From 6fba79495278c399042e2195d21805be4e9fd99d Mon Sep 17 00:00:00 2001 From: "yuqi.pyq" Date: Thu, 15 Jun 2023 17:03:32 +0800 Subject: [PATCH 1/6] feat: impl page rank --- .github/workflows/ci.yml | 31 + .gitignore | 5 + .husky/commit-msg | 4 + .husky/pre-commit | 4 + CHANGELOG.md | 93 -- README-zh_CN.md | 40 - README.md | 87 +- jest.config.js | 30 + package.json | 57 +- packages/graph-gpu/.prettierrc.js | 5 - packages/graph-gpu/package.json | 9 +- packages/graph-gpu/src/index.ts | 1 + .../graph-gpu/src/link-analysis/pageRank.ts | 14 +- packages/graph-rust/Cargo.toml | 5 + packages/graph-rust/README.md | 0 packages/graph-rust/rustfmt.toml | 8 + packages/graph-rust/src/lib.rs | 5 + packages/graph-rust/src/page_rank.rs | 184 +++ packages/graph-rust/src/prelude.rs | 4 + packages/graph-rust/src/utils.rs | 1 + packages/graph-wasm/.gitignore | 5 - packages/graph-wasm/Cargo.lock | 44 +- packages/graph-wasm/Cargo.toml | 2 +- packages/graph-wasm/rust-src/lib.rs | 4 +- packages/graph-wasm/tsconfig.json | 24 + packages/graph/.prettierrc.js | 5 - packages/graph/jest.config.js | 15 - packages/graph/package.json | 44 +- packages/graph/src/adjacent-matrix.ts | 38 - packages/graph/src/asyncIndex.ts | 69 - packages/graph/src/bfs.ts | 89 -- packages/graph/src/connected-component.ts | 113 -- packages/graph/src/constants/time.ts | 2 - packages/graph/src/cosine-similarity.ts | 27 - packages/graph/src/degree.ts | 51 - packages/graph/src/detect-cycle.ts | 346 ----- packages/graph/src/dfs.ts | 76 -- packages/graph/src/dijkstra.ts | 105 -- packages/graph/src/find-path.ts | 70 - packages/graph/src/floydWarshall.ts | 34 - packages/graph/src/gSpan/gSpan.ts | 954 ------------- packages/graph/src/gSpan/struct.ts | 114 -- packages/graph/src/gaddi.ts | 1211 ----------------- packages/graph/src/i-louvain.ts | 28 - packages/graph/src/index.ts | 89 +- packages/graph/src/k-core.ts | 37 - packages/graph/src/k-means.ts | 216 --- packages/graph/src/label-propagation.ts | 151 -- packages/graph/src/louvain.ts | 401 ------ packages/graph/src/mts.ts | 116 -- packages/graph/src/nodes-cosine-similarity.ts | 50 - packages/graph/src/pageRank.ts | 54 +- packages/graph/src/structs/binary-heap.ts | 90 -- packages/graph/src/structs/linked-list.ts | 245 ---- packages/graph/src/structs/queue.ts | 46 - packages/graph/src/structs/stack.ts | 65 - packages/graph/src/structs/union-find.ts | 45 - packages/graph/src/types.ts | 113 +- packages/graph/src/util.ts | 59 - .../graph/src/utils/data-preprocessing.ts | 110 -- packages/graph/src/utils/node-properties.ts | 78 -- packages/graph/src/utils/vector.ts | 159 --- packages/graph/src/workers/algorithm.ts | 16 - packages/graph/src/workers/constant.ts | 31 - packages/graph/src/workers/createWorker.ts | 33 - packages/graph/src/workers/index.ts | 253 ---- packages/graph/src/workers/index.worker.ts | 27 - packages/graph/tsconfig.json | 1 + site/benchmark/index.html | 4 +- site/benchmark/main.ts | 16 +- site/benchmark/page-rank.ts | 6 +- site/datasets.ts | 15 +- site/types.ts | 2 +- tsconfig.json | 11 + tslint.json | 21 + 75 files changed, 530 insertions(+), 6087 deletions(-) create mode 100644 .github/workflows/ci.yml create mode 100644 .husky/commit-msg create mode 100644 .husky/pre-commit delete mode 100644 CHANGELOG.md delete mode 100644 README-zh_CN.md create mode 100644 jest.config.js delete mode 100644 packages/graph-gpu/.prettierrc.js create mode 100644 packages/graph-rust/README.md create mode 100644 packages/graph-rust/rustfmt.toml create mode 100644 packages/graph-rust/src/lib.rs create mode 100644 packages/graph-rust/src/page_rank.rs create mode 100644 packages/graph-rust/src/prelude.rs create mode 100644 packages/graph-rust/src/utils.rs delete mode 100644 packages/graph-wasm/.gitignore create mode 100644 packages/graph-wasm/tsconfig.json delete mode 100644 packages/graph/.prettierrc.js delete mode 100644 packages/graph/jest.config.js delete mode 100644 packages/graph/src/adjacent-matrix.ts delete mode 100644 packages/graph/src/asyncIndex.ts delete mode 100644 packages/graph/src/bfs.ts delete mode 100644 packages/graph/src/connected-component.ts delete mode 100644 packages/graph/src/constants/time.ts delete mode 100644 packages/graph/src/cosine-similarity.ts delete mode 100644 packages/graph/src/degree.ts delete mode 100644 packages/graph/src/detect-cycle.ts delete mode 100644 packages/graph/src/dfs.ts delete mode 100644 packages/graph/src/dijkstra.ts delete mode 100644 packages/graph/src/find-path.ts delete mode 100644 packages/graph/src/floydWarshall.ts delete mode 100644 packages/graph/src/gSpan/gSpan.ts delete mode 100644 packages/graph/src/gSpan/struct.ts delete mode 100644 packages/graph/src/gaddi.ts delete mode 100644 packages/graph/src/i-louvain.ts delete mode 100644 packages/graph/src/k-core.ts delete mode 100644 packages/graph/src/k-means.ts delete mode 100644 packages/graph/src/label-propagation.ts delete mode 100644 packages/graph/src/louvain.ts delete mode 100644 packages/graph/src/mts.ts delete mode 100644 packages/graph/src/nodes-cosine-similarity.ts delete mode 100644 packages/graph/src/structs/binary-heap.ts delete mode 100644 packages/graph/src/structs/linked-list.ts delete mode 100644 packages/graph/src/structs/queue.ts delete mode 100644 packages/graph/src/structs/stack.ts delete mode 100644 packages/graph/src/structs/union-find.ts delete mode 100644 packages/graph/src/util.ts delete mode 100644 packages/graph/src/utils/data-preprocessing.ts delete mode 100644 packages/graph/src/utils/node-properties.ts delete mode 100644 packages/graph/src/utils/vector.ts delete mode 100644 packages/graph/src/workers/algorithm.ts delete mode 100644 packages/graph/src/workers/constant.ts delete mode 100644 packages/graph/src/workers/createWorker.ts delete mode 100644 packages/graph/src/workers/index.ts delete mode 100644 packages/graph/src/workers/index.worker.ts create mode 100644 tsconfig.json create mode 100644 tslint.json diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 0000000..ec72c12 --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,31 @@ +name: CI + +on: ["push", "pull_request"] + +jobs: + ci: + runs-on: ubuntu-20.04 + strategy: + matrix: + node-version: [15] + steps: + - uses: actions/checkout@v3 + - uses: pnpm/action-setup@v2 + with: + version: 7 + - name: Use Node.js ${{ matrix.node-version }} + uses: actions/setup-node@v3 + with: + node-version: ${{ matrix.node-version }} + cache: "pnpm" + - name: Install dependencies + run: pnpm install + - name: lint + run: | + pnpm lint + - name: build + run: | + pnpm build:ci + - name: test + run: | + pnpm test diff --git a/.gitignore b/.gitignore index 04afe08..759f228 100644 --- a/.gitignore +++ b/.gitignore @@ -13,3 +13,8 @@ dist !mock-cert.pem pnpm-lock.yaml tsconfig.tsbuildinfo +target +Cargo.lock +pkg +pkg-node +pkg-parallel diff --git a/.husky/commit-msg b/.husky/commit-msg new file mode 100644 index 0000000..62aa592 --- /dev/null +++ b/.husky/commit-msg @@ -0,0 +1,4 @@ +#!/bin/sh +. "$(dirname "$0")/_/husky.sh" + +npx --no-install commitlint --edit "$1" \ No newline at end of file diff --git a/.husky/pre-commit b/.husky/pre-commit new file mode 100644 index 0000000..c37466e --- /dev/null +++ b/.husky/pre-commit @@ -0,0 +1,4 @@ +#!/bin/sh +. "$(dirname "$0")/_/husky.sh" + +npx lint-staged \ No newline at end of file diff --git a/CHANGELOG.md b/CHANGELOG.md deleted file mode 100644 index 77bd6ce..0000000 --- a/CHANGELOG.md +++ /dev/null @@ -1,93 +0,0 @@ -# ChangeLog -#### 0.1.25 - -- feat: Optimized data preprocessing coding - when the feature values are all numerical, use the original values (plus normalization), and do not use one-hot coding -#### 0.1.24 - -- fix: i-louvain without cluster problem; -#### 0.1.23 - -- perf: k-means algorithm: set K to minimum -#### 0.1.22 - -- fix: k-means algorithm, perf: louvain -- support specified parameters such as propertyKey,involvedKeys and uninvolvedKeys -#### 0.1.21 - -- perf: k-means algorithm -- Optimize parameters and return - -#### 0.1.20 - -- feat: add k-means algorithm for nodes clustering - -#### 0.1.19 - -- fix: GADDI matched failed problem; - -#### 0.1.18 - -- feat: add one-hot data preprocessing; - -#### 0.1.17 - -- feat: add consine-similarity algorithm and nodes-consine-similarity algorithm; - -#### 0.1.16 - -- feat: add i-louvain based on louvain according to academic; - -#### 0.1.15 - -- feat: k-core algorithm; - -#### 0.1.14 - -- fix: GADDI with proper begin p node; -- feat: louvain with property similarity measure - -#### 0.1.10 - -- fix: GADDI with better accuracy; - -#### 0.1.9 - -- chore: separate sync and async functions into different entries; - -#### 0.1.8 - -- fix: CPU usage increases due to 0.1.3-beta ~ 0.1.3 with publicPath configuration; -- fix: CPU usage increases due to 0.1.6 ~ 0.17 with browser output; -- feat: export fix: export detectAllCycles, detectAllDirectedCycle, detectAllUndirectedCycle; - -#### 0.1.6 - -- fix: louvain with increased clusterId and node with correct new clusterId; - -#### 0.1.5 - -- fix: worker async problem; -- chore: unify allPath and allPaths; - -#### 0.1.2 - -- fix: failed to find result problem in dijkstra; - -#### 0.1.1 - -- fix: shortestPath with wrong result; - -#### 0.1.0 - -- fix: findShortestPath undefined is not interatable; - -#### 0.1.0-beta.3 - -- fix: cannot read degree of undefined problem of GADDI; - -#### 0.1.0-beta - -- feat: worker for algorithms; -- feat: gaddi for graph pattern matching; - -#### 0.0.7 - -- feat: dijkstra supports finding multiple shortest paths; diff --git a/README-zh_CN.md b/README-zh_CN.md deleted file mode 100644 index 59bfce3..0000000 --- a/README-zh_CN.md +++ /dev/null @@ -1,40 +0,0 @@ -### AntV Algorithm - -AntV 算法包，包括图算法及其他各类算法。 - -graph 包下面包括的都是图算法。 - -AntV 共支持以下图算法： -- **社区发现** - - k-core: K-Core社区发现算法 -- 找到符合指定核心度K的密切相关子图结构 - - louvain: LOUVAIN 算法 -- 根据模块度划分社区 - - i-louvain: I-LOUVAIN 算法 -- 根据模块度和惯性模块度（属性相似度）划分社区 - - labelPropagation: 标签传播算法 - - minimumSpanningTree: 图的最小生成树 - -- **节点聚类** - - k-means: K-Means算法 - 根据节点之间的距离将节点分为K个簇 - -- **相似性** - - cosineSimilarity: 余弦相似度算法 -- 计算两个元素的余弦相似度 - - nodesCosineSimilarity: 节点余弦相似度算法 -- 计算节点与种子节点之间的余弦相似度 - - -- **中心性** - - pageRank: 节点排序的页面排序算法 - - degree: 计算节点的入度、出度和总度 - -- **路径** - - dijkstra: Dijkstra 最短路径算法 - - findPath: 通过Dijkstra找到两个节点的最短路径和所有路径 - - floydWarshall: 弗洛伊德最短路径算法 - -- **其它** - - neighbors: 在图中查找节点的邻居 - - GADDI: 图结构和语义模式匹配算法 - - detectCycle: 环路检测 - - dfs: D深度优先遍历 - - adjacentMatrix: 邻接矩阵 - - connectedComponent: 联通子图 - -并支持在 web-worker 中计算上述算法 diff --git a/README.md b/README.md index 54dd385..6332e29 100644 --- a/README.md +++ b/README.md @@ -1,35 +1,64 @@ -### AntV Algorithm +

+AntV Algorithm +

-It is an algorithm package of AntV, mainly includes graph related algorithms: -- **Community Detection** - - k-core: K-Core community detection algorithm -- Find the closely related subgraph structure that conforms to the specified core degree K - - louvain: LOUVAIN algorithm -- Divide communities according to Modularity - - i-louvain: I-LOUVAIN algorithm -- Divide communities according to Modularity and Inertial Modularity (properties similarity) - - labelPropagation: Label Propagation(LP) clustering algorithm - - minimumSpanningTree: Generate the minimum spanning tree for a graph +[![Build Status](https://github.com/antvis/algorithm/workflows/build/badge.svg?branch=next)](https://github.com/antvis//actions) +[![Coverage Status](https://img.shields.io/coveralls/github/antvis/algorithm/next.svg)](https://coveralls.io/github/antvis/algorithm?branch=next) +[![npm Download](https://img.shields.io/npm/dm/@antv/algorithm.svg)](https://www.npmjs.com/package/@antv/algorithm) +[![npm License](https://img.shields.io/npm/l/@antv/algorithm.svg)](https://www.npmjs.com/package/@antv/algorithm) -- **nodes clustering** - - k-means: K-Means algorithm - Cluster nodes into K clusters according to the distance between node +- [@antv/graph](./packages/graph/README.md) [![npm Version](https://img.shields.io/npm/v/@antv/graph/alpha)](https://www.npmjs.com/package/@antv/graph) Implemented with TypeScript. [Online Demo](https://observablehq.com/d/2db6b0cc5e97d8d6) +- [@antv/graph-rust](./packages/graph-rust/README.md) Implemented with Rust. +- [@antv/graph-wasm](./packages/graph-wasm/README.md) [![npm Version](https://img.shields.io/npm/v/@antv/graph-wasm)](https://www.npmjs.com/package/@antv/graph-wasm) Provide a WASM binding of `@antv/graph-rust`. [Online Demo](https://observablehq.com/d/288c16a54543a141) +- [@antv/graph-gpu](./packages/graph-gpu/README.md) [![npm Version](https://img.shields.io/npm/v/@antv/graph-gpu)](https://www.npmjs.com/package/@antv/graph-gpu) Accelerate some parallelizable algorithms such as Fruchterman with WebGPU which has a better performance under large amount of data. -- **Similarity** - - cosineSimilarity: Cosine Similarity algorithm -- Calculate cosine similarity - - nodesCosineSimilarity: Nodes Cosine Similarity algorithm -- Calculate the cosine similarity between other nodes and seed node +It is an algorithm package of AntV, mainly includes graph related algorithms: - **Centrality** - pageRank: page rank algorithm for nodes ranking - - degree: calculate the in degree, out degree, and total degree for nodes - -- **Path** - - dijkstra: Dijkstra shortest path algorithm - - findPath: Find the shortest paths and all paths for two nodes by Dijkstra - - floydWarshall: Floyd Warshall shortest path algorithm - -- **Other** - - neighbors: Find the neighbors for a node in the graph - - GADDI: graph structural and semantic pattern matching algorithm - - detectCycle: Detect the cycles of the graph data - - dfs: Depth-First search algorithm - - adjacentMatrix: calculate the adjacency matrix for graph data - - connectedComponent: Calculate the connected components for graph data - -All the algorithms above supports to be calculated with web-worker. \ No newline at end of file + +## Development + +We use [Vite](https://vitejs.dev/) to start a dev server: + +```bash +$ pnpm dev +``` + +## Test + +Run all the test cases with Jest: + +```bash +$ pnpm test +``` + +## Publish + +Using Changesets with pnpm: https://pnpm.io/next/using-changesets + +The generated markdown files in the .changeset directory should be committed to the repository. + +```bash +pnpm changeset +``` + +This will bump the versions of the packages previously specified with pnpm changeset (and any dependents of those) and update the changelog files. + +```bash +pnpm changeset version +``` + +Commit the changes. This command will publish all packages that have bumped versions not yet present in the registry. + +```bash +pnpm publish -r +``` + +If you want to publish versions for test: + +```bash +pnpm changeset pre enter alpha +pnpm changeset pre enter beta +pnpm changeset pre enter rc +``` diff --git a/jest.config.js b/jest.config.js new file mode 100644 index 0000000..3f84e26 --- /dev/null +++ b/jest.config.js @@ -0,0 +1,30 @@ +// module.exports = { + +// preset: "ts-jest", +// collectCoverage: false, +// collectCoverageFrom: [ +// "packages/layout/src/**/*.{ts,js}", +// "!**/node_modules/**", +// "!**/vendor/**", +// ], + +/** @type {import('ts-jest').JestConfigWithTsJest} */ +module.exports = { + testEnvironment: "jsdom", + testRegex: "__tests__/.*test\\.ts?$", + moduleDirectories: ["node_modules", "src", "es"], + moduleFileExtensions: ["js", "ts", "json"], + moduleNameMapper: { + "@antv/algorithm/(.*)": "/src/$1", + }, + transform: { + // '^.+\\.[tj]sx?$' to process js/ts with `ts-jest` + // '^.+\\.m?[tj]sx?$' to process js/ts/mjs/mts with `ts-jest` + "^.+\\.tsx?$": [ + "ts-jest", + { + diagnostics: false, + }, + ], + }, +}; diff --git a/package.json b/package.json index 0708270..2ce7e1a 100644 --- a/package.json +++ b/package.json @@ -1,26 +1,69 @@ { "name": "@antv/algorithm", "private": true, + "homepage": "https://github.com/antvis/algorithm", + "bugs": { + "url": "https://github.com/antvis/algorithm/issues" + }, + "repository": { + "type": "git", + "url": "https://github.com/antvis/algorithm.git" + }, + "license": "MIT", "scripts": { "dev": "vite", + "lint:es": "eslint --ext .js --fix", + "lint:ts": "tslint -c tslint.json -p packages/layout/tsconfig.json --fix", + "lint": "npm run lint:ts && npm run lint:es", + "lint-staged": "lint-staged", "build": "pnpm -r run build", - "lint": "pnpm -r run lint", + "build:ci": "pnpm -r run build:ci", + "prepare": "husky install", "test": "pnpm -r run test --no-private", - "prettier": "prettier --write '**/*.{js,jsx,tsx,ts,less,md,json}'", - "pretty-quick": "pretty-quick", - "clean": "pnpm -r run clean", - "clean:modules": "rimraf node_modules", - "ls": "pnpm -r list", + "coverage": "jest --coverage", "build:site": "vite build", - "deploy": "gh-pages -d site/dist" + "deploy": "gh-pages -d site/dist", + "preview": "vite preview --port 9092" + }, + "lint-staged": { + "*.js": [ + "eslint --fix" + ], + "packages/**/*/src/**/*.ts": [ + "tslint -c tslint.json -p ./tsconfig.json --fix" + ] }, "devDependencies": { "@antv/graphlib": "^2.0.0", + "@changesets/cli": "^2.26.1", + "cross-env": "^7.0.3", + "eslint": "^7.32.0", + "eslint-config-airbnb-base": "^14.2.1", + "eslint-config-prettier": "^6.15.0", + "eslint-plugin-import": "^2.27.5", + "gh-pages": "^5.0.0", "graphology": "^0.25.1", "graphology-generators": "^0.11.2", "graphology-types": "^0.24.7", "graphology-metrics": "^2.1.0", "graphology-shortest-path": "^2.0.2", + "husky": "^7.0.4", + "jest": "^29.5.0", + "jest-environment-jsdom": "29.5.0", + "lint-staged": "^10.5.4", + "npm-run-all": "^4.1.5", + "rimraf": "^3.0.2", + "ts-jest": "^29.1.0", + "ts-loader": "^8.4.0", + "tslint": "^6.1.3", + "tslint-config-airbnb": "^5.11.2", + "tslint-config-prettier": "^1.18.0", + "tslint-eslint-rules": "^5.4.0", + "typescript": "^4.9.5", "vite": "^4.3.8" + }, + "publishConfig": { + "access": "public", + "registry": "https://registry.npmjs.org" } } diff --git a/packages/graph-gpu/.prettierrc.js b/packages/graph-gpu/.prettierrc.js deleted file mode 100644 index 7b597d7..0000000 --- a/packages/graph-gpu/.prettierrc.js +++ /dev/null @@ -1,5 +0,0 @@ -const fabric = require('@umijs/fabric'); - -module.exports = { - ...fabric.prettier, -}; diff --git a/packages/graph-gpu/package.json b/packages/graph-gpu/package.json index 8eb5c94..f383505 100644 --- a/packages/graph-gpu/package.json +++ b/packages/graph-gpu/package.json @@ -31,15 +31,10 @@ "dev:umd": "webpack --config webpack.dev.config.js --mode development", "ci": "npm run build && npm run coverage", "clean": "rimraf lib dist", - "coverage": "jest --coverage", "lint": "eslint --ext .js,.jsx,.ts,.tsx --format=pretty \"./\"", "lint:src": "eslint --ext .ts --format=pretty \"./src\"", "prettier": "prettier -c --write \"**/*\"", - "test": "npm run build:umd && jest", - "test-live": "npm run build:umd && DEBUG_MODE=1 jest --watch ./tests/unit/louvain-spec.ts", - "test-live:async": "npm run build:umd && DEBUG_MODE=1 jest --watch ./tests/unit/louvain-async-spec.ts", - "lint-staged:js": "eslint --ext .js,.jsx,.ts,.tsx", - "cdn": "antv-bin upload -n @antv/webgpu-graph" + "lint-staged:js": "eslint --ext .js,.jsx,.ts,.tsx" }, "homepage": "https://g6.antv.vision", "bugs": { @@ -59,9 +54,7 @@ "@types/jest": "^26.0.18", "@umijs/fabric": "^2.5.6", "babel-loader": "^8.2.2", - "jest": "^26.6.3", "rimraf": "^3.0.2", - "ts-jest": "^26.4.4", "ts-loader": "^8.0.14", "tslint": "^6.1.3", "typescript": "^4.1.3", diff --git a/packages/graph-gpu/src/index.ts b/packages/graph-gpu/src/index.ts index 70508e2..fb741ab 100644 --- a/packages/graph-gpu/src/index.ts +++ b/packages/graph-gpu/src/index.ts @@ -1,3 +1,4 @@ export * from './WebGPUGraph'; export * from './link-analysis'; export * from './traversal'; +export * from './types'; diff --git a/packages/graph-gpu/src/link-analysis/pageRank.ts b/packages/graph-gpu/src/link-analysis/pageRank.ts index ba2eeb5..5cad8b2 100644 --- a/packages/graph-gpu/src/link-analysis/pageRank.ts +++ b/packages/graph-gpu/src/link-analysis/pageRank.ts @@ -1,7 +1,7 @@ -import { DeviceRenderer } from '@antv/g-webgpu'; -import { Kernel } from '@antv/g-plugin-gpgpu'; -import { convertGraphData2CSC } from '../util'; -import { Graph } from '../types'; +import { DeviceRenderer } from "@antv/g-webgpu"; +import { Kernel } from "@antv/g-plugin-gpgpu"; +import { convertGraphData2CSC } from "../util"; +import { Graph } from "../types"; const { BufferUsage } = DeviceRenderer; @@ -18,9 +18,9 @@ const { BufferUsage } = DeviceRenderer; export async function pageRank( device: DeviceRenderer.Device, graphData: Graph, - eps = 1e-5, + tolerance = 1e-5, alpha = 0.85, - maxIteration = 1000, + maxIteration = 1000 ) { const BLOCK_SIZE = 1; const BLOCKS = 256; @@ -152,7 +152,7 @@ fn main( const last = (await readback.readBuffer(rLastBuffer)) as Float32Array; const result = last.reduce((prev, cur) => prev + cur, 0); - if (result < eps) { + if (result < tolerance) { break; } } diff --git a/packages/graph-rust/Cargo.toml b/packages/graph-rust/Cargo.toml index 7a4b3d4..39ebbd5 100644 --- a/packages/graph-rust/Cargo.toml +++ b/packages/graph-rust/Cargo.toml @@ -17,7 +17,12 @@ lto = true opt-level = 's' [dependencies] +atomic_float = "0.1.0" graph_builder = "0.3.1" rayon = "1.5.1" +serde = { optional = true } + +[dev-dependencies] +graph_builder = { version = "^0.3.1", features = ["gdl"] } diff --git a/packages/graph-rust/README.md b/packages/graph-rust/README.md new file mode 100644 index 0000000..e69de29 diff --git a/packages/graph-rust/rustfmt.toml b/packages/graph-rust/rustfmt.toml new file mode 100644 index 0000000..6df7c47 --- /dev/null +++ b/packages/graph-rust/rustfmt.toml @@ -0,0 +1,8 @@ +hard_tabs = false +newline_style = "unix" + +unstable_features = true +format_code_in_doc_comments = true +format_macro_bodies = true +format_macro_matchers = true +format_strings = true diff --git a/packages/graph-rust/src/lib.rs b/packages/graph-rust/src/lib.rs new file mode 100644 index 0000000..6f978b0 --- /dev/null +++ b/packages/graph-rust/src/lib.rs @@ -0,0 +1,5 @@ +pub mod page_rank; +pub mod prelude; +pub mod utils; + +const DEFAULT_PARALLELISM: usize = 4; diff --git a/packages/graph-rust/src/page_rank.rs b/packages/graph-rust/src/page_rank.rs new file mode 100644 index 0000000..dde9605 --- /dev/null +++ b/packages/graph-rust/src/page_rank.rs @@ -0,0 +1,184 @@ +use crate::{prelude::*, DEFAULT_PARALLELISM}; + +use atomic_float::AtomicF64; +use graph_builder::SharedMut; +use rayon::prelude::*; + +use std::sync::atomic::Ordering; +use std::thread::available_parallelism; + +const CHUNK_SIZE: usize = 16384; + +#[derive(Copy, Clone, Debug)] +#[cfg_attr(feature = "serde", derive(serde::Serialize, serde::Deserialize))] +pub struct PageRankConfig { + /// The maximum number of page rank iterations. + pub max_iterations: usize, + + /// If the sum of page rank deltas per iteration is + /// below the tolerance value, the computation stop. + pub tolerance: f64, + + /// Imagining a random surfer clicking links, the + /// damping factor defines the probability if the + /// surfer will continue at any step. + pub damping_factor: f32, +} + +impl Default for PageRankConfig { + fn default() -> Self { + Self { + max_iterations: Self::DEFAULT_MAX_ITERATIONS, + tolerance: Self::DEFAULT_TOLERANCE, + damping_factor: Self::DEFAULT_DAMPING_FACTOR, + } + } +} + +impl PageRankConfig { + pub const DEFAULT_MAX_ITERATIONS: usize = 20; + pub const DEFAULT_TOLERANCE: f64 = 1E-4; + pub const DEFAULT_DAMPING_FACTOR: f32 = 0.85; + + pub fn new(max_iterations: usize, tolerance: f64, damping_factor: f32) -> Self { + Self { + max_iterations, + tolerance, + damping_factor, + } + } +} + +pub fn page_rank(graph: &G, config: PageRankConfig) -> (Vec, usize, f64) +where + NI: Idx, + G: Graph + DirectedDegrees + DirectedNeighbors + Sync, +{ + let PageRankConfig { + max_iterations, + tolerance, + damping_factor, + } = config; + + let node_count = graph.node_count().index(); + let init_score = 1_f32 / node_count as f32; + let base_score = (1.0_f32 - damping_factor) / node_count as f32; + + let mut out_scores = Vec::with_capacity(node_count); + + (0..node_count) + .into_par_iter() + .map(NI::new) + .map(|node| init_score / graph.out_degree(node).index() as f32) + .collect_into_vec(&mut out_scores); + + let mut scores = vec![init_score; node_count]; + + let scores_ptr = SharedMut::new(scores.as_mut_ptr()); + let out_scores_ptr = SharedMut::new(out_scores.as_mut_ptr()); + + let mut iteration = 0; + + loop { + let error = page_rank_iteration( + graph, + base_score, + damping_factor, + &out_scores_ptr, + &scores_ptr, + ); + + iteration += 1; + + if error < tolerance || iteration == max_iterations { + return (scores, iteration, error); + } + } +} + +fn page_rank_iteration( + graph: &G, + base_score: f32, + damping_factor: f32, + out_scores: &SharedMut, + scores: &SharedMut, +) -> f64 +where + NI: Idx, + G: Graph + DirectedDegrees + DirectedNeighbors + Sync, +{ + let next_chunk = Atomic::new(NI::zero()); + let total_error = AtomicF64::new(0_f64); + + std::thread::scope(|s| { + let num_threads = available_parallelism().map_or(DEFAULT_PARALLELISM, |p| p.get()); + + for _ in 0..num_threads { + s.spawn(|| { + let mut error = 0_f64; + + loop { + let start = NI::fetch_add(&next_chunk, NI::new(CHUNK_SIZE), Ordering::AcqRel); + if start >= graph.node_count() { + break; + } + + let end = (start + NI::new(CHUNK_SIZE)).min(graph.node_count()); + + for u in start.range(end) { + let incoming_total = graph + .in_neighbors(u) + .map(|v| unsafe { out_scores.add(v.index()).read() }) + .sum::(); + + let old_score = unsafe { scores.add(u.index()).read() }; + let new_score = base_score + damping_factor * incoming_total; + + unsafe { scores.add(u.index()).write(new_score) }; + let diff = (new_score - old_score) as f64; + error += f64::abs(diff); + + unsafe { + out_scores + .add(u.index()) + .write(new_score / graph.out_degree(u).index() as f32) + } + } + } + total_error.fetch_add(error, Ordering::SeqCst); + }); + } + }); + + total_error.load(Ordering::SeqCst) +} + +#[cfg(test)] +mod tests { + use super::*; + use crate::prelude::{CsrLayout, GraphBuilder}; + + #[test] + fn test_pr_two_components() { + let gdl = "(a)-->()-->()<--(a),(b)-->()-->()<--(b)"; + + let graph: DirectedCsrGraph = GraphBuilder::new() + .csr_layout(CsrLayout::Sorted) + .gdl_str::(gdl) + .build() + .unwrap(); + + let (scores, _, _) = page_rank(&graph, PageRankConfig::default()); + + let expected: Vec = vec![ + 0.024999997, + 0.035624996, + 0.06590624, + 0.024999997, + 0.035624996, + 0.06590624, + ]; + + assert_eq!(scores, expected); + } +} diff --git a/packages/graph-rust/src/prelude.rs b/packages/graph-rust/src/prelude.rs new file mode 100644 index 0000000..e151dda --- /dev/null +++ b/packages/graph-rust/src/prelude.rs @@ -0,0 +1,4 @@ +pub use crate::page_rank::*; +pub use crate::utils::*; + +pub use graph_builder::prelude::*; diff --git a/packages/graph-rust/src/utils.rs b/packages/graph-rust/src/utils.rs new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/packages/graph-rust/src/utils.rs @@ -0,0 +1 @@ + diff --git a/packages/graph-wasm/.gitignore b/packages/graph-wasm/.gitignore deleted file mode 100644 index 63392d8..0000000 --- a/packages/graph-wasm/.gitignore +++ /dev/null @@ -1,5 +0,0 @@ -target -pkg -pkg-node -pkg-parallel -*.lock \ No newline at end of file diff --git a/packages/graph-wasm/Cargo.lock b/packages/graph-wasm/Cargo.lock index 8a9f789..d27fd0a 100644 --- a/packages/graph-wasm/Cargo.lock +++ b/packages/graph-wasm/Cargo.lock @@ -3,24 +3,22 @@ version = 3 [[package]] -name = "ahash" -version = "0.8.3" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2c99f64d1e06488f620f932677e24bc6e2897582980441ae90a671415bd7ec2f" +name = "antv-graph" +version = "0.0.1" dependencies = [ - "cfg-if 1.0.0", - "getrandom", - "once_cell", - "version_check", + "atomic_float", + "graph_builder", + "rayon", + "serde", ] [[package]] name = "antv-graph-wasm" version = "0.0.1" dependencies = [ + "antv-graph", "console_error_panic_hook", "getrandom", - "graph", "js-sys", "serde", "serde-wasm-bindgen", @@ -210,22 +208,6 @@ dependencies = [ "wasm-bindgen", ] -[[package]] -name = "graph" -version = "0.3.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "624b74cfef1d6e08adeac4b5947e8e79351d0a53491b07b9d342701f8e58b68f" -dependencies = [ - "ahash", - "atomic_float", - "graph_builder", - "log", - "nanorand", - "num-format", - "rayon", - "serde", -] - [[package]] name = "graph_builder" version = "0.3.1" @@ -342,12 +324,6 @@ version = "0.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "8452105ba047068f40ff7093dd1d9da90898e63dd61736462e9cdda6a90ad3c3" -[[package]] -name = "nanorand" -version = "0.7.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6a51313c5820b0b02bd422f4b44776fbf47961755c74ce64afc73bfad10226c3" - [[package]] name = "num" version = "0.4.0" @@ -646,12 +622,6 @@ version = "1.0.9" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "b15811caf2415fb889178633e7724bad2509101cde276048e013b9def5e51fa0" -[[package]] -name = "version_check" -version = "0.9.4" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f" - [[package]] name = "wasi" version = "0.11.0+wasi-snapshot-preview1" diff --git a/packages/graph-wasm/Cargo.toml b/packages/graph-wasm/Cargo.toml index c0166f0..ebc25d7 100644 --- a/packages/graph-wasm/Cargo.toml +++ b/packages/graph-wasm/Cargo.toml @@ -24,7 +24,7 @@ path = "rust-src/lib.rs" [dependencies] getrandom = { version = "0.2", features = ["js"] } -graph = { version = "0.3.0", features = ["serde"] } +antv-graph = { path = "../graph-rust/", features = ["serde"] } console_error_panic_hook = "0.1" js-sys = "0.3.51" serde-wasm-bindgen = "0.5" diff --git a/packages/graph-wasm/rust-src/lib.rs b/packages/graph-wasm/rust-src/lib.rs index c08f7ae..e2aedf4 100644 --- a/packages/graph-wasm/rust-src/lib.rs +++ b/packages/graph-wasm/rust-src/lib.rs @@ -1,4 +1,4 @@ -use graph::prelude::*; +use antv_graph::prelude::*; use js_sys::Array; use wasm_bindgen::prelude::*; @@ -42,7 +42,7 @@ pub fn page_rank(val: JsValue) -> Array { ]) .build(); - let (ranks, iterations, _) = graph::prelude::page_rank( + let (ranks, iterations, _) = antv_graph::prelude::page_rank( &graph, PageRankConfig::new( options.max_iterations, diff --git a/packages/graph-wasm/tsconfig.json b/packages/graph-wasm/tsconfig.json new file mode 100644 index 0000000..02c8ba0 --- /dev/null +++ b/packages/graph-wasm/tsconfig.json @@ -0,0 +1,24 @@ +{ + "compilerOptions": { + "rootDir": "./src", + "composite": true, + "module": "esnext", + "declaration": true, + "sourceMap": true, + "target": "es5", + "outDir": "lib", + "jsx": "react", + "importHelpers": true, + "moduleResolution": "node", + "allowSyntheticDefaultImports": true, + "resolveJsonModule": true, + "esModuleInterop": true, + "lib": ["esnext", "dom"], + "experimentalDecorators": false /* Enables experimental support for ES7 decorators. */, + // "emitDecoratorMetadata": true, /* Enables experimental support for emitting type metadata for decorators. */ + "downlevelIteration": true, + "skipLibCheck": true + }, + "include": ["src/**/*"], + "exclude": ["src/**/*.spec.ts"] +} diff --git a/packages/graph/.prettierrc.js b/packages/graph/.prettierrc.js deleted file mode 100644 index 7b597d7..0000000 --- a/packages/graph/.prettierrc.js +++ /dev/null @@ -1,5 +0,0 @@ -const fabric = require('@umijs/fabric'); - -module.exports = { - ...fabric.prettier, -}; diff --git a/packages/graph/jest.config.js b/packages/graph/jest.config.js deleted file mode 100644 index 74a1e59..0000000 --- a/packages/graph/jest.config.js +++ /dev/null @@ -1,15 +0,0 @@ -module.exports = { - runner: 'jest-electron/runner', - testEnvironment: 'jest-electron/environment', - preset: 'ts-jest', - collectCoverage: false, - collectCoverageFrom: ['src/**/*.{ts,js}', '!**/node_modules/**', '!**/vendor/**'], - testRegex: '/tests/.*-spec\\.ts?$', - moduleDirectories: ['node_modules', 'src'], - moduleFileExtensions: ['js', 'ts', 'json'], - globals: { - 'ts-jest': { - diagnostics: false, - }, - }, -}; diff --git a/packages/graph/package.json b/packages/graph/package.json index 6c1754f..b9096a6 100644 --- a/packages/graph/package.json +++ b/packages/graph/package.json @@ -1,12 +1,11 @@ { - "name": "@antv/algorithm", - "version": "0.1.25", + "name": "@antv/graph", + "version": "0.0.1", "description": "graph algorithm", "keywords": [ "graph", "algorithm", - "antv", - "G6" + "antv" ], "files": [ "package.json", @@ -15,26 +14,19 @@ "LICENSE", "README.md" ], + "sideEffects": false, "main": "dist/index.min.js", "module": "lib/index.js", "types": "lib/index.d.ts", "unpkg": "dist/index.min.js", "scripts": { + "clean": "rimraf dist lib", + "dev": "webpack --config webpack.dev.config.js --mode development", "build": "npm run clean && npm run build:esm && npm run build:umd", + "build:ci": "npm run build", "build:esm": "tsc", "build:umd": "webpack --config webpack.config.js --mode production", - "dev:umd": "webpack --config webpack.dev.config.js --mode development", - "ci": "npm run build && npm run coverage", - "clean": "rimraf lib dist", - "coverage": "jest --coverage", - "lint": "eslint --ext .js,.jsx,.ts,.tsx --format=pretty \"./\"", - "lint:src": "eslint --ext .ts --format=pretty \"./src\"", - "prettier": "prettier -c --write \"**/*\"", - "test": "npm run build:umd && jest", - "test-live": "npm run build:umd && DEBUG_MODE=1 jest --watch ./tests/unit/louvain-spec.ts", - "test-live:async": "npm run build:umd && DEBUG_MODE=1 jest --watch ./tests/unit/louvain-async-spec.ts", - "lint-staged:js": "eslint --ext .js,.jsx,.ts,.tsx", - "cdn": "antv-bin upload -n @antv/algorithm" + "publish:alpha": "npm publish --tag alpha" }, "homepage": "https://g6.antv.vision", "bugs": { @@ -47,25 +39,19 @@ "license": "MIT", "author": "https://github.com/orgs/antvis/people", "devDependencies": { - "@babel/core": "^7.12.10", - "@babel/plugin-proposal-class-properties": "^7.12.1", - "@babel/preset-env": "^7.12.7", - "@babel/preset-typescript": "^7.12.7", - "@types/jest": "^26.0.18", - "@umijs/fabric": "^2.5.6", - "babel-loader": "^8.2.2", - "jest": "^26.6.3", - "rimraf": "^3.0.2", - "ts-jest": "^26.4.4", - "ts-loader": "^8.0.14", - "tslint": "^6.1.3", - "typescript": "^4.1.3", + "@babel/core": "^7.7.7", + "@babel/plugin-proposal-class-properties": "^7.1.0", + "@types/d3-force": "^3.0.4", + "babel-loader": "^8.0.6", + "ts-loader": "^7.0.3", + "typescript": "^4.0.3", "webpack": "^5.38.1", "webpack-cli": "^5.0.2", "worker-loader": "^3.0.7" }, "dependencies": { "@antv/util": "^2.0.13", + "@antv/graphlib": "^2.0.0", "tslib": "^2.5.2" } } diff --git a/packages/graph/src/adjacent-matrix.ts b/packages/graph/src/adjacent-matrix.ts deleted file mode 100644 index 6c484b4..0000000 --- a/packages/graph/src/adjacent-matrix.ts +++ /dev/null @@ -1,38 +0,0 @@ -import { GraphData, Matrix } from "./types"; - -const adjMatrix = (graphData: GraphData, directed?: boolean): Matrix[] => { - const { nodes, edges } = graphData; - const matrix: Matrix[] = []; - // map node with index in data.nodes - const nodeMap: { - [key: string]: number; - } = {}; - - if (!nodes) { - throw new Error("invalid nodes data!"); - } - - if (nodes) { - nodes.forEach((node, i) => { - nodeMap[node.id] = i; - const row: number[] = []; - matrix.push(row); - }); - } - - if (edges) { - edges.forEach((edge) => { - const { source, target } = edge; - const sIndex = nodeMap[source as string]; - const tIndex = nodeMap[target as string]; - if ((!sIndex && sIndex !== 0) || (!tIndex && tIndex !== 0)) return; - matrix[sIndex][tIndex] = 1; - if (!directed) { - matrix[tIndex][sIndex] = 1; - } - }); - } - return matrix; -}; - -export default adjMatrix; diff --git a/packages/graph/src/asyncIndex.ts b/packages/graph/src/asyncIndex.ts deleted file mode 100644 index 1ee629b..0000000 --- a/packages/graph/src/asyncIndex.ts +++ /dev/null @@ -1,69 +0,0 @@ -import { - getAdjMatrixAsync, - connectedComponentAsync, - getDegreeAsync, - getInDegreeAsync, - getOutDegreeAsync, - detectCycleAsync, - detectAllCyclesAsync, - detectAllDirectedCycleAsync, - detectAllUndirectedCycleAsync, - dijkstraAsync, - findAllPathAsync, - findShortestPathAsync, - floydWarshallAsync, - labelPropagationAsync, - louvainAsync, - minimumSpanningTreeAsync, - pageRankAsync, - getNeighborsAsync, - GADDIAsync, -} from './workers/index'; - -const detectDirectedCycleAsync = detectCycleAsync; - -export { - getAdjMatrixAsync, - connectedComponentAsync, - getDegreeAsync, - getInDegreeAsync, - getOutDegreeAsync, - detectCycleAsync, - detectDirectedCycleAsync, - detectAllCyclesAsync, - detectAllDirectedCycleAsync, - detectAllUndirectedCycleAsync, - dijkstraAsync, - findAllPathAsync, - findShortestPathAsync, - floydWarshallAsync, - labelPropagationAsync, - louvainAsync, - minimumSpanningTreeAsync, - pageRankAsync, - getNeighborsAsync, - GADDIAsync, -}; - -export default { - getAdjMatrixAsync, - connectedComponentAsync, - getDegreeAsync, - getInDegreeAsync, - getOutDegreeAsync, - detectCycleAsync, - detectDirectedCycleAsync, - detectAllCyclesAsync, - detectAllDirectedCycleAsync, - detectAllUndirectedCycleAsync, - dijkstraAsync, - findAllPathAsync, - findShortestPathAsync, - floydWarshallAsync, - labelPropagationAsync, - louvainAsync, - minimumSpanningTreeAsync, - pageRankAsync, - getNeighborsAsync, - GADDIAsync, -}; \ No newline at end of file diff --git a/packages/graph/src/bfs.ts b/packages/graph/src/bfs.ts deleted file mode 100644 index 69df6d2..0000000 --- a/packages/graph/src/bfs.ts +++ /dev/null @@ -1,89 +0,0 @@ -import Queue from './structs/queue' -import { GraphData, IAlgorithmCallbacks } from './types'; -import { getNeighbors } from './util'; - -/** - * - * @param callbacks - * allowTraversal: 确定 BFS 是否从顶点沿着边遍历到其邻居，默认情况下，同一个节点只能遍历一次 - * enterNode: 当 BFS 访问某个节点时调用 - * leaveNode: 当 BFS 访问访问结束某个节点时调用 - */ -function initCallbacks(callbacks: IAlgorithmCallbacks = {} as IAlgorithmCallbacks) { - const initiatedCallback = callbacks; - - const stubCallback = () => {}; - - const allowTraversalCallback = (() => { - const seen = {}; - return ({ next }) => { - const id = next; - if (!seen[id]) { - seen[id] = true; - return true; - } - return false; - }; - })(); - - initiatedCallback.allowTraversal = callbacks.allowTraversal || allowTraversalCallback; - initiatedCallback.enter = callbacks.enter || stubCallback; - initiatedCallback.leave = callbacks.leave || stubCallback; - - return initiatedCallback; -} - -/** - * 广度优先遍历图 - * @param graph Graph 图实例 - * @param startNode 开始遍历的节点 - * @param originalCallbacks 回调 - */ -const breadthFirstSearch = ( - graphData: GraphData, - startNodeId: string, - originalCallbacks?: IAlgorithmCallbacks, - directed: boolean = true -) => { - const callbacks = initCallbacks(originalCallbacks); - const nodeQueue = new Queue(); - - const { edges = [] } = graphData - - // 初始化队列元素 - nodeQueue.enqueue(startNodeId); - - let previousNode = ''; - - // 遍历队列中的所有顶点 - while (!nodeQueue.isEmpty()) { - const currentNode: string = nodeQueue.dequeue(); - callbacks.enter({ - current: currentNode, - previous: previousNode, - }); - - // 将所有邻居添加到队列中以便遍历 - getNeighbors(currentNode, edges, directed ? 'target' : undefined).forEach((nextNode) => { - if ( - callbacks.allowTraversal({ - previous: previousNode, - current: currentNode, - next: nextNode, - }) - ) { - nodeQueue.enqueue(nextNode); - } - }); - - callbacks.leave({ - current: currentNode, - previous: previousNode, - }); - - // 下一次循环之前存储当前顶点 - previousNode = currentNode; - } -}; - -export default breadthFirstSearch; diff --git a/packages/graph/src/connected-component.ts b/packages/graph/src/connected-component.ts deleted file mode 100644 index 4db77be..0000000 --- a/packages/graph/src/connected-component.ts +++ /dev/null @@ -1,113 +0,0 @@ -import { GraphData, NodeConfig } from "./types"; -import { getNeighbors } from "./util"; - -/** - * Generate all connected components for an undirected graph - * @param graph - */ -export const detectConnectedComponents = (graphData: GraphData): NodeConfig[][] => { - const { nodes = [], edges = [] } = graphData - const allComponents: NodeConfig[][] = []; - const visited = {}; - const nodeStack: NodeConfig[] = []; - - const getComponent = (node: NodeConfig) => { - nodeStack.push(node); - visited[node.id] = true; - const neighbors = getNeighbors(node.id, edges); - for (let i = 0; i < neighbors.length; ++i) { - const neighbor = neighbors[i]; - if (!visited[neighbor]) { - const targetNode = nodes.filter(node => node.id === neighbor) - if (targetNode.length > 0) { - getComponent(targetNode[0]); - } - } - } - }; - - for (let i = 0; i < nodes.length; i++) { - const node = nodes[i]; - if (!visited[node.id]) { - // 对于无向图进行dfs遍历，每一次调用后都得到一个连通分量 - getComponent(node); - const component = []; - while (nodeStack.length > 0) { - component.push(nodeStack.pop()); - } - allComponents.push(component); - } - } - return allComponents; -} - -/** - * Tarjan's Algorithm 复杂度 O(|V|+|E|) - * For directed graph only - * a directed graph is said to be strongly connected if "every vertex is reachable from every other vertex". - * refer: http://en.wikipedia.org/wiki/Tarjan%27s_strongly_connected_components_algorithm - * @param graph - * @return a list of strongly connected components - */ -export const detectStrongConnectComponents = (graphData: GraphData): NodeConfig[][] => { - const { nodes = [], edges = [] } = graphData - const nodeStack: NodeConfig[] = []; - const inStack = {}; // 辅助判断是否已经在stack中，减少查找开销 - const indices = {}; - const lowLink = {}; - const allComponents: NodeConfig[][] = []; - let index = 0; - - const getComponent = (node: NodeConfig) => { - // Set the depth index for v to the smallest unused index - indices[node.id] = index; - lowLink[node.id] = index; - index += 1; - nodeStack.push(node); - inStack[node.id] = true; - - // 考虑每个邻接点 - const neighbors = getNeighbors(node.id, edges, 'target').filter((n) => nodes.map(node => node.id).indexOf(n) > -1); - for (let i = 0; i < neighbors.length; i++) { - const targetNodeID = neighbors[i]; - if (!indices[targetNodeID] && indices[targetNodeID] !== 0) { - const targetNode = nodes.filter(node => node.id === targetNodeID) - if (targetNode.length > 0) { - getComponent(targetNode[0]); - } - // tree edge - lowLink[node.id] = Math.min(lowLink[node.id], lowLink[targetNodeID]); - } else if (inStack[targetNodeID]) { - // back edge, target node is in the current SCC - lowLink[node.id] = Math.min(lowLink[node.id], indices[targetNodeID]); - } - } - - // If node is a root node, generate an SCC - if (lowLink[node.id] === indices[node.id]) { - const component = []; - while (nodeStack.length > 0) { - const tmpNode = nodeStack.pop(); - inStack[tmpNode.id] = false; - component.push(tmpNode); - if (tmpNode === node) break; - } - if (component.length > 0) { - allComponents.push(component); - } - } - }; - - for (const node of nodes) { - if (!indices[node.id] && indices[node.id] !== 0) { - getComponent(node); - } - } - - return allComponents; -} - -export default function getConnectedComponents(graphData: GraphData, directed?: boolean): NodeConfig[][] { - if (directed) return detectStrongConnectComponents(graphData); - return detectConnectedComponents(graphData); -} diff --git a/packages/graph/src/constants/time.ts b/packages/graph/src/constants/time.ts deleted file mode 100644 index 383bcae..0000000 --- a/packages/graph/src/constants/time.ts +++ /dev/null @@ -1,2 +0,0 @@ -export const secondReg = /^(\d{1,4})(-|\/)(\d{1,2})\2(\d{1,2})$/; -export const dateReg = /^(\d{1,4})(-|\/)(\d{1,2})\2(\d{1,2}) (\d{1,2}):(\d{1,2}):(\d{1,2})$/; diff --git a/packages/graph/src/cosine-similarity.ts b/packages/graph/src/cosine-similarity.ts deleted file mode 100644 index 2b6e25c..0000000 --- a/packages/graph/src/cosine-similarity.ts +++ /dev/null @@ -1,27 +0,0 @@ -import Vector from './utils/vector'; -/** - * cosine-similarity算法 计算余弦相似度 - * @param item 元素 - * @param targetItem 目标元素 - */ -const cosineSimilarity = ( - item: number[], - targetItem: number[], -): number => { - // 目标元素向量 - const targetItemVector = new Vector(targetItem); - // 目标元素向量的模长 - const targetNodeNorm2 = targetItemVector.norm2(); - // 元素向量 - const itemVector = new Vector(item); - // 元素向量的模长 - const itemNorm2 = itemVector.norm2(); - // 计算元素向量和目标元素向量的点积 - const dot = targetItemVector.dot(itemVector); - const norm2Product = targetNodeNorm2 * itemNorm2; - // 计算元素向量和目标元素向量的余弦相似度 - const cosineSimilarity = norm2Product ? dot / norm2Product : 0; - return cosineSimilarity; -} - -export default cosineSimilarity; diff --git a/packages/graph/src/degree.ts b/packages/graph/src/degree.ts deleted file mode 100644 index 8a58adc..0000000 --- a/packages/graph/src/degree.ts +++ /dev/null @@ -1,51 +0,0 @@ -import { GraphData, DegreeType } from "./types"; - -const degree = (graphData: GraphData): DegreeType => { - const degrees: DegreeType = {}; - const { nodes = [], edges = [] } = graphData - - nodes.forEach((node) => { - degrees[node.id] = { - degree: 0, - inDegree: 0, - outDegree: 0, - }; - }); - - edges.forEach((edge) => { - degrees[edge.source].degree++; - degrees[edge.source].outDegree++; - degrees[edge.target].degree++; - degrees[edge.target].inDegree++; - }); - - return degrees; -}; - -export default degree; - -/** - * 获取指定节点的入度 - * @param graphData 图数据 - * @param nodeId 节点ID - */ -export const getInDegree = (graphData: GraphData, nodeId: string): number => { - const nodeDegree = degree(graphData) - if (nodeDegree[nodeId]) { - return degree(graphData)[nodeId].inDegree - } - return 0 -} - -/** - * 获取指定节点的出度 - * @param graphData 图数据 - * @param nodeId 节点ID - */ -export const getOutDegree = (graphData: GraphData, nodeId: string): number => { - const nodeDegree = degree(graphData) - if (nodeDegree[nodeId]) { - return degree(graphData)[nodeId].outDegree - } - return 0 -} diff --git a/packages/graph/src/detect-cycle.ts b/packages/graph/src/detect-cycle.ts deleted file mode 100644 index e6f1b25..0000000 --- a/packages/graph/src/detect-cycle.ts +++ /dev/null @@ -1,346 +0,0 @@ -import dfs from './dfs'; -import getConnectedComponents, { detectStrongConnectComponents } from './connected-component'; -import { GraphData, IAlgorithmCallbacks, NodeConfig } from './types'; -import { getNeighbors } from './util'; - -const detectDirectedCycle = (graphData: GraphData): { - [key: string]: string; -} => { - let cycle: { - [key: string]: string; - } = null; - - const { nodes = [] } = graphData - - const dfsParentMap = {}; - - // 所有没有被访问的节点集合 - const unvisitedSet = {}; - - // 正在被访问的节点集合 - const visitingSet = {}; - - // 所有已经被访问过的节点集合 - const visitedSet = {}; - - // 初始化 unvisitedSet - nodes.forEach((node) => { - unvisitedSet[node.id] = node; - }); - - const callbacks: IAlgorithmCallbacks = { - enter: ({ current: currentNode, previous: previousNode }) => { - if (visitingSet[currentNode]) { - // 如果当前节点正在访问中，则说明检测到环路了 - cycle = {}; - - let currentCycleNode = currentNode; - let previousCycleNode = previousNode; - - while (previousCycleNode !== currentNode) { - cycle[currentCycleNode] = previousCycleNode; - currentCycleNode = previousCycleNode; - previousCycleNode = dfsParentMap[previousCycleNode]; - } - - cycle[currentCycleNode] = previousCycleNode; - } else { - // 如果不存在正在访问集合中，则将其放入正在访问集合，并从未访问集合中删除 - visitingSet[currentNode] = currentNode; - delete unvisitedSet[currentNode]; - - // 更新 DSF parents 列表 - dfsParentMap[currentNode] = previousNode; - } - }, - leave: ({ current: currentNode }) => { - // 如果所有的节点的子节点都已经访问过了，则从正在访问集合中删除掉，并将其移入到已访问集合中， - // 同时也意味着当前节点的所有邻居节点都被访问过了 - visitedSet[currentNode] = currentNode; - delete visitingSet[currentNode]; - }, - allowTraversal: ({ next: nextNode }) => { - // 如果检测到环路则需要终止所有进一步的遍历，否则会导致无限循环遍历 - if (cycle) { - return false; - } - - // 仅允许遍历没有访问的节点，visitedSet 中的都已经访问过了 - return !visitedSet[nextNode]; - }, - }; - - // 开始遍历节点 - while (Object.keys(unvisitedSet).length) { - // 从第一个节点开始进行 DFS 遍历 - const firsetUnVisitedKey = Object.keys(unvisitedSet)[0]; - - dfs(graphData, firsetUnVisitedKey, callbacks); - } - - return cycle; -}; - -/** - * 检测无向图中的所有Base cycles - * refer: https://www.codeproject.com/Articles/1158232/Enumerating-All-Cycles-in-an-Undirected-Graph - * @param graph - * @param nodeIds 节点 ID 的数组 - * @param include 包含或排除指定的节点 - * @return [{[key: string]: INode}] 返回一组base cycles - */ -export const detectAllUndirectedCycle = (graphData: GraphData, nodeIds?: string[], include = true) => { - const allCycles = []; - const components = getConnectedComponents(graphData, false); - - // loop through all connected components - for (const component of components) { - if (!component.length) continue; - const root = component[0]; - const rootId = root.id; - - const stack = [root]; - const parent = { [rootId]: root }; - const used = { [rootId]: new Set() }; - - // walk a spanning tree to find cycles - while (stack.length > 0) { - const curNode = stack.pop(); - const curNodeId = curNode.id; - const neighbors = getNeighbors(curNodeId, graphData.edges); - for (let i = 0; i < neighbors.length; i += 1) { - const neighborId = neighbors[i]; - const neighbor = graphData.nodes.find(node => node.id === neighborId) - // const neighborId = neighbor.get('id'); - if (neighborId === curNodeId) { - // 自环 - allCycles.push({ [neighborId]: curNode }); - } else if (!(neighborId in used)) { - // visit a new node - parent[neighborId] = curNode; - stack.push(neighbor); - used[neighborId] = new Set([curNode]); - } else if (!used[curNodeId].has(neighbor)) { - // a cycle found - let cycleValid = true; - const cyclePath = [neighbor, curNode]; - let p = parent[curNodeId]; - while (used[neighborId].size && !used[neighborId].has(p)) { - cyclePath.push(p); - if (p === parent[p.id]) break; - else p = parent[p.id]; - } - cyclePath.push(p); - - if (nodeIds && include) { - // 如果有指定包含的节点 - cycleValid = false; - if (cyclePath.findIndex((node) => nodeIds.indexOf(node.id) > -1) > -1) { - cycleValid = true; - } - } else if (nodeIds && !include) { - // 如果有指定不包含的节点 - if (cyclePath.findIndex((node) => nodeIds.indexOf(node.id) > -1) > -1) { - cycleValid = false; - } - } - - // 把 node list 形式转换为 cycle 的格式 - if (cycleValid) { - const cycle = {}; - for (let index = 1; index < cyclePath.length; index += 1) { - cycle[cyclePath[index - 1].id] = cyclePath[index]; - } - if (cyclePath.length) { - cycle[cyclePath[cyclePath.length - 1].id] = cyclePath[0]; - } - allCycles.push(cycle); - } - - used[neighborId].add(curNode); - } - } - } - } - - return allCycles; -}; - -/** - * Johnson's algorithm, 时间复杂度 O((V + E)(C + 1))$ and space bounded by O(V + E) - * refer: https://www.cs.tufts.edu/comp/150GA/homeworks/hw1/Johnson%2075.PDF - * refer: https://networkx.github.io/documentation/stable/_modules/networkx/algorithms/cycles.html#simple_cycles - * @param graph - * @param nodeIds 节点 ID 的数组 - * @param include 包含或排除指定的节点 - * @return [{[key: string]: INode}] 返回所有的 simple cycles - */ -export const detectAllDirectedCycle = (graphData: GraphData, nodeIds?: string[], include = true) => { - const path = []; // stack of nodes in current path - const blocked = new Set(); - const B = []; // remember portions of the graph that yield no elementary circuit - const allCycles = []; - const idx2Node: { - [key: string]: NodeConfig; - } = {}; - const node2Idx = {}; - - // 辅助函数： unblock all blocked nodes - const unblock = (thisNode: NodeConfig) => { - const stack = [thisNode]; - while (stack.length > 0) { - const node = stack.pop(); - if (blocked.has(node)) { - blocked.delete(node); - B[node.id].forEach((n) => { - stack.push(n); - }); - B[node.id].clear(); - } - } - }; - - const circuit = (node: NodeConfig, start: NodeConfig, adjList) => { - let closed = false; // whether a path is closed - if (nodeIds && include === false && nodeIds.indexOf(node.id) > -1) return closed; - path.push(node); - blocked.add(node); - - const neighbors = adjList[node.id]; - for (let i = 0; i < neighbors.length; i += 1) { - const neighbor = idx2Node[neighbors[i]]; - if (neighbor === start) { - const cycle = {}; - for (let index = 1; index < path.length; index += 1) { - cycle[path[index - 1].id] = path[index]; - } - if (path.length) { - cycle[path[path.length - 1].id] = path[0]; - } - allCycles.push(cycle); - closed = true; - } else if (!blocked.has(neighbor)) { - if (circuit(neighbor, start, adjList)) { - closed = true; - } - } - } - - if (closed) { - unblock(node); - } else { - for (let i = 0; i < neighbors.length; i += 1) { - const neighbor = idx2Node[neighbors[i]]; - if (!B[neighbor.id].has(node)) { - B[neighbor.id].add(node); - } - } - } - path.pop(); - return closed; - }; - - const { nodes = [] } = graphData; - - // Johnson's algorithm 要求给节点赋顺序，先按节点在数组中的顺序 - for (let i = 0; i < nodes.length; i += 1) { - const node = nodes[i]; - const nodeId = node.id; - node2Idx[nodeId] = i; - idx2Node[i] = node; - } - // 如果有指定包含的节点，则把指定节点排序在前，以便提早结束搜索 - if (nodeIds && include) { - for (let i = 0; i < nodeIds.length; i++) { - const nodeId = nodeIds[i]; - node2Idx[nodes[i].id] = node2Idx[nodeId]; - node2Idx[nodeId] = 0; - idx2Node[0] = nodes.find(node => node.id === nodeId); - idx2Node[node2Idx[nodes[i].id]] = nodes[i]; - } - } - - // 返回 节点顺序 >= nodeOrder 的强连通分量的adjList - const getMinComponentAdj = (components: NodeConfig[][]) => { - let minCompIdx; - let minIdx = Infinity; - - // Find least component and the lowest node - for (let i = 0; i < components.length; i += 1) { - const comp = components[i]; - for (let j = 0; j < comp.length; j++) { - const nodeIdx = node2Idx[comp[j].id]; - if (nodeIdx < minIdx) { - minIdx = nodeIdx; - minCompIdx = i; - } - } - } - - const component = components[minCompIdx]; - const adjList = []; - for (let i = 0; i < component.length; i += 1) { - const node = component[i]; - adjList[node.id] = []; - for (const neighbor of getNeighbors(node.id, graphData.edges, 'target').filter((n) => component.map(c => c.id).indexOf(n) > -1)) { - // 对自环情况 (点连向自身) 特殊处理：记录自环，但不加入adjList - if (neighbor === node.id && !(include === false && nodeIds.indexOf(node.id) > -1)) { - allCycles.push({ [node.id]: node }); - } else { - adjList[node.id].push(node2Idx[neighbor]); - } - } - } - - return { - component, - adjList, - minIdx, - }; - }; - - let nodeIdx = 0; - while (nodeIdx < nodes.length) { - const subgraphNodes = nodes.filter((n) => node2Idx[n.id] >= nodeIdx); - const sccs = detectStrongConnectComponents({ nodes: subgraphNodes, edges: graphData.edges }).filter( - (component) => component.length > 1, - ); - if (sccs.length === 0) break; - - const scc = getMinComponentAdj(sccs); - const { minIdx, adjList, component } = scc; - if (component.length > 1) { - component.forEach((node) => { - B[node.id] = new Set(); - }); - const startNode = idx2Node[minIdx]; - // startNode 不在指定要包含的节点中，提前结束搜索 - if (nodeIds && include && nodeIds.indexOf(startNode.id) === -1) return allCycles; - circuit(startNode, startNode, adjList); - nodeIdx = minIdx + 1; - } else { - break; - } - } - return allCycles; -}; - -/** - * 查找图中所有满足要求的圈 - * @param graph - * @param directed 是否为有向图 - * @param nodeIds 节点 ID 的数组，若不指定，则返回图中所有的圈 - * @param include 包含或排除指定的节点 - * @return [{[key: string]: Node}] 包含所有环的数组，每个环用一个Object表示，其中key为节点id，value为该节点在环中指向的下一个节点 - */ -export const detectAllCycles = ( - graphData: GraphData, - directed?: boolean, - nodeIds?: string[], - include = true, -) => { - if (directed) return detectAllDirectedCycle(graphData, nodeIds, include); - return detectAllUndirectedCycle(graphData, nodeIds, include); -}; - -export default detectDirectedCycle; diff --git a/packages/graph/src/dfs.ts b/packages/graph/src/dfs.ts deleted file mode 100644 index cb0166c..0000000 --- a/packages/graph/src/dfs.ts +++ /dev/null @@ -1,76 +0,0 @@ -import { IAlgorithmCallbacks, GraphData } from './types' -import { getNeighbors } from './util' - -function initCallbacks(callbacks: IAlgorithmCallbacks = {} as IAlgorithmCallbacks) { - const initiatedCallback = callbacks; - - const stubCallback = () => {}; - - const allowTraversalCallback = (() => { - const seen = {}; - return ({ next }) => { - if (!seen[next]) { - seen[next] = true; - return true; - } - return false; - }; - })(); - - initiatedCallback.allowTraversal = callbacks.allowTraversal || allowTraversalCallback; - initiatedCallback.enter = callbacks.enter || stubCallback; - initiatedCallback.leave = callbacks.leave || stubCallback; - - return initiatedCallback; -} - -/** - * @param {Graph} graph - * @param {GraphNode} currentNode - * @param {GraphNode} previousNode - * @param {Callbacks} callbacks - */ -function depthFirstSearchRecursive( - graphData: GraphData, - currentNode: string, - previousNode: string, - callbacks: IAlgorithmCallbacks, -) { - callbacks.enter({ - current: currentNode, - previous: previousNode, - }); - - const { edges = [] } = graphData - - getNeighbors(currentNode, edges, 'target').forEach((nextNode) => { - if ( - callbacks.allowTraversal({ - previous: previousNode, - current: currentNode, - next: nextNode, - }) - ) { - depthFirstSearchRecursive(graphData, nextNode, currentNode, callbacks); - } - }); - - callbacks.leave({ - current: currentNode, - previous: previousNode, - }); -} - -/** - * 深度优先遍历图 - * @param data GraphData 图数据 - * @param startNodeId 开始遍历的节点的 ID - * @param originalCallbacks 回调 - */ -export default function depthFirstSearch( - graphData: GraphData, - startNodeId: string, - callbacks?: IAlgorithmCallbacks, -) { - depthFirstSearchRecursive(graphData, startNodeId, '', initCallbacks(callbacks)); -} diff --git a/packages/graph/src/dijkstra.ts b/packages/graph/src/dijkstra.ts deleted file mode 100644 index a557215..0000000 --- a/packages/graph/src/dijkstra.ts +++ /dev/null @@ -1,105 +0,0 @@ -import { isArray } from '@antv/util'; -import { GraphData, NodeConfig, EdgeConfig } from './types'; -import { getOutEdgesNodeId, getEdgesByNodeId } from './util'; - -const minVertex = ( - D: { [key: string]: number }, - nodes: NodeConfig[], - marks: { [key: string]: boolean }, -): NodeConfig => { - // 找出最小的点 - let minDis = Infinity; - let minNode; - for (let i = 0; i < nodes.length; i++) { - const nodeId = nodes[i].id; - if (!marks[nodeId] && D[nodeId] <= minDis) { - minDis = D[nodeId]; - minNode = nodes[i]; - } - } - return minNode; -}; - -const dijkstra = ( - graphData: GraphData, - source: string, - directed?: boolean, - weightPropertyName?: string, -) => { - const { nodes = [], edges = [] } = graphData; - const nodeIds = []; - const marks = {}; - const D = {}; - const prevs = {}; // key: 顶点, value: 顶点的前驱点数组（可能有多条等长的最短路径） - nodes.forEach((node, i) => { - const id = node.id; - nodeIds.push(id); - D[id] = Infinity; - if (id === source) D[id] = 0; - }); - - const nodeNum = nodes.length; - for (let i = 0; i < nodeNum; i++) { - // Process the vertices - const minNode = minVertex(D, nodes, marks); - const minNodeId = minNode.id; - marks[minNodeId] = true; - - if (D[minNodeId] === Infinity) continue; // Unreachable vertices cannot be the intermediate point - - let relatedEdges: EdgeConfig[] = []; - if (directed) relatedEdges = getOutEdgesNodeId(minNodeId, edges); - else relatedEdges = getEdgesByNodeId(minNodeId, edges); - - relatedEdges.forEach(edge => { - const edgeTarget = edge.target; - const edgeSource = edge.source; - const w = edgeTarget === minNodeId ? edgeSource : edgeTarget; - const weight = weightPropertyName && edge[weightPropertyName] ? edge[weightPropertyName] : 1; - if (D[w] > D[minNode.id] + weight) { - D[w] = D[minNode.id] + weight; - prevs[w] = [minNode.id]; - } else if (D[w] === D[minNode.id] + weight) { - prevs[w].push(minNode.id); - } - }); - } - - prevs[source] = [source]; - // 每个节点存可能存在多条最短路径 - const paths = {}; - for (const target in D) { - if (D[target] !== Infinity) { - findAllPaths(source, target, prevs, paths); - } - } - - // 兼容之前单路径 - const path = {}; - for (const target in paths) { - path[target] = paths[target][0]; - } - return { length: D, path, allPath: paths }; -}; - -export default dijkstra; - -function findAllPaths(source, target, prevs, foundPaths) { - if (source === target) { - return [source]; - } - if (foundPaths[target]) { - return foundPaths[target]; - } - const paths = []; - for (let prev of prevs[target]) { - const prevPaths = findAllPaths(source, prev, prevs, foundPaths); - if (!prevPaths) return; - for (let prePath of prevPaths) { - if (isArray(prePath)) paths.push([...prePath, target]); - else paths.push([prePath, target]); - } - } - foundPaths[target] = paths; - return foundPaths[target]; -} diff --git a/packages/graph/src/find-path.ts b/packages/graph/src/find-path.ts deleted file mode 100644 index 846d46e..0000000 --- a/packages/graph/src/find-path.ts +++ /dev/null @@ -1,70 +0,0 @@ -import dijkstra from './dijkstra'; -import { GraphData } from './types'; -import { getNeighbors } from './util'; - -export const findShortestPath = ( - graphData: GraphData, - start: string, - end: string, - directed?: boolean, - weightPropertyName?: string -) => { - const { length, path, allPath } = dijkstra( - graphData, - start, - directed, - weightPropertyName - ); - return { length: length[end], path: path[end], allPath: allPath[end] }; -}; - -export const findAllPath = ( - graphData: GraphData, - start: string, - end: string, - directed?: boolean -) => { - if (start === end) return [[start]]; - - const { edges = [] } = graphData; - - const visited = [start]; - const isVisited = { [start]: true }; - const stack: string[][] = []; // 辅助栈，用于存储访问过的节点的邻居节点 - const allPath = []; - let neighbors = directed - ? getNeighbors(start, edges, 'target') - : getNeighbors(start, edges); - stack.push(neighbors); - - while (visited.length > 0 && stack.length > 0) { - const children = stack[stack.length - 1]; - if (children.length) { - const child = children.shift(); - if (child) { - visited.push(child); - isVisited[child] = true; - neighbors = directed - ? getNeighbors(child, edges, 'target') - : getNeighbors(child, edges); - stack.push(neighbors.filter(neighbor => !isVisited[neighbor])); - } - } else { - const node = visited.pop(); - isVisited[node] = false; - stack.pop(); - continue; - } - - if (visited[visited.length - 1] === end) { - const path = visited.map(node => node); - allPath.push(path); - - const node = visited.pop(); - isVisited[node] = false; - stack.pop(); - } - } - - return allPath; -}; diff --git a/packages/graph/src/floydWarshall.ts b/packages/graph/src/floydWarshall.ts deleted file mode 100644 index 70e2ffe..0000000 --- a/packages/graph/src/floydWarshall.ts +++ /dev/null @@ -1,34 +0,0 @@ -import getAdjMatrix from "./adjacent-matrix"; -import { GraphData, Matrix } from "./types"; - -const floydWarshall = (graphData: GraphData, directed?: boolean) => { - const adjacentMatrix = getAdjMatrix(graphData, directed); - - const dist: Matrix[] = []; - const size = adjacentMatrix.length; - for (let i = 0; i < size; i += 1) { - dist[i] = []; - for (let j = 0; j < size; j += 1) { - if (i === j) { - dist[i][j] = 0; - } else if (adjacentMatrix[i][j] === 0 || !adjacentMatrix[i][j]) { - dist[i][j] = Infinity; - } else { - dist[i][j] = adjacentMatrix[i][j]; - } - } - } - // floyd - for (let k = 0; k < size; k += 1) { - for (let i = 0; i < size; i += 1) { - for (let j = 0; j < size; j += 1) { - if (dist[i][j] > dist[i][k] + dist[k][j]) { - dist[i][j] = dist[i][k] + dist[k][j]; - } - } - } - } - return dist; -}; - -export default floydWarshall; diff --git a/packages/graph/src/gSpan/gSpan.ts b/packages/graph/src/gSpan/gSpan.ts deleted file mode 100644 index 6e68cd8..0000000 --- a/packages/graph/src/gSpan/gSpan.ts +++ /dev/null @@ -1,954 +0,0 @@ -import { GraphData } from "../types"; -import { clone } from "@antv/util"; -import { - Graph, - Edge, - VACANT_NODE_LABEL, - VACANT_GRAPH_ID, - Node, - VACANT_EDGE_LABEL, -} from "./struct"; - -export interface EdgeMap { - [key: string]: { - // key 的格式为 source-target - idx: number; // 该边在原图 graphData.edges 的序号 - edge: any; - }; -} - -export interface NodeMap { - [key: string]: { - // key 格式为 node.id - idx: number; // 该j客店在原图 graphData.nodes 的序号 - node: any; - degree: number; - inDegree: number; - outDegree: number; - }; -} - -interface PDFS { - graphId: number; - edge: any; - preNode: any; -} - -class DFSedge { - public fromNode: number; - public toNode: number; - public nodeEdgeNodeLabel: { - nodeLabel1: string; - edgeLabel: string; - nodeLabel2: string; - }; - - constructor( - fromNode: number, - toNode: number, - fromNodeLabel: string, - edgeLabel: string, - toNodeLabel: string - ) { - this.fromNode = fromNode; - this.toNode = toNode; - this.nodeEdgeNodeLabel = { - nodeLabel1: fromNodeLabel || VACANT_NODE_LABEL, - edgeLabel: edgeLabel || VACANT_EDGE_LABEL, - nodeLabel2: toNodeLabel || VACANT_NODE_LABEL, - }; - } - - equalTo(other) { - return ( - this.fromNode === other.formNode && - this.toNode === other.toNode && - this.nodeEdgeNodeLabel === other.nodeEdgeNodeLabel - ); - } - - notEqualTo(other) { - return !this.equalTo(other); - } -} - -// DFScode 是 DESedge 的数组 -class DFScode { - public dfsEdgeList: DFSedge[]; - public rmpath: any; - - constructor() { - this.rmpath = []; - this.dfsEdgeList = []; - } - - equalTo(other) { - const aLength = this.dfsEdgeList.length; - const bLength = other.length; - if (aLength !== bLength) return false; - for (let i = 0; i < aLength; i++) { - if (this.dfsEdgeList[i] !== other[i]) return false; - } - return true; - } - - notEqualTo(other) { - return !this.equalTo(other); - } - - /** 增加一条 edge 到 DFScode */ - pushBack(fromNode, toNode, fromNodeLabel, edgeLabel, toNodeLabel) { - this.dfsEdgeList.push( - new DFSedge(fromNode, toNode, fromNodeLabel, edgeLabel, toNodeLabel) - ); - return this.dfsEdgeList; - } - - /** 根据 dfs 构建图 */ - toGraph(graphId: number = VACANT_GRAPH_ID, directed = false) { - const graph = new Graph(graphId, true, directed); - this.dfsEdgeList.forEach((dfsEdge) => { - const fromNodeId = dfsEdge.fromNode; - const toNodeId = dfsEdge.toNode; - const { nodeLabel1, edgeLabel, nodeLabel2 } = dfsEdge.nodeEdgeNodeLabel; - - if (nodeLabel1 !== VACANT_NODE_LABEL) graph.addNode(fromNodeId, nodeLabel1); - if (nodeLabel2 !== VACANT_NODE_LABEL) graph.addNode(toNodeId, nodeLabel2); - if (nodeLabel1 !== VACANT_NODE_LABEL && nodeLabel2 !== nodeLabel1) graph.addEdge(undefined, fromNodeId, toNodeId, edgeLabel); - }); - return graph; - } - - // 建立 rightmost path - buildRmpath() { - this.rmpath = []; - let oldFrom = undefined; - const selfLength = this.dfsEdgeList.length; - for (let i = selfLength - 1; i >= 0; i--) { - const dfsEdge = this.dfsEdgeList[i]; - const fromNodeIdx = dfsEdge.fromNode; - const toNodeIdx = dfsEdge.toNode; - if ( - fromNodeIdx < toNodeIdx && - (oldFrom === undefined || toNodeIdx === oldFrom) - ) { - this.rmpath.push(i); - oldFrom = fromNodeIdx; - } - } - return this.rmpath; - } - - getNodeNum() { - const nodeMap = {}; - this.dfsEdgeList.forEach((dfsEdge) => { - if (!nodeMap[dfsEdge.fromNode]) nodeMap[dfsEdge.fromNode] = true; - if (!nodeMap[dfsEdge.toNode]) nodeMap[dfsEdge.toNode] = true; - }); - return Object.keys(nodeMap).length; - } -} - -class History { - public his: object; - public edges: Edge[]; - public nodesUsed: object; - public edgesUsed: object; - - constructor(pdfs: PDFS) { - this.his = {}; - this.nodesUsed = {}; - this.edgesUsed = {}; - this.edges = []; - if (!pdfs) return; - while (pdfs) { - const e = pdfs.edge; - this.edges.push(e); - this.nodesUsed[e.from] = 1; - this.nodesUsed[e.to] = 1; - this.edgesUsed[e.id] = 1; - pdfs = pdfs.preNode; - } - // 倒序 - this.edges = this.edges.reverse(); - } - - hasNode(node: Node) { - return this.nodesUsed[node.id] === 1; - } - - hasEdge(edge: Edge) { - return this.edgesUsed[edge.id] === 1; - } -} - -interface Root { - [key: string]: { - projected: PDFS[]; - nodeLabel1?: string; - edgeLabel?: string; - nodeLabel2?: string; - fromNodeId?: number; - toNodeId?: number; - }; -} - -interface GraphDataMap { - [key: string]: GraphData; -} -interface GraphMap { - [key: number]: Graph; -} - -interface AlgorithmProps { - graphs: GraphMap; // 图数据 - minSupport: number; // 算法参数，最小支持数量，根据 graphs 内图的数量指定 - directed?: boolean; // 是否有向图，默认为 false - minNodeNum?: number; // 每个子图中边的最少个数，默认为 1 - maxNodeNum?: number; // 每个子图中边的最多个数，默认为 4 - top?: number; // 返回前 top 个频繁子图，默认为 10 - verbose?: boolean; -} - -class GSpan { - public graphs: GraphMap; - public dfsCode: DFScode; - public support: number; - public frequentSize1Subgraphs: GraphData[]; - public frequentSubgraphs: Graph[]; - public reportDF: []; - public maxNodeNum: number; - public minNodeNum: number; - public minSupport: number; - public top: number; - public directed: boolean; - private counter: number; // 用于生成图的 id，自增 - public verbose: boolean; - - constructor({ - graphs, - minSupport = 2, - minNodeNum = 1, - maxNodeNum = 4, - top = 10, - directed = false, - verbose = false, - }: AlgorithmProps) { - // -------- 第零步，初始化------- - this.graphs = graphs; - this.dfsCode = new DFScode(); - this.support = 0; - this.frequentSize1Subgraphs = []; - this.frequentSubgraphs = []; - this.minSupport = minSupport; - this.top = top; - this.directed = directed; - this.counter = 0; - // TODO? timestamp = {} - this.maxNodeNum = maxNodeNum; - this.minNodeNum = minNodeNum; - this.verbose = verbose; - if (this.maxNodeNum < this.minNodeNum) this.maxNodeNum = this.minNodeNum; - this.reportDF = []; // matrix - } - - // Line 352 - findForwardRootEdges(graph: Graph, fromNode: Node): Edge[] { - const result = []; - const nodeMap = graph.nodeMap; - fromNode.edges.forEach((edge) => { - if (this.directed || fromNode.label <= nodeMap[edge.to].label) - result.push(edge); - }); - - return result; - } - - findBackwardEdge( - graph: Graph, - edge1: Edge, - edge2: Edge, - history: History - ): Edge { - if (!this.directed && edge1 === edge2) return null; - const nodeMap = graph.nodeMap; - const edge2To = nodeMap[edge2.to]; - const edge2ToEdges = edge2To.edges; - const edgeLength = edge2ToEdges.length; - for (let i = 0; i < edgeLength; i++) { - const edge = edge2ToEdges[i]; - if (history.hasEdge(edge) || edge.to !== edge1.from) continue; - if (!this.directed) { - if ( - edge1.label < edge.label || - (edge1.label === edge.label && - nodeMap[edge1.to].label <= nodeMap[edge2.to].label) - ) { - return edge; - } - } else { - if ( - nodeMap[edge1.from].label < nodeMap[edge2.to].label || - (nodeMap[edge1.from].label === nodeMap[edge2.to].label && - edge1.label <= edge.label) - ) { - return edge; - } - } - } - return null; - } - - findForwardPureEdges( - graph, - rightmostEdge, - minNodeLabel, - history: History - ): Edge[] { - const result = []; - const rightmostEdgeToId = rightmostEdge.to; - const edges = graph.nodeMap[rightmostEdgeToId].edges; - const edgeLength = edges.length; - for (let i = 0; i < edgeLength; i++) { - const edge = edges[i]; - const toNode = graph.nodeMap[edge.to]; - if (minNodeLabel <= toNode.label && !history.hasNode(toNode)) { - result.push(edge); - } - } - return result; - } - - findForwardRmpathEdges( - graph: Graph, - rightmostEdge: Edge, - minNodeLabel: string, - history: History - ): Edge[] { - const result = []; - const nodeMap = graph.nodeMap; - const toNodeLabel = nodeMap[rightmostEdge.to].label; - const fromNode = nodeMap[rightmostEdge.from]; - const edges = fromNode.edges; - const edgeLength = edges.length; - for (let i = 0; i < edgeLength; i++) { - const edge = edges[i]; - const newToNodeLabel = nodeMap[edge.to].label; - if ( - rightmostEdge.to === edge.to || - minNodeLabel > newToNodeLabel || - history.hasNode(nodeMap[edge.to]) - ) { - continue; - } - if ( - rightmostEdge.label < edge.label || - (rightmostEdge.label === edge.label && toNodeLabel <= newToNodeLabel) - ) { - result.push(edge); - } - } - return result; - } - - getSupport(projected: PDFS[]): number { - const graphMap = {}; - projected.forEach((pro) => { - if (!graphMap[pro.graphId]) graphMap[pro.graphId] = true; - }); - return Object.keys(graphMap).length; - } - - findMinLabel( - obj: Root - ): { - nodeLabel1?: string; - edgeLabel: string; - nodeLabel2?: string; - } { - let minLabel = undefined; - Object.keys(obj).forEach((nodeEdgeNodeLabel) => { - const { nodeLabel1, edgeLabel, nodeLabel2 } = obj[nodeEdgeNodeLabel]; - if (!minLabel) { - minLabel = { - nodeLabel1, - edgeLabel, - nodeLabel2, - }; - return; - } - if ( - nodeLabel1 < minLabel.nodeLabel1 || - (nodeLabel1 === minLabel.nodeLabel1 && - edgeLabel < minLabel.edgeLabel) || - (nodeLabel1 === minLabel.nodeLabel1 && - edgeLabel === minLabel.edgeLabel && - nodeLabel2 < minLabel.nodeLabel2) - ) { - minLabel = { - nodeLabel1, - edgeLabel, - nodeLabel2, - }; - } - }); - return minLabel; - } - - isMin() { - const dfsCode = this.dfsCode; - if (this.verbose) console.log("isMin checking", dfsCode); - if (dfsCode.dfsEdgeList.length === 1) return true; - const directed = this.directed; - const graph = dfsCode.toGraph(VACANT_GRAPH_ID, directed); - const nodeMap = graph.nodeMap; - const dfsCodeMin = new DFScode(); - const root: Root = {}; - graph.nodes.forEach((node) => { - const forwardEdges = this.findForwardRootEdges(graph, node); - forwardEdges.forEach((edge) => { - let otherNode = nodeMap[edge.to]; - const nodeEdgeNodeLabel = `${node.label}-${edge.label}-${otherNode.label}`; - if (!root[nodeEdgeNodeLabel]) - root[nodeEdgeNodeLabel] = { - projected: [], - nodeLabel1: node.label, - edgeLabel: edge.label, - nodeLabel2: otherNode.label, - }; - const pdfs: PDFS = { - graphId: graph.id, - edge, - preNode: null, - }; - root[nodeEdgeNodeLabel].projected.push(pdfs); - }); - }); - - // 比较 root 中每一项的 nodeEdgeNodeLabel 大小，按照 nodeLabel1、edgeLabe、nodeLabel2 的顺序比较 - let minLabel = this.findMinLabel(root); // line 419 - if (!minLabel) return; - dfsCodeMin.dfsEdgeList.push( - new DFSedge( - 0, - 1, - minLabel.nodeLabel1, - minLabel.edgeLabel, - minLabel.nodeLabel2 - ) - ); - - // line 423 - const projectIsMin = (projected: PDFS[]) => { - // right most path - const rmpath = dfsCodeMin.buildRmpath(); - const minNodeLabel = - dfsCodeMin.dfsEdgeList[0].nodeEdgeNodeLabel.nodeLabel1; - const maxToC = dfsCodeMin.dfsEdgeList[rmpath[0]].toNode; // node id - - const backwardRoot: Root = {}; - let flag = false, - newTo = 0; - let end = directed ? -1 : 0; // 遍历到 1 还是到 0 - for (let i = rmpath.length - 1; i > end; i--) { - if (flag) break; - // line 435 - projected.forEach((p) => { - const history = new History(p); - const backwardEdge = this.findBackwardEdge( - graph, - history.edges[rmpath[i]], - history.edges[rmpath[0]], - history - ); - if (backwardEdge) { - // Line 441 - if (!backwardRoot[backwardEdge.label]) { - backwardRoot[backwardEdge.label] = { - projected: [], - edgeLabel: backwardEdge.label, - }; - } - backwardRoot[backwardEdge.label].projected.push({ - graphId: graph.id, - edge: backwardRoot, - preNode: p, - }); - newTo = dfsCodeMin.dfsEdgeList[rmpath[i]].fromNode; - flag = true; - } - }); - } - - if (flag) { - const minBackwardEdgeLabel = this.findMinLabel(backwardRoot); - dfsCodeMin.dfsEdgeList.push( - new DFSedge( - maxToC, - newTo, - VACANT_NODE_LABEL, - minBackwardEdgeLabel.edgeLabel, - VACANT_NODE_LABEL - ) - ); - const idx = dfsCodeMin.dfsEdgeList.length - 1; - if (this.dfsCode.dfsEdgeList[idx] !== dfsCodeMin.dfsEdgeList[idx]) - return false; - return projectIsMin( - backwardRoot[minBackwardEdgeLabel.edgeLabel].projected - ); - } - const forwardRoot: Root = {}; - flag = false; - let newFrom = 0; - projected.forEach((p) => { - const history = new History(p); - const forwardPureEdges = this.findForwardPureEdges( - graph, - history.edges[rmpath[0]], - minNodeLabel, - history - ); - if (forwardPureEdges.length > 0) { - flag = true; - newFrom = maxToC; - forwardPureEdges.forEach((edge) => { - const key = `${edge.label}-${nodeMap[edge.to].label}`; - if (!forwardRoot[key]) - forwardRoot[key] = { - projected: [], - edgeLabel: edge.label, - nodeLabel2: nodeMap[edge.to].label, - }; - forwardRoot[key].projected.push({ - graphId: graph.id, - edge, - preNode: p, - }); - }); - } - }); - - const pathLength = rmpath.length; - for (let i = 0; i < pathLength; i++) { - if (flag) break; - const value = rmpath[i]; - projected.forEach((p) => { - const history = new History(p); - const forwardRmpathEdges = this.findForwardRmpathEdges( - graph, - history.edges[value], - minNodeLabel, - history - ); - if (forwardRmpathEdges.length > 0) { - flag = true; - newFrom = dfsCodeMin.dfsEdgeList[value].fromNode; - forwardRmpathEdges.forEach((edge) => { - const key = `${edge.label}-${nodeMap[edge.to].label}`; - if (!forwardRoot[key]) - forwardRoot[key] = { - projected: [], - edgeLabel: edge.label, - nodeLabel2: nodeMap[edge.to].label, - }; - forwardRoot[key].projected.push({ - graphId: graph.id, - edge, - preNode: p, - }); - }); - } - }); - } - - if (!flag) return true; - - const forwardMinEdgeNodeLabel = this.findMinLabel(forwardRoot); - dfsCodeMin.dfsEdgeList.push( - new DFSedge( - newFrom, - maxToC + 1, - VACANT_NODE_LABEL, - forwardMinEdgeNodeLabel.edgeLabel, - forwardMinEdgeNodeLabel.nodeLabel2 - ) - ); - const idx = dfsCodeMin.dfsEdgeList.length - 1; - if (dfsCode.dfsEdgeList[idx] !== dfsCodeMin.dfsEdgeList[idx]) - return false; - return projectIsMin( - forwardRoot[ - `${forwardMinEdgeNodeLabel.edgeLabel}-${forwardMinEdgeNodeLabel.nodeLabel2}` - ].projected - ); - }; - const key = `${minLabel.nodeLabel1}-${minLabel.edgeLabel}-${minLabel.nodeLabel2}`; - return projectIsMin(root[key].projected); - } - - report() { - if (this.dfsCode.getNodeNum() < this.minNodeNum) return; - this.counter++; - const graph = this.dfsCode.toGraph(this.counter, this.directed); - this.frequentSubgraphs.push(clone(graph)); - } - - subGraphMining(projected) { - const support = this.getSupport(projected); - if (support < this.minSupport) return; - if (!this.isMin()) return; - this.report(); - - const nodeNum = this.dfsCode.getNodeNum(); - const rmpath = this.dfsCode.buildRmpath(); - const maxToC = this.dfsCode.dfsEdgeList[rmpath[0]].toNode; - const minNodeLabel = this.dfsCode.dfsEdgeList[0].nodeEdgeNodeLabel - .nodeLabel1; - - const forwardRoot: Root = {}; - const backwardRoot: Root = {}; - - projected.forEach((p) => { - const graph = this.graphs[p.graphId]; - const nodeMap = graph.nodeMap; - const history = new History(p); - // backward Line 526 - for (let i = rmpath.length - 1; i >= 0; i--) { - const backwardEdge = this.findBackwardEdge( - graph, - history.edges[rmpath[i]], - history.edges[rmpath[0]], - history - ); - if (backwardEdge) { - const key = `${this.dfsCode.dfsEdgeList[rmpath[i]].fromNode}-${ - backwardEdge.label - }`; - if (!backwardRoot[key]) - backwardRoot[key] = { - projected: [], - toNodeId: this.dfsCode.dfsEdgeList[rmpath[i]].fromNode, - edgeLabel: backwardEdge.label, - }; - backwardRoot[key].projected.push({ - graphId: p.graphId, - edge: backwardEdge, - preNode: p, - }); - } - } - - // pure forward - if (nodeNum >= this.maxNodeNum) return; - const forwardPureEdges = this.findForwardPureEdges( - graph, - history.edges[rmpath[0]], - minNodeLabel, - history - ); - forwardPureEdges.forEach((edge) => { - const key = `${maxToC}-${edge.label}-${nodeMap[edge.to].label}`; - if (!forwardRoot[key]) - forwardRoot[key] = { - projected: [], - fromNodeId: maxToC, - edgeLabel: edge.label, - nodeLabel2: nodeMap[edge.to].label, - }; - forwardRoot[key].projected.push({ - graphId: p.graphId, - edge, - preNode: p, - }); - }); - - // rmpath forward - for (let i = 0; i < rmpath.length; i++) { - const forwardRmpathEdges = this.findForwardRmpathEdges( - graph, - history.edges[rmpath[i]], - minNodeLabel, - history - ); - forwardRmpathEdges.forEach((edge) => { - const key = `${this.dfsCode.dfsEdgeList[rmpath[i]].fromNode}-${ - edge.label - }-${nodeMap[edge.to].label}`; - if (!forwardRoot[key]) - forwardRoot[key] = { - projected: [], - fromNodeId: this.dfsCode.dfsEdgeList[rmpath[i]].fromNode, - edgeLabel: edge.label, - nodeLabel2: nodeMap[edge.to].label, - }; - forwardRoot[key].projected.push({ - graphId: p.graphId, - edge, - preNode: p, - }); - }); - } - }); - - // backward - Object.keys(backwardRoot).forEach((key) => { - const { toNodeId, edgeLabel } = backwardRoot[key]; - this.dfsCode.dfsEdgeList.push( - new DFSedge(maxToC, toNodeId, "-1", edgeLabel, "-1") - ); - this.subGraphMining(backwardRoot[key].projected); - this.dfsCode.dfsEdgeList.pop(); - }); - - // forward - Object.keys(forwardRoot).forEach((key) => { - const { fromNodeId, edgeLabel, nodeLabel2 } = forwardRoot[key]; - this.dfsCode.dfsEdgeList.push( - new DFSedge( - fromNodeId, - maxToC + 1, - VACANT_NODE_LABEL, - edgeLabel, - nodeLabel2 - ) - ); - this.subGraphMining(forwardRoot[key].projected); - this.dfsCode.dfsEdgeList.pop(); - }); - } - - generate1EdgeFrequentSubGraphs() { - const graphs = this.graphs; - const directed = this.directed; - const minSupport = this.minSupport; - const frequentSize1Subgraphs = this.frequentSize1Subgraphs; - let nodeLabelCounter = {}, - nodeEdgeNodeCounter = {}; - // 保存各个图和各自节点的关系 map，key 格式为 graphKey-node类型 - const nodeLableCounted = {}; - // 保存各个图和各自边的关系 map，key 格式为 graphKey-fromNode类型-edge类型-toNode类型 - const nodeEdgeNodeLabelCounted = {}; - Object.keys(graphs).forEach((key) => { - // Line 271 - const graph = graphs[key]; - const nodeMap = graph.nodeMap; - // 遍历节点，记录对应图 与 每个节点的 label 到 nodeLableCounted - graph.nodes.forEach((node, i) => { - // Line 272 - const nodeLabel = node.label; - const graphNodeKey = `${key}-${nodeLabel}`; - if (!nodeLableCounted[graphNodeKey]) { - let counter = nodeLabelCounter[nodeLabel] || 0; - counter++; - nodeLabelCounter[nodeLabel] = counter; - } - nodeLableCounted[graphNodeKey] = { - graphKey: key, - label: nodeLabel, - }; - // 遍历该节点的所有边，记录各个图和各自边的关系到 nodeEdgeNodeLabelCounted. Line 276 - node.edges.forEach((edge) => { - let nodeLabel1 = nodeLabel; - let nodeLabel2 = nodeMap[edge.to].label; - if (!directed && nodeLabel1 > nodeLabel2) { - const tmp = nodeLabel2; - nodeLabel2 = nodeLabel1; - nodeLabel1 = tmp; - } - const edgeLabel = edge.label; - - const graphNodeEdgeNodeKey = `${key}-${nodeLabel1}-${edgeLabel}-${nodeLabel2}`; - const nodeEdgeNodeKey = `${nodeLabel1}-${edgeLabel}-${nodeLabel2}`; - - if (!nodeEdgeNodeCounter[nodeEdgeNodeKey]) { - let counter = nodeEdgeNodeCounter[nodeEdgeNodeKey] || 0; - counter++; - nodeEdgeNodeCounter[nodeEdgeNodeKey] = counter; // Line281 - } - nodeEdgeNodeLabelCounted[graphNodeEdgeNodeKey] = { - graphId: key, - nodeLabel1, - edgeLabel, - nodeLabel2, - }; - }); - }); - }); - - // 计算频繁的节点 - Object.keys(nodeLabelCounter).forEach((label) => { - const count = nodeLabelCounter[label]; - if (count < minSupport) return; - const g = { nodes: [], edges: [] }; - g.nodes.push({ - id: "0", - label, - }); - frequentSize1Subgraphs.push(g); - // if (minNodeNum <= 1) reportSize1 TODO - }); - - return frequentSize1Subgraphs; - } - - run() { - // -------- 第一步, _generate_1edge_frequent_subgraphs：频繁的单个节点------- - this.frequentSize1Subgraphs = this.generate1EdgeFrequentSubGraphs(); - - if (this.maxNodeNum < 2) return; - - const graphs = this.graphs; - const directed = this.directed; - - // PDFS 数组的 map Line 304 - const root: Root = {}; - Object.keys(graphs).forEach((graphId: any) => { - const graph = graphs[graphId]; - const nodeMap = graph.nodeMap; - // Line 306 - graph.nodes.forEach((node) => { - const forwardRootEdges = this.findForwardRootEdges(graph, node); - // Line 308 - forwardRootEdges.forEach((edge) => { - let toNode = nodeMap[edge.to]; - const nodeEdgeNodeLabel = `${node.label}-${edge.label}-${toNode.label}`; - if (!root[nodeEdgeNodeLabel]) - root[nodeEdgeNodeLabel] = { - projected: [], - nodeLabel1: node.label as string, - edgeLabel: edge.label as string, - nodeLabel2: toNode.label as string, - }; - const pdfs: PDFS = { - graphId, - edge, - preNode: null, - }; - root[nodeEdgeNodeLabel].projected.push(pdfs); - }); - }); - }); - - // Line 313 - Object.keys(root).forEach((nodeEdgeNodeLabel) => { - const { projected, nodeLabel1, edgeLabel, nodeLabel2 } = root[ - nodeEdgeNodeLabel - ]; - - this.dfsCode.dfsEdgeList.push( - new DFSedge(0, 1, nodeLabel1, edgeLabel, nodeLabel2) - ); - this.subGraphMining(projected); - this.dfsCode.dfsEdgeList.pop(); - }); - } -} - -const formatGraphs = ( - graphs: GraphDataMap, - directed: boolean, - nodeLabelProp: string, - edgeLabelProp: string -): GraphMap => { - const result: { [key: number]: Graph } = {}; - Object.keys(graphs).forEach((key, i) => { - const graph = graphs[key]; - const fGraph = new Graph(i, true, directed); - const nodeIdxMap = {}; - graph.nodes.forEach((node, j) => { - fGraph.addNode(j, node[nodeLabelProp]); - nodeIdxMap[node.id] = j; - }); - graph.edges.forEach((edge, k) => { - const sourceIdx = nodeIdxMap[edge.source]; - const targetIdx = nodeIdxMap[edge.target]; - fGraph.addEdge(-1, sourceIdx, targetIdx, edge[edgeLabelProp]); - }); - if (fGraph && fGraph.getNodeNum()) result[fGraph.id] = fGraph; - }); - return result; -}; - -const toGraphDatas = ( - graphs: Graph[], - nodeLabelProp: string, - edgeLabelProp: string -) => { - const result = []; - graphs.forEach((graph) => { - const graphData = { nodes: [], edges: [] }; - graph.nodes.forEach((node) => { - graphData.nodes.push({ - id: `${node.id}`, - [nodeLabelProp]: node.label, - }); - }); - graph.edges.forEach((edge) => { - graphData.edges.push({ - source: `${edge.from}`, - target: `${edge.to}`, - [edgeLabelProp]: edge.label, - }); - }); - result.push(graphData); - }); - return result; -}; - -interface Props { - graphs: GraphDataMap; // 图数据 - minSupport: number; // 算法参数，最小支持数量，根据 graphs 内图的数量指定 - directed?: boolean; // 是否有向图，默认为 false - nodeLabelProp?: string; // 节点类型的属性名 - edgeLabelProp?: string; // 边类型的属性名 - minNodeNum?: number; // 每个子图中节点的最少个数，默认为 1 - maxNodeNum?: number; // 每个子图中节点的最多个数，默认为 4 - top?: number; // 返回前 top 个频繁子图，默认为 10 - verbose?: boolean; -} - -const DEFAULT_LABEL_NAME = "cluster"; - -/** - * gSpan 频繁子图计算算法（frequent graph mining） - * @param params 参数 - */ -const gSpan = (params: Props): GraphData[] => { - // ------- 将图数据 GraphData 的 map 转换为格式 ------- - const { - graphs, - directed = false, - nodeLabelProp = DEFAULT_LABEL_NAME, - edgeLabelProp = DEFAULT_LABEL_NAME, - } = params; - const formattedGraphs = formatGraphs( - graphs, - directed, - nodeLabelProp, - edgeLabelProp - ); - const { minSupport, maxNodeNum, minNodeNum, verbose, top } = params; - - // ------- 初始化与执行算法 ------- - const algoParams = { - graphs: formattedGraphs, - minSupport, - maxNodeNum, - minNodeNum, - top, - verbose, - directed, - }; - const calculator = new GSpan(algoParams); - calculator.run(); - - const result = toGraphDatas( - calculator.frequentSubgraphs, - nodeLabelProp, - edgeLabelProp - ); - return result; -}; - -export default gSpan; diff --git a/packages/graph/src/gSpan/struct.ts b/packages/graph/src/gSpan/struct.ts deleted file mode 100644 index 03de226..0000000 --- a/packages/graph/src/gSpan/struct.ts +++ /dev/null @@ -1,114 +0,0 @@ -import { indexOf } from "@antv/util"; - -export const VACANT_EDGE_ID = -1; -export const VACANT_NODE_ID = -1; -export const VACANT_EDGE_LABEL = "-1"; -export const VACANT_NODE_LABEL = "-1"; -export const VACANT_GRAPH_ID = -1; -export const AUTO_EDGE_ID = "-1"; - -export class Edge { - public id: number; - public from: number; - public to: number; - public label: string; - - constructor( - id = VACANT_EDGE_ID, - from = VACANT_NODE_ID, - to = VACANT_NODE_ID, - label = VACANT_EDGE_LABEL - ) { - this.id = id; - this.from = from; - this.to = to; - this.label = label; - } -} - -export class Node { - public id: number; - public from: number; - public to: number; - public label: string; - public edges: Edge[]; - public edgeMap: {}; - - constructor(id = VACANT_NODE_ID, label = VACANT_NODE_LABEL) { - this.id = id; - this.label = label; - this.edges = []; - this.edgeMap = {}; - } - - addEdge(edge) { - this.edges.push(edge); - this.edgeMap[edge.id] = edge; - } -} - -export class Graph { - public id: number; - public from: number; - public to: number; - public label: string; - public edgeIdAutoIncrease: boolean; - public nodes: Node[]; - public edges: Edge[]; - public nodeMap: {}; - public edgeMap: {}; - public nodeLabelMap: {}; // key 是 label，value 是节点 id 的数组 - public edgeLabelMap: {}; - private counter: number; // 自增用于自动生成边 id - public directed: boolean; - - constructor( - id = VACANT_NODE_ID, - edgeIdAutoIncrease = true, - directed = false - ) { - this.id = id; - this.edgeIdAutoIncrease = edgeIdAutoIncrease; - this.edges = []; - this.nodes = []; - this.nodeMap = {}; - this.edgeMap = {}; - this.nodeLabelMap = {}; - this.edgeLabelMap = {}; - this.counter = 0; - this.directed = directed; - } - - getNodeNum() { - return this.nodes.length; - } - - addNode(id: number, label: string) { - if (this.nodeMap[id]) return; - const node = new Node(id, label); - this.nodes.push(node); - this.nodeMap[id] = node; - if (!this.nodeLabelMap[label]) this.nodeLabelMap[label] = []; - this.nodeLabelMap[label].push(id); - } - - addEdge(id: number, from: number, to: number, label: string) { - if (this.edgeIdAutoIncrease || id === undefined) id = this.counter++; - if (this.nodeMap[from] && this.nodeMap[to] && this.nodeMap[to].edgeMap[id]) - return; - const edge = new Edge(id, from, to, label); - this.edges.push(edge); - this.edgeMap[id] = edge; - - this.nodeMap[from].addEdge(edge); - - if (!this.edgeLabelMap[label]) this.edgeLabelMap[label] = []; - this.edgeLabelMap[label].push(edge); - - if (!this.directed) { - const rEdge = new Edge(id, to, from, label); - this.nodeMap[to].addEdge(rEdge); - this.edgeLabelMap[label].push(rEdge); - } - } -} diff --git a/packages/graph/src/gaddi.ts b/packages/graph/src/gaddi.ts deleted file mode 100644 index b9a61bf..0000000 --- a/packages/graph/src/gaddi.ts +++ /dev/null @@ -1,1211 +0,0 @@ -import floydWarshall from './floydWarshall'; -import { GraphData, Matrix } from './types'; -import gSpan, { EdgeMap, NodeMap } from './gSpan/gSpan'; -import dijkstra from './dijkstra'; -import { uniqueId } from './util'; - -/** 节点对 map */ -interface NodePairMap { - [key: string]: { - // key 的格式为 startNodeIdx-endNodeIdx - start: number; // 第一个节点的 idx - end: number; // 第二个节点的 idx - distance: number; // 两节点最短路径长度 - }; -} - -interface LabelMap { - [label: string]: any; -} - -/** 邻居单元类型 */ -interface NeighborUnit { - nodeId: string; - nodeIdx: number; - nodeIdxs: number[]; // the first one is nodeIdx - neighbors: any[]; // - neighborNum: number; - nodeLabelCountMap: { - [label: string]: { - count: number; - dists: number[]; // 按照从小到大排序的距离数组 - }; - }; -} - -/** 节点对的邻居交集的诱导子图 map */ -interface InterGraphMap { - [key: string]: GraphData; // key 格式由节点对的 idx 组成：beginIdx-endIdx，和 nodePairMap 对应 -} - -/** - * 为 graphData 中每个节点生成邻居单元数组 - * @param graphData - * @param spm - * @param nodeLabelProp - * @param k k-近邻 - */ -const findKNeighborUnits = ( - graphData: GraphData, - spm: Matrix[], - nodeLabelProp: string = 'cluster', - k: number = 2, -): NeighborUnit[] => { - const units: NeighborUnit[] = []; - const nodes = graphData.nodes; - spm.forEach((row: number[], i) => { - units.push(findKNeighborUnit(nodes, row, i, nodeLabelProp, k)); - }); - return units; -}; - -const findKNeighborUnit = (nodes, row, i, nodeLabelProp, k) => { - const unitNodeIdxs = [i]; - const neighbors = []; - const labelCountMap = {}; - row.forEach((v, j) => { - if (v <= k && i !== j) { - unitNodeIdxs.push(j); - neighbors.push(nodes[j]); - const label = nodes[j][nodeLabelProp]; - if (!labelCountMap[label]) labelCountMap[label] = { count: 1, dists: [v] }; - else { - labelCountMap[label].count++; - labelCountMap[label].dists.push(v); - } - } - }); - // 将 labelCountMap 中的 dists 按照从小到大排序，方便后面使用 - Object.keys(labelCountMap).forEach(label => { - labelCountMap[label].dists = labelCountMap[label].dists.sort((a, b) => a - b); - }); - return { - nodeIdx: i, - nodeId: nodes[i].id, - nodeIdxs: unitNodeIdxs, - neighbors, - neighborNum: unitNodeIdxs.length - 1, - nodeLabelCountMap: labelCountMap, - }; -}; - -/** - * 随机寻找点对，满足距离小于 k - * @param k 参数 k，表示 k-近邻 - * @param nodeNum 参数 length - * @param maxNodePairNum 寻找点对的数量不超过 maxNodePairNum - * @param spm 最短路径矩阵 - */ -const findNodePairsRandomly = ( - k: number, - nodeNum: number, - maxNodePairNum: number, - kNeighborUnits: NeighborUnit[], - spm: Matrix[], -): NodePairMap => { - // 每个节点需要随机找出的点对数 - let nodePairNumEachNode = Math.ceil(maxNodePairNum / nodeNum); - const nodePairMap = {}; - let foundNodePairCount = 0; - - // 遍历节点，为每个节点随机找出 nodePairNumEachNode 个点对，满足距离小于 k。找到的点对数量超过 maxNodePairNum 或所有节点遍历结束时终止 - kNeighborUnits.forEach((unit, i) => { - // 若未达到 nodePairNumEachNode，或循环次数小于最大循环次数(2 * nodeNum)，继续循环 - let nodePairForICount = 0; - let outerLoopCount = 0; - const neighbors = unit.nodeIdxs; // the first one is the center node - const neighborNum = unit.neighborNum - 1; - while (nodePairForICount < nodePairNumEachNode) { - // 另一端节点在节点数组中的的 index - let oidx = neighbors[1 + Math.floor(Math.random() * neighborNum)]; - let innerLoopCount = 0; - // 若随机得到的另一端 idx 不符合条件，则继续 random。条件是不是同一个节点、这个点对没有被记录过、距离小于 k - while (nodePairMap[`${i}-${oidx}`] || nodePairMap[`${oidx}-${i}`]) { - oidx = Math.floor(Math.random() * nodeNum); - innerLoopCount++; - if (innerLoopCount > 2 * nodeNum) break; // 循环次数大于最大循环次数(2 * nodeNum)跳出循环，避免死循环 - } - if (innerLoopCount < 2 * nodeNum) { - // 未达到最大循环次数，说明找到了合适的另一端 - nodePairMap[`${i}-${oidx}`] = { - start: i, - end: oidx, - distance: spm[i][oidx], - }; - nodePairForICount++; - foundNodePairCount++; - // 如果当前找到的点对数量达到了上限，返回结果 - if (foundNodePairCount >= maxNodePairNum) return nodePairMap; - } - outerLoopCount++; - if (outerLoopCount > 2 * nodeNum) break; // 循环次数大于最大循环次数(2 * nodeNum)跳出循环，避免死循环 - } - // 这个节点没有找到足够 nodePairNumEachNode 的点对。更新 nodePairNumEachNode，让后续节点找更多的点对 - if (nodePairForICount < nodePairNumEachNode) { - const gap = nodePairNumEachNode - nodePairForICount; - nodePairNumEachNode = (nodePairNumEachNode + gap) / (nodeNum - i - 1); - } - }); - return nodePairMap; -}; - -/** - * 计算所有 nodePairMap 中节点对的相交邻居诱导子图 - * @param nodePairMap 节点对 map，key 为 node1.id-node2.id，value 为 { startNodeIdx, endNodeIdx, distance } - * @param neighborUnits 每个节点的邻居元数组 - * @param graphData 原图数据 - * @param edgeMap 边的 map，方便检索 - * @param cachedInducedGraphMap 缓存的结果，下次进入该函数将继续更新该缓存，若 key 在缓存中存在则不需要重复计算 - */ -const getIntersectNeighborInducedGraph = ( - nodePairMap: NodePairMap, - neighborUnits: NeighborUnit[], - graphData: GraphData, - cachedInducedGraphMap?: InterGraphMap, -): InterGraphMap => { - const nodes = graphData.nodes; - if (!cachedInducedGraphMap) cachedInducedGraphMap = {}; - Object.keys(nodePairMap).forEach(key => { - if (cachedInducedGraphMap && cachedInducedGraphMap[key]) return; - cachedInducedGraphMap[key] = { nodes: [], edges: [] }; - const pair = nodePairMap[key]; - const startUnitNodeIds = neighborUnits[pair.start]?.nodeIdxs; - const endUnitNodeIds = neighborUnits[pair.end]?.nodeIdxs; - if (!startUnitNodeIds || !endUnitNodeIds) return; // 不存在邻元，返回空图 - const endSet = new Set(endUnitNodeIds); - const intersect = startUnitNodeIds.filter(x => endSet.has(x)); // 可能会爆栈（在 1580 + 6 nodes full-connected 时出现） - if (!intersect || !intersect.length) return; // 没有交集，返回空图 - const intersectIdMap = {}; - const intersectLength = intersect.length; - for (let i = 0; i < intersectLength; i++) { - const node = nodes[intersect[i]]; - cachedInducedGraphMap[key].nodes.push(node); // 将交集中的点加入诱导子图 - intersectIdMap[node.id] = true; - } - // 遍历所有边数据，如果边的两端都在交集中，将该边加入诱导子图 - graphData.edges.forEach(edge => { - if (intersectIdMap[edge.source] && intersectIdMap[edge.target]) - cachedInducedGraphMap[key].edges.push(edge); - }); - }); - return cachedInducedGraphMap; -}; - -/** - * 计算 strcutre 在 graph 上的匹配数量 - * @param graph 图数据 - * @param structure 目前支持只有两个节点一条边的最简单结构 - * @param nodeLabelProp 节点类型字段名 - * @param edgeLabelProp 边类型字段名 - */ -const getMatchedCount = (graph, structure, nodeLabelProp, edgeLabelProp) => { - const nodeMap = {}; - graph.nodes.forEach(node => { - nodeMap[node.id] = node; - }); - let count = 0; - if (!structure?.edges?.length || structure?.nodes?.length < 2) return 0; - graph.edges.forEach(e => { - const sourceLabel = nodeMap[e.source][nodeLabelProp]; - const targetLabel = nodeMap[e.target][nodeLabelProp]; - const strNodeLabel1 = structure?.nodes[0][nodeLabelProp]; - const strNodeLabel2 = structure?.nodes[1][nodeLabelProp]; - const strEdgeLabel = structure?.edges[0][edgeLabelProp]; - - if (e[edgeLabelProp] !== strEdgeLabel) return; - if ( - (sourceLabel === strNodeLabel1 && targetLabel === strNodeLabel2) || - (sourceLabel === strNodeLabel2 && targetLabel === strNodeLabel1) - ) { - count++; - } - }); - return count; -}; - -/** - * structures 中寻找最具有代表性的一个。这个结构是使得 matchedCountMap 的分组方式类内间距最小，类间间距最大 - * @param matchedCountMap 每个 structure 分类后的各图匹配数量，格式 { [strcture.idx]: { [interInducedGraphKey]: count } } - * @param structureNum strcuture 个数，与 matchedCountMap.length 对应 - * @param structures - */ -const findRepresentStructure = (matchedCountMap, structureNum, structures) => { - let maxOffset = Infinity, - representClusterType = 0; - for (let i = 0; i < structureNum; i++) { - // 一种分组的 map，key 是 intGraph 的 key，value 是 structures[i] 的匹配个数 - const countMapI = matchedCountMap[i]; - // 按照 value 为该组排序，生成 keys 的数组： - const sortedGraphKeys = Object.keys(countMapI).sort((a, b) => { - return countMapI[a] - countMapI[b]; - }); - - // 共 100 个 graphKeys，将 graphKeys 按顺序分为 groupNum 组 - const groupNum = 10; - const clusters = []; // 总共有 groupNum 个项 - sortedGraphKeys.forEach((key, j) => { - if (!clusters[j % groupNum]) - clusters[j % groupNum] = { graphs: [], totalCount: 0, aveCount: 0 }; - clusters[j % groupNum].graphs.push(key); - clusters[j % groupNum].totalCount += countMapI[key]; - }); - - // 计算 cluster 与 cluster 之间的距离 innerDist，每个 cluster 内部的距离 intraDist - let aveIntraDist = 0; // 该类的类内平均值 - const aveCounts = []; // 类内平均匹配数量，将用于计算类间距离 - clusters.forEach(graphsInCluster => { - // 类内均值 - const aveCount = graphsInCluster.totalCount / graphsInCluster.graphs.length; - graphsInCluster.aveCount = aveCount; - aveCounts.push(aveCount); - - // 对于每类，计算类内间距平均值 - let aveIntraPerCluster = 0; - const graphsNum = graphsInCluster.length; - graphsInCluster.graphs.forEach((graphKey1, j) => { - const graph1Count = countMapI[graphKey1]; - graphsInCluster.graphs.forEach((graphKey2, k) => { - if (j === k) return; - aveIntraPerCluster += Math.abs(graph1Count - countMapI[graphKey2]); - }); - }); - aveIntraPerCluster /= (graphsNum * (graphsNum - 1)) / 2; - aveIntraDist += aveIntraPerCluster; - }); - - aveIntraDist /= clusters.length; - - // 用类内均值计算类间距 - let aveInterDist = 0; // 类间间距平均值 - aveCounts.forEach((aveCount1, j) => { - aveCounts.forEach((aveCount2, k) => { - if (j === k) return; - aveInterDist += Math.abs(aveCount1 - aveCount2); - }); - aveInterDist /= (aveCounts.length * (aveCounts.length - 1)) / 2; - }); - - // 寻找 (类间间距均值-类内间距均值) 最大的一种分组方式（对应的 structure 就是最终要找的唯一 DS(G)） - const offset = aveInterDist - aveIntraDist; - if (maxOffset < offset) { - maxOffset = offset; - representClusterType = i; - } - } - return { - structure: structures[representClusterType], - structureCountMap: matchedCountMap[representClusterType], - }; -}; - -const getNodeMaps = (nodes, nodeLabelProp): { nodeMap: NodeMap; nodeLabelMap: LabelMap } => { - const nodeMap: NodeMap = {}, - nodeLabelMap: LabelMap = {}; - nodes.forEach((node, i) => { - nodeMap[node.id] = { idx: i, node, degree: 0, inDegree: 0, outDegree: 0 }; - const label = node[nodeLabelProp]; - if (!nodeLabelMap[label]) nodeLabelMap[label] = []; - nodeLabelMap[label].push(node); - }); - return { nodeMap, nodeLabelMap }; -}; - -const getEdgeMaps = ( - edges, - edgeLabelProp, - nodeMap: NodeMap, -): { edgeMap: EdgeMap; edgeLabelMap: LabelMap } => { - const edgeMap = {}, - edgeLabelMap = {}; - edges.forEach((edge, i) => { - edgeMap[`${uniqueId}`] = { idx: i, edge }; - const label = edge[edgeLabelProp]; - if (!edgeLabelMap[label]) edgeLabelMap[label] = []; - edgeLabelMap[label].push(edge); - - const sourceNode = nodeMap[edge.source]; - if (sourceNode) { - sourceNode.degree++; - sourceNode.outDegree++; - } - const targetNode = nodeMap[edge.target]; - if (targetNode) { - targetNode.degree++; - targetNode.inDegree++; - } - }); - return { edgeMap, edgeLabelMap }; -}; - -/** - * 输出最短路径的 map，key 为 sourceNode.id-targetNode.id，value 为这两个节点的最短路径长度 - * @param nodes - * @param spm - * @param directed - */ -const getSpmMap = (nodes, spm, directed): { [key: string]: number } => { - const length = spm.length; - const map = {}; - spm.forEach((row, i) => { - const start = directed ? 0 : i + 1; - const iId = nodes[i].id; - for (let j = start; j < length; j++) { - if (i === j) continue; - const jId = nodes[j].id; - const dist = row[j]; - map[`${iId}-${jId}`] = dist; - if (!directed) map[`${jId}-${iId}`] = dist; - } - }); - return map; -}; - -/** - * 计算一对节点（node1，node2）的 NDS 距离 - * @param graph 原图数据 - * @param node1 - * @param node2 - */ -const getNDSDist = ( - graph, - node1, - node2, - nodeMap, - spDist, - kNeighborUnits, - structure, - nodeLabelProp, - edgeLabelProp, - cachedNDSMap, - cachedInterInducedGraph, -) => { - const key = `${node1.id}-${node2.id}`; - if (cachedNDSMap && cachedNDSMap[key]) return cachedNDSMap[key]; - let interInducedGraph = cachedInterInducedGraph ? cachedInterInducedGraph[key] : undefined; - // 若没有缓存相交邻居诱导子图，计算 - if (!interInducedGraph) { - const pairMap: NodePairMap = { - [key]: { - start: nodeMap[node1.id].idx, - end: nodeMap[node2.id].idx, - distance: spDist, - }, - }; - - cachedInterInducedGraph = getIntersectNeighborInducedGraph( - pairMap, - kNeighborUnits, - graph, - cachedInterInducedGraph, - ); - interInducedGraph = cachedInterInducedGraph[key]; - } - - return getMatchedCount(interInducedGraph, structure, nodeLabelProp, edgeLabelProp); -}; - -/** - * 计算 pattern 上绩点的度数并存储到 minPatternNodeLabelDegreeMap - */ -const stashPatternNodeLabelDegreeMap = (minPatternNodeLabelDegreeMap, neighborLabel, patternNodeMap, patternNodeLabelMap) => { - let minPatternNodeLabelDegree = minPatternNodeLabelDegreeMap[neighborLabel]?.degree; - let minPatternNodeLabelInDegree = minPatternNodeLabelDegreeMap[neighborLabel]?.inDegree; - let minPatternNodeLabelOutDegree = minPatternNodeLabelDegreeMap[neighborLabel]?.outDegree; - - if (minPatternNodeLabelDegreeMap[neighborLabel] === undefined) { - minPatternNodeLabelDegree = Infinity; - minPatternNodeLabelInDegree = Infinity; - minPatternNodeLabelOutDegree = Infinity; - patternNodeLabelMap[neighborLabel].forEach(patternNodeWithLabel => { - const patternNodeDegree = patternNodeMap[patternNodeWithLabel.id].degree; - if (minPatternNodeLabelDegree > patternNodeDegree) - minPatternNodeLabelDegree = patternNodeDegree; - const patternNodeInDegree = patternNodeMap[patternNodeWithLabel.id].inDegree; - if (minPatternNodeLabelInDegree > patternNodeInDegree) - minPatternNodeLabelInDegree = patternNodeInDegree; - const patternNodeOutDegree = patternNodeMap[patternNodeWithLabel.id].outDegree; - if (minPatternNodeLabelOutDegree > patternNodeOutDegree) - minPatternNodeLabelOutDegree = patternNodeOutDegree; - }); - minPatternNodeLabelDegreeMap[neighborLabel] = { - degree: minPatternNodeLabelDegree, - inDegree: minPatternNodeLabelInDegree, - outDegree: minPatternNodeLabelOutDegree - }; - } - - return { - minPatternNodeLabelDegree, - minPatternNodeLabelInDegree, - minPatternNodeLabelOutDegree - } -} - -/** - * GADDI 模式匹配 - * @param graphData 原图数据 - * @param pattern 搜索图（需要在原图上搜索的模式）数据 - * @param directed 是否计算有向图，默认 false - * @param k 参数 k，表示 k-近邻 - * @param length 参数 length - * @param nodeLabelProp 节点数据中代表节点标签（分类信息）的属性名。默认为 cluster - * @param edgeLabelProp 边数据中代表边标签（分类信息）的属性名。默认为 cluster - */ -const GADDI = ( - graphData: GraphData, - pattern: GraphData, - directed: boolean = false, - k: number, - length: number, - nodeLabelProp: string = 'cluster', - edgeLabelProp: string = 'cluster', -): GraphData[] => { - if (!graphData || !graphData.nodes) return; - // 分为三步： - // 0. 预计算：节点/边数，邻接矩阵、最短路径矩阵 - // 1. 处理原图 graphData。再分为 1~5 小步 - // 2. 匹配 - - // console.log("----- stage-pre: preprocessing -------"); - - // -------- 第零步，预计算：节点/边数，邻接矩阵、最短路径矩阵------- - const nodeNum = graphData.nodes.length; - if (!nodeNum) return; - // console.log("----- stage-pre.1: calc shortest path matrix for graph -------"); - const spm = floydWarshall(graphData, directed); - // console.log( - // "----- stage-pre.2: calc shortest path matrix for pattern -------" - // ); - const patternSpm = floydWarshall(pattern, directed); - // console.log( - // "----- stage-pre.3: calc shortest path matrix map for graph -------" - // ); - const spmMap = getSpmMap(graphData.nodes, spm, directed); - // console.log( - // "----- stage-pre.4: calc shortest path matrix map for pattern -------" - // ); - const patternSpmMap = getSpmMap(pattern.nodes, patternSpm, directed); - - // console.log("----- stage-pre.5: establish maps -------"); - // 节点的 map，以 id 为 id 映射，方便后续快速检索 - const { nodeMap, nodeLabelMap } = getNodeMaps(graphData.nodes, nodeLabelProp); - const { nodeMap: patternNodeMap, nodeLabelMap: patternNodeLabelMap } = getNodeMaps( - pattern.nodes, - nodeLabelProp, - ); - - // 计算节点度数 - getEdgeMaps(graphData.edges, edgeLabelProp, nodeMap); - - const { edgeLabelMap: patternEdgeLabelMap } = getEdgeMaps( - pattern.edges, - edgeLabelProp, - patternNodeMap, - ); - - // 若未指定 length，自动计算 pattern 半径（最短路径最大值） - let patternSpmSpread = []; - patternSpm?.forEach(row => { - patternSpmSpread = patternSpmSpread.concat(row); - }) - if (!length) length = Math.max(...patternSpmSpread, 2); - if (!k) k = length; - - // console.log("params", directed, length, k); - - // console.log("----- stage-pre.6: calc k neighbor units -------"); - // 计算每个节点的 k 邻元集合 - const kNeighborUnits = findKNeighborUnits(graphData, spm, nodeLabelProp, k); - const patternKNeighborUnits = findKNeighborUnits(pattern, patternSpm, nodeLabelProp, k); - - // console.log( - // "----- stage0: going to processing graph and find intersect neighbor induced graphs -------" - // ); - - // console.log("----- stage0.1: going to select random node pairs -------"); - // -------- 第一步，处理原图 graphData------- - - // 1.1. 随机选择最多 100 个点对，满足距离小于 Length 和 k - // 当 graphData 少于 20 个节点，则不能找出 100 个点对，只找出不多于 n(n-1)/2 个点对 - const maxNodePairNum = Math.min(100, (nodeNum * (nodeNum - 1)) / 2); - const nodePairsMap = findNodePairsRandomly( - k, - nodeNum, - maxNodePairNum, - kNeighborUnits, - spm, - ); - - // console.log( - // "----- stage0.2: going to calculate intersect neighbor induced graphs -------" - // ); - // 1.2. 生成上面节点对的相应相交邻居诱导子图。格式为 {'beginNodeIdx-endNodeIdx': {nodes: [], edges: []}} - let intGMap = getIntersectNeighborInducedGraph(nodePairsMap, kNeighborUnits, graphData); - // 1.3. 使用 gSpan 算法（frequent graph mining）计算 ISIntG 的前 10 个频率最高的子结构（3-4条边） - const top = 10, - minSupport = 1, - minNodeNum = 1, - maxNodeNum = 4; - const params = { - graphs: intGMap, - nodeLabelProp, - edgeLabelProp, - minSupport, - minNodeNum, - maxNodeNum, - directed, - }; - - // console.log( - // "----- stage1: (gSpan) going to find frequent structure dsG -------" - // ); - // console.log("----- stage1.1: going to run gSpan -------"); - // 暂时假设生成的 sub structure 都只有一条边 - const freStructures = gSpan(params).slice(0, top); - // structureNum 可能小于 top - const structureNum = freStructures.length; - - // 1.4. 计算上述 10 个子结构在 intGMap 中每个诱导子图的匹配个数 - const matchedCountMap = []; - freStructures.forEach((structure, i) => { - matchedCountMap[i] = {}; - Object.keys(intGMap).forEach(key => { - const graph = intGMap[key]; - const subStructureCount = getMatchedCount(graph, structure, nodeLabelProp, edgeLabelProp); - matchedCountMap[i][key] = subStructureCount; - }); - }); - - // console.log( - // "----- stage1.1: going to find the most represent strucutre -------" - // ); - - // 1.5. 对于每个子结构，根据匹配个数为 intGMap 中的诱导子图分组，生成 structureNum 种分组 - // 计算每种分组的类间距和类内间距，找到类间距最大、类内间距最小的一种分组，这种分组对应的子结构被选为唯一代表性子结构 DS(G) - const { structure: dsG, structureCountMap: ndsDist } = findRepresentStructure( - matchedCountMap, - structureNum, - freStructures, - ); - - // -------- 第二步，匹配------- - // 2.1 找到从 Q 中的一个节点作为起始节点，寻找 G 中的匹配。这个其实节点的标签可以在 G 中找到最多的节点 - let beginPNode = pattern.nodes[0], - candidates = [], - label = pattern.nodes[0]?.[nodeLabelProp], - maxNodeNumWithSameLabel = -Infinity; - pattern.nodes.forEach(node => { - const pLabel = node[nodeLabelProp]; - const nodesWithSameLabel = nodeLabelMap[pLabel] - if (nodesWithSameLabel?.length > maxNodeNumWithSameLabel) { - maxNodeNumWithSameLabel = nodesWithSameLabel.length; - candidates = nodesWithSameLabel; - label = pLabel; - beginPNode = node; - } - }); - - // console.log("----- stage2: going to find candidates -------"); - - // 全局缓存，避免重复计算 - const minPatternNodeLabelDegreeMap = {}; // key 是 label，value 是该 label 节点的最小度数 - let patternIntGraphMap = {}, - patternNDSDist = {}, // key 为 node.id-node.id - patternNDSDistMap = {}; // key 为 node.id-label2，value nds距离值数组（按从大到小排序，无需关心具体对应哪个 node2） - // 2.2.2 对于 Q 中的另一个标签的 k 个节点，计算它们到 node 的最短路径以及 NDS 距离 - const patternSpDist = {}; - const patternSpDistBack = {}; - Object.keys(patternNodeLabelMap).forEach((label2, j) => { - patternSpDist[label2] = []; - if (directed) { - patternSpDistBack[label2] = []; - } - let maxDist = -Infinity; - const patternNodesWithLabel2 = patternNodeLabelMap[label2]; - const patternNodePairMap = {}; - patternNodesWithLabel2.forEach(nodeWithLabel2 => { - const dist = patternSpmMap[`${beginPNode.id}-${nodeWithLabel2.id}`]; - dist && patternSpDist[label2].push(dist); - if (maxDist < dist) maxDist = dist; - patternNodePairMap[`${beginPNode.id}-${nodeWithLabel2.id}`] = { - start: 0, - end: patternNodeMap[nodeWithLabel2.id].idx, - distance: dist, - }; - if (directed) { - const distBack = patternSpmMap[`${nodeWithLabel2.id}-${beginPNode.id}`]; - distBack && patternSpDistBack[label2].push(distBack); - } - }); - - // spDist[label2] 按照从小到大排序 - patternSpDist[label2] = patternSpDist[label2].sort((a, b) => a - b); - if (directed) patternSpDistBack[label2] = patternSpDistBack[label2].sort((a, b) => a - b); - - // 计算 Q 中所有 label2 节点到 beginPNode 的 NDS 距离 - // 所有 label2 节点到 beginPNode 的邻居相交诱导子图： - // key: node1.id-node2.id - patternIntGraphMap = getIntersectNeighborInducedGraph( - patternNodePairMap, - patternKNeighborUnits, - pattern, - patternIntGraphMap, - ); - // pattern 中 beginNode 到当前 label2 节点 的 NDS 距离（数组，无需关心具体对应到哪个节点） - let currentPatternNDSDistArray = []; - Object.keys(patternNodePairMap).forEach(key => { - if (patternNDSDist[key]) { - currentPatternNDSDistArray.push(patternNDSDist[key]); - return; // 缓存过则不需要再次计算 - } - const patternIntGraph = patternIntGraphMap[key]; - patternNDSDist[key] = getMatchedCount(patternIntGraph, dsG, nodeLabelProp, edgeLabelProp); - currentPatternNDSDistArray.push(patternNDSDist[key]); - }); - - // 根据值为 currentPatternNDSDist 从大到小排序 - currentPatternNDSDistArray = currentPatternNDSDistArray.sort((a, b) => b - a); - patternNDSDistMap[`${beginPNode.id}-${label2}`] = currentPatternNDSDistArray; - - if (label2 === label) return; - - const candidatesNum = candidates?.length || 0; - for (let m = candidatesNum - 1; m >= 0; m--) { - const cNode = candidates[m]; - - // prune1：若 candidates 中节点 cNode 的 kNeighborUnits 中标签为 label2 的节点个数少于 pattern 中 label2 个数，删去它 - const graphNeighborUnit = kNeighborUnits[nodeMap[cNode.id].idx]; - const graphNeighborUnitCountMap = graphNeighborUnit.nodeLabelCountMap[label2]; - const patternLabel2Num = patternNodeLabelMap[label2].length; - if (!graphNeighborUnitCountMap || graphNeighborUnitCountMap.count < patternLabel2Num) { - candidates.splice(m, 1); - continue; - } - - // prune2：若 candidates 中节点 cNode 到 kNeighborUnits 中标签为 label2 的节点最短路径大于 patternSpDist[label2]，删去它 - // (prune2 规则即：candidate 相关的最短路径的最大 spDist[label2].length 个，按照大小顺序依次和 patternSpDist[label2] 中的值比较，只要遇到一个是 G > Q 的，就删去这个 candidate) - let prune2Invalid = false; - for (let n = 0; n < patternLabel2Num; n++) { - if (graphNeighborUnitCountMap.dists[n] > patternSpDist[label2][n]) { - prune2Invalid = true; - break; - } - } - if (prune2Invalid) { - candidates.splice(m, 1); - continue; - } - - // prune3：若 candidates 中节点 cNode 到 kNeighborUnits 中标签为 label2 的节点 NDS 距离小于 patternNDSDist[beginNode.id-label2]，删去它 - // TODO：prune3，currentPatternNDSDistArray 与 currentNDSDist 的比较 - - // 计算 G 中所有 label2 节点到 cNode 的 NDS 距离 - // 所有 label2 节点到 cNode 的邻居相交诱导子图： - const cNodePairMap = {}; - graphNeighborUnit.neighbors.forEach(neighborNode => { - const dist = spmMap[`${cNode.id}-${neighborNode.id}`]; - cNodePairMap[`${cNode.id}-${neighborNode.id}`] = { - start: nodeMap[cNode.id].idx, - end: nodeMap[neighborNode.id].idx, - distance: dist, - }; - }); - // 更新 intGMap - intGMap = getIntersectNeighborInducedGraph(cNodePairMap, kNeighborUnits, graphData, intGMap); - // candidate 到它周围 label2 节点的 NDS 距离, key 是 node.id-node.id - let currentNDSDistArray = []; - Object.keys(cNodePairMap).forEach(key => { - if (ndsDist[key]) { - currentNDSDistArray.push(ndsDist[key]); - return; // 缓存过则不需要再次计算 - } - const intGraph = intGMap[key]; - ndsDist[key] = getMatchedCount(intGraph, dsG, nodeLabelProp, edgeLabelProp); - currentNDSDistArray.push(ndsDist[key]); - }); - - // 根据值为 currentNDSDistArray 从大到小排序 - currentNDSDistArray = currentNDSDistArray.sort((a, b) => b - a); - - let prune3Invalid = false; - for (let n = 0; n < patternLabel2Num; n++) { - if (currentNDSDistArray[n] < currentPatternNDSDistArray[n]) { - prune3Invalid = true; - break; - } - } - if (prune3Invalid) { - candidates.splice(m, 1); - continue; - } - } - }); - - const candidateGraphs = []; - - // console.log( - // "----- stage3: going to splice neighbors for each candidate graph -------" - // ); - - // candidates 经过筛选后，以每个 candidate 为中心，生成 Length-neighbor 的邻居诱导子图 - // 并在诱导子图中去除不可能在 Q 上找到匹配的点：在 Q 上不存在的 label，其他 label 到 candidate 的最大最短距离符合 Q、NDS 距离符合 Q - candidates?.forEach(candidate => { - const nodeIdx = nodeMap[candidate.id].idx; - const lengthNeighborUnit = findKNeighborUnit( - graphData.nodes, - spm[nodeIdx], - nodeIdx, - nodeLabelProp, - length, - ); - - const neighborNodes = lengthNeighborUnit.neighbors; - - // 删除不可能找到匹配的邻居点 - const neighborNum = neighborNodes.length; - let unmatched = false; - for (let i = neighborNum - 1; i >= 0; i--) { - // 如果通过裁剪，符合条件的节点数量已过少，说明不能匹配这个 candidate 相关的图 - if (neighborNodes.length + 1 < pattern.nodes.length) { - unmatched = true; - return; - } - const neighborNode = neighborNodes[i]; - const neighborLabel = neighborNode[nodeLabelProp]; - // prune1: 若该邻居点的 label 不存在于 pattern 中，移除这个点 - if (!patternNodeLabelMap[neighborLabel] || !patternNodeLabelMap[neighborLabel].length) { - neighborNodes.splice(i, 1); - continue; - } - - // prune2: 若该邻居点到 candidate 的最短路径比和它有相同 label 的节点到 beginPNode 的最大最短路径长度长，移除这个点 - // prune2.1: 如果没有这个标签到 beginPNode 的距离记录，说明 pattern 上（可能 beginPNode 是这个 label）没有其他这个 label 的节点 - if (!patternSpDist[neighborLabel] || !patternSpDist[neighborLabel].length) { - neighborNodes.splice(i, 1); - continue; - } - - const key = `${candidate.id}-${neighborNode.id}`; - - // prune2.2 - const distToCandidate = spmMap[key]; - let idx = patternSpDist[neighborLabel].length - 1; - let maxDistWithLabelInPattern = patternSpDist[neighborLabel][idx]; // patternSpDist[neighborLabel] 已经按照从小到大排序 - if (distToCandidate > maxDistWithLabelInPattern) { - neighborNodes.splice(i, 1); - continue; - } - - if (directed) { - const keyBack = `${neighborNode.id}-${candidate.id}`; - const distFromCandidate = spmMap[keyBack]; - idx = patternSpDistBack[neighborLabel].length - 1; - let maxBackDistWithLabelInPattern = patternSpDistBack[neighborLabel][idx]; - if (distFromCandidate > maxBackDistWithLabelInPattern) { - neighborNodes.splice(i, 1); - continue; - } - } - - // prune3: 若该邻居点到 candidate 的 NDS 距离比和它有相同 label 的节点到 beginPNode 的最小 NDS 距离小，移除这个点 - const ndsToCandidate = ndsDist[key] - ? ndsDist[key] - : getNDSDist( - graphData, - candidate, - neighborNode, - nodeMap, - distToCandidate, - kNeighborUnits, - dsG, - nodeLabelProp, - edgeLabelProp, - ndsDist, - intGMap, - ); - const patternKey = `${beginPNode.id}-${neighborLabel}`; - const minNdsWithLabelInPattern = - patternNDSDistMap[patternKey][patternNDSDistMap[patternKey].length - 1]; // patternNDSDist[key] 一定存在 - if (ndsToCandidate < minNdsWithLabelInPattern) { - neighborNodes.splice(i, 1); - continue; - } - - // prune4: 若该邻居点的度数小于 pattern 同 label 节点最小度数，删去该点 - const { - minPatternNodeLabelDegree, - minPatternNodeLabelInDegree, - minPatternNodeLabelOutDegree - } = stashPatternNodeLabelDegreeMap(minPatternNodeLabelDegreeMap, neighborLabel, patternNodeMap,patternNodeLabelMap); - - if (nodeMap[neighborNode.id].degree < minPatternNodeLabelDegree) { - neighborNodes.splice(i, 1); - continue; - } - } - - // 节点在个数上符合匹配（不少于 pattern 的节点个数），现在筛选相关边 - if (!unmatched) { - candidateGraphs.push({ - nodes: [candidate].concat(neighborNodes), - }); - } - }); - - // console.log( - // "----- stage4: going to splice edges and neighbors for each candidate graph -------" - // ); - - const { length: undirectedLengthsToBeginPNode } = dijkstra(pattern, beginPNode.id, false); - - let undirectedLengthsToBeginPNodeLabelMap = {}; - if (directed) { - Object.keys(undirectedLengthsToBeginPNode).forEach(nodeId => { - const nodeLabel = patternNodeMap[nodeId].node[nodeLabelProp]; - if (!undirectedLengthsToBeginPNodeLabelMap[nodeLabel]) - undirectedLengthsToBeginPNodeLabelMap[nodeLabel] = [undirectedLengthsToBeginPNode[nodeId]]; - else - undirectedLengthsToBeginPNodeLabelMap[nodeLabel].push( - undirectedLengthsToBeginPNode[nodeId], - ); - }); - Object.keys(undirectedLengthsToBeginPNodeLabelMap).forEach(pLabel => { - undirectedLengthsToBeginPNodeLabelMap[pLabel].sort((a, b) => a - b); - }); - } else { - undirectedLengthsToBeginPNodeLabelMap = patternSpDist; - } - - // 现在 candidateGraphs 里面只有节点，进行边的筛选 - let candidateGraphNum = candidateGraphs.length; - for (let i = candidateGraphNum - 1; i >= 0; i--) { - const candidateGraph = candidateGraphs[i]; - const candidate = candidateGraph.nodes[0]; - - const candidateNodeLabelCountMap = {}; - const candidateNodeMap = {}; - candidateGraph.nodes.forEach((node, q) => { - candidateNodeMap[node.id] = { - idx: q, - node, - degree: 0, - inDegree: 0, - outDegree: 0 - }; - const cNodeLabel = node[nodeLabelProp]; - if (!candidateNodeLabelCountMap[cNodeLabel]) candidateNodeLabelCountMap[cNodeLabel] = 1; - else candidateNodeLabelCountMap[cNodeLabel]++; - }); - - // 根据 candidate 和 neighborNodes 中的节点生成 G 的诱导子图 - // 即，将 graphData 上两端都在 candidateGraph.nodes 中的边放入 candidateEdges - const candidateEdges = []; - const edgeLabelCountMap = {}; - graphData.edges.forEach(edge => { - if (candidateNodeMap[edge.source] && candidateNodeMap[edge.target]) { - candidateEdges.push(edge); - if (!edgeLabelCountMap[edge[edgeLabelProp]]) edgeLabelCountMap[edge[edgeLabelProp]] = 1; - else edgeLabelCountMap[edge[edgeLabelProp]]++; - candidateNodeMap[edge.source].degree++; - candidateNodeMap[edge.target].degree++; - candidateNodeMap[edge.source].outDegree++; - candidateNodeMap[edge.target].inDegree++; - } - }); - - // prune：若有一个 edgeLabel 在 candidateGraph 上的个数少于 pattern，去除该图 - const pattenrEdgeLabelNum = Object.keys(patternEdgeLabelMap).length; - let prunedByEdgeLabel = false; - for (let e = 0; e < pattenrEdgeLabelNum; e++) { - const label = Object.keys(patternEdgeLabelMap)[e]; - if ( - !edgeLabelCountMap[label] || - edgeLabelCountMap[label] < patternEdgeLabelMap[label].length - ) { - prunedByEdgeLabel = true; - break; - } - } - if (prunedByEdgeLabel) { - candidateGraphs.splice(i, 1); - continue; - } - - // 遍历 candidateEdges，进行边的筛选 - let candidateEdgeNum = candidateEdges.length; - - // prune：若边数过少，去除该图 - if (candidateEdgeNum < pattern.edges.length) { - candidateGraphs.splice(i, 1); - break; - } - let candidateGraphInvalid = false; - for (let e = candidateEdgeNum - 1; e >= 0; e--) { - const edge = candidateEdges[e]; - const edgeLabel = edge[edgeLabelProp]; - const patternEdgesWithLabel = patternEdgeLabelMap[edgeLabel]; - - // prune 1: 若边的 label 不存在于 pattern 边 label 中，去除该边 - if (!patternEdgesWithLabel || !patternEdgesWithLabel.length) { - edgeLabelCountMap[edgeLabel]--; - // 若这个 label 的 count 减少之后，该 label 的边数不足，去除该图 - if (patternEdgesWithLabel && edgeLabelCountMap[edgeLabel] < patternEdgesWithLabel.length) { - candidateGraphInvalid = true; - break; - } - candidateEdges.splice(e, 1); - candidateNodeMap[edge.source].degree--; - candidateNodeMap[edge.target].degree--; - candidateNodeMap[edge.source].outDegree--; - candidateNodeMap[edge.target].inDegree--; - continue; - } - - // prune 2: 若边的 label +两端 label 的三元组关系不能在 pattern 中找到，去除该边 - const sourceLabel = candidateNodeMap[edge.source].node[nodeLabelProp]; - const targetLabel = candidateNodeMap[edge.target].node[nodeLabelProp]; - - let edgeMatched = false; - patternEdgesWithLabel.forEach(patternEdge => { - const patternSource = patternNodeMap[patternEdge.source].node; - const patternTarget = patternNodeMap[patternEdge.target].node; - if ( - patternSource[nodeLabelProp] === sourceLabel && - patternTarget[nodeLabelProp] === targetLabel - ) - edgeMatched = true; - if ( - !directed && - patternSource[nodeLabelProp] === targetLabel && - patternTarget[nodeLabelProp] === sourceLabel - ) - edgeMatched = true; - }); - if (!edgeMatched) { - edgeLabelCountMap[edgeLabel]--; - // 若这个 label 的 count 减少之后，该 label 的边数不足，去除该图 - if (patternEdgesWithLabel && edgeLabelCountMap[edgeLabel] < patternEdgesWithLabel.length) { - candidateGraphInvalid = true; - break; - } - candidateEdges.splice(e, 1); - candidateNodeMap[edge.source].degree--; - candidateNodeMap[edge.target].degree--; - candidateNodeMap[edge.source].outDegree--; - candidateNodeMap[edge.target].inDegree--; - continue; - } - } - - // prune2: 删除边的过程中，发现边数过少/边 label 数过少时，去除该图 - if (candidateGraphInvalid) { - candidateGraphs.splice(i, 1); - continue; - } - - candidateGraph.edges = candidateEdges; - - const { length: lengthsToCandidate } = dijkstra( - candidateGraph, - candidateGraph.nodes[0].id, - false, // 此处计算路径长度用于判断是否连通，因此使用无向图 - ); - Object.keys(lengthsToCandidate) - .reverse() - .forEach(targetId => { - if (targetId === candidateGraph.nodes[0].id || candidateGraphInvalid) return; - // prune4: 通过上述裁剪，可能导致该邻居子图变为不连通。裁剪掉目前在这个邻居子图中和 candidate（第一个节点）不连通的节点 - if (lengthsToCandidate[targetId] === Infinity) { - const targetNodeLabel = candidateNodeMap[targetId].node[nodeLabelProp]; - candidateNodeLabelCountMap[targetNodeLabel]--; - if ( - candidateNodeLabelCountMap[targetNodeLabel] < - patternNodeLabelMap[targetNodeLabel].length - ) { - candidateGraphInvalid = true; - return; - } - const idx = candidateGraph.nodes.indexOf(candidateNodeMap[targetId].node); - candidateGraph.nodes.splice(idx, 1); - candidateNodeMap[targetId] = undefined; - return; - } - // prune5: 经过边裁剪后，可能又出现了最短路径过长的节点 （比 pattern 中同 label 的节点到 beginNode 最大最短距离远），删去这些节点 - const nLabel = nodeMap[targetId].node[nodeLabelProp]; - if ( - !undirectedLengthsToBeginPNodeLabelMap[nLabel] || - !undirectedLengthsToBeginPNodeLabelMap[nLabel].length || - lengthsToCandidate[targetId] > - undirectedLengthsToBeginPNodeLabelMap[nLabel][ - undirectedLengthsToBeginPNodeLabelMap[nLabel].length - 1 - ] - ) { - const targetNodeLabel = candidateNodeMap[targetId].node[nodeLabelProp]; - candidateNodeLabelCountMap[targetNodeLabel]--; - if ( - candidateNodeLabelCountMap[targetNodeLabel] < - patternNodeLabelMap[targetNodeLabel].length - ) { - candidateGraphInvalid = true; - return; - } - const idx = candidateGraph.nodes.indexOf(candidateNodeMap[targetId].node); - candidateGraph.nodes.splice(idx, 1); - candidateNodeMap[targetId] = undefined; - } - }); - - if (candidateGraphInvalid) { - candidateGraphs.splice(i, 1); - continue; - } - - let degreeChanged = true; - let loopCount = 0; - while (degreeChanged && !candidateGraphInvalid) { - degreeChanged = false; - - // candidate 度数不足，删去该图 - const condition = directed ? (candidateNodeMap[candidate.id].degree < patternNodeMap[beginPNode.id].degree || - candidateNodeMap[candidate.id].inDegree < patternNodeMap[beginPNode.id].inDegree || - candidateNodeMap[candidate.id].outDegree < patternNodeMap[beginPNode.id].outDegree) : - candidateNodeMap[candidate.id].degree < patternNodeMap[beginPNode.id].degree; - if (condition) { - candidateGraphInvalid = true; - break; - } - // candidate label 个数不足，删去该图 - if ( - candidateNodeLabelCountMap[candidate[nodeLabelProp]] < - patternNodeLabelMap[candidate[nodeLabelProp]].length - ) { - candidateGraphInvalid = true; - break; - } - - // prune6：去除度数过小的节点 - const currentCandidateNodeNum = candidateGraph.nodes.length; - for (let o = currentCandidateNodeNum - 1; o >= 0; o--) { - const cgNode = candidateGraph.nodes[o]; - const nodeDegree = candidateNodeMap[cgNode.id].degree; - const nodeInDegree = candidateNodeMap[cgNode.id].inDegree; - const nodeOutDegree = candidateNodeMap[cgNode.id].outDegree; - const cNodeLabel = cgNode[nodeLabelProp]; - - const { - minPatternNodeLabelDegree, - minPatternNodeLabelInDegree, - minPatternNodeLabelOutDegree - } = stashPatternNodeLabelDegreeMap(minPatternNodeLabelDegreeMap, cNodeLabel, patternNodeMap,patternNodeLabelMap); - - const deleteCondition = directed ? (nodeDegree < minPatternNodeLabelDegree || - nodeInDegree < minPatternNodeLabelInDegree || - nodeOutDegree < minPatternNodeLabelOutDegree) : - nodeDegree < minPatternNodeLabelDegree; - if (deleteCondition) { - candidateNodeLabelCountMap[cgNode[nodeLabelProp]]--; - // 节点 label 个数不足 - if ( - candidateNodeLabelCountMap[cgNode[nodeLabelProp]] < - patternNodeLabelMap[cgNode[nodeLabelProp]].length - ) { - candidateGraphInvalid = true; - break; - } - candidateGraph.nodes.splice(o, 1); - candidateNodeMap[cgNode.id] = undefined; - degreeChanged = true; - } - } - if (candidateGraphInvalid || (!degreeChanged && loopCount !== 0)) break; - // 经过 prune5 节点裁剪，删去端点已经不在 candidateGraph 中的边 - candidateEdgeNum = candidateEdges.length; - for (let y = candidateEdgeNum - 1; y >= 0; y--) { - const cedge = candidateEdges[y]; - if (!candidateNodeMap[cedge.source] || !candidateNodeMap[cedge.target]) { - candidateEdges.splice(y, 1); - const edgeLabel = cedge[edgeLabelProp]; - edgeLabelCountMap[edgeLabel]--; - if (candidateNodeMap[cedge.source]) { - candidateNodeMap[cedge.source].degree--; - candidateNodeMap[cedge.source].outDegree--; - } - if (candidateNodeMap[cedge.target]) { - candidateNodeMap[cedge.target].degree--; - candidateNodeMap[cedge.target].inDegree--; - } - // 边 label 数量不足 - if ( - patternEdgeLabelMap[edgeLabel] && - edgeLabelCountMap[edgeLabel] < patternEdgeLabelMap[edgeLabel].length - ) { - candidateGraphInvalid = true; - break; - } - degreeChanged = true; - } - } - loopCount++; - } - - if (candidateGraphInvalid) { - candidateGraphs.splice(i, 1); - continue; - } - - // prune: 若节点/边数过少，节点/边 label 过少，去掉这个图 - if ( - candidateGraphInvalid || - candidateGraph.nodes.length < pattern.nodes.length || - candidateEdges.length < pattern.edges.length - ) { - candidateGraphs.splice(i, 1); - continue; - } - } - - // 此时已经生成的多个 candidateGraphs，可能有重复 - - // console.log( - // "----- stage5: going to splice dulplicated candidate graphs -------" - // ); - - // 删去 candidateGraphs 中一模一样的子图，通过边的 node-node-edgeLabel 作为 key，这类边个数作为 value，进行匹配 - let currentLength = candidateGraphs.length; - for (let i = 0; i <= currentLength - 1; i++) { - const cg1 = candidateGraphs[i]; - const cg1EdgeMap = {}; // [node1.id-node2.id-edge.label]: count - cg1.edges.forEach(edge => { - const key = `${edge.source}-${edge.target}-${edge.label}`; - if (!cg1EdgeMap[key]) cg1EdgeMap[key] = 1; - else cg1EdgeMap[key]++; - }); - - for (let j = currentLength - 1; j > i; j--) { - const cg2 = candidateGraphs[j]; - const cg2EdgeMap = {}; // [node1.id-node2.id-edge.label]: count - cg2.edges.forEach(edge => { - const key = `${edge.source}-${edge.target}-${edge.label}`; - if (!cg2EdgeMap[key]) cg2EdgeMap[key] = 1; - else cg2EdgeMap[key]++; - }); - - let same = true; - if (Object.keys(cg2EdgeMap).length !== Object.keys(cg1EdgeMap).length) { - same = false; - } else { - Object.keys(cg1EdgeMap).forEach(key => { - if (cg2EdgeMap[key] !== cg1EdgeMap[key]) same = false; - }); - } - if (same) { - candidateGraphs.splice(j, 1); - } - } - currentLength = candidateGraphs.length; - } - - return candidateGraphs; -}; - -export default GADDI; diff --git a/packages/graph/src/i-louvain.ts b/packages/graph/src/i-louvain.ts deleted file mode 100644 index f6f6898..0000000 --- a/packages/graph/src/i-louvain.ts +++ /dev/null @@ -1,28 +0,0 @@ -import louvain from './louvain'; -import type { ClusterData, GraphData } from './types'; - -/** - * 社区发现 i-louvain 算法：模块度 + 惯性模块度（即节点属性相似性） - * @param graphData 图数据 - * @param directed 是否有向图，默认为 false - * @param weightPropertyName 权重的属性字段 - * @param threshold 差值阈值 - * @param propertyKey 属性的字段名 - * @param involvedKeys 参与计算的key集合 - * @param uninvolvedKeys 不参与计算的key集合 - * @param inertialWeight 惯性模块度权重 - */ -const iLouvain = ( - graphData: GraphData, - directed: boolean = false, - weightPropertyName: string = 'weight', - threshold: number = 0.0001, - propertyKey: string = undefined, - involvedKeys: string[] = [], - uninvolvedKeys: string[] = ['id'], - inertialWeight: number = 1, - ): ClusterData => { - return louvain(graphData, directed, weightPropertyName, threshold, true, propertyKey, involvedKeys, uninvolvedKeys, inertialWeight); -} - -export default iLouvain; diff --git a/packages/graph/src/index.ts b/packages/graph/src/index.ts index a0b8833..d80201a 100644 --- a/packages/graph/src/index.ts +++ b/packages/graph/src/index.ts @@ -1,88 +1 @@ -import getAdjMatrix from './adjacent-matrix'; -import breadthFirstSearch from './bfs'; -import connectedComponent from './connected-component'; -import getDegree from './degree'; -import { getInDegree, getOutDegree } from './degree'; -import detectCycle, { detectAllCycles, detectAllDirectedCycle, detectAllUndirectedCycle } from './detect-cycle'; -import depthFirstSearch from './dfs'; -import dijkstra from './dijkstra'; -import { findAllPath, findShortestPath } from './find-path'; -import floydWarshall from './floydWarshall'; -import labelPropagation from './label-propagation'; -import louvain from './louvain'; -import iLouvain from './i-louvain'; -import kCore from './k-core'; -import kMeans from './k-means'; -import cosineSimilarity from './cosine-similarity'; -import nodesCosineSimilarity from './nodes-cosine-similarity'; -import minimumSpanningTree from './mts'; -import pageRank from './pageRank'; -import GADDI from './gaddi'; -import Stack from './structs/stack'; -import { getNeighbors } from './util'; -import { IAlgorithm } from './types'; - -const detectDirectedCycle = detectCycle; - -export { - getAdjMatrix, - breadthFirstSearch, - connectedComponent, - getDegree, - getInDegree, - getOutDegree, - detectCycle, - detectDirectedCycle, - detectAllCycles, - detectAllDirectedCycle, - detectAllUndirectedCycle, - depthFirstSearch, - dijkstra, - findAllPath, - findShortestPath, - floydWarshall, - labelPropagation, - louvain, - iLouvain, - kCore, - kMeans, - cosineSimilarity, - nodesCosineSimilarity, - minimumSpanningTree, - pageRank, - getNeighbors, - Stack, - GADDI, - IAlgorithm -}; - -export default { - getAdjMatrix, - breadthFirstSearch, - connectedComponent, - getDegree, - getInDegree, - getOutDegree, - detectCycle, - detectDirectedCycle, - detectAllCycles, - detectAllDirectedCycle, - detectAllUndirectedCycle, - depthFirstSearch, - dijkstra, - findAllPath, - findShortestPath, - floydWarshall, - labelPropagation, - louvain, - iLouvain, - kCore, - kMeans, - cosineSimilarity, - nodesCosineSimilarity, - minimumSpanningTree, - pageRank, - getNeighbors, - Stack, - GADDI, -}; \ No newline at end of file +export * from "./pageRank"; diff --git a/packages/graph/src/k-core.ts b/packages/graph/src/k-core.ts deleted file mode 100644 index e62d4d4..0000000 --- a/packages/graph/src/k-core.ts +++ /dev/null @@ -1,37 +0,0 @@ - -import { clone } from '@antv/util'; -import degree from './degree'; -import { GraphData } from './types'; -/** - * k-core算法 找出符合指定核心度的紧密关联的子图结构 - * @param graphData 图数据 - * @param k 核心度数 - */ -const kCore = ( - graphData: GraphData, - k: number = 1, - ): GraphData => { - const data = clone(graphData); - const { nodes = [] } = data; - let { edges = [] } = data; - while (true) { - // 获取图中节点的度数 - const degrees = degree({ nodes, edges}); - const nodeIds = Object.keys(degrees); - // 按照度数进行排序 - nodeIds.sort((a, b) => degrees[a]?.degree - degrees[b]?.degree); - const minIndexId = nodeIds[0]; - if (!nodes.length || degrees[minIndexId]?.degree >= k) { - break; - } - const originIndex = nodes.findIndex(node => node.id === minIndexId); - // 移除度数小于k的节点 - nodes.splice(originIndex, 1); - // 移除度数小于k的节点相关的边 - edges = edges.filter(edge => !(edge.source === minIndexId || edge.target === minIndexId)); - } - - return { nodes, edges }; -} - -export default kCore; diff --git a/packages/graph/src/k-means.ts b/packages/graph/src/k-means.ts deleted file mode 100644 index be017c4..0000000 --- a/packages/graph/src/k-means.ts +++ /dev/null @@ -1,216 +0,0 @@ -import { isEqual, uniq } from '@antv/util'; -import { getAllProperties } from './utils/node-properties'; -import { oneHot, getDistance } from './utils/data-preprocessing'; -import Vector from './utils/vector'; -import { GraphData, ClusterData, DistanceType } from './types'; - -// 获取质心 -const getCentroid = (distanceType, allPropertiesWeight, index) => { - let centroid = []; - switch (distanceType) { - case DistanceType.EuclideanDistance: - centroid = allPropertiesWeight[index]; - break; - default: - centroid = []; - break; - } - return centroid; -} - -/** - * k-means算法 根据节点之间的距离将节点聚类为K个簇 - * @param data 图数据 - * @param k 质心（聚类中心）个数 - * @param propertyKey 属性的字段名 - * @param involvedKeys 参与计算的key集合 - * @param uninvolvedKeys 不参与计算的key集合 - * @param distanceType 距离类型 默认节点属性的欧式距离 - */ -const kMeans = ( - data: GraphData, - k: number = 3, - propertyKey: string = undefined, - involvedKeys: string[] = [], - uninvolvedKeys: string[] = ['id'], - distanceType: DistanceType = DistanceType.EuclideanDistance, -) : ClusterData => { - const { nodes = [], edges = [] } = data; - - const defaultClusterInfo = { - clusters: [ - { - id: "0", - nodes, - } - ], - clusterEdges: [] - }; - - // 距离类型为欧式距离且没有属性时，直接return - if (distanceType === DistanceType.EuclideanDistance && !nodes.every(node => node.hasOwnProperty(propertyKey))){ - return defaultClusterInfo; - } - - // 所有节点属性集合 - let properties = []; - // 所有节点属性one-hot特征向量集合 - let allPropertiesWeight = []; - if (distanceType === DistanceType.EuclideanDistance) { - properties = getAllProperties(nodes, propertyKey); - allPropertiesWeight = oneHot(properties, involvedKeys, uninvolvedKeys); - } - if (!allPropertiesWeight.length) { - return defaultClusterInfo; - } - const allPropertiesWeightUniq = uniq(allPropertiesWeight.map(item => item.join(''))); - // 当输入节点数量或者属性集合的长度小于k时，k调整为其中最小的值 - const finalK = Math.min(k, nodes.length, allPropertiesWeightUniq.length); - - // 记录节点的原始index，与allPropertiesWeight对应 - for (let i = 0; i < nodes.length; i++) { - nodes[i].originIndex = i; - } - // 初始化质心（聚类中心） - const centroids = []; - const centroidIndexList = []; - const clusters = []; - for (let i = 0; i < finalK; i++) { - if (i === 0) { - // 随机选取质心（聚类中心） - const randomIndex = Math.floor(Math.random() * nodes.length); - switch (distanceType) { - case DistanceType.EuclideanDistance: - centroids[i] = allPropertiesWeight[randomIndex]; - break; - default: - centroids[i] = []; - break; - } - centroidIndexList.push(randomIndex); - clusters[i] = [nodes[randomIndex]]; - nodes[randomIndex].clusterId = String(i); - } else { - let maxDistance = -Infinity; - let maxDistanceNodeIndex = 0; - // 选取与已有质心平均距离最远的点做为新的质心 - for (let m = 0; m < nodes.length; m++) { - if (!centroidIndexList.includes(m)) { - let totalDistance = 0; - for (let j = 0; j < centroids.length; j++) { - // 求节点到质心的距离（默认节点属性的欧式距离） - let distance = 0; - switch (distanceType) { - case DistanceType.EuclideanDistance: - distance = getDistance(allPropertiesWeight[nodes[m].originIndex], centroids[j], distanceType); - break; - default: - break; - } - totalDistance += distance; - } - // 节点到各质心的平均距离（默认欧式距离） - const avgDistance = totalDistance / centroids.length; - // 记录到已有质心最远的的距离和节点索引 - if (avgDistance > maxDistance && - !centroids.find(centroid => isEqual(centroid, getCentroid(distanceType, allPropertiesWeight, nodes[m].originIndex)))) { - maxDistance = avgDistance; - maxDistanceNodeIndex = m; - } - } - } - - centroids[i] = getCentroid(distanceType, allPropertiesWeight, maxDistanceNodeIndex); - centroidIndexList.push(maxDistanceNodeIndex); - clusters[i] = [nodes[maxDistanceNodeIndex]]; - nodes[maxDistanceNodeIndex].clusterId = String(i); - } - } - - - let iterations = 0; - while (true) { - for (let i = 0; i < nodes.length; i++) { - let minDistanceIndex = 0; - let minDistance = Infinity; - if (!(iterations === 0 && centroidIndexList.includes(i))) { - for (let j = 0; j < centroids.length; j++) { - // 求节点到质心的距离（默认节点属性的欧式距离） - let distance = 0; - switch (distanceType) { - case DistanceType.EuclideanDistance: - distance = getDistance(allPropertiesWeight[i], centroids[j], distanceType); - break; - default: - break; - } - // 记录节点最近的质心的索引 - if (distance < minDistance) { - minDistance = distance; - minDistanceIndex = j; - } - } - - // 从原来的类别删除节点 - if (nodes[i].clusterId !== undefined) { - for (let n = clusters[Number(nodes[i].clusterId)].length - 1; n >= 0 ; n--) { - if (clusters[Number(nodes[i].clusterId)][n].id === nodes[i].id) { - clusters[Number(nodes[i].clusterId)].splice(n, 1); - } - } - } - // 将节点划分到距离最小的质心（聚类中心）所对应的类中 - nodes[i].clusterId = String(minDistanceIndex); - clusters[minDistanceIndex].push(nodes[i]); - } - } - - // 是否存在质心（聚类中心）移动 - let centroidsEqualAvg = false; - for (let i = 0; i < clusters.length; i ++) { - const clusterNodes = clusters[i]; - let totalVector = new Vector([]); - for (let j = 0; j < clusterNodes.length; j++) { - totalVector = totalVector.add(new Vector(allPropertiesWeight[clusterNodes[j].originIndex])); - } - // 计算每个类别的均值向量 - const avgVector = totalVector.avg(clusterNodes.length); - // 如果均值向量不等于质心向量 - if (!avgVector.equal(new Vector(centroids[i]))) { - centroidsEqualAvg = true; - // 移动/更新每个类别的质心（聚类中心）到该均值向量 - centroids[i] = avgVector.getArr(); - } - } - iterations++; - // 如果每个节点都归属了类别，且不存在质心（聚类中心）移动或者迭代次数超过1000，则停止 - if (nodes.every(node => node.clusterId !== undefined) && centroidsEqualAvg || iterations >= 1000) { - break; - } - } - - // get the cluster edges - const clusterEdges = []; - const clusterEdgeMap = {}; - edges.forEach(edge => { - const { source, target } = edge; - const sourceClusterId = nodes.find(node => node.id === source)?.clusterId; - const targetClusterId = nodes.find(node => node.id === target)?.clusterId; - const newEdgeId = `${sourceClusterId}---${targetClusterId}`; - if (clusterEdgeMap[newEdgeId]) { - clusterEdgeMap[newEdgeId].count++; - } else { - const newEdge = { - source: sourceClusterId, - target: targetClusterId, - count: 1 - }; - clusterEdgeMap[newEdgeId] = newEdge; - clusterEdges.push(newEdge); - } - }); - - return { clusters, clusterEdges }; -} - -export default kMeans; diff --git a/packages/graph/src/label-propagation.ts b/packages/graph/src/label-propagation.ts deleted file mode 100644 index ea5dc3c..0000000 --- a/packages/graph/src/label-propagation.ts +++ /dev/null @@ -1,151 +0,0 @@ - -import getAdjMatrix from './adjacent-matrix' -import { uniqueId } from './util'; -import { GraphData, ClusterData } from './types'; - -/** - * 标签传播算法 - * @param graphData 图数据 - * @param directed 是否有向图，默认为 false - * @param weightPropertyName 权重的属性字段 - * @param maxIteration 最大迭代次数 - */ -const labelPropagation = ( - graphData: GraphData, - directed: boolean = false, - weightPropertyName: string = 'weight', - maxIteration: number = 1000 -): ClusterData => { - // the origin data - const { nodes = [], edges = [] } = graphData; - - const clusters = {}; - const nodeMap = {}; - // init the clusters and nodeMap - nodes.forEach((node, i) => { - const cid: string = uniqueId(); - node.clusterId = cid; - clusters[cid] = { - id: cid, - nodes: [node] - }; - nodeMap[node.id] = { - node, - idx: i - }; - }); - - // the adjacent matrix of calNodes inside clusters - const adjMatrix = getAdjMatrix(graphData, directed); - // the sum of each row in adjacent matrix - const ks = []; - /** - * neighbor nodes (id for key and weight for value) for each node - * neighbors = { - * id(node_id): { id(neighbor_1_id): weight(weight of the edge), id(neighbor_2_id): weight(weight of the edge), ... }, - * ... - * } - */ - const neighbors = {}; - adjMatrix.forEach((row, i) => { - let k = 0; - const iid = nodes[i].id; - neighbors[iid] = {}; - row.forEach((entry, j) => { - if (!entry) return; - k += entry; - const jid = nodes[j].id; - neighbors[iid][jid] = entry; - }); - ks.push(k); - }); - - let iter = 0; - - while (iter < maxIteration) { - let changed = false; - nodes.forEach(node => { - const neighborClusters = {}; - Object.keys(neighbors[node.id]).forEach(neighborId => { - const neighborWeight = neighbors[node.id][neighborId]; - const neighborNode = nodeMap[neighborId].node; - const neighborClusterId = neighborNode.clusterId; - if (!neighborClusters[neighborClusterId]) neighborClusters[neighborClusterId] = 0; - neighborClusters[neighborClusterId] += neighborWeight; - }); - // find the cluster with max weight - let maxWeight = -Infinity; - let bestClusterIds = []; - Object.keys(neighborClusters).forEach(clusterId => { - if (maxWeight < neighborClusters[clusterId]) { - maxWeight = neighborClusters[clusterId]; - bestClusterIds = [clusterId]; - } else if (maxWeight === neighborClusters[clusterId]) { - bestClusterIds.push(clusterId); - } - }); - if (bestClusterIds.length === 1 && bestClusterIds[0] === node.clusterId) return; - const selfClusterIdx = bestClusterIds.indexOf(node.clusterId); - if (selfClusterIdx >= 0) bestClusterIds.splice(selfClusterIdx, 1); - if (bestClusterIds && bestClusterIds.length) { - changed = true; - - // remove from origin cluster - const selfCluster = clusters[node.clusterId as string]; - const nodeInSelfClusterIdx = selfCluster.nodes.indexOf(node); - selfCluster.nodes.splice(nodeInSelfClusterIdx, 1); - - // move the node to the best cluster - const randomIdx = Math.floor(Math.random() * bestClusterIds.length); - const bestCluster = clusters[bestClusterIds[randomIdx]]; - bestCluster.nodes.push(node); - node.clusterId = bestCluster.id; - } - }); - if (!changed) break; - iter++; - } - - // delete the empty clusters - Object.keys(clusters).forEach(clusterId => { - const cluster = clusters[clusterId]; - if (!cluster.nodes || !cluster.nodes.length) { - delete clusters[clusterId]; - } - }); - - // get the cluster edges - const clusterEdges = []; - const clusterEdgeMap = {}; - edges.forEach(edge => { - const { source, target } = edge; - const weight = edge[weightPropertyName] || 1; - const sourceClusterId = nodeMap[source].node.clusterId; - const targetClusterId = nodeMap[target].node.clusterId; - const newEdgeId = `${sourceClusterId}---${targetClusterId}`; - if (clusterEdgeMap[newEdgeId]) { - clusterEdgeMap[newEdgeId].weight += weight; - clusterEdgeMap[newEdgeId].count++; - } else { - const newEdge = { - source: sourceClusterId, - target: targetClusterId, - weight, - count: 1 - }; - clusterEdgeMap[newEdgeId] = newEdge; - clusterEdges.push(newEdge); - } - }); - - const clustersArray = []; - Object.keys(clusters).forEach(clusterId => { - clustersArray.push(clusters[clusterId]); - }); - return { - clusters: clustersArray, - clusterEdges - } -} - -export default labelPropagation; diff --git a/packages/graph/src/louvain.ts b/packages/graph/src/louvain.ts deleted file mode 100644 index 75abc49..0000000 --- a/packages/graph/src/louvain.ts +++ /dev/null @@ -1,401 +0,0 @@ -import { clone } from '@antv/util'; -import getAdjMatrix from './adjacent-matrix'; -import { NodeConfig, ClusterData, GraphData, ClusterMap } from './types'; -import Vector from './utils/vector'; -import { getAllProperties } from './utils/node-properties'; -import { oneHot } from './utils/data-preprocessing'; - -const getModularity = ( - nodes: NodeConfig[], - adjMatrix: number[][], - ks: number[], - m: number -) => { - const length = adjMatrix.length; - const param = 2 * m; - let modularity = 0; - for (let i = 0; i < length; i++) { - const clusteri = nodes[i].clusterId; - for (let j = 0; j < length; j++) { - const clusterj = nodes[j].clusterId; - if (clusteri !== clusterj) continue; - const entry = adjMatrix[i][j] || 0; - const ki = ks[i] || 0; - const kj = ks[j] || 0; - modularity += (entry - ki * kj / param); - } - } - modularity *= (1 / param); - return modularity; -} - -// 模块惯性度，衡量属性相似度 -const getInertialModularity = ( - nodes: NodeConfig[] = [], - allPropertiesWeight: number[][], -) => { - const length = nodes.length; - let totalProperties = new Vector([]); - for (let i = 0; i < length; i++) { - totalProperties = totalProperties.add(new Vector(allPropertiesWeight[i])); - } - // 均值向量 - const avgProperties = totalProperties.avg(length); - - avgProperties.normalize(); - // 节点集合的方差: 节点v与均值向量的平方欧式距离之和 - let variance: number = 0; - for (let i = 0; i < length; i++) { - const propertiesi = new Vector(allPropertiesWeight[i]); - const squareEuclideanDistance = propertiesi.squareEuclideanDistance(avgProperties); - variance += squareEuclideanDistance; - } - - // 任意两点间的欧式平方距离 - let squareEuclideanDistanceInfo = []; - nodes.forEach(() => { - squareEuclideanDistanceInfo.push([]); - }); - for (let i = 0; i < length; i++) { - const propertiesi = new Vector(allPropertiesWeight[i]); - nodes[i]['clusterInertial'] = 0; - for (let j = 0; j < length; j++) { - if ( i === j) { - squareEuclideanDistanceInfo[i][j] = 0; - continue; - } - const propertiesj = new Vector(allPropertiesWeight[j]); - squareEuclideanDistanceInfo[i][j] = propertiesi.squareEuclideanDistance(propertiesj); - nodes[i]['clusterInertial'] += squareEuclideanDistanceInfo[i][j]; - } - } - - // 计算模块惯性度 - let inertialModularity: number = 0; - const param = 2 * length * variance; - for (let i = 0; i < length; i++) { - const clusteri = nodes[i].clusterId; - for (let j = 0; j < length; j++) { - const clusterj = nodes[j].clusterId; - if ( i === j || clusteri !== clusterj) continue; - const inertial = (nodes[i].clusterInertial * nodes[j].clusterInertial) / Math.pow(param, 2) - squareEuclideanDistanceInfo[i][j] / param; - inertialModularity += inertial; - } - } - return Number(inertialModularity.toFixed(4)); -} - - -/** - * 社区发现 louvain 算法 - * @param graphData 图数据 - * @param directed 是否有向图，默认为 false - * @param weightPropertyName 权重的属性字段 - * @param threshold 差值阈值 - * @param inertialModularity 是否使用惯性模块度（即节点属性相似性） - * @param propertyKey 属性的字段名 - * @param involvedKeys 参与计算的key集合 - * @param uninvolvedKeys 不参与计算的key集合 - * @param inertialWeight 惯性模块度权重 - */ -const louvain = ( - graphData: GraphData, - directed: boolean = false, - weightPropertyName: string = 'weight', - threshold: number = 0.0001, - inertialModularity: boolean = false, - propertyKey: string = undefined, - involvedKeys: string[] = [], - uninvolvedKeys: string[] = ['id'], - inertialWeight: number = 1, -): ClusterData => { - // the origin data - const { nodes = [], edges = [] } = graphData; - - let allPropertiesWeight = []; - if (inertialModularity) { - nodes.forEach((node, index) => { - node.properties = node.properties || {}; - node.originIndex = index; - }) - - let nodeTypeInfo = []; - if (nodes.every(node => node.hasOwnProperty('nodeType'))) { - nodeTypeInfo = Array.from(new Set(nodes.map(node => node.nodeType))); - nodes.forEach(node => { - node.properties.nodeType = nodeTypeInfo.findIndex(nodeType => nodeType === node.nodeType); - }) - } - // 所有节点属性集合 - const properties = getAllProperties(nodes, propertyKey); - // 所有节点属性one-hot特征向量集合 - allPropertiesWeight = oneHot(properties, involvedKeys, uninvolvedKeys); - } - - let uniqueId = 1; - - const clusters: ClusterMap = {}; - const nodeMap = {}; - // init the clusters and nodeMap - nodes.forEach((node, i) => { - const cid: string = String(uniqueId++); - node.clusterId = cid; - clusters[cid] = { - id: cid, - nodes: [node] - }; - nodeMap[node.id] = { - node, - idx: i - }; - }); - // the adjacent matrix of calNodes inside clusters - const adjMatrix = getAdjMatrix(graphData, directed); - // the sum of each row in adjacent matrix - const ks = []; - /** - * neighbor nodes (id for key and weight for value) for each node - * neighbors = { - * id(node_id): { id(neighbor_1_id): weight(weight of the edge), id(neighbor_2_id): weight(weight of the edge), ... }, - * ... - * } - */ - const neighbors = {}; - // the sum of the weights of all edges in the graph - let m = 0; - adjMatrix.forEach((row, i) => { - let k = 0; - const iid = nodes[i].id; - neighbors[iid] = {}; - row.forEach((entry, j) => { - if (!entry) return; - k += entry; - const jid = nodes[j].id; - neighbors[iid][jid] = entry; - m += entry; - }); - ks.push(k); - }); - - m /= 2; - - let totalModularity = Infinity; - let previousModularity = Infinity; - let iter = 0; - - let finalNodes = []; - let finalClusters = {}; - while (true) { - if (inertialModularity && nodes.every(node => node.hasOwnProperty('properties'))) { - totalModularity = getModularity(nodes, adjMatrix, ks, m) + getInertialModularity(nodes, allPropertiesWeight) * inertialWeight; - } else { - totalModularity = getModularity(nodes, adjMatrix, ks, m); - } - - // 第一次迭代previousModularity直接赋值 - if (iter === 0) { - previousModularity = totalModularity; - finalNodes = nodes; - finalClusters = clusters; - } - - const increaseWithinThreshold = totalModularity > 0 && totalModularity > previousModularity && totalModularity - previousModularity < threshold; - // 总模块度增加才更新最优解 - if (totalModularity > previousModularity) { - finalNodes = nodes.map(node => ({ - node, - clusterId: node.clusterId - })); - finalClusters = clone(clusters); - previousModularity = totalModularity; - } - - // whether to terminate the iterations - if ( increaseWithinThreshold || iter > 100) { - break; - }; - iter++; - // pre compute some values for current clusters - Object.keys(clusters).forEach(clusterId => { - // sum of weights of edges to nodes in cluster - let sumTot = 0; - edges.forEach(edge => { - const { source, target } = edge; - const sourceClusterId = nodeMap[source].node.clusterId; - const targetClusterId = nodeMap[target].node.clusterId; - if ((sourceClusterId === clusterId && targetClusterId !== clusterId) - || (targetClusterId === clusterId && sourceClusterId !== clusterId)) { - sumTot = sumTot + (edge[weightPropertyName] as number || 1); - } - }); - clusters[clusterId].sumTot = sumTot; - }); - - - // move the nodes to increase the delta modularity - nodes.forEach((node, i) => { - const selfCluster = clusters[node.clusterId as string]; - let bestIncrease = 0; - let bestCluster; - - const commonParam = ks[i] / (2 * m); - - // sum of weights of edges from node to nodes in cluster - let kiin = 0; - const selfClusterNodes = selfCluster.nodes; - selfClusterNodes.forEach(scNode => { - const scNodeIdx = nodeMap[scNode.id].idx; - kiin += adjMatrix[i][scNodeIdx] || 0; - }); - // the modurarity for **removing** the node i from the origin cluster of node i - const removeModurarity = kiin - selfCluster.sumTot * commonParam; - // nodes for **removing** node i into this neighbor cluster - const selfClusterNodesAfterRemove = selfClusterNodes.filter(scNode => scNode.id !== node.id); - let propertiesWeightRemove = []; - selfClusterNodesAfterRemove.forEach((nodeRemove, index) => { - propertiesWeightRemove[index] = allPropertiesWeight[nodeRemove.originIndex]; - }) - // the inertialModularity for **removing** the node i from the origin cluster of node i - const removeInertialModularity = getInertialModularity(selfClusterNodesAfterRemove, allPropertiesWeight) * inertialWeight; - - // the neightbors of the node - const nodeNeighborIds = neighbors[node.id]; - Object.keys(nodeNeighborIds).forEach(neighborNodeId => { - const neighborNode = nodeMap[neighborNodeId].node; - const neighborClusterId = neighborNode.clusterId; - - // if the node and the neighbor of node are in the same cluster, reutrn - if (neighborClusterId === node.clusterId) return; - const neighborCluster = clusters[neighborClusterId]; - const clusterNodes = neighborCluster.nodes; - - // if the cluster is empty, remove the cluster and return - if (!clusterNodes || !clusterNodes.length) return; - - // sum of weights of edges from node to nodes in cluster - let neighborClusterKiin = 0; - clusterNodes.forEach(cNode => { - const cNodeIdx = nodeMap[cNode.id].idx; - neighborClusterKiin += adjMatrix[i][cNodeIdx] || 0; - }); - - // the modurarity for **adding** node i into this neighbor cluster - const addModurarity = neighborClusterKiin - neighborCluster.sumTot * commonParam; - // nodes for **adding** node i into this neighbor cluster - const clusterNodesAfterAdd= clusterNodes.concat([node]); - let propertiesWeightAdd = []; - clusterNodesAfterAdd.forEach((nodeAdd, index) => { - propertiesWeightAdd[index] = allPropertiesWeight[nodeAdd.originIndex]; - }) - // the inertialModularity for **adding** node i into this neighbor cluster - const addInertialModularity = getInertialModularity(clusterNodesAfterAdd, allPropertiesWeight) * inertialWeight; - - // the increase modurarity is the difference between addModurarity and removeModurarity - let increase = addModurarity - removeModurarity; - if (inertialModularity) { - increase = (addModurarity + addInertialModularity) - (removeModurarity + removeInertialModularity); - } - - // find the best cluster to move node i into - if (increase > bestIncrease) { - bestIncrease = increase; - bestCluster = neighborCluster; - } - }); - - // if found a best cluster to move into - if (bestIncrease > 0) { - bestCluster.nodes.push(node); - const previousClusterId = node.clusterId; - node.clusterId = bestCluster.id; - // move the node to the best cluster - const nodeInSelfClusterIdx = selfCluster.nodes.indexOf(node); - // remove from origin cluster - selfCluster.nodes.splice(nodeInSelfClusterIdx, 1); - // update sumTot for clusters - // sum of weights of edges to nodes in cluster - let neighborClusterSumTot = 0; - let selfClusterSumTot = 0; - edges.forEach(edge => { - const { source, target } = edge; - const sourceClusterId = nodeMap[source].node.clusterId; - const targetClusterId = nodeMap[target].node.clusterId; - if ((sourceClusterId === bestCluster.id && targetClusterId !== bestCluster.id) - || (targetClusterId === bestCluster.id && sourceClusterId !== bestCluster.id)) { - neighborClusterSumTot = neighborClusterSumTot + (edge[weightPropertyName] as number || 1); - } - if ((sourceClusterId === previousClusterId && targetClusterId !== previousClusterId) - || (targetClusterId === previousClusterId && sourceClusterId !== previousClusterId)) { - selfClusterSumTot = selfClusterSumTot + (edge[weightPropertyName] as number || 1); - } - }); - - // the nodes of the clusters to move into and remove are changed, update their sumTot - bestCluster.sumTot = neighborClusterSumTot; - selfCluster.sumTot = selfClusterSumTot; - } - }); - } - - // delete the empty clusters, assign increasing clusterId - const newClusterIdMap = {} - let clusterIdx = 0; - Object.keys(finalClusters).forEach((clusterId) => { - const cluster = finalClusters[clusterId]; - if (!cluster.nodes || !cluster.nodes.length) { - delete finalClusters[clusterId]; - return; - } - const newId = String(clusterIdx + 1); - if (newId === clusterId) { - return; - } - cluster.id = newId; - cluster.nodes = cluster.nodes.map(item => ({ id: item.id, clusterId: newId })); - finalClusters[newId] = cluster; - newClusterIdMap[clusterId] = newId; - delete finalClusters[clusterId]; - clusterIdx ++; - }); - // restore node clusterId - finalNodes.forEach(nodeInfo => { - const { node, clusterId } = nodeInfo; - if (!node) return; - node.clusterId = clusterId; - if (node.clusterId && newClusterIdMap[node.clusterId]) node.clusterId = newClusterIdMap[node.clusterId] - }) - // get the cluster edges - const clusterEdges = []; - const clusterEdgeMap = {}; - edges.forEach(edge => { - const { source, target } = edge; - const weight = edge[weightPropertyName] || 1; - const sourceClusterId = nodeMap[source].node.clusterId; - const targetClusterId = nodeMap[target].node.clusterId; - if (!sourceClusterId || !targetClusterId) return; - const newEdgeId = `${sourceClusterId}---${targetClusterId}`; - if (clusterEdgeMap[newEdgeId]) { - clusterEdgeMap[newEdgeId].weight += weight; - clusterEdgeMap[newEdgeId].count++; - } else { - const newEdge = { - source: sourceClusterId, - target: targetClusterId, - weight, - count: 1 - }; - clusterEdgeMap[newEdgeId] = newEdge; - clusterEdges.push(newEdge); - } - }); - const clustersArray = []; - Object.keys(finalClusters).forEach(clusterId => { - clustersArray.push(finalClusters[clusterId]); - }); - return { - clusters: clustersArray, - clusterEdges - } -} - -export default louvain; diff --git a/packages/graph/src/mts.ts b/packages/graph/src/mts.ts deleted file mode 100644 index e97edad..0000000 --- a/packages/graph/src/mts.ts +++ /dev/null @@ -1,116 +0,0 @@ -import UnionFind from './structs/union-find'; -import MinBinaryHeap from './structs/binary-heap'; -import { GraphData, EdgeConfig } from './types'; -import { getEdgesByNodeId } from './util'; - -/** - * Prim algorithm，use priority queue，复杂度 O(E+V*logV), V: 节点数量，E: 边的数量 - * refer: https://en.wikipedia.org/wiki/Prim%27s_algorithm - * @param graph - * @param weight 指定用于作为边权重的属性，若不指定，则认为所有边权重一致 - */ -const primMST = (graphData: GraphData, weight?: string) => { - const selectedEdges = []; - const { nodes = [], edges = [] } = graphData; - if (nodes.length === 0) { - return selectedEdges; - } - - // 从nodes[0]开始 - const currNode = nodes[0]; - const visited = new Set(); - visited.add(currNode); - - // 用二叉堆维护距已加入节点的其他节点的边的权值 - const compareWeight = (a: EdgeConfig, b: EdgeConfig) => { - if (weight) { - return a.weight - b.weight; - } - return 0; - - }; - const edgeQueue = new MinBinaryHeap(compareWeight); - getEdgesByNodeId(currNode.id, edges).forEach((edge) => { - edgeQueue.insert(edge); - }); - - while (!edgeQueue.isEmpty()) { - // 选取与已加入的结点之间边权最小的结点 - const currEdge: EdgeConfig = edgeQueue.delMin(); - const source = currEdge.source; - const target = currEdge.target; - if (visited.has(source) && visited.has(target)) continue; - selectedEdges.push(currEdge); - - if (!visited.has(source)) { - visited.add(source); - getEdgesByNodeId(source, edges).forEach((edge) => { - edgeQueue.insert(edge); - }); - } - if (!visited.has(target)) { - visited.add(target); - getEdgesByNodeId(target, edges).forEach((edge) => { - edgeQueue.insert(edge); - }); - } - } - return selectedEdges; -}; - -/** - * Kruskal algorithm，复杂度 O(E*logE), E: 边的数量 - * refer: https://en.wikipedia.org/wiki/Kruskal%27s_algorithm - * @param graph - * @param weight 指定用于作为边权重的属性，若不指定，则认为所有边权重一致 - * @return IEdge[] 返回构成MST的边的数组 - */ -const kruskalMST = (graphData: GraphData, weight?: string): EdgeConfig[] => { - const selectedEdges = []; - const { nodes = [], edges = [] } = graphData - if (nodes.length === 0) { - return selectedEdges; - } - - // 若指定weight，则将所有的边按权值从小到大排序 - const weightEdges = edges.map((edge) => edge); - if (weight) { - weightEdges.sort((a, b) => { - return a.weight - b.weight; - }); - } - const disjointSet = new UnionFind(nodes.map((n) => n.id)); - - // 从权值最小的边开始，如果这条边连接的两个节点于图G中不在同一个连通分量中，则添加这条边 - // 直到遍历完所有点或边 - while (weightEdges.length > 0) { - const curEdge = weightEdges.shift(); - const source = curEdge.source; - const target = curEdge.target; - if (!disjointSet.connected(source, target)) { - selectedEdges.push(curEdge); - disjointSet.union(source, target); - } - } - return selectedEdges; -}; - -/** - * 最小生成树 - * refer: https://en.wikipedia.org/wiki/Kruskal%27s_algorithm - * @param graph - * @param weight 指定用于作为边权重的属性，若不指定，则认为所有边权重一致 - * @param algo 'prim' | 'kruskal' 算法类型 - * @return EdgeConfig[] 返回构成MST的边的数组 - */ -const minimumSpanningTree = (graphData: GraphData, weight?: string, algo?: string): EdgeConfig[] => { - const algos = { - prim: primMST, - kruskal: kruskalMST, - }; - if (!algo) return kruskalMST(graphData, weight); - - return algos[algo](graphData, weight); -} - -export default minimumSpanningTree diff --git a/packages/graph/src/nodes-cosine-similarity.ts b/packages/graph/src/nodes-cosine-similarity.ts deleted file mode 100644 index 2e593eb..0000000 --- a/packages/graph/src/nodes-cosine-similarity.ts +++ /dev/null @@ -1,50 +0,0 @@ -import { clone } from '@antv/util'; -import { NodeConfig } from './types'; -import { getAllProperties } from './utils/node-properties'; -import { oneHot } from './utils/data-preprocessing'; -import cosineSimilarity from './cosine-similarity'; -/** - * nodes-cosine-similarity算法 基于节点属性计算余弦相似度(基于种子节点寻找相似节点) - * @param nodes 图节点数据 - * @param seedNode 种子节点 - * @param propertyKey 属性的字段名 - * @param involvedKeys 参与计算的key集合 - * @param uninvolvedKeys 不参与计算的key集合 - */ -const nodesCosineSimilarity = ( - nodes: NodeConfig[] = [], - seedNode: NodeConfig, - propertyKey: string = undefined, - involvedKeys: string[] = [], - uninvolvedKeys: string[] = [], -): { - allCosineSimilarity: number[], - similarNodes: NodeConfig[], -} => { - const similarNodes = clone(nodes.filter(node => node.id !== seedNode.id)); - const seedNodeIndex = nodes.findIndex(node => node.id === seedNode.id); - // 所有节点属性集合 - const properties = getAllProperties(nodes, propertyKey); - // 所有节点属性one-hot特征向量集合 - const allPropertiesWeight = oneHot(properties, involvedKeys, uninvolvedKeys); - // 种子节点属性 - const seedNodeProperties = allPropertiesWeight[seedNodeIndex]; - - const allCosineSimilarity: number[] = []; - similarNodes.forEach((node, index) => { - if (node.id !== seedNode.id) { - // 节点属性 - const nodeProperties = allPropertiesWeight[index]; - // 计算节点向量和种子节点向量的余弦相似度 - const cosineSimilarityValue = cosineSimilarity(nodeProperties, seedNodeProperties); - allCosineSimilarity.push(cosineSimilarityValue); - node.cosineSimilarity = cosineSimilarityValue; - } - }); - - // 将返回的节点按照余弦相似度大小排序 - similarNodes.sort((a, b) => b.cosineSimilarity - a.cosineSimilarity); - return { allCosineSimilarity, similarNodes }; -} - -export default nodesCosineSimilarity; diff --git a/packages/graph/src/pageRank.ts b/packages/graph/src/pageRank.ts index bda8cfd..d18d38f 100644 --- a/packages/graph/src/pageRank.ts +++ b/packages/graph/src/pageRank.ts @@ -1,40 +1,40 @@ -import { GraphData } from "./types"; -import degree from './degree' -import { getNeighbors } from "./util"; +import { ID } from "@antv/graphlib"; +import { Graph } from "./types"; /** * PageRank https://en.wikipedia.org/wiki/PageRank * refer: https://github.com/anvaka/ngraph.pagerank - * @param graph - * @param epsilon 判断是否收敛的精度值，默认 0.000001 - * @param linkProb 阻尼系数（dumping factor），指任意时刻，用户访问到某节点后继续访问该节点链接的下一个节点的概率，经验值 0.85 + * @param graph + * @param tolerance + * @param alpha + * @param maxIterations */ -const pageRank = (graphData: GraphData, epsilon?: number, linkProb?: number): { - [key: string]: number; -} => { - if (typeof epsilon !== 'number') epsilon = 0.000001; - if (typeof linkProb !== 'number') linkProb = 0.85; - +export const pageRank = ( + graph: Graph, + tolerance = 1e-5, + alpha = 0.85, + maxIterations = 1000 +): { id: ID; score: number }[] => { let distance = 1; let leakedRank = 0; - let maxIterations = 1000; - const { nodes = [], edges = [] } = graphData; + const nodes = graph.getAllNodes(); + const edges = graph.getAllEdges(); const nodesCount = nodes.length; - let currentRank; - const curRanks = {}; - const prevRanks = {} + let currentRank: number; + const curRanks: Record = {}; + const prevRanks: Record = {}; // Initialize pageranks 初始化 for (let j = 0; j < nodesCount; ++j) { const node = nodes[j]; const nodeId = node.id; - curRanks[nodeId] = (1 / nodesCount) - prevRanks[nodeId] = (1 / nodesCount) + curRanks[nodeId] = 1 / nodesCount; + prevRanks[nodeId] = 1 / nodesCount; } - const nodeDegree = degree(graphData) - while (maxIterations > 0 && distance > epsilon) { + const nodeDegree = degree(graphData); + while (maxIterations > 0 && distance > tolerance) { leakedRank = 0; for (let j = 0; j < nodesCount; ++j) { const node = nodes[j]; @@ -43,13 +43,13 @@ const pageRank = (graphData: GraphData, epsilon?: number, linkProb?: number): { if (nodeDegree[node.id].inDegree === 0) { curRanks[nodeId] = 0; } else { - const neighbors = getNeighbors(nodeId, edges, 'source'); + const neighbors = graph.getRelatedEdges(nodeId, "in"); for (let i = 0; i < neighbors.length; ++i) { const neighbor = neighbors[i]; const outDegree: number = nodeDegree[neighbor].outDegree; - if (outDegree > 0) currentRank += (prevRanks[neighbor] / outDegree); + if (outDegree > 0) currentRank += prevRanks[neighbor] / outDegree; } - curRanks[nodeId] = linkProb * currentRank; + curRanks[nodeId] = alpha * currentRank; leakedRank += curRanks[nodeId]; } } @@ -63,10 +63,8 @@ const pageRank = (graphData: GraphData, epsilon?: number, linkProb?: number): { distance += Math.abs(currentRank - prevRanks[nodeId]); prevRanks[nodeId] = currentRank; } - maxIterations -= 1 + maxIterations -= 1; } return prevRanks; -} - -export default pageRank +}; diff --git a/packages/graph/src/structs/binary-heap.ts b/packages/graph/src/structs/binary-heap.ts deleted file mode 100644 index bf3eb70..0000000 --- a/packages/graph/src/structs/binary-heap.ts +++ /dev/null @@ -1,90 +0,0 @@ -const defaultCompare = (a, b) => { - return a - b; -}; - -export default class MinBinaryHeap { - list: any[]; - - compareFn: (a: any, b: any) => number; - - constructor(compareFn = defaultCompare) { - this.compareFn = compareFn; - this.list = []; - } - - getLeft(index) { - return 2 * index + 1; - } - - getRight(index) { - return 2 * index + 2; - } - - getParent(index) { - if (index === 0) { - return null; - } - return Math.floor((index - 1) / 2); - } - - isEmpty() { - return this.list.length <= 0; - } - - top() { - return this.isEmpty() ? undefined : this.list[0]; - } - - delMin() { - const top = this.top(); - const bottom = this.list.pop(); - if (this.list.length > 0) { - this.list[0] = bottom; - this.moveDown(0); - } - return top; - } - - insert(value) { - if (value !== null) { - this.list.push(value); - const index = this.list.length - 1; - this.moveUp(index); - return true; - } - return false; - } - - moveUp(index) { - let parent = this.getParent(index); - while (index && index > 0 && this.compareFn(this.list[parent], this.list[index]) > 0) { - // swap - const tmp = this.list[parent]; - this.list[parent] = this.list[index]; - this.list[index] = tmp; - // [this.list[index], this.list[parent]] = [this.list[parent], this.list[index]] - index = parent; - parent = this.getParent(index); - } - } - - moveDown(index) { - let element = index; - const left = this.getLeft(index); - const right = this.getRight(index); - const size = this.list.length; - if (left !== null && left < size && this.compareFn(this.list[element], this.list[left]) > 0) { - element = left; - } else if ( - right !== null && - right < size && - this.compareFn(this.list[element], this.list[right]) > 0 - ) { - element = right; - } - if (index !== element) { - [this.list[index], this.list[element]] = [this.list[element], this.list[index]]; - this.moveDown(element); - } - } -} diff --git a/packages/graph/src/structs/linked-list.ts b/packages/graph/src/structs/linked-list.ts deleted file mode 100644 index b4ebee6..0000000 --- a/packages/graph/src/structs/linked-list.ts +++ /dev/null @@ -1,245 +0,0 @@ -const defaultComparator = (a, b) => { - if (a === b) { - return true; - } - - return false; -} - -/** - * 链表中单个元素节点 - */ -export class LinkedListNode { - public value; - - public next: LinkedListNode; - - constructor(value, next: LinkedListNode = null) { - this.value = value; - this.next = next; - } - - toString(callback?: any) { - return callback ? callback(this.value) : `${this.value}`; - } -} - -export default class LinkedList { - public head: LinkedListNode; - - public tail: LinkedListNode; - - public compare: Function; - - constructor(comparator = defaultComparator) { - this.head = null; - this.tail = null; - this.compare = comparator; - } - - /** - * 将指定元素添加到链表头部 - * @param value - */ - prepend(value) { - // 在头部添加一个节点 - const newNode = new LinkedListNode(value, this.head); - this.head = newNode; - - if (!this.tail) { - this.tail = newNode; - } - - return this; - } - - /** - * 将指定元素添加到链表中 - * @param value - */ - append(value) { - const newNode = new LinkedListNode(value); - - // 如果不存在头节点，则将创建的新节点作为头节点 - if (!this.head) { - this.head = newNode; - this.tail = newNode; - - return this; - } - - // 将新节点附加到链表末尾 - this.tail.next = newNode; - this.tail = newNode; - - return this; - } - - /** - * 删除指定元素 - * @param value 要删除的元素 - */ - delete(value): LinkedListNode { - if (!this.head) { - return null; - } - - let deleteNode = null; - - // 如果删除的是头部元素，则将next作为头元素 - while (this.head && this.compare(this.head.value, value)) { - deleteNode = this.head; - this.head = this.head.next; - } - - let currentNode = this.head; - - if (currentNode !== null) { - // 如果删除了节点以后，将next节点前移 - while (currentNode.next) { - if (this.compare(currentNode.next.value, value)) { - deleteNode = currentNode.next; - currentNode.next = currentNode.next.next; - } else { - currentNode = currentNode.next; - } - } - } - - // 检查尾部节点是否被删除 - if (this.compare(this.tail.value, value)) { - this.tail = currentNode; - } - - return deleteNode; - } - - /** - * 查找指定的元素 - * @param param0 - */ - find({ value = undefined, callback = undefined }): LinkedListNode { - if (!this.head) { - return null; - } - - let currentNode = this.head; - - while (currentNode) { - // 如果指定了 callback，则按指定的 callback 查找 - if (callback && callback(currentNode.value)) { - return currentNode; - } - - // 如果指定了 value，则按 value 查找 - if (value !== undefined && this.compare(currentNode.value, value)) { - return currentNode; - } - - currentNode = currentNode.next; - } - - return null; - } - - /** - * 删除尾部节点 - */ - deleteTail() { - const deletedTail = this.tail; - - if (this.head === this.tail) { - // 链表中只有一个元素 - this.head = null; - this.tail = null; - return deletedTail; - } - - let currentNode = this.head; - while (currentNode.next) { - if (!currentNode.next.next) { - currentNode.next = null; - } else { - currentNode = currentNode.next; - } - } - - this.tail = currentNode; - - return deletedTail; - } - - /** - * 删除头部节点 - */ - deleteHead() { - if (!this.head) { - return null; - } - - const deletedHead = this.head; - - if (this.head.next) { - this.head = this.head.next; - } else { - this.head = null; - this.tail = null; - } - - return deletedHead; - } - - /** - * 将一组元素转成链表中的节点 - * @param values 链表中的元素 - */ - fromArray(values) { - values.forEach((value) => this.append(value)); - return this; - } - - /** - * 将链表中的节点转成数组元素 - */ - toArray() { - const nodes = []; - - let currentNode = this.head; - - while (currentNode) { - nodes.push(currentNode); - currentNode = currentNode.next; - } - - return nodes; - } - - /** - * 反转链表中的元素节点 - */ - reverse() { - let currentNode = this.head; - let prevNode = null; - let nextNode = null; - while (currentNode) { - // 存储下一个元素节点 - nextNode = currentNode.next; - - // 更改当前节点的下一个节点，以便将它连接到上一个节点上 - currentNode.next = prevNode; - - // 将 prevNode 和 currentNode 向前移动一步 - prevNode = currentNode; - currentNode = nextNode; - } - - this.tail = this.head; - this.head = prevNode; - } - - toString(callback = undefined) { - return this.toArray() - .map((node) => node.toString(callback)) - .toString(); - } -} diff --git a/packages/graph/src/structs/queue.ts b/packages/graph/src/structs/queue.ts deleted file mode 100644 index f265e0c..0000000 --- a/packages/graph/src/structs/queue.ts +++ /dev/null @@ -1,46 +0,0 @@ -import LinkedList from './linked-list'; - -export default class Queue { - public linkedList: LinkedList; - - constructor() { - this.linkedList = new LinkedList(); - } - - /** - * 队列是否为空 - */ - public isEmpty() { - return !this.linkedList.head; - } - - /** - * 读取队列头部的元素， 不删除队列中的元素 - */ - public peek() { - if (!this.linkedList.head) { - return null; - } - return this.linkedList.head.value; - } - - /** - * 在队列的尾部新增一个元素 - * @param value - */ - public enqueue(value) { - this.linkedList.append(value); - } - - /** - * 删除队列中的头部元素，如果队列为空，则返回 null - */ - public dequeue() { - const removeHead = this.linkedList.deleteHead(); - return removeHead ? removeHead.value : null; - } - - public toString(callback?: any) { - return this.linkedList.toString(callback); - } -} diff --git a/packages/graph/src/structs/stack.ts b/packages/graph/src/structs/stack.ts deleted file mode 100644 index af60cb3..0000000 --- a/packages/graph/src/structs/stack.ts +++ /dev/null @@ -1,65 +0,0 @@ -import LinkedList from './linked-list'; - -export default class Stack { - - private linkedList: LinkedList; - - private maxStep: number; - - constructor(maxStep: number = 10) { - this.linkedList = new LinkedList(); - this.maxStep = maxStep; - } - - get length() { - return this.linkedList.toArray().length; - } - - /** - * 判断栈是否为空，如果链表中没有头部元素，则栈为空 - */ - isEmpty() { - return !this.linkedList.head; - } - - /** - * 是否到定义的栈的最大长度，如果达到最大长度后，不再允许入栈 - */ - isMaxStack() { - return this.toArray().length >= this.maxStep; - } - - /** - * 访问顶端元素 - */ - peek() { - if (this.isEmpty()) { - return null; - } - - // 返回头部元素，不删除元素 - return this.linkedList.head.value; - } - - push(value) { - this.linkedList.prepend(value); - if (this.length > this.maxStep) { - this.linkedList.deleteTail(); - } - } - - pop() { - const removeHead = this.linkedList.deleteHead(); - return removeHead ? removeHead.value : null; - } - - toArray() { - return this.linkedList.toArray().map((node) => node.value); - } - - clear() { - while (!this.isEmpty()) { - this.pop(); - } - } -} diff --git a/packages/graph/src/structs/union-find.ts b/packages/graph/src/structs/union-find.ts deleted file mode 100644 index 940ed6d..0000000 --- a/packages/graph/src/structs/union-find.ts +++ /dev/null @@ -1,45 +0,0 @@ -/** - * 并查集 Disjoint set to support quick union - */ -export default class UnionFind { - count: number; - - parent: {}; - - constructor(items: (number | string)[]) { - this.count = items.length; - this.parent = {}; - for (const i of items) { - this.parent[i] = i; - } - } - - // find the root of the item - find(item) { - while (this.parent[item] !== item) { - item = this.parent[item]; - } - return item; - } - - union(a, b) { - const rootA = this.find(a); - const rootB = this.find(b); - - if (rootA === rootB) return; - - // make the element with smaller root the parent - if (rootA < rootB) { - if (this.parent[b] !== b) this.union(this.parent[b], a); - this.parent[b] = this.parent[a]; - } else { - if (this.parent[a] !== a) this.union(this.parent[a], b); - this.parent[a] = this.parent[b]; - } - } - - // whether a and b are connected, i.e. a and b have the same root - connected(a, b) { - return this.find(a) === this.find(b); - } -} diff --git a/packages/graph/src/types.ts b/packages/graph/src/types.ts index 47a03fc..88318c3 100644 --- a/packages/graph/src/types.ts +++ b/packages/graph/src/types.ts @@ -1,114 +1,9 @@ +import { Graph as IGraph, PlainObject } from "@antv/graphlib"; -export type Matrix = number[]; +export interface NodeData extends PlainObject {} -export interface NodeConfig { - id: string; - clusterId?: string; - [key: string]: any; -} - -export interface EdgeConfig { - source: string; - target: string; +export interface EdgeData extends PlainObject { weight?: number; - [key: string]: any; -} - -export interface GraphData { - nodes?: NodeConfig[]; - edges?: EdgeConfig[]; -} - -export interface Cluster { - id: string; - nodes: NodeConfig[]; - sumTot?: number; -} - -export interface ClusterData { - clusters: Cluster[]; - clusterEdges: EdgeConfig[]; -} - -export interface ClusterMap { - [key: string]: Cluster -} - -// 图算法回调方法接口定义 -export interface IAlgorithmCallbacks { - enter?: (param: { current: string; previous: string }) => void; - leave?: (param: { current: string; previous?: string }) => void; - allowTraversal?: (param: { previous?: string; current?: string; next: string }) => boolean; -} - -export interface DegreeType { - [key: string]: { - degree: number; - inDegree: number; - outDegree: number; - } -} - -export enum DistanceType { - EuclideanDistance = 'euclideanDistance', -} - -export interface PlainObject { - [key: string]: any; -} - -// 数据集中属性/特征值分布的map -export interface KeyValueMap { - [key:string]: any[]; } -export interface IAlgorithm { - getAdjMatrix: (graphData: GraphData, directed?: boolean) => Matrix[], - breadthFirstSearch: ( - graphData: GraphData, - startNodeId: string, - originalCallbacks?: IAlgorithmCallbacks, - directed?: boolean - ) => void, - connectedComponent: (graphData: GraphData, directed?: boolean) => NodeConfig[][], - getDegree: (graphData: GraphData) => DegreeType, - getInDegree: (graphData: GraphData, nodeId: string) => number, - getOutDegree: (graphData: GraphData, nodeId: string) => number, - detectCycle: (graphData: GraphData) => { [key: string]: string }, - detectDirectedCycle: (graphData: GraphData) => { [key: string]: string }, - detectAllCycles: (graphData: GraphData, directed?: boolean, nodeIds?: string[], include?: boolean) => any, - detectAllDirectedCycle: (graphData: GraphData, nodeIds?: string[], include?: boolean) => any, - detectAllUndirectedCycle: (graphData: GraphData, nodeIds?: string[], include?: boolean) => any, - depthFirstSearch: (graphData: GraphData, startNodeId: string, callbacks?: IAlgorithmCallbacks) => void, - dijkstra: (graphData: GraphData, source: string, directed?: boolean, weightPropertyName?: string) => { length: object, allPath: object, path: object}, - findAllPath: (graphData: GraphData, start: string, end: string, directed?: boolean) => any, - findShortestPath: (graphData: GraphData, start: string, end: string, directed?: boolean, weightPropertyName?: string) => any, - floydWarshall: (graphData: GraphData, directed?: boolean) => Matrix[], - labelPropagation: (graphData: GraphData, directed?: boolean, weightPropertyName?: string, maxIteration?: number) => ClusterData, - louvain: (graphData: GraphData, directed: boolean, weightPropertyName: string, threshold: number) => ClusterData, - minimumSpanningTree: (graphData: GraphData, weight?: string, algo?: string) => EdgeConfig[], - pageRank: (graphData: GraphData, epsilon?: number, linkProb?: number) => { [key: string]: number}, - getNeighbors: (nodeId: string, edges?: EdgeConfig[], type?: 'target' | 'source' | undefined) => string[], - Stack: any, - GADDI: (graphData: GraphData, pattern: GraphData, directed: boolean, k: number, length: number, nodeLabelProp: string, edgeLabelProp: string) => GraphData[], - getAdjMatrixAsync: (graphData: GraphData, directed?: boolean) => Matrix[], - connectedComponentAsync: (graphData: GraphData, directed?: boolean) => NodeConfig[][], - getDegreeAsync: (graphData: GraphData) => DegreeType, - getInDegreeAsync: (graphData: GraphData, nodeId: string) => number, - getOutDegreeAsync: (graphData: GraphData, nodeId: string) => number, - detectCycleAsync: (graphData: GraphData) => { [key: string]: string }, - detectDirectedCycleAsync: (graphData: GraphData) => { [key: string]: string }, - detectAllCyclesAsync: (graphData: GraphData, directed?: boolean, nodeIds?: string[], include?: boolean) => any, - detectAllDirectedCycleAsync: (graphData: GraphData, nodeIds?: string[], include?: boolean) => any, - detectAllUndirectedCycleAsync: (graphData: GraphData, nodeIds?: string[], include?: boolean) => any, - dijkstraAsync: (graphData: GraphData, source: string, directed?: boolean, weightPropertyName?: string) => { length: object, allPath: object, path: object}, - findAllPathAsync: (graphData: GraphData, start: string, end: string, directed?: boolean) => any, - findShortestPathAsync: (graphData: GraphData, start: string, end: string, directed?: boolean, weightPropertyName?: string) => any, - floydWarshallAsync: (graphData: GraphData, directed?: boolean) => Matrix[], - labelPropagationAsync: (graphData: GraphData, directed?: boolean, weightPropertyName?: string, maxIteration?: number) => ClusterData, - louvainAsync: (graphData: GraphData, directed: boolean, weightPropertyName: string, threshold: number) => ClusterData, - minimumSpanningTreeAsync: (graphData: GraphData, weight?: string, algo?: string) => EdgeConfig[], - pageRankAsync: (graphData: GraphData, epsilon?: number, linkProb?: number) => { [key: string]: number}, - getNeighborsAsync: (nodeId: string, edges?: EdgeConfig[], type?: 'target' | 'source' | undefined) => string[], - GADDIAsync: (graphData: GraphData, pattern: GraphData, directed: boolean, k: number, length: number, nodeLabelProp: string, edgeLabelProp: string) => GraphData[], -} \ No newline at end of file +export type Graph = IGraph; diff --git a/packages/graph/src/util.ts b/packages/graph/src/util.ts deleted file mode 100644 index 35ae015..0000000 --- a/packages/graph/src/util.ts +++ /dev/null @@ -1,59 +0,0 @@ -import { EdgeConfig, GraphData, Matrix } from './types' - -/** - * 获取指定节点的所有邻居 - * @param nodeId 节点 ID - * @param edges 图中的所有边数据 - * @param type 邻居类型 - */ -export const getNeighbors = (nodeId: string, edges: EdgeConfig[] = [], type?: 'target' | 'source' | undefined): string[] => { - const currentEdges = edges.filter(edge => edge.source === nodeId || edge.target === nodeId) - if (type === 'target') { - // 当前节点为 source，它所指向的目标节点 - const neighhborsConverter = (edge: EdgeConfig) => { - return edge.source === nodeId; - }; - return currentEdges.filter(neighhborsConverter).map((edge) => edge.target); - } - if (type === 'source') { - // 当前节点为 target，它所指向的源节点 - const neighhborsConverter = (edge: EdgeConfig) => { - return edge.target === nodeId; - }; - return currentEdges.filter(neighhborsConverter).map((edge) => edge.source); - } - - // 若未指定 type ，则返回所有邻居 - const neighhborsConverter = (edge: EdgeConfig) => { - return edge.source === nodeId ? edge.target : edge.source; - }; - return currentEdges.map(neighhborsConverter); -} - -/** - * 获取指定节点的出边 - * @param nodeId 节点 ID - * @param edges 图中的所有边数据 - */ -export const getOutEdgesNodeId = (nodeId: string, edges: EdgeConfig[]) => { - return edges.filter(edge => edge.source === nodeId) -} - -/** - * 获取指定节点的边，包括出边和入边 - * @param nodeId 节点 ID - * @param edges 图中的所有边数据 - */ -export const getEdgesByNodeId = (nodeId: string, edges: EdgeConfig[]) => { - return edges.filter(edge => edge.source === nodeId || edge.target === nodeId) -} - -/** - * 生成唯一的 ID，规则是序号 + 时间戳 - * @param index 序号 - */ -export const uniqueId = (index: number = 0) => { - const random1 = `${Math.random()}`.split('.')[1].substr(0, 5); - const random2 = `${Math.random()}`.split('.')[1].substr(0, 5); - return `${index}-${random1}${random2}` -}; diff --git a/packages/graph/src/utils/data-preprocessing.ts b/packages/graph/src/utils/data-preprocessing.ts deleted file mode 100644 index fcf54cd..0000000 --- a/packages/graph/src/utils/data-preprocessing.ts +++ /dev/null @@ -1,110 +0,0 @@ -import { uniq } from '@antv/util'; -import { PlainObject, DistanceType, GraphData, KeyValueMap } from '../types'; -import Vector from './vector'; - -/** - * 获取数据中所有的属性及其对应的值 - * @param dataList 数据集 - * @param involvedKeys 参与计算的key集合 - * @param uninvolvedKeys 不参与计算的key集合 - */ -export const getAllKeyValueMap = (dataList: PlainObject[], involvedKeys?: string[], uninvolvedKeys?: string[]) => { - let keys = []; - // 指定了参与计算的keys时，使用指定的keys - if (involvedKeys?.length) { - keys = involvedKeys; - } else { - // 未指定抽取的keys时，提取数据中所有的key - dataList.forEach(data => { - keys = keys.concat(Object.keys(data)); - }) - keys = uniq(keys); - } - // 获取所有值非空的key的value数组 - const allKeyValueMap: KeyValueMap = {}; - keys.forEach(key => { - let value = []; - dataList.forEach(data => { - if (data[key] !== undefined && data[key] !== '') { - value.push(data[key]); - } - }) - if (value.length && !uninvolvedKeys?.includes(key)) { - allKeyValueMap[key] = uniq(value); - } - }) - - return allKeyValueMap; -} - -/** - * one-hot编码：数据特征提取 - * @param dataList 数据集 - * @param involvedKeys 参与计算的的key集合 - * @param uninvolvedKeys 不参与计算的key集合 - */ -export const oneHot = (dataList: PlainObject[], involvedKeys?: string[], uninvolvedKeys?: string[]) => { - // 获取数据中所有的属性/特征及其对应的值 - const allKeyValueMap = getAllKeyValueMap(dataList, involvedKeys, uninvolvedKeys); - const oneHotCode = []; - if (!Object.keys(allKeyValueMap).length) { - return oneHotCode; - } - - // 获取所有的属性/特征值 - const allValue = Object.values(allKeyValueMap); - // 是否所有属性/特征的值都是数值型 - const isAllNumber = allValue.every(value => value.every(item => (typeof(item) === 'number'))); - - // 对数据进行one-hot编码 - dataList.forEach((data, index) => { - let code = []; - Object.keys(allKeyValueMap).forEach(key => { - const keyValue = data[key]; - const allKeyValue = allKeyValueMap[key]; - const valueIndex = allKeyValue.findIndex(value => keyValue === value); - let subCode = []; - // 如果属性/特征所有的值都能转成数值型，不满足分箱，则直接用值（todo: 为了收敛更快，需做归一化处理） - if (isAllNumber) { - subCode.push(keyValue); - } else { - // 进行one-hot编码 - for(let i = 0; i < allKeyValue.length; i++) { - if (i === valueIndex) { - subCode.push(1); - } else { - subCode.push(0); - } - } - } - code = code.concat(subCode); - }) - oneHotCode[index] = code; - }) - return oneHotCode; -} - -/** - * getDistance：获取两个元素之间的距离 - * @param item - * @param otherItem - * @param distanceType 距离类型 - * @param graphData 图数据 - */ -export const getDistance = (item, otherItem, distanceType: DistanceType = DistanceType.EuclideanDistance, graphData?: GraphData) => { - let distance = 0; - switch (distanceType) { - case DistanceType.EuclideanDistance: - distance = new Vector(item).euclideanDistance(new Vector(otherItem)); - break; - default: - break; - } - return distance; -} - -export default { - getAllKeyValueMap, - oneHot, - getDistance, -} diff --git a/packages/graph/src/utils/node-properties.ts b/packages/graph/src/utils/node-properties.ts deleted file mode 100644 index 3fc53a7..0000000 --- a/packages/graph/src/utils/node-properties.ts +++ /dev/null @@ -1,78 +0,0 @@ -import { NodeConfig } from '../types'; -import { secondReg, dateReg } from '../constants/time'; - -// 获取所有属性并排序 -export const getAllSortProperties = (nodes: NodeConfig[] = [], n: number = 100) => { - const propertyKeyInfo = {}; - nodes.forEach(node => { - if (!node.properties) { - return; - } - Object.keys(node.properties).forEach(propertyKey => { - // 目前过滤只保留可以转成数值型的或日期型的, todo: 统一转成one-hot特征向量或者embedding - if (propertyKey === 'id' || !`${node.properties[propertyKey]}`.match(secondReg) && - !`${node.properties[propertyKey]}`.match(dateReg) && - isNaN(Number(node.properties[propertyKey]))) { - if (propertyKeyInfo.hasOwnProperty(propertyKey)) { - delete propertyKeyInfo[propertyKey]; - } - return; - } - if (propertyKeyInfo.hasOwnProperty(propertyKey)) { - propertyKeyInfo[propertyKey] += 1; - } else { - propertyKeyInfo[propertyKey] = 1; - } - }) - }) - - // 取top50的属性 - const sortKeys = Object.keys(propertyKeyInfo).sort((a,b) => propertyKeyInfo[b] - propertyKeyInfo[a]); - return sortKeys.length < n ? sortKeys : sortKeys.slice(0, n); -} - -const processProperty = (properties, propertyKeys) => propertyKeys.map(key => { - if (properties.hasOwnProperty(key)) { - // // 可以转成数值的直接转成数值 - // if (!isNaN(Number(properties[key]))) { - // return Number(properties[key]); - // } - // // 时间型的转成时间戳 - // if (properties[key].match(secondReg) || properties[key].match(dateReg)) { - // // @ts-ignore - // return Number(Date.parse(new Date(properties[key]))) / 1000; - // } - return properties[key]; - } - return 0; -}) - -// 获取属性特征权重 -export const getPropertyWeight = (nodes: NodeConfig[]) => { - const propertyKeys = getAllSortProperties(nodes); - let allPropertiesWeight = []; - for (let i = 0; i < nodes.length; i++) { - allPropertiesWeight[i] = processProperty(nodes[i].properties, propertyKeys); - } - return allPropertiesWeight; -} - -// 获取所有节点的属性集合 -export const getAllProperties = (nodes, key = undefined) => { - const allProperties = []; - nodes.forEach(node => { - if (key === undefined) { - allProperties.push(node); - } - if (node[key] !== undefined) { - allProperties.push(node[key]); - } - }) - return allProperties; -} - -export default { - getAllSortProperties, - getPropertyWeight, - getAllProperties -} diff --git a/packages/graph/src/utils/vector.ts b/packages/graph/src/utils/vector.ts deleted file mode 100644 index 1b61849..0000000 --- a/packages/graph/src/utils/vector.ts +++ /dev/null @@ -1,159 +0,0 @@ - -/** - * 向量运算 - */ -import { clone } from '@antv/util'; - -class Vector { - arr: number[]; - - constructor(arr) { - this.arr = arr; - } - - getArr() { - return this.arr || []; - } - - add(otherVector) { - const otherArr = otherVector.arr; - if (!this.arr?.length) { - return new Vector(otherArr); - } - if (!otherArr?.length) { - return new Vector(this.arr); - } - if (this.arr.length === otherArr.length) { - let res = []; - for (let index in this.arr) { - res[index] = this.arr[index] + otherArr[index]; - } - return new Vector(res); - } - } - - subtract(otherVector) { - const otherArr = otherVector.arr; - if (!this.arr?.length) { - return new Vector(otherArr); - } - if (!otherArr?.length) { - return new Vector(this.arr); - } - if (this.arr.length === otherArr.length) { - let res = []; - for (let index in this.arr) { - res[index] = this.arr[index] - otherArr[index]; - } - return new Vector(res); - } - } - - avg(length) { - let res = []; - if (length !== 0) { - for (let index in this.arr) { - res[index] = this.arr[index] / length; - } - } - return new Vector(res); - } - - negate() { - let res = []; - for (let index in this.arr) { - res[index] = - this.arr[index]; - } - return new Vector(res); - } - - // 平方欧式距离 - squareEuclideanDistance(otherVector) { - const otherArr = otherVector.arr; - if (!this.arr?.length || !otherArr?.length) { - return 0; - } - if (this.arr.length === otherArr.length) { - let res = 0; - for (let index in this.arr) { - res += Math.pow(this.arr[index] - otherVector.arr[index], 2); - } - return res; - } - } - - // 欧式距离 - euclideanDistance(otherVector) { - const otherArr = otherVector.arr; - if (!this.arr?.length || !otherArr?.length) { - return 0; - } - if (this.arr.length === otherArr.length) { - let res = 0; - for (let index in this.arr) { - res += Math.pow(this.arr[index] - otherVector.arr[index], 2); - } - return Math.sqrt(res); - } else { - console.error('The two vectors are unequal in length.') - } - } - - // 归一化处理 - normalize() { - let res = []; - const cloneArr = clone(this.arr); - cloneArr.sort((a, b) => a - b); - const max = cloneArr[cloneArr.length - 1]; - const min = cloneArr[0]; - for (let index in this.arr) { - res[index] = (this.arr[index] - min) / (max - min); - } - return new Vector(res); - } - - // 2范数 or 模长 - norm2() { - if (!this.arr?.length) { - return 0; - } - let res = 0; - for (let index in this.arr) { - res += Math.pow(this.arr[index], 2); - } - return Math.sqrt(res); - } - - // 两个向量的点积 - dot(otherVector) { - const otherArr = otherVector.arr; - if (!this.arr?.length || !otherArr?.length) { - return 0; - } - if (this.arr.length === otherArr.length) { - let res = 0; - for (let index in this.arr) { - res += this.arr[index] * otherVector.arr[index]; - } - return res; - } else { - console.error('The two vectors are unequal in length.') - } - } - - // 两个向量比较 - equal(otherVector) { - const otherArr = otherVector.arr; - if (this.arr?.length !== otherArr?.length) { - return false; - } - for (let index in this.arr) { - if (this.arr[index] !== otherArr[index]) { - return false; - } - } - return true; - } -} - -export default Vector; diff --git a/packages/graph/src/workers/algorithm.ts b/packages/graph/src/workers/algorithm.ts deleted file mode 100644 index acade39..0000000 --- a/packages/graph/src/workers/algorithm.ts +++ /dev/null @@ -1,16 +0,0 @@ -export { default as getAdjMatrix } from '../adjacent-matrix'; -export { default as breadthFirstSearch } from '../bfs'; -export { default as connectedComponent } from '../connected-component'; -export { default as getDegree } from '../degree'; -export { getInDegree, getOutDegree } from '../degree'; -export { default as detectCycle } from '../detect-cycle'; -export { default as depthFirstSearch } from '../dfs'; -export { default as dijkstra } from '../dijkstra'; -export { findAllPath, findShortestPath } from '../find-path'; -export { default as floydWarshall } from '../floydWarshall'; -export { default as labelPropagation } from '../label-propagation'; -export { default as louvain } from '../louvain'; -export { default as minimumSpanningTree } from '../mts'; -export { default as pageRank } from '../pageRank'; -export { default as GADDI } from '../gaddi'; -export { getNeighbors } from '../util'; diff --git a/packages/graph/src/workers/constant.ts b/packages/graph/src/workers/constant.ts deleted file mode 100644 index cceaec6..0000000 --- a/packages/graph/src/workers/constant.ts +++ /dev/null @@ -1,31 +0,0 @@ -export const ALGORITHM = { - pageRank: 'pageRank', - breadthFirstSearch: 'breadthFirstSearch', - connectedComponent: 'connectedComponent', - depthFirstSearch: 'depthFirstSearch', - detectCycle: 'detectCycle', - detectDirectedCycle: 'detectDirectedCycle', - detectAllCycles: 'detectAllCycles', - detectAllDirectedCycle: 'detectAllDirectedCycle', - detectAllUndirectedCycle: 'detectAllUndirectedCycle', - dijkstra: 'dijkstra', - findAllPath: 'findAllPath', - findShortestPath: 'findShortestPath', - floydWarshall: 'floydWarshall', - getAdjMatrix: 'getAdjMatrix', - getDegree: 'getDegree', - getInDegree: 'getInDegree', - getNeighbors: 'getNeighbors', - getOutDegree: 'getOutDegree', - labelPropagation: 'labelPropagation', - louvain: 'louvain', - GADDI: 'GADDI', - minimumSpanningTree: 'minimumSpanningTree', - SUCCESS: 'SUCCESS', - FAILURE: 'FAILURE', -}; - -export const MESSAGE = { - SUCCESS: 'SUCCESS', - FAILURE: 'FAILURE', -}; diff --git a/packages/graph/src/workers/createWorker.ts b/packages/graph/src/workers/createWorker.ts deleted file mode 100644 index 37f8112..0000000 --- a/packages/graph/src/workers/createWorker.ts +++ /dev/null @@ -1,33 +0,0 @@ -import { MESSAGE } from './constant'; -import Worker from './index.worker'; - -interface Event { - type: string; - data: any; -} - -/** - * 创建一个在worker中运行的算法 - * @param type 算法类型 - */ -const createWorker = (type: string) => (...data) => - new Promise((resolve, reject) => { - const worker = new Worker(); - worker.postMessage({ - _algorithmType:type, - data, - }); - - worker.onmessage = (event: Event) => { - const { data, _algorithmType } = event.data; - if (MESSAGE.SUCCESS === _algorithmType) { - resolve(data); - } else { - reject(); - } - - worker.terminate(); - }; - }); - -export default createWorker; diff --git a/packages/graph/src/workers/index.ts b/packages/graph/src/workers/index.ts deleted file mode 100644 index 467a320..0000000 --- a/packages/graph/src/workers/index.ts +++ /dev/null @@ -1,253 +0,0 @@ -import { - GraphData, - DegreeType, - Matrix, - ClusterData, - EdgeConfig, - NodeConfig, -} from '../types'; -import createWorker from './createWorker'; -import { ALGORITHM } from './constant'; - -/** - * @param graphData 图数据 - * @param directed 是否为有向图 - */ -const getAdjMatrixAsync = (graphData: GraphData, directed?: boolean) => - createWorker(ALGORITHM.getAdjMatrix)(...[graphData, directed]); - -/** - * 图的连通分量 - * @param graphData 图数据 - * @param directed 是否为有向图 - */ -const connectedComponentAsync = (graphData: GraphData, directed?: boolean) => - createWorker(ALGORITHM.connectedComponent)(...[graphData, directed]); - -/** - * 获取节点的度 - * @param graphData 图数据 - */ -const getDegreeAsync = (graphData: GraphData) => - createWorker(ALGORITHM.getDegree)(graphData); - -/** - * 获取节点的入度 - * @param graphData 图数据 - * @param nodeId 节点ID - */ -const getInDegreeAsync = (graphData: GraphData, nodeId: string) => - createWorker(ALGORITHM.getInDegree)(graphData, nodeId); - -/** - * 获取节点的出度 - * @param graphData 图数据 - * @param nodeId 节点ID - */ -const getOutDegreeAsync = (graphData: GraphData, nodeId: string) => - createWorker(ALGORITHM.getOutDegree)(graphData, nodeId); - -/** - * 检测图中的(有向) Cycle - * @param graphData 图数据 - */ -const detectCycleAsync = (graphData: GraphData) => - createWorker<{ - [key: string]: string; - }>(ALGORITHM.detectCycle)(graphData); - -/** - * 检测图中的(无向) Cycle - * @param graphData 图数据 - */ - const detectAllCyclesAsync = (graphData: GraphData) => - createWorker<{ - [key: string]: string; - }>(ALGORITHM.detectAllCycles)(graphData); - -/** - * 检测图中的所有(有向) Cycle - * @param graphData 图数据 - */ - const detectAllDirectedCycleAsync = (graphData: GraphData) => - createWorker<{ - [key: string]: string; - }>(ALGORITHM.detectAllDirectedCycle)(graphData); - -/** - * 检测图中的所有(无向) Cycle - * @param graphData 图数据 - */ - const detectAllUndirectedCycleAsync = (graphData: GraphData) => - createWorker<{ - [key: string]: string; - }>(ALGORITHM.detectAllUndirectedCycle)(graphData); - -/** - * Dijkstra's algorithm, See {@link https://en.wikipedia.org/wiki/Dijkstra%27s_algorithm} - * @param graphData 图数据 - */ -const dijkstraAsync = ( - graphData: GraphData, - source: string, - directed?: boolean, - weightPropertyName?: string, -) => - createWorker<{ - length: number; - path: any; - allPath: any; - }>(ALGORITHM.dijkstra)(...[graphData, source, directed, weightPropertyName]); - -/** - * 查找两点之间的所有路径 - * @param graphData 图数据 - * @param start 路径起始点ID - * @param end 路径终点ID - * @param directed 是否为有向图 - */ -const findAllPathAsync = (graphData: GraphData, start: string, end: string, directed?: boolean) => - createWorker(ALGORITHM.findAllPath)(...[graphData, start, end, directed]); - -/** - * 查找两点之间的所有路径 - * @param graphData 图数据 - * @param start 路径起始点ID - * @param end 路径终点ID - * @param directed 是否为有向图 - * @param weightPropertyName 边权重的属名称，若数据中没有权重，则默认每条边权重为 1 - */ -const findShortestPathAsync = ( - graphData: GraphData, - start: string, - end: string, - directed?: boolean, - weightPropertyName?: string, -) => - createWorker<{ - length: number; - path: any; - allPath: any; - }>(ALGORITHM.findShortestPath)(...[graphData, start, end, directed, weightPropertyName]); - -/** - * Floyd–Warshall algorithm, See {@link https://en.wikipedia.org/wiki/Floyd%E2%80%93Warshall_algorithm} - * @param graphData 图数据 - * @param directed 是否为有向图 - */ -const floydWarshallAsync = (graphData: GraphData, directed?: boolean) => - createWorker(ALGORITHM.floydWarshall)(...[graphData, directed]); - -/** - * 标签传播算法 - * @param graphData 图数据 - * @param directed 是否有向图，默认为 false - * @param weightPropertyName 权重的属性字段 - * @param maxIteration 最大迭代次数 - */ -const labelPropagationAsync = ( - graphData: GraphData, - directed: boolean, - weightPropertyName: string, - maxIteration: number = 1000, -) => - createWorker(ALGORITHM.labelPropagation)( - graphData, - directed, - weightPropertyName, - maxIteration, - ); - -/** - * 社区发现 louvain 算法 - * @param graphData 图数据 - * @param directed 是否有向图，默认为 false - * @param weightPropertyName 权重的属性字段 - * @param threshold - */ -const louvainAsync = ( - graphData: GraphData, - directed: boolean, - weightPropertyName: string, - threshold: number, -) => - createWorker(ALGORITHM.louvain)(graphData, directed, weightPropertyName, threshold); - -/** - * 最小生成树，See {@link https://en.wikipedia.org/wiki/Kruskal%27s_algorithm} - * @param graph - * @param weight 指定用于作为边权重的属性，若不指定，则认为所有边权重一致 - * @param algo 'prim' | 'kruskal' 算法类型 - * @return EdgeConfig[] 返回构成MST的边的数组 - */ -const minimumSpanningTreeAsync = (graphData: GraphData, weight?: boolean, algo?: string) => - createWorker(ALGORITHM.minimumSpanningTree)(...[graphData, weight, algo]); - -/** - * PageRank https://en.wikipedia.org/wiki/PageRank - * refer: https://github.com/anvaka/ngraph.pagerank - * @param graph - * @param epsilon 判断是否收敛的精度值，默认 0.000001 - * @param linkProb 阻尼系数（dumping factor），指任意时刻，用户访问到某节点后继续访问该节点链接的下一个节点的概率，经验值 0.85 - */ -const pageRankAsync = (graphData: GraphData, epsilon?: number, linkProb?: number) => - createWorker<{ - [key: string]: number; - }>(ALGORITHM.pageRank)(...[graphData, epsilon, linkProb]); - -/** - * 获取指定节点的所有邻居 - * @param nodeId 节点 ID - * @param edges 图中的所有边数据 - * @param type 邻居类型 - */ -const getNeighborsAsync = ( - nodeId: string, - edges: EdgeConfig[], - type?: 'target' | 'source' | undefined, -) => createWorker(ALGORITHM.getNeighbors)(...[nodeId, edges, type]); - -/** - * GADDI 图模式匹配 - * @param graphData 原图数据 - * @param pattern 搜索图（需要在原图上搜索的模式）数据 - * @param directed 是否计算有向图，默认 false - * @param k 参数 k，表示 k-近邻 - * @param length 参数 length - * @param nodeLabelProp 节点数据中代表节点标签（分类信息）的属性名。默认为 cluster - * @param edgeLabelProp 边数据中代表边标签（分类信息）的属性名。默认为 cluster - */ -const GADDIAsync = ( - graphData: GraphData, - pattern: GraphData, - directed: boolean = false, - k: number, - length: number, - nodeLabelProp: string = 'cluster', - edgeLabelProp: string = 'cluster', -) => - createWorker(ALGORITHM.GADDI)( - ...[graphData, pattern, directed, k, length, nodeLabelProp, edgeLabelProp], - ); - -export { - getAdjMatrixAsync, - connectedComponentAsync, - getDegreeAsync, - getInDegreeAsync, - getOutDegreeAsync, - detectCycleAsync, - detectAllCyclesAsync, - detectAllDirectedCycleAsync, - detectAllUndirectedCycleAsync, - dijkstraAsync, - findAllPathAsync, - findShortestPathAsync, - floydWarshallAsync, - labelPropagationAsync, - louvainAsync, - minimumSpanningTreeAsync, - pageRankAsync, - getNeighborsAsync, - GADDIAsync, -}; diff --git a/packages/graph/src/workers/index.worker.ts b/packages/graph/src/workers/index.worker.ts deleted file mode 100644 index dbdb581..0000000 --- a/packages/graph/src/workers/index.worker.ts +++ /dev/null @@ -1,27 +0,0 @@ -import * as algorithm from './algorithm'; -import { MESSAGE } from './constant'; - -const ctx: Worker = (typeof self !== 'undefined') ? self : {} as any; - -interface Event { - type: string; - data: any; -} - -ctx.onmessage = (event: Event) => { - const { _algorithmType, data } = event.data; - // 如果发送内容没有私有类型。说明不是自己发的。不管 - // fix: https://github.com/antvis/algorithm/issues/25 - if(!_algorithmType){ - return; - } - if (typeof algorithm[_algorithmType] === 'function') { - const result = algorithm[_algorithmType](...data); - ctx.postMessage({ _algorithmType: MESSAGE.SUCCESS, data: result }); - return; - } - ctx.postMessage({ _algorithmType: MESSAGE.FAILURE }); -}; - -// https://stackoverflow.com/questions/50210416/webpack-worker-loader-fails-to-compile-typescript-worker -export default null as any; diff --git a/packages/graph/tsconfig.json b/packages/graph/tsconfig.json index ba439d3..2ccebef 100644 --- a/packages/graph/tsconfig.json +++ b/packages/graph/tsconfig.json @@ -1,4 +1,5 @@ { + "extends": "../../tsconfig.json", "compilerOptions": { "rootDir": "./src", "composite": true, diff --git a/site/benchmark/index.html b/site/benchmark/index.html index 7a1e793..d0a428a 100644 --- a/site/benchmark/index.html +++ b/site/benchmark/index.html @@ -170,8 +170,8 @@
-
-
@antv/webgpu-graph
+
+
@antv/graph-gpu
diff --git a/site/benchmark/main.ts b/site/benchmark/main.ts index d875fd6..e08981e 100644 --- a/site/benchmark/main.ts +++ b/site/benchmark/main.ts @@ -15,10 +15,10 @@ const TestsConfig = [ name: TestName.ANTV_ALGORITHM, }, { - name: TestName.ANTV_WEBGPU_GRAPH, + name: TestName.ANTV_GRAPH_GPU, }, { - name: TestName.ANTV_WEBGPU_GRAPH, + name: TestName.ANTV_GRAPH_WASM, }, ]; @@ -63,7 +63,7 @@ const $results = TestsConfig.map(({ name }) => { }, }, { - name: TestName.ANTV_WEBGPU_GRAPH, + name: TestName.ANTV_GRAPH_GPU, methods: { pageRank: webgpuPageRank, sssp: webgpuSSSP, @@ -72,7 +72,7 @@ const $results = TestsConfig.map(({ name }) => { { name: TestName.ANTV_GRAPH_WASM, methods: { - // pageRank: webgpuPageRank, + // pageRank: wasmPageRank, // sssp: webgpuSSSP, }, }, @@ -82,10 +82,10 @@ const $results = TestsConfig.map(({ name }) => { const dataset = datasets[$dataset.value]; const algorithmName = $algorithm.value; let options = null; - if (algorithmName === "sssp") { - const graph = dataset[TestName.ANTV_WEBGPU_GRAPH]; - options = graph.getAllNodes()[1].id; - } + // if (algorithmName === "sssp") { + // const graph = dataset[TestName.ANTV_WEBGPU_GRAPH]; + // options = graph.getAllNodes()[1].id; + // } await Promise.all( layoutConfig.map(async ({ name, methods }: any, i: number) => { diff --git a/site/benchmark/page-rank.ts b/site/benchmark/page-rank.ts index 8e3246b..a47433c 100644 --- a/site/benchmark/page-rank.ts +++ b/site/benchmark/page-rank.ts @@ -1,5 +1,7 @@ +import { Graph } from "@antv/graphlib"; import pagerank from "graphology-metrics/centrality/pagerank"; -import { WebGPUGraph } from "../../packages/graph-gpu/src"; +import { WebGPUGraph } from "../../packages/graph-gpu"; +import { Threads } from "../../packages/graph-wasm"; interface Options { alpha: number; @@ -29,7 +31,7 @@ export async function graphology(graph: any, options: Partial) { } export async function webgpu( - graph: any, + graph: Graph, options: Partial, webgpuGraph: WebGPUGraph ) { diff --git a/site/datasets.ts b/site/datasets.ts index c65d72c..8a3573a 100644 --- a/site/datasets.ts +++ b/site/datasets.ts @@ -17,17 +17,8 @@ export const loadDatasets = async () => { clusters: 5, }); graph.edges().forEach(function(edge, i) { - // graph.setEdgeAttribute(edge, "weight", i > EDGES / 2 ? 1 : 100); graph.setEdgeAttribute(edge, "weight", 1); }); - // graph.nodes().forEach(function (node) { - // graph.setNodeAttribute(node, "x", Math.random() * CANVAS_SIZE); - // graph.setNodeAttribute(node, "y", Math.random() * CANVAS_SIZE); - - // if (dimensions === 3) { - // graph.setNodeAttribute(node, "z", Math.random() * CANVAS_SIZE); - // } - // }); const antvgraph = graphology2antv(graph); @@ -36,7 +27,8 @@ export const loadDatasets = async () => { "Creates a graph with the desired number of nodes & edges and having a given number of clusters. Generated by Graphology Generators.", [TestName.GRAPHOLOGY]: graph, [TestName.ANTV_ALGORITHM]: antvgraph, - [TestName.ANTV_WEBGPU_GRAPH]: antvgraph, + [TestName.ANTV_GRAPH_GPU]: antvgraph, + [TestName.ANTV_GRAPH_WASM]: antvgraph, }; }; @@ -94,7 +86,8 @@ export const loadDatasets = async () => { desc, [TestName.GRAPHOLOGY]: graphlibModel, [TestName.ANTV_ALGORITHM]: oldG6GraphFormat, - [TestName.ANTV_WEBGPU_GRAPH]: antvGraphModel, + [TestName.ANTV_GRAPH_GPU]: antvGraphModel, + [TestName.ANTV_GRAPH_WASM]: antvGraphModel, }; }; }; diff --git a/site/types.ts b/site/types.ts index 75f046e..761db8f 100644 --- a/site/types.ts +++ b/site/types.ts @@ -1,6 +1,6 @@ export enum TestName { GRAPHOLOGY = "graphology", ANTV_ALGORITHM = "@antv/algorithm", - ANTV_WEBGPU_GRAPH = "@antv/webgpu-graph", + ANTV_GRAPH_GPU = "@antv/graph-gpu", ANTV_GRAPH_WASM = "@antv/graph-wasm", } diff --git a/tsconfig.json b/tsconfig.json new file mode 100644 index 0000000..03e2ca5 --- /dev/null +++ b/tsconfig.json @@ -0,0 +1,11 @@ +{ + "compilerOptions": { + "noImplicitAny": true, + "module": "esnext", + "target": "es5", + "jsx": "react", + "allowJs": true, + "moduleResolution": "node", + "allowSyntheticDefaultImports": true + } +} diff --git a/tslint.json b/tslint.json new file mode 100644 index 0000000..31d6c78 --- /dev/null +++ b/tslint.json @@ -0,0 +1,21 @@ +{ + "extends": [ + "tslint-config-airbnb", + "tslint-eslint-rules", + "tslint-config-prettier" + ], + "linterOptions": { + "exclude": ["**/es/**/*.d.ts", "**/lib/**/*.d.ts"] + }, + "rules": { + "no-construct": true, + "no-debugger": true, + "no-reference": true, + "import-name": false, + "semicolon": [true, "always"], + "arrow-parens": true, + "no-this-assignment": false, + "no-increment-decrement": false, + "object-shorthand-properties-first": false + } +} From 8d7f23a08e10ab78dc56fa03eaecb2947e92d0d8 Mon Sep 17 00:00:00 2001 From: "yuqi.pyq" Date: Thu, 29 Jun 2023 15:20:42 +0800 Subject: [PATCH 2/6] feat: sssp impl --- packages/graph-rust/src/lib.rs | 1 + packages/graph-rust/src/prelude.rs | 1 + packages/graph-rust/src/sssp.rs | 303 +++++++++++++++++++++++++ packages/graph-wasm/README.md | 117 ++++++++++ packages/graph-wasm/rust-src/lib.rs | 11 + packages/graph-wasm/src/wasm-worker.js | 12 +- 6 files changed, 439 insertions(+), 6 deletions(-) create mode 100644 packages/graph-rust/src/sssp.rs diff --git a/packages/graph-rust/src/lib.rs b/packages/graph-rust/src/lib.rs index 6f978b0..63d2d12 100644 --- a/packages/graph-rust/src/lib.rs +++ b/packages/graph-rust/src/lib.rs @@ -1,5 +1,6 @@ pub mod page_rank; pub mod prelude; +pub mod sssp; pub mod utils; const DEFAULT_PARALLELISM: usize = 4; diff --git a/packages/graph-rust/src/prelude.rs b/packages/graph-rust/src/prelude.rs index e151dda..836519f 100644 --- a/packages/graph-rust/src/prelude.rs +++ b/packages/graph-rust/src/prelude.rs @@ -1,4 +1,5 @@ pub use crate::page_rank::*; +pub use crate::sssp::*; pub use crate::utils::*; pub use graph_builder::prelude::*; diff --git a/packages/graph-rust/src/sssp.rs b/packages/graph-rust/src/sssp.rs new file mode 100644 index 0000000..29add5c --- /dev/null +++ b/packages/graph-rust/src/sssp.rs @@ -0,0 +1,303 @@ +use crate::prelude::*; + +use atomic_float::AtomicF32; +use rayon::prelude::*; + +use std::sync::atomic::{AtomicUsize, Ordering}; + +const INF: f32 = f32::MAX; +const NO_BIN: usize = usize::MAX; +const BIN_SIZE_THRESHOLD: usize = 1000; + +const BATCH_SIZE: usize = 64; + +#[derive(Copy, Clone, Debug)] +#[cfg_attr(feature = "serde", derive(serde::Serialize, serde::Deserialize))] +pub struct DeltaSteppingConfig { + /// The node for which to compute distances to all reachable nodes. + pub start_node: usize, + + /// Defines the "bucket width". A bucket maintains nodes with the + /// same tentative distance to the start node. + pub delta: f32, +} + +impl DeltaSteppingConfig { + pub fn new(start_node: usize, delta: f32) -> Self { + Self { start_node, delta } + } +} + +pub fn delta_stepping(graph: &G, config: DeltaSteppingConfig) -> Vec +where + NI: Idx, + G: Graph + DirectedNeighborsWithValues + Sync, +{ + let DeltaSteppingConfig { start_node, delta } = config; + + let node_count = graph.node_count().index(); + let thread_count = rayon::current_num_threads(); + + let mut distance: Vec = Vec::with_capacity(node_count); + distance.resize_with(node_count, || AtomicF32::new(INF)); + distance[start_node.index()].store(0.0, Ordering::Release); + + let mut frontier = vec![NI::zero(); graph.edge_count().index()]; + frontier[0] = NI::new(start_node); + let frontier_idx = AtomicUsize::new(0); + let mut frontier_len = 1; + + let mut local_bins = Vec::with_capacity(thread_count); + local_bins.resize_with(thread_count, ThreadLocalBins::::new); + + let mut curr_bin = 0; + + while curr_bin != NO_BIN { + frontier_idx.store(0, Ordering::Relaxed); + + let next_bin = local_bins + .par_iter_mut() + .map(|local_bins| { + process_shared_bin( + local_bins, + curr_bin, + graph, + (&frontier, &frontier_idx, frontier_len), + &distance, + delta, + ) + }) + .map(|local_bins| process_local_bins(local_bins, curr_bin, graph, &distance, delta)) + .map(|local_bins| min_non_empty_bin(local_bins, curr_bin)) + .min_by(|x, y| x.cmp(y)) + .unwrap_or(NO_BIN); + + // copy next local bins into shared global bin + frontier_len = frontier_slices(&mut frontier, &local_bins, next_bin) + .par_iter_mut() + .zip(local_bins.par_iter_mut()) + .filter(|(_, local_bins)| local_bins.contains(next_bin)) + .map(|(slice, local_bins)| { + slice.copy_from_slice(local_bins.slice(next_bin)); + local_bins.clear(next_bin); + slice.len() + }) + .sum(); + + curr_bin = next_bin; + } + + distance +} + +fn process_shared_bin<'bins, NI, G>( + bins: &'bins mut ThreadLocalBins, + curr_bin: usize, + graph: &G, + (frontier, frontier_idx, frontier_len): (&[NI], &AtomicUsize, usize), + distance: &[AtomicF32], + delta: f32, +) -> &'bins mut ThreadLocalBins +where + NI: Idx, + G: Graph + DirectedNeighborsWithValues + Sync, +{ + loop { + let offset = frontier_idx.fetch_add(BATCH_SIZE, Ordering::AcqRel); + + if offset >= frontier_len { + break; + } + + let limit = usize::min(offset + BATCH_SIZE, frontier_len); + + for node in frontier[offset..limit].iter() { + if distance[node.index()].load(Ordering::Acquire) >= delta * curr_bin as f32 { + relax_edges(graph, distance, bins, *node, delta); + } + } + } + bins +} + +fn process_local_bins<'bins, NI, G>( + bins: &'bins mut ThreadLocalBins, + curr_bin: usize, + graph: &G, + distance: &[AtomicF32], + delta: f32, +) -> &'bins mut ThreadLocalBins +where + NI: Idx, + G: Graph + DirectedNeighborsWithValues + Sync, +{ + while curr_bin < bins.len() + && !bins.is_empty(curr_bin) + && bins.bin_len(curr_bin) < BIN_SIZE_THRESHOLD + { + let current_bin_copy = bins.clone(curr_bin); + bins.clear(curr_bin); + + for node in current_bin_copy { + relax_edges(graph, distance, bins, node, delta); + } + } + bins +} + +fn min_non_empty_bin(local_bins: &mut ThreadLocalBins, curr_bin: usize) -> usize { + let mut next_local_bin = NO_BIN; + for bin in curr_bin..local_bins.len() { + if !local_bins.is_empty(bin) { + next_local_bin = bin; + break; + } + } + next_local_bin +} + +fn relax_edges( + graph: &G, + distances: &[AtomicF32], + local_bins: &mut ThreadLocalBins, + node: NI, + delta: f32, +) where + NI: Idx, + G: Graph + DirectedNeighborsWithValues + Sync, +{ + for Target { target, value } in graph.out_neighbors_with_values(node) { + let mut old_distance = distances[target.index()].load(Ordering::Acquire); + let new_distance = distances[node.index()].load(Ordering::Acquire) + value; + + while new_distance < old_distance { + match distances[target.index()].compare_exchange_weak( + old_distance, + new_distance, + Ordering::Release, + Ordering::Relaxed, + ) { + Ok(_) => { + let dest_bin = (new_distance / delta) as usize; + if dest_bin >= local_bins.len() { + local_bins.resize(dest_bin + 1); + } + local_bins.push(dest_bin, *target); + break; + } + // CAX failed -> retry with new min distance + Err(min_distance) => old_distance = min_distance, + } + } + } +} + +fn frontier_slices<'a, NI: Idx>( + frontier: &'a mut [NI], + bins: &[ThreadLocalBins], + next_bin: usize, +) -> Vec<&'a mut [NI]> { + let mut slices = Vec::with_capacity(bins.len()); + let mut tail = frontier; + + for local_bins in bins.iter() { + if local_bins.contains(next_bin) { + let (head, remainder) = tail.split_at_mut(local_bins.bin_len(next_bin)); + slices.push(head); + tail = remainder; + } else { + slices.push(&mut []); + } + } + + slices +} + +#[derive(Debug)] +struct ThreadLocalBins { + bins: Vec>, +} + +impl ThreadLocalBins +where + T: Clone, +{ + fn new() -> Self { + Self { bins: vec![vec![]] } + } + + fn contains(&self, bin: usize) -> bool { + self.len() > bin + } + + fn len(&self) -> usize { + self.bins.len() + } + + fn bin_len(&self, bin: usize) -> usize { + self.bins[bin].len() + } + + fn is_empty(&self, bin: usize) -> bool { + self.bins[bin].is_empty() + } + + fn clone(&self, bin: usize) -> Vec { + self.bins[bin].clone() + } + + fn clear(&mut self, bin: usize) { + self.bins[bin].clear(); + } + + fn slice(&self, bin: usize) -> &[T] { + &self.bins[bin] + } + + fn resize(&mut self, new_len: usize) { + self.bins.resize_with(new_len, Vec::new) + } + + fn push(&mut self, bin: usize, val: T) { + self.bins[bin].push(val); + } +} + +#[cfg(test)] +mod tests { + use super::*; + use crate::prelude::{CsrLayout, GraphBuilder}; + + #[test] + fn test_sssp() { + let gdl = "(a:A) + (b:B) + (c:C) + (d:D) + (e:E) + (f:F) + (a)-[{cost: 4.0 }]->(b) + (a)-[{cost: 2.0 }]->(c) + (b)-[{cost: 5.0 }]->(c) + (b)-[{cost: 10.0 }]->(d) + (c)-[{cost: 3.0 }]->(e) + (d)-[{cost: 11.0 }]->(f) + (e)-[{cost: 4.0 }]->(d)"; + + let graph: DirectedCsrGraph = GraphBuilder::new() + .csr_layout(CsrLayout::Deduplicated) + .gdl_str::(gdl) + .build() + .unwrap(); + + let config = DeltaSteppingConfig::new(0, 3.0); + + let actual: Vec = delta_stepping(&graph, config) + .into_iter() + .map(|d| d.load(Ordering::Relaxed)) + .collect(); + let expected: Vec = vec![0.0, 4.0, 2.0, 9.0, 5.0, 20.0]; + + assert_eq!(actual, expected); + } +} diff --git a/packages/graph-wasm/README.md b/packages/graph-wasm/README.md index e69de29..43694a9 100644 --- a/packages/graph-wasm/README.md +++ b/packages/graph-wasm/README.md @@ -0,0 +1,117 @@ +# @antv/graph-wasm + +A WASM binding of `@antv/graph-rust`. We used [wasm-bindgen-rayon](https://github.com/GoogleChromeLabs/wasm-bindgen-rayon) to implement data parallelism with WebWorkers. + +- [Use with Webpack](#webpack) +- [Use with Vite](#vite) + +## Usage + +Since [cross origin workers are blocked](https://stackoverflow.com/questions/58098143/why-are-cross-origin-workers-blocked-and-why-is-the-workaround-ok/60015898#60015898), we do not recommand the UMD way of using it for now. You can opt to ESM usage with bundler such as [Webpack](#webpack) or [Vite](#vite). + +### ESM + +```js +import { initThreads, supportsThreads } from "@antv/graph-wasm"; +``` + +Since [Not all browsers](https://webassembly.org/roadmap/) support WebAssembly threads yet, we need to use feature detection to choose the right one on the JavaScript side. + +```js +const supported = await supportsThreads(); // `true` means we can use multithreads now! +const threads = await initThreads(supported); +``` + +```js +import { Graph } from "@antv/graphlib"; + +const results = await threads.pageRank( + graph, + { + tolerance: 1e-5, + alpha: 0.85, + maxIterations: 1000 + } +); +``` + +### Use WASM with multithreads + +First of all, in order to use SharedArrayBuffer on the Web, you need to enable [cross-origin isolation policies](https://web.dev/coop-coep/). Check out the linked article for details. + +To opt in to a cross-origin isolated state, you need to send the following HTTP headers on the main document: + +``` +Cross-Origin-Embedder-Policy: require-corp +Cross-Origin-Opener-Policy: same-origin +``` + +If you can't control the server, try this hacky workaround which implemented with ServiceWorker: https://github.com/orgs/community/discussions/13309#discussioncomment-3844940. Here's an example on [Stackblitz](https://stackblitz.com/edit/github-wpncwj-fxmffg?file=src/index.js). + +### Webpack + +Webpack has good support for Webworker, here's an example on [Stackblitz](https://stackblitz.com/edit/github-wpncwj?file=src/index.js). We use [statikk](https://www.npmjs.com/package/statikk) as static server in this example since it has a good support of cross-origin isolation headers. For more information, please refer to [Use WASM with multithreads](#use-wasm-with-multithreads). + +### Vite + +Vite also provides [worker options](https://vitejs.dev/config/worker-options.html) in its config. To let Vite [process URL correctly](https://vitejs.dev/guide/dep-pre-bundling.html#customizing-the-behavior) when creating WebWorker in third-party packages, we need to add the package to `optimizeDeps.exclude`: + +```js +// vite.config.js +optimizeDeps: { + exclude: ['@antv/graph-wasm'], +}, +``` + +To enable COOP & COEP headers, we can set them with `plugins`: + +```js +// vite.config.js +plugins: [ + { + name: 'isolation', + configureServer(server) { + // @see https://gist.github.com/mizchi/afcc5cf233c9e6943720fde4b4579a2b + server.middlewares.use((_req, res, next) => { + res.setHeader('Cross-Origin-Opener-Policy', 'same-origin'); + res.setHeader('Cross-Origin-Embedder-Policy', 'require-corp'); + next(); + }); + }, + }, +], +``` + +Here's a complete example on [Stackblitz](https://stackblitz.com/edit/vite-6b9ga6?file=README.md). + +If you can't control the server, try this hacky workaround which implemented with ServiceWorker: https://github.com/orgs/community/discussions/13309#discussioncomment-3844940 + +## API Reference + +### PageRank + +* `tolerance` Set the tolerance the approximation, this parameter should be a small magnitude value. The lower the tolerance the better the approximation. +* `alpha` The damping factor alpha represents the probability to follow an outgoing edge, standard value is 0.85. +* `maxIterations` Set the maximum number of iterations. + +### SSSP + +## Build + +Install [wasm-pack](https://rustwasm.github.io/wasm-pack/installer/) first. + +Then run the command `npm run build`, the compiled package will be outputted under the `/dist` directory. + +```bash +$ npm run build +``` + +## Publish + +```bash +$ npm publish +``` + +## License + +The scripts and documentation in this project are released under the [MIT License](LICENSE). diff --git a/packages/graph-wasm/rust-src/lib.rs b/packages/graph-wasm/rust-src/lib.rs index e2aedf4..722725d 100644 --- a/packages/graph-wasm/rust-src/lib.rs +++ b/packages/graph-wasm/rust-src/lib.rs @@ -1,3 +1,4 @@ +use std::sync::atomic::Ordering; use antv_graph::prelude::*; use js_sys::Array; use wasm_bindgen::prelude::*; @@ -14,6 +15,16 @@ pub fn start() { console_error_panic_hook::set_once(); } +#[wasm_bindgen(js_name = "sssp")] +pub fn sssp(val: JsValue) -> Array { + let graph: DirectedCsrGraph = GraphBuilder::new().edges_with_values(vec![]).build(); + let config = DeltaSteppingConfig::new(0, 3.0); + let result: Vec = antv_graph::prelude::delta_stepping(&graph, config).into_iter() + .map(|d| d.load(Ordering::Relaxed)) + .collect(); + result.into_iter().map(JsValue::from).collect() +} + #[wasm_bindgen(js_name = "pageRank")] pub fn page_rank(val: JsValue) -> Array { let options: PageRankConfig = serde_wasm_bindgen::from_value(val).unwrap(); diff --git a/packages/graph-wasm/src/wasm-worker.js b/packages/graph-wasm/src/wasm-worker.js index ff2fbb2..3103352 100644 --- a/packages/graph-wasm/src/wasm-worker.js +++ b/packages/graph-wasm/src/wasm-worker.js @@ -1,4 +1,4 @@ -import * as Comlink from "comlink"; +import * as Comlink from 'comlink'; const DEFAULT_PAGE_RANK_OPTIONS = { max_iterations: 10, @@ -6,8 +6,8 @@ const DEFAULT_PAGE_RANK_OPTIONS = { damping_factor: 0.85, }; -const wrapTransfer = (page_rank) => { - return (options) => { +const wrapTransfer = page_rank => { + return options => { const ranks = page_rank({ ...DEFAULT_PAGE_RANK_OPTIONS, ...options, @@ -23,20 +23,20 @@ const wrapTransfer = (page_rank) => { // Wrap wasm-bindgen exports (the `generate` function) to add time measurement. function wrapExports({ page_rank }) { return { - page_rank: wrapTransfer(page_rank), + pageRank: wrapTransfer(page_rank), }; } async function initHandlers(useMultiThread) { if (useMultiThread) { // @ts-ignore - const multiThread = await import("../pkg-parallel/antv_graph_wasm.js"); + const multiThread = await import('../pkg-parallel/antv_graph_wasm.js'); await multiThread.default(); await multiThread.initThreadPool(navigator.hardwareConcurrency); return Comlink.proxy(wrapExports(multiThread)); } else { // @ts-ignore - const singleThread = await import("../pkg/antv_graph_wasm.js"); + const singleThread = await import('../pkg/antv_graph_wasm.js'); await singleThread.default(); return Comlink.proxy(wrapExports(singleThread)); } From 3a3d98d7ac774dbe1b9804b9f171f218f80a1fd8 Mon Sep 17 00:00:00 2001 From: "yuqi.pyq" Date: Tue, 11 Jul 2023 11:49:19 +0800 Subject: [PATCH 3/6] fix: use rayon to spawn threads instead of std:threads --- README.md | 4 +- __tests__/unit/pageRank.spec.ts | 172 + jest.config.js | 4 +- package.json | 10 +- packages/graph-gpu/package.json | 10 +- packages/graph-gpu/src/WebGPUGraph.ts | 6 +- .../graph-gpu/src/link-analysis/pageRank.ts | 18 +- packages/graph-gpu/tsconfig.json | 1 + packages/graph-rust/Cargo.toml | 37 +- packages/graph-rust/README.md | 3 + .../graph-rust/src/graph_builder/builder.rs | 540 + .../graph-rust/src/graph_builder/compat.rs | 109 + .../graph-rust/src/graph_builder/graph/csr.rs | 873 + .../graph-rust/src/graph_builder/graph/mod.rs | 1 + .../graph-rust/src/graph_builder/graph_ops.rs | 627 + .../graph-rust/src/graph_builder/index.rs | 103 + .../src/graph_builder/input/edgelist.rs | 258 + .../graph-rust/src/graph_builder/input/mod.rs | 93 + packages/graph-rust/src/graph_builder/mod.rs | 171 + .../graph-rust/src/graph_builder/prelude.rs | 32 + packages/graph-rust/src/lib.rs | 1 + packages/graph-rust/src/page_rank.rs | 43 +- packages/graph-rust/src/prelude.rs | 2 +- packages/graph-rust/src/sssp.rs | 39 - packages/graph-wasm/Cargo.lock | 133 +- packages/graph-wasm/README.md | 6 +- packages/graph-wasm/package.json | 9 - packages/graph-wasm/rust-src/lib.rs | 60 +- packages/graph-wasm/src/interface.ts | 22 +- packages/graph-wasm/src/wasm-worker.js | 40 +- packages/graph-wasm/tsconfig.json | 1 + packages/graph/package.json | 7 +- packages/graph/src/pageRank.ts | 36 +- .../tests/unit/adjacent-matrix-async-spec.ts | 116 - .../graph/tests/unit/adjacent-matrix-spec.ts | 114 - packages/graph/tests/unit/bfs-spec.ts | 175 - .../unit/connected-component-async-spec.ts | 112 - .../tests/unit/connected-component-spec.ts | 106 - .../graph/tests/unit/cosineSimilarity-spec.ts | 41 - .../tests/unit/data/cluster-origin-data.json | 1 - .../data/cluster-origin-properties-data.json | 370 - packages/graph/tests/unit/data/test-data.ts | 38635 ---------------- .../graph/tests/unit/degree-async-spec.ts | 119 - packages/graph/tests/unit/degree-spec.ts | 139 - .../tests/unit/detect-cycle-async-spec.ts | 74 - .../graph/tests/unit/detect-cycle-spec.ts | 508 - packages/graph/tests/unit/dfs-spec.ts | 170 - .../graph/tests/unit/find-path-async-spec.ts | 132 - packages/graph/tests/unit/find-path-spec.ts | 122 - .../tests/unit/floydWarshall-async-spec.ts | 110 - .../graph/tests/unit/floydWarshall-spec.ts | 108 - packages/graph/tests/unit/gSpan-spec.ts | 483 - packages/graph/tests/unit/gaddi-async-spec.ts | 388 - packages/graph/tests/unit/gaddi-spec.ts | 1110 - packages/graph/tests/unit/kMeans-spec.ts | 236 - .../unit/label-propagation-async-spec.ts | 89 - .../tests/unit/label-propagation-spec.ts | 54 - packages/graph/tests/unit/linked-list-spec.ts | 88 - .../graph/tests/unit/louvain-async-spec.ts | 67 - packages/graph/tests/unit/louvain-spec.ts | 67 - packages/graph/tests/unit/mst-spec.ts | 84 - .../tests/unit/nodesCosineSimilarity-spec.ts | 104 - .../graph/tests/unit/pagerank-async-spec.ts | 138 - packages/graph/tests/unit/pagerank-spec.ts | 137 - packages/graph/tests/unit/queue-spec.ts | 65 - packages/graph/tests/unit/stack-spec.ts | 85 - packages/graph/tests/unit/util-spec.ts | 116 - packages/graph/tests/unit/utils.ts | 20 - packages/graph/webpack.config.js | 64 +- site/benchmark/index.html | 4 +- site/benchmark/main.ts | 30 +- site/benchmark/page-rank.ts | 64 +- site/datasets.ts | 2 +- site/index.html | 2 +- site/types.ts | 2 +- vite.config.js | 14 + 76 files changed, 3316 insertions(+), 44820 deletions(-) create mode 100644 __tests__/unit/pageRank.spec.ts create mode 100644 packages/graph-rust/src/graph_builder/builder.rs create mode 100644 packages/graph-rust/src/graph_builder/compat.rs create mode 100644 packages/graph-rust/src/graph_builder/graph/csr.rs create mode 100644 packages/graph-rust/src/graph_builder/graph/mod.rs create mode 100644 packages/graph-rust/src/graph_builder/graph_ops.rs create mode 100644 packages/graph-rust/src/graph_builder/index.rs create mode 100644 packages/graph-rust/src/graph_builder/input/edgelist.rs create mode 100644 packages/graph-rust/src/graph_builder/input/mod.rs create mode 100644 packages/graph-rust/src/graph_builder/mod.rs create mode 100644 packages/graph-rust/src/graph_builder/prelude.rs delete mode 100644 packages/graph/tests/unit/adjacent-matrix-async-spec.ts delete mode 100644 packages/graph/tests/unit/adjacent-matrix-spec.ts delete mode 100644 packages/graph/tests/unit/bfs-spec.ts delete mode 100644 packages/graph/tests/unit/connected-component-async-spec.ts delete mode 100644 packages/graph/tests/unit/connected-component-spec.ts delete mode 100644 packages/graph/tests/unit/cosineSimilarity-spec.ts delete mode 100644 packages/graph/tests/unit/data/cluster-origin-data.json delete mode 100644 packages/graph/tests/unit/data/cluster-origin-properties-data.json delete mode 100644 packages/graph/tests/unit/data/test-data.ts delete mode 100644 packages/graph/tests/unit/degree-async-spec.ts delete mode 100644 packages/graph/tests/unit/degree-spec.ts delete mode 100644 packages/graph/tests/unit/detect-cycle-async-spec.ts delete mode 100644 packages/graph/tests/unit/detect-cycle-spec.ts delete mode 100644 packages/graph/tests/unit/dfs-spec.ts delete mode 100644 packages/graph/tests/unit/find-path-async-spec.ts delete mode 100644 packages/graph/tests/unit/find-path-spec.ts delete mode 100644 packages/graph/tests/unit/floydWarshall-async-spec.ts delete mode 100644 packages/graph/tests/unit/floydWarshall-spec.ts delete mode 100644 packages/graph/tests/unit/gSpan-spec.ts delete mode 100644 packages/graph/tests/unit/gaddi-async-spec.ts delete mode 100644 packages/graph/tests/unit/gaddi-spec.ts delete mode 100644 packages/graph/tests/unit/kMeans-spec.ts delete mode 100644 packages/graph/tests/unit/label-propagation-async-spec.ts delete mode 100644 packages/graph/tests/unit/label-propagation-spec.ts delete mode 100644 packages/graph/tests/unit/linked-list-spec.ts delete mode 100644 packages/graph/tests/unit/louvain-async-spec.ts delete mode 100644 packages/graph/tests/unit/louvain-spec.ts delete mode 100644 packages/graph/tests/unit/mst-spec.ts delete mode 100644 packages/graph/tests/unit/nodesCosineSimilarity-spec.ts delete mode 100644 packages/graph/tests/unit/pagerank-async-spec.ts delete mode 100644 packages/graph/tests/unit/pagerank-spec.ts delete mode 100644 packages/graph/tests/unit/queue-spec.ts delete mode 100644 packages/graph/tests/unit/stack-spec.ts delete mode 100644 packages/graph/tests/unit/util-spec.ts delete mode 100644 packages/graph/tests/unit/utils.ts diff --git a/README.md b/README.md index 6332e29..428e1dc 100644 --- a/README.md +++ b/README.md @@ -4,8 +4,8 @@ [![Build Status](https://github.com/antvis/algorithm/workflows/build/badge.svg?branch=next)](https://github.com/antvis//actions) [![Coverage Status](https://img.shields.io/coveralls/github/antvis/algorithm/next.svg)](https://coveralls.io/github/antvis/algorithm?branch=next) -[![npm Download](https://img.shields.io/npm/dm/@antv/algorithm.svg)](https://www.npmjs.com/package/@antv/algorithm) -[![npm License](https://img.shields.io/npm/l/@antv/algorithm.svg)](https://www.npmjs.com/package/@antv/algorithm) +[![npm Download](https://img.shields.io/npm/dm/@antv/graph.svg)](https://www.npmjs.com/package/@antv/graph) +[![npm License](https://img.shields.io/npm/l/@antv/graph.svg)](https://www.npmjs.com/package/@antv/graph) - [@antv/graph](./packages/graph/README.md) [![npm Version](https://img.shields.io/npm/v/@antv/graph/alpha)](https://www.npmjs.com/package/@antv/graph) Implemented with TypeScript. [Online Demo](https://observablehq.com/d/2db6b0cc5e97d8d6) - [@antv/graph-rust](./packages/graph-rust/README.md) Implemented with Rust. diff --git a/__tests__/unit/pageRank.spec.ts b/__tests__/unit/pageRank.spec.ts new file mode 100644 index 0000000..ac0bfd6 --- /dev/null +++ b/__tests__/unit/pageRank.spec.ts @@ -0,0 +1,172 @@ +import { Graph } from "@antv/graphlib"; +import { pageRank } from "../../packages/graph/src"; + +describe('Calculate pagerank of graph nodes', () => { + test('calculate pagerank', () => { + const graph = new Graph({ + nodes: [ + { + id: 'A', + data: {} + }, + { + id: 'B', + data: {} + }, + { + id: 'C', + data: {} + }, + { + id: 'D', + data: {} + }, + { + id: 'E', + data: {} + }, + { + id: 'F', + data: {} + }, + { + id: 'G', + data: {} + }, + { + id: 'H', + data: {} + }, + { + id: 'I', + data: {} + }, + { + id: 'J', + data: {} + }, + { + id: 'K', + data: {} + } + ], + edges: [ + { + id: 'e0', + source: 'D', + target: 'A', + data: {} + }, + { + id: 'e1', + source: 'D', + target: 'B', + data: {} + }, + { + id: 'e2', + source: 'B', + target: 'C', + data: {} + }, + { + id: 'e3', + source: 'C', + target: 'B', + data: {} + }, + { + id: 'e4', + source: 'F', + target: 'B', + data: {} + }, + { + id: 'e5', + source: 'F', + target: 'E', + data: {} + }, + { + id: 'e6', + source: 'E', + target: 'F', + data: {} + }, + { + id: 'e7', + source: 'E', + target: 'D', + data: {} + }, + { + id: 'e8', + source: 'E', + target: 'B', + data: {} + }, + { + id: 'e9', + source: 'K', + target: 'E', + data: {} + }, + { + id: 'e10', + source: 'J', + target: 'E', + data: {} + }, + { + id: 'e11', + source: 'I', + target: 'E', + data: {} + }, + { + id: 'e12', + source: 'H', + target: 'E', + data: {} + }, + { + id: 'e13', + source: 'G', + target: 'E', + data: {} + }, + { + id: 'e14', + source: 'G', + target: 'B', + data: {} + }, + { + id: 'e15', + source: 'H', + target: 'B', + data: {} + }, + { + id: 'e16', + source: 'I', + target: 'B', + data: {} + }, + ], + }); + + const result = pageRank(graph); + + let maxNodeId; + let maxVal = 0; + for (let nodeId in result) { + const val = result[nodeId]; + if (val >= maxVal) { + maxNodeId = nodeId; + maxVal = val + } + } + expect(maxNodeId).toBe('B') + }) +}); \ No newline at end of file diff --git a/jest.config.js b/jest.config.js index 3f84e26..646d8b3 100644 --- a/jest.config.js +++ b/jest.config.js @@ -11,11 +11,11 @@ /** @type {import('ts-jest').JestConfigWithTsJest} */ module.exports = { testEnvironment: "jsdom", - testRegex: "__tests__/.*test\\.ts?$", + testRegex: "__tests__/.*spec\\.ts?$", moduleDirectories: ["node_modules", "src", "es"], moduleFileExtensions: ["js", "ts", "json"], moduleNameMapper: { - "@antv/algorithm/(.*)": "/src/$1", + "@antv/graph/(.*)": "/src/$1", }, transform: { // '^.+\\.[tj]sx?$' to process js/ts with `ts-jest` diff --git a/package.json b/package.json index 2ce7e1a..439a852 100644 --- a/package.json +++ b/package.json @@ -1,5 +1,4 @@ { - "name": "@antv/algorithm", "private": true, "homepage": "https://github.com/antvis/algorithm", "bugs": { @@ -13,13 +12,13 @@ "scripts": { "dev": "vite", "lint:es": "eslint --ext .js --fix", - "lint:ts": "tslint -c tslint.json -p packages/layout/tsconfig.json --fix", + "lint:ts": "tslint -c tslint.json -p packages/graph/tsconfig.json --fix", "lint": "npm run lint:ts && npm run lint:es", "lint-staged": "lint-staged", "build": "pnpm -r run build", "build:ci": "pnpm -r run build:ci", "prepare": "husky install", - "test": "pnpm -r run test --no-private", + "test": "jest", "coverage": "jest --coverage", "build:site": "vite build", "deploy": "gh-pages -d site/dist", @@ -36,6 +35,7 @@ "devDependencies": { "@antv/graphlib": "^2.0.0", "@changesets/cli": "^2.26.1", + "@types/jest": "latest", "cross-env": "^7.0.3", "eslint": "^7.32.0", "eslint-config-airbnb-base": "^14.2.1", @@ -60,7 +60,9 @@ "tslint-config-prettier": "^1.18.0", "tslint-eslint-rules": "^5.4.0", "typescript": "^4.9.5", - "vite": "^4.3.8" + "vite": "^4.3.8", + "webpack": "^5.38.1", + "webpack-cli": "^5.0.2" }, "publishConfig": { "access": "public", diff --git a/packages/graph-gpu/package.json b/packages/graph-gpu/package.json index f383505..177e9a3 100644 --- a/packages/graph-gpu/package.json +++ b/packages/graph-gpu/package.json @@ -51,15 +51,7 @@ "@babel/plugin-proposal-class-properties": "^7.12.1", "@babel/preset-env": "^7.12.7", "@babel/preset-typescript": "^7.12.7", - "@types/jest": "^26.0.18", - "@umijs/fabric": "^2.5.6", - "babel-loader": "^8.2.2", - "rimraf": "^3.0.2", - "ts-loader": "^8.0.14", - "tslint": "^6.1.3", - "typescript": "^4.1.3", - "webpack": "^5.38.1", - "webpack-cli": "^5.0.2" + "babel-loader": "^8.2.2" }, "dependencies": { "@antv/g": "^5.16.26", diff --git a/packages/graph-gpu/src/WebGPUGraph.ts b/packages/graph-gpu/src/WebGPUGraph.ts index a75208f..d1b1c2d 100644 --- a/packages/graph-gpu/src/WebGPUGraph.ts +++ b/packages/graph-gpu/src/WebGPUGraph.ts @@ -1,7 +1,7 @@ import { Canvas } from '@antv/g'; import { Renderer } from '@antv/g-webgpu'; import { Plugin } from '@antv/g-plugin-gpgpu'; -import { pageRank } from './link-analysis'; +import { PageRankParams, pageRank } from './link-analysis'; import { sssp } from './traversal'; import { Graph } from './types'; @@ -41,9 +41,9 @@ export class WebGPUGraph { return plugin.getDevice(); } - async pageRank(graphData: Graph, eps = 1e-5, alpha = 0.85, maxIteration = 1000) { + async pageRank(graphData: Graph, params?: PageRankParams) { const device = await this.getDevice(); - return pageRank(device, graphData, eps, alpha, maxIteration); + return pageRank(device, graphData, params); } async sssp(graphData: Graph, sourceId: string, weightPropertyName: string = 'weight') { diff --git a/packages/graph-gpu/src/link-analysis/pageRank.ts b/packages/graph-gpu/src/link-analysis/pageRank.ts index 5cad8b2..d948145 100644 --- a/packages/graph-gpu/src/link-analysis/pageRank.ts +++ b/packages/graph-gpu/src/link-analysis/pageRank.ts @@ -5,6 +5,12 @@ import { Graph } from "../types"; const { BufferUsage } = DeviceRenderer; +export interface PageRankParams { + alpha: number; + maxIterations: number; + tolerance: number; +} + /** * Pagerank using power method, ported from CUDA * @@ -18,10 +24,14 @@ const { BufferUsage } = DeviceRenderer; export async function pageRank( device: DeviceRenderer.Device, graphData: Graph, - tolerance = 1e-5, - alpha = 0.85, - maxIteration = 1000 + params?: PageRankParams ) { + let { + tolerance = 1e-5, + alpha = 0.85, + maxIterations = 1000 + } = params || {}; + const BLOCK_SIZE = 1; const BLOCKS = 256; @@ -145,7 +155,7 @@ fn main( const grids = Math.ceil(V.length / (BLOCKS * BLOCK_SIZE)); - while (maxIteration--) { + while (maxIterations--) { storeKernel.dispatch(grids, 1); matmulKernel.dispatch(grids, 1); rankDiffKernel.dispatch(grids, 1); diff --git a/packages/graph-gpu/tsconfig.json b/packages/graph-gpu/tsconfig.json index ba439d3..2ccebef 100644 --- a/packages/graph-gpu/tsconfig.json +++ b/packages/graph-gpu/tsconfig.json @@ -1,4 +1,5 @@ { + "extends": "../../tsconfig.json", "compilerOptions": { "rootDir": "./src", "composite": true, diff --git a/packages/graph-rust/Cargo.toml b/packages/graph-rust/Cargo.toml index 39ebbd5..7f4302c 100644 --- a/packages/graph-rust/Cargo.toml +++ b/packages/graph-rust/Cargo.toml @@ -17,12 +17,43 @@ lto = true opt-level = 's' [dependencies] +atoi = "2.0.0" +atomic = "0.5.1" atomic_float = "0.1.0" -graph_builder = "0.3.1" +byte-slice-cast = "1.2.2" +dashmap = "5.4.0" +delegate = "0.8.0" +fast-float = "0.2.0" +fxhash = "0.2.1" +gdl = { version = "0.2.7", optional = true} rayon = "1.5.1" serde = { optional = true } -[dev-dependencies] -graph_builder = { version = "^0.3.1", features = ["gdl"] } +[dependencies.linereader] +version = "0.4.0" + +[dependencies.log] +version = "0.4.17" + +[dependencies.memmap2] +version = "0.5.8" + +[dependencies.num] +version = "0.4.0" + +[dependencies.num-format] +version = "0.4.3" + +[dependencies.num_cpus] +version = "1.14.0" + +[dependencies.page_size] +version = "0.4.2" + +[dependencies.parking_lot] +version = "0.12.1" + +[dependencies.thiserror] +version = "1.0.37" diff --git a/packages/graph-rust/README.md b/packages/graph-rust/README.md index e69de29..e2794fb 100644 --- a/packages/graph-rust/README.md +++ b/packages/graph-rust/README.md @@ -0,0 +1,3 @@ +# @antv/graph-rust + +This crate builds on top of the [graph_builder](https://docs.rs/graph_builder/latest/graph_builder/) crate, which can be used as a building block for custom graph algorithms. \ No newline at end of file diff --git a/packages/graph-rust/src/graph_builder/builder.rs b/packages/graph-rust/src/graph_builder/builder.rs new file mode 100644 index 0000000..727273f --- /dev/null +++ b/packages/graph-rust/src/graph_builder/builder.rs @@ -0,0 +1,540 @@ +use std::{convert::TryFrom, marker::PhantomData}; + +use super::{ + graph::csr::{CsrLayout, NodeValues}, + index::Idx, + input::{edgelist::EdgeList, InputCapabilities, InputPath}, + prelude::edgelist::{EdgeIterator, EdgeWithValueIterator}, + Error, +}; +use std::path::Path as StdPath; + +pub struct Uninitialized { + csr_layout: CsrLayout, +} + +pub struct FromEdges +where + NI: Idx, + Edges: IntoIterator, +{ + csr_layout: CsrLayout, + edges: Edges, + _node: PhantomData, +} + +pub struct FromEdgeListAndNodeValues +where + NI: Idx, +{ + csr_layout: CsrLayout, + node_values: NodeValues, + edge_list: EdgeList, +} + +pub struct FromEdgesWithValues +where + NI: Idx, + Edges: IntoIterator, +{ + csr_layout: CsrLayout, + edges: Edges, + _node: PhantomData, +} + +#[cfg(feature = "gdl")] +#[cfg_attr(all(feature = "gdl", has_doc_cfg), doc(cfg(feature = "gdl")))] +pub struct FromGdlString +where + NI: Idx, +{ + csr_layout: CsrLayout, + gdl: String, + _node: PhantomData, +} + +#[cfg(feature = "gdl")] +#[cfg_attr(all(feature = "gdl", has_doc_cfg), doc(cfg(feature = "gdl")))] +pub struct FromGdlGraph<'a, NI> +where + NI: Idx, +{ + csr_layout: CsrLayout, + gdl_graph: &'a gdl::Graph, + _node: PhantomData, +} + +pub struct FromInput +where + P: AsRef, + NI: Idx, + Format: InputCapabilities, + Format::GraphInput: TryFrom>, +{ + csr_layout: CsrLayout, + _idx: PhantomData, + _path: PhantomData

, + _format: PhantomData, +} + +pub struct FromPath +where + P: AsRef, + NI: Idx, + Format: InputCapabilities, + Format::GraphInput: TryFrom>, +{ + csr_layout: CsrLayout, + path: P, + _idx: PhantomData, + _format: PhantomData, +} + +/// A builder to create graphs in a type-safe way. +/// +/// The builder implementation uses different states to allow staged building of +/// graphs. Each individual state enables stage-specific methods on the builder. +/// +/// # Examples +/// +/// Create a directed graph from a vec of edges: +/// +/// ``` +/// use graph_builder::prelude::*; +/// +/// let graph: DirectedCsrGraph = GraphBuilder::new() +/// .edges(vec![(0, 1), (0, 2), (1, 2), (1, 3), (2, 3)]) +/// .build(); +/// +/// assert_eq!(graph.node_count(), 4); +/// ``` +/// +/// Create an undirected graph from a vec of edges: +/// +/// ``` +/// use graph_builder::prelude::*; +/// +/// let graph: UndirectedCsrGraph = GraphBuilder::new() +/// .edges(vec![(0, 1), (0, 2), (1, 2), (1, 3), (2, 3)]) +/// .build(); +/// +/// assert_eq!(graph.node_count(), 4); +/// ``` +pub struct GraphBuilder { + state: State, +} + +impl Default for GraphBuilder { + fn default() -> Self { + GraphBuilder::new() + } +} + +impl GraphBuilder { + /// Creates a new builder + pub fn new() -> Self { + Self { + state: Uninitialized { + csr_layout: CsrLayout::default(), + }, + } + } + + /// Sets the [`CsrLayout`] to use during CSR construction. + /// + /// # Examples + /// + /// Store the neighbors sorted: + /// + /// ``` + /// use graph_builder::prelude::*; + /// + /// let graph: UndirectedCsrGraph = GraphBuilder::new() + /// .csr_layout(CsrLayout::Sorted) + /// .edges(vec![(0, 7), (0, 3), (0, 3), (0, 1)]) + /// .build(); + /// + /// assert_eq!(graph.neighbors(0).copied().collect::>(), &[1, 3, 3, 7]); + /// ``` + /// + /// Store the neighbors sorted and deduplicated: + /// + /// ``` + /// use graph_builder::prelude::*; + /// + /// let graph: UndirectedCsrGraph = GraphBuilder::new() + /// .csr_layout(CsrLayout::Deduplicated) + /// .edges(vec![(0, 7), (0, 3), (0, 3), (0, 1)]) + /// .build(); + /// + /// assert_eq!(graph.neighbors(0).copied().collect::>(), &[1, 3, 7]); + /// ``` + #[must_use] + pub fn csr_layout(mut self, csr_layout: CsrLayout) -> Self { + self.state.csr_layout = csr_layout; + self + } + + /// Create a graph from the given edge tuples. + /// + /// # Example + /// + /// ``` + /// use graph_builder::prelude::*; + /// + /// let graph: DirectedCsrGraph = GraphBuilder::new() + /// .edges(vec![(0, 1), (0, 2), (1, 2), (1, 3), (2, 3)]) + /// .build(); + /// + /// assert_eq!(graph.node_count(), 4); + /// assert_eq!(graph.edge_count(), 5); + /// ``` + pub fn edges(self, edges: Edges) -> GraphBuilder> + where + NI: Idx, + Edges: IntoIterator, + { + GraphBuilder { + state: FromEdges { + csr_layout: self.state.csr_layout, + edges, + _node: PhantomData, + }, + } + } + + /// Create a graph from the given edge triplets. + /// + /// # Example + /// + /// ``` + /// use graph_builder::prelude::*; + /// + /// let graph: DirectedCsrGraph = GraphBuilder::new() + /// .edges_with_values(vec![(0, 1, 0.1), (0, 2, 0.2), (1, 2, 0.3), (1, 3, 0.4), (2, 3, 0.5)]) + /// .build(); + /// + /// assert_eq!(graph.node_count(), 4); + /// assert_eq!(graph.edge_count(), 5); + /// ``` + pub fn edges_with_values( + self, + edges: Edges, + ) -> GraphBuilder> + where + NI: Idx, + Edges: IntoIterator, + { + GraphBuilder { + state: FromEdgesWithValues { + csr_layout: self.state.csr_layout, + edges, + _node: PhantomData, + }, + } + } + + /// Creates a graph using Graph Definition Language (GDL). + /// + /// Creating graphs from GDL is recommended for small graphs only, e.g., + /// during testing. The graph construction is **not** parallelized. + /// + /// See [GDL on crates.io](https://crates.io/crates/gdl) for more + /// information on how to define graphs using GDL. + /// + /// # Example + /// + /// ``` + /// use graph_builder::prelude::*; + /// + /// let g: UndirectedCsrGraph = GraphBuilder::new() + /// .gdl_str::("(a)-->(),(a)-->()") + /// .build() + /// .unwrap(); + /// + /// assert_eq!(g.node_count(), 3); + /// assert_eq!(g.edge_count(), 2); + /// ``` + /// + /// One can also create weighted graphs using GDL. There needs to be exactly + /// one edge property with the same type as specified for the edge value. + /// The property key is not relevant. + /// + /// ``` + /// use graph_builder::prelude::*; + /// + /// let g: UndirectedCsrGraph = GraphBuilder::new() + /// .csr_layout(CsrLayout::Sorted) + /// .gdl_str::("(a)-[{f: 0.42}]->(),(a)-[{f: 13.37}]->()") + /// .build() + /// .unwrap(); + /// + /// assert_eq!(g.node_count(), 3); + /// assert_eq!(g.edge_count(), 2); + /// + /// let mut neighbors = g.neighbors_with_values(0); + /// assert_eq!(neighbors.next(), Some(&Target::new(1, 0.42))); + /// assert_eq!(neighbors.next(), Some(&Target::new(2, 13.37))); + /// assert_eq!(neighbors.next(), None); + /// ``` + #[cfg(feature = "gdl")] + #[cfg_attr(all(feature = "gdl", has_doc_cfg), doc(cfg(feature = "gdl")))] + pub fn gdl_str(self, gdl: S) -> GraphBuilder> + where + NI: Idx, + S: Into, + { + GraphBuilder { + state: FromGdlString { + csr_layout: self.state.csr_layout, + gdl: gdl.into(), + _node: PhantomData, + }, + } + } + + /// Creates a graph from an already constructed GDL graph. + /// + /// Creating graphs from GDL is recommended for small graphs only, e.g., + /// during testing. The graph construction is **not** parallelized. + /// + /// See [GDL on crates.io](https://crates.io/crates/gdl) for more + /// information on how to define graphs using GDL. + /// + /// # Example + /// + /// ``` + /// use graph_builder::prelude::*; + /// + /// let gdl_graph = "(a)-->(),(a)-->()".parse::<::gdl::Graph>().unwrap(); + /// + /// let g: DirectedCsrGraph = GraphBuilder::new() + /// .gdl_graph::(&gdl_graph) + /// .build() + /// .unwrap(); + /// + /// assert_eq!(g.node_count(), 3); + /// assert_eq!(g.edge_count(), 2); + /// + /// let id_a = gdl_graph.get_node("a").unwrap().id(); + /// + /// assert_eq!(g.out_neighbors(id_a).len(), 2); + /// ``` + #[cfg(feature = "gdl")] + #[cfg_attr(all(feature = "gdl", has_doc_cfg), doc(cfg(feature = "gdl")))] + pub fn gdl_graph(self, gdl_graph: &::gdl::Graph) -> GraphBuilder> + where + NI: Idx, + { + GraphBuilder { + state: FromGdlGraph { + csr_layout: self.state.csr_layout, + gdl_graph, + _node: PhantomData, + }, + } + } + + /// Creates a graph by reading it from the given file format. + /// + /// # Examples + /// + /// Read a directed graph from an edge list file: + /// + /// ``` + /// use std::path::PathBuf; + /// + /// use graph_builder::prelude::*; + /// + /// let path = [env!("CARGO_MANIFEST_DIR"), "resources", "example.el"] + /// .iter() + /// .collect::(); + /// + /// let graph: DirectedCsrGraph = GraphBuilder::new() + /// .file_format(EdgeListInput::default()) + /// .path(path) + /// .build() + /// .expect("loading failed"); + /// + /// assert_eq!(graph.node_count(), 4); + /// assert_eq!(graph.edge_count(), 5); + /// ``` + pub fn file_format( + self, + _format: Format, + ) -> GraphBuilder> + where + Path: AsRef, + NI: Idx, + Format: InputCapabilities, + Format::GraphInput: TryFrom>, + { + GraphBuilder { + state: FromInput { + csr_layout: self.state.csr_layout, + _idx: PhantomData, + _path: PhantomData, + _format: PhantomData, + }, + } + } +} + +impl GraphBuilder> +where + NI: Idx, + Edges: IntoIterator, +{ + pub fn node_values( + self, + node_values: I, + ) -> GraphBuilder> + where + I: IntoIterator, + { + let edge_list = EdgeList::from(EdgeIterator(self.state.edges)); + let node_values = node_values.into_iter().collect::>(); + + GraphBuilder { + state: FromEdgeListAndNodeValues { + csr_layout: self.state.csr_layout, + node_values, + edge_list, + }, + } + } + + /// Build the graph from the given vec of edges. + pub fn build(self) -> Graph + where + Graph: From<(EdgeList, CsrLayout)>, + { + Graph::from(( + EdgeList::from(EdgeIterator(self.state.edges)), + self.state.csr_layout, + )) + } +} + +impl GraphBuilder> +where + NI: Idx, + EV: Sync, + Edges: IntoIterator, +{ + pub fn node_values( + self, + node_values: I, + ) -> GraphBuilder> + where + I: IntoIterator, + { + let edge_list = EdgeList::from(EdgeWithValueIterator(self.state.edges)); + let node_values = node_values.into_iter().collect::>(); + + GraphBuilder { + state: FromEdgeListAndNodeValues { + csr_layout: self.state.csr_layout, + node_values, + edge_list, + }, + } + } + + /// Build the graph from the given vec of edges. + pub fn build(self) -> Graph + where + Graph: From<(EdgeList, CsrLayout)>, + { + Graph::from(( + EdgeList::new(self.state.edges.into_iter().collect()), + self.state.csr_layout, + )) + } +} + +impl GraphBuilder> { + pub fn build(self) -> Graph + where + Graph: From<(NodeValues, EdgeList, CsrLayout)>, + { + Graph::from(( + self.state.node_values, + self.state.edge_list, + self.state.csr_layout, + )) + } +} + +#[cfg(feature = "gdl")] +#[cfg_attr(all(feature = "gdl", has_doc_cfg), doc(cfg(feature = "gdl")))] +impl GraphBuilder> +where + NI: Idx, +{ + /// Builds the graph from the given GDL string. + pub fn build(self) -> Result + where + Graph: From<(gdl::Graph, CsrLayout)>, + { + let gdl_graph = self.state.gdl.parse::()?; + let graph = Graph::from((gdl_graph, self.state.csr_layout)); + Ok(graph) + } +} + +#[cfg(feature = "gdl")] +#[cfg_attr(all(feature = "gdl", has_doc_cfg), doc(cfg(feature = "gdl")))] +impl<'a, NI> GraphBuilder> +where + NI: Idx, +{ + /// Build the graph from the given GDL graph. + pub fn build(self) -> Result + where + Graph: From<(&'a gdl::Graph, CsrLayout)>, + { + Ok(Graph::from((self.state.gdl_graph, self.state.csr_layout))) + } +} + +impl GraphBuilder> +where + Path: AsRef, + NI: Idx, + Format: InputCapabilities, + Format::GraphInput: TryFrom>, +{ + /// Set the location where the graph is stored. + pub fn path(self, path: Path) -> GraphBuilder> { + GraphBuilder { + state: FromPath { + csr_layout: self.state.csr_layout, + path, + _idx: PhantomData, + _format: PhantomData, + }, + } + } +} + +impl GraphBuilder> +where + Path: AsRef, + NI: Idx, + Format: InputCapabilities, + Format::GraphInput: TryFrom>, + super::Error: From<>>::Error>, +{ + /// Build the graph from the given input format and path. + pub fn build(self) -> Result + where + Graph: TryFrom<(Format::GraphInput, CsrLayout)>, + super::Error: From, + { + let input = Format::GraphInput::try_from(InputPath(self.state.path))?; + let graph = Graph::try_from((input, self.state.csr_layout))?; + + Ok(graph) + } +} \ No newline at end of file diff --git a/packages/graph-rust/src/graph_builder/compat.rs b/packages/graph-rust/src/graph_builder/compat.rs new file mode 100644 index 0000000..5dcdf25 --- /dev/null +++ b/packages/graph-rust/src/graph_builder/compat.rs @@ -0,0 +1,109 @@ +use std::mem::MaybeUninit; + +pub(crate) trait MaybeUninitWriteSliceExt { + fn write_slice_compat<'a>(this: &'a mut [MaybeUninit], src: &[T]) -> &'a mut [T] + where + T: Copy; +} + +#[cfg(not(has_maybe_uninit_write_slice))] +impl MaybeUninitWriteSliceExt for MaybeUninit { + fn write_slice_compat<'a>(this: &'a mut [MaybeUninit], src: &[T]) -> &'a mut [T] + where + T: Copy, + { + // SAFETY: &[T] and &[MaybeUninit] have the same layout + let uninit_src: &[MaybeUninit] = unsafe { std::mem::transmute(src) }; + + this.copy_from_slice(uninit_src); + + // SAFETY: Valid elements have just been copied into `this` so it is initialized + // SAFETY: similar to safety notes for `slice_get_ref`, but we have a + // mutable reference which is also guaranteed to be valid for writes. + unsafe { &mut *(this as *mut [MaybeUninit] as *mut [T]) } + } +} + +#[cfg(has_maybe_uninit_write_slice)] +impl MaybeUninitWriteSliceExt for MaybeUninit { + fn write_slice_compat<'a>(this: &'a mut [MaybeUninit], src: &[T]) -> &'a mut [T] + where + T: Copy, + { + MaybeUninit::write_slice(this, src) + } +} + +pub(crate) trait NewUninitExt { + fn new_uninit_slice_compat(len: usize) -> Box<[MaybeUninit]>; + + unsafe fn assume_init_compat(self) -> Box<[T]>; +} + +#[cfg(not(has_new_uninit))] +impl NewUninitExt for Box<[MaybeUninit]> { + fn new_uninit_slice_compat(len: usize) -> Box<[MaybeUninit]> { + use std::mem::ManuallyDrop; + use std::slice::from_raw_parts_mut; + + let vec = Vec::::with_capacity(len); + let mut vec = ManuallyDrop::new(vec); + + unsafe { + let slice = from_raw_parts_mut(vec.as_mut_ptr() as *mut MaybeUninit, len); + Box::from_raw(slice) + } + } + + unsafe fn assume_init_compat(self) -> Box<[T]> { + unsafe { Box::from_raw(Box::into_raw(self) as *mut [T]) } + } +} + +#[cfg(has_new_uninit)] +impl NewUninitExt for Box<[MaybeUninit]> { + fn new_uninit_slice_compat(len: usize) -> Box<[MaybeUninit]> { + Box::<[T]>::new_uninit_slice(len) + } + + unsafe fn assume_init_compat(self) -> Box<[T]> { + unsafe { self.assume_init() } + } +} + +pub(crate) trait SlicePartitionDedupExt { + fn partition_dedup_compat(&mut self) -> (&mut [T], &mut [T]); +} + +#[cfg(not(has_slice_partition_dedup))] +impl SlicePartitionDedupExt for [T] { + fn partition_dedup_compat(&mut self) -> (&mut [T], &mut [T]) { + let len = self.len(); + if len <= 1 { + return (self, &mut []); + } + + let ptr = self.as_mut_ptr(); + let mut next_read: usize = 1; + let mut next_write: usize = 1; + + unsafe { + while next_read < len { + let ptr_read = ptr.add(next_read); + let prev_ptr_write = ptr.add(next_write - 1); + // Changed from if `!same_bucket(&mut *ptr_read, &mut *prev_ptr_write)` + // as the original implementation is copied from `partition_dedup_by`. + if *ptr_read != *prev_ptr_write { + if next_read != next_write { + let ptr_write = prev_ptr_write.offset(1); + core::ptr::swap(ptr_read, ptr_write); + } + next_write += 1; + } + next_read += 1; + } + } + + self.split_at_mut(next_write) + } +} diff --git a/packages/graph-rust/src/graph_builder/graph/csr.rs b/packages/graph-rust/src/graph_builder/graph/csr.rs new file mode 100644 index 0000000..ee194cd --- /dev/null +++ b/packages/graph-rust/src/graph_builder/graph/csr.rs @@ -0,0 +1,873 @@ +use atomic::Atomic; +use byte_slice_cast::{AsByteSlice, AsMutByteSlice, ToByteSlice, ToMutByteSlice}; +use std::{ + convert::TryFrom, + fs::File, + io::{BufReader, Read, Write}, + iter::FromIterator, + mem::{ManuallyDrop, MaybeUninit}, + path::PathBuf, + sync::atomic::Ordering::Acquire, +}; + +use rayon::prelude::*; + +use super::super::compat::*; +use super::super::{ + graph_ops::{DeserializeGraphOp, SerializeGraphOp, ToUndirectedOp}, + index::Idx, + input::{edgelist::Edges, Direction}, + DirectedDegrees, DirectedNeighbors, DirectedNeighborsWithValues, Error, Graph, + NodeValues as NodeValuesTrait, SharedMut, UndirectedDegrees, UndirectedNeighbors, + UndirectedNeighborsWithValues, +}; + +/// Defines how the neighbor list of individual nodes are organized within the +/// CSR target array. +#[derive(Clone, Copy, Debug)] +pub enum CsrLayout { + /// Neighbor lists are sorted and may contain duplicate target ids. This is + /// the default representation. + Sorted, + /// Neighbor lists are not in any particular order. + Unsorted, + /// Neighbor lists are sorted and do not contain duplicate target ids. + /// Self-loops, i.e., edges in the form of `(u, u)` are removed. + Deduplicated, +} + +impl Default for CsrLayout { + fn default() -> Self { + CsrLayout::Unsorted + } +} + +/// A Compressed-Sparse-Row data structure to represent sparse graphs. +/// +/// The data structure is composed of two arrays: `offsets` and `targets`. For a +/// graph with node count `n` and edge count `m`, `offsets` has exactly `n + 1` +/// and `targets` exactly `m` entries. +/// +/// For a given node `u`, `offsets[u]` stores the start index of the neighbor +/// list of `u` in `targets`. The degree of `u`, i.e., the length of the +/// neighbor list is defined by `offsets[u + 1] - offsets[u]`. The neighbor list +/// of `u` is defined by the slice `&targets[offsets[u]..offsets[u + 1]]`. +#[derive(Debug)] +pub struct Csr { + offsets: Box<[Index]>, + targets: Box<[Target]>, +} + +/// Represents the target of an edge and its associated value. +#[derive(Clone, Copy, Debug)] +#[repr(C)] +pub struct Target { + pub target: NI, + pub value: EV, +} + +impl Ord for Target { + fn cmp(&self, other: &Self) -> std::cmp::Ordering { + self.target.cmp(&other.target) + } +} + +impl PartialOrd for Target { + fn partial_cmp(&self, other: &Self) -> Option { + self.target.partial_cmp(&other.target) + } +} + +impl PartialEq for Target { + fn eq(&self, other: &Self) -> bool { + self.target.eq(&other.target) + } +} + +impl Eq for Target {} + +impl Target { + pub fn new(target: T, value: EV) -> Self { + Self { target, value } + } +} + +impl Csr { + pub(crate) fn new(offsets: Box<[Index]>, targets: Box<[Target]>) -> Self { + Self { offsets, targets } + } + + #[inline] + pub(crate) fn node_count(&self) -> Index { + Index::new(self.offsets.len() - 1) + } + + #[inline] + pub(crate) fn edge_count(&self) -> Index { + Index::new(self.targets.len()) + } + + #[inline] + pub(crate) fn degree(&self, i: Index) -> Index { + let from = self.offsets[i.index()]; + let to = self.offsets[(i + Index::new(1)).index()]; + + to - from + } + + #[inline] + pub(crate) fn targets_with_values(&self, i: Index) -> &[Target] { + let from = self.offsets[i.index()]; + let to = self.offsets[(i + Index::new(1)).index()]; + + &self.targets[from.index()..to.index()] + } +} + +impl Csr { + #[inline] + pub(crate) fn targets(&self, i: Index) -> &[NI] { + assert_eq!( + std::mem::size_of::>(), + std::mem::size_of::() + ); + assert_eq!( + std::mem::align_of::>(), + std::mem::align_of::() + ); + let from = self.offsets[i.index()]; + let to = self.offsets[(i + Index::new(1)).index()]; + + let len = (to - from).index(); + + let targets = &self.targets[from.index()..to.index()]; + + // SAFETY: len is within bounds as it is calculated above as `to - from`. + // The types Target and T are verified to have the same + // size and alignment. + unsafe { std::slice::from_raw_parts(targets.as_ptr() as *const _, len) } + } +} + +pub trait SwapCsr { + fn swap_csr(&mut self, csr: Csr) -> &mut Self; +} + +impl From<(&'_ E, NI, Direction, CsrLayout)> for Csr +where + NI: Idx, + EV: Copy + Send + Sync, + E: Edges, +{ + fn from( + (edge_list, node_count, direction, csr_layout): (&'_ E, NI, Direction, CsrLayout), + ) -> Self { + let degrees = edge_list.degrees(node_count, direction); + let offsets = prefix_sum_atomic(degrees); + let edge_count = offsets[node_count.index()].load(Acquire).index(); + let mut targets = Vec::>::with_capacity(edge_count); + let targets_ptr = SharedMut::new(targets.as_mut_ptr()); + + // The following loop writes all targets into their correct position. + // The offsets are a prefix sum of all degrees, which will produce + // non-overlapping positions for all node values. + // + // SAFETY: for any (s, t) tuple from the same edge_list we use the + // prefix_sum to find a unique position for the target value, so that we + // only write once into each position and every thread that might run + // will write into different positions. + if matches!(direction, Direction::Outgoing | Direction::Undirected) { + edge_list.edges().for_each(|(s, t, v)| { + let offset = NI::get_and_increment(&offsets[s.index()], Acquire); + + unsafe { + targets_ptr.add(offset.index()).write(Target::new(t, v)); + } + }) + } + + if matches!(direction, Direction::Incoming | Direction::Undirected) { + edge_list.edges().for_each(|(s, t, v)| { + let offset = NI::get_and_increment(&offsets[t.index()], Acquire); + + unsafe { + targets_ptr.add(offset.index()).write(Target::new(s, v)); + } + }) + } + + // SAFETY: The previous loops iterated the input edge list once (twice + // for undirected) and inserted one node id for each edge. The + // `edge_count` is defined by the highest offset value. + unsafe { + targets.set_len(edge_count); + } + let mut offsets = ManuallyDrop::new(offsets); + let (ptr, len, cap) = (offsets.as_mut_ptr(), offsets.len(), offsets.capacity()); + + // SAFETY: NI and NI::Atomic have the same memory layout + let mut offsets = unsafe { + let ptr = ptr as *mut _; + Vec::from_raw_parts(ptr, len, cap) + }; + + // Each insert into the target array in the previous loops incremented + // the offset for the corresponding node by one. As a consequence the + // offset values are shifted one index to the right. We need to correct + // this in order to get correct offsets. + offsets.rotate_right(1); + offsets[0] = NI::zero(); + + let (offsets, targets) = match csr_layout { + CsrLayout::Unsorted => (offsets, targets), + CsrLayout::Sorted => { + sort_targets(&offsets, &mut targets); + (offsets, targets) + } + CsrLayout::Deduplicated => { + let offsets_targets = sort_and_deduplicate_targets(&offsets, &mut targets[..]); + offsets_targets + } + }; + + Csr { + offsets: offsets.into_boxed_slice(), + targets: targets.into_boxed_slice(), + } + } +} + +unsafe impl ToByteSlice for Target +where + NI: ToByteSlice, + EV: ToByteSlice, +{ + fn to_byte_slice + ?Sized>(slice: &S) -> &[u8] { + let slice = slice.as_ref(); + let len = slice.len() * std::mem::size_of::>(); + unsafe { std::slice::from_raw_parts(slice.as_ptr() as *const u8, len) } + } +} + +unsafe impl ToMutByteSlice for Target +where + NI: ToMutByteSlice, + EV: ToMutByteSlice, +{ + fn to_mut_byte_slice + ?Sized>(slice: &mut S) -> &mut [u8] { + let slice = slice.as_mut(); + let len = slice.len() * std::mem::size_of::>(); + unsafe { std::slice::from_raw_parts_mut(slice.as_mut_ptr() as *mut u8, len) } + } +} + +impl Csr +where + NI: Idx + ToByteSlice, + EV: ToByteSlice, +{ + fn serialize(&self, output: &mut W) -> Result<(), Error> { + let type_name = std::any::type_name::().as_bytes(); + output.write_all([type_name.len()].as_byte_slice())?; + output.write_all(type_name)?; + + let node_count = self.node_count(); + let edge_count = self.edge_count(); + let meta = [node_count, edge_count]; + output.write_all(meta.as_byte_slice())?; + + output.write_all(self.offsets.as_byte_slice())?; + output.write_all(self.targets.as_byte_slice())?; + + Ok(()) + } +} + +impl Csr +where + NI: Idx + ToMutByteSlice, + EV: ToMutByteSlice, +{ + fn deserialize(read: &mut R) -> Result, Error> { + let mut type_name_len = [0_usize; 1]; + read.read_exact(type_name_len.as_mut_byte_slice())?; + let [type_name_len] = type_name_len; + + let mut type_name = vec![0_u8; type_name_len]; + read.read_exact(type_name.as_mut_byte_slice())?; + let type_name = String::from_utf8(type_name).expect("could not read type name"); + + let expected_type_name = std::any::type_name::().to_string(); + + if type_name != expected_type_name { + return Err(Error::InvalidIdType { + expected: expected_type_name, + actual: type_name, + }); + } + + let mut meta = [NI::zero(); 2]; + read.read_exact(meta.as_mut_byte_slice())?; + + let [node_count, edge_count] = meta; + + let mut offsets = Box::new_uninit_slice_compat(node_count.index() + 1); + let offsets_ptr = offsets.as_mut_ptr() as *mut NI; + let offsets_ptr = + unsafe { std::slice::from_raw_parts_mut(offsets_ptr, node_count.index() + 1) }; + read.read_exact(offsets_ptr.as_mut_byte_slice())?; + + let mut targets = Box::new_uninit_slice_compat(edge_count.index()); + let targets_ptr = targets.as_mut_ptr() as *mut Target; + let targets_ptr = + unsafe { std::slice::from_raw_parts_mut(targets_ptr, edge_count.index()) }; + read.read_exact(targets_ptr.as_mut_byte_slice())?; + + let offsets = unsafe { offsets.assume_init_compat() }; + let targets = unsafe { targets.assume_init_compat() }; + + Ok(Csr::new(offsets, targets)) + } +} + +pub struct NodeValues(Box<[NV]>); + +impl NodeValues { + pub fn new(node_values: Vec) -> Self { + Self(node_values.into_boxed_slice()) + } +} + +impl FromIterator for NodeValues { + fn from_iter>(iter: T) -> Self { + Self(iter.into_iter().collect::>().into_boxed_slice()) + } +} + +impl NodeValues +where + NV: ToByteSlice, +{ + fn serialize(&self, output: &mut W) -> Result<(), Error> { + let node_count = self.0.len(); + let meta = [node_count]; + output.write_all(meta.as_byte_slice())?; + output.write_all(self.0.as_byte_slice())?; + Ok(()) + } +} + +impl NodeValues +where + NV: ToMutByteSlice, +{ + fn deserialize(read: &mut R) -> Result { + let mut meta = [0_usize; 1]; + read.read_exact(meta.as_mut_byte_slice())?; + let [node_count] = meta; + + let mut node_values = Box::new_uninit_slice_compat(node_count); + let node_values_ptr = node_values.as_mut_ptr() as *mut NV; + let node_values_slice = + unsafe { std::slice::from_raw_parts_mut(node_values_ptr, node_count.index()) }; + read.read_exact(node_values_slice.as_mut_byte_slice())?; + + let offsets = unsafe { node_values.assume_init_compat() }; + + Ok(NodeValues(offsets)) + } +} + +pub struct DirectedCsrGraph { + node_values: NodeValues, + csr_out: Csr, + csr_inc: Csr, +} + +impl DirectedCsrGraph { + pub fn new( + node_values: NodeValues, + csr_out: Csr, + csr_inc: Csr, + ) -> Self { + let g = Self { + node_values, + csr_out, + csr_inc, + }; + + g + } +} + +impl ToUndirectedOp for DirectedCsrGraph +where + NI: Idx, + NV: Clone + Send + Sync, + EV: Copy + Send + Sync, +{ + type Undirected = UndirectedCsrGraph; + + fn to_undirected(&self, layout: impl Into>) -> Self::Undirected { + let node_values = NodeValues::new(self.node_values.0.to_vec()); + let layout = layout.into().unwrap_or_default(); + let edges = ToUndirectedEdges { g: self }; + + UndirectedCsrGraph::from((node_values, edges, layout)) + } +} + +struct ToUndirectedEdges<'g, NI: Idx, NV, EV> { + g: &'g DirectedCsrGraph, +} + +impl<'g, NI, NV, EV> Edges for ToUndirectedEdges<'g, NI, NV, EV> +where + NI: Idx, + NV: Send + Sync, + EV: Copy + Send + Sync, +{ + type NI = NI; + + type EV = EV; + + type EdgeIter<'a> = ToUndirectedEdgesIter<'a, NI, NV, EV> + where + Self: 'a; + + fn edges(&self) -> Self::EdgeIter<'_> { + ToUndirectedEdgesIter { g: self.g } + } + + fn max_node_id(&self) -> Self::NI { + self.g.node_count() - NI::new(1) + } + + #[cfg(test)] + fn len(&self) -> usize { + unimplemented!("This type is not used in tests") + } +} + +struct ToUndirectedEdgesIter<'g, NI: Idx, NV, EV> { + g: &'g DirectedCsrGraph, +} + +impl<'g, NI: Idx, NV: Send + Sync, EV: Copy + Send + Sync> ParallelIterator + for ToUndirectedEdgesIter<'g, NI, NV, EV> +{ + type Item = (NI, NI, EV); + + fn drive_unindexed(self, consumer: C) -> C::Result + where + C: rayon::iter::plumbing::UnindexedConsumer, + { + let par_iter = (0..self.g.node_count().index()) + .into_par_iter() + .flat_map_iter(|n| { + let n = NI::new(n); + self.g + .out_neighbors_with_values(n) + .map(move |t| (n, t.target, t.value)) + }); + par_iter.drive_unindexed(consumer) + } +} + +impl Graph for DirectedCsrGraph { + delegate::delegate! { + to self.csr_out { + fn node_count(&self) -> NI; + fn edge_count(&self) -> NI; + } + } +} + +impl NodeValuesTrait for DirectedCsrGraph { + fn node_value(&self, node: NI) -> &NV { + &self.node_values.0[node.index()] + } +} + +impl DirectedDegrees for DirectedCsrGraph { + fn out_degree(&self, node: NI) -> NI { + self.csr_out.degree(node) + } + + fn in_degree(&self, node: NI) -> NI { + self.csr_inc.degree(node) + } +} + +impl DirectedNeighbors for DirectedCsrGraph { + type NeighborsIterator<'a> = std::slice::Iter<'a, NI> where NV: 'a; + + fn out_neighbors(&self, node: NI) -> Self::NeighborsIterator<'_> { + self.csr_out.targets(node).iter() + } + + fn in_neighbors(&self, node: NI) -> Self::NeighborsIterator<'_> { + self.csr_inc.targets(node).iter() + } +} + +impl DirectedNeighborsWithValues for DirectedCsrGraph { + type NeighborsIterator<'a> = std::slice::Iter<'a, Target> where NV:'a, EV: 'a; + + fn out_neighbors_with_values(&self, node: NI) -> Self::NeighborsIterator<'_> { + self.csr_out.targets_with_values(node).iter() + } + + fn in_neighbors_with_values(&self, node: NI) -> Self::NeighborsIterator<'_> { + self.csr_inc.targets_with_values(node).iter() + } +} + +impl From<(E, CsrLayout)> for DirectedCsrGraph +where + NI: Idx, + EV: Copy + Send + Sync, + E: Edges, +{ + fn from((edge_list, csr_option): (E, CsrLayout)) -> Self { + let node_count = edge_list.max_node_id() + NI::new(1); + + let node_values = NodeValues::new(vec![(); node_count.index()]); + + let csr_out = Csr::from((&edge_list, node_count, Direction::Outgoing, csr_option)); + let csr_inc = Csr::from((&edge_list, node_count, Direction::Incoming, csr_option)); + + DirectedCsrGraph::new(node_values, csr_out, csr_inc) + } +} + +impl From<(NodeValues, E, CsrLayout)> for DirectedCsrGraph +where + NI: Idx, + EV: Copy + Send + Sync, + E: Edges, +{ + fn from((node_values, edge_list, csr_option): (NodeValues, E, CsrLayout)) -> Self { + let node_count = edge_list.max_node_id() + NI::new(1); + + assert!( + node_values.0.len() >= node_count.index(), + "number of node values ({}) does not match node count of edge list ({})", + node_values.0.len(), + node_count.index() + ); + + let csr_out = Csr::from((&edge_list, node_count, Direction::Outgoing, csr_option)); + let csr_inc = Csr::from((&edge_list, node_count, Direction::Incoming, csr_option)); + + DirectedCsrGraph::new(node_values, csr_out, csr_inc) + } +} + + +impl SerializeGraphOp for DirectedCsrGraph +where + W: Write, + NI: Idx + ToByteSlice, + NV: ToByteSlice, + EV: ToByteSlice, +{ + fn serialize(&self, mut output: W) -> Result<(), Error> { + let DirectedCsrGraph { + node_values, + csr_out, + csr_inc, + } = self; + + node_values.serialize(&mut output)?; + csr_out.serialize(&mut output)?; + csr_inc.serialize(&mut output)?; + + Ok(()) + } +} + +impl DeserializeGraphOp for DirectedCsrGraph +where + R: Read, + NI: Idx + ToMutByteSlice, + NV: ToMutByteSlice, + EV: ToMutByteSlice, +{ + fn deserialize(mut read: R) -> Result { + let node_values: NodeValues = NodeValues::deserialize(&mut read)?; + let csr_out: Csr = Csr::deserialize(&mut read)?; + let csr_inc: Csr = Csr::deserialize(&mut read)?; + Ok(DirectedCsrGraph::new(node_values, csr_out, csr_inc)) + } +} + +impl TryFrom<(PathBuf, CsrLayout)> for DirectedCsrGraph +where + NI: Idx + ToMutByteSlice, + EV: ToMutByteSlice, +{ + type Error = Error; + + fn try_from((path, _): (PathBuf, CsrLayout)) -> Result { + let reader = BufReader::new(File::open(path)?); + let graph = DirectedCsrGraph::deserialize(reader)?; + + Ok(graph) + } +} + +pub struct UndirectedCsrGraph { + node_values: NodeValues, + csr: Csr, +} + +impl From> for UndirectedCsrGraph { + fn from(csr: Csr) -> Self { + UndirectedCsrGraph::new(NodeValues::new(vec![(); csr.node_count().index()]), csr) + } +} + +impl UndirectedCsrGraph { + pub fn new(node_values: NodeValues, csr: Csr) -> Self { + let g = Self { node_values, csr }; + + g + } +} + +impl Graph for UndirectedCsrGraph { + fn node_count(&self) -> NI { + self.csr.node_count() + } + + fn edge_count(&self) -> NI { + self.csr.edge_count() / NI::new(2) + } +} + +impl NodeValuesTrait for UndirectedCsrGraph { + fn node_value(&self, node: NI) -> &NV { + &self.node_values.0[node.index()] + } +} + +impl UndirectedDegrees for UndirectedCsrGraph { + fn degree(&self, node: NI) -> NI { + self.csr.degree(node) + } +} + +impl UndirectedNeighbors for UndirectedCsrGraph { + type NeighborsIterator<'a> = std::slice::Iter<'a, NI> where NV: 'a; + + fn neighbors(&self, node: NI) -> Self::NeighborsIterator<'_> { + self.csr.targets(node).iter() + } +} + +impl UndirectedNeighborsWithValues for UndirectedCsrGraph { + type NeighborsIterator<'a> = std::slice::Iter<'a, Target> where NV: 'a, EV: 'a; + + fn neighbors_with_values(&self, node: NI) -> Self::NeighborsIterator<'_> { + self.csr.targets_with_values(node).iter() + } +} + +impl SwapCsr for UndirectedCsrGraph { + fn swap_csr(&mut self, mut csr: Csr) -> &mut Self { + std::mem::swap(&mut self.csr, &mut csr); + self + } +} + +impl From<(E, CsrLayout)> for UndirectedCsrGraph +where + NI: Idx, + EV: Copy + Send + Sync, + E: Edges, +{ + fn from((edge_list, csr_option): (E, CsrLayout)) -> Self { + let node_count = edge_list.max_node_id() + NI::new(1); + + let node_values = NodeValues::new(vec![(); node_count.index()]); + + let csr = Csr::from((&edge_list, node_count, Direction::Undirected, csr_option)); + + UndirectedCsrGraph::new(node_values, csr) + } +} + +impl From<(NodeValues, E, CsrLayout)> for UndirectedCsrGraph +where + NI: Idx, + EV: Copy + Send + Sync, + E: Edges, +{ + fn from((node_values, edge_list, csr_option): (NodeValues, E, CsrLayout)) -> Self { + let node_count = edge_list.max_node_id() + NI::new(1); + + let csr = Csr::from((&edge_list, node_count, Direction::Undirected, csr_option)); + + UndirectedCsrGraph::new(node_values, csr) + } +} + +impl SerializeGraphOp for UndirectedCsrGraph +where + W: Write, + NI: Idx + ToByteSlice, + NV: ToByteSlice, + EV: ToByteSlice, +{ + fn serialize(&self, mut output: W) -> Result<(), Error> { + let UndirectedCsrGraph { node_values, csr } = self; + + node_values.serialize(&mut output)?; + csr.serialize(&mut output)?; + + Ok(()) + } +} + +impl DeserializeGraphOp for UndirectedCsrGraph +where + R: Read, + NI: Idx + ToMutByteSlice, + NV: ToMutByteSlice, + EV: ToMutByteSlice, +{ + fn deserialize(mut read: R) -> Result { + let node_values = NodeValues::deserialize(&mut read)?; + let csr: Csr = Csr::deserialize(&mut read)?; + Ok(UndirectedCsrGraph::new(node_values, csr)) + } +} + +impl TryFrom<(PathBuf, CsrLayout)> for UndirectedCsrGraph +where + NI: Idx + ToMutByteSlice, + EV: ToMutByteSlice, +{ + type Error = Error; + + fn try_from((path, _): (PathBuf, CsrLayout)) -> Result { + let reader = BufReader::new(File::open(path)?); + UndirectedCsrGraph::deserialize(reader) + } +} + +fn prefix_sum_atomic(degrees: Vec>) -> Vec> { + let mut last = degrees.last().unwrap().load(Acquire); + let mut sums = degrees + .into_iter() + .scan(NI::zero(), |total, degree| { + let value = *total; + *total += degree.into_inner(); + Some(Atomic::new(value)) + }) + .collect::>(); + + last += sums.last().unwrap().load(Acquire); + sums.push(Atomic::new(last)); + + sums +} + +pub(crate) fn prefix_sum(degrees: Vec) -> Vec { + let mut last = *degrees.last().unwrap(); + let mut sums = degrees + .into_iter() + .scan(NI::zero(), |total, degree| { + let value = *total; + *total += degree; + Some(value) + }) + .collect::>(); + last += *sums.last().unwrap(); + sums.push(last); + sums +} + +pub(crate) fn sort_targets(offsets: &[NI], targets: &mut [Target]) +where + NI: Idx, + T: Copy + Send + Ord, + EV: Send, +{ + to_mut_slices(offsets, targets) + .par_iter_mut() + .for_each(|list| list.sort_unstable()); +} + +fn sort_and_deduplicate_targets( + offsets: &[NI], + targets: &mut [Target], +) -> (Vec, Vec>) +where + NI: Idx, + EV: Copy + Send, +{ + let node_count = offsets.len() - 1; + + let mut new_degrees = Vec::with_capacity(node_count); + let mut target_slices = to_mut_slices(offsets, targets); + + target_slices + .par_iter_mut() + .enumerate() + .map(|(node, slice)| { + slice.sort_unstable(); + // deduplicate + let (dedup, _) = slice.partition_dedup_compat(); + let mut new_degree = dedup.len(); + // remove self loops .. there is at most once occurence of node inside dedup + if let Ok(idx) = dedup.binary_search_by_key(&NI::new(node), |t| t.target) { + dedup[idx..].rotate_left(1); + new_degree -= 1; + } + NI::new(new_degree) + }) + .collect_into_vec(&mut new_degrees); + + let new_offsets = prefix_sum(new_degrees); + debug_assert_eq!(new_offsets.len(), node_count + 1); + + let edge_count = new_offsets[node_count].index(); + let mut new_targets: Vec> = Vec::with_capacity(edge_count); + let new_target_slices = to_mut_slices(&new_offsets, new_targets.spare_capacity_mut()); + + target_slices + .into_par_iter() + .zip(new_target_slices.into_par_iter()) + .for_each(|(old_slice, new_slice)| { + MaybeUninit::write_slice_compat(new_slice, &old_slice[..new_slice.len()]); + }); + + // SAFETY: We copied all (potentially shortened) target ids from the old + // target list to the new one. + unsafe { + new_targets.set_len(edge_count); + } + + (new_offsets, new_targets) +} + +fn to_mut_slices<'targets, NI: Idx, T>( + offsets: &[NI], + targets: &'targets mut [T], +) -> Vec<&'targets mut [T]> { + let node_count = offsets.len() - 1; + let mut target_slices = Vec::with_capacity(node_count); + let mut tail = targets; + let mut prev_offset = offsets[0]; + + for &offset in &offsets[1..] { + let (list, remainder) = tail.split_at_mut((offset - prev_offset).index()); + target_slices.push(list); + tail = remainder; + prev_offset = offset; + } + + target_slices +} diff --git a/packages/graph-rust/src/graph_builder/graph/mod.rs b/packages/graph-rust/src/graph_builder/graph/mod.rs new file mode 100644 index 0000000..571c09b --- /dev/null +++ b/packages/graph-rust/src/graph_builder/graph/mod.rs @@ -0,0 +1 @@ +pub mod csr; \ No newline at end of file diff --git a/packages/graph-rust/src/graph_builder/graph_ops.rs b/packages/graph-rust/src/graph_builder/graph_ops.rs new file mode 100644 index 0000000..06b2d9c --- /dev/null +++ b/packages/graph-rust/src/graph_builder/graph_ops.rs @@ -0,0 +1,627 @@ +use rayon::prelude::*; + +use super::graph::csr::{prefix_sum, Csr, SwapCsr, Target}; +use super::index::Idx; +use super::{ + CsrLayout, DirectedDegrees, DirectedNeighborsWithValues, Error, Graph, SharedMut, + UndirectedDegrees, UndirectedNeighborsWithValues, +}; + +use std::ops::Range; +use std::sync::Arc; + +/// Partition the node set based on the degrees of the nodes. +pub trait DegreePartitionOp { + /// Creates a range-based degree partition of the nodes. + /// + /// Divide the nodes into `concurrency` number of ranges such that these + /// ranges have roughly equal total degree. That is, the sum of the degrees + /// of the nodes of each range should be roughly equal to the extent that + /// that's actually possible. + /// The length of the returned vector will never exceed `concurrency`. + fn degree_partition(&self, concurrency: usize) -> Vec>; +} + +/// Partition the node set based on the out degrees of the nodes. +pub trait OutDegreePartitionOp { + /// Creates a range-based out degree partition of the nodes. + /// + /// Divide the nodes into `concurrency` number of ranges such that these + /// ranges have roughly equal total out degree. That is, the sum of the out + /// degrees of the nodes of each range should be roughly equal to the extent + /// that that's actually possible. + /// The length of the returned vector will never exceed `concurrency`. + fn out_degree_partition(&self, concurrency: usize) -> Vec>; +} + +/// Partition the node set based on the in degrees of the nodes. +pub trait InDegreePartitionOp { + /// Creates a range-based in degree partition of the nodes. + /// + /// Divide the nodes into `concurrency` number of ranges such that these + /// ranges have roughly equal total in degree. That is, the sum of the in + /// degrees of the nodes of each range should be roughly equal to the extent + /// that that's actually possible. + /// The length of the returned vector will never exceed `concurrency`. + fn in_degree_partition(&self, concurrency: usize) -> Vec>; +} + +/// Call a particular function for each node with its corresponding state in parallel. +pub trait ForEachNodeParallelOp { + /// For each node calls `node_fn` with the node and its corresponding mutable + /// state in parallel. + /// + /// For every node `n` in the graph `node_fn(&self, n, node_values[n.index()])` + /// will be called. + /// + /// `node_values` must have length exactly equal to the number of nodes in + /// the graph. + /// + /// # Example + /// + /// ``` + /// # use graph_builder::prelude::*; + /// # use std::ops::Range; + /// let graph: DirectedCsrGraph = GraphBuilder::new() + /// .edges(vec![(0, 1), (0, 2), (1, 2)]) + /// .build(); + /// let mut node_values = vec![0; 3]; + /// + /// graph. + /// for_each_node_par(&mut node_values, |g, node, node_state| { + /// *node_state = g.out_degree(node); + /// }); + /// + /// assert_eq!(node_values[0], 2); + /// assert_eq!(node_values[1], 1); + /// assert_eq!(node_values[2], 0); + /// ``` + fn for_each_node_par(&self, node_values: &mut [T], node_fn: F) -> Result<(), Error> + where + T: Send, + F: Fn(&Self, NI, &mut T) + Send + Sync; +} + +/// Call a particular function for each node with its corresponding state in parallel based on a +/// partition. +pub trait ForEachNodeParallelByPartitionOp { + /// For each node calls `node_fn` with the node and its corresponding + /// mutable state in parallel, using `partition` as a parallelization hint. + /// + /// For every node `n` in the graph `node_fn(&self, n, node_values[n.index()])` + /// will be called. + /// + /// `node_values` must have length exactly equal to the number of nodes in + /// the graph. + /// + /// The parallelization will be implemented such that the work for a set of + /// nodes represented by each range in `partition` will correspond to a task + /// that will run in a single thread. + /// + /// # Example + /// + /// ``` + /// # use graph_builder::prelude::*; + /// # use std::ops::Range; + /// let graph: DirectedCsrGraph = GraphBuilder::new() + /// .edges(vec![(0, 1), (0, 2), (1, 2)]) + /// .build(); + /// let mut node_values = vec![0; 3]; + /// let partition: Vec> = graph.out_degree_partition(num_cpus::get()); + /// + /// graph. + /// for_each_node_par_by_partition(&partition, &mut node_values, |g, node, node_state| { + /// *node_state = g.out_degree(node); + /// }); + /// + /// assert_eq!(node_values[0], 2); + /// assert_eq!(node_values[1], 1); + /// assert_eq!(node_values[2], 0); + /// ``` + fn for_each_node_par_by_partition( + &self, + partition: &[Range], + node_values: &mut [T], + node_fn: F, + ) -> Result<(), Error> + where + T: Send, + F: Fn(&Self, NI, &mut T) + Send + Sync; +} + +pub trait RelabelByDegreeOp { + /// Creates a new graph by relabeling the node ids of the given graph. + /// + /// Ids are relabaled using descending degree-order, i.e., given `n` nodes, + /// the node with the largest degree will become node id `0`, the node with + /// the smallest degree will become node id `n - 1`. + /// + /// Note, that this method creates a new graph with the same space + /// requirements as the input graph. + /// + /// # Example + /// + /// ``` + /// use graph_builder::prelude::*; + /// + /// let mut graph: UndirectedCsrGraph = GraphBuilder::new() + /// .edges(vec![(0, 1), (1, 2), (1, 3), (3, 0)]) + /// .build(); + /// + /// assert_eq!(graph.degree(0), 2); + /// assert_eq!(graph.degree(1), 3); + /// assert_eq!(graph.degree(2), 1); + /// assert_eq!(graph.degree(3), 2); + /// + /// let mut neighbors = graph.neighbors(0); + /// assert_eq!(neighbors.next(), Some(&1)); + /// assert_eq!(neighbors.next(), Some(&3)); + /// assert_eq!(neighbors.next(), None); + /// + /// graph.make_degree_ordered(); + /// + /// assert_eq!(graph.degree(0), 3); + /// assert_eq!(graph.degree(1), 2); + /// assert_eq!(graph.degree(2), 2); + /// assert_eq!(graph.degree(3), 1); + /// + /// assert_eq!(graph.neighbors(0).as_slice(), &[1, 2, 3]); + /// ``` + fn make_degree_ordered(&mut self); +} + +pub trait ToUndirectedOp { + type Undirected; + + /// Creates a new undirected graph from the edges of an existing graph. + /// + /// Note, that this method creates a new graph with the same space + /// requirements as the input graph. + /// + /// # Example + /// + /// ``` + /// use graph_builder::prelude::*; + /// + /// let graph: DirectedCsrGraph = GraphBuilder::new() + /// .edges(vec![(0, 1), (2, 0)]) + /// .build(); + /// + /// assert_eq!(graph.out_degree(0), 1); + /// assert_eq!(graph.out_neighbors(0).as_slice(), &[1]); + /// + /// assert_eq!(graph.in_degree(0), 1); + /// assert_eq!(graph.in_neighbors(0).as_slice(), &[2]); + /// + /// let graph = graph.to_undirected(None); + /// + /// assert_eq!(graph.degree(0), 2); + /// assert_eq!(graph.neighbors(0).as_slice(), &[1, 2]); + /// ``` + /// + /// This method accepts an optional [`CsrLayout`] as second parameter, + /// which has the same effect as described in [`GraphBuilder::csr_layout`] + + /// # Example + /// + /// ``` + /// use graph_builder::prelude::*; + /// + /// let graph: DirectedCsrGraph = GraphBuilder::new() + /// .edges(vec![(0, 2), (1, 0), (2, 0)]) + /// .build(); + /// + /// // No layout specified, a default layput is chosen + /// let un_graph = graph.to_undirected(None); + /// assert_eq!(un_graph.neighbors(0).as_slice(), &[2, 1, 2]); + /// + /// // The `Sorted` layout + /// let un_graph = graph.to_undirected(CsrLayout::Sorted); + /// assert_eq!(un_graph.neighbors(0).as_slice(), &[1, 2, 2]); + /// + /// // The `Deduplicated` layout + /// let un_graph = graph.to_undirected(CsrLayout::Deduplicated); + /// assert_eq!(un_graph.neighbors(0).as_slice(), &[1, 2]); + /// ``` + fn to_undirected(&self, layout: impl Into>) -> Self::Undirected; +} + +pub trait SerializeGraphOp { + fn serialize(&self, write: W) -> Result<(), Error>; +} + +pub trait DeserializeGraphOp { + fn deserialize(read: R) -> Result; +} + +impl RelabelByDegreeOp for G +where + NI: Idx, + EV: Copy + Ord + Sync, + G: Graph + + UndirectedDegrees + + UndirectedNeighborsWithValues + + SwapCsr + + Sync, +{ + fn make_degree_ordered(&mut self) { + relabel_by_degree(self) + } +} + +impl ForEachNodeParallelOp for G +where + NI: Idx, + G: Graph + Sync, +{ + /// For each node calls a given function with the node and its corresponding + /// mutable state in parallel. + /// + /// The parallelization is done by means of a [rayon](https://docs.rs/rayon/) + /// based fork join with a task for each node. + fn for_each_node_par(&self, node_values: &mut [T], node_fn: F) -> Result<(), Error> + where + T: Send, + F: Fn(&Self, NI, &mut T) + Send + Sync, + { + if node_values.len() != self.node_count().index() { + return Err(Error::InvalidNodeValues); + } + + let node_fn = Arc::new(node_fn); + + node_values + .into_par_iter() + .enumerate() + .for_each(|(i, node_state)| node_fn(self, NI::new(i), node_state)); + + Ok(()) + } +} + +impl ForEachNodeParallelByPartitionOp for G +where + NI: Idx, + G: Graph + Sync, +{ + /// For each node calls a given function with the node and its corresponding + /// mutable state in parallel based on the provided node partition. + /// + /// The parallelization is done by means of a [rayon](https://docs.rs/rayon/) + /// based fork join with a task for each range in the provided node partition. + fn for_each_node_par_by_partition( + &self, + partition: &[Range], + node_values: &mut [T], + node_fn: F, + ) -> Result<(), Error> + where + T: Send, + F: Fn(&Self, NI, &mut T) + Send + Sync, + { + if node_values.len() != self.node_count().index() { + return Err(Error::InvalidNodeValues); + } + + if partition.iter().map(|r| r.end - r.start).sum::() != self.node_count() { + return Err(Error::InvalidPartitioning); + } + + let node_fn = Arc::new(node_fn); + + let node_value_splits = split_by_partition(partition, node_values); + + node_value_splits + .into_par_iter() + .zip(partition.into_par_iter()) + .for_each_with(node_fn, |node_fn, (mutable_chunk, range)| { + for (node_state, node) in mutable_chunk.iter_mut().zip(range.start.range(range.end)) + { + node_fn(self, node, node_state); + } + }); + + Ok(()) + } +} + +impl DegreePartitionOp for U +where + NI: Idx, + U: Graph + UndirectedDegrees + UndirectedNeighborsWithValues, +{ + /// Creates a greedy range-based degree partition of the nodes. + /// + /// It is greedy in the sense that it goes through the node set only once + /// and simply adds a new range to the result whenever the current range's + /// nodes' degrees sum up to at least the average node degree. + /// + /// # Example + /// + /// ``` + /// # use graph_builder::prelude::*; + /// # use std::ops::Range; + /// let graph: UndirectedCsrGraph = GraphBuilder::new() + /// .edges(vec![(0, 1), (0, 2), (0, 3), (0, 3)]) + /// .build(); + /// + /// let partition: Vec> = graph.degree_partition(2); + /// + /// assert_eq!(partition.len(), 2); + /// assert_eq!(partition[0], 0..1); + /// assert_eq!(partition[1], 1..4); + /// ``` + fn degree_partition(&self, concurrency: usize) -> Vec> { + let batch_size = ((self.edge_count().index() * 2) as f64 / concurrency as f64).ceil(); + greedy_node_map_partition( + |node| self.degree(node).index(), + self.node_count(), + batch_size as usize, + concurrency, + ) + } +} + +impl OutDegreePartitionOp for D +where + NI: Idx, + D: Graph + DirectedDegrees + DirectedNeighborsWithValues, +{ + /// Creates a greedy range-based out degree partition of the nodes. + /// + /// It is greedy in the sense that it goes through the node set only once + /// and simply adds a new range to the result whenever the current range's + /// nodes' out degrees sum up to at least the average node out degree. + /// + /// # Example + /// + /// ``` + /// # use graph_builder::prelude::*; + /// # use std::ops::Range; + /// let graph: DirectedCsrGraph = GraphBuilder::new() + /// .edges(vec![(0, 1), (0, 2), (2, 1), (2, 3)]) + /// .build(); + /// + /// let partition: Vec> = graph.out_degree_partition(2); + /// + /// assert_eq!(partition.len(), 2); + /// assert_eq!(partition[0], 0..1); + /// assert_eq!(partition[1], 1..4); + /// ``` + fn out_degree_partition(&self, concurrency: usize) -> Vec> { + let batch_size = (self.edge_count().index() as f64 / concurrency as f64).ceil(); + greedy_node_map_partition( + |node| self.out_degree(node).index(), + self.node_count(), + batch_size as usize, + concurrency, + ) + } +} + +impl InDegreePartitionOp for D +where + NI: Idx, + D: Graph + DirectedDegrees + DirectedNeighborsWithValues, +{ + /// Creates a greedy range-based in degree partition of the nodes. + /// + /// It is greedy in the sense that it goes through the node set only once + /// and simply adds a new range to the result whenever the current range's + /// nodes' in degrees sum up to at least the average node in degree. + /// + /// # Example + /// + /// ``` + /// # use graph_builder::prelude::*; + /// # use std::ops::Range; + /// let graph: DirectedCsrGraph = GraphBuilder::new() + /// .edges(vec![(1, 0), (1, 2), (2, 0), (3, 2)]) + /// .build(); + /// + /// let partition: Vec> = graph.in_degree_partition(2); + /// + /// assert_eq!(partition.len(), 2); + /// assert_eq!(partition[0], 0..1); + /// assert_eq!(partition[1], 1..4); + /// ``` + fn in_degree_partition(&self, concurrency: usize) -> Vec> { + let batch_size = (self.edge_count().index() as f64 / concurrency as f64).ceil(); + greedy_node_map_partition( + |node| self.in_degree(node).index(), + self.node_count(), + batch_size as usize, + concurrency, + ) + } +} + +// Split input slice into a vector of partition.len() disjoint slices such that +// the slice at index i in the output vector has the same length as the range at +// index i in the input partition. +fn split_by_partition<'a, NI: Idx, T>( + partition: &[Range], + slice: &'a mut [T], +) -> Vec<&'a mut [T]> { + debug_assert_eq!( + partition + .iter() + .map(|r| r.end - r.start) + .sum::() + .index(), + slice.len() + ); + + let mut splits = Vec::with_capacity(partition.len()); + + let mut remainder = slice; + let mut current_start = NI::zero(); + for range in partition.iter() { + let next_end = range.end - current_start; + current_start += next_end; + + let (left, right) = remainder.split_at_mut(next_end.index()); + + splits.push(left); + remainder = right; + } + + splits +} + +// Partition nodes 0..node_count().index() into at most max_batches ranges such +// that the sums of node_map(node) for each range are roughly equal. It does so +// greedily and therefore does not guarantee an optimally balanced range-based +// partition. +fn greedy_node_map_partition( + node_map: F, + node_count: NI, + batch_size: usize, + max_batches: usize, +) -> Vec> +where + F: Fn(NI) -> usize, + NI: Idx, +{ + let mut partitions = Vec::with_capacity(max_batches); + + let mut partition_size = 0; + let mut partition_start = NI::zero(); + let upper_bound = node_count - NI::new(1); + + for node in NI::zero().range(node_count) { + partition_size += node_map(node); + + if (partitions.len() < max_batches - 1 && partition_size >= batch_size) + || node == upper_bound + { + let partition_end = node + NI::new(1); + partitions.push(partition_start..partition_end); + partition_size = 0; + partition_start = partition_end; + } + } + + partitions +} + +fn relabel_by_degree(graph: &mut G) +where + NI: Idx, + G: Graph + + UndirectedDegrees + + UndirectedNeighborsWithValues + + SwapCsr + + Sync, + EV: Copy + Ord + Sync, +{ + let degree_node_pairs = sort_by_degree_desc(graph); + let (degrees, nodes) = unzip_degrees_and_nodes(degree_node_pairs); + let offsets = prefix_sum(degrees); + let targets = relabel_targets(graph, nodes, &offsets); + + graph.swap_csr(Csr::new( + offsets.into_boxed_slice(), + targets.into_boxed_slice(), + )); +} + +// Extracts (degree, node_id) pairs from the given graph and sorts them by +// degree descending. +fn sort_by_degree_desc(graph: &G) -> Vec<(NI, NI)> +where + NI: Idx, + G: Graph + UndirectedDegrees + UndirectedNeighborsWithValues + Sync, +{ + let node_count = graph.node_count().index(); + let mut degree_node_pairs = Vec::with_capacity(node_count); + + (0..node_count) + .into_par_iter() + .map(NI::new) + .map(|node_id| (graph.degree(node_id), node_id)) + .collect_into_vec(&mut degree_node_pairs); + degree_node_pairs.par_sort_unstable_by(|left, right| left.cmp(right).reverse()); + + degree_node_pairs +} + +// Unzips (degree, node-id) pairs into `degrees` and `nodes` +// +// `degrees` maps a new node id to its degree. +// `nodes` maps the previous node id to the new node id. +fn unzip_degrees_and_nodes(degree_node_pairs: Vec<(NI, NI)>) -> (Vec, Vec) { + let node_count = degree_node_pairs.len(); + let mut degrees = Vec::::with_capacity(node_count); + let mut nodes = Vec::::with_capacity(node_count); + let nodes_ptr = SharedMut::new(nodes.as_mut_ptr()); + + (0..node_count) + .into_par_iter() + .map(|n| { + let (degree, node) = degree_node_pairs[n]; + + // SAFETY: node is the node_id from degree_node_pairs which is + // created from 0..node_count -- the values are all distinct and we + // will not write into the same location in parallel + unsafe { + nodes_ptr.add(node.index()).write(NI::new(n)); + } + + degree + }) + .collect_into_vec(&mut degrees); + + // SAFETY: degree_node_pairs contains each value in 0..node_count once + unsafe { + nodes.set_len(node_count); + } + + (degrees, nodes) +} + +// Relabel target ids according to the given node mapping and offsets. +fn relabel_targets(graph: &G, nodes: Vec, offsets: &[NI]) -> Vec> +where + NI: Idx, + G: Graph + UndirectedNeighborsWithValues + Sync, + EV: Copy + Ord + Sync, +{ + let node_count = graph.node_count().index(); + let edge_count = offsets[node_count].index(); + let mut targets = Vec::>::with_capacity(edge_count); + let targets_ptr = SharedMut::new(targets.as_mut_ptr()); + + (0..node_count).into_par_iter().map(NI::new).for_each(|u| { + let new_u = nodes[u.index()]; + let start_offset = offsets[new_u.index()].index(); + let mut end_offset = start_offset; + + for &v in graph.neighbors_with_values(u) { + let new_v = nodes[v.target.index()]; + // SAFETY: a node u is processed by at most one thread. We write + // into a non-overlapping range defined by the offsets for that + // node. No two threads will write into the same range. + unsafe { + targets_ptr + .add(end_offset) + .write(Target::new(new_v, v.value)); + } + end_offset += 1; + } + + // SAFETY: start_offset..end_offset is a non-overlapping range for + // a node u which is processed by exactly one thread. + unsafe { + std::slice::from_raw_parts_mut(targets_ptr.add(start_offset), end_offset - start_offset) + } + .sort_unstable(); + }); + + // SAFETY: we inserted every relabeled target id of which there are edge_count many. + unsafe { + targets.set_len(edge_count); + } + + targets +} diff --git a/packages/graph-rust/src/graph_builder/index.rs b/packages/graph-rust/src/graph_builder/index.rs new file mode 100644 index 0000000..8f7c7c0 --- /dev/null +++ b/packages/graph-rust/src/graph_builder/index.rs @@ -0,0 +1,103 @@ +use std::fmt::Debug; +use std::iter::Sum; +use std::ops::{Range, RangeInclusive}; +use std::sync::atomic::Ordering; + +use atoi::FromRadix10; +use atomic::Atomic; + +pub trait Idx: + Copy + + std::ops::Add + + std::ops::AddAssign + + std::ops::Sub + + std::ops::Div + + std::ops::Mul + + Ord + + Debug + + Send + + Sum + + Sync + + Sized + + 'static +{ + fn new(idx: usize) -> Self; + + fn zero() -> Self; + + fn index(self) -> usize; + + type RangeIter: Iterator; + + fn range(self, end: Self) -> Self::RangeIter; + + type RangeInclusiveIter: Iterator; + + fn range_inclusive(self, end: Self) -> Self::RangeInclusiveIter; + + fn parse(bytes: &[u8]) -> (Self, usize); + + fn get_and_increment(this: &Atomic, order: Ordering) -> Self { + Self::fetch_add(this, Self::new(1), order) + } + + fn fetch_add(this: &Atomic, val: Self, order: Ordering) -> Self; +} + +macro_rules! impl_idx { + ($TYPE:ty) => { + impl Idx for $TYPE { + #[inline] + fn new(idx: usize) -> Self { + assert!(idx <= <$TYPE>::MAX as usize); + idx as $TYPE + } + + #[inline] + fn zero() -> Self { + 0 + } + + #[inline] + fn index(self) -> usize { + self as usize + } + + type RangeIter = Range; + + #[inline] + fn range(self, end: Self) -> Self::RangeIter { + self..end + } + + type RangeInclusiveIter = RangeInclusive; + + #[inline] + fn range_inclusive(self, end: Self) -> Self::RangeInclusiveIter { + self..=end + } + + #[inline] + fn parse(bytes: &[u8]) -> (Self, usize) { + FromRadix10::from_radix_10(bytes) + } + + #[inline] + fn fetch_add(this: &Atomic<$TYPE>, val: $TYPE, order: Ordering) -> $TYPE { + this.fetch_add(val, order) + } + } + }; +} + +impl_idx!(u8); +impl_idx!(u16); +impl_idx!(u32); +impl_idx!(u64); +impl_idx!(usize); + +impl_idx!(i8); +impl_idx!(i16); +impl_idx!(i32); +impl_idx!(i64); +impl_idx!(isize); \ No newline at end of file diff --git a/packages/graph-rust/src/graph_builder/input/edgelist.rs b/packages/graph-rust/src/graph_builder/input/edgelist.rs new file mode 100644 index 0000000..552d4a7 --- /dev/null +++ b/packages/graph-rust/src/graph_builder/input/edgelist.rs @@ -0,0 +1,258 @@ +use atomic::Atomic; +use std::{convert::TryFrom, fs::File, marker::PhantomData, path::Path, sync::Arc}; + +use parking_lot::Mutex; +use rayon::prelude::*; +use std::sync::atomic::Ordering::AcqRel; + +use crate::prelude::{Idx, Error}; + +use super::{InputCapabilities, InputPath, ParseValue, Direction}; + +/// Reads a graph from a file that contains an edge per line. +/// +/// An edge is represented by a source node id and a target node id. The two +/// node ids must be separated by a 1-byte character (e.g. whitespace or tab). +/// +/// The node count of the resulting graph is the highest node id within the file +/// plus one. The edge count will be twice the number of lines in the file. +/// +/// # Example +/// +/// ```ignore +/// > cat my_graph.edgelist +/// 0 1 +/// 0 2 +/// 1 3 +/// 2 0 +/// ``` +pub struct EdgeListInput { + _idx: PhantomData<(NI, EV)>, +} + +impl Default for EdgeListInput { + fn default() -> Self { + Self { _idx: PhantomData } + } +} + +impl InputCapabilities for EdgeListInput { + type GraphInput = EdgeList; +} + +#[allow(clippy::len_without_is_empty)] +pub trait Edges { + type NI: Idx; + type EV; + + type EdgeIter<'a>: ParallelIterator + where + Self: 'a; + + fn edges(&self) -> Self::EdgeIter<'_>; + + fn max_node_id(&self) -> Self::NI { + default_max_node_id(self) + } + + fn degrees(&self, node_count: Self::NI, direction: Direction) -> Vec> { + let mut degrees = Vec::with_capacity(node_count.index()); + degrees.resize_with(node_count.index(), || Atomic::new(Self::NI::zero())); + + if matches!(direction, Direction::Outgoing | Direction::Undirected) { + self.edges().for_each(|(s, _, _)| { + Self::NI::get_and_increment(°rees[s.index()], AcqRel); + }); + } + + if matches!(direction, Direction::Incoming | Direction::Undirected) { + self.edges().for_each(|(_, t, _)| { + Self::NI::get_and_increment(°rees[t.index()], AcqRel); + }); + } + + degrees + } + + #[cfg(test)] + fn len(&self) -> usize; +} + +fn default_max_node_id(edges: &E) -> E::NI { + edges + .edges() + .into_par_iter() + .map(|(s, t, _)| E::NI::max(s, t)) + .reduce(E::NI::zero, E::NI::max) +} + +#[derive(Debug)] +pub struct EdgeList { + list: Box<[(NI, NI, EV)]>, + max_node_id: Option, +} + +impl EdgeList { + pub fn new(edges: Vec<(NI, NI, EV)>) -> Self { + Self { + list: edges.into_boxed_slice(), + max_node_id: None, + } + } + + pub fn with_max_node_id(edges: Vec<(NI, NI, EV)>, max_node_id: NI) -> Self { + Self { + list: edges.into_boxed_slice(), + max_node_id: Some(max_node_id), + } + } +} + +impl Edges for EdgeList { + type NI = NI; + + type EV = EV; + + type EdgeIter<'a> = rayon::iter::Copied> + where + Self: 'a; + + fn edges(&self) -> Self::EdgeIter<'_> { + self.list.into_par_iter().copied() + } + + #[cfg(test)] + fn len(&self) -> usize { + self.list.len() + } + + fn max_node_id(&self) -> Self::NI { + match self.max_node_id { + Some(id) => id, + None => default_max_node_id(self), + } + } +} + +pub(crate) struct EdgeIterator>(pub I); + +impl From> for EdgeList +where + NI: Idx, + I: IntoIterator, +{ + fn from(iter: EdgeIterator) -> Self { + EdgeList::new(iter.0.into_iter().map(|(s, t)| (s, t, ())).collect()) + } +} + +pub(crate) struct EdgeWithValueIterator>(pub I); + +impl From> for EdgeList +where + NI: Idx, + EV: Sync, + I: IntoIterator, +{ + fn from(iter: EdgeWithValueIterator) -> Self { + EdgeList::new(iter.0.into_iter().map(|(s, t, v)| (s, t, v)).collect()) + } +} + +impl TryFrom> for EdgeList +where + P: AsRef, + NI: Idx, + EV: ParseValue + std::fmt::Debug + Send + Sync, +{ + type Error = Error; + + fn try_from(path: InputPath

) -> Result { + let file = File::open(path.0.as_ref())?; + let mmap = unsafe { memmap2::MmapOptions::new().populate().map(&file)? }; + EdgeList::try_from(mmap.as_ref()) + } +} + +impl TryFrom<&[u8]> for EdgeList +where + NI: Idx, + EV: ParseValue + std::fmt::Debug + Send + Sync, +{ + type Error = Error; + + fn try_from(bytes: &[u8]) -> Result { + let page_size = page_size::get(); + let cpu_count = num_cpus::get_physical(); + let chunk_size = + (usize::max(1, bytes.len() / cpu_count) + (page_size - 1)) & !(page_size - 1); + + let all_edges = Arc::new(Mutex::new(Vec::new())); + + let new_line_bytes = new_line_bytes(bytes); + + rayon::scope(|s| { + for start in (0..bytes.len()).step_by(chunk_size) { + let all_edges = Arc::clone(&all_edges); + s.spawn(move |_| { + let mut end = usize::min(start + chunk_size, bytes.len()); + while end <= bytes.len() && bytes[end - 1] != b'\n' { + end += 1; + } + + let mut start = start; + if start != 0 { + while bytes[start - 1] != b'\n' { + start += 1; + } + } + + let mut edges = Vec::new(); + let mut chunk = &bytes[start..end]; + while !chunk.is_empty() { + let (source, source_bytes) = NI::parse(chunk); + chunk = &chunk[source_bytes + 1..]; + + let (target, target_bytes) = NI::parse(chunk); + chunk = &chunk[target_bytes..]; + + let value = match chunk.strip_prefix(b" ") { + Some(value_chunk) => { + let (value, value_bytes) = EV::parse(value_chunk); + chunk = &value_chunk[value_bytes + new_line_bytes..]; + value + } + None => { + chunk = &chunk[new_line_bytes..]; + // if the input does not have a value, the default for EV is used + EV::parse(&[]).0 + } + }; + + edges.push((source, target, value)); + } + + let mut all_edges = all_edges.lock(); + all_edges.append(&mut edges); + }); + } + }); + + let edges = Arc::try_unwrap(all_edges).unwrap().into_inner(); + + Ok(EdgeList::new(edges)) + } +} + +// Returns the OS-dependent number of bytes for newline: +// +// `1` for Linux/macOS style (b'\n') +// '2' for Windows style (b'\r\n') +fn new_line_bytes(bytes: &[u8]) -> usize { + 1 + bytes + .iter() + .position(|b| *b == b'\n') + .and_then(|idx| idx.checked_sub(1)) + .and_then(|idx| bytes.get(idx).copied()) + .map_or(0, |b| (b == b'\r') as usize) +} diff --git a/packages/graph-rust/src/graph_builder/input/mod.rs b/packages/graph-rust/src/graph_builder/input/mod.rs new file mode 100644 index 0000000..77ea902 --- /dev/null +++ b/packages/graph-rust/src/graph_builder/input/mod.rs @@ -0,0 +1,93 @@ +pub mod edgelist; + + +pub use edgelist::EdgeList; +pub use edgelist::EdgeListInput; +pub use edgelist::Edges; + +use super::index::Idx; + +pub struct InputPath

(pub(crate) P); + +pub trait InputCapabilities { + type GraphInput; +} + +#[derive(Debug, Clone, Copy)] +pub enum Direction { + Outgoing, + Incoming, + Undirected, +} + +/// Used by input formats to read node or edge values from bytes. +pub trait ParseValue: Default + Sized { + /// Parses a value from a slice. + /// + /// # Example + /// + /// ``` + /// use graph_builder::input::ParseValue; + /// + /// let bytes = "13.37".as_bytes(); + /// + /// let (number, len) = f32::parse(bytes); + /// + /// assert_eq!(number, 13.37); + /// assert_eq!(len, 5); + /// ``` + /// + /// # Return + /// + /// Returns a tuple containing two entries. The first is the parsed value, + /// the second is the index of the byte right after the parsed value. + fn parse(bytes: &[u8]) -> (Self, usize); +} + +impl ParseValue for () { + fn parse(_bytes: &[u8]) -> (Self, usize) { + ((), 0) + } +} + +macro_rules! impl_parse_value { + ($atoi:path, $($ty:ty),+ $(,)?) => { + $( + impl $crate::graph_builder::input::ParseValue for $ty { + fn parse(bytes: &[u8]) -> (Self, usize) { + if bytes.len() == 0 { + (<$ty as ::std::default::Default>::default(), 0) + } else { + $atoi(bytes) + } + } + } + )+ + }; +} + +impl_parse_value!( + ::atoi::FromRadix10::from_radix_10, + u8, + u16, + u32, + u64, + u128, + usize, +); + +impl_parse_value!( + ::atoi::FromRadix10Signed::from_radix_10_signed, + i8, + i16, + i32, + i64, + i128, + isize, +); + +impl_parse_value!(parse_float, f32, f64); + +fn parse_float(bytes: &[u8]) -> (T, usize) { + fast_float::parse_partial(bytes).unwrap() +} \ No newline at end of file diff --git a/packages/graph-rust/src/graph_builder/mod.rs b/packages/graph-rust/src/graph_builder/mod.rs new file mode 100644 index 0000000..62aeab7 --- /dev/null +++ b/packages/graph-rust/src/graph_builder/mod.rs @@ -0,0 +1,171 @@ + + +pub mod builder; +mod compat; +pub mod graph; +pub mod graph_ops; +pub mod index; +pub mod input; +pub mod prelude; + +pub use self::builder::GraphBuilder; +pub use self::graph::csr::CsrLayout; +pub use self::graph::csr::DirectedCsrGraph; +pub use self::graph::csr::UndirectedCsrGraph; + +use std::convert::Infallible; + +use self::graph::csr::Target; +use thiserror::Error; + +use self::index::Idx; + +#[derive(Error, Debug)] +pub enum Error { + #[error("error while loading graph")] + IoError { + #[from] + source: std::io::Error, + }, + #[error("incompatible index type")] + IdxError { + #[from] + source: std::num::TryFromIntError, + }, + #[error("invalid partitioning")] + InvalidPartitioning, + #[error("number of node values must be the same as node count")] + InvalidNodeValues, + #[error("invalid id size, expected {expected:?} bytes, got {actual:?} bytes")] + InvalidIdType { expected: String, actual: String }, +} + +impl From for Error { + fn from(_: Infallible) -> Self { + unreachable!() + } +} + +/// A graph is a tuple `(N, E)`, where `N` is a set of nodes and `E` a set of +/// edges. Each edge connects exactly two nodes. +/// +/// `Graph` is parameterized over the node index type `Node` which is used to +/// uniquely identify a node. An edge is a tuple of node identifiers. +pub trait Graph { + /// Returns the number of nodes in the graph. + fn node_count(&self) -> NI; + + /// Returns the number of edges in the graph. + fn edge_count(&self) -> NI; +} + +/// A graph that allows storing a value per node. +pub trait NodeValues { + fn node_value(&self, node: NI) -> &NV; +} + +pub trait UndirectedDegrees { + /// Returns the number of edges connected to the given node. + fn degree(&self, node: NI) -> NI; +} + +/// Returns the neighbors of a given node. +/// +/// The edge `(42, 1337)` is equivalent to the edge `(1337, 42)`. +pub trait UndirectedNeighbors { + type NeighborsIterator<'a>: Iterator + where + Self: 'a; + + /// Returns an iterator of all nodes connected to the given node. + fn neighbors(&self, node: NI) -> Self::NeighborsIterator<'_>; +} + +/// Returns the neighbors of a given node. +/// +/// The edge `(42, 1337)` is equivalent to the edge `(1337, 42)`. +pub trait UndirectedNeighborsWithValues { + type NeighborsIterator<'a>: Iterator> + where + Self: 'a, + EV: 'a; + + /// Returns an iterator of all nodes connected to the given node + /// including the value of the connecting edge. + fn neighbors_with_values(&self, node: NI) -> Self::NeighborsIterator<'_>; +} + +pub trait DirectedDegrees { + /// Returns the number of edges where the given node is a source node. + fn out_degree(&self, node: NI) -> NI; + + /// Returns the number of edges where the given node is a target node. + fn in_degree(&self, node: NI) -> NI; +} + +/// Returns the neighbors of a given node either in outgoing or incoming direction. +/// +/// An edge tuple `e = (u, v)` has a source node `u` and a target node `v`. From +/// the perspective of `u`, the edge `e` is an **outgoing** edge. From the +/// perspective of node `v`, the edge `e` is an **incoming** edge. The edges +/// `(u, v)` and `(v, u)` are not considered equivalent. +pub trait DirectedNeighbors { + type NeighborsIterator<'a>: Iterator + where + Self: 'a; + + /// Returns an iterator of all nodes which are connected in outgoing direction + /// to the given node, i.e., the given node is the source node of the + /// connecting edge. + fn out_neighbors(&self, node: NI) -> Self::NeighborsIterator<'_>; + + /// Returns an iterator of all nodes which are connected in incoming direction + /// to the given node, i.e., the given node is the target node of the + /// connecting edge. + fn in_neighbors(&self, node: NI) -> Self::NeighborsIterator<'_>; +} + +/// Returns the neighbors of a given node either in outgoing or incoming direction. +/// +/// An edge tuple `e = (u, v)` has a source node `u` and a target node `v`. From +/// the perspective of `u`, the edge `e` is an **outgoing** edge. From the +/// perspective of node `v`, the edge `e` is an **incoming** edge. The edges +/// `(u, v)` and `(v, u)` are not considered equivale +pub trait DirectedNeighborsWithValues { + type NeighborsIterator<'a>: Iterator> + where + Self: 'a, + EV: 'a; + + /// Returns an iterator of all nodes which are connected in outgoing direction + /// to the given node, i.e., the given node is the source node of the + /// connecting edge. For each connected node, the value of the connecting + /// edge is also returned. + fn out_neighbors_with_values(&self, node: NI) -> Self::NeighborsIterator<'_>; + + /// Returns an iterator of all nodes which are connected in incoming direction + /// to the given node, i.e., the given node is the target node of the + /// connecting edge. For each connected node, the value of the connecting + /// edge is also returned. + fn in_neighbors_with_values(&self, node: NI) -> Self::NeighborsIterator<'_>; +} + +#[repr(transparent)] +pub struct SharedMut(*mut T); +unsafe impl Send for SharedMut {} +unsafe impl Sync for SharedMut {} + +impl SharedMut { + pub fn new(ptr: *mut T) -> Self { + SharedMut(ptr) + } + + delegate::delegate! { + to self.0 { + /// # Safety + /// + /// Ensure that `count` does not exceed the capacity of the Vec. + pub unsafe fn add(&self, count: usize) -> *mut T; + } + } +} \ No newline at end of file diff --git a/packages/graph-rust/src/graph_builder/prelude.rs b/packages/graph-rust/src/graph_builder/prelude.rs new file mode 100644 index 0000000..a6a225c --- /dev/null +++ b/packages/graph-rust/src/graph_builder/prelude.rs @@ -0,0 +1,32 @@ +pub use super::builder::GraphBuilder; + +pub use super::graph::csr::CsrLayout; +pub use super::graph::csr::DirectedCsrGraph; +pub use super::graph::csr::Target; +pub use super::graph::csr::UndirectedCsrGraph; + +pub use super::graph_ops::DegreePartitionOp; +pub use super::graph_ops::DeserializeGraphOp; +pub use super::graph_ops::ForEachNodeParallelByPartitionOp; +pub use super::graph_ops::ForEachNodeParallelOp; +pub use super::graph_ops::InDegreePartitionOp; +pub use super::graph_ops::OutDegreePartitionOp; +pub use super::graph_ops::RelabelByDegreeOp; +pub use super::graph_ops::SerializeGraphOp; +pub use super::graph_ops::ToUndirectedOp; + +pub use super::index::Idx; +pub use atomic::Atomic; + +pub use super::input::*; + +pub use super::DirectedDegrees; +pub use super::DirectedNeighbors; +pub use super::DirectedNeighborsWithValues; +pub use super::Graph; +pub use super::NodeValues; +pub use super::UndirectedDegrees; +pub use super::UndirectedNeighbors; +pub use super::UndirectedNeighborsWithValues; + +pub use super::Error; \ No newline at end of file diff --git a/packages/graph-rust/src/lib.rs b/packages/graph-rust/src/lib.rs index 63d2d12..e18da0b 100644 --- a/packages/graph-rust/src/lib.rs +++ b/packages/graph-rust/src/lib.rs @@ -2,5 +2,6 @@ pub mod page_rank; pub mod prelude; pub mod sssp; pub mod utils; +pub mod graph_builder; const DEFAULT_PARALLELISM: usize = 4; diff --git a/packages/graph-rust/src/page_rank.rs b/packages/graph-rust/src/page_rank.rs index dde9605..735ffdd 100644 --- a/packages/graph-rust/src/page_rank.rs +++ b/packages/graph-rust/src/page_rank.rs @@ -1,11 +1,10 @@ -use crate::{prelude::*, DEFAULT_PARALLELISM}; +use super::graph_builder::{prelude::*, SharedMut}; +use crate::DEFAULT_PARALLELISM; use atomic_float::AtomicF64; -use graph_builder::SharedMut; use rayon::prelude::*; use std::sync::atomic::Ordering; -use std::thread::available_parallelism; const CHUNK_SIZE: usize = 16384; @@ -36,7 +35,7 @@ impl Default for PageRankConfig { } impl PageRankConfig { - pub const DEFAULT_MAX_ITERATIONS: usize = 20; + pub const DEFAULT_MAX_ITERATIONS: usize = 1000; pub const DEFAULT_TOLERANCE: f64 = 1E-4; pub const DEFAULT_DAMPING_FACTOR: f32 = 0.85; @@ -110,11 +109,11 @@ where let next_chunk = Atomic::new(NI::zero()); let total_error = AtomicF64::new(0_f64); - std::thread::scope(|s| { - let num_threads = available_parallelism().map_or(DEFAULT_PARALLELISM, |p| p.get()); + rayon::scope(|s| { + let num_threads = DEFAULT_PARALLELISM; for _ in 0..num_threads { - s.spawn(|| { + s.spawn(|_| { let mut error = 0_f64; loop { @@ -152,33 +151,3 @@ where total_error.load(Ordering::SeqCst) } - -#[cfg(test)] -mod tests { - use super::*; - use crate::prelude::{CsrLayout, GraphBuilder}; - - #[test] - fn test_pr_two_components() { - let gdl = "(a)-->()-->()<--(a),(b)-->()-->()<--(b)"; - - let graph: DirectedCsrGraph = GraphBuilder::new() - .csr_layout(CsrLayout::Sorted) - .gdl_str::(gdl) - .build() - .unwrap(); - - let (scores, _, _) = page_rank(&graph, PageRankConfig::default()); - - let expected: Vec = vec![ - 0.024999997, - 0.035624996, - 0.06590624, - 0.024999997, - 0.035624996, - 0.06590624, - ]; - - assert_eq!(scores, expected); - } -} diff --git a/packages/graph-rust/src/prelude.rs b/packages/graph-rust/src/prelude.rs index 836519f..541de1d 100644 --- a/packages/graph-rust/src/prelude.rs +++ b/packages/graph-rust/src/prelude.rs @@ -2,4 +2,4 @@ pub use crate::page_rank::*; pub use crate::sssp::*; pub use crate::utils::*; -pub use graph_builder::prelude::*; +pub use super::graph_builder::prelude::*; diff --git a/packages/graph-rust/src/sssp.rs b/packages/graph-rust/src/sssp.rs index 29add5c..ea95035 100644 --- a/packages/graph-rust/src/sssp.rs +++ b/packages/graph-rust/src/sssp.rs @@ -262,42 +262,3 @@ where self.bins[bin].push(val); } } - -#[cfg(test)] -mod tests { - use super::*; - use crate::prelude::{CsrLayout, GraphBuilder}; - - #[test] - fn test_sssp() { - let gdl = "(a:A) - (b:B) - (c:C) - (d:D) - (e:E) - (f:F) - (a)-[{cost: 4.0 }]->(b) - (a)-[{cost: 2.0 }]->(c) - (b)-[{cost: 5.0 }]->(c) - (b)-[{cost: 10.0 }]->(d) - (c)-[{cost: 3.0 }]->(e) - (d)-[{cost: 11.0 }]->(f) - (e)-[{cost: 4.0 }]->(d)"; - - let graph: DirectedCsrGraph = GraphBuilder::new() - .csr_layout(CsrLayout::Deduplicated) - .gdl_str::(gdl) - .build() - .unwrap(); - - let config = DeltaSteppingConfig::new(0, 3.0); - - let actual: Vec = delta_stepping(&graph, config) - .into_iter() - .map(|d| d.load(Ordering::Relaxed)) - .collect(); - let expected: Vec = vec![0.0, 4.0, 2.0, 9.0, 5.0, 20.0]; - - assert_eq!(actual, expected); - } -} diff --git a/packages/graph-wasm/Cargo.lock b/packages/graph-wasm/Cargo.lock index d27fd0a..b3a6368 100644 --- a/packages/graph-wasm/Cargo.lock +++ b/packages/graph-wasm/Cargo.lock @@ -6,10 +6,25 @@ version = 3 name = "antv-graph" version = "0.0.1" dependencies = [ + "atoi", + "atomic", "atomic_float", - "graph_builder", + "byte-slice-cast", + "dashmap", + "delegate", + "fast-float", + "fxhash", + "linereader", + "log", + "memmap2", + "num", + "num-format", + "num_cpus", + "page_size", + "parking_lot", "rayon", "serde", + "thiserror", ] [[package]] @@ -30,9 +45,9 @@ dependencies = [ [[package]] name = "arrayvec" -version = "0.7.2" +version = "0.7.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8da52d66c7071e2e3fa2a1e5c6d088fec47b593032b254f5e980de8ea54454d6" +checksum = "96d30a06541fbafbc7f82ed10c06164cfbd2c401138f6addd8404629c4b16711" [[package]] name = "atoi" @@ -208,31 +223,6 @@ dependencies = [ "wasm-bindgen", ] -[[package]] -name = "graph_builder" -version = "0.3.1" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3bed82dbbf80a458a59ee9fa11b03e194e1429b36d94da2ac59356b44eb926d7" -dependencies = [ - "atoi", - "atomic", - "byte-slice-cast", - "dashmap", - "delegate", - "fast-float", - "fxhash", - "linereader", - "log", - "memmap2", - "num", - "num-format", - "num_cpus", - "page_size", - "parking_lot", - "rayon", - "thiserror", -] - [[package]] name = "hashbrown" version = "0.12.3" @@ -280,9 +270,9 @@ dependencies = [ [[package]] name = "lock_api" -version = "0.4.9" +version = "0.4.10" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "435011366fe56583b16cf956f9df0095b405b82d76425bc8981c0e22e60ec4df" +checksum = "c1cc9717a20b1bb222f333e6a92fd32f7d8a18ddc5a3191a11af45dcbf4dcd16" dependencies = [ "autocfg", "scopeguard", @@ -448,31 +438,31 @@ dependencies = [ [[package]] name = "parking_lot_core" -version = "0.9.7" +version = "0.9.8" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9069cbb9f99e3a5083476ccb29ceb1de18b9118cafa53e90c9551235de2b9521" +checksum = "93f00c865fe7cabf650081affecd3871070f26767e7b2070a3ffae14c654b447" dependencies = [ "cfg-if 1.0.0", "libc", "redox_syscall", "smallvec", - "windows-sys", + "windows-targets", ] [[package]] name = "proc-macro2" -version = "1.0.59" +version = "1.0.64" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6aeca18b86b413c660b781aa319e4e2648a3e6f9eadc9b47e9038e6fe9f3451b" +checksum = "78803b62cbf1f46fde80d7c0e803111524b9877184cfe7c3033659490ac7a7da" dependencies = [ "unicode-ident", ] [[package]] name = "quote" -version = "1.0.28" +version = "1.0.29" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1b9ab9c7eadfd8df19006f1cf1a4aed13540ed5cbc047010ece5826e10825488" +checksum = "573015e8ab27661678357f27dc26460738fd2b6c86e46f386fde94cb5d913105" dependencies = [ "proc-macro2", ] @@ -501,9 +491,9 @@ dependencies = [ [[package]] name = "redox_syscall" -version = "0.2.16" +version = "0.3.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "fb5a58c1855b4b6819d59012155603f0b22ad30cad752600aadfcb695265519a" +checksum = "567664f262709473930a4bf9e51bf2ebf3348f2e748ccc50dea20646858f8f29" dependencies = [ "bitflags", ] @@ -548,7 +538,7 @@ checksum = "8c805777e3930c8883389c602315a24224bcc738b63905ef87cd1420353ea93e" dependencies = [ "proc-macro2", "quote", - "syn 2.0.18", + "syn 2.0.25", ] [[package]] @@ -564,9 +554,9 @@ dependencies = [ [[package]] name = "smallvec" -version = "1.10.0" +version = "1.11.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a507befe795404456341dfab10cef66ead4c041f62b8b11bbb92bffe5d0953e0" +checksum = "62bb4feee49fdd9f707ef802e22365a35de4b7b299de4763d44bfea899442ff9" [[package]] name = "spmc" @@ -587,9 +577,9 @@ dependencies = [ [[package]] name = "syn" -version = "2.0.18" +version = "2.0.25" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "32d41677bcbe24c20c52e7c70b0d8db04134c5d1066bf98662e2871ad200ea3e" +checksum = "15e3fc8c0c74267e2df136e5e5fb656a464158aa57624053375eb9c8c6e25ae2" dependencies = [ "proc-macro2", "quote", @@ -598,22 +588,22 @@ dependencies = [ [[package]] name = "thiserror" -version = "1.0.40" +version = "1.0.43" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "978c9a314bd8dc99be594bc3c175faaa9794be04a5a5e153caba6915336cebac" +checksum = "a35fc5b8971143ca348fa6df4f024d4d55264f3468c71ad1c2f365b0a4d58c42" dependencies = [ "thiserror-impl", ] [[package]] name = "thiserror-impl" -version = "1.0.40" +version = "1.0.43" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f9456a42c5b0d803c8cd86e73dd7cc9edd429499f37a3550d286d5e86720569f" +checksum = "463fe12d7993d3b327787537ce8dd4dfa058de32fc2b195ef3cde03dc4771e8f" dependencies = [ "proc-macro2", "quote", - "syn 2.0.18", + "syn 2.0.25", ] [[package]] @@ -651,7 +641,7 @@ dependencies = [ "once_cell", "proc-macro2", "quote", - "syn 2.0.18", + "syn 2.0.25", "wasm-bindgen-shared", ] @@ -673,7 +663,7 @@ checksum = "e128beba882dd1eb6200e1dc92ae6c5dbaa4311aa7bb211ca035779e5efc39f8" dependencies = [ "proc-macro2", "quote", - "syn 2.0.18", + "syn 2.0.25", "wasm-bindgen-backend", "wasm-bindgen-shared", ] @@ -730,20 +720,11 @@ version = "0.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f" -[[package]] -name = "windows-sys" -version = "0.45.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "75283be5efb2831d37ea142365f009c02ec203cd29a3ebecbc093d52315b66d0" -dependencies = [ - "windows-targets", -] - [[package]] name = "windows-targets" -version = "0.42.2" +version = "0.48.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8e5180c00cd44c9b1c88adb3693291f1cd93605ded80c250a75d472756b4d071" +checksum = "05d4b17490f70499f20b9e791dcf6a299785ce8af4d709018206dc5b4953e95f" dependencies = [ "windows_aarch64_gnullvm", "windows_aarch64_msvc", @@ -756,42 +737,42 @@ dependencies = [ [[package]] name = "windows_aarch64_gnullvm" -version = "0.42.2" +version = "0.48.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "597a5118570b68bc08d8d59125332c54f1ba9d9adeedeef5b99b02ba2b0698f8" +checksum = "91ae572e1b79dba883e0d315474df7305d12f569b400fcf90581b06062f7e1bc" [[package]] name = "windows_aarch64_msvc" -version = "0.42.2" +version = "0.48.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e08e8864a60f06ef0d0ff4ba04124db8b0fb3be5776a5cd47641e942e58c4d43" +checksum = "b2ef27e0d7bdfcfc7b868b317c1d32c641a6fe4629c171b8928c7b08d98d7cf3" [[package]] name = "windows_i686_gnu" -version = "0.42.2" +version = "0.48.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c61d927d8da41da96a81f029489353e68739737d3beca43145c8afec9a31a84f" +checksum = "622a1962a7db830d6fd0a69683c80a18fda201879f0f447f065a3b7467daa241" [[package]] name = "windows_i686_msvc" -version = "0.42.2" +version = "0.48.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "44d840b6ec649f480a41c8d80f9c65108b92d89345dd94027bfe06ac444d1060" +checksum = "4542c6e364ce21bf45d69fdd2a8e455fa38d316158cfd43b3ac1c5b1b19f8e00" [[package]] name = "windows_x86_64_gnu" -version = "0.42.2" +version = "0.48.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8de912b8b8feb55c064867cf047dda097f92d51efad5b491dfb98f6bbb70cb36" +checksum = "ca2b8a661f7628cbd23440e50b05d705db3686f894fc9580820623656af974b1" [[package]] name = "windows_x86_64_gnullvm" -version = "0.42.2" +version = "0.48.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "26d41b46a36d453748aedef1486d5c7a85db22e56aff34643984ea85514e94a3" +checksum = "7896dbc1f41e08872e9d5e8f8baa8fdd2677f29468c4e156210174edc7f7b953" [[package]] name = "windows_x86_64_msvc" -version = "0.42.2" +version = "0.48.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9aec5da331524158c6d1a4ac0ab1541149c0b9505fde06423b02f5ef0106b9f0" +checksum = "1a515f5799fe4961cb532f983ce2b23082366b898e52ffbce459c86f67c8378a" diff --git a/packages/graph-wasm/README.md b/packages/graph-wasm/README.md index 43694a9..0d90557 100644 --- a/packages/graph-wasm/README.md +++ b/packages/graph-wasm/README.md @@ -5,6 +5,8 @@ A WASM binding of `@antv/graph-rust`. We used [wasm-bindgen-rayon](https://githu - [Use with Webpack](#webpack) - [Use with Vite](#vite) +![pagerank](https://mdn.alipayobjects.com/huamei_qa8qxu/afts/img/A*klB7TKFwbskAAAAAAAAAAAAADmJ7AQ/original) + ## Usage Since [cross origin workers are blocked](https://stackoverflow.com/questions/58098143/why-are-cross-origin-workers-blocked-and-why-is-the-workaround-ok/60015898#60015898), we do not recommand the UMD way of using it for now. You can opt to ESM usage with bundler such as [Webpack](#webpack) or [Vite](#vite). @@ -90,9 +92,9 @@ If you can't control the server, try this hacky workaround which implemented wit ### PageRank -* `tolerance` Set the tolerance the approximation, this parameter should be a small magnitude value. The lower the tolerance the better the approximation. +* `tolerance` Set the tolerance the approximation, this parameter should be a small magnitude value. The lower the tolerance the better the approximation. The default value is 0.0001. * `alpha` The damping factor alpha represents the probability to follow an outgoing edge, standard value is 0.85. -* `maxIterations` Set the maximum number of iterations. +* `maxIterations` Set the maximum number of iterations. The default value is 1000. ### SSSP diff --git a/packages/graph-wasm/package.json b/packages/graph-wasm/package.json index 9ff17cd..383fcee 100644 --- a/packages/graph-wasm/package.json +++ b/packages/graph-wasm/package.json @@ -38,14 +38,5 @@ "comlink": "^4.3.1", "wasm-feature-detect": "^1.2.10", "tslib": "^2.5.0" - }, - "devDependencies": { - "cross-env": "^7.0.3", - "npm-run-all": "^4.1.5", - "rimraf": "^3.0.2", - "ts-loader": "^7.0.3", - "typescript": "^4.0.3", - "webpack": "^5.38.1", - "webpack-cli": "^5.0.2" } } diff --git a/packages/graph-wasm/rust-src/lib.rs b/packages/graph-wasm/rust-src/lib.rs index 722725d..62d7ca1 100644 --- a/packages/graph-wasm/rust-src/lib.rs +++ b/packages/graph-wasm/rust-src/lib.rs @@ -2,6 +2,7 @@ use std::sync::atomic::Ordering; use antv_graph::prelude::*; use js_sys::Array; use wasm_bindgen::prelude::*; +use serde::{Deserialize, Serialize}; #[cfg(feature = "parallel")] pub use wasm_bindgen_rayon::init_thread_pool; @@ -15,45 +16,23 @@ pub fn start() { console_error_panic_hook::set_once(); } -#[wasm_bindgen(js_name = "sssp")] -pub fn sssp(val: JsValue) -> Array { - let graph: DirectedCsrGraph = GraphBuilder::new().edges_with_values(vec![]).build(); - let config = DeltaSteppingConfig::new(0, 3.0); - let result: Vec = antv_graph::prelude::delta_stepping(&graph, config).into_iter() - .map(|d| d.load(Ordering::Relaxed)) - .collect(); - result.into_iter().map(JsValue::from).collect() +#[derive(Serialize, Deserialize)] +pub struct PageRankParams { + pub max_iterations: usize, + pub tolerance: f64, + pub damping_factor: f32, + pub edgelist: Vec<(usize, usize)>, } #[wasm_bindgen(js_name = "pageRank")] pub fn page_rank(val: JsValue) -> Array { - let options: PageRankConfig = serde_wasm_bindgen::from_value(val).unwrap(); + let options: PageRankParams = serde_wasm_bindgen::from_value(val).unwrap(); let graph: DirectedCsrGraph = GraphBuilder::new() - .edges(vec![ - (1, 2), // B->C - (2, 1), // C->B - (4, 0), // D->A - (4, 1), // D->B - (5, 4), // E->D - (5, 1), // E->B - (5, 6), // E->F - (6, 1), // F->B - (6, 5), // F->E - (7, 1), // G->B - (7, 5), // F->E - (8, 1), // G->B - (8, 5), // G->E - (9, 1), // H->B - (9, 5), // H->E - (10, 1), // I->B - (10, 5), // I->E - (11, 5), // J->B - (12, 5), // K->B - ]) + .edges(options.edgelist) .build(); - let (ranks, iterations, _) = antv_graph::prelude::page_rank( + let (ranks, _, _) = antv_graph::prelude::page_rank( &graph, PageRankConfig::new( options.max_iterations, @@ -65,3 +44,22 @@ pub fn page_rank(val: JsValue) -> Array { // @see https://stackoverflow.com/a/58996628 ranks.into_iter().map(JsValue::from).collect() } + +#[derive(Serialize, Deserialize)] +pub struct SSSPParams { + pub start_node: usize, + pub delta: f32, + pub edgelist: Vec<(usize, usize, f32)>, +} + +#[wasm_bindgen(js_name = "sssp")] +pub fn sssp(val: JsValue) -> Array { + let options: SSSPParams = serde_wasm_bindgen::from_value(val).unwrap(); + + let graph: DirectedCsrGraph = GraphBuilder::new().edges_with_values(options.edgelist).build(); + let config = DeltaSteppingConfig::new(options.start_node, options.delta); + let result: Vec = antv_graph::prelude::delta_stepping(&graph, config).into_iter() + .map(|d| d.load(Ordering::Relaxed)) + .collect(); + result.into_iter().map(JsValue::from).collect() +} diff --git a/packages/graph-wasm/src/interface.ts b/packages/graph-wasm/src/interface.ts index 6ce1c7c..960ce97 100644 --- a/packages/graph-wasm/src/interface.ts +++ b/packages/graph-wasm/src/interface.ts @@ -1,3 +1,23 @@ +export interface PageRankParams { + maxIterations?: number; + alpha?: number; + tolerance?: number; + /** + * [source, target] + */ + edgelist: [number, number][]; +} + +export interface SSSPParams { + startNode?: number; + delta?: number; + /** + * [source, target, weight] + */ + edgelist: [number, number, number][]; +} + export interface Threads { - page_rank: (options: any) => Promise<{ ranks: number[] }>; + pageRank: (options: PageRankParams) => Promise; + sssp: (options: SSSPParams) => Promise<{ ranks: number[] }>; } diff --git a/packages/graph-wasm/src/wasm-worker.js b/packages/graph-wasm/src/wasm-worker.js index 3103352..fc3e785 100644 --- a/packages/graph-wasm/src/wasm-worker.js +++ b/packages/graph-wasm/src/wasm-worker.js @@ -1,29 +1,39 @@ import * as Comlink from 'comlink'; -const DEFAULT_PAGE_RANK_OPTIONS = { - max_iterations: 10, - tolerance: 0.0001, - damping_factor: 0.85, +const wrapTransferPageRank = pageRank => { + return options => { + const params = { + max_iterations: options.maxIterations || 1000, + tolerance: options.tolerance || 0.0001, + damping_factor: options.alpha || 0.85, + edgelist: options.edgelist + }; + + const ranks = pageRank(params); + + return Comlink.transfer(ranks, []); + }; }; -const wrapTransfer = page_rank => { +const wrapTransferSSSP = sssp => { return options => { - const ranks = page_rank({ - ...DEFAULT_PAGE_RANK_OPTIONS, - ...options, - }); - - return { - // Little perf boost to transfer data to the main thread w/o copying. - ranks: Comlink.transfer(ranks, [ranks]), + const params = { + start_node: options.startNode || 0, + delta: options.delta || 3, + edgelist: options.edgelist }; + + const ranks = sssp(params); + + return Comlink.transfer(ranks, []); }; }; // Wrap wasm-bindgen exports (the `generate` function) to add time measurement. -function wrapExports({ page_rank }) { +function wrapExports({ pageRank, sssp }) { return { - pageRank: wrapTransfer(page_rank), + pageRank: wrapTransferPageRank(pageRank), + sssp: wrapTransferSSSP(sssp), }; } diff --git a/packages/graph-wasm/tsconfig.json b/packages/graph-wasm/tsconfig.json index 02c8ba0..6663048 100644 --- a/packages/graph-wasm/tsconfig.json +++ b/packages/graph-wasm/tsconfig.json @@ -1,4 +1,5 @@ { + "extends": "../../tsconfig.json", "compilerOptions": { "rootDir": "./src", "composite": true, diff --git a/packages/graph/package.json b/packages/graph/package.json index b9096a6..ea5fecb 100644 --- a/packages/graph/package.json +++ b/packages/graph/package.json @@ -42,12 +42,7 @@ "@babel/core": "^7.7.7", "@babel/plugin-proposal-class-properties": "^7.1.0", "@types/d3-force": "^3.0.4", - "babel-loader": "^8.0.6", - "ts-loader": "^7.0.3", - "typescript": "^4.0.3", - "webpack": "^5.38.1", - "webpack-cli": "^5.0.2", - "worker-loader": "^3.0.7" + "babel-loader": "^8.0.6" }, "dependencies": { "@antv/util": "^2.0.13", diff --git a/packages/graph/src/pageRank.ts b/packages/graph/src/pageRank.ts index d18d38f..f2e63db 100644 --- a/packages/graph/src/pageRank.ts +++ b/packages/graph/src/pageRank.ts @@ -1,31 +1,37 @@ import { ID } from "@antv/graphlib"; import { Graph } from "./types"; +interface Params { + alpha: number; + maxIterations: number; + tolerance: number; +} + /** * PageRank https://en.wikipedia.org/wiki/PageRank * refer: https://github.com/anvaka/ngraph.pagerank * @param graph - * @param tolerance - * @param alpha - * @param maxIterations + * @param params */ export const pageRank = ( graph: Graph, - tolerance = 1e-5, - alpha = 0.85, - maxIterations = 1000 -): { id: ID; score: number }[] => { + params?: Params, +): Record => { + const { + tolerance = 1e-5, + alpha = 0.85, + maxIterations = 1000 + } = params || {}; + let distance = 1; let leakedRank = 0; const nodes = graph.getAllNodes(); - const edges = graph.getAllEdges(); const nodesCount = nodes.length; let currentRank: number; const curRanks: Record = {}; const prevRanks: Record = {}; - // Initialize pageranks 初始化 for (let j = 0; j < nodesCount; ++j) { const node = nodes[j]; const nodeId = node.id; @@ -33,21 +39,21 @@ export const pageRank = ( prevRanks[nodeId] = 1 / nodesCount; } - const nodeDegree = degree(graphData); - while (maxIterations > 0 && distance > tolerance) { + let iterations = maxIterations; + while (iterations > 0 && distance > tolerance) { leakedRank = 0; for (let j = 0; j < nodesCount; ++j) { const node = nodes[j]; const nodeId = node.id; currentRank = 0; - if (nodeDegree[node.id].inDegree === 0) { + if (graph.getDegree(nodeId, 'in') === 0) { curRanks[nodeId] = 0; } else { const neighbors = graph.getRelatedEdges(nodeId, "in"); for (let i = 0; i < neighbors.length; ++i) { const neighbor = neighbors[i]; - const outDegree: number = nodeDegree[neighbor].outDegree; - if (outDegree > 0) currentRank += prevRanks[neighbor] / outDegree; + const outDegree: number = graph.getDegree(neighbor.source, 'out'); + if (outDegree > 0) currentRank += prevRanks[neighbor.source] / outDegree; } curRanks[nodeId] = alpha * currentRank; leakedRank += curRanks[nodeId]; @@ -63,7 +69,7 @@ export const pageRank = ( distance += Math.abs(currentRank - prevRanks[nodeId]); prevRanks[nodeId] = currentRank; } - maxIterations -= 1; + iterations -= 1; } return prevRanks; diff --git a/packages/graph/tests/unit/adjacent-matrix-async-spec.ts b/packages/graph/tests/unit/adjacent-matrix-async-spec.ts deleted file mode 100644 index ccdd4a7..0000000 --- a/packages/graph/tests/unit/adjacent-matrix-async-spec.ts +++ /dev/null @@ -1,116 +0,0 @@ -import { getAlgorithm } from './utils'; - -const data = { - nodes: [ - { - id: 'A', - label: '0', - }, - { - id: 'B', - label: '1', - }, - { - id: 'C', - label: '2', - }, - { - id: 'D', - label: '3', - }, - { - id: 'E', - label: '4', - }, - { - id: 'F', - label: '5', - }, - { - id: 'G', - label: '6', - }, - { - id: 'H', - label: '7', - }, - ], - edges: [ - { - source: 'A', - target: 'B', - }, - { - source: 'B', - target: 'C', - }, - { - source: 'C', - target: 'G', - }, - { - source: 'A', - target: 'D', - }, - { - source: 'A', - target: 'E', - }, - { - source: 'E', - target: 'F', - }, - { - source: 'F', - target: 'D', - }, - ], -}; - -describe('(Async) Adjacency Matrix', () => { - it('undirected', async () => { - const { getAdjMatrixAsync } = await getAlgorithm(); - const matrix = await getAdjMatrixAsync(data); - expect(Object.keys(matrix).length).toBe(8); - const node0Adj = matrix[0]; - expect(node0Adj.length).toBe(5); - expect(node0Adj[0]).toBe(undefined); - expect(node0Adj[1]).toBe(1); - expect(node0Adj[2]).toBe(undefined); - expect(node0Adj[3]).toBe(1); - expect(node0Adj[4]).toBe(1); - - const node1Adj = matrix[1]; - expect(node1Adj.length).toBe(3); - expect(node1Adj[0]).toBe(1); - expect(node1Adj[1]).toBe(undefined); - expect(node1Adj[2]).toBe(1); - - const node5Adj = matrix[5]; - expect(node5Adj.length).toBe(5); - expect(node5Adj[0]).toBe(undefined); - expect(node5Adj[1]).toBe(undefined); - expect(node5Adj[2]).toBe(undefined); - expect(node5Adj[3]).toBe(1); - expect(node5Adj[4]).toBe(1); - }); - - it('directed', async () => { - const { getAdjMatrixAsync } = await getAlgorithm(); - const matrix = await getAdjMatrixAsync(data, true); - expect(Object.keys(matrix).length).toBe(8); - const node0Adj = matrix[0]; - expect(node0Adj.length).toBe(5); - expect(node0Adj[0]).toBe(undefined); - expect(node0Adj[1]).toBe(1); - expect(node0Adj[2]).toBe(undefined); - expect(node0Adj[3]).toBe(1); - expect(node0Adj[4]).toBe(1); - - const node1Adj = matrix[1]; - expect(node1Adj.length).toBe(3); - expect(node1Adj[0]).toBe(undefined); - expect(node1Adj[1]).toBe(undefined); - expect(node1Adj[2]).toBe(1); - }); -}); diff --git a/packages/graph/tests/unit/adjacent-matrix-spec.ts b/packages/graph/tests/unit/adjacent-matrix-spec.ts deleted file mode 100644 index ec485a8..0000000 --- a/packages/graph/tests/unit/adjacent-matrix-spec.ts +++ /dev/null @@ -1,114 +0,0 @@ -import { getAdjMatrix } from '../../src'; - -const data = { - nodes: [ - { - id: 'A', - label: '0', - }, - { - id: 'B', - label: '1', - }, - { - id: 'C', - label: '2', - }, - { - id: 'D', - label: '3', - }, - { - id: 'E', - label: '4', - }, - { - id: 'F', - label: '5', - }, - { - id: 'G', - label: '6', - }, - { - id: 'H', - label: '7', - }, - ], - edges: [ - { - source: 'A', - target: 'B', - }, - { - source: 'B', - target: 'C', - }, - { - source: 'C', - target: 'G', - }, - { - source: 'A', - target: 'D', - }, - { - source: 'A', - target: 'E', - }, - { - source: 'E', - target: 'F', - }, - { - source: 'F', - target: 'D', - }, - ], -}; - -describe('Adjacency Matrix', () => { - it('undirected', () => { - const matrix = getAdjMatrix(data); - expect(Object.keys(matrix).length).toBe(8); - const node0Adj = matrix[0]; - expect(node0Adj.length).toBe(5); - expect(node0Adj[0]).toBe(undefined); - expect(node0Adj[1]).toBe(1); - expect(node0Adj[2]).toBe(undefined); - expect(node0Adj[3]).toBe(1); - expect(node0Adj[4]).toBe(1); - - const node1Adj = matrix[1]; - expect(node1Adj.length).toBe(3); - expect(node1Adj[0]).toBe(1); - expect(node1Adj[1]).toBe(undefined); - expect(node1Adj[2]).toBe(1); - - const node5Adj = matrix[5]; - expect(node5Adj.length).toBe(5); - expect(node5Adj[0]).toBe(undefined); - expect(node5Adj[1]).toBe(undefined); - expect(node5Adj[2]).toBe(undefined); - expect(node5Adj[3]).toBe(1); - expect(node5Adj[4]).toBe(1); - }); - - it('directed', () => { - const matrix = getAdjMatrix(data, true); - expect(Object.keys(matrix).length).toBe(8); - const node0Adj = matrix[0]; - expect(node0Adj.length).toBe(5); - expect(node0Adj[0]).toBe(undefined); - expect(node0Adj[1]).toBe(1); - expect(node0Adj[2]).toBe(undefined); - expect(node0Adj[3]).toBe(1); - expect(node0Adj[4]).toBe(1); - - const node1Adj = matrix[1]; - expect(node1Adj.length).toBe(3); - expect(node1Adj[0]).toBe(undefined); - expect(node1Adj[1]).toBe(undefined); - expect(node1Adj[2]).toBe(1); - }); -}); diff --git a/packages/graph/tests/unit/bfs-spec.ts b/packages/graph/tests/unit/bfs-spec.ts deleted file mode 100644 index 68a5c8c..0000000 --- a/packages/graph/tests/unit/bfs-spec.ts +++ /dev/null @@ -1,175 +0,0 @@ -import { breadthFirstSearch } from '../../src'; - -const data = { - nodes: [ - { - id: 'A', - }, - { - id: 'B', - }, - { - id: 'C', - }, - { - id: 'D', - }, - { - id: 'E', - }, - { - id: 'F', - }, - { - id: 'G', - }, - { - id: 'H', - }, - ], - edges: [ - { - source: 'A', - target: 'B', - }, - { - source: 'B', - target: 'C', - }, - { - source: 'C', - target: 'G', - }, - { - source: 'A', - target: 'D', - }, - { - source: 'A', - target: 'E', - }, - { - source: 'E', - target: 'F', - }, - { - source: 'F', - target: 'D', - }, - ], -}; - -describe('breadthFirstSearch', () => { - it('should perform BFS operation on graph', () => { - const enterNodeCallback = jest.fn(); - const leaveNodeCallback = jest.fn(); - - // Traverse graphs without callbacks first. - breadthFirstSearch(data, 'A'); - - // Traverse graph with enterNode and leaveNode callbacks. - breadthFirstSearch(data, 'A', { - enter: enterNodeCallback, - leave: leaveNodeCallback, - }); - - expect(enterNodeCallback).toHaveBeenCalledTimes(7); - expect(leaveNodeCallback).toHaveBeenCalledTimes(7); - - const nodeA = 'A'; - const nodeB = 'B'; - const nodeC = 'C'; - const nodeD = 'D'; - const nodeE = 'E'; - const nodeF = 'F'; - const nodeG = 'G'; - - const enterNodeParamsMap = [ - { currentNode: nodeA, previousNode: '' }, - { currentNode: nodeB, previousNode: nodeA }, - { currentNode: nodeD, previousNode: nodeB }, - { currentNode: nodeE, previousNode: nodeD }, - { currentNode: nodeC, previousNode: nodeE }, - { currentNode: nodeF, previousNode: nodeC }, - { currentNode: nodeG, previousNode: nodeF }, - ]; - - for (let callIndex = 0; callIndex < 6; callIndex += 1) { - const params = enterNodeCallback.mock.calls[callIndex][0]; - expect(params.current).toEqual(enterNodeParamsMap[callIndex].currentNode); - expect(params.previous).toEqual( - enterNodeParamsMap[callIndex].previousNode && - enterNodeParamsMap[callIndex].previousNode, - ); - } - - const leaveNodeParamsMap = [ - { currentNode: nodeA, previousNode: '' }, - { currentNode: nodeB, previousNode: nodeA }, - { currentNode: nodeD, previousNode: nodeB }, - { currentNode: nodeE, previousNode: nodeD }, - { currentNode: nodeC, previousNode: nodeE }, - { currentNode: nodeF, previousNode: nodeC }, - { currentNode: nodeG, previousNode: nodeF }, - ]; - - for (let callIndex = 0; callIndex < 6; callIndex += 1) { - const params = leaveNodeCallback.mock.calls[callIndex][0]; - expect(params.current).toEqual(leaveNodeParamsMap[callIndex].currentNode); - expect(params.previous).toEqual( - leaveNodeParamsMap[callIndex].previousNode && - leaveNodeParamsMap[callIndex].previousNode, - ); - } - }); - - it('should allow to create custom node visiting logic', () => { - - const enterNodeCallback = jest.fn(); - const leaveNodeCallback = jest.fn(); - - // Traverse graph with enterNode and leaveNode callbacks. - breadthFirstSearch(data, 'A', { - enter: enterNodeCallback, - leave: leaveNodeCallback, - allowTraversal: ({ current, next }) => { - return !(current === 'A' && next === 'B'); - }, - }); - - expect(enterNodeCallback).toHaveBeenCalledTimes(5); - expect(leaveNodeCallback).toHaveBeenCalledTimes(5); - - const enterNodeParamsMap = [ - { currentNode: 'A', previousNode: '' }, - { currentNode: 'D', previousNode: 'A' }, - { currentNode: 'E', previousNode: 'D' }, - { currentNode: 'F', previousNode: 'E' }, - { currentNode: 'D', previousNode: 'F' }, - ]; - - for (let callIndex = 0; callIndex < 5; callIndex += 1) { - const params = enterNodeCallback.mock.calls[callIndex][0]; - expect(params.current).toEqual(enterNodeParamsMap[callIndex].currentNode); - expect(params.previous).toEqual( - enterNodeParamsMap[callIndex].previousNode, - ); - } - - const leaveNodeParamsMap = [ - { currentNode: 'A', previousNode: '' }, - { currentNode: 'D', previousNode: 'A' }, - { currentNode: 'E', previousNode: 'D' }, - { currentNode: 'F', previousNode: 'E' }, - { currentNode: 'D', previousNode: 'F' }, - ]; - - for (let callIndex = 0; callIndex < 5; callIndex += 1) { - const params = leaveNodeCallback.mock.calls[callIndex][0]; - expect(params.current).toEqual(leaveNodeParamsMap[callIndex].currentNode); - expect(params.previous).toEqual( - leaveNodeParamsMap[callIndex].previousNode, - ); - } - }); -}); diff --git a/packages/graph/tests/unit/connected-component-async-spec.ts b/packages/graph/tests/unit/connected-component-async-spec.ts deleted file mode 100644 index bea990a..0000000 --- a/packages/graph/tests/unit/connected-component-async-spec.ts +++ /dev/null @@ -1,112 +0,0 @@ -import { getAlgorithm } from './utils'; - -const data = { - nodes: [ - { - id: 'A', - }, - { - id: 'B', - }, - { - id: 'C', - }, - { - id: 'D', - }, - { - id: 'E', - }, - { - id: 'F', - }, - { - id: 'G', - }, - { - id: 'H', - }, - ], - edges: [ - { - source: 'A', - target: 'B', - }, - { - source: 'B', - target: 'C', - }, - { - source: 'A', - target: 'C', - }, - { - source: 'D', - target: 'A', - }, - { - source: 'D', - target: 'E', - }, - { - source: 'E', - target: 'F', - }, - { - source: 'F', - target: 'D', - }, - { - source: 'G', - target: 'H', - }, - { - source: 'H', - target: 'G', - }, - ], -}; - -describe('(Async) find connected components', () => { - it('detect strongly connected components in undirected graph', async done => { - const { connectedComponentAsync } = await getAlgorithm(); - let result = await connectedComponentAsync(data, false); - expect(result.length).toEqual(2); - expect(result[0].map(node => node.id).sort()).toEqual(['A', 'B', 'C', 'D', 'E', 'F']); - expect(result[1].map(node => node.id).sort()).toEqual(['G', 'H']); - done(); - }); - - it('detect strongly connected components in directed graph', async done => { - const { connectedComponentAsync } = await getAlgorithm(); - let result = await connectedComponentAsync(data, true); - expect(result.length).toEqual(5); - expect(result[3].map(node => node.id).sort()).toEqual(['D', 'E', 'F']); - expect(result[4].map(node => node.id).sort()).toEqual(['G', 'H']); - done(); - }); - - it('test connected components detection performance using large graph', async done => { - fetch('https://gw.alipayobjects.com/os/basement_prod/da5a1b47-37d6-44d7-8d10-f3e046dabf82.json') - .then(res => res.json()) - .then(async data => { - const { connectedComponentAsync } = await getAlgorithm(); - - data.nodes.forEach(node => { - node.label = node.olabel; - node.degree = 0; - data.edges.forEach(edge => { - if (edge.source === node.id || edge.target === node.id) { - node.degree++; - } - }); - }); - - let directedComps = await connectedComponentAsync(data, true); - let undirectedComps = await connectedComponentAsync(data, false); - expect(directedComps.length).toEqual(1589); - expect(undirectedComps.length).toEqual(396); - done(); - }); - }); -}); diff --git a/packages/graph/tests/unit/connected-component-spec.ts b/packages/graph/tests/unit/connected-component-spec.ts deleted file mode 100644 index abf7346..0000000 --- a/packages/graph/tests/unit/connected-component-spec.ts +++ /dev/null @@ -1,106 +0,0 @@ -import { connectedComponent } from '../../src' - -const data = { - nodes: [ - { - id: 'A', - }, - { - id: 'B', - }, - { - id: 'C', - }, - { - id: 'D', - }, - { - id: 'E', - }, - { - id: 'F', - }, - { - id: 'G', - }, - { - id: 'H', - }, - ], - edges: [ - { - source: 'A', - target: 'B', - }, - { - source: 'B', - target: 'C', - }, - { - source: 'A', - target: 'C', - }, - { - source: 'D', - target: 'A', - }, - { - source: 'D', - target: 'E', - }, - { - source: 'E', - target: 'F', - }, - { - source: 'F', - target: 'D', - }, - { - source: 'G', - target: 'H', - }, - { - source: 'H', - target: 'G', - }, - ], -}; - -describe('find connected components', () => { - - it('detect strongly connected components in undirected graph', () => { - let result = connectedComponent(data, false); - expect(result.length).toEqual(2); - expect(result[0].map((node) => node.id).sort()).toEqual(['A', 'B', 'C', 'D', 'E', 'F']); - expect(result[1].map((node) => node.id).sort()).toEqual(['G', 'H']); - }); - - it('detect strongly connected components in directed graph', () => { - let result = connectedComponent(data, true); - expect(result.length).toEqual(5); - expect(result[3].map((node) => node.id).sort()).toEqual(['D', 'E', 'F']); - expect(result[4].map((node) => node.id).sort()).toEqual(['G', 'H']); - }); - - it('test connected components detection performance using large graph', () => { - fetch('https://gw.alipayobjects.com/os/basement_prod/da5a1b47-37d6-44d7-8d10-f3e046dabf82.json') - .then((res) => res.json()) - .then((data) => { - data.nodes.forEach((node) => { - node.label = node.olabel; - node.degree = 0; - data.edges.forEach((edge) => { - if (edge.source === node.id || edge.target === node.id) { - node.degree++; - } - }); - }); - - let directedComps = connectedComponent(data, true); - let undirectedComps = connectedComponent(data, false); - expect(directedComps.length).toEqual(1589); - expect(undirectedComps.length).toEqual(396); - }); - }); -}); diff --git a/packages/graph/tests/unit/cosineSimilarity-spec.ts b/packages/graph/tests/unit/cosineSimilarity-spec.ts deleted file mode 100644 index 3824680..0000000 --- a/packages/graph/tests/unit/cosineSimilarity-spec.ts +++ /dev/null @@ -1,41 +0,0 @@ -import { cosineSimilarity } from '../../src'; - -describe('cosineSimilarity abnormal demo: ', () => { - it('item contains only zeros: ', () => { - const item = [0, 0, 0]; - const targetTtem = [3, 1, 1]; - const cosineSimilarityValue = cosineSimilarity(item, targetTtem); - expect(cosineSimilarityValue).toBe(0); - }); - it('targetTtem contains only zeros: ', () => { - const item = [3, 5, 2]; - const targetTtem = [0, 0, 0]; - const cosineSimilarityValue = cosineSimilarity(item, targetTtem); - expect(cosineSimilarityValue).toBe(0); - }); - it('item and targetTtem both contains only zeros: ', () => { - const item = [0, 0, 0]; - const targetTtem = [0, 0, 0]; - const cosineSimilarityValue = cosineSimilarity(item, targetTtem); - expect(cosineSimilarityValue).toBe(0); - }); -}); - -describe('cosineSimilarity normal demo: ', () => { - it('demo similar: ', () => { - const item = [30, 0, 100]; - const targetTtem = [32, 1, 120]; - const cosineSimilarityValue = cosineSimilarity(item, targetTtem); - expect(cosineSimilarityValue).toBeGreaterThanOrEqual(0); - expect(cosineSimilarityValue).toBeLessThan(1); - expect(Number(cosineSimilarityValue.toFixed(3))).toBe(0.999); - }); - it('demo dissimilar: ', () => { - const item = [10, 300, 2]; - const targetTtem = [1, 2, 30]; - const cosineSimilarityValue = cosineSimilarity(item, targetTtem); - expect(cosineSimilarityValue).toBeGreaterThanOrEqual(0); - expect(cosineSimilarityValue).toBeLessThan(1); - expect(Number(cosineSimilarityValue.toFixed(3))).toBe(0.074); - }); -}); diff --git a/packages/graph/tests/unit/data/cluster-origin-data.json b/packages/graph/tests/unit/data/cluster-origin-data.json deleted file mode 100644 index 9e26dfe..0000000 --- a/packages/graph/tests/unit/data/cluster-origin-data.json +++ /dev/null @@ -1 +0,0 @@ -{} \ No newline at end of file diff --git a/packages/graph/tests/unit/data/cluster-origin-properties-data.json b/packages/graph/tests/unit/data/cluster-origin-properties-data.json deleted file mode 100644 index e3349f2..0000000 --- a/packages/graph/tests/unit/data/cluster-origin-properties-data.json +++ /dev/null @@ -1,370 +0,0 @@ -{ - "nodes": [ - { - "id": "node-0", - "label": "node-0", - "properties": { - "city": "110000", - "age": 20, - "amount": 100, - "wifi": "wifi-0" - } - }, - { - "id": "node-1", - "label": "node-1", - "properties": { - "city": "110000", - "age": 22, - "amount": 100, - "wifi": "wifi-1" - } - }, - { - "id": "node-2", - "label": "node-2", - "properties": { - "city": "110000", - "age": 20, - "amount": 100, - "wifi": "wifi-2" - } - }, - { - "id": "node-3", - "label": "node-3", - "properties": { - "city": "110000", - "age": 21, - "amount": 100, - "wifi": "wifi-3" - } - }, - { - "id": "node-4", - "label": "node-4", - "properties": { - "city": "110000", - "age": 22, - "amount": 100, - "wifi": "wifi-4" - } - }, - { - "id": "node-5", - "label": "node-5", - "properties": { - "city": "310000", - "age": 30, - "amount": 1000, - "wifi": "wifi-5" - } - }, - { - "id": "node-6", - "label": "node-6", - "properties": { - "city": "310000", - "age": 31, - "amount": 1000, - "wifi": "wifi-6" - } - }, - { - "id": "node-7", - "label": "node-7", - "properties": { - "city": "310000", - "age": 31, - "amount": 1000, - "wifi": "wifi-7" - } - }, - { - "id": "node-8", - "label": "node-8", - "properties": { - "city": "310000", - "age": 32, - "amount": 1000, - "wifi": "wifi-8" - } - }, - { - "id": "node-9", - "label": "node-9", - "properties": { - "city": "310000", - "age": 30, - "amount": 1000, - "wifi": "wifi-9" - } - }, - { - "id": "node-10", - "label": "node-10", - "properties": { - "city": "310000", - "age": 30, - "amount": 1000, - "wifi": "wifi-10" - } - }, - { - "id": "node-11", - "label": "node-11", - "properties": { - "city": "440300", - "age": 40, - "amount": 10000, - "wifi": "wifi-11" - } - }, - { - "id": "node-12", - "label": "node-12", - "properties": { - "city": "440300", - "age": 40, - "amount": 10000, - "wifi": "wifi-12" - } - }, - { - "id": "node-13", - "label": "node-13", - "properties": { - "city": "440300", - "age": 41, - "amount": 10000, - "wifi": "wifi-13" - } - }, - { - "id": "node-14", - "label": "node-14", - "properties": { - "city": "440300", - "age": 42, - "amount": 10000, - "wifi": "wifi-14" - } - }, - { - "id": "node-15", - "label": "node-15", - "properties": { - "city": "440300", - "age": 41, - "amount": 10000, - "wifi": "wifi-15" - } - }, - { - "id": "node-16", - "label": "node-16", - "properties": { - "city": "440300", - "age": 43, - "amount": 10000, - "wifi": "wifi-16" - } - } - ], - "edges": [ - { - "id": "edge-0", - "source": "node-0", - "target": "node-1" - }, - { - "id": "edge-1", - "source": "node-0", - "target": "node-2" - }, - { - "id": "edge-2", - "source": "node-0", - "target": "node-3" - }, - { - "id": "edge-3", - "source": "node-0", - "target": "node-4" - }, - { - "id": "edge-4", - "source": "node-1", - "target": "node-2" - }, - { - "id": "edge-5", - "source": "node-1", - "target": "node-3" - }, - { - "id": "edge-6", - "source": "node-1", - "target": "node-4" - }, - { - "id": "edge-7", - "source": "node-2", - "target": "node-3" - }, - { - "id": "edge-8", - "source": "node-2", - "target": "node-4" - }, - { - "id": "edge-9", - "source": "node-3", - "target": "node-4" - }, - - - { - "id": "edge-10", - "source": "node-5", - "target": "node-6" - }, - { - "id": "edge-11", - "source": "node-5", - "target": "node-7" - }, - { - "id": "edge-12", - "source": "node-5", - "target": "node-8" - }, - { - "id": "edge-13", - "source": "node-5", - "target": "node-9" - }, - { - "id": "edge-14", - "source": "node-6", - "target": "node-7" - }, - { - "id": "edge-15", - "source": "node-6", - "target": "node-8" - }, - { - "id": "edge-16", - "source": "node-6", - "target": "node-9" - }, - { - "id": "edge-17", - "source": "node-7", - "target": "node-8" - }, - { - "id": "edge-18", - "source": "node-7", - "target": "node-9" - }, - { - "id": "edge-19", - "source": "node-8", - "target": "node-9" - }, - { - "id": "edge-20", - "source": "node-9", - "target": "node-10" - }, - { - "id": "edge-40", - "source": "node-10", - "target": "node-5" - }, - - - { - "id": "edge-21", - "source": "node-11", - "target": "node-12" - }, - { - "id": "edge-22", - "source": "node-11", - "target": "node-13" - }, - { - "id": "edge-23", - "source": "node-11", - "target": "node-14" - }, - { - "id": "edge-24", - "source": "node-11", - "target": "node-15" - }, - { - "id": "edge-25", - "source": "node-12", - "target": "node-13" - }, - { - "id": "edge-26", - "source": "node-12", - "target": "node-14" - }, - { - "id": "edge-27", - "source": "node-12", - "target": "node-15" - }, - { - "id": "edge-28", - "source": "node-13", - "target": "node-14" - }, - { - "id": "edge-29", - "source": "node-13", - "target": "node-15" - }, - { - "id": "edge-30", - "source": "node-14", - "target": "node-15" - }, - { - "id": "edge-31", - "source": "node-0", - "target": "node-5" - }, - { - "id": "edge-32", - "source": "node-5", - "target": "node-11" - }, - { - "id": "edge-33", - "source": "node-11", - "target": "node-0" - }, - { - "id": "edge-34", - "source": "node-16", - "target": "node-0" - }, - { - "id": "edge-35", - "source": "node-16", - "target": "node-5" - }, - { - "id": "edge-36", - "source": "node-16", - "target": "node-11" - } - ] -} \ No newline at end of file diff --git a/packages/graph/tests/unit/data/test-data.ts b/packages/graph/tests/unit/data/test-data.ts deleted file mode 100644 index 8657282..0000000 --- a/packages/graph/tests/unit/data/test-data.ts +++ /dev/null @@ -1,38635 +0,0 @@ -export const nodes20 = 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"source":"1005","target":"2025","dataType":"Enterprise2Enterprise#Guarantee"},{"id":"edge-1005|2026|Enterprise2Enterprise#Guarantee|1608187864","source":"1005","target":"2026","dataType":"Enterprise2Enterprise#Guarantee"},{"id":"edge-1005|2025|Enterprise2Enterprise#Guarantee|1610530400","source":"1005","target":"2025","dataType":"Enterprise2Enterprise#Guarantee"},{"id":"edge-1005|2026|Enterprise2Enterprise#Guarantee|1610530400","source":"1005","target":"2026","dataType":"Enterprise2Enterprise#Guarantee"},{"id":"edge-1005|2025|Enterprise2Enterprise#Guarantee|1612412941","source":"1005","target":"2025","dataType":"Enterprise2Enterprise#Guarantee"},{"id":"edge-1005|2026|Enterprise2Enterprise#Guarantee|1612412941","source":"1005","target":"2026","dataType":"Enterprise2Enterprise#Guarantee"},{"id":"edge-1005|2025|Enterprise2Enterprise#Investment|1608187864","source":"1005","target":"2025","dataType":"Enterprise2Enterprise#Investment"},{"id":"edge-1005|2026|Enterprise2Enterprise#Investment|1608187864","source":"1005","target":"2026","dataType":"Enterprise2Enterprise#Investment"},{"id":"edge-1005|2025|Enterprise2Enterprise#Investment|1610530400","source":"1005","target":"2025","dataType":"Enterprise2Enterprise#Investment"},{"id":"edge-1005|2026|Enterprise2Enterprise#Investment|1610530400","source":"1005","target":"2026","dataType":"Enterprise2Enterprise#Investment"},{"id":"edge-1005|2025|Enterprise2Enterprise#Investment|1612412941","source":"1005","target":"2025","dataType":"Enterprise2Enterprise#Investment"},{"id":"edge-1005|2026|Enterprise2Enterprise#Investment|1612412941","source":"1005","target":"2026","dataType":"Enterprise2Enterprise#Investment"},{"id":"edge-1005|2025|Enterprise2Enterprise#Level|1608187864","source":"1005","target":"2025","dataType":"Enterprise2Enterprise#Level"},{"id":"edge-1005|2026|Enterprise2Enterprise#Level|1608187864","source":"1005","target":"2026","dataType":"Enterprise2Enterprise#Level"},{"id":"edge-1005|2025|Enterprise2Enterprise#Level|1610530400","source":"1005","target":"2025","dataType":"Enterprise2Enterprise#Level"},{"id":"edge-1005|2026|Enterprise2Enterprise#Level|1610530400","source":"1005","target":"2026","dataType":"Enterprise2Enterprise#Level"},{"id":"edge-1005|2025|Enterprise2Enterprise#Level|1612412941","source":"1005","target":"2025","dataType":"Enterprise2Enterprise#Level"},{"id":"edge-1005|2026|Enterprise2Enterprise#Level|1612412941","source":"1005","target":"2026","dataType":"Enterprise2Enterprise#Level"},{"id":"edge-1006|2026|Enterprise2Enterprise#Guarantee|1608187864","source":"1006","target":"2026","dataType":"Enterprise2Enterprise#Guarantee"},{"id":"edge-1006|2027|Enterprise2Enterprise#Guarantee|1608187864","source":"1006","target":"2027","dataType":"Enterprise2Enterprise#Guarantee"},{"id":"edge-1006|2026|Enterprise2Enterprise#Guarantee|1610530400","source":"1006","target":"2026","dataType":"Enterprise2Enterprise#Guarantee"},{"id":"edge-1006|2027|Enterprise2Enterprise#Guarantee|1610530400","source":"1006","target":"2027","dataType":"Enterprise2Enterprise#Guarantee"},{"id":"edge-1006|2026|Enterprise2Enterprise#Guarantee|1612412941","source":"1006","target":"2026","dataType":"Enterprise2Enterprise#Guarantee"},{"id":"edge-1006|2027|Enterprise2Enterprise#Guarantee|1612412941","source":"1006","target":"2027","dataType":"Enterprise2Enterprise#Guarantee"},{"id":"edge-1006|2026|Enterprise2Enterprise#Investment|1608187864","source":"1006","target":"2026","dataType":"Enterprise2Enterprise#Investment"},{"id":"edge-1006|2027|Enterprise2Enterprise#Investment|1608187864","source":"1006","target":"2027","dataType":"Enterprise2Enterprise#Investment"},{"id":"edge-1006|2026|Enterprise2Enterprise#Investment|1610530400","source":"1006","target":"2026","dataType":"Enterprise2Enterprise#Investment"},{"id":"edge-1006|2027|Enterprise2Enterprise#Investment|1610530400","source":"1006","target":"2027","dataType":"Enterprise2Enterprise#Investment"},{"id":"edge-1006|2026|Enterprise2Enterprise#Investment|1612412941","source":"1006","target":"2026","dataType":"Enterprise2Enterprise#Investment"},{"id":"edge-1006|2027|Enterprise2Enterprise#Investment|1612412941","source":"1006","target":"2027","dataType":"Enterprise2Enterprise#Investment"},{"id":"edge-1006|2026|Enterprise2Enterprise#Level|1608187864","source":"1006","target":"2026","dataType":"Enterprise2Enterprise#Level"},{"id":"edge-1006|2027|Enterprise2Enterprise#Level|1608187864","source":"1006","target":"2027","dataType":"Enterprise2Enterprise#Level"},{"id":"edge-1006|2026|Enterprise2Enterprise#Level|1610530400","source":"1006","target":"2026","dataType":"Enterprise2Enterprise#Level"},{"id":"edge-1006|2027|Enterprise2Enterprise#Level|1610530400","source":"1006","target":"2027","dataType":"Enterprise2Enterprise#Level"},{"id":"edge-1006|2026|Enterprise2Enterprise#Level|1612412941","source":"1006","target":"2026","dataType":"Enterprise2Enterprise#Level"},{"id":"edge-1006|2027|Enterprise2Enterprise#Level|1612412941","source":"1006","target":"2027","dataType":"Enterprise2Enterprise#Level"}]} - -export const nodes77 = { - nodes: [ - { id: "0", cluster: "A", label: "0-A" }, - { id: "1", cluster: "B", label: "1-B" }, - { id: "2", cluster: "C", label: "2-C" }, - { id: "3", cluster: "C", label: "3-C" }, - { id: "4", cluster: "C", label: "4-C" }, - { id: "5", cluster: "B", label: "5-B" }, - { id: "6", cluster: "C", label: "6-C" }, - { id: "7", cluster: "B", label: "7-B" }, - { id: "8", cluster: "A", label: "8-A" }, - { id: "9", cluster: "A", label: "9-A" }, - { id: "10", cluster: "B", label: "10-B" }, - { id: "11", cluster: "B", label: "11-B" }, - { id: "12", cluster: "C", label: "12-C" }, - { id: "13", cluster: "B", label: "13-B" }, - { id: "14", cluster: "B", label: "14-B" }, - { id: "15", cluster: "B", label: "15-B" }, - { id: "16", cluster: "B", label: "16-B" }, - { id: "17", cluster: "B", label: "17-B" }, - { id: "18", cluster: "B", label: "18-B" }, - { id: "19", cluster: "C", label: "19-C" }, - { id: "20", cluster: "B", label: "20-B" }, - { id: "21", cluster: "A", label: "21-A" }, - { id: "22", cluster: "B", label: "22-B" }, - { id: "23", cluster: "B", label: "23-B" }, - { id: "24", cluster: "C", label: "24-C" }, - { id: "25", cluster: "C", label: "25-C" }, - { id: "26", cluster: "B", label: "26-B" }, - { id: "27", cluster: "A", label: "27-A" }, - { id: "28", cluster: "C", label: "28-C" }, - { id: "29", cluster: "C", label: "29-C" }, - { id: "30", cluster: "B", label: "30-B" }, - { id: "31", cluster: "B", label: "31-B" }, - { id: "32", cluster: "C", label: "32-C" }, - { id: "33", cluster: "A", label: "33-A" }, - { id: "34", cluster: "A", label: "34-A" }, - { id: "35", cluster: "C", label: "35-C" }, - { id: "36", cluster: "A", label: "36-A" }, - { id: "37", cluster: "C", label: "37-C" }, - { id: "38", cluster: "C", label: "38-C" }, - { id: "39", cluster: "B", label: "39-B" }, - { id: "40", cluster: "C", label: "40-C" }, - { id: "41", cluster: "B", label: "41-B" }, - { id: "42", cluster: "B", label: "42-B" }, - { id: "43", cluster: "A", label: "43-A" }, - { id: "44", cluster: "C", label: "44-C" }, - { id: "45", cluster: "B", label: "45-B" }, - { id: "46", cluster: "B", label: "46-B" }, - { id: "47", cluster: "C", label: "47-C" }, - { id: "48", cluster: "B", label: "48-B" }, - { id: "49", cluster: "C", label: "49-C" }, - { id: "50", cluster: "A", label: "50-A" }, - { id: "51", cluster: "C", label: "51-C" }, - { id: "52", cluster: "C", label: "52-C" }, - { id: "53", cluster: "C", label: "53-C" }, - { id: "54", cluster: "C", label: "54-C" }, - { id: "55", cluster: "A", label: "55-A" }, - { id: "56", cluster: "B", label: "56-B" }, - { id: "57", cluster: "A", label: "57-A" }, - { id: "58", cluster: "B", label: "58-B" }, - { id: "59", cluster: "C", label: "59-C" }, - { id: "60", cluster: "B", label: "60-B" }, - { id: "61", cluster: "B", label: "61-B" }, - { id: "62", cluster: "C", label: "62-C" }, - { id: "63", cluster: "B", label: "63-B" }, - { id: "64", cluster: "B", label: "64-B" }, - { id: "65", cluster: "A", label: "65-A" }, - { id: 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1, cluster: "a", label: "a" }, - { source: "76", target: "63", value: 1, cluster: "a", label: "a" }, - { source: "76", target: "62", value: 1, cluster: "a", label: "a" }, - { source: "76", target: "48", value: 1, cluster: "a", label: "a" }, - { source: "76", target: "58", value: 1, cluster: "a", label: "a" }, - ], -}; - -export const nodes202 = { - nodes: [ - { - id: "1", - label: "1-A", - cluster: "A", - x: 301.20880899273163, - y: 16.498563471350245, - }, - { - id: "2", - label: "2-B", - cluster: "B", - x: 167.71579022730245, - y: 21.169092644111863, - }, - { - id: "3", - label: "3-C", - cluster: "C", - x: 225.60113755765104, - y: 53.38237357832761, - }, - { - id: "4", - label: "4-D", - cluster: "D", - x: 257.2171264302781, - y: 10.65803240773092, - }, - { - id: "5", - label: "5-E", - cluster: "E", - x: 631.9192989141275, - y: 16.185060075215628, - }, - { - id: "6", - label: "6-A", - cluster: "A", - x: 147.70380559678026, - y: 22.309088056991207, - }, - { - id: "7", - label: "7-B", - cluster: "B", - x: 127.84189789787449, - y: 93.67277180968523, - }, - { - id: "8", - label: "8-C", - cluster: "C", - x: 707.7325190040664, - y: 6.916731320922539, - }, - { - id: "9", - label: "9-D", - cluster: "D", - x: 235.0228391142811, - y: 4.721612635411866, - }, - { - id: "10", - label: "10-E", - cluster: "E", - x: 112.17360443437231, - y: 85.14322322856475, - }, - { - id: "11", - label: "11-A", - cluster: "A", - x: 151.94058879507244, - y: 39.805144202813125, - }, - { - id: "12", - label: "12-B", - cluster: "B", - x: 222.2986880590628, - y: 88.06947603346353, - }, - { - id: "13", - label: "13-C", - cluster: "C", - x: 604.6951590389173, - y: -53.95978614928713, - }, - { - id: "14", - label: "14-D", - cluster: "D", - x: 78.13869258561154, - y: 53.854113269521804, - }, - { - id: "15", - label: "15-E", - cluster: "E", - x: 57.32017518529654, - y: 104.76288631835605, - }, - { - id: "16", - label: "16-A", - cluster: "A", - x: 673.6741242664087, - y: 26.82550911323939, - }, - { - id: "17", - label: "17-B", - cluster: "B", - x: 155.47170625632668, - y: 116.73379987079107, - }, - { - id: "18", - label: "18-C", - cluster: "C", - x: 659.8004935950742, - y: -4.488657283902915, - }, - { - id: "19", - label: "19-D", - cluster: "D", - x: 599.0010245474674, - y: -20.64496545181059, - }, - { - id: "20", - label: "20-E", - cluster: "E", - x: 592.751970574288, - y: 75.641401815118, - }, - { - id: "21", - label: "21-A", - cluster: "A", - x: 430.06880990239205, - y: 31.849250143249904, - }, - { - id: "22", - label: "22-B", - cluster: "B", - x: 233.90199011505297, - y: 29.14332300354274, - }, - { - id: "23", - label: "23-C", - cluster: "C", - x: 140.53417335176366, - y: 104.24293269089377, - }, - { - id: "24", - label: "24-D", - cluster: "D", - x: 657.6323691943008, - y: -77.4386558440363, - }, - { - id: "25", - label: "25-E", - cluster: "E", - x: 104.62839595086363, - y: 34.708443038044265, - }, - { - id: "26", - label: "26-A", - cluster: "A", - x: 246.65151766730597, - y: 100.61314350776709, - }, - { - id: "27", - label: "27-B", - cluster: "B", - x: 287.73976326614627, - y: 93.6794945238267, - }, - { - id: "28", - label: "28-C", - cluster: "C", - x: 701.5483534740976, - y: -35.947008798702385, - }, - { - id: "29", - label: "29-D", - cluster: "D", - x: 18.817352550124035, - y: 81.91483226407264, - }, - { - id: "30", - label: "30-E", - cluster: "E", - x: 252.54666325089096, - y: -198.63655309420574, - }, - { - id: "31", - label: "31-A", - cluster: "A", - x: 733.8237869966578, - y: -90.26277289379352, - }, - { - id: "32", - label: "32-B", - cluster: "B", - x: 674.3876779304654, - y: -56.10785937643712, - }, - { - id: "33", - label: "33-C", - cluster: "C", - x: 199.6492065642083, - y: 1.7727263515040845, - }, - { - id: "34", - label: "34-D", - cluster: "D", - x: 574.8062458666107, - y: 23.966554376971402, - }, - { - id: "35", - label: "35-E", - cluster: "E", - x: 167.98611042812948, - y: 172.15142154155532, - }, - { - id: "36", - label: "36-A", - cluster: "A", - x: 1283.9532146261135, - y: 155.858407876654, - }, - { - id: "37", - label: "37-B", - cluster: "B", - x: 588.7131468576222, - y: 52.64924625939446, - }, - { - id: "38", - label: "38-C", - cluster: "C", - x: 691.8047077339269, - y: -132.2652032838732, - }, - { - id: "39", - label: "39-D", - cluster: "D", - x: 138.21798305095118, - y: -101.64990039655224, - }, - { - id: "40", - label: "40-E", - cluster: "E", - x: 203.00175801495834, - y: 22.5563777520993, - }, - { - id: "41", - label: "41-A", - cluster: "A", - x: 161.11913453893496, - y: -5.513899552777263, - }, - { - id: "42", - label: "42-B", - cluster: "B", - x: 683.1449997888833, - y: -26.836451326762237, - }, - { - id: "43", - label: "43-C", - cluster: "C", - x: -300.084433851007, - y: -329.3475097692899, - }, - { - id: "44", - label: "44-D", - cluster: "D", - x: 740.9106679320191, - y: -39.796159644362206, - }, - { - id: "45", - label: "45-E", - cluster: "E", - x: 678.1922622322952, - y: 89.31025514147821, - }, - { - id: "46", - label: "46-A", - cluster: "A", - x: 706.9247977830264, - y: 83.30216828609257, - }, - { - id: "47", - label: "47-B", - cluster: "B", - x: 223.76942665280342, - y: -163.6813672134135, - }, - { - id: "48", - label: "48-C", - cluster: "C", - x: 94.61061490581231, - y: -91.41876243605611, - }, - { - id: "49", - label: "49-D", - cluster: "D", - x: 235.24424301409536, - y: -99.86663382097574, - }, - { - id: "50", - label: "50-E", - cluster: "E", - x: 19.627144223819307, - y: 36.28745839469572, - }, - { - id: "51", - label: "51-A", - cluster: "A", - x: 218.6666943227235, - y: 143.02882889214789, - }, - { - id: "52", - label: "52-B", - cluster: "B", - x: 821.3004836613433, - y: -30.61921565291595, - }, - { - id: "53", - label: "53-C", - cluster: "C", - x: 238.08249656023094, - y: -164.657891404515, - }, - { - id: "54", - label: "54-D", - cluster: "D", - x: 10.678175610522628, - y: 102.03121522445221, - }, - { - id: "55", - label: "55-E", - cluster: "E", - x: 74.78892208872713, - y: 93.32603724694751, - }, - { - id: "56", - label: "56-A", - cluster: "A", - x: 86.5481979982473, - y: 152.77723217737145, - }, - { - id: "57", - label: "57-B", - cluster: "B", - x: -50.53758659577995, - y: 66.17163295696331, - }, - { - id: "58", - label: "58-C", - cluster: "C", - x: 124.99232912102912, - y: 49.17014499847617, - }, - { - id: "59", - label: "59-D", - cluster: "D", - x: 239.03934495453748, - y: 128.19542560190095, - }, - { - id: "60", - label: "60-E", - cluster: "E", - x: 177.46567825384528, - y: 77.58436899474053, - }, - { - id: "61", - label: "61-A", - cluster: "A", - x: 47.80720410493432, - y: 26.910816917159025, - }, - { - id: "62", - label: "62-B", - cluster: "B", - x: 180.75866443546886, - y: -25.603485857861273, - }, - { - id: "63", - label: "63-C", - cluster: "C", - x: 79.94308772846239, - y: 30.250594698990923, - }, - { - id: "64", - label: "64-D", - cluster: "D", - x: 256.69482468295365, - y: 66.62642141029733, - }, - { - id: "65", - label: "65-E", - cluster: "E", - x: -56.27184094162641, - y: 100.60158868441853, - }, - { - id: "66", - label: "66-A", - cluster: "A", - x: 1163.118843617073, - y: 137.54073131117298, - }, - { - id: "67", - label: "67-B", - cluster: "B", - x: 935.6722362869774, - y: 10.961269762472613, - }, - { - id: "68", - label: "68-C", - cluster: "C", - x: 877.6388891428642, - y: -54.423553799531945, - }, - { - id: "69", - label: "69-D", - cluster: "D", - x: 862.5620555673153, - y: 68.21871413386326, - }, - { - id: "70", - label: "70-E", - cluster: "E", - x: 651.8117046813284, - y: 383.43786860491366, - }, - { - id: "71", - label: "71-A", - cluster: "A", - x: 112.32321798605142, - y: 110.57036191354275, - }, - { - id: "72", - label: "72-B", - cluster: "B", - x: 163.22223644436053, - y: 306.97878145497214, - }, - { - id: "73", - label: "73-C", - cluster: "C", - x: 73.09128707297499, - y: 73.28475817485352, - }, - { - id: "74", - label: "74-D", - cluster: "D", - x: 149.37488556005434, - y: 56.86691119191546, - }, - { - id: "75", - label: "75-E", - cluster: "E", - x: 208.1151118841309, - y: 45.62303635045838, - }, - { - id: "76", - label: "76-A", - cluster: "A", - x: 155.72918363379713, - y: 182.62425088813723, - }, - { - id: "77", - label: "77-B", - cluster: "B", - x: 131.51716435242332, - y: 26.29232947924133, - }, - { - id: "78", - label: "78-C", - cluster: "C", - x: 137.17854905360056, - y: 130.72293947212546, - }, - { - id: "79", - label: "79-D", - cluster: "D", - x: 201.57554128119486, - y: 179.7740851197805, - }, - { - id: "80", - label: "80-E", - cluster: "E", - x: 201.7639359765842, - y: 80.30550969861244, - }, - { - id: "81", - label: "81-A", - cluster: "A", - x: 193.08525675227216, - y: -26.776909498595103, - }, - { - id: "82", - label: "82-B", - cluster: "B", - x: 176.2257737238614, - y: 119.09358069641392, - }, - { - id: "83", - label: "83-C", - cluster: "C", - x: 123.36955853851471, - y: 72.90227074539227, - }, - { - id: "84", - label: "84-D", - cluster: "D", - x: 95.64731600310219, - y: 191.94832453165574, - }, - { - id: "85", - label: "85-E", - cluster: "E", - x: 257.49904006196067, - y: 162.90681458635993, - }, - { - id: "86", - label: "86-A", - cluster: "A", - x: 159.89629572452498, - y: 139.17657479670177, - }, - { - id: "87", - label: "87-B", - cluster: "B", - x: 242.21787636263187, - y: 180.37532154393148, - }, - { - id: "88", - label: "88-C", - cluster: "C", - x: 153.51557429284753, - y: 219.4644332165533, - }, - { - id: "89", - label: "89-D", - cluster: "D", - x: 212.52903527794774, - y: 162.10562812559996, - }, - { - id: "90", - label: "90-E", - cluster: "E", - x: 114.4364042216654, - y: 157.9470622335633, - }, - { - id: "91", - label: "91-A", - cluster: "A", - x: 168.67221661354546, - y: 147.51719703393715, - }, - { - id: "92", - label: "92-B", - cluster: "B", - x: 218.7011415961873, - y: 63.98091093584418, - }, - { - id: "93", - label: "93-C", - cluster: "C", - x: 191.80778191120422, - y: 230.90752723217858, - }, - { - id: "94", - label: "94-D", - cluster: "D", - x: 86.33718673366937, - y: 121.1409627480123, - }, - { - id: "95", - label: "95-E", - cluster: "E", - x: 151.00866403910925, - y: -25.318171679581756, - }, - { - id: "96", - label: "96-A", - cluster: "A", - x: 87.6034441569486, - y: 221.12987808165747, - }, - { - id: "97", - label: "97-B", - cluster: "B", - x: 189.98824266912817, - y: 100.82865551344841, - }, - { - id: "98", - label: "98-C", - cluster: "C", - x: 175.75892612938924, - y: 199.98300035294818, - }, - { - id: "99", - label: "99-D", - cluster: "D", - x: 203.27976655688812, - y: 126.51763569908216, - }, - { - id: "100", - label: "100-E", - cluster: "E", - x: 765.5355367329136, - y: 21.991836134813855, - }, - { - id: "101", - label: "101-A", - cluster: "A", - x: 551.8236283021658, - y: 72.3733197711641, - }, - { - id: "102", - label: "102-B", - cluster: "B", - x: 674.3850330350368, - y: 106.79756526421562, - }, - { - id: "103", - label: "103-C", - cluster: "C", - x: 111.07370967244908, - y: -9.790899903800316, - }, - { - id: "104", - label: "104-D", - cluster: "D", - x: 119.21985296306136, - y: 178.81172825379036, - }, - { - id: "105", - label: "105-E", - cluster: "E", - x: 214.86617576389293, - y: -43.19275406620191, - }, - { - id: "106", - label: "106-A", - cluster: "A", - x: 30.289142228062424, - y: -61.72078405043325, - }, - { - id: "107", - label: "107-B", - cluster: "B", - x: 1025.3920882208713, - y: 13.502860193287079, - }, - { - id: "108", - label: "108-C", - cluster: "C", - x: 786.6692472601269, - y: 115.72166424829832, - }, - { - id: "109", - label: "109-D", - cluster: "D", - x: 1024.6034606822714, - y: 220.8015852158882, - }, - { - id: "110", - label: "110-E", - cluster: "E", - x: 615.6865253904227, - y: 419.9760884117146, - }, - { - id: "111", - label: "111-A", - cluster: "A", - x: 971.4477618233167, - y: 187.43451740080653, - }, - { - id: "112", - label: "112-B", - cluster: "B", - x: 945.8801867385047, - y: 92.19746645363625, - }, - { - id: "113", - label: "113-C", - cluster: "C", - x: -353.411964141735, - y: 15.557630395473382, - }, - { - id: "114", - label: "114-D", - cluster: "D", - x: 1088.652155541285, - y: 18.818088004958867, - }, - { - id: "115", - label: "115-E", - cluster: "E", - x: 1086.728613491952, - y: -95.63408676603015, - }, - { - id: "116", - label: "116-A", - cluster: "A", - x: 926.7945186040679, - y: -61.18983090733566, - }, - { - id: "117", - label: "117-B", - cluster: "B", - x: 820.5732912157398, - y: 267.31458070683175, - }, - { - id: "118", - label: "118-C", - cluster: "C", - x: 935.1903441769451, - y: 63.67984213485708, - }, - { - id: "119", - label: "119-D", - cluster: "D", - x: 1024.758652171975, - y: -84.44385070311073, - }, - { - id: "120", - label: "120-E", - cluster: "E", - x: 757.0664354811632, - y: 302.42111840057305, - }, - { - id: "121", - label: "121-A", - cluster: "A", - x: 1007.7437119515743, - y: 109.49839233278878, - }, - { - id: "122", - label: "122-B", - cluster: "B", - x: 1252.2492355396016, - y: 286.24593655305375, - }, - { - 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label: "a" }, - { id: "edge-7400", source: "40", target: "95", cluster: "c", label: "c" }, - { id: "edge-7420", source: "97", target: "77", cluster: "a", label: "a" }, - { id: "edge-7440", source: "97", target: "169", cluster: "a", label: "a" }, - { id: "edge-7460", source: "97", target: "183", cluster: "c", label: "c" }, - { id: "edge-7480", source: "41", target: "75", cluster: "a", label: "a" }, - { id: "edge-7500", source: "41", target: "48", cluster: "c", label: "c" }, - { id: "edge-7520", source: "41", target: "99", cluster: "c", label: "c" }, - { id: "edge-7540", source: "173", target: "128", cluster: "a", label: "a" }, - { id: "edge-7560", source: "173", target: "49", cluster: "c", label: "c" }, - { id: "edge-7580", source: "102", target: "144", cluster: "c", label: "c" }, - { id: "edge-7600", source: "157", target: "58", cluster: "a", label: "a" }, - { id: "edge-7620", source: "157", target: "99", cluster: "a", label: "a" }, - { id: "edge-7640", source: "46", target: "108", cluster: "c", label: "c" }, - { id: "edge-7660", source: "2", target: "105", cluster: "c", label: "c" }, - { id: "edge-7680", source: "2", target: "155", cluster: "a", label: "a" }, - { id: "edge-7700", source: "73", target: "7", cluster: "c", label: "c" }, - { id: "edge-7720", source: "73", target: "168", cluster: "c", label: "c" }, - { id: "edge-7740", source: "7", target: "77", cluster: "c", label: "c" }, - { id: "edge-7760", source: "7", target: "166", cluster: "c", label: "c" }, - { id: "edge-7780", source: "9", target: "12", cluster: "c", label: "c" }, - { id: "edge-7800", source: "9", target: "172", cluster: "c", label: "c" }, - { id: "edge-7820", source: "9", target: "183", cluster: "c", label: "c" }, - { id: "edge-7840", source: "104", target: "99", cluster: "a", label: "a" }, - { id: "edge-7860", source: "11", target: "76", cluster: "c", label: "c" }, - { id: "edge-7880", source: "11", target: "22", cluster: "c", label: "c" }, - { id: "edge-7900", source: "11", target: "48", cluster: "c", label: "c" }, - { id: "edge-7920", source: "12", target: "98", cluster: "c", label: "c" }, - { id: "edge-7940", source: "12", target: "91", cluster: "c", label: "c" }, - { id: "edge-7960", source: "13", target: "178", cluster: "c", label: "c" }, - { id: "edge-7980", source: "14", target: "77", cluster: "c", label: "c" }, - { id: "edge-8000", source: "14", target: "166", cluster: "a", label: "a" }, - { id: "edge-8020", source: "76", target: "141", cluster: "c", label: "c" }, - { id: "edge-8040", source: "130", target: "48", cluster: "c", label: "c" }, - { id: "edge-8060", source: "77", target: "81", cluster: "c", label: "c" }, - { id: "edge-8080", source: "77", target: "95", cluster: "c", label: "c" }, - { id: "edge-8100", source: "106", target: "48", cluster: "c", label: "c" }, - { id: "edge-8120", source: "128", target: "74", cluster: "c", label: "c" }, - { id: "edge-8140", source: "128", target: "95", cluster: "c", label: "c" }, - { id: "edge-8160", source: "86", target: "83", cluster: "a", label: "a" }, - { id: "edge-8180", source: "86", target: "94", cluster: "a", label: "a" }, - { id: "edge-8200", source: "164", target: "4", cluster: "a", label: "a" }, - { id: "edge-8220", source: "164", target: "58", cluster: "c", label: "c" }, - { id: "edge-8240", source: "164", target: "60", cluster: "c", label: "c" }, - { id: "edge-8260", source: "166", target: "187", cluster: "c", label: "c" }, - { id: "edge-8280", source: "166", target: "183", cluster: "c", label: "c" }, - { id: "edge-8300", source: "89", target: "78", cluster: "a", label: "a" }, - { id: "edge-8320", source: "89", target: "184", cluster: "a", label: "a" }, - { id: "edge-8340", source: "158", target: "28", cluster: "a", label: "a" }, - { id: "edge-8360", source: "155", target: "15", cluster: "a", label: "a" }, - { id: "edge-8380", source: "155", target: "95", cluster: "a", label: "a" }, - { id: "edge-8400", source: "60", target: "82", cluster: "a", label: "a" }, - { id: "edge-8420", source: "60", target: "169", cluster: "a", label: "a" }, - { id: "edge-8440", source: "61", target: "58", cluster: "c", label: "c" }, - { id: "edge-8460", source: "91", target: "153", cluster: "c", label: "c" }, - { id: "edge-8480", source: "91", target: "92", cluster: "c", label: "c" }, - { id: "edge-8500", source: "143", target: "99", cluster: "c", label: "c" }, - { id: "edge-8520", source: "99", target: "6", cluster: "c", label: "c" }, - { id: "edge-8540", source: "137", target: "58", cluster: "c", label: "c" }, - { id: "edge-8560", source: "136", target: "74", cluster: "c", label: "c" }, - { id: "edge-8580", source: "185", target: "84", cluster: "c", label: "c" }, - { id: "edge-8600", source: "4", target: "127", cluster: "a", label: "a" }, - { id: "edge-8620", source: "6", target: "78", cluster: "c", label: "c" }, - { id: "edge-8640", source: "6", target: "184", cluster: "c", label: "c" }, - { id: "edge-8660", source: "52", target: "100", cluster: "c", label: "c" }, - { id: "edge-8680", source: "74", target: "64", cluster: "a", label: "a" }, - { id: "edge-8700", source: "10", target: "27", cluster: "a", label: "a" }, - { id: "edge-8720", source: "10", target: "54", cluster: "a", label: "a" }, - { id: "edge-8740", source: "92", target: "82", cluster: "a", label: "a" }, - { id: "edge-8760", source: "49", target: "21", cluster: "c", label: "c" }, - { id: "edge-8780", source: "169", target: "168", cluster: "c", label: "c" }, - { id: "edge-8800", source: "78", target: "172", cluster: "c", label: "c" }, - { id: "edge-8820", source: "79", target: "58", cluster: "a", label: "a" }, - { id: "edge-8840", source: "141", target: "87", cluster: "c", label: "c" }, - { id: "edge-8860", source: "105", target: "22", cluster: "c", label: "c" }, - { id: "edge-8880", source: "87", target: "93", cluster: "c", label: "c" }, - { id: "edge-8900", source: "27", target: "21", cluster: "c", label: "c" }, - { id: "edge-8920", source: "93", target: "84", cluster: "a", label: "a" }, - { id: "edge-8940", source: "127", target: "48", cluster: "a", label: "a" }, - { id: "edge-8960", source: "98", target: "142", cluster: "c", label: "c" }, - { id: "edge-8980", source: "153", target: "55", cluster: "a", label: "a" }, - { id: "edge-9000", source: "64", target: "21", cluster: "c", label: "c" }, - { id: "edge-9020", source: "82", target: "84", cluster: "c", label: "c" }, - { id: "edge-9040", source: "58", target: "172", cluster: "c", label: "c" }, - { id: "edge-9060", source: "142", target: "88", cluster: "c", label: "c" }, - { id: "edge-9080", source: "132", target: "56", cluster: "c", label: "c" }, - { id: "edge-9100", source: "132", target: "133", cluster: "a", label: "a" }, - { id: "edge-9120", source: "1", target: "13", cluster: "c", label: "c" }, - { id: "edge-9140", source: "42", target: "13", cluster: "a", label: "a" }, - { id: "edge-9160", source: "18", target: "44", cluster: "c", label: "c" }, - { id: "edge-9180", source: "50", target: "106", cluster: "a", label: "a" }, - { id: "edge-9200", source: "195", target: "108", cluster: "c", label: "c" }, - { id: "edge-9220", source: "72", target: "93", cluster: "c", label: "c" }, - { id: "edge-9240", source: "19", target: "32", cluster: "c", label: "c" }, - { id: "edge-9260", source: "56", target: "11", cluster: "c", label: "c" }, - { id: "edge-9280", source: "56", target: "154", cluster: "c", label: "c" }, - { id: "edge-9300", source: "56", target: "59", cluster: "a", label: "a" }, - { id: "edge-9320", source: "56", target: "97", cluster: "c", label: "c" }, - { id: "edge-9340", source: "100", target: "37", cluster: "c", label: "c" }, - { id: "edge-9360", source: "23", target: "79", cluster: "a", label: "a" }, - { id: "edge-9380", source: "23", target: "164", cluster: "c", label: "c" }, - { id: "edge-9400", source: "23", target: "143", cluster: "c", label: "c" }, - { id: "edge-9420", source: "25", target: "3", cluster: "a", label: "a" }, - { id: "edge-9440", source: "25", target: "54", cluster: "a", label: "a" }, - { id: "edge-9460", source: "25", target: "127", cluster: "a", label: "a" }, - { id: "edge-9480", source: "25", target: "157", cluster: "c", label: "c" }, - { id: "edge-9500", source: "62", target: "172", cluster: "a", label: "a" }, - { id: "edge-9520", source: "26", target: "9", cluster: "a", label: "a" }, - { id: "edge-9540", source: "26", target: "86", cluster: "c", label: "c" }, - { id: "edge-9560", source: "26", target: "97", cluster: "c", label: "c" }, - { id: "edge-9580", source: "85", target: "79", cluster: "a", label: "a" }, - { id: "edge-9600", source: "85", target: "89", cluster: "a", label: "a" }, - { id: "edge-9620", source: "85", target: "157", cluster: "c", label: "c" }, - { id: "edge-9640", source: "167", target: "125", cluster: "c", label: "c" }, - { id: "edge-9660", source: "90", target: "153", cluster: "a", label: "a" }, - { id: "edge-9680", source: "90", target: "89", cluster: "a", label: "a" }, - { id: "edge-9700", source: "90", target: "98", cluster: "a", label: "a" }, - { id: "edge-9720", source: "133", target: "103", cluster: "c", label: "c" }, - { id: "edge-9740", source: "133", target: "64", cluster: "c", label: "c" }, - { id: "edge-9760", source: "133", target: "168", cluster: "c", label: "c" }, - { id: "edge-9780", source: "133", target: "155", cluster: "a", label: "a" }, - { id: "edge-9800", source: "34", target: "46", cluster: "c", label: "c" }, - { id: "edge-9820", source: "35", target: "80", cluster: "c", label: "c" }, - { id: "edge-9840", source: "35", target: "89", cluster: "c", label: "c" }, - { id: "edge-9860", source: "35", target: "143", cluster: "c", label: "c" }, - { id: "edge-9880", source: "125", target: "21", cluster: "c", label: "c" }, - { id: "edge-9900", source: "126", target: "5", cluster: "c", label: "c" }, - { id: "edge-9920", source: "37", target: "45", cluster: "a", label: "a" }, - { id: "edge-9940", source: "40", target: "3", cluster: "a", label: "a" }, - { id: "edge-9960", source: "40", target: "55", cluster: "a", label: "a" }, - { id: "edge-9980", source: "40", target: "95", cluster: "c", label: "c" }, - { id: "edge-10000", source: "97", target: "14", cluster: "c", label: "c" }, - { id: "edge-10020", source: "97", target: "59", cluster: "a", label: "a" }, - { id: "edge-10040", source: "97", target: "60", cluster: "a", label: "a" }, - { id: "edge-10060", source: "41", target: "77", cluster: "a", label: "a" }, - { id: "edge-10080", source: "41", target: "166", cluster: "a", label: "a" }, - { id: "edge-10100", source: "173", target: "73", cluster: "a", label: "a" }, - { id: "edge-10120", source: "173", target: "55", cluster: "c", label: "c" }, - { id: "edge-10140", source: "173", target: "61", cluster: "a", label: "a" }, - { - id: "edge-10160", - source: "102", - target: "101", - cluster: "c", - label: "c", - }, - { id: "edge-10180", source: "157", target: "15", cluster: "a", label: "a" }, - { id: "edge-10200", source: "157", target: "86", cluster: "a", label: "a" }, - { id: "edge-10220", source: "157", target: "99", cluster: "a", label: "a" }, - { id: "edge-10240", source: "2", target: "73", cluster: "c", label: "c" }, - { id: "edge-10260", source: "2", target: "83", cluster: "a", label: "a" }, - { id: "edge-10280", source: "2", target: "92", cluster: "c", label: "c" }, - { id: "edge-10300", source: "51", target: "12", cluster: "a", label: "a" }, - { id: "edge-10320", source: "51", target: "166", cluster: "a", label: "a" }, - { - id: "edge-10340", - source: "103", - target: "106", - cluster: "a", - label: "a", - }, - { id: "edge-10360", source: "73", target: "6", cluster: "c", label: "c" }, - { id: "edge-10380", source: "73", target: "58", cluster: "c", label: "c" }, - { id: "edge-10400", source: "7", target: "27", cluster: "c", label: "c" }, - { id: "edge-10420", source: "7", target: "58", cluster: "c", label: "c" }, - { id: "edge-10440", source: "7", target: "136", cluster: "c", label: "c" }, - { id: "edge-10460", source: "9", target: "11", cluster: "a", label: "a" }, - { id: "edge-10480", source: "9", target: "21", cluster: "c", label: "c" }, - { id: "edge-10500", source: "9", target: "95", cluster: "a", label: "a" }, - { id: "edge-10520", source: "178", target: "28", cluster: "c", label: "c" }, - { id: "edge-10540", source: "165", target: "22", cluster: "c", label: "c" }, - { id: "edge-10560", source: "11", target: "3", cluster: "c", label: "c" }, - { id: "edge-10580", source: "11", target: "142", cluster: "c", label: "c" }, - { id: "edge-10600", source: "12", target: "4", cluster: "a", label: "a" }, - { id: "edge-10620", source: "12", target: "193", cluster: "c", label: "c" }, - { id: "edge-10640", source: "12", target: "94", cluster: "a", label: "a" }, - { id: "edge-10660", source: "13", target: "32", cluster: "a", label: "a" }, - { id: "edge-10680", source: "14", target: "55", cluster: "a", label: "a" }, - { id: "edge-10700", source: "76", target: "27", cluster: "a", label: "a" }, - { id: "edge-10720", source: "76", target: "87", cluster: "c", label: "c" }, - { id: "edge-10740", source: "130", target: "49", cluster: "c", label: "c" }, - { id: "edge-10760", source: "77", target: "54", cluster: "a", label: "a" }, - { id: "edge-10780", source: "77", target: "142", cluster: "a", label: "a" }, - { id: "edge-10800", source: "77", target: "99", cluster: "c", label: "c" }, - { id: "edge-10820", source: "45", target: "20", cluster: "a", label: "a" }, - { id: "edge-10840", source: "86", target: "79", cluster: "a", label: "a" }, - { id: "edge-10860", source: "86", target: "88", cluster: "c", label: "c" }, - { id: "edge-10880", source: "86", target: "99", cluster: "c", label: "c" }, - { id: "edge-10900", source: "164", target: "82", cluster: "c", label: "c" }, - { - id: "edge-10920", - source: "164", - target: "136", - cluster: "c", - label: "c", - }, - { id: "edge-10940", source: "166", target: "79", cluster: "a", label: "a" }, - { id: "edge-10960", source: "166", target: "94", cluster: "c", label: "c" }, - { id: "edge-10980", source: "89", target: "10", cluster: "c", label: "c" }, - { id: "edge-11000", source: "89", target: "87", cluster: "c", label: "c" }, - { id: "edge-11020", source: "158", target: "20", cluster: "a", label: "a" }, - { - id: "edge-11040", - source: "155", - target: "153", - cluster: "a", - label: "a", - }, - { id: "edge-11060", source: "155", target: "61", cluster: "a", label: "a" }, - { id: "edge-11080", source: "60", target: "17", cluster: "c", label: "c" }, - { id: "edge-11100", source: "60", target: "91", cluster: "c", label: "c" }, - { id: "edge-11120", source: "61", target: "153", cluster: "a", label: "a" }, - { id: "edge-11140", source: "61", target: "94", cluster: "a", label: "a" }, - { id: "edge-11160", source: "91", target: "55", cluster: "c", label: "c" }, - { id: "edge-11180", source: "143", target: "27", cluster: "c", label: "c" }, - { - id: "edge-11200", - source: "143", - target: "142", - cluster: "a", - label: "a", - }, - { id: "edge-11220", source: "99", target: "3", cluster: "a", label: "a" }, - { id: "edge-11240", source: "99", target: "93", cluster: "a", label: "a" }, - { id: "edge-11260", source: "95", target: "193", cluster: "a", label: "a" }, - { id: "edge-11280", source: "136", target: "80", cluster: "a", label: "a" }, - { id: "edge-11300", source: "136", target: "92", cluster: "a", label: "a" }, - { id: "edge-11320", source: "4", target: "21", cluster: "c", label: "c" }, - { id: "edge-11340", source: "6", target: "27", cluster: "a", label: "a" }, - { id: "edge-11360", source: "6", target: "172", cluster: "a", label: "a" }, - { id: "edge-11380", source: "52", target: "67", cluster: "a", label: "a" }, - { id: "edge-11400", source: "74", target: "78", cluster: "c", label: "c" }, - { id: "edge-11420", source: "74", target: "94", cluster: "a", label: "a" }, - { id: "edge-11440", source: "10", target: "172", cluster: "c", label: "c" }, - { id: "edge-11460", source: "92", target: "59", cluster: "c", label: "c" }, - { id: 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label: "a" }, - { id: "edge-11740", source: "94", target: "84", cluster: "c", label: "c" }, - { id: "edge-11760", source: "39", target: "48", cluster: "c", label: "c" }, - { id: "edge-11780", source: "98", target: "172", cluster: "c", label: "c" }, - { - id: "edge-11800", - source: "153", - target: "168", - cluster: "c", - label: "c", - }, - { id: "edge-11820", source: "80", target: "58", cluster: "a", label: "a" }, - { id: "edge-11840", source: "193", target: "58", cluster: "a", label: "a" }, - { id: "edge-11860", source: "55", target: "154", cluster: "c", label: "c" }, - { id: "edge-11880", source: "172", target: "22", cluster: "c", label: "c" }, - ], -}; - -export const nodes1589 = { - nodes: [ - { - id: "0", - olabel: "Kuperman_M", - x: 26.22602890442184, - y: 33.48766498594824, - cluster: "A", - label: "0-A", - degree: 1.4422495703074083, - }, - { - id: "1", - olabel: "Acebron_J", - x: 762.9747722969743, - y: 1076.5655474780835, - cluster: "B", - label: "1-B", - degree: 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}, - { - source: "1559", - target: "218", - cluster: "B", - label: "B", - color: "#333", - id: "edge2681", - }, - { - source: "1560", - target: "1559", - cluster: "C", - label: "C", - color: "#333", - id: "edge2682", - }, - { - source: "1560", - target: "1144", - cluster: "B", - label: "B", - color: "#333", - id: "edge2683", - }, - { - source: "1560", - target: "218", - cluster: "C", - label: "C", - color: "#333", - id: "edge2684", - }, - { - source: "1561", - target: "62", - cluster: "A", - label: "A", - color: "#333", - id: "edge2685", - }, - { - source: "1561", - target: "61", - cluster: "C", - label: "C", - color: "#333", - id: "edge2686", - }, - { - source: "1562", - target: "1561", - cluster: "A", - label: "A", - color: "#333", - id: "edge2687", - }, - { - source: "1562", - target: "62", - cluster: "B", - label: "B", - color: "#333", - id: "edge2688", - }, - { - source: "1562", - target: "61", - cluster: "A", - label: "A", - color: "#333", - id: "edge2689", - }, - { - source: "1563", - target: "1561", - cluster: "B", - label: "B", - color: "#333", - id: "edge2690", - }, - { - source: "1563", - target: "1562", - cluster: "C", - label: "C", - color: "#333", - id: "edge2691", - }, - { - source: "1563", - target: "62", - cluster: "C", - label: "C", - color: "#333", - id: "edge2692", - }, - { - source: "1563", - target: "61", - cluster: "B", - label: "B", - color: "#333", - id: "edge2693", - }, - { - source: "1564", - target: "1561", - cluster: "C", - label: "C", - color: "#333", - id: "edge2694", - }, - { - source: "1564", - target: "1562", - cluster: "A", - label: "A", - color: "#333", - id: "edge2695", - }, - { - source: "1564", - target: "1563", - cluster: "B", - label: "B", - color: "#333", - id: "edge2696", - }, - { - source: "1564", - target: "62", - cluster: "A", - label: "A", - color: "#333", - id: "edge2697", - }, - { - source: "1564", - target: "61", - cluster: "C", - label: "C", - color: "#333", - id: "edge2698", - }, - { - source: "1565", - target: "1561", - cluster: "A", - label: "A", - color: "#333", - id: "edge2699", - }, - { - source: "1565", - target: "1562", - cluster: "B", - label: "B", - color: "#333", - id: "edge2700", - }, - { - source: "1565", - target: "1563", - cluster: "C", - label: "C", - color: "#333", - id: "edge2701", - }, - { - source: "1565", - target: "1564", - cluster: "A", - label: "A", - color: "#333", - id: "edge2702", - }, - { - source: "1565", - target: "62", - cluster: "B", - label: "B", - color: "#333", - id: "edge2703", - }, - { - source: "1565", - target: "61", - cluster: "A", - label: "A", - color: "#333", - id: "edge2704", - }, - { - source: "1566", - target: "1561", - cluster: "B", - label: "B", - color: "#333", - id: "edge2705", - }, - { - source: "1566", - target: "1562", - cluster: "C", - label: "C", - color: "#333", - id: "edge2706", - }, - { - source: "1566", - target: "1563", - cluster: "A", - label: "A", - color: "#333", - id: "edge2707", - }, - { - source: "1566", - target: "1564", - cluster: "B", - label: "B", - color: "#333", - id: "edge2708", - }, - { - source: "1566", - target: "1565", - cluster: "C", - label: "C", - color: "#333", - id: "edge2709", - }, - { - source: "1566", - target: "62", - cluster: "C", - label: "C", - color: "#333", - id: "edge2710", - }, - { - source: "1566", - target: "61", - cluster: "B", - label: "B", - color: "#333", - id: "edge2711", - }, - { - source: "1568", - target: "1567", - cluster: "A", - label: "A", - color: "#333", - id: "edge2712", - }, - { - source: "1569", - target: "336", - cluster: "A", - label: "A", - color: "#333", - id: "edge2713", - }, - { - source: "1569", - target: "630", - cluster: "A", - label: "A", - color: "#333", - id: "edge2714", - }, - { - source: "1570", - target: "336", - cluster: "B", - label: "B", - color: "#333", - id: "edge2715", - }, - { - source: "1570", - target: "630", - cluster: "B", - label: "B", - color: "#333", - id: "edge2716", - }, - { - source: "1570", - target: "1569", - cluster: "B", - label: "B", - color: "#333", - id: "edge2717", - }, - { - source: "1571", - target: "336", - cluster: "C", - label: "C", - color: "#333", - id: "edge2718", - }, - { - source: "1571", - target: "630", - cluster: "C", - label: "C", - color: "#333", - id: "edge2719", - }, - { - source: "1571", - target: "1569", - cluster: "C", - label: "C", - color: "#333", - id: "edge2720", - }, - { - source: "1571", - target: "1570", - cluster: "A", - label: "A", - color: "#333", - id: "edge2721", - }, - { - source: "1572", - target: "336", - cluster: "A", - label: "A", - color: "#333", - id: "edge2722", - }, - { - source: "1572", - target: "630", - cluster: "A", - label: "A", - color: "#333", - id: "edge2723", - }, - { - source: "1572", - target: "1569", - cluster: "A", - label: "A", - color: "#333", - id: "edge2724", - }, - { - source: "1572", - target: "1570", - cluster: "B", - label: "B", - color: "#333", - id: "edge2725", - }, - { - source: "1572", - target: "1571", - cluster: "C", - label: "C", - color: "#333", - id: "edge2726", - }, - { - source: "1573", - target: "630", - cluster: "B", - label: "B", - color: "#333", - id: "edge2727", - }, - { - source: "1573", - target: "782", - cluster: "A", - label: "A", - color: "#333", - id: "edge2728", - }, - { - source: "1575", - target: "1574", - cluster: "C", - label: "C", - color: "#333", - id: "edge2729", - }, - { - source: "1576", - target: "1574", - cluster: "A", - label: "A", - color: "#333", - id: "edge2730", - }, - { - source: "1576", - target: "1575", - cluster: "B", - label: "B", - color: "#333", - id: "edge2731", - }, - { - source: "1577", - target: "1574", - cluster: "B", - label: "B", - color: "#333", - id: "edge2732", - }, - { - source: "1577", - target: "1575", - cluster: "C", - label: "C", - color: "#333", - id: "edge2733", - }, - { - source: "1577", - target: "1576", - cluster: "A", - label: "A", - color: "#333", - id: "edge2734", - }, - { - source: "1578", - target: "630", - cluster: "A", - label: "A", - color: "#333", - id: "edge2735", - }, - { - source: "1578", - target: "629", - cluster: "C", - label: "C", - color: "#333", - id: "edge2736", - }, - { - source: "1580", - target: "1579", - cluster: "A", - label: "A", - color: "#333", - id: "edge2737", - }, - { - source: "1583", - target: "1582", - cluster: "A", - label: "A", - color: "#333", - id: "edge2738", - }, - { - source: "1585", - target: "1584", - cluster: "B", - label: "B", - color: "#333", - id: "edge2739", - }, - { - source: "1586", - target: "1584", - cluster: "C", - label: "C", - color: "#333", - id: "edge2740", - }, - { - source: "1587", - target: "521", - cluster: "C", - label: "C", - color: "#333", - id: "edge2741", - }, - { - source: "1587", - target: "75", - cluster: "A", - label: "A", - color: "#333", - id: "edge2742", - }, - ], -}; diff --git a/packages/graph/tests/unit/degree-async-spec.ts b/packages/graph/tests/unit/degree-async-spec.ts deleted file mode 100644 index e9debc2..0000000 --- a/packages/graph/tests/unit/degree-async-spec.ts +++ /dev/null @@ -1,119 +0,0 @@ -import { getAlgorithm } from './utils'; - -const data = { - nodes: [ - { - id: 'A', - }, - { - id: 'B', - }, - { - id: 'C', - }, - { - id: 'D', - }, - { - id: 'E', - }, - { - id: 'F', - }, - { - id: 'G', - }, - { - id: 'H', - }, - ], - edges: [ - { - source: 'A', - target: 'B', - }, - { - source: 'B', - target: 'C', - }, - { - source: 'A', - target: 'C', - }, - { - source: 'D', - target: 'A', - }, - { - source: 'D', - target: 'E', - }, - { - source: 'E', - target: 'F', - }, - { - source: 'F', - target: 'D', - }, - { - source: 'G', - target: 'H', - }, - { - source: 'H', - target: 'G', - }, - ], -}; - -describe('degree async algorithm', () => { - it('getDegreeAsync', async () => { - const degree = { - A: { - degree: 3, - inDegree: 1, - outDegree: 2, - }, - B: { - degree: 2, - inDegree: 1, - outDegree: 1, - }, - C: { - degree: 2, - inDegree: 2, - outDegree: 0, - }, - D: { - degree: 3, - inDegree: 1, - outDegree: 2, - }, - E: { - degree: 2, - inDegree: 1, - outDegree: 1, - }, - F: { - degree: 2, - inDegree: 1, - outDegree: 1, - }, - G: { - degree: 2, - inDegree: 1, - outDegree: 1, - }, - H: { - degree: 2, - inDegree: 1, - outDegree: 1, - }, - }; - - const { getDegreeAsync } = await getAlgorithm(); - const result = await getDegreeAsync(data); - expect(result).toEqual(degree); - }); -}); diff --git a/packages/graph/tests/unit/degree-spec.ts b/packages/graph/tests/unit/degree-spec.ts deleted file mode 100644 index 3fedf65..0000000 --- a/packages/graph/tests/unit/degree-spec.ts +++ /dev/null @@ -1,139 +0,0 @@ -import { getDegree, getInDegree, getOutDegree } from '../../src' - -const data = { - nodes: [ - { - id: 'A', - }, - { - id: 'B', - }, - { - id: 'C', - }, - { - id: 'D', - }, - { - id: 'E', - }, - { - id: 'F', - }, - { - id: 'G', - }, - { - id: 'H', - }, - ], - edges: [ - { - source: 'A', - target: 'B', - }, - { - source: 'B', - target: 'C', - }, - { - source: 'A', - target: 'C', - }, - { - source: 'D', - target: 'A', - }, - { - source: 'D', - target: 'E', - }, - { - source: 'E', - target: 'F', - }, - { - source: 'F', - target: 'D', - }, - { - source: 'G', - target: 'H', - }, - { - source: 'H', - target: 'G', - }, - ], -}; - -describe('degree algorithm', () => { - it('getDegree', () => { - const degree = { - A: { - degree: 3, - inDegree: 1, - outDegree: 2 - }, - B: { - degree: 2, - inDegree: 1, - outDegree: 1 - }, - C: { - degree: 2, - inDegree: 2, - outDegree: 0 - }, - D: { - degree: 3, - inDegree: 1, - outDegree: 2 - }, - E: { - degree: 2, - inDegree: 1, - outDegree: 1 - }, - F: { - degree: 2, - inDegree: 1, - outDegree: 1 - }, - G: { - degree: 2, - inDegree: 1, - outDegree: 1 - }, - H: { - degree: 2, - inDegree: 1, - outDegree: 1 - } - } - let result = getDegree(data); - expect(result).toEqual(degree); - }); - - it('getInDegree', () => { - let result = getInDegree(data, 'A'); - expect(result).toBe(1); - - result = getInDegree(data, 'C') - expect(result).toBe(2) - - result = getInDegree(data, 'E') - expect(result).toBe(1) - }); - - it('getOutDegree', () => { - let result = getOutDegree(data, 'A'); - expect(result).toEqual(2); - - result = getOutDegree(data, 'D'); - expect(result).toEqual(2); - - result = getOutDegree(data, 'F'); - expect(result).toEqual(1); - }); -}); diff --git a/packages/graph/tests/unit/detect-cycle-async-spec.ts b/packages/graph/tests/unit/detect-cycle-async-spec.ts deleted file mode 100644 index f469fda..0000000 --- a/packages/graph/tests/unit/detect-cycle-async-spec.ts +++ /dev/null @@ -1,74 +0,0 @@ -import { getAlgorithm } from './utils'; - -const data = { - nodes: [ - { - id: 'A', - }, - { - id: 'B', - }, - { - id: 'C', - }, - { - id: 'D', - }, - { - id: 'E', - }, - { - id: 'F', - }, - { - id: 'G', - }, - ], - edges: [ - { - source: 'A', - target: 'B', - }, - { - source: 'B', - target: 'C', - }, - { - source: 'A', - target: 'C', - }, - { - source: 'D', - target: 'A', - }, - { - source: 'D', - target: 'E', - }, - { - source: 'E', - target: 'F', - }, - ], -}; - -describe('(Async) detectDirectedCycle', () => { - it('should detect directed cycle', async () => { - const { detectCycleAsync } = await getAlgorithm(); - - let result = await detectCycleAsync(data); - expect(result).toBeNull(); - - data.edges.push({ - source: 'F', - target: 'D', - }); - - result = await detectCycleAsync(data); - expect(result).toEqual({ - D: 'F', - F: 'E', - E: 'D', - }); - }); -}); diff --git a/packages/graph/tests/unit/detect-cycle-spec.ts b/packages/graph/tests/unit/detect-cycle-spec.ts deleted file mode 100644 index 8bbabc2..0000000 --- a/packages/graph/tests/unit/detect-cycle-spec.ts +++ /dev/null @@ -1,508 +0,0 @@ -import detectDirectedCycle, { detectAllCycles } from '../../src/detect-cycle'; - -const data = { - nodes: [ - { - id: 'A', - }, - { - id: 'B', - }, - { - id: 'C', - }, - { - id: 'D', - }, - { - id: 'E', - }, - { - id: 'F', - }, - { - id: 'G', - }, - ], - edges: [ - { - source: 'A', - target: 'B', - }, - { - source: 'B', - target: 'C', - }, - { - source: 'A', - target: 'C', - }, - { - source: 'D', - target: 'A', - }, - { - source: 'D', - target: 'E', - }, - { - source: 'E', - target: 'F', - }, - ], -}; - -describe('detectDirectedCycle', () => { - it('should detect directed cycle', () => { - let result = detectDirectedCycle(data); - // debugger - expect(result).toBeNull(); - - data.edges.push({ - source: 'F', - target: 'D', - }); - - // 返回格式： - // { currentNodeId: prevNode } - result = detectDirectedCycle(data); - expect(result).toEqual({ - D: 'F', - F: 'E', - E: 'D', - }); - }); - it('detect all cycles in directed graph', () => { - data.edges.push({ - source: 'C', - target: 'D', - }); - - const result = detectAllCycles(data, true); - expect(result.length).toEqual(3); - - const result2 = detectAllCycles(data, true, ['B']); - expect(result2.length).toEqual(1); - - expect(result2[0]).toEqual({ - A: { id: 'B' }, - B: { id: 'C' }, - C: { id: 'D' }, - D: { id: 'A' }, - }); - }); - it('detect cycle in undirected graph', () => { - const result = detectAllCycles(data); - expect(result.length).toEqual(3); - const result2 = detectAllCycles(data, false, ['B'], false); - expect(Object.keys(result2[0]).sort()).toEqual(['D', 'E', 'F']); - }); - it('test another graph', () => { - const graphData = { - nodes: [ - { - id: '0', - label: '0', - }, - { - id: '1', - label: '1', - }, - { - id: '2', - label: '2', - }, - { - id: '3', - label: '3', - }, - { - id: '4', - label: '4', - }, - { - id: '5', - label: '5', - }, - { - id: '6', - label: '6', - }, - { - id: '7', - label: '7', - }, - { - id: '8', - label: '8', - }, - { - id: '9', - label: '9', - }, - { - id: '10', - label: '10', - }, - { - id: '11', - label: '11', - }, - { - id: '12', - label: '12', - }, - { - id: '13', - label: '13', - }, - { - id: '14', - label: '14', - }, - { - id: '15', - label: '15', - }, - { - id: '16', - label: '16', - }, - { - id: '17', - label: '17', - }, - { - id: '18', - label: '18', - }, - { - id: '19', - label: '19', - }, - { - id: '20', - label: '20', - }, - { - id: '21', - label: '21', - }, - { - id: '22', - label: '22', - }, - { - id: '23', - label: '23', - }, - { - id: '24', - label: '24', - }, - { - id: '25', - label: '25', - }, - { - id: '26', - label: '26', - }, - { - id: '27', - label: '27', - }, - { - id: '28', - label: '28', - }, - { - id: '29', - label: '29', - }, - { - id: '30', - label: '30', - }, - { - id: '31', - label: '31', - }, - { - id: '32', - label: '32', - }, - { - id: '33', - label: '33', - }, - ], - edges: [ - { - source: '0', - target: '1', - }, - { - source: '0', - target: '2', - }, - { - source: '3', - target: '0', - }, - { - source: '0', - target: '4', - }, - { - source: '5', - target: '0', - }, - { - source: '0', - target: '7', - }, - { - source: '0', - target: '8', - }, - { - source: '0', - target: '9', - }, - { - source: '0', - target: '10', - }, - { - source: '0', - target: '11', - }, - { - source: '0', - target: '13', - }, - { - source: '14', - target: '0', - }, - { - source: '0', - target: '15', - }, - { - source: '0', - target: '16', - }, - { - source: '2', - target: '3', - }, - { - source: '4', - target: '5', - }, - { - source: '4', - target: '6', - }, - { - source: '5', - target: '6', - }, - { - source: '7', - target: '13', - }, - { - source: '8', - target: '14', - }, - { - source: '9', - target: '10', - }, - { - source: '10', - target: '22', - }, - { - source: '10', - target: '14', - }, - { - source: '10', - target: '12', - }, - { - source: '10', - target: '24', - }, - { - source: '10', - target: '21', - }, - { - source: '10', - target: '20', - }, - { - source: '11', - target: '24', - }, - { - source: '11', - target: '22', - }, - { - source: '11', - target: '14', - }, - { - source: '12', - target: '13', - }, - { - source: '16', - target: '17', - }, - { - source: '16', - target: '18', - }, - { - source: '16', - target: '21', - }, - { - source: '16', - target: '22', - }, - { - source: '17', - target: '18', - }, - { - source: '17', - target: '20', - }, - { - source: '18', - target: '19', - }, - { - source: '19', - target: '20', - }, - { - source: '19', - target: '33', - }, - { - source: '19', - target: '22', - }, - { - source: '19', - target: '23', - }, - { - source: '20', - target: '21', - }, - { - source: '21', - target: '22', - }, - { - source: '22', - target: '24', - }, - { - source: '22', - target: '25', - }, - { - source: '22', - target: '26', - }, - { - source: '22', - target: '23', - }, - { - source: '22', - target: '28', - }, - { - source: '22', - target: '30', - }, - { - source: '22', - target: '31', - }, - { - source: '22', - target: '32', - }, - { - source: '22', - target: '33', - }, - { - source: '23', - target: '28', - }, - { - source: '23', - target: '27', - }, - { - source: '23', - target: '29', - }, - { - source: '23', - target: '30', - }, - { - source: '23', - target: '31', - }, - { - source: '23', - target: '33', - }, - { - source: '32', - target: '33', - }, - ], - }; - const result = detectAllCycles(graphData, true, ['14']); - const result2 = detectAllCycles(graphData); - expect(result.length).toEqual(4); - expect(result2.length).toEqual(27); - }); - it('test a large graph', () => { - fetch('https://gw.alipayobjects.com/os/basement_prod/da5a1b47-37d6-44d7-8d10-f3e046dabf82.json') - .then((res) => res.json()) - .then((data) => { - data.nodes.forEach((node) => { - node.label = node.olabel; - node.degree = 0; - data.edges.forEach((edge) => { - if (edge.source === node.id || edge.target === node.id) { - node.degree++; - } - }); - }); - - const directedCycles = detectAllCycles(data, true); - expect(directedCycles.length).toEqual(0); - const undirectedCycles = detectAllCycles(data, false, ['1084'], false); - expect(undirectedCycles.length).toEqual(1548); - }); - }); -}); diff --git a/packages/graph/tests/unit/dfs-spec.ts b/packages/graph/tests/unit/dfs-spec.ts deleted file mode 100644 index 9afc547..0000000 --- a/packages/graph/tests/unit/dfs-spec.ts +++ /dev/null @@ -1,170 +0,0 @@ -import { depthFirstSearch } from '../../src'; - -const data = { - nodes: [ - { - id: 'A', - }, - { - id: 'B', - }, - { - id: 'C', - }, - { - id: 'D', - }, - { - id: 'E', - }, - { - id: 'F', - }, - { - id: 'G', - }, - ], - edges: [ - { - source: 'A', - target: 'B', - }, - { - source: 'B', - target: 'C', - }, - { - source: 'C', - target: 'G', - }, - { - source: 'A', - target: 'D', - }, - { - source: 'A', - target: 'E', - }, - { - source: 'E', - target: 'F', - }, - { - source: 'F', - target: 'D', - }, - { - source: 'D', - target: 'G', - }, - ], -}; - -describe('depthFirstSearch', () => { - it('should perform DFS operation on graph', () => { - - const enterNodeCallback = jest.fn(); - const leaveNodeCallback = jest.fn(); - - // Traverse graphs without callbacks first to check default ones. - depthFirstSearch(data, 'A'); - - // Traverse graph with enterNode and leaveNode callbacks. - depthFirstSearch(data, 'A', { - enter: enterNodeCallback, - leave: leaveNodeCallback, - }); - - expect(enterNodeCallback).toHaveBeenCalledTimes(data.nodes.length); - expect(leaveNodeCallback).toHaveBeenCalledTimes(data.nodes.length); - - const enterNodeParamsMap = [ - { currentNode: 'A', previousNode: '' }, - { currentNode: 'B', previousNode: 'A' }, - { currentNode: 'C', previousNode: 'B' }, - { currentNode: 'G', previousNode: 'C' }, - { currentNode: 'D', previousNode: 'A' }, - { currentNode: 'E', previousNode: 'A' }, - { currentNode: 'F', previousNode: 'E' }, - ]; - - for (let callIndex = 0; callIndex < data.nodes.length; callIndex += 1) { - const params = enterNodeCallback.mock.calls[callIndex][0]; - expect(params.current).toEqual(enterNodeParamsMap[callIndex].currentNode); - expect(params.previous).toEqual( - enterNodeParamsMap[callIndex].previousNode, - ); - } - - const leaveNodeParamsMap = [ - { currentNode: 'G', previousNode: 'C' }, - { currentNode: 'C', previousNode: 'B' }, - { currentNode: 'B', previousNode: 'A' }, - { currentNode: 'D', previousNode: 'A' }, - { currentNode: 'F', previousNode: 'E' }, - { currentNode: 'E', previousNode: 'A' }, - { currentNode: 'A', previousNode: '' }, - ]; - - for (let callIndex = 0; callIndex < data.nodes.length; callIndex += 1) { - const params = leaveNodeCallback.mock.calls[callIndex][0]; - expect(params.current).toEqual(leaveNodeParamsMap[callIndex].currentNode); - expect(params.previous).toEqual( - leaveNodeParamsMap[callIndex].previousNode, - ); - } - }); - - it('allow users to redefine node visiting logic', () => { - - const enterNodeCallback = jest.fn(); - const leaveNodeCallback = jest.fn(); - - depthFirstSearch(data, 'A', { - enter: enterNodeCallback, - leave: leaveNodeCallback, - allowTraversal: ({ current: currentNode, next: nextNode }) => { - return !(currentNode === 'A' && nextNode === 'B'); - }, - }); - - expect(enterNodeCallback).toHaveBeenCalledTimes(7); - expect(leaveNodeCallback).toHaveBeenCalledTimes(7); - - const enterNodeParamsMap = [ - { currentNode: 'A', previousNode: '' }, - { currentNode: 'D', previousNode: 'A' }, - { currentNode: 'G', previousNode: 'D' }, - { currentNode: 'E', previousNode: 'A' }, - { currentNode: 'F', previousNode: 'E' }, - { currentNode: 'D', previousNode: 'F' }, - { currentNode: 'G', previousNode: 'D' }, - ]; - - for (let callIndex = 0; callIndex < data.nodes.length; callIndex += 1) { - const params = enterNodeCallback.mock.calls[callIndex][0]; - expect(params.current).toEqual(enterNodeParamsMap[callIndex].currentNode); - expect(params.previous && params.previous).toEqual( - enterNodeParamsMap[callIndex].previousNode, - ); - } - - const leaveNodeParamsMap = [ - { currentNode: 'G', previousNode: 'D' }, - { currentNode: 'D', previousNode: 'A' }, - { currentNode: 'G', previousNode: 'D' }, - { currentNode: 'D', previousNode: 'F' }, - { currentNode: 'F', previousNode: 'E' }, - { currentNode: 'E', previousNode: 'A' }, - { currentNode: 'A', previousNode: '' }, - ]; - - for (let callIndex = 0; callIndex < data.nodes.length; callIndex += 1) { - const params = leaveNodeCallback.mock.calls[callIndex][0]; - expect(params.current).toEqual(leaveNodeParamsMap[callIndex].currentNode); - expect(params.previous).toEqual( - leaveNodeParamsMap[callIndex].previousNode, - ); - } - }); -}); diff --git a/packages/graph/tests/unit/find-path-async-spec.ts b/packages/graph/tests/unit/find-path-async-spec.ts deleted file mode 100644 index ef99e05..0000000 --- a/packages/graph/tests/unit/find-path-async-spec.ts +++ /dev/null @@ -1,132 +0,0 @@ -import { getAlgorithm } from './utils'; - -const data = { - nodes: [ - { - id: 'A', - label: 'A', - }, - { - id: 'B', - label: 'B', - }, - { - id: 'C', - label: 'C', - }, - { - id: 'D', - label: 'D', - }, - { - id: 'E', - label: 'E', - }, - { - id: 'F', - label: 'F', - }, - { - id: 'G', - label: 'G', - }, - { - id: 'H', - label: 'H', - }, - ], - edges: [ - { - source: 'A', - target: 'B', - }, - { - source: 'B', - target: 'C', - }, - { - source: 'C', - target: 'G', - }, - { - source: 'A', - target: 'D', - }, - { - source: 'A', - target: 'E', - }, - { - source: 'E', - target: 'F', - }, - { - source: 'F', - target: 'D', - }, - { - source: 'D', - target: 'E', - }, - ], -}; - -describe('(Async) Shortest Path from source to target on graph', () => { - it('find the shortest path', async done => { - const { findShortestPathAsync } = await getAlgorithm(); - const { length, path } = await findShortestPathAsync(data, 'A', 'C'); - expect(length).toBe(2); - expect(path).toStrictEqual(['A', 'B', 'C']); - done(); - }); - - it('find all shortest paths', async done => { - const { findShortestPathAsync } = await getAlgorithm(); - const { length, allPath } = await findShortestPathAsync(data, 'A', 'F'); - expect(length).toBe(2); - expect(allPath[0]).toStrictEqual(['A', 'E', 'F']); - expect(allPath[1]).toStrictEqual(['A', 'D', 'F']); - - const { - length: directedLenght, - path: directedPath, - allPath: directedAllPath, - } = await findShortestPathAsync(data, 'A', 'F', true); - expect(directedLenght).toBe(2); - expect(directedAllPath[0]).toStrictEqual(['A', 'E', 'F']); - expect(directedPath).toStrictEqual(['A', 'E', 'F']); - done(); - }); - - it('find all paths', async done => { - const { findAllPathAsync } = await getAlgorithm(); - const allPath = await findAllPathAsync(data, 'A', 'E'); - expect(allPath.length).toBe(3); - expect(allPath[0]).toStrictEqual(['A', 'D', 'F', 'E']); - expect(allPath[1]).toStrictEqual(['A', 'D', 'E']); - expect(allPath[2]).toStrictEqual(['A', 'E']); - done(); - }); - - it('find all paths in directed graph', async done => { - const { findAllPathAsync } = await getAlgorithm(); - const allPath = await findAllPathAsync(data, 'A', 'E', true); - expect(allPath.length).toStrictEqual(2); - expect(allPath[0]).toStrictEqual(['A', 'D', 'E']); - expect(allPath[1]).toStrictEqual(['A', 'E']); - done(); - }); - - it('find all shortest paths in weighted graph', async done => { - const { findShortestPathAsync } = await getAlgorithm(); - data.edges.forEach((edge: any, i) => { - edge.weight = ((i % 2) + 1) * 2; - if (edge.source === 'F' && edge.target === 'D') edge.weight = 10; - }); - const { length, path, allPath } = await findShortestPathAsync(data, 'A', 'F', false, 'weight'); - expect(length).toBe(6); - expect(allPath[0]).toStrictEqual(['A', 'E', 'F']); - expect(path).toStrictEqual(['A', 'E', 'F']); - done(); - }); -}); diff --git a/packages/graph/tests/unit/find-path-spec.ts b/packages/graph/tests/unit/find-path-spec.ts deleted file mode 100644 index e2dde9f..0000000 --- a/packages/graph/tests/unit/find-path-spec.ts +++ /dev/null @@ -1,122 +0,0 @@ -import { findAllPath, findShortestPath } from '../../src'; - -const data = { - nodes: [ - { - id: 'A', - label: 'A', - }, - { - id: 'B', - label: 'B', - }, - { - id: 'C', - label: 'C', - }, - { - id: 'D', - label: 'D', - }, - { - id: 'E', - label: 'E', - }, - { - id: 'F', - label: 'F', - }, - { - id: 'G', - label: 'G', - }, - { - id: 'H', - label: 'H', - }, - ], - edges: [ - { - source: 'A', - target: 'B', - }, - { - source: 'B', - target: 'C', - }, - { - source: 'C', - target: 'G', - }, - { - source: 'A', - target: 'D', - }, - { - source: 'A', - target: 'E', - }, - { - source: 'E', - target: 'F', - }, - { - source: 'F', - target: 'D', - }, - { - source: 'D', - target: 'E', - }, - ], -}; - -describe('Shortest Path from source to target on graph', () => { - it('find the shortest path', () => { - const { length, path } = findShortestPath(data, 'A', 'C'); - expect(length).toBe(2); - expect(path).toStrictEqual(['A', 'B', 'C']); - }); - - it('find all shortest paths', () => { - const { length, allPath } = findShortestPath(data, 'A', 'F'); - expect(length).toBe(2); - expect(allPath[0]).toStrictEqual(['A', 'E', 'F']); - expect(allPath[1]).toStrictEqual(['A', 'D', 'F']); - - const { - length: directedLenght, - path: directedPath, - allPath: directedAllPath, - } = findShortestPath(data, 'A', 'F', true); - expect(directedLenght).toBe(2); - expect(directedAllPath[0]).toStrictEqual(['A', 'E', 'F']); - expect(directedPath).toStrictEqual(['A', 'E', 'F']); - }); - - it('find all paths', () => { - const allPath = findAllPath(data, 'A', 'E'); - expect(allPath.length).toBe(3); - expect(allPath[0]).toStrictEqual(['A', 'D', 'F', 'E']); - expect(allPath[1]).toStrictEqual(['A', 'D', 'E']); - expect(allPath[2]).toStrictEqual(['A', 'E']); - }); - - it('find all paths in directed graph', () => { - const allPath = findAllPath(data, 'A', 'E', true); - expect(allPath.length).toStrictEqual(2); - expect(allPath[0]).toStrictEqual(['A', 'D', 'E']); - expect(allPath[1]).toStrictEqual(['A', 'E']); - }); - - it('find all shortest paths in weighted graph', () => { - data.edges.forEach((edge: any, i) => { - edge.weight = ((i % 2) + 1) * 2; - if (edge.source === 'F' && edge.target === 'D') edge.weight = 10; - }); - const { length, path, allPath } = findShortestPath(data, 'A', 'F', false, 'weight'); - expect(length).toBe(6); - expect(allPath[0]).toStrictEqual(['A', 'E', 'F']); - expect(path).toStrictEqual(['A', 'E', 'F']); - }); -}); diff --git a/packages/graph/tests/unit/floydWarshall-async-spec.ts b/packages/graph/tests/unit/floydWarshall-async-spec.ts deleted file mode 100644 index f33b939..0000000 --- a/packages/graph/tests/unit/floydWarshall-async-spec.ts +++ /dev/null @@ -1,110 +0,0 @@ -import { getAlgorithm } from './utils'; - -const data = { - nodes: [ - { - id: 'A', - label: '0', - }, - { - id: 'B', - label: '1', - }, - { - id: 'C', - label: '2', - }, - { - id: 'D', - label: '3', - }, - { - id: 'E', - label: '4', - }, - { - id: 'F', - label: '5', - }, - { - id: 'G', - label: '6', - }, - { - id: 'H', - label: '7', - }, - ], - edges: [ - { - source: 'A', - target: 'B', - }, - { - source: 'B', - target: 'C', - }, - { - source: 'C', - target: 'G', - }, - { - source: 'A', - target: 'D', - }, - { - source: 'A', - target: 'E', - }, - { - source: 'E', - target: 'F', - }, - { - source: 'F', - target: 'D', - }, - ], -}; - -describe('(Async) Adjacency Matrix by Algorithm', () => { - it('get graph shortestpath matrix', async () => { - const { floydWarshallAsync } = await getAlgorithm(); - const matrix = await floydWarshallAsync(data); - expect(Object.keys(matrix).length).toBe(8); - const node0 = matrix[0]; - expect(node0.length).toBe(8); - expect(node0[0]).toBe(0); - expect(node0[1]).toBe(1); - expect(node0[2]).toBe(2); - expect(node0[3]).toBe(1); - expect(node0[4]).toBe(1); - expect(node0[5]).toBe(2); - expect(node0[6]).toBe(3); - expect(node0[7]).toBe(Infinity); - expect(matrix[1][7]).toBe(Infinity); - expect(matrix[2][7]).toBe(Infinity); - expect(matrix[3][7]).toBe(Infinity); - }); - - it('directed', async () => { - // directed - const { floydWarshallAsync } = await getAlgorithm(); - const matrix = await floydWarshallAsync(data, true); - expect(Object.keys(matrix).length).toBe(8); - const node0 = matrix[0]; - expect(node0.length).toBe(8); - expect(node0[0]).toBe(0); - expect(node0[1]).toBe(1); - expect(node0[2]).toBe(2); - expect(node0[3]).toBe(1); - expect(node0[4]).toBe(1); - expect(node0[5]).toBe(2); - expect(node0[6]).toBe(3); - expect(node0[7]).toBe(Infinity); - const node8 = matrix[6]; - expect(node8.length).toBe(8); - expect(node8[1]).toBe(Infinity); - expect(node8[6]).toBe(0); - }); -}); diff --git a/packages/graph/tests/unit/floydWarshall-spec.ts b/packages/graph/tests/unit/floydWarshall-spec.ts deleted file mode 100644 index 1fe4c44..0000000 --- a/packages/graph/tests/unit/floydWarshall-spec.ts +++ /dev/null @@ -1,108 +0,0 @@ -import { floydWarshall } from '../../src'; - -const data = { - nodes: [ - { - id: 'A', - label: '0', - }, - { - id: 'B', - label: '1', - }, - { - id: 'C', - label: '2', - }, - { - id: 'D', - label: '3', - }, - { - id: 'E', - label: '4', - }, - { - id: 'F', - label: '5', - }, - { - id: 'G', - label: '6', - }, - { - id: 'H', - label: '7', - }, - ], - edges: [ - { - source: 'A', - target: 'B', - }, - { - source: 'B', - target: 'C', - }, - { - source: 'C', - target: 'G', - }, - { - source: 'A', - target: 'D', - }, - { - source: 'A', - target: 'E', - }, - { - source: 'E', - target: 'F', - }, - { - source: 'F', - target: 'D', - }, - ], -}; - -describe('Adjacency Matrix by Algorithm', () => { - it('get graph shortestpath matrix', () => { - const matrix = floydWarshall(data); - expect(Object.keys(matrix).length).toBe(8); - const node0 = matrix[0]; - expect(node0.length).toBe(8); - expect(node0[0]).toBe(0); - expect(node0[1]).toBe(1); - expect(node0[2]).toBe(2); - expect(node0[3]).toBe(1); - expect(node0[4]).toBe(1); - expect(node0[5]).toBe(2); - expect(node0[6]).toBe(3); - expect(node0[7]).toBe(Infinity); - expect(matrix[1][7]).toBe(Infinity); - expect(matrix[2][7]).toBe(Infinity); - expect(matrix[3][7]).toBe(Infinity); - }); - - it('directed', () => { - // directed - const matrix = floydWarshall(data, true); - expect(Object.keys(matrix).length).toBe(8); - const node0 = matrix[0]; - expect(node0.length).toBe(8); - expect(node0[0]).toBe(0); - expect(node0[1]).toBe(1); - expect(node0[2]).toBe(2); - expect(node0[3]).toBe(1); - expect(node0[4]).toBe(1); - expect(node0[5]).toBe(2); - expect(node0[6]).toBe(3); - expect(node0[7]).toBe(Infinity); - const node8 = matrix[6]; - expect(node8.length).toBe(8); - expect(node8[1]).toBe(Infinity); - expect(node8[6]).toBe(0); - }); -}); diff --git a/packages/graph/tests/unit/gSpan-spec.ts b/packages/graph/tests/unit/gSpan-spec.ts deleted file mode 100644 index c201a80..0000000 --- a/packages/graph/tests/unit/gSpan-spec.ts +++ /dev/null @@ -1,483 +0,0 @@ -import gSpan from "../../src/gSpan/gSpan"; - -const data1 = { - nodes: [ - { - id: "0", - cluster: "B", - }, - { - id: "1", - cluster: "B", - }, - { - id: "2", - cluster: "B", - }, - { - id: "3", - cluster: "C", - }, - { - id: "4", - cluster: "B", - }, - { - id: "5", - cluster: "D", - }, - { - id: "6", - cluster: "B", - }, - { - id: "7", - cluster: "C", - }, - { - id: "8", - cluster: "C", - }, - { - id: "9", - cluster: "C", - }, - { - id: "10", - cluster: "B", - }, - { - id: "11", - cluster: "B", - }, - { - id: "12", - cluster: "B", - }, - { - id: "13", - cluster: "B", - }, - { - id: "14", - cluster: "B", - }, - { - id: "15", - cluster: "B", - }, - { - id: "16", - cluster: "B", - }, - { - id: "17", - cluster: "B", - }, - { - id: "18", - cluster: "B", - }, - ], - edges: [ - { - source: "0", - target: "1", - cluster: "b", - }, - { - source: "0", - target: "2", - cluster: "b", - }, - { - source: "2", - target: "3", - cluster: "c", - }, - { - source: "2", - target: "4", - cluster: "b", - }, - { - source: "3", - target: "5", - cluster: "b", - }, - { - source: "4", - target: "6", - cluster: "b", - }, - { - source: "5", - target: "7", - cluster: "b", - }, - { - source: "5", - target: "8", - cluster: "b", - }, - { - source: "5", - target: "9", - cluster: "b", - }, - { - source: "6", - target: "10", - cluster: "b", - }, - { - source: "6", - target: "9", - cluster: "c", - }, - { - source: "7", - target: "11", - cluster: "c", - }, - { - source: "8", - target: "12", - cluster: "c", - }, - { - source: "10", - target: "13", - cluster: "b", - }, - { - source: "11", - target: "14", - cluster: "b", - }, - { - source: "11", - target: "15", - cluster: "b", - }, - { - source: "12", - target: "16", - cluster: "b", - }, - { - source: "12", - target: "15", - cluster: "b", - }, - { - source: "14", - target: "17", - cluster: "b", - }, - { - source: "16", - target: "18", - cluster: "b", - }, - ], -}; -const data2 = { - nodes: [ - { - id: "0", - cluster: "B", - }, - { - id: "1", - cluster: "B", - }, - { - id: "2", - cluster: "F", - }, - { - id: "3", - cluster: "F", - }, - { - id: "4", - cluster: "C", - }, - { - id: "5", - cluster: "C", - }, - { - id: "6", - cluster: "C", - }, - { - id: "7", - cluster: "C", - }, - { - id: "8", - cluster: "C", - }, - { - id: "9", - cluster: "C", - }, - ], - edges: [ - { - source: "0", - target: "1", - cluster: "b", - }, - { - source: "0", - target: "2", - cluster: "b", - }, - { - source: "1", - target: "3", - cluster: "b", - }, - { - source: "2", - target: "4", - cluster: "c", - }, - { - source: "2", - target: "5", - cluster: "c", - }, - { - source: "2", - target: "6", - cluster: "b", - }, - { - source: "3", - target: "7", - cluster: "c", - }, - { - source: "3", - target: "8", - cluster: "c", - }, - { - source: "3", - target: "9", - cluster: "b", - }, - ], -}; -const data3 = { - nodes: [ - { - id: "0", - cluster: "F", - }, - { - id: "1", - cluster: "F", - }, - { - id: "2", - cluster: "B", - }, - { - id: "3", - cluster: "B", - }, - { - id: "4", - cluster: "B", - }, - { - id: "5", - cluster: "B", - }, - { - id: "6", - cluster: "B", - }, - { - id: "7", - cluster: "B", - }, - { - id: "8", - cluster: "B", - }, - { - id: "9", - cluster: "B", - }, - { - id: "10", - cluster: "B", - }, - { - id: "11", - cluster: "B", - }, - { - id: "12", - cluster: "B", - }, - { - id: "13", - cluster: "B", - }, - { - id: "14", - cluster: "C", - }, - { - id: "15", - cluster: "C", - }, - { - id: "16", - cluster: "B", - }, - { - id: "17", - cluster: "C", - }, - { - id: "18", - cluster: "C", - }, - { - id: "19", - cluster: "B", - }, - ], - edges: [ - { - source: "0", - target: "1", - cluster: "b", - }, - { - source: "0", - target: "2", - cluster: "b", - }, - { - source: "1", - target: "3", - cluster: "b", - }, - { - source: "2", - target: "4", - cluster: "e", - }, - { - source: "2", - target: "5", - cluster: "e", - }, - { - source: "3", - target: "6", - cluster: "e", - }, - { - source: "3", - target: "7", - cluster: "e", - }, - { - source: "4", - target: "2", - cluster: "b", - }, - { - source: "4", - target: "9", - cluster: "e", - }, - { - source: "5", - target: "10", - cluster: "e", - }, - { - source: "6", - target: "11", - cluster: "b", - }, - { - source: "6", - target: "12", - cluster: "e", - }, - { - source: "7", - target: "13", - cluster: "e", - }, - { - source: "8", - target: "14", - cluster: "c", - }, - { - source: "8", - target: "15", - cluster: "b", - }, - { - source: "9", - target: "16", - cluster: "e", - }, - { - source: "10", - target: "16", - cluster: "e", - }, - { - source: "11", - target: "17", - cluster: "c", - }, - { - source: "11", - target: "18", - cluster: "b", - }, - { - source: "12", - target: "19", - cluster: "e", - }, - { - source: "13", - target: "19", - cluster: "e", - }, - ], -}; - -describe("gSpan", () => { - it("gSpan first test", () => { - const graphDataMap = { - "a-name": data1, - "b-name": data2, - "c-name": data3, - }; - const result = gSpan({ - graphs: graphDataMap, - minSupport: 3, - minNodeNum: 2, - maxNodeNum: 4, - }); - console.log(result); - }); -}); diff --git a/packages/graph/tests/unit/gaddi-async-spec.ts b/packages/graph/tests/unit/gaddi-async-spec.ts deleted file mode 100644 index 2d65c9b..0000000 --- a/packages/graph/tests/unit/gaddi-async-spec.ts +++ /dev/null @@ -1,388 +0,0 @@ -import { getAlgorithm } from './utils'; -import { nodes77, nodes202 } from './data/test-data'; - -const data3 = { - nodes: [ - { - id: '0', - cluster: 'F', - }, - { - id: '1', - cluster: 'F', - }, - { - id: '2', - cluster: 'B', - }, - { - id: '3', - cluster: 'B', - }, - { - id: '4', - cluster: 'B', - }, - { - id: '5', - cluster: 'B', - }, - { - id: '6', - cluster: 'B', - }, - { - id: '7', - cluster: 'B', - }, - { - id: '8', - cluster: 'B', - }, - { - id: '9', - cluster: 'B', - }, - { - id: '10', - cluster: 'B', - }, - { - id: '11', - cluster: 'B', - }, - { - id: '12', - cluster: 'B', - }, - { - id: '13', - cluster: 'B', - }, - { - id: '14', - cluster: 'C', - }, - { - id: '15', - cluster: 'C', - }, - { - id: '16', - cluster: 'B', - }, - { - id: '17', - cluster: 'C', - }, - { - id: '18', - cluster: 'C', - }, - { - id: '19', - cluster: 'B', - }, - ], - edges: [ - { - source: '0', - target: '1', - cluster: 'b', - }, - { - source: '0', - target: '2', - cluster: 'b', - }, - { - source: '1', - target: '3', - cluster: 'b', - }, - { - source: '2', - target: '4', - cluster: 'e', - }, - { - source: '2', - target: '5', - cluster: 'e', - }, - { - source: '3', - target: '6', - cluster: 'e', - }, - { - source: '3', - target: '7', - cluster: 'e', - }, - { - source: '4', - target: '2', - cluster: 'b', - }, - { - source: '4', - target: '9', - cluster: 'e', - }, - { - source: '5', - target: '10', - cluster: 'e', - }, - { - source: '6', - target: '11', - cluster: 'b', - }, - { - source: '6', - target: '12', - cluster: 'e', - }, - { - source: '7', - target: '13', - cluster: 'e', - }, - { - source: '8', - target: '14', - cluster: 'c', - }, - { - source: '8', - target: '15', - cluster: 'b', - }, - { - source: '9', - target: '16', - cluster: 'e', - }, - { - source: '10', - target: '16', - cluster: 'e', - }, - { - source: '11', - target: '17', - cluster: 'c', - }, - { - source: '11', - target: '18', - cluster: 'c', - }, - { - source: '12', - target: '19', - cluster: 'e', - }, - { - source: '13', - target: '19', - cluster: 'e', - }, - ], -}; - -const pattern1 = { - nodes: [ - { - id: '0', - cluster: 'F', - }, - { - id: '1', - cluster: 'F', - }, - { - id: '2', - cluster: 'B', - }, - ], - edges: [ - { - source: '0', - target: '1', - cluster: 'b', - }, - { - source: '0', - target: '2', - cluster: 'b', - }, - ], -}; - -describe('(Async) gSpan', () => { - it('gSpan match pattern 1', async () => { - const { GADDIAsync } = await getAlgorithm(); - const matchedSubGraphs = await GADDIAsync( - data3, - pattern1, - false, - undefined, - undefined, - 'cluster', - 'cluster', - ); - expect(matchedSubGraphs.length).toBe(2); - matchedSubGraphs.forEach(graph => { - expect(graph.nodes[0].cluster).toBe('F'); - expect(graph.nodes[1].cluster).toBe('F'); - expect(graph.nodes[2].cluster).toBe('B'); - expect(graph.edges[0].cluster).toBe('b'); - expect(graph.edges[1].cluster).toBe('b'); - }); - }); -}); - -describe('(Async) Performance: gSpan 77 nodes G', () => { - it('pattern 10 nodes', async () => { - const patternWith10Nodes = { - nodes: [ - { id: 'pn1', cluster: 'B' }, - { id: 'pn2', cluster: 'B' }, - { id: 'pn3', cluster: 'B' }, - { id: 'pn4', cluster: 'C' }, - { id: 'pn5', cluster: 'B' }, - { id: 'pn6', cluster: 'A' }, - { id: 'pn7', cluster: 'B' }, - { id: 'pn8', cluster: 'B' }, - { id: 'pn9', cluster: 'A' }, - { id: 'pn10', cluster: 'B' }, - ], - edges: [ - { source: 'pn1', target: 'pn2', cluster: 'b' }, - { source: 'pn1', target: 'pn3', cluster: 'b' }, - { source: 'pn1', target: 'pn4', cluster: 'b' }, - { source: 'pn1', target: 'pn5', cluster: 'b' }, - { source: 'pn1', target: 'pn6', cluster: 'b' }, - { source: 'pn1', target: 'pn7', cluster: 'b' }, - { source: 'pn1', target: 'pn8', cluster: 'b' }, - - { source: 'pn2', target: 'pn3', cluster: 'b' }, - { source: 'pn2', target: 'pn4', cluster: 'b' }, - { source: 'pn2', target: 'pn5', cluster: 'b' }, - { source: 'pn2', target: 'pn6', cluster: 'b' }, - { source: 'pn2', target: 'pn7', cluster: 'b' }, - { source: 'pn2', target: 'pn8', cluster: 'b' }, - - { source: 'pn3', target: 'pn4', cluster: 'b' }, - { source: 'pn3', target: 'pn5', cluster: 'b' }, - { source: 'pn3', target: 'pn6', cluster: 'b' }, - { source: 'pn3', target: 'pn7', cluster: 'b' }, - { source: 'pn3', target: 'pn8', cluster: 'b' }, - - { source: 'pn4', target: 'pn5', cluster: 'b' }, - { source: 'pn4', target: 'pn6', cluster: 'b' }, - { source: 'pn4', target: 'pn7', cluster: 'b' }, - { source: 'pn4', target: 'pn8', cluster: 'b' }, - - { source: 'pn5', target: 'pn6', cluster: 'b' }, - { source: 'pn5', target: 'pn7', cluster: 'b' }, - { source: 'pn5', target: 'pn8', cluster: 'b' }, - - { source: 'pn6', target: 'pn7', cluster: 'b' }, - { source: 'pn6', target: 'pn8', cluster: 'b' }, - - { source: 'pn7', target: 'pn8', cluster: 'b' }, - - { source: 'pn8', target: 'pn9', cluster: 'a' }, - { source: 'pn8', target: 'pn10', cluster: 'a' }, - ], - }; - const begin = performance.now(); - const { GADDIAsync } = await getAlgorithm(); - const result = await GADDIAsync( - nodes77, - patternWith10Nodes, - false, - undefined, - undefined, - 'cluster', - 'cluster', - ); - console.log( - '77 nodes graph matching 10 nodes pattern', - performance.now() - begin, - result.length, - ); - result.forEach(re => { - console.log(JSON.stringify(re)); - }); - expect(result.length).toBe(3); - - expect(result[0].nodes[0].id).toBe('16'); - expect(result[1].nodes[0].id).toBe('17'); - expect(result[2].nodes[0].id).toBe('23'); - }); -}); - -describe('(Async) Performance: 202 nodes G', () => { - it('pattern with 14 nodes, directed', async () => { - const patternWith14Nodes = { - nodes: [ - { id: 'pn1', cluster: 'D' }, - { id: 'pn2', cluster: 'C' }, - { id: 'pn3', cluster: 'D' }, - { id: 'pn4', cluster: 'D' }, - { id: 'pn5', cluster: 'C' }, - { id: 'pn6', cluster: 'B' }, - { id: 'pn7', cluster: 'E' }, - { id: 'pn8', cluster: 'C' }, - { id: 'pn9', cluster: 'C' }, - { id: 'pn10', cluster: 'B' }, - { id: 'pn11', cluster: 'B' }, - { id: 'pn12', cluster: 'A' }, - { id: 'pn13', cluster: 'E' }, - { id: 'pn14', cluster: 'B' }, - ], - edges: [ - { source: 'pn2', target: 'pn1', cluster: 'c' }, - { source: 'pn3', target: 'pn1', cluster: 'a' }, - { source: 'pn4', target: 'pn1', cluster: 'c' }, - { source: 'pn1', target: 'pn5', cluster: 'c' }, - { source: 'pn6', target: 'pn1', cluster: 'c' }, - { source: 'pn7', target: 'pn1', cluster: 'c' }, - { source: 'pn8', target: 'pn1', cluster: 'c' }, - { source: 'pn1', target: 'pn9', cluster: 'a' }, - { source: 'pn10', target: 'pn1', cluster: 'c' }, - { source: 'pn11', target: 'pn1', cluster: 'a' }, - { source: 'pn1', target: 'pn12', cluster: 'c' }, - { source: 'pn1', target: 'pn13', cluster: 'c' }, - { source: 'pn14', target: 'pn13', cluster: 'c' }, - ], - }; - const begin = performance.now(); - const { GADDIAsync } = await getAlgorithm(); - const result = await GADDIAsync( - nodes202, - patternWith14Nodes, - true, - undefined, - undefined, - 'cluster', - 'cluster', - ); - - console.log( - '202 nodes graph matching 14 nodes pattern, directed', - performance.now() - begin, - result.length, - ); - result.forEach(re => { - console.log(JSON.stringify(re)); - }); - expect(result.length).toBe(1); - expect(result[0].nodes[0].id).toBe('49'); - }); -}); diff --git a/packages/graph/tests/unit/gaddi-spec.ts b/packages/graph/tests/unit/gaddi-spec.ts deleted file mode 100644 index 03f2383..0000000 --- a/packages/graph/tests/unit/gaddi-spec.ts +++ /dev/null @@ -1,1110 +0,0 @@ -import GADDI from '../../src/gaddi'; -import { nodes77, nodes202, nodes1589, nodes20 } from './data/test-data'; - -const data3 = { - nodes: [ - { - id: '0', - cluster: 'F', - }, - { - id: '1', - cluster: 'F', - }, - { - id: '2', - cluster: 'B', - }, - { - id: '3', - cluster: 'B', - }, - { - id: '4', - cluster: 'B', - }, - { - id: '5', - cluster: 'B', - }, - { - id: '6', - cluster: 'B', - }, - { - id: '7', - cluster: 'B', - }, - { - id: '8', - cluster: 'B', - }, - { - id: '9', - cluster: 'B', - }, - { - id: '10', - cluster: 'B', - }, - { - id: '11', - cluster: 'B', - }, - { - id: '12', - cluster: 'B', - }, - { - id: '13', - cluster: 'B', - }, - { - id: '14', - cluster: 'C', - }, - { - id: '15', - cluster: 'C', - }, - { - id: '16', - cluster: 'B', - }, - { - id: '17', - cluster: 'C', - }, - { - id: '18', - cluster: 'C', - }, - { - id: '19', - cluster: 'B', - }, - ], - edges: [ - { - source: '0', - target: '1', - cluster: 'b', - }, - { - source: '0', - target: '2', - cluster: 'b', - }, - { - source: '1', - target: '3', - cluster: 'b', - }, - { - source: '2', - target: '4', - cluster: 'e', - }, - { - source: '2', - target: '5', - cluster: 'e', - }, - { - source: '3', - target: '6', - cluster: 'e', - }, - { - source: '3', - target: '7', - cluster: 'e', - }, - { - source: '4', - target: '2', - cluster: 'b', - }, - { - source: '4', - target: '9', - cluster: 'e', - }, - { - source: '5', - target: '10', - cluster: 'e', - }, - { - source: '6', - target: '11', - cluster: 'b', - }, - { - source: '6', - target: '12', - cluster: 'e', - }, - { - source: '7', - target: '13', - cluster: 'e', - }, - { - source: '8', - target: '14', - cluster: 'c', - }, - { - source: '8', - target: '15', - cluster: 'b', - }, - { - source: '9', - target: '16', - cluster: 'e', - }, - { - source: '10', - target: '16', - cluster: 'e', - }, - { - source: '11', - target: '17', - cluster: 'c', - }, - { - source: '11', - target: '18', - cluster: 'c', - }, - { - source: '12', - target: '19', - cluster: 'e', - }, - { - source: '13', - target: '19', - cluster: 'e', - }, - ], -}; - -const pattern1 = { - nodes: [ - { - id: '0', - cluster: 'F', - }, - { - id: '1', - cluster: 'F', - }, - { - id: '2', - cluster: 'B', - }, - ], - edges: [ - { - source: '0', - target: '1', - cluster: 'b', - }, - { - source: '0', - target: '2', - cluster: 'b', - }, - ], -}; - -const pattern2 = { - nodes: [ - { - id: '11', - cluster: 'B', - }, - { - id: '17', - cluster: 'C', - }, - { - id: '18', - cluster: 'C', - }, - ], - edges: [ - { - source: '11', - target: '17', - cluster: 'c', - }, - { - source: '11', - target: '18', - cluster: 'b', - }, - ], -}; - -const circlePattern = { - nodes: [ - { id: '1', cluster: 'B' }, - { id: '2', cluster: 'B' }, - { id: '3', cluster: 'B' }, - { id: '4', cluster: 'B' }, - { id: '5', cluster: 'B' }, - { id: '6', cluster: 'B' }, - ], - edges: [ - { source: '1', target: '2', cluster: 'e' }, - { source: '2', target: '3', cluster: 'e' }, - { source: '3', target: '4', cluster: 'e' }, - { source: '4', target: '5', cluster: 'e' }, - { source: '5', target: '6', cluster: 'e' }, - { source: '6', target: '1', cluster: 'e' }, - ], -}; - -describe('gSpan', () => { - it('gSpan match pattern 1', () => { - const matchedSubGraphs = GADDI( - data3, - pattern1, - false, - undefined, - undefined, - 'cluster', - 'cluster', - ); - console.log('test1', matchedSubGraphs); - expect(matchedSubGraphs.length).toBe(2); - matchedSubGraphs.forEach(graph => { - expect(graph.nodes[0].cluster).toBe('B'); - expect(graph.nodes[1].cluster).toBe('F'); - expect(graph.nodes[2].cluster).toBe('F'); - expect(graph.edges[0].cluster).toBe('b'); - expect(graph.edges[1].cluster).toBe('b'); - }); - }); - it('gSpan match pattern 2', () => { - const matchedSubGraphs = GADDI(data3, pattern2, false, 2, 1, 'cluster', 'cluster'); - console.log('test2', matchedSubGraphs); - expect(matchedSubGraphs.length).toBe(1); - // expect(matchedSubGraphs.nodes) - }); - it('gSpan match circular', () => { - const matchedSubGraphs = GADDI( - data3, - circlePattern, - false, - undefined, - undefined, - 'cluster', - 'cluster', - ); - expect(matchedSubGraphs.length).toBe(2); - matchedSubGraphs.forEach(graph => { - graph.nodes.forEach(node => { - expect(node.cluster).toBe('B'); - }); - graph.edges.forEach(edge => { - expect(edge.cluster).toBe('e'); - }); - }); - }); - it('gSpan match circular2 with a parallel edge', () => { - const circlePattern2 = { - nodes: [ - { id: '1', cluster: 'B' }, - { id: '2', cluster: 'B' }, - { id: '3', cluster: 'B' }, - { id: '4', cluster: 'B' }, - { id: '5', cluster: 'B' }, - { id: '6', cluster: 'B' }, - ], - edges: [ - { source: '1', target: '2', cluster: 'e' }, - { source: '2', target: '3', cluster: 'e' }, - { source: '3', target: '4', cluster: 'e' }, - { source: '4', target: '5', cluster: 'e' }, // 平行边 - { source: '4', target: '5', cluster: 'b' }, // 平行边 - { source: '5', target: '6', cluster: 'e' }, - { source: '6', target: '1', cluster: 'e' }, - ], - }; - const matchedSubGraphs = GADDI( - data3, - circlePattern2, - false, - undefined, - undefined, - 'cluster', - 'cluster', - ); - console.log('circle 2', matchedSubGraphs); - expect(matchedSubGraphs.length).toBe(1); - - matchedSubGraphs[0].nodes.forEach(node => { - expect(node.cluster).toBe('B'); - }); - matchedSubGraphs[0].edges.forEach((edge, i) => { - if (i === 2) { - expect(edge.cluster).toBe('b'); - return; - } - expect(edge.cluster).toBe('e'); - }); - }); - // 平行边可能被匹配成多条单独边 - it('gSpan match two parallel edges', () => { - const pattern3 = { - nodes: [ - { id: 'node1', cluster: 'B' }, - { id: 'node2', cluster: 'B' }, - ], - edges: [ - { source: 'node1', target: 'node2', cluster: 'b' }, - { source: 'node1', target: 'node2', cluster: 'e' }, - ], - }; - const matchedSubGraphs = GADDI( - data3, - pattern3, - false, - undefined, - undefined, - 'cluster', - 'cluster', - ); - console.log('test3', matchedSubGraphs); - // expect(matchedSubGraphs.length).toBe(2); - // matchedSubGraphs.forEach((graph) => { - // expect(graph.nodes[0].cluster).toBe("F"); - // expect(graph.nodes[1].cluster).toBe("F"); - // expect(graph.nodes[2].cluster).toBe("B"); - // expect(graph.edges[0].cluster).toBe("b"); - // expect(graph.edges[1].cluster).toBe("b"); - // }); - }); -}); - -describe('gSpan directed', () => { - it('gSpan match pattern 1', () => { - const pattern11 = { - nodes: [ - { - id: '0', - cluster: 'F', - }, - { - id: '1', - cluster: 'F', - }, - { - id: '2', - cluster: 'B', - }, - ], - edges: [ - { - source: '0', - target: '1', - cluster: 'b', - }, - { - source: '0', - target: '2', - cluster: 'b', - }, - ], - }; - const matchedSubGraphs = GADDI( - data3, - pattern11, - true, - undefined, - undefined, - 'cluster', - 'cluster', - ); - expect(matchedSubGraphs.length).toBe(2); - expect(matchedSubGraphs[0].nodes[0].id).toBe('2'); - expect(matchedSubGraphs[0].nodes[1].id).toBe('0'); - expect(matchedSubGraphs[0].nodes[2].id).toBe('1'); - }); -}); - -describe('GADDI switch nodes', () => { - it('gSpan match pattern 1', () => { - const pattern1 = { - nodes: [ - { id: 'Person', dataType: 'Person' }, - { id: 'Enterprise', dataType: 'Enterprise' }, - ], - edges: [ - { - id: 'edge-1613700998017', - source: 'Person', - target: 'Enterprise', - dataType: 'Person2Enterprise#Guarantee', - rules: [], - }, - ], - }; - const res1 = GADDI(nodes20, pattern1, true, undefined, undefined, 'dataType', 'dataType'); - expect(res1.length).toBe(6); - const pattern2 = { - nodes: [ - { id: 'Enterprise', dataType: 'Enterprise' }, - { id: 'Person', dataType: 'Person' }, - ], - edges: [ - { - id: 'edge-1613700998017', - source: 'Person', - target: 'Enterprise', - dataType: 'Person2Enterprise#Guarantee', - rules: [], - }, - ], - }; - const res2 = GADDI(nodes20, pattern2, true, undefined, undefined, 'dataType', 'dataType'); - expect(res2.length).toBe(6); - }); -}); - -describe('Performance: gSpan 77 nodes G', () => { - // 100ms - it('pattern 3 nodes', () => { - const patternWith3Nodes = { - nodes: [ - { id: 'pn1', cluster: 'A' }, - { id: 'pn2', cluster: 'B' }, - { id: 'pn3', cluster: 'A' }, - ], - edges: [ - { source: 'pn1', target: 'pn2', cluster: 'b' }, - { source: 'pn1', target: 'pn3', cluster: 'a' }, - ], - }; - const begin = performance.now(); - const result = GADDI( - nodes77, - patternWith3Nodes, - false, - undefined, - undefined, - 'cluster', - 'cluster', - ); - console.log('77 nodes graph matching 3 nodes pattern', performance.now() - begin); - result.forEach(re => { - console.log(JSON.stringify(re)); - }); - - expect(result.length).toBe(5); - expect(result[0].nodes[0].id).toBe('11'); - expect(result[1].nodes[0].id).toBe('48'); - expect(result[2].nodes[0].id).toBe('60'); - expect(result[3].nodes[0].id).toBe('63'); - expect(result[4].nodes[0].id).toBe('66'); - - expect(result[3].nodes.length).toBe(4); - expect(result[4].nodes.length).toBe(3); - }); - // 100ms - it('pattern 5 nodes', () => { - const patternWith5Nodes = { - nodes: [ - { id: 'pn1', cluster: 'A' }, - { id: 'pn2', cluster: 'C' }, - { id: 'pn3', cluster: 'C' }, - { id: 'pn4', cluster: 'B' }, - ], - edges: [ - { source: 'pn1', target: 'pn2', cluster: 'c' }, - { source: 'pn1', target: 'pn3', cluster: 'c' }, - { source: 'pn3', target: 'pn2', cluster: 'c' }, - { source: 'pn3', target: 'pn4', cluster: 'b' }, - { source: 'pn2', target: 'pn4', cluster: 'b' }, - { source: 'pn1', target: 'pn4', cluster: 'c' }, - ], - }; - const begin = performance.now(); - const result = GADDI( - nodes77, - patternWith5Nodes, - false, - undefined, - undefined, - 'cluster', - 'cluster', - ); - console.log('77 nodes graph matching 5 nodes pattern', performance.now() - begin); - result.forEach(re => { - console.log(JSON.stringify(re)); - }); - expect(result.length).toBe(2); - expect(result[0].nodes[0].id).toBe('11'); - expect(result[1].nodes[0].id).toBe('26'); - - expect(result[0].nodes.length).toBe(7); - expect(result[1].nodes.length).toBe(4); - }); - it('pattern 10 nodes', () => { - const patternWith10Nodes = { - nodes: [ - { id: 'pn1', cluster: 'B' }, - { id: 'pn2', cluster: 'B' }, - { id: 'pn3', cluster: 'B' }, - { id: 'pn4', cluster: 'C' }, - { id: 'pn5', cluster: 'B' }, - { id: 'pn6', cluster: 'A' }, - { id: 'pn7', cluster: 'B' }, - { id: 'pn8', cluster: 'B' }, - { id: 'pn9', cluster: 'A' }, - { id: 'pn10', cluster: 'B' }, - ], - edges: [ - { source: 'pn1', target: 'pn2', cluster: 'b' }, - { source: 'pn1', target: 'pn3', cluster: 'b' }, - { source: 'pn1', target: 'pn4', cluster: 'b' }, - { source: 'pn1', target: 'pn5', cluster: 'b' }, - { source: 'pn1', target: 'pn6', cluster: 'b' }, - { source: 'pn1', target: 'pn7', cluster: 'b' }, - { source: 'pn1', target: 'pn8', cluster: 'b' }, - - { source: 'pn2', target: 'pn3', cluster: 'b' }, - { source: 'pn2', target: 'pn4', cluster: 'b' }, - { source: 'pn2', target: 'pn5', cluster: 'b' }, - { source: 'pn2', target: 'pn6', cluster: 'b' }, - { source: 'pn2', target: 'pn7', cluster: 'b' }, - { source: 'pn2', target: 'pn8', cluster: 'b' }, - - { source: 'pn3', target: 'pn4', cluster: 'b' }, - { source: 'pn3', target: 'pn5', cluster: 'b' }, - { source: 'pn3', target: 'pn6', cluster: 'b' }, - { source: 'pn3', target: 'pn7', cluster: 'b' }, - { source: 'pn3', target: 'pn8', cluster: 'b' }, - - { source: 'pn4', target: 'pn5', cluster: 'b' }, - { source: 'pn4', target: 'pn6', cluster: 'b' }, - { source: 'pn4', target: 'pn7', cluster: 'b' }, - { source: 'pn4', target: 'pn8', cluster: 'b' }, - - { source: 'pn5', target: 'pn6', cluster: 'b' }, - { source: 'pn5', target: 'pn7', cluster: 'b' }, - { source: 'pn5', target: 'pn8', cluster: 'b' }, - - { source: 'pn6', target: 'pn7', cluster: 'b' }, - { source: 'pn6', target: 'pn8', cluster: 'b' }, - - { source: 'pn7', target: 'pn8', cluster: 'b' }, - - { source: 'pn8', target: 'pn9', cluster: 'a' }, - { source: 'pn8', target: 'pn10', cluster: 'a' }, - ], - }; - const begin = performance.now(); - const result = GADDI( - nodes77, - patternWith10Nodes, - false, - undefined, - undefined, - 'cluster', - 'cluster', - ); - console.log( - '77 nodes graph matching 10 nodes pattern', - performance.now() - begin, - result.length, - ); - result.forEach(re => { - console.log(JSON.stringify(re)); - }); - expect(result.length).toBe(3); - - expect(result[0].nodes[0].id).toBe('16'); - expect(result[1].nodes[0].id).toBe('17'); - expect(result[2].nodes[0].id).toBe('23'); - }); -}); - -describe('Performance: 202 nodes G', () => { - it('pattern with 4 nodes', () => { - const patternWith4Nodes = { - nodes: [ - { id: 'pn1', cluster: 'E' }, - { id: 'pn2', cluster: 'D' }, - { id: 'pn3', cluster: 'B' }, - { id: 'pn4', cluster: 'B' }, - ], - edges: [ - { source: 'pn1', target: 'pn2', cluster: 'c' }, - { source: 'pn2', target: 'pn3', cluster: 'a' }, - { source: 'pn3', target: 'pn4', cluster: 'a' }, - { source: 'pn1', target: 'pn4', cluster: 'c' }, - ], - }; - const begin = performance.now(); - const result = GADDI( - nodes202, - patternWith4Nodes, - false, - undefined, - undefined, - 'cluster', - 'cluster', - ); - console.log('202 nodes graph matching 4 nodes pattern', performance.now() - begin); - result.forEach(re => { - console.log(JSON.stringify(re)); - }); - expect(result.length).toBe(1); - expect(result[0].nodes[0].id).toBe('67'); - expect(result[0].nodes.length).toBe(4); - }); - it('pattern with 7 nodes', () => { - const patternWith7Nodes = { - nodes: [ - { id: 'pn1', cluster: 'B' }, - { id: 'pn2', cluster: 'C' }, - { id: 'pn3', cluster: 'C' }, - { id: 'pn4', cluster: 'D' }, - { id: 'pn5', cluster: 'E' }, - { id: 'pn6', cluster: 'C' }, - { id: 'pn7', cluster: 'B' }, - ], - edges: [ - { source: 'pn1', target: 'pn2', cluster: 'c' }, - { source: 'pn2', target: 'pn3', cluster: 'c' }, - { source: 'pn3', target: 'pn4', cluster: 'a' }, - { source: 'pn4', target: 'pn5', cluster: 'c' }, - { source: 'pn5', target: 'pn1', cluster: 'c' }, - { source: 'pn4', target: 'pn6', cluster: 'a' }, - { source: 'pn4', target: 'pn7', cluster: 'a' }, - { source: 'pn6', target: 'pn7', cluster: 'c' }, - ], - }; - const begin = performance.now(); - const result = GADDI( - nodes202, - patternWith7Nodes, - false, - undefined, - undefined, - 'cluster', - 'cluster', - ); - console.log('202 nodes graph matching 7 nodes pattern', performance.now() - begin); - result.forEach(re => { - console.log(JSON.stringify(re)); - }); - expect(result.length).toBe(6); - expect(result[0].nodes[0].id).toBe('2'); - expect(result[1].nodes[0].id).toBe('77'); - expect(result[2].nodes[0].id).toBe('87'); - expect(result[3].nodes[0].id).toBe('132'); - expect(result[4].nodes[0].id).toBe('157'); - expect(result[5].nodes[0].id).toBe('167'); - }); - it('pattern with 7 nodes, directed', () => { - const patternWith7Nodes = { - nodes: [ - { id: 'pn1', cluster: 'B' }, - { id: 'pn2', cluster: 'C' }, - { id: 'pn3', cluster: 'C' }, - { id: 'pn4', cluster: 'D' }, - { id: 'pn5', cluster: 'E' }, - { id: 'pn6', cluster: 'C' }, - { id: 'pn7', cluster: 'B' }, - ], - edges: [ - { source: 'pn1', target: 'pn2', cluster: 'c' }, - { source: 'pn1', target: 'pn5', cluster: 'c' }, - { source: 'pn3', target: 'pn2', cluster: 'c' }, - { source: 'pn4', target: 'pn3', cluster: 'a' }, - { source: 'pn5', target: 'pn4', cluster: 'c' }, - { source: 'pn4', target: 'pn6', cluster: 'a' }, - { source: 'pn4', target: 'pn7', cluster: 'a' }, - { source: 'pn7', target: 'pn6', cluster: 'c' }, - ], - }; - const begin = performance.now(); - const result = GADDI( - nodes202, - patternWith7Nodes, - true, - undefined, - undefined, - 'cluster', - 'cluster', - ); - console.log('202 nodes graph matching 7 nodes pattern, directed', performance.now() - begin); - result.forEach(re => { - console.log(JSON.stringify(re)); - }); - expect(result.length).toBe(1); - expect(result[0].nodes[0].id).toBe('167'); - expect(result[0].nodes.length).toBe(7); - }); - it('pattern with 14 nodes, directed', () => { - const patternWith14Nodes = { - nodes: [ - { id: 'pn1', cluster: 'D' }, - { id: 'pn2', cluster: 'C' }, - { id: 'pn3', cluster: 'D' }, - { id: 'pn4', cluster: 'D' }, - { id: 'pn5', cluster: 'C' }, - { id: 'pn6', cluster: 'B' }, - { id: 'pn7', cluster: 'E' }, - { id: 'pn8', cluster: 'C' }, - { id: 'pn9', cluster: 'C' }, - { id: 'pn10', cluster: 'B' }, - { id: 'pn11', cluster: 'B' }, - { id: 'pn12', cluster: 'A' }, - { id: 'pn13', cluster: 'E' }, - { id: 'pn14', cluster: 'B' }, - ], - edges: [ - { source: 'pn2', target: 'pn1', cluster: 'c' }, - { source: 'pn3', target: 'pn1', cluster: 'a' }, - { source: 'pn4', target: 'pn1', cluster: 'c' }, - { source: 'pn1', target: 'pn5', cluster: 'c' }, - { source: 'pn6', target: 'pn1', cluster: 'c' }, - { source: 'pn7', target: 'pn1', cluster: 'c' }, - { source: 'pn8', target: 'pn1', cluster: 'c' }, - { source: 'pn1', target: 'pn9', cluster: 'a' }, - { source: 'pn10', target: 'pn1', cluster: 'c' }, - { source: 'pn11', target: 'pn1', cluster: 'a' }, - { source: 'pn1', target: 'pn12', cluster: 'c' }, - { source: 'pn1', target: 'pn13', cluster: 'c' }, - { source: 'pn14', target: 'pn13', cluster: 'c' }, - ], - }; - const begin = performance.now(); - const result = GADDI( - nodes202, - patternWith14Nodes, - true, - undefined, - undefined, - 'cluster', - 'cluster', - ); - - console.log( - '202 nodes graph matching 14 nodes pattern, directed', - performance.now() - begin, - result.length, - ); - result.forEach(re => { - console.log(JSON.stringify(re)); - }); - // expect(result.length).toBe(8); - // expect(result[7].nodes[0].id).toBe("100"); - }); -}); -describe('Performance: 1589 nodes G', () => { - it('pattern with 4 nodes', () => { - const patternWith4Nodes = { - nodes: [ - { id: 'pn1', cluster: 'A' }, - { id: 'pn2', cluster: 'B' }, - { id: 'pn3', cluster: 'C' }, - { id: 'pn4', cluster: 'A' }, - ], - edges: [ - { source: 'pn1', target: 'pn2', cluster: 'B' }, - { source: 'pn1', target: 'pn3', cluster: 'C' }, - { source: 'pn2', target: 'pn3', cluster: 'A' }, - { source: 'pn3', target: 'pn4', cluster: 'C' }, - ], - }; - const begin = performance.now(); - const result = GADDI( - nodes1589, - patternWith4Nodes, - false, - undefined, - undefined, - 'cluster', - 'cluster', - ); - console.log( - '1589 nodes graph matching 4 nodes pattern', - performance.now() - begin, - result.length, - ); - result.forEach(re => { - console.log(JSON.stringify(re)); - }); - - expect(result.length).toBe(163); - }); - // TODO: 爆栈 - xit('pattern with 6 nodes full-connected', () => { - const patternWith6Nodes = { - nodes: [ - { id: 'pn1', cluster: 'B' }, - { id: 'pn2', cluster: 'C' }, - { id: 'pn3', cluster: 'A' }, - { id: 'pn4', cluster: 'C' }, - { id: 'pn4', cluster: 'B' }, - { id: 'pn4', cluster: 'A' }, - ], - edges: [ - { source: 'pn1', target: 'pn2', cluster: 'A' }, - { source: 'pn1', target: 'pn3', cluster: 'B' }, - { source: 'pn1', target: 'pn4', cluster: 'A' }, - { source: 'pn1', target: 'pn5', cluster: 'C' }, - { source: 'pn1', target: 'pn6', cluster: 'B' }, - - { source: 'pn2', target: 'pn3', cluster: 'C' }, - { source: 'pn2', target: 'pn4', cluster: 'B' }, - { source: 'pn2', target: 'pn5', cluster: 'A' }, - { source: 'pn2', target: 'pn6', cluster: 'C' }, - - { source: 'pn3', target: 'pn3', cluster: 'C' }, - { source: 'pn3', target: 'pn5', cluster: 'B' }, - { source: 'pn3', target: 'pn6', cluster: 'A' }, - - { source: 'pn4', target: 'pn5', cluster: 'A' }, - { source: 'pn4', target: 'pn6', cluster: 'C' }, - - { source: 'pn5', target: 'pn6', cluster: 'B' }, - ], - }; - const begin = performance.now(); - const result = GADDI( - nodes1589, - patternWith6Nodes, - false, - undefined, - undefined, - 'cluster', - 'cluster', - ); - console.log( - '1589 nodes graph matching 6 nodes full-connected pattern', - performance.now() - begin, - result.length, - ); - result.forEach(re => { - console.log(JSON.stringify(re)); - }); - }); -}); - -describe('Prune', () => { - it('Prune', () => { - const dataPrune = { - "nodes":[ - { - "id":"0", - "cluster":"B" - }, - { - "id":"1", - "cluster":"B" - }, - { - "id":"2", - "cluster":"B" - }, - { - "id":"3", - "cluster":"C" - }, - ], - "edges":[ - { - "source":"0", - "target":"1", - "cluster":"b" - }, - { - "source":"1", - "target":"2", - "cluster":"b" - }, - { - "source":"1", - "target":"3", - "cluster":"b" - }, - ] - } - - const dataPrune2 = { - "nodes":[ - { - "id":"0", - "cluster":"B" - }, - { - "id":"1", - "cluster":"B" - }, - { - "id":"2", - "cluster":"B" - }, - { - "id":"3", - "cluster":"B" - }, - { - "id":"4", - "cluster":"B" - }, - { - "id":"5", - "cluster":"B" - }, - { - "id":"6", - "cluster":"B" - }, - { - "id":"7", - "cluster":"B" - }, - { - "id":"8", - "cluster":"B" - }, - { - "id":"9", - "cluster":"B" - }, - { - "id":"10", - "cluster":"B" - }, - { - "id":"11", - "cluster":"C" - }, - ], - "edges":[ - { - "source":"0", - "target":"6", - "cluster":"b" - }, - { - "source":"1", - "target":"6", - "cluster":"b" - }, - { - "source":"2", - "target":"6", - "cluster":"b" - }, - { - "source":"3", - "target":"6", - "cluster":"b" - }, - { - "source":"4", - "target":"6", - "cluster":"b" - }, - { - "source":"5", - "target":"6", - "cluster":"b" - }, - { - "source":"6", - "target":"7", - "cluster":"b" - }, - { - "source":"6", - "target":"8", - "cluster":"b" - }, - { - "source":"6", - "target":"9", - "cluster":"b" - }, - { - "source":"6", - "target":"10", - "cluster":"b" - }, - { - "source":"6", - "target":"11", - "cluster":"b" - }, - ] - } - const p = { - nodes: [ - { - id: '0', - cluster: 'B', - }, - { - id: '1', - cluster: 'B', - }, - { - id: '2', - cluster: 'B', - }, - { - id: '3', - cluster: 'C', - }, - ], - edges: [ - { - source: '0', - target: '1', - cluster: 'b', - }, - { - source: '2', - target: '1', - cluster: 'b', - }, - { - source: '1', - target: '3', - cluster: 'b', - }, - ], - }; - - const result = GADDI( - dataPrune2, - p, - true, - undefined, - undefined, - 'cluster', - 'cluster', - ); - - // console.log('res', result); - // // console.log(JSON.stringify(data3)); - - // result.forEach(re => { - // console.log(JSON.stringify(re)); - // }); - expect(result.length).toBe(1); - }) -}); \ No newline at end of file diff --git a/packages/graph/tests/unit/kMeans-spec.ts b/packages/graph/tests/unit/kMeans-spec.ts deleted file mode 100644 index 7e9ed1d..0000000 --- a/packages/graph/tests/unit/kMeans-spec.ts +++ /dev/null @@ -1,236 +0,0 @@ -import { kMeans } from '../../src'; -import { GraphData, NodeConfig } from '../../src/types'; -import propertiesGraphData from './data/cluster-origin-properties-data.json'; - -describe('kMeans abnormal demo', () => { - it('no properties demo: ', () => { - const noPropertiesData = { - nodes: [ - { - id: 'node-0', - }, - { - id: 'node-1', - }, - { - id: 'node-2', - }, - { - id: 'node-3', - } - ], - edges: [], - } - const { clusters, clusterEdges } = kMeans(noPropertiesData, 2); - expect(clusters.length).toBe(1); - expect(clusterEdges.length).toBe(0); - }); -}); - -describe('kMeans normal demo', () => { - const simpleGraphData = { - nodes: [ - { - id: 'node-0', - properties: { - amount: 10, - city: '10001', - } - }, - { - id: 'node-1', - properties: { - amount: 10000, - city: '10002', - } - }, - { - id: 'node-2', - properties: { - amount: 3000, - city: '10003', - } - }, - { - id: 'node-3', - properties: { - amount: 3200, - city: '10003', - } - }, - { - id: 'node-4', - properties: { - amount: 2000, - city: '10003', - } - } - ], - edges: [ - { - id: 'edge-0', - source: 'node-0', - target: 'node-1', - }, - { - id: 'edge-1', - source: 'node-0', - target: 'node-2', - }, - { - id: 'edge-4', - source: 'node-3', - target: 'node-2', - }, - { - id: 'edge-5', - source: 'node-2', - target: 'node-1', - }, - { - id: 'edge-6', - source: 'node-4', - target: 'node-1', - }, - ] - } - it('simple data demo: ', () => { - const nodes = simpleGraphData.nodes as NodeConfig[]; - const { clusters } = kMeans(simpleGraphData, 3, 'properties'); - expect(clusters.length).toBe(3); - expect(nodes[2].clusterId).toEqual(nodes[3].clusterId); - expect(nodes[2].clusterId).toEqual(nodes[4].clusterId); - }); - - it('complex data demo: ', () => { - const nodes = propertiesGraphData.nodes as NodeConfig[]; - const { clusters } = kMeans(propertiesGraphData as GraphData, 3, 'properties'); - expect(clusters.length).toBe(3); - expect(nodes[0].clusterId).toEqual(nodes[1].clusterId); - expect(nodes[0].clusterId).toEqual(nodes[2].clusterId); - expect(nodes[0].clusterId).toEqual(nodes[3].clusterId); - expect(nodes[0].clusterId).toEqual(nodes[4].clusterId); - expect(nodes[5].clusterId).toEqual(nodes[6].clusterId); - expect(nodes[5].clusterId).toEqual(nodes[7].clusterId); - expect(nodes[5].clusterId).toEqual(nodes[8].clusterId); - expect(nodes[5].clusterId).toEqual(nodes[9].clusterId); - expect(nodes[5].clusterId).toEqual(nodes[10].clusterId); - expect(nodes[11].clusterId).toEqual(nodes[12].clusterId); - expect(nodes[11].clusterId).toEqual(nodes[13].clusterId); - expect(nodes[11].clusterId).toEqual(nodes[14].clusterId); - expect(nodes[11].clusterId).toEqual(nodes[15].clusterId); - expect(nodes[11].clusterId).toEqual(nodes[16].clusterId); - }); - - - it('demo use involvedKeys: ', () => { - const involvedKeys = ['amount']; - const nodes = simpleGraphData.nodes as NodeConfig[]; - const { clusters } = kMeans(simpleGraphData, 3, 'properties', involvedKeys); - expect(clusters.length).toBe(3); - expect(nodes[2].clusterId).toEqual(nodes[3].clusterId); - expect(nodes[2].clusterId).toEqual(nodes[4].clusterId); - }); - - it('demo use uninvolvedKeys: ', () => { - const uninvolvedKeys = ['id', 'city']; - const nodes = simpleGraphData.nodes as NodeConfig[]; - const { clusters } = kMeans(simpleGraphData, 3, 'properties', [], uninvolvedKeys); - expect(clusters.length).toBe(3); - expect(nodes[2].clusterId).toEqual(nodes[3].clusterId); - expect(nodes[2].clusterId).toEqual(nodes[4].clusterId); - }); -}); - -describe('kMeans All properties values are numeric demo', () => { - it('all properties values are numeric demo: ', () => { - const allPropertiesValuesNumericData = { - nodes: [ - { - id: 'node-0', - properties: { - max: 1000000, - mean: 900000, - min: 800000, - } - }, - { - id: 'node-1', - properties: { - max: 1600000, - mean: 1100000, - min: 600000, - } - }, - { - id: 'node-2', - properties: { - max: 5000, - mean: 3500, - min: 2000, - } - }, - { - id: 'node-3', - properties: { - max: 9000, - mean: 7500, - min: 6000, - } - } - ], - edges: [], - } - const { clusters, clusterEdges } = kMeans(allPropertiesValuesNumericData, 2, 'properties'); - expect(clusters.length).toBe(2); - expect(clusterEdges.length).toBe(0); - const nodes = allPropertiesValuesNumericData.nodes as NodeConfig[]; - expect(nodes[0].clusterId).toEqual(nodes[1].clusterId); - expect(nodes[2].clusterId).toEqual(nodes[3].clusterId); - }); - - it('only one property and the value are numeric demo: ', () => { - const allPropertiesValuesNumericData = { - nodes: [ - { - id: 'node-0', - properties: { - num: 10, - } - }, - { - id: 'node-1', - properties: { - num: 12, - } - }, - { - id: 'node-2', - properties: { - num: 56, - } - }, - { - id: 'node-3', - properties: { - num: 300, - } - }, - { - id: 'node-4', - properties: { - num: 350, - } - } - ], - edges: [], - } - const { clusters, clusterEdges } = kMeans(allPropertiesValuesNumericData, 2, 'properties'); - expect(clusters.length).toBe(2); - expect(clusterEdges.length).toBe(0); - const nodes = allPropertiesValuesNumericData.nodes as NodeConfig[]; - expect(nodes[0].clusterId).toEqual(nodes[1].clusterId); - expect(nodes[0].clusterId).toEqual(nodes[2].clusterId); - expect(nodes[3].clusterId).toEqual(nodes[4].clusterId); - }); -}); diff --git a/packages/graph/tests/unit/label-propagation-async-spec.ts b/packages/graph/tests/unit/label-propagation-async-spec.ts deleted file mode 100644 index f2d5401..0000000 --- a/packages/graph/tests/unit/label-propagation-async-spec.ts +++ /dev/null @@ -1,89 +0,0 @@ -import { getAlgorithm } from './utils'; -import { GraphData } from '../../src/types'; - -describe('(Async) label propagation', () => { - it('simple label propagation', async done => { - const { labelPropagationAsync } = await getAlgorithm(); - const data: GraphData = { - nodes: [ - { id: '0' }, - { id: '1' }, - { id: '2' }, - { id: '3' }, - { id: '4' }, - { id: '5' }, - { id: '6' }, - { id: '7' }, - { id: '8' }, - { id: '9' }, - { id: '10' }, - { id: '11' }, - { id: '12' }, - { id: '13' }, - { id: '14' }, - ], - edges: [ - { source: '0', target: '1' }, - { source: '0', target: '2' }, - { source: '0', target: '3' }, - { source: '0', target: '4' }, - { source: '1', target: '2' }, - { source: '1', target: '3' }, - { source: '1', target: '4' }, - { source: '2', target: '3' }, - { source: '2', target: '4' }, - { source: '3', target: '4' }, - { source: '0', target: '0' }, - { source: '0', target: '0' }, - { source: '0', target: '0' }, - - { source: '5', target: '6', weight: 5 }, - { source: '5', target: '7' }, - { source: '5', target: '8' }, - { source: '5', target: '9' }, - { source: '6', target: '7' }, - { source: '6', target: '8' }, - { source: '6', target: '9' }, - { source: '7', target: '8' }, - { source: '7', target: '9' }, - { source: '8', target: '9' }, - - { source: '10', target: '11' }, - { source: '10', target: '12' }, - { source: '10', target: '13' }, - { source: '10', target: '14' }, - { source: '11', target: '12' }, - { source: '11', target: '13' }, - { source: '11', target: '14' }, - { source: '12', target: '13' }, - { source: '12', target: '14' }, - { source: '13', target: '14', weight: 5 }, - - { source: '0', target: '5' }, - { source: '5', target: '10' }, - { source: '10', target: '0' }, - { source: '10', target: '0' }, - ], - }; - const clusteredData = await labelPropagationAsync(data, false, 'weight'); - expect(clusteredData.clusters.length).not.toBe(0); - expect(clusteredData.clusterEdges.length).not.toBe(0); - done(); - }); - it('label propagation with large graph', () => { - // https://gw.alipayobjects.com/os/antvdemo/assets/data/relations.json - fetch('https://gw.alipayobjects.com/os/basement_prod/da5a1b47-37d6-44d7-8d10-f3e046dabf82.json') - .then(res => res.json()) - .then(async data => { - // 1589 nodes, 2747 edges - const { labelPropagationAsync } = await getAlgorithm(); - const clusteredData = await labelPropagationAsync(data, false, 'weight'); - // console.log(`Call to doSomething took ${t1 - t0} milliseconds.`); - - // 9037.91999999521 ms - - expect(clusteredData.clusters.length).toBe(472); - expect(clusteredData.clusterEdges.length).toBe(444); - }); - }); -}); diff --git a/packages/graph/tests/unit/label-propagation-spec.ts b/packages/graph/tests/unit/label-propagation-spec.ts deleted file mode 100644 index 87ad625..0000000 --- a/packages/graph/tests/unit/label-propagation-spec.ts +++ /dev/null @@ -1,54 +0,0 @@ -import { labelPropagation } from '../../src'; -import { GraphData } from '../../src/types'; - -describe('label propagation', () => { - it('simple label propagation', () => { - const data: GraphData = { - nodes: [ - { id: '0' }, { id: '1' }, { id: '2' }, { id: '3' }, { id: '4' }, - { id: '5' }, { id: '6' }, { id: '7' }, { id: '8' }, { id: '9' }, - { id: '10' }, { id: '11' }, { id: '12' }, { id: '13' }, { id: '14' }, - ], - edges: [ - { source: '0', target: '1' }, { source: '0', target: '2' }, { source: '0', target: '3' }, { source: '0', target: '4' }, - { source: '1', target: '2' }, { source: '1', target: '3' }, { source: '1', target: '4' }, - { source: '2', target: '3' }, { source: '2', target: '4' }, - { source: '3', target: '4' }, - { source: '0', target: '0' }, - { source: '0', target: '0' }, - { source: '0', target: '0' }, - - { source: '5', target: '6', weight: 5 }, { source: '5', target: '7' }, { source: '5', target: '8' }, { source: '5', target: '9' }, - { source: '6', target: '7' }, { source: '6', target: '8' }, { source: '6', target: '9' }, - { source: '7', target: '8' }, { source: '7', target: '9' }, - { source: '8', target: '9' }, - - { source: '10', target: '11' }, { source: '10', target: '12' }, { source: '10', target: '13' }, { source: '10', target: '14' }, - { source: '11', target: '12' }, { source: '11', target: '13' }, { source: '11', target: '14' }, - { source: '12', target: '13' }, { source: '12', target: '14' }, - { source: '13', target: '14', weight: 5 }, - - { source: '0', target: '5' }, - { source: '5', target: '10' }, - { source: '10', target: '0' }, - { source: '10', target: '0' }, - ] - } - const clusteredData = labelPropagation(data, false, 'weight'); - expect(clusteredData.clusters.length).not.toBe(0); - expect(clusteredData.clusterEdges.length).not.toBe(0); - }); - it('label propagation with large graph', () => { // https://gw.alipayobjects.com/os/antvdemo/assets/data/relations.json - fetch('https://gw.alipayobjects.com/os/basement_prod/da5a1b47-37d6-44d7-8d10-f3e046dabf82.json') - .then((res) => res.json()) - .then((data) => { // 1589 nodes, 2747 edges - const clusteredData = labelPropagation(data, false, 'weight'); - // console.log(`Call to doSomething took ${t1 - t0} milliseconds.`); - - // 9037.91999999521 ms - - expect(clusteredData.clusters.length).toBe(472); - expect(clusteredData.clusterEdges.length).toBe(444); - }); - }); -}); diff --git a/packages/graph/tests/unit/linked-list-spec.ts b/packages/graph/tests/unit/linked-list-spec.ts deleted file mode 100644 index 381ab27..0000000 --- a/packages/graph/tests/unit/linked-list-spec.ts +++ /dev/null @@ -1,88 +0,0 @@ -import LinkedList, { LinkedListNode } from '../../src/structs/linked-list' - -describe('linked list struct', () => { - it('init linedListNode', () => { - const linkedNode1 = new LinkedListNode(1) - const linkedNode2 = new LinkedListNode(2, linkedNode1) - - expect(linkedNode1.value).toBe(1) - expect(linkedNode1.next).toBe(null) - expect(linkedNode1.toString()).toEqual('1') - - expect(linkedNode2.value).toBe(2) - expect(linkedNode2.next).toBe(linkedNode1) - expect(linkedNode2.toString()).toBe('2') - }) - - const linkedList = new LinkedList() - it('init linked list', () => { - expect(linkedList).not.toBe(undefined) - }) - - it('find & append', () => { - let node1 = linkedList.find({ value: 1 }) - expect(node1).toBe(null) - - // append node - linkedList.append(1) - node1 = linkedList.find({ value: 1 }) - - expect(node1).not.toBe(null) - expect(node1.value).toBe(1) - }) - - it('prepend', () => { - linkedList.prepend(2) - - const node1 = linkedList.find({ value: 1 }) - const node2 = linkedList.find({ value: 2 }) - expect(linkedList.toArray()).toEqual([node2, node1]) - expect(linkedList.toString()).toEqual('2,1') - }) - - it('deleteHead', () => { - const deleteHead = linkedList.deleteHead() - expect(deleteHead).not.toBe(undefined) - expect(deleteHead.value).toEqual(2) - expect(deleteHead.next).toEqual({ next: null, value: 1 }) - }) - - it('deleteTail', () => { - linkedList.prepend(3) - - const deleteTail = linkedList.deleteTail() - expect(deleteTail).not.toBe(undefined) - expect(deleteTail.value).toBe(1) - expect(deleteTail.next).toBe(null) - }) - - it('delete', () => { - linkedList.append(5) - linkedList.append(6) - - const node3 = linkedList.find({ value: 3 }) - const node5 = linkedList.find({ value: 5 }) - const node6 = linkedList.find({ value: 6 }) - expect(linkedList.toArray()).toEqual([node3, node5, node6]) - expect(linkedList.toString()).toEqual('3,5,6') - - // 删除一个不存在的元素 - let deleteNode = linkedList.delete(8) - expect(deleteNode).toBe(null) - - // 删除存在的元素 - deleteNode = linkedList.delete(5) - expect(deleteNode).not.toBe(null) - expect(deleteNode.value).toBe(5) - expect(deleteNode.next).toEqual({ next: null, value: 6 }) - - deleteNode = linkedList.find({ value: 5 }) - expect(deleteNode).toBe(null) - }) - - it('reverse', () => { - expect(linkedList.toString()).toEqual('3,6') - linkedList.reverse() - expect(linkedList.toString()).toEqual('6,3') - }) -}) \ No newline at end of file diff --git a/packages/graph/tests/unit/louvain-async-spec.ts b/packages/graph/tests/unit/louvain-async-spec.ts deleted file mode 100644 index ae0b39e..0000000 --- a/packages/graph/tests/unit/louvain-async-spec.ts +++ /dev/null @@ -1,67 +0,0 @@ -import { louvain } from '../../src'; -import { GraphData } from '../../src/types'; -import propertiesGraphData from './data/cluster-origin-properties-data.json'; - -describe('(Async) louvain', () => { - - it('simple louvain', () => { - const data: GraphData = { - nodes: [ - { id: '0' }, { id: '1' }, { id: '2' }, { id: '3' }, { id: '4' }, - { id: '5' }, { id: '6' }, { id: '7' }, { id: '8' }, { id: '9' }, - { id: '10' }, { id: '11' }, { id: '12' }, { id: '13' }, { id: '14' }, - ], - edges: [ - { source: '0', target: '1' }, { source: '0', target: '2' }, { source: '0', target: '3' }, { source: '0', target: '4' }, - { source: '1', target: '2' }, { source: '1', target: '3' }, { source: '1', target: '4' }, - { source: '2', target: '3' }, { source: '2', target: '4' }, - { source: '3', target: '4' }, - { source: '0', target: '0' }, - { source: '0', target: '0' }, - { source: '0', target: '0' }, - - { source: '5', target: '6', weight: 5 }, { source: '5', target: '7' }, { source: '5', target: '8' }, { source: '5', target: '9' }, - { source: '6', target: '7' }, { source: '6', target: '8' }, { source: '6', target: '9' }, - { source: '7', target: '8' }, { source: '7', target: '9' }, - { source: '8', target: '9' }, - - { source: '10', target: '11' }, { source: '10', target: '12' }, { source: '10', target: '13' }, { source: '10', target: '14' }, - { source: '11', target: '12' }, { source: '11', target: '13' }, { source: '11', target: '14' }, - { source: '12', target: '13' }, { source: '12', target: '14' }, - { source: '13', target: '14', weight: 5 }, - - { source: '0', target: '5' }, - { source: '5', target: '10' }, - { source: '10', target: '0' }, - { source: '10', target: '0' }, - ] - } - const clusteredData = louvain(data, false, 'weight'); - expect(clusteredData.clusters.length).toBe(3); - expect(clusteredData.clusters[0].sumTot).toBe(3); - expect(clusteredData.clusters[1].sumTot).toBe(2); - expect(clusteredData.clusterEdges.length).toBe(6); - expect(clusteredData.clusterEdges[0].count).toBe(13); - expect(clusteredData.clusterEdges[1].count).toBe(10); - expect(clusteredData.clusterEdges[1].weight).toBe(14); - }); - - it('louvain with large graph', () => { // https://gw.alipayobjects.com/os/antvdemo/assets/data/relations.json - fetch('https://gw.alipayobjects.com/os/basement_prod/da5a1b47-37d6-44d7-8d10-f3e046dabf82.json') - .then((res) => res.json()) - .then((data) => { // 1589 nodes, 2747 edges - const clusteredData = louvain(data, false, 'weight'); - expect(clusteredData.clusters.length).toBe(495); - expect(clusteredData.clusterEdges.length).toBe(505); - }); - }); - - it('louvain: add inertialModularity', () => { - const clusteredData = louvain(propertiesGraphData as GraphData, false, 'weight', 0.01, true, 'properties'); - expect(clusteredData.clusters.length).toBe(3); - expect(clusteredData.clusters[0].sumTot).toBe(3); - expect(clusteredData.clusters[1].sumTot).toBe(3); - expect(clusteredData.clusters[2].sumTot).toBe(4); - expect(clusteredData.clusterEdges.length).toBe(7); - }); -}); diff --git a/packages/graph/tests/unit/louvain-spec.ts b/packages/graph/tests/unit/louvain-spec.ts deleted file mode 100644 index 386e934..0000000 --- a/packages/graph/tests/unit/louvain-spec.ts +++ /dev/null @@ -1,67 +0,0 @@ -import { louvain, iLouvain } from '../../src'; -import { GraphData } from '../../src/types'; -import propertiesGraphData from './data/cluster-origin-properties-data.json'; - -describe('louvain', () => { - - it('simple louvain', () => { - const data: GraphData = { - nodes: [ - { id: '0' }, { id: '1' }, { id: '2' }, { id: '3' }, { id: '4' }, - { id: '5' }, { id: '6' }, { id: '7' }, { id: '8' }, { id: '9' }, - { id: '10' }, { id: '11' }, { id: '12' }, { id: '13' }, { id: '14' }, - ], - edges: [ - { source: '0', target: '1' }, { source: '0', target: '2' }, { source: '0', target: '3' }, { source: '0', target: '4' }, - { source: '1', target: '2' }, { source: '1', target: '3' }, { source: '1', target: '4' }, - { source: '2', target: '3' }, { source: '2', target: '4' }, - { source: '3', target: '4' }, - { source: '0', target: '0' }, - { source: '0', target: '0' }, - { source: '0', target: '0' }, - - { source: '5', target: '6', weight: 5 }, { source: '5', target: '7' }, { source: '5', target: '8' }, { source: '5', target: '9' }, - { source: '6', target: '7' }, { source: '6', target: '8' }, { source: '6', target: '9' }, - { source: '7', target: '8' }, { source: '7', target: '9' }, - { source: '8', target: '9' }, - - { source: '10', target: '11' }, { source: '10', target: '12' }, { source: '10', target: '13' }, { source: '10', target: '14' }, - { source: '11', target: '12' }, { source: '11', target: '13' }, { source: '11', target: '14' }, - { source: '12', target: '13' }, { source: '12', target: '14' }, - { source: '13', target: '14', weight: 5 }, - - { source: '0', target: '5' }, - { source: '5', target: '10' }, - { source: '10', target: '0' }, - { source: '10', target: '0' }, - ] - } - const clusteredData = louvain(data, false, 'weight'); - expect(clusteredData.clusters.length).toBe(3); - expect(clusteredData.clusters[0].sumTot).toBe(3); - expect(clusteredData.clusters[1].sumTot).toBe(2); - expect(clusteredData.clusterEdges.length).toBe(6); - expect(clusteredData.clusterEdges[0].count).toBe(13); - expect(clusteredData.clusterEdges[1].count).toBe(10); - expect(clusteredData.clusterEdges[1].weight).toBe(14); - }); - - it('louvain with large graph', () => { // https://gw.alipayobjects.com/os/antvdemo/assets/data/relations.json - fetch('https://gw.alipayobjects.com/os/basement_prod/da5a1b47-37d6-44d7-8d10-f3e046dabf82.json') - .then((res) => res.json()) - .then((data) => { // 1589 nodes, 2747 edges - const clusteredData = louvain(data, false, 'weight'); - expect(clusteredData.clusters.length).toBe(495); - expect(clusteredData.clusterEdges.length).toBe(505); - }); - }); - - it('louvain: add inertialModularity', () => { - const clusteredData = iLouvain(propertiesGraphData as GraphData, false, 'weight', 0.01, 'properties'); - expect(clusteredData.clusters.length).toBe(3); - expect(clusteredData.clusters[0].sumTot).toBe(3); - expect(clusteredData.clusters[1].sumTot).toBe(3); - expect(clusteredData.clusters[2].sumTot).toBe(4); - expect(clusteredData.clusterEdges.length).toBe(7); - }); -}); \ No newline at end of file diff --git a/packages/graph/tests/unit/mst-spec.ts b/packages/graph/tests/unit/mst-spec.ts deleted file mode 100644 index fcedaee..0000000 --- a/packages/graph/tests/unit/mst-spec.ts +++ /dev/null @@ -1,84 +0,0 @@ -import { minimumSpanningTree } from '../../src'; - -const data = { - nodes: [ - { - id: 'A', - }, - { - id: 'B', - }, - { - id: 'C', - }, - { - id: 'D', - }, - { - id: 'E', - }, - { - id: 'F', - }, - { - id: 'G', - }, - ], - edges: [ - { - source: 'A', - target: 'B', - weight: 1, - }, - { - source: 'B', - target: 'C', - weight: 1, - }, - { - source: 'A', - target: 'C', - weight: 2, - }, - { - source: 'D', - target: 'A', - weight: 3, - }, - { - source: 'D', - target: 'E', - weight: 4, - }, - { - source: 'E', - target: 'F', - weight: 2, - }, - { - source: 'F', - target: 'D', - weight: 3, - }, - ], -}; - -describe('minimumSpanningTree', () => { - it('test kruskal algorithm', () => { - let result = minimumSpanningTree(data, 'weight'); - let totalWeight = 0; - for (let edge of result) { - totalWeight += edge.weight; - } - expect(totalWeight).toEqual(10); - }); - - it('test prim algorithm', () => { - let result = minimumSpanningTree(data, 'weight', 'prim'); - let totalWeight = 0; - for (let edge of result) { - totalWeight += edge.weight; - } - expect(totalWeight).toEqual(10); - }); -}); diff --git a/packages/graph/tests/unit/nodesCosineSimilarity-spec.ts b/packages/graph/tests/unit/nodesCosineSimilarity-spec.ts deleted file mode 100644 index 470e1e6..0000000 --- a/packages/graph/tests/unit/nodesCosineSimilarity-spec.ts +++ /dev/null @@ -1,104 +0,0 @@ -import { nodesCosineSimilarity } from '../../src'; -import { NodeConfig } from '../../src/types'; -import propertiesGraphData from './data/cluster-origin-properties-data.json'; - -describe('nodesCosineSimilarity abnormal demo', () => { - it('no properties demo: ', () => { - const nodes = [ - { - id: 'node-0', - }, - { - id: 'node-1', - }, - { - id: 'node-2', - }, - { - id: 'node-3', - } - ]; - const { allCosineSimilarity, similarNodes } = nodesCosineSimilarity(nodes as NodeConfig[], nodes[0]); - expect(allCosineSimilarity.length).toBe(3); - expect(similarNodes.length).toBe(3); - expect(allCosineSimilarity[0]).toBe(1); - expect(allCosineSimilarity[1]).toBe(0); - expect(allCosineSimilarity[2]).toBe(0); - }); -}); - -describe('nodesCosineSimilarity normal demo', () => { - it('simple demo: ', () => { - const nodes = [ - { - id: 'node-0', - properties: { - amount: 10, - } - }, - { - id: 'node-2', - properties: { - amount: 100, - } - }, - { - id: 'node-3', - properties: { - amount: 1000, - } - }, - { - id: 'node-4', - properties: { - amount: 50, - } - } - ]; - const { allCosineSimilarity, similarNodes } = nodesCosineSimilarity(nodes as NodeConfig[], nodes[0], 'properties'); - expect(allCosineSimilarity.length).toBe(3); - expect(similarNodes.length).toBe(3); - allCosineSimilarity.forEach(data => { - expect(data).toBeGreaterThanOrEqual(0); - expect(data).toBeLessThanOrEqual(1); - }) - }); - - it('complex demo: ', () => { - const { nodes } = propertiesGraphData; - const { allCosineSimilarity, similarNodes } = nodesCosineSimilarity(nodes as NodeConfig[], nodes[16], 'properties'); - expect(allCosineSimilarity.length).toBe(16); - expect(similarNodes.length).toBe(16); - allCosineSimilarity.forEach(data => { - expect(data).toBeGreaterThanOrEqual(0); - expect(data).toBeLessThanOrEqual(1); - }) - }); - - - it('demo use involvedKeys: ', () => { - const involvedKeys = ['amount', 'wifi']; - const { nodes } = propertiesGraphData; - const { allCosineSimilarity, similarNodes } = nodesCosineSimilarity(nodes as NodeConfig[], nodes[16], 'properties', involvedKeys); - expect(allCosineSimilarity.length).toBe(16); - expect(similarNodes.length).toBe(16); - allCosineSimilarity.forEach(data => { - expect(data).toBeGreaterThanOrEqual(0); - expect(data).toBeLessThanOrEqual(1); - }) - expect(similarNodes[0].id).toBe('node-11'); - }); - - it('demo use uninvolvedKeys: ', () => { - const uninvolvedKeys = ['amount']; - const { nodes } = propertiesGraphData; - const { allCosineSimilarity, similarNodes } = nodesCosineSimilarity(nodes as NodeConfig[], nodes[16], 'properties', [], uninvolvedKeys); - expect(allCosineSimilarity.length).toBe(16); - expect(similarNodes.length).toBe(16); - allCosineSimilarity.forEach(data => { - expect(data).toBeGreaterThanOrEqual(0); - expect(data).toBeLessThanOrEqual(1); - }) - expect(similarNodes[0].id).toBe('node-11'); - }); -}); diff --git a/packages/graph/tests/unit/pagerank-async-spec.ts b/packages/graph/tests/unit/pagerank-async-spec.ts deleted file mode 100644 index ab78386..0000000 --- a/packages/graph/tests/unit/pagerank-async-spec.ts +++ /dev/null @@ -1,138 +0,0 @@ -import { getAlgorithm } from './utils'; - -const data = { - nodes: [ - { - id: 'A', - label: 'A', - }, - { - id: 'B', - label: 'B', - }, - { - id: 'C', - label: 'C', - }, - { - id: 'D', - label: 'D', - }, - { - id: 'E', - label: 'E', - }, - { - id: 'F', - label: 'F', - }, - { - id: 'G', - label: 'G', - }, - { - id: 'H', - label: 'H', - }, - { - id: 'I', - label: 'I', - }, - { - id: 'J', - label: 'J', - }, - { - id: 'K', - label: 'K', - } - ], - edges: [ - { - source: 'D', - target: 'A', - }, - { - source: 'D', - target: 'B', - }, - { - source: 'B', - target: 'C', - }, - { - source: 'C', - target: 'B', - }, - { - source: 'F', - target: 'B', - }, - { - source: 'F', - target: 'E', - }, - { - source: 'E', - target: 'F', - }, - { - source: 'E', - target: 'D', - }, - { - source: 'E', - target: 'B', - }, - { - source: 'K', - target: 'E', - }, - { - source: 'J', - target: 'E', - }, - { - source: 'I', - target: 'E', - }, - { - source: 'H', - target: 'E', - }, - { - source: 'G', - target: 'E', - }, - { - source: 'G', - target: 'B', - }, - { - source: 'H', - target: 'B', - }, - { - source: 'I', - target: 'B', - }, - ], -}; - -describe('(Async) Calculate pagerank of graph nodes', () => { - - it('calculate pagerank', async () => { - const { pageRankAsync } = await getAlgorithm(); - const result = await pageRankAsync(data); - let maxNodeId; - let maxVal = 0; - for (let nodeId in result) { - const val = result[nodeId]; - if (val >= maxVal) { - maxNodeId = nodeId; - maxVal = val - } - } - expect(maxNodeId).toBe('B') - }); -}); diff --git a/packages/graph/tests/unit/pagerank-spec.ts b/packages/graph/tests/unit/pagerank-spec.ts deleted file mode 100644 index 8d2dc92..0000000 --- a/packages/graph/tests/unit/pagerank-spec.ts +++ /dev/null @@ -1,137 +0,0 @@ -import { pageRank } from '../../src'; - -const data = { - nodes: [ - { - id: 'A', - label: 'A', - }, - { - id: 'B', - label: 'B', - }, - { - id: 'C', - label: 'C', - }, - { - id: 'D', - label: 'D', - }, - { - id: 'E', - label: 'E', - }, - { - id: 'F', - label: 'F', - }, - { - id: 'G', - label: 'G', - }, - { - id: 'H', - label: 'H', - }, - { - id: 'I', - label: 'I', - }, - { - id: 'J', - label: 'J', - }, - { - id: 'K', - label: 'K', - } - ], - edges: [ - { - source: 'D', - target: 'A', - }, - { - source: 'D', - target: 'B', - }, - { - source: 'B', - target: 'C', - }, - { - source: 'C', - target: 'B', - }, - { - source: 'F', - target: 'B', - }, - { - source: 'F', - target: 'E', - }, - { - source: 'E', - target: 'F', - }, - { - source: 'E', - target: 'D', - }, - { - source: 'E', - target: 'B', - }, - { - source: 'K', - target: 'E', - }, - { - source: 'J', - target: 'E', - }, - { - source: 'I', - target: 'E', - }, - { - source: 'H', - target: 'E', - }, - { - source: 'G', - target: 'E', - }, - { - source: 'G', - target: 'B', - }, - { - source: 'H', - target: 'B', - }, - { - source: 'I', - target: 'B', - }, - ], -}; - -describe('Calculate pagerank of graph nodes', () => { - - it('calculate pagerank', () => { - const result = pageRank(data); - let maxNodeId; - let maxVal = 0; - for (let nodeId in result) { - const val = result[nodeId]; - if (val >= maxVal) { - maxNodeId = nodeId; - maxVal = val - } - } - expect(maxNodeId).toBe('B') - }); -}); diff --git a/packages/graph/tests/unit/queue-spec.ts b/packages/graph/tests/unit/queue-spec.ts deleted file mode 100644 index d998481..0000000 --- a/packages/graph/tests/unit/queue-spec.ts +++ /dev/null @@ -1,65 +0,0 @@ -import Queue from '../../src/structs/queue'; - -describe('Queue', () => { - it('should create empty queue', () => { - const queue = new Queue(); - expect(queue).not.toBeNull(); - expect(queue.linkedList).not.toBeNull(); - }); - - it('should enqueue data to queue', () => { - const queue = new Queue(); - - queue.enqueue(1); - queue.enqueue(2); - - expect(queue.toString()).toBe('1,2'); - }); - - it('should be possible to enqueue/dequeue objects', () => { - const queue = new Queue(); - - queue.enqueue({ value: 'test1', key: 'key1' }); - queue.enqueue({ value: 'test2', key: 'key2' }); - - const stringifier = (value) => `${value.key}:${value.value}`; - - expect(queue.toString(stringifier)).toBe('key1:test1,key2:test2'); - expect(queue.dequeue().value).toBe('test1'); - expect(queue.dequeue().value).toBe('test2'); - }); - - it('should peek data from queue', () => { - const queue = new Queue(); - - expect(queue.peek()).toBeNull(); - - queue.enqueue(1); - queue.enqueue(2); - - expect(queue.peek()).toBe(1); - expect(queue.peek()).toBe(1); - }); - - it('should check if queue is empty', () => { - const queue = new Queue(); - - expect(queue.isEmpty()).toBe(true); - - queue.enqueue(1); - - expect(queue.isEmpty()).toBe(false); - }); - - it('should dequeue from queue in FIFO order', () => { - const queue = new Queue(); - - queue.enqueue(1); - queue.enqueue(2); - - expect(queue.dequeue()).toBe(1); - expect(queue.dequeue()).toBe(2); - expect(queue.dequeue()).toBeNull(); - expect(queue.isEmpty()).toBe(true); - }); -}); diff --git a/packages/graph/tests/unit/stack-spec.ts b/packages/graph/tests/unit/stack-spec.ts deleted file mode 100644 index c2cc948..0000000 --- a/packages/graph/tests/unit/stack-spec.ts +++ /dev/null @@ -1,85 +0,0 @@ -import Stack from '../../src/structs/stack'; - -describe('stack unit test', () => { - it('init stack', () => { - const stack = new Stack(); - for (let i = 0; i < 4; i++) { - stack.push({ - nodes: [ - { - id: `node${i}`, - }, - ], - }); - } - - const result = stack.pop(); - // console.log(stack.toArray()); - expect(result).toEqual({ - nodes: [ - { - id: 'node3', - }, - ], - }); - - expect(stack.peek()).toEqual({ - nodes: [ - { - id: 'node2', - }, - ], - }); - - expect(stack.isMaxStack()).toBe(false); - expect(stack.isEmpty()).toBe(false); - - stack.push({ - nodes: [ - { - id: 'node5', - }, - ], - }); - stack.push({ - nodes: [ - { - id: 'node6', - }, - ], - }); - - expect(stack.isMaxStack()).toBe(false); - stack.clear() - expect(stack.length).toBe(0) - }); - - it('init stack with maxStep', () => { - const stack = new Stack(3); - for (let i = 0; i < 5; i++) { - stack.push({ - nodes: [ - { - id: `node${i}`, - }, - ], - }); - } - expect(stack.length).toBe(3); - - expect(stack.toArray()).toEqual([ - { - nodes: [{ id: 'node4'}] - }, - { - nodes: [{ id: 'node3'}] - }, - { - nodes: [{ id: 'node2'}] - } - ]) - - stack.clear() - expect(stack.length).toBe(0) - }); -}); diff --git a/packages/graph/tests/unit/util-spec.ts b/packages/graph/tests/unit/util-spec.ts deleted file mode 100644 index bb2ec3f..0000000 --- a/packages/graph/tests/unit/util-spec.ts +++ /dev/null @@ -1,116 +0,0 @@ -import { getNeighbors, getEdgesByNodeId, getOutEdgesNodeId } from '../../src/util' - -const data = { - nodes: [ - { - id: 'A', - }, - { - id: 'B', - }, - { - id: 'C', - }, - { - id: 'D', - }, - { - id: 'E', - }, - { - id: 'F', - }, - { - id: 'G', - }, - { - id: 'H', - }, - ], - edges: [ - { - source: 'A', - target: 'B', - }, - { - source: 'B', - target: 'C', - }, - { - source: 'A', - target: 'C', - }, - { - source: 'D', - target: 'A', - }, - { - source: 'D', - target: 'E', - }, - { - source: 'E', - target: 'F', - }, - { - source: 'F', - target: 'D', - }, - { - source: 'G', - target: 'H', - }, - { - source: 'H', - target: 'G', - }, - ], -}; - -describe('algorithm util method', () => { - it('getNeighbors', () => { - - let result = getNeighbors('A', data.edges); - expect(result).toEqual(['B', 'C', 'D']); - - result = getNeighbors('A', data.edges, 'source') - expect(result).toEqual(['D']) - - result = getNeighbors('A', data.edges, 'target') - expect(result).toEqual(['B', 'C']) - }); - - it('getEdgesByNodeId', () => { - const aEdges = [ - { - source: 'A', - target: 'B', - }, - { - source: 'A', - target: 'C', - }, - { - source: 'D', - target: 'A', - }, - ] - let result = getEdgesByNodeId('A', data.edges); - expect(result).toEqual(aEdges); - }); - - it('getOutEdgesNodeId', () => { - const aEdges = [ - { - source: 'A', - target: 'B', - }, - { - source: 'A', - target: 'C', - } - ] - let result = getOutEdgesNodeId('A', data.edges); - expect(result).toEqual(aEdges); - }); -}); diff --git a/packages/graph/tests/unit/utils.ts b/packages/graph/tests/unit/utils.ts deleted file mode 100644 index eed2d5a..0000000 --- a/packages/graph/tests/unit/utils.ts +++ /dev/null @@ -1,20 +0,0 @@ -import algorithm from '../../src/'; - -type IAlgorithm = typeof algorithm; -declare const window: Window & { - Algorithm: IAlgorithm; -}; - -export const getAlgorithm = () => - new Promise(resolve => { - if (window.Algorithm) { - resolve(window.Algorithm); - } - const script = document.createElement('script'); - script.type = 'text/javascript'; - script.src = `${process.cwd()}/dist/index.min.js`; - script.onload = function() { - resolve(window.Algorithm); - }; - document.body.append(script); - }); \ No newline at end of file diff --git a/packages/graph/webpack.config.js b/packages/graph/webpack.config.js index 4858a47..baaa168 100644 --- a/packages/graph/webpack.config.js +++ b/packages/graph/webpack.config.js @@ -1,22 +1,15 @@ -const webpack = require('webpack'); const resolve = require('path').resolve; module.exports = { - entry: { - index: './src/index.ts', - async: './src/asyncIndex.ts' - }, + entry: './src/index.ts', output: { - filename: '[name].min.js', - library: 'Algorithm', + filename: 'index.min.js', + library: 'GraphAlgorithm', libraryTarget: 'umd', - libraryExport: 'default', - path: resolve(process.cwd(), 'dist/'), + path: resolve(process.cwd(), 'dist'), globalObject: 'this', - publicPath: './dist', - }, - watchOptions: { - ignored: /node_modules/ + publicPath: '', + clean: true, }, resolve: { extensions: ['.ts', '.js'], @@ -24,50 +17,11 @@ module.exports = { module: { rules: [ { - test: /\.worker\.ts$/, - exclude: /(node_modules)/, - use: [ - { - loader: 'worker-loader', - options: { - inline: 'fallback', - filename: 'index.worker.js', - }, - }, - ], - }, - { - test: /\.js$/, - include: /node_modules/, - use: { - loader: 'babel-loader', - options: { - presets: [ - [ - '@babel/preset-env', - { - loose: true, - modules: false, - }, - ], - { - plugins: ['@babel/plugin-proposal-class-properties'], - }, - ], - }, - }, - }, - { - test: /\.ts$/, - use: { - loader: 'ts-loader', - options: { - transpileOnly: true, - }, - }, + test: /\.tsx?$/, + use: "ts-loader", + exclude: /node_modules/, }, ], }, - plugins: [new webpack.NoEmitOnErrorsPlugin(), new webpack.optimize.AggressiveMergingPlugin()], devtool: 'source-map', }; diff --git a/site/benchmark/index.html b/site/benchmark/index.html index d0a428a..30b377d 100644 --- a/site/benchmark/index.html +++ b/site/benchmark/index.html @@ -165,8 +165,8 @@

-
-
@antv/algorithm
+
+
@antv/graph
diff --git a/site/benchmark/main.ts b/site/benchmark/main.ts index e08981e..3a944fd 100644 --- a/site/benchmark/main.ts +++ b/site/benchmark/main.ts @@ -3,9 +3,12 @@ import { loadDatasets } from "../datasets"; import { TestName } from "../types"; import { graphology as graphologyPageRank, + antv as antvPageRank, webgpu as webgpuPageRank, + wasm as wasmPageRank } from "./page-rank"; import { graphology as graphologySSSP, webgpu as webgpuSSSP } from "./sssp"; +import { initThreads } from "../../packages/graph-wasm"; const TestsConfig = [ { @@ -31,6 +34,13 @@ const $results = TestsConfig.map(({ name }) => { return [$div.querySelector(".console")!, $div.querySelector(".time")!]; }); +const initThreadsPool = async () => { + const singleThread = await initThreads(false); + const multiThreads = await initThreads(true); + + return [singleThread, multiThreads]; +}; + (async () => { $run.innerHTML = "Loading..."; $run.disabled = true; @@ -44,7 +54,10 @@ const $results = TestsConfig.map(({ name }) => { // initialize WebGPU context const graph = new WebGPUGraph(); - $run.innerHTML = "Run layouts"; + console.time("Init WASM threads"); + const [forceSingleThread, forceMultiThreads] = await initThreadsPool(); + console.timeEnd("Init WASM threads"); + $run.innerHTML = 'Run layouts'; $run.disabled = false; const layoutConfig: any = [ @@ -52,27 +65,27 @@ const $results = TestsConfig.map(({ name }) => { name: TestName.GRAPHOLOGY, methods: { pageRank: graphologyPageRank, - sssp: graphologySSSP, + // sssp: graphologySSSP, }, }, { name: TestName.ANTV_ALGORITHM, methods: { - // pageRank: graphologyForceatlas2, + pageRank: antvPageRank, // sssp: graphologyFruchterman, }, }, { name: TestName.ANTV_GRAPH_GPU, methods: { - pageRank: webgpuPageRank, - sssp: webgpuSSSP, + // pageRank: webgpuPageRank, + // sssp: webgpuSSSP, }, }, { name: TestName.ANTV_GRAPH_WASM, methods: { - // pageRank: wasmPageRank, + pageRank: wasmPageRank, // sssp: webgpuSSSP, }, }, @@ -81,7 +94,7 @@ const $results = TestsConfig.map(({ name }) => { $run.onclick = async () => { const dataset = datasets[$dataset.value]; const algorithmName = $algorithm.value; - let options = null; + let options = {}; // if (algorithmName === "sssp") { // const graph = dataset[TestName.ANTV_WEBGPU_GRAPH]; // options = graph.getAllNodes()[1].id; @@ -94,7 +107,8 @@ const $results = TestsConfig.map(({ name }) => { const result = await methods[algorithmName]( dataset[name], options, - graph + graph, + forceMultiThreads ); $results[i][1].innerHTML = `${(performance.now() - start).toFixed( 2 diff --git a/site/benchmark/page-rank.ts b/site/benchmark/page-rank.ts index a47433c..fc9ff37 100644 --- a/site/benchmark/page-rank.ts +++ b/site/benchmark/page-rank.ts @@ -1,8 +1,13 @@ -import { Graph } from "@antv/graphlib"; +import { Graph, ID } from "@antv/graphlib"; import pagerank from "graphology-metrics/centrality/pagerank"; +import { pageRank } from "../../packages/graph"; import { WebGPUGraph } from "../../packages/graph-gpu"; import { Threads } from "../../packages/graph-wasm"; +function format(records: { id: ID; score: number}[]) { + return records.map(({ id, score }) => ({ id, score: score.toFixed(6) })); +} + interface Options { alpha: number; maxIterations: number; @@ -27,7 +32,23 @@ export async function graphology(graph: any, options: Partial) { score: result[key], })); - return r.sort((a, b) => b.score - a.score).slice(0, 10); // {id: 'Valjean', score: 0.1} + return format(r.sort((a, b) => b.score - a.score).slice(0, 10)); // {id: 'Valjean', score: 0.1} +} + +export async function antv( + graph: Graph, + options: Partial,) { + const result = pageRank(graph, { + ...DEFAULT_OPTIONS, + ...options, + }); + + const r = Object.keys(result).map((key) => ({ + id: key, + score: result[key], + })); + + return format(r.sort((a, b) => b.score - a.score).slice(0, 10)); // {id: 'Valjean', score: 0.1} } export async function webgpu( @@ -35,16 +56,39 @@ export async function webgpu( options: Partial, webgpuGraph: WebGPUGraph ) { - const { alpha, tolerance, maxIterations } = { - ...DEFAULT_OPTIONS, - ...options, - }; const result = await webgpuGraph.pageRank( graph, - tolerance, - alpha, - maxIterations + { + ...DEFAULT_OPTIONS, + ...options, + } ); - return result.slice(0, 10); // {id: 'Valjean', score: 0.1} + return format(result.slice(0, 10)); // {id: 'Valjean', score: 0.1} } + +export async function wasm( + graph: Graph, + options: Partial, + _: any, + threads: Threads +): Promise { + const edgelist: [number, number][] = []; + const nodeIdxMap: Record = {}; + const idxNodeMap: Record = {}; + const edges = graph.getAllEdges(); + graph.getAllNodes().forEach((node, i) => { + nodeIdxMap[node.id] = i; + idxNodeMap[i] = node.id; + }); + // convert graph to edgelist + edges.forEach((edge) => { + edgelist.push([nodeIdxMap[edge.source], nodeIdxMap[edge.target]]); + }); + const ranks = await threads.pageRank({ + ...options, + edgelist + }); + const formatted = ranks.map((rank, i) => ({ id: idxNodeMap[i], score: rank })); + return format(formatted.sort((a, b) => b.score - a.score).slice(0, 10)); // {id: 'Valjean', score: 0.1} +} \ No newline at end of file diff --git a/site/datasets.ts b/site/datasets.ts index 8a3573a..0203d3a 100644 --- a/site/datasets.ts +++ b/site/datasets.ts @@ -85,7 +85,7 @@ export const loadDatasets = async () => { return { desc, [TestName.GRAPHOLOGY]: graphlibModel, - [TestName.ANTV_ALGORITHM]: oldG6GraphFormat, + [TestName.ANTV_ALGORITHM]: antvGraphModel, [TestName.ANTV_GRAPH_GPU]: antvGraphModel, [TestName.ANTV_GRAPH_WASM]: antvGraphModel, }; diff --git a/site/index.html b/site/index.html index 2258375..d4c1a8d 100644 --- a/site/index.html +++ b/site/index.html @@ -8,7 +8,7 @@ Here are some examples using - @antv/algorithm. + @antv/graph.
  • Benchmarks between CPU, WASM and GPU diff --git a/site/types.ts b/site/types.ts index 761db8f..d63bbb6 100644 --- a/site/types.ts +++ b/site/types.ts @@ -1,6 +1,6 @@ export enum TestName { GRAPHOLOGY = "graphology", - ANTV_ALGORITHM = "@antv/algorithm", + ANTV_ALGORITHM = "@antv/graph", ANTV_GRAPH_GPU = "@antv/graph-gpu", ANTV_GRAPH_WASM = "@antv/graph-wasm", } diff --git a/vite.config.js b/vite.config.js index 3a81ae7..9ca6531 100644 --- a/vite.config.js +++ b/vite.config.js @@ -16,4 +16,18 @@ export default defineConfig({ }, }, }, + plugins: [ + { + name: "isolation", + configureServer(server) { + // The multithreads version of @antv/layout-wasm needs to use SharedArrayBuffer, which should be used in a secure context. + // @see https://gist.github.com/mizchi/afcc5cf233c9e6943720fde4b4579a2b + server.middlewares.use((_req, res, next) => { + res.setHeader("Cross-Origin-Opener-Policy", "same-origin"); + res.setHeader("Cross-Origin-Embedder-Policy", "require-corp"); + next(); + }); + }, + }, + ], }); From 5a14aff8dbf30d16bd5c33b8b79434bd8a9616ba Mon Sep 17 00:00:00 2001 From: "yuqi.pyq" Date: Tue, 11 Jul 2023 11:51:21 +0800 Subject: [PATCH 4/6] chore: commit pnpm lockfile --- .gitignore | 1 - pnpm-lock.yaml | 7616 ++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 7616 insertions(+), 1 deletion(-) create mode 100644 pnpm-lock.yaml diff --git a/.gitignore b/.gitignore index 759f228..bdd640c 100644 --- a/.gitignore +++ b/.gitignore @@ -11,7 +11,6 @@ es dist *.pem !mock-cert.pem -pnpm-lock.yaml tsconfig.tsbuildinfo target Cargo.lock diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml new file mode 100644 index 0000000..3935168 --- /dev/null +++ b/pnpm-lock.yaml @@ -0,0 +1,7616 @@ +lockfileVersion: '6.0' + +importers: + + .: + devDependencies: + '@antv/graphlib': + specifier: ^2.0.0 + version: 2.0.0 + '@changesets/cli': + specifier: ^2.26.1 + version: 2.26.1 + '@types/jest': + specifier: latest + version: 29.5.2 + cross-env: + specifier: ^7.0.3 + version: 7.0.3 + eslint: + specifier: ^7.32.0 + version: 7.32.0 + eslint-config-airbnb-base: + specifier: ^14.2.1 + version: 14.2.1(eslint-plugin-import@2.27.5)(eslint@7.32.0) + eslint-config-prettier: + specifier: ^6.15.0 + version: 6.15.0(eslint@7.32.0) + eslint-plugin-import: + specifier: ^2.27.5 + version: 2.27.5(eslint@7.32.0) + gh-pages: + specifier: ^5.0.0 + version: 5.0.0 + graphology: + specifier: ^0.25.1 + version: 0.25.1(graphology-types@0.24.7) + graphology-generators: + specifier: ^0.11.2 + version: 0.11.2(graphology-types@0.24.7) + graphology-metrics: + specifier: ^2.1.0 + version: 2.1.0(graphology-types@0.24.7) + graphology-shortest-path: + specifier: ^2.0.2 + version: 2.0.2(graphology-types@0.24.7) + graphology-types: + specifier: ^0.24.7 + version: 0.24.7 + husky: + specifier: ^7.0.4 + version: 7.0.4 + jest: + specifier: ^29.5.0 + version: 29.5.0 + jest-environment-jsdom: + specifier: 29.5.0 + version: 29.5.0 + lint-staged: + specifier: ^10.5.4 + version: 10.5.4 + npm-run-all: + specifier: ^4.1.5 + version: 4.1.5 + rimraf: + specifier: ^3.0.2 + version: 3.0.2 + ts-jest: + specifier: ^29.1.0 + version: 29.1.0(@babel/core@7.22.1)(jest@29.5.0)(typescript@4.9.5) + ts-loader: + specifier: ^8.4.0 + version: 8.4.0(typescript@4.9.5)(webpack@5.38.1) + tslint: + specifier: ^6.1.3 + version: 6.1.3(typescript@4.9.5) + tslint-config-airbnb: + specifier: ^5.11.2 + version: 5.11.2(tslint@6.1.3)(typescript@4.9.5) + tslint-config-prettier: + specifier: ^1.18.0 + version: 1.18.0 + tslint-eslint-rules: + specifier: ^5.4.0 + version: 5.4.0(tslint@6.1.3)(typescript@4.9.5) + typescript: + specifier: ^4.9.5 + version: 4.9.5 + vite: + specifier: ^4.3.8 + version: 4.3.8 + webpack: + specifier: ^5.38.1 + version: 5.38.1(webpack-cli@5.0.2) + webpack-cli: + specifier: ^5.0.2 + version: 5.0.2(webpack@5.38.1) + + packages/graph: + dependencies: + '@antv/graphlib': + specifier: ^2.0.0 + version: 2.0.0 + '@antv/util': + specifier: ^2.0.13 + version: 2.0.13 + tslib: + specifier: ^2.5.2 + 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Date: Wed, 12 Jul 2023 11:03:41 +0800 Subject: [PATCH 5/6] feat: js impl fo louvain --- .../data/cluster-origin-properties-data.json | 404 +++++++++++++++++ __tests__/unit/findPath.spec.ts | 139 ++++++ __tests__/unit/louvain.spec.ts | 67 +++ packages/graph-gpu/src/traversal/sssp.ts | 2 +- packages/graph/src/adjMatrix.ts | 29 ++ packages/graph/src/dijkstra.ts | 107 +++++ packages/graph/src/findPath.ts | 68 +++ packages/graph/src/iLouvain.ts | 24 + packages/graph/src/index.ts | 3 + packages/graph/src/louvain.ts | 420 ++++++++++++++++++ packages/graph/src/types.ts | 28 +- packages/graph/src/utils.ts | 81 ++++ packages/graph/src/vector.ts | 156 +++++++ site/benchmark/main.ts | 14 +- site/benchmark/page-rank.ts | 16 +- site/benchmark/sssp.ts | 28 +- site/benchmark/util.ts | 20 + tsconfig.json | 1 + 18 files changed, 1582 insertions(+), 25 deletions(-) create mode 100644 __tests__/data/cluster-origin-properties-data.json create mode 100644 __tests__/unit/findPath.spec.ts create mode 100644 __tests__/unit/louvain.spec.ts create mode 100644 packages/graph/src/adjMatrix.ts create mode 100644 packages/graph/src/dijkstra.ts create mode 100644 packages/graph/src/findPath.ts create mode 100644 packages/graph/src/iLouvain.ts create mode 100644 packages/graph/src/louvain.ts create mode 100644 packages/graph/src/utils.ts create mode 100644 packages/graph/src/vector.ts create mode 100644 site/benchmark/util.ts diff --git a/__tests__/data/cluster-origin-properties-data.json b/__tests__/data/cluster-origin-properties-data.json new file mode 100644 index 0000000..f174b90 --- /dev/null +++ b/__tests__/data/cluster-origin-properties-data.json @@ -0,0 +1,404 @@ +{ + "nodes": [ + { + "id": "node-0", + "label": "node-0", + "data": { + "city": "110000", + "age": 20, + "amount": 100, + "wifi": "wifi-0" + } + }, + { + "id": "node-1", + "label": "node-1", + "data": { + "city": "110000", + "age": 22, + "amount": 100, + "wifi": "wifi-1" + } + }, + { + "id": "node-2", + "label": "node-2", + "data": { + "city": "110000", + "age": 20, + "amount": 100, + "wifi": "wifi-2" + } + }, + { + "id": "node-3", + "label": "node-3", + "data": { + "city": "110000", + "age": 21, + "amount": 100, + "wifi": "wifi-3" + } + }, + { + "id": "node-4", + "label": "node-4", + "data": { + "city": "110000", + "age": 22, + "amount": 100, + "wifi": "wifi-4" + } + }, + { + "id": "node-5", + "label": "node-5", + "data": { + "city": "310000", + "age": 30, + "amount": 1000, + "wifi": "wifi-5" + } + }, + { + "id": "node-6", + "label": "node-6", + "data": { + "city": "310000", + "age": 31, + "amount": 1000, + "wifi": "wifi-6" + } + }, + { + "id": "node-7", + "label": "node-7", + "data": { + "city": "310000", + "age": 31, + "amount": 1000, + "wifi": "wifi-7" + } + }, + { + "id": "node-8", + "label": "node-8", + "data": { + "city": "310000", + "age": 32, + "amount": 1000, + "wifi": "wifi-8" + } + }, + { + "id": "node-9", + "label": "node-9", + "data": { + "city": "310000", + "age": 30, + "amount": 1000, + "wifi": "wifi-9" + } + }, + { + "id": "node-10", + "label": "node-10", + "data": { + "city": "310000", + "age": 30, + "amount": 1000, + "wifi": "wifi-10" + } + }, + { + "id": "node-11", + "label": "node-11", + "data": { + "city": "440300", + "age": 40, + "amount": 10000, + "wifi": "wifi-11" + } + }, + { + "id": "node-12", + "label": "node-12", + "data": { + "city": "440300", + "age": 40, + "amount": 10000, + "wifi": "wifi-12" + } + }, + { + "id": "node-13", + "label": "node-13", + "data": { + "city": "440300", + "age": 41, + "amount": 10000, + "wifi": "wifi-13" + } + }, + { + "id": "node-14", + "label": "node-14", + "data": { + "city": "440300", + "age": 42, + "amount": 10000, + "wifi": "wifi-14" + } + }, + { + "id": "node-15", + "label": "node-15", + "data": { + "city": "440300", + "age": 41, + "amount": 10000, + "wifi": "wifi-15" + } + }, + { + "id": "node-16", + "label": "node-16", + "data": { + "city": "440300", + "age": 43, + "amount": 10000, + "wifi": "wifi-16" + } + } + ], + "edges": [ + { + "id": "edge-0", + "source": "node-0", + "target": "node-1", + "data": {} + }, + { + "id": "edge-1", + "source": "node-0", + "target": "node-2", + "data": {} + }, + { + "id": "edge-2", + "source": "node-0", + "target": "node-3", + "data": {} + }, + { + "id": "edge-3", + "source": "node-0", + "target": "node-4", + "data": {} + }, + { + "id": "edge-4", + "source": "node-1", + "target": "node-2", + "data": {} + }, + { + "id": "edge-5", + "source": "node-1", + "target": "node-3", + "data": {} + }, + { + "id": "edge-6", + "source": "node-1", + "target": "node-4", + "data": {} + }, + { + "id": "edge-7", + "source": "node-2", + "target": "node-3", + "data": {} + }, + { + "id": "edge-8", + "source": "node-2", + "target": "node-4", + "data": {} + }, + { + "id": "edge-9", + "source": "node-3", + "target": "node-4", + "data": {} + }, + { + "id": "edge-10", + "source": "node-5", + "target": "node-6", + "data": {} + }, + { + "id": "edge-11", + "source": "node-5", + "target": "node-7", + "data": {} + }, + { + "id": "edge-12", + "source": "node-5", + "target": "node-8", + "data": {} + }, + { + "id": "edge-13", + "source": "node-5", + "target": "node-9", + "data": {} + }, + { + "id": "edge-14", + "source": "node-6", + "target": "node-7", + "data": {} + }, + { + "id": "edge-15", + "source": "node-6", + "target": "node-8", + "data": {} + }, + { + "id": "edge-16", + "source": "node-6", + "target": "node-9", + "data": {} + }, + { + "id": "edge-17", + "source": "node-7", + "target": "node-8", + "data": {} + }, + { + "id": "edge-18", + "source": "node-7", + "target": "node-9", + "data": {} + }, + { + "id": "edge-19", + "source": "node-8", + "target": "node-9", + "data": {} + }, + { + "id": "edge-20", + "source": "node-9", + "target": "node-10", + "data": {} + }, + { + "id": "edge-40", + "source": "node-10", + "target": "node-5", + "data": {} + }, + { + "id": "edge-21", + "source": "node-11", + "target": "node-12", + "data": {} + }, + { + "id": "edge-22", + "source": "node-11", + "target": "node-13", + "data": {} + }, + { + "id": "edge-23", + "source": "node-11", + "target": "node-14", + "data": {} + }, + { + "id": "edge-24", + "source": "node-11", + "target": "node-15", + "data": {} + }, + { + "id": "edge-25", + "source": "node-12", + "target": "node-13", + "data": {} + }, + { + "id": "edge-26", + "source": "node-12", + "target": "node-14", + "data": {} + }, + { + "id": "edge-27", + "source": "node-12", + "target": "node-15", + "data": {} + }, + { + "id": "edge-28", + "source": "node-13", + "target": "node-14", + "data": {} + }, + { + "id": "edge-29", + "source": "node-13", + "target": "node-15", + "data": {} + }, + { + "id": "edge-30", + "source": "node-14", + "target": "node-15", + "data": {} + }, + { + "id": "edge-31", + "source": "node-0", + "target": "node-5", + "data": {} + }, + { + "id": "edge-32", + "source": "node-5", + "target": "node-11", + "data": {} + }, + { + "id": "edge-33", + "source": "node-11", + "target": "node-0", + "data": {} + }, + { + "id": "edge-34", + "source": "node-16", + "target": "node-0", + "data": {} + }, + { + "id": "edge-35", + "source": "node-16", + "target": "node-5", + "data": {} + }, + { + "id": "edge-36", + "source": "node-16", + "target": "node-11", + "data": {} + } + ] +} \ No newline at end of file diff --git a/__tests__/unit/findPath.spec.ts b/__tests__/unit/findPath.spec.ts new file mode 100644 index 0000000..e6278a6 --- /dev/null +++ b/__tests__/unit/findPath.spec.ts @@ -0,0 +1,139 @@ +import { Graph } from "@antv/graphlib"; +import { findShortestPath, findAllPath } from "../../packages/graph/src"; + +const graph = new Graph({ + nodes: [ + { + id: 'A', + data: {} + }, + { + id: 'B', + data: {} + }, + { + id: 'C', + data: {} + }, + { + id: 'D', + data: {} + }, + { + id: 'E', + data: {} + }, + { + id: 'F', + data: {} + }, + { + id: 'G', + data: {} + }, + { + id: 'H', + data: {} + }, + ], + edges: [ + { + id: 'e1', + source: 'A', + target: 'B', + data: {} + }, + { + id: 'e2', + source: 'B', + target: 'C', + data: {} + }, + { + id: 'e3', + source: 'C', + target: 'G', + data: {} + }, + { + id: 'e4', + source: 'A', + target: 'D', + data: {} + }, + { + id: 'e5', + source: 'A', + target: 'E', + data: {} + }, + { + id: 'e6', + source: 'E', + target: 'F', + data: {} + }, + { + id: 'e7', + source: 'F', + target: 'D', + data: {} + }, + { + id: 'e8', + source: 'D', + target: 'E', + data: {} + }, + ], +}); + +describe('Shortest Path from source to target on graph', () => { + it('find the shortest path', () => { + const { length, path } = findShortestPath(graph, 'A', 'C'); + expect(length).toBe(2); + expect(path).toStrictEqual(['A', 'B', 'C']); + }); + + it('find all shortest paths', () => { + const { length, allPath } = findShortestPath(graph, 'A', 'F'); + expect(length).toBe(2); + expect(allPath[0]).toStrictEqual(['A', 'E', 'F']); + expect(allPath[1]).toStrictEqual(['A', 'D', 'F']); + + const { + length: directedLenght, + path: directedPath, + allPath: directedAllPath, + } = findShortestPath(graph, 'A', 'F', true); + expect(directedLenght).toBe(2); + expect(directedAllPath[0]).toStrictEqual(['A', 'E', 'F']); + expect(directedPath).toStrictEqual(['A', 'E', 'F']); + }); + + it('find all paths', () => { + const allPath = findAllPath(graph, 'A', 'E'); + expect(allPath.length).toBe(3); + expect(allPath[0]).toStrictEqual(['A', 'D', 'F', 'E']); + expect(allPath[1]).toStrictEqual(['A', 'D', 'E']); + expect(allPath[2]).toStrictEqual(['A', 'E']); + }); + + it('find all paths in directed graph', () => { + const allPath = findAllPath(graph, 'A', 'E', true); + expect(allPath.length).toStrictEqual(2); + expect(allPath[0]).toStrictEqual(['A', 'D', 'E']); + expect(allPath[1]).toStrictEqual(['A', 'E']); + }); + + it('find all shortest paths in weighted graph', () => { + graph.getAllEdges().forEach((edge, i) => { + edge.data.weight = ((i % 2) + 1) * 2; + if (edge.source === 'F' && edge.target === 'D') edge.data.weight = 10; + }); + const { length, path, allPath } = findShortestPath(graph, 'A', 'F', false, 'weight'); + expect(length).toBe(6); + expect(allPath[0]).toStrictEqual(['A', 'E', 'F']); + expect(path).toStrictEqual(['A', 'E', 'F']); + }); +}); \ No newline at end of file diff --git a/__tests__/unit/louvain.spec.ts b/__tests__/unit/louvain.spec.ts new file mode 100644 index 0000000..9f9185f --- /dev/null +++ b/__tests__/unit/louvain.spec.ts @@ -0,0 +1,67 @@ +import { Graph } from "@antv/graphlib"; +import { louvain, iLouvain } from "../../packages/graph/src"; +import * as propertiesGraphData from "../data/cluster-origin-properties-data.json"; + +describe('Louvain', () => { + it('simple louvain', () => { + const graph = new Graph({ + nodes: [ + { id: '0', data: {} }, { id: '1', data: {} }, { id: '2', data: {} }, { id: '3', data: {} }, { id: '4', data: {} }, + { id: '5', data: {} }, { id: '6', data: {} }, { id: '7', data: {} }, { id: '8', data: {} }, { id: '9', data: {} }, + { id: '10', data: {} }, { id: '11', data: {} }, { id: '12', data: {} }, { id: '13', data: {} }, { id: '14', data: {} }, + ], + edges: [ + { id: 'e1', source: '0', target: '1', data: {} }, { id: 'e2', source: '0', target: '2', data: {} }, { id: 'e3', source: '0', target: '3', data: {} }, { id: 'e4', source: '0', target: '4', data: {} }, + { id: 'e5', source: '1', target: '2', data: {} }, { id: 'e6', source: '1', target: '3', data: {} }, { id: 'e7', source: '1', target: '4', data: {} }, + { id: 'e8', source: '2', target: '3', data: {} }, { id: 'e9', source: '2', target: '4', data: {} }, + { id: 'e10', source: '3', target: '4', data: {} }, + { id: 'e11', source: '0', target: '0', data: {} }, + { id: 'e12', source: '0', target: '0', data: {} }, + { id: 'e13', source: '0', target: '0', data: {} }, + + { id: 'e14', source: '5', target: '6', data: {weight: 5} }, { id: 'e15', source: '5', target: '7', data: {} }, { id: 'e16', source: '5', target: '8', data: {} }, { id: 'e17', source: '5', target: '9', data: {} }, + { id: 'e18', source: '6', target: '7', data: {} }, { id: 'e19', source: '6', target: '8', data: {} }, { id: 'e20', source: '6', target: '9', data: {} }, + { id: 'e21', source: '7', target: '8', data: {} }, { id: 'e22', source: '7', target: '9', data: {} }, + { id: 'e23',source: '8', target: '9', data: {} }, + + { id: 'e24',source: '10', target: '11', data: {} }, { id: 'e25',source: '10', target: '12', data: {} }, { id: 'e26',source: '10', target: '13', data: {} }, { id: 'e27',source: '10', target: '14', data: {} }, + { id: 'e28',source: '11', target: '12', data: {} }, { id: 'e29',source: '11', target: '13', data: {} }, { id: 'e30',source: '11', target: '14', data: {} }, + { id: 'e31',source: '12', target: '13', data: {} }, { id: 'e32',source: '12', target: '14', data: {} }, + { id: 'e33',source: '13', target: '14', data: { weight: 5 } }, + + { id: 'e34',source: '0', target: '5', data: {}}, + { id: 'e35',source: '5', target: '10', data: {} }, + { id: 'e36',source: '10', target: '0', data: {} }, + { id: 'e37',source: '10', target: '0', data: {} }, + ], + }); + const clusteredData = louvain(graph, false, 'weight'); + expect(clusteredData.clusters.length).toBe(3); + expect(clusteredData.clusters[0].sumTot).toBe(3); + expect(clusteredData.clusters[1].sumTot).toBe(2); + expect(clusteredData.clusterEdges.length).toBe(6); + expect(clusteredData.clusterEdges[0].data.count).toBe(13); + expect(clusteredData.clusterEdges[1].data.count).toBe(10); + expect(clusteredData.clusterEdges[1].data.weight).toBe(14); + }); + + // it('louvain with large graph', () => { // https://gw.alipayobjects.com/os/antvdemo/assets/data/relations.json + // fetch('https://gw.alipayobjects.com/os/basement_prod/da5a1b47-37d6-44d7-8d10-f3e046dabf82.json') + // .then((res) => res.json()) + // .then((data) => { // 1589 nodes, 2747 edges + // const clusteredData = louvain(data, false, 'weight'); + // expect(clusteredData.clusters.length).toBe(495); + // expect(clusteredData.clusterEdges.length).toBe(505); + // }); + // }); + + it('louvain: add inertialModularity', () => { + const graph = new Graph(propertiesGraphData); + const clusteredData = iLouvain(graph, false, 'weight', 0.01); + expect(clusteredData.clusters.length).toBe(3); + expect(clusteredData.clusters[0].sumTot).toBe(3); + expect(clusteredData.clusters[1].sumTot).toBe(3); + expect(clusteredData.clusters[2].sumTot).toBe(4); + expect(clusteredData.clusterEdges.length).toBe(7); + }); +}); \ No newline at end of file diff --git a/packages/graph-gpu/src/traversal/sssp.ts b/packages/graph-gpu/src/traversal/sssp.ts index 82638ae..cb20ee6 100644 --- a/packages/graph-gpu/src/traversal/sssp.ts +++ b/packages/graph-gpu/src/traversal/sssp.ts @@ -196,7 +196,7 @@ fn main( updatePredKernel.dispatch(grids, 1); const out = (await readback.readBuffer(DiOutBuffer)) as Float32Array; - const predecessor = await readback.readBuffer(POutBuffer); + const predecessor = await readback.readBuffer(POutBuffer) as Float32Array; return Array.from(out).map((distance, i) => ({ target: graphData.getAllNodes()[V[i]].id, diff --git a/packages/graph/src/adjMatrix.ts b/packages/graph/src/adjMatrix.ts new file mode 100644 index 0000000..6e607ab --- /dev/null +++ b/packages/graph/src/adjMatrix.ts @@ -0,0 +1,29 @@ +import { Graph, Matrix } from "./types"; + +export function graph2AdjacencyMatrix(graph: Graph, directed?: boolean): Matrix[] { + const matrix: Matrix[] = []; + // map node with index in data.nodes + const nodeMap: { + [key: string]: number; + } = {}; + + graph.getAllNodes().forEach((node, i) => { + nodeMap[node.id] = i; + const row: number[] = []; + matrix.push(row); + }); + + + graph.getAllEdges().forEach((edge) => { + const { source, target } = edge; + const sIndex = nodeMap[source as string]; + const tIndex = nodeMap[target as string]; + if ((!sIndex && sIndex !== 0) || (!tIndex && tIndex !== 0)) return; + matrix[sIndex][tIndex] = 1; + if (!directed) { + matrix[tIndex][sIndex] = 1; + } + }); + + return matrix; +} \ No newline at end of file diff --git a/packages/graph/src/dijkstra.ts b/packages/graph/src/dijkstra.ts new file mode 100644 index 0000000..5ffa2d9 --- /dev/null +++ b/packages/graph/src/dijkstra.ts @@ -0,0 +1,107 @@ +import { Edge, ID, Node } from "@antv/graphlib"; +import { isArray } from '@antv/util'; +import { EdgeData, Graph, NodeData } from "./types"; + +function minVertex( + D: { [key: ID]: number }, + nodes: Node[], + marks: { [key: string]: boolean }, +): Node { + let minDis = Infinity; + let minNode; + for (let i = 0; i < nodes.length; i++) { + const nodeId = nodes[i].id; + if (!marks[nodeId] && D[nodeId] <= minDis) { + minDis = D[nodeId]; + minNode = nodes[i]; + } + } + return minNode; +} + +function findAllPaths(source: ID, target: ID, prevs: Record, foundPaths: Record): ID[] { + if (source === target) { + return [source]; + } + if (foundPaths[target]) { + // @ts-ignore + return foundPaths[target]; + } + const paths: ID[][] = []; + for (const prev of prevs[target]) { + const prevPaths = findAllPaths(source, prev, prevs, foundPaths); + if (!prevPaths) return; + for (const prePath of prevPaths) { + if (isArray(prePath)) paths.push([...prePath, target]); + else paths.push([prePath, target]); + } + } + foundPaths[target] = paths; + // @ts-ignore + return foundPaths[target]; +} + +export function dijkstra( + graph: Graph, + source: ID, + directed?: boolean, + weightPropertyName?: string, +) { + const nodes = graph.getAllNodes(); + const nodeIds: ID[] = []; + const marks: Record = {}; + const D: Record = {}; + const prevs: Record = {}; // key: 顶点, value: 顶点的前驱点数组（可能有多条等长的最短路径） + nodes.forEach((node, i) => { + const id = node.id; + nodeIds.push(id); + D[id] = Infinity; + if (id === source) D[id] = 0; + }); + + const nodeNum = nodes.length; + for (let i = 0; i < nodeNum; i++) { + // Process the vertices + const minNode = minVertex(D, nodes, marks); + const minNodeId = minNode.id; + marks[minNodeId] = true; + + if (D[minNodeId] === Infinity) continue; // Unreachable vertices cannot be the intermediate point + + let relatedEdges: Edge[] = []; + if (directed) { + relatedEdges = graph.getRelatedEdges(minNodeId, 'out'); + } else { + relatedEdges = graph.getRelatedEdges(minNodeId, 'both'); + } + + relatedEdges.forEach((edge) => { + const edgeTarget = edge.target; + const edgeSource = edge.source; + const w = edgeTarget === minNodeId ? edgeSource : edgeTarget; + const weight = weightPropertyName && edge.data[weightPropertyName] as number ? edge.data[weightPropertyName] as number : 1; + if (D[w] > D[minNode.id] + weight) { + D[w] = D[minNode.id] + weight; + prevs[w] = [minNode.id]; + } else if (D[w] === D[minNode.id] + weight) { + prevs[w].push(minNode.id); + } + }); + } + + prevs[source] = [source]; + // 每个节点存可能存在多条最短路径 + const paths: Record = {}; + for (const target in D) { + if (D[target] !== Infinity) { + findAllPaths(source, target, prevs, paths); + } + } + + // 兼容之前单路径 + const path: Record = {}; + for (const target in paths) { + path[target] = paths[target][0]; + } + return { length: D, path, allPath: paths }; +} \ No newline at end of file diff --git a/packages/graph/src/findPath.ts b/packages/graph/src/findPath.ts new file mode 100644 index 0000000..b0a5e55 --- /dev/null +++ b/packages/graph/src/findPath.ts @@ -0,0 +1,68 @@ +import { ID, Node } from "@antv/graphlib"; +import { Graph, NodeData } from "./types"; +import { dijkstra } from "./dijkstra"; + +export const findShortestPath = ( + graph: Graph, + start: ID, + end: ID, + directed?: boolean, + weightPropertyName?: string +) => { + const { length, path, allPath } = dijkstra( + graph, + start, + directed, + weightPropertyName + ); + return { length: length[end], path: path[end], allPath: allPath[end] }; +}; + +export const findAllPath = ( + graph: Graph, + start: ID, + end: ID, + directed?: boolean +) => { + if (start === end) return [[start]]; + + const visited = [start]; + const isVisited = { [start]: true }; + const stack: Node[][] = []; // 辅助栈，用于存储访问过的节点的邻居节点 + const allPath = []; + let neighbors = directed + ? graph.getSuccessors(start) + : graph.getNeighbors(start); + stack.push(neighbors); + + while (visited.length > 0 && stack.length > 0) { + const children = stack[stack.length - 1]; + if (children.length) { + const child = children.shift(); + if (child) { + visited.push(child.id); + isVisited[child.id] = true; + neighbors = directed + ? graph.getSuccessors(child.id) + : graph.getNeighbors(child.id); + stack.push(neighbors.filter((neighbor) => !isVisited[neighbor.id])); + } + } else { + const node = visited.pop(); + isVisited[node] = false; + stack.pop(); + continue; + } + + if (visited[visited.length - 1] === end) { + const path = visited.map((node) => node); + allPath.push(path); + + const node = visited.pop(); + isVisited[node] = false; + stack.pop(); + } + } + + return allPath; +}; \ No newline at end of file diff --git a/packages/graph/src/iLouvain.ts b/packages/graph/src/iLouvain.ts new file mode 100644 index 0000000..2ad40b5 --- /dev/null +++ b/packages/graph/src/iLouvain.ts @@ -0,0 +1,24 @@ +import { louvain } from './louvain'; +import type { ClusterData, Graph } from "./types"; + +/** + * 社区发现 i-louvain 算法：模块度 + 惯性模块度（即节点属性相似性） + * @param graphData 图数据 + * @param directed 是否有向图，默认为 false + * @param weightPropertyName 权重的属性字段 + * @param threshold 差值阈值 + * @param involvedKeys 参与计算的key集合 + * @param uninvolvedKeys 不参与计算的key集合 + * @param inertialWeight 惯性模块度权重 + */ +export function iLouvain( + graph: Graph, + directed: boolean = false, + weightPropertyName: string = 'weight', + threshold: number = 0.0001, + involvedKeys: string[] = [], + uninvolvedKeys: string[] = ['id'], + inertialWeight: number = 1, +): ClusterData { + return louvain(graph, directed, weightPropertyName, threshold, true, involvedKeys, uninvolvedKeys, inertialWeight); +} \ No newline at end of file diff --git a/packages/graph/src/index.ts b/packages/graph/src/index.ts index d80201a..ab5387c 100644 --- a/packages/graph/src/index.ts +++ b/packages/graph/src/index.ts @@ -1 +1,4 @@ export * from "./pageRank"; +export * from "./findPath"; +export * from "./louvain"; +export * from "./iLouvain"; diff --git a/packages/graph/src/louvain.ts b/packages/graph/src/louvain.ts new file mode 100644 index 0000000..dfb477c --- /dev/null +++ b/packages/graph/src/louvain.ts @@ -0,0 +1,420 @@ +import { ID, Node } from "@antv/graphlib"; +import { clone } from "@antv/util"; +import { Cluster, ClusterData, ClusterMap, Graph, NodeData } from "./types"; +import { getAllProperties, oneHot } from "./utils"; +import { graph2AdjacencyMatrix } from "./adjMatrix"; +import { Vector } from "./vector"; + +/** + * The quality of the communities referred as partitions hereafter is measured by Modularity of the partition. + * @see https://medium.com/walmartglobaltech/demystifying-louvains-algorithm-and-its-implementation-in-gpu-9a07cdd3b010 + */ +function getModularity( + nodes: Node[], + adjMatrix: number[][], + ks: number[], + m: number +) { + const length = adjMatrix.length; + const param = 2 * m; // number if links + let modularity = 0; + for (let i = 0; i < length; i++) { + const clusteri = nodes[i].data.clusterId as string; + for (let j = 0; j < length; j++) { + const clusterj = nodes[j].data.clusterId as string; + if (clusteri !== clusterj) continue; // 1 if x = y and 0 otherwise + const entry = adjMatrix[i][j] || 0; // Aij: the weightof the edge between i & j + const ki = ks[i] || 0; // Ki: degree of the node + const kj = ks[j] || 0; + modularity += (entry - ki * kj / param); + } + } + modularity *= (1 / param); + return modularity; +} + +// 模块惯性度，衡量属性相似度 +function getInertialModularity( + nodes: Node[] = [], + allPropertiesWeight: number[][], +) { + const length = nodes.length; + let totalProperties = new Vector([]); + for (let i = 0; i < length; i++) { + totalProperties = totalProperties.add(new Vector(allPropertiesWeight[i])); + } + // 均值向量 + const avgProperties = totalProperties.avg(length); + + avgProperties.normalize(); + // 节点集合的方差: 节点v与均值向量的平方欧式距离之和 + let variance: number = 0; + for (let i = 0; i < length; i++) { + const propertiesi = new Vector(allPropertiesWeight[i]); + const squareEuclideanDistance = propertiesi.squareEuclideanDistance(avgProperties); + variance += squareEuclideanDistance; + } + + // 任意两点间的欧式平方距离 + const squareEuclideanDistanceInfo: number[][] = []; + nodes.forEach(() => { + squareEuclideanDistanceInfo.push([]); + }); + for (let i = 0; i < length; i++) { + const propertiesi = new Vector(allPropertiesWeight[i]); + nodes[i].data['clusterInertial'] = 0; + for (let j = 0; j < length; j++) { + if ( i === j) { + squareEuclideanDistanceInfo[i][j] = 0; + continue; + } + const propertiesj = new Vector(allPropertiesWeight[j]); + squareEuclideanDistanceInfo[i][j] = propertiesi.squareEuclideanDistance(propertiesj); + (nodes[i].data['clusterInertial'] as number) += squareEuclideanDistanceInfo[i][j]; + } + } + + // 计算模块惯性度 + let inertialModularity = 0; + const param = 2 * length * variance; + for (let i = 0; i < length; i++) { + const clusteri = nodes[i].data.clusterId; + for (let j = 0; j < length; j++) { + const clusterj = nodes[j].data.clusterId; + if ( i === j || clusteri !== clusterj) continue; + const inertial = ((nodes[i].data.clusterInertial as number) * (nodes[j].data.clusterInertial as number)) + / Math.pow(param, 2) - squareEuclideanDistanceInfo[i][j] / param; + inertialModularity += inertial; + } + } + return Number(inertialModularity.toFixed(4)); +} + +/** + * 社区发现 louvain 算法 + * @param graphData 图数据 + * @param directed 是否有向图，默认为 false + * @param weightPropertyName 权重的属性字段 + * @param threshold 差值阈值 + * @param inertialModularity 是否使用惯性模块度（即节点属性相似性） + * @param propertyKey 属性的字段名 + * @param involvedKeys 参与计算的key集合 + * @param uninvolvedKeys 不参与计算的key集合 + * @param inertialWeight 惯性模块度权重 + */ +export function louvain( + graph: Graph, + directed: boolean = false, + weightPropertyName: string = 'weight', + threshold: number = 0.0001, + inertialModularity: boolean = false, + involvedKeys: string[] = [], + uninvolvedKeys: string[] = ['id'], + inertialWeight: number = 1, +): ClusterData { + const nodes = graph.getAllNodes(); + const edges = graph.getAllEdges(); + + let allPropertiesWeight: number[][] = []; + if (inertialModularity) { + nodes.forEach((node, index) => { + node.data.originIndex = index; + }); + + let nodeTypeInfo: string[] = []; + if (nodes.every((node) => 'nodeType' in node.data)) { + nodeTypeInfo = Array.from(new Set(nodes.map((node) => node.data.nodeType as string))); + nodes.forEach((node) => { + node.data.nodeType = nodeTypeInfo.findIndex((nodeType) => nodeType === node.data.nodeType); + }); + } + // 所有节点属性集合 + const properties = getAllProperties(nodes); + + // 所有节点属性one-hot特征向量集合 + allPropertiesWeight = oneHot(properties, involvedKeys, uninvolvedKeys) as number[][]; + } + + /** + * 1. To start with each node is assigned to a different community or partition. + * The number of partitions is equal to number of nodes N. + */ + let uniqueId = 1; + const clusters: ClusterMap = {}; + const nodeMap: Record; idx: number }> = {}; + nodes.forEach((node, i) => { + const cid: string = String(uniqueId++); + node.data.clusterId = cid; + clusters[cid] = { + id: cid, + nodes: [node] + }; + nodeMap[node.id] = { + node, + idx: i + }; + }); + // the adjacent matrix of calNodes inside clusters + const adjMatrix = graph2AdjacencyMatrix(graph, directed); + // the sum of each row in adjacent matrix + const ks: number[] = []; + /** + * neighbor nodes (id for key and weight for value) for each node + * neighbors = { + * id(node_id): { id(neighbor_1_id): weight(weight of the edge), id(neighbor_2_id): weight(weight of the edge), ... }, + * ... + * } + */ + const neighbors: Record> = {}; + // the sum of the weights of all edges in the graph + let m = 0; + adjMatrix.forEach((row, i) => { + let k = 0; + const iid = nodes[i].id; + neighbors[iid] = {}; + row.forEach((entry, j) => { + if (!entry) return; + k += entry; + const jid = nodes[j].id; + neighbors[iid][jid] = entry; + m += entry; + }); + ks.push(k); + }); + + m /= 2; + + let totalModularity = Infinity; + let previousModularity = Infinity; + let iter = 0; + + let finalNodes: Node[] = []; + let finalClusters: ClusterMap = {}; + while (true) { + if (inertialModularity && nodes.every((node) => node.hasOwnProperty('properties'))) { + totalModularity = getModularity(nodes, adjMatrix, ks, m) + getInertialModularity(nodes, allPropertiesWeight) * inertialWeight; + } else { + totalModularity = getModularity(nodes, adjMatrix, ks, m); + } + + // 第一次迭代previousModularity直接赋值 + if (iter === 0) { + previousModularity = totalModularity; + finalNodes = nodes; + finalClusters = clusters; + } + + const increaseWithinThreshold = totalModularity > 0 && totalModularity > previousModularity && totalModularity - previousModularity < threshold; + // 总模块度增加才更新最优解 + if (totalModularity > previousModularity) { + finalClusters = clone(clusters); + previousModularity = totalModularity; + } + + // whether to terminate the iterations + if (increaseWithinThreshold || iter > 100) { + break; + } + iter++; + // pre compute some values for current clusters + Object.keys(clusters).forEach((clusterId) => { + // sum of weights of edges to nodes in cluster + let sumTot = 0; + edges.forEach((edge) => { + const { source, target } = edge; + const sourceClusterId = nodeMap[source].node.data.clusterId; + const targetClusterId = nodeMap[target].node.data.clusterId; + if ((sourceClusterId === clusterId && targetClusterId !== clusterId) + || (targetClusterId === clusterId && sourceClusterId !== clusterId)) { + sumTot = sumTot + (edge.data[weightPropertyName] as number || 1); + } + }); + clusters[clusterId].sumTot = sumTot; + }); + + + // move the nodes to increase the delta modularity + nodes.forEach((node, i) => { + const selfCluster = clusters[node.data.clusterId]; + let bestIncrease = 0; + let bestCluster: Cluster; + + const commonParam = ks[i] / (2 * m); + + // sum of weights of edges from node to nodes in cluster + let kiin = 0; + const selfClusterNodes = selfCluster.nodes; + selfClusterNodes.forEach((scNode) => { + const scNodeIdx = nodeMap[scNode.id].idx; + kiin += adjMatrix[i][scNodeIdx] || 0; + }); + // the modurarity for **removing** the node i from the origin cluster of node i + const removeModurarity = kiin - selfCluster.sumTot * commonParam; + // nodes for **removing** node i into this neighbor cluster + const selfClusterNodesAfterRemove = selfClusterNodes.filter((scNode) => scNode.id !== node.id); + const propertiesWeightRemove: number[][] = []; + selfClusterNodesAfterRemove.forEach((nodeRemove, index) => { + propertiesWeightRemove[index] = allPropertiesWeight[nodeRemove.data.originIndex as number]; + }); + // the inertialModularity for **removing** the node i from the origin cluster of node i + const removeInertialModularity = getInertialModularity(selfClusterNodesAfterRemove, allPropertiesWeight) * inertialWeight; + + // the neightbors of the node + const nodeNeighborIds = neighbors[node.id]; + Object.keys(nodeNeighborIds).forEach((neighborNodeId) => { + const neighborNode = nodeMap[neighborNodeId].node; + const neighborClusterId = neighborNode.data.clusterId; + + // if the node and the neighbor of node are in the same cluster, reutrn + if (neighborClusterId === node.data.clusterId) return; + const neighborCluster = clusters[neighborClusterId]; + const clusterNodes = neighborCluster.nodes; + + // if the cluster is empty, remove the cluster and return + if (!clusterNodes || !clusterNodes.length) return; + + // sum of weights of edges from node to nodes in cluster + let neighborClusterKiin = 0; + clusterNodes.forEach((cNode) => { + const cNodeIdx = nodeMap[cNode.id].idx; + neighborClusterKiin += adjMatrix[i][cNodeIdx] || 0; + }); + + // the modurarity for **adding** node i into this neighbor cluster + const addModurarity = neighborClusterKiin - neighborCluster.sumTot * commonParam; + // nodes for **adding** node i into this neighbor cluster + const clusterNodesAfterAdd= clusterNodes.concat([node]); + const propertiesWeightAdd: number[][] = []; + clusterNodesAfterAdd.forEach((nodeAdd, index) => { + propertiesWeightAdd[index] = allPropertiesWeight[nodeAdd.data.originIndex as number]; + }); + // the inertialModularity for **adding** node i into this neighbor cluster + const addInertialModularity = getInertialModularity(clusterNodesAfterAdd, allPropertiesWeight) * inertialWeight; + + // the increase modurarity is the difference between addModurarity and removeModurarity + let increase = addModurarity - removeModurarity; + if (inertialModularity) { + increase = (addModurarity + addInertialModularity) - (removeModurarity + removeInertialModularity); + } + + // find the best cluster to move node i into + if (increase > bestIncrease) { + bestIncrease = increase; + bestCluster = neighborCluster; + } + }); + + // if found a best cluster to move into + if (bestIncrease > 0) { + bestCluster.nodes.push(node); + const previousClusterId = node.data.clusterId; + node.data.clusterId = bestCluster.id; + // move the node to the best cluster + const nodeInSelfClusterIdx = selfCluster.nodes.indexOf(node); + // remove from origin cluster + selfCluster.nodes.splice(nodeInSelfClusterIdx, 1); + // update sumTot for clusters + // sum of weights of edges to nodes in cluster + let neighborClusterSumTot = 0; + let selfClusterSumTot = 0; + edges.forEach((edge) => { + const { source, target } = edge; + const sourceClusterId = nodeMap[source].node.data.clusterId; + const targetClusterId = nodeMap[target].node.data.clusterId; + if ((sourceClusterId === bestCluster.id && targetClusterId !== bestCluster.id) + || (targetClusterId === bestCluster.id && sourceClusterId !== bestCluster.id)) { + neighborClusterSumTot = neighborClusterSumTot + (edge.data[weightPropertyName] as number || 1); + } + if ((sourceClusterId === previousClusterId && targetClusterId !== previousClusterId) + || (targetClusterId === previousClusterId && sourceClusterId !== previousClusterId)) { + selfClusterSumTot = selfClusterSumTot + (edge.data[weightPropertyName] as number || 1); + } + }); + + // the nodes of the clusters to move into and remove are changed, update their sumTot + bestCluster.sumTot = neighborClusterSumTot; + selfCluster.sumTot = selfClusterSumTot; + } + }); + } + + // delete the empty clusters, assign increasing clusterId + const newClusterIdMap: Record = {}; + let clusterIdx = 0; + Object.keys(finalClusters).forEach((clusterId) => { + const cluster = finalClusters[clusterId]; + if (!cluster.nodes || !cluster.nodes.length) { + delete finalClusters[clusterId]; + return; + } + const newId = String(clusterIdx + 1); + if (newId === clusterId) { + return; + } + cluster.id = newId; + cluster.nodes.forEach((node) => { + node.data.clusterId = newId; + }); + finalClusters[newId] = cluster; + newClusterIdMap[clusterId] = newId; + delete finalClusters[clusterId]; + clusterIdx ++; + }); + // restore node clusterId + finalNodes.forEach((node) => { + if (node.data.clusterId && newClusterIdMap[node.data.clusterId]) { + node.data.clusterId = newClusterIdMap[node.data.clusterId]; + } + }); + // get the cluster edges + const clusterEdges: { + id: ID; + source: string; + target: string; + data: { + weight: number; + count: number; + } + }[] = []; + const clusterEdgeMap: Record = {}; + edges.forEach((edge) => { + const { source, target } = edge; + const weight = edge.data[weightPropertyName] as number || 1; + const sourceClusterId = nodeMap[source].node.data.clusterId; + const targetClusterId = nodeMap[target].node.data.clusterId; + if (!sourceClusterId || !targetClusterId) return; + const newEdgeId = `${sourceClusterId}---${targetClusterId}`; + if (clusterEdgeMap[newEdgeId]) { + clusterEdgeMap[newEdgeId].data.weight += weight; + clusterEdgeMap[newEdgeId].data.count++; + } else { + const newEdge = { + id: edge.id, + source: sourceClusterId, + target: targetClusterId, + data: { + weight, + count: 1 + } + }; + clusterEdgeMap[newEdgeId] = newEdge; + clusterEdges.push(newEdge); + } + }); + const clustersArray: Cluster[] = []; + Object.keys(finalClusters).forEach((clusterId) => { + clustersArray.push(finalClusters[clusterId]); + }); + return { + clusters: clustersArray, + clusterEdges + }; +} diff --git a/packages/graph/src/types.ts b/packages/graph/src/types.ts index 88318c3..8fe9dce 100644 --- a/packages/graph/src/types.ts +++ b/packages/graph/src/types.ts @@ -1,9 +1,33 @@ -import { Graph as IGraph, PlainObject } from "@antv/graphlib"; +import { Edge, Graph as IGraph, Node, PlainObject } from "@antv/graphlib"; -export interface NodeData extends PlainObject {} +// 数据集中属性/特征值分布的map +export interface KeyValueMap { + [key:string]: any[]; +} + +export interface NodeData extends PlainObject { + clusterId?: string; +} export interface EdgeData extends PlainObject { weight?: number; } +export interface Cluster { + id: string; + nodes: Node[]; + sumTot?: number; +} + +export interface ClusterData { + clusters: Cluster[]; + clusterEdges: Edge[]; +} + +export interface ClusterMap { + [key: string]: Cluster; +} + export type Graph = IGraph; + +export type Matrix = number[]; \ No newline at end of file diff --git a/packages/graph/src/utils.ts b/packages/graph/src/utils.ts new file mode 100644 index 0000000..80470f3 --- /dev/null +++ b/packages/graph/src/utils.ts @@ -0,0 +1,81 @@ +import { Node, PlainObject } from "@antv/graphlib"; +import { KeyValueMap, NodeData } from "./types"; +import { uniq } from "@antv/util"; + +export const getAllProperties = (nodes: Node[]) => { + const allProperties: NodeData[] = []; + nodes.forEach((node) => { + allProperties.push(node.data); + }); + return allProperties; +}; + +export const getAllKeyValueMap = (dataList: PlainObject[], involvedKeys?: string[], uninvolvedKeys?: string[]) => { + let keys: string[] = []; + // 指定了参与计算的keys时，使用指定的keys + if (involvedKeys?.length) { + keys = involvedKeys; + } else { + // 未指定抽取的keys时，提取数据中所有的key + dataList.forEach((data) => { + keys = keys.concat(Object.keys(data)); + }); + keys = uniq(keys); + } + // 获取所有值非空的key的value数组 + const allKeyValueMap: KeyValueMap = {}; + keys.forEach((key) => { + const value: unknown[] = []; + dataList.forEach((data) => { + if (data[key] !== undefined && data[key] !== '') { + value.push(data[key]); + } + }); + if (value.length && !uninvolvedKeys?.includes(key)) { + allKeyValueMap[key] = uniq(value); + } + }); + + return allKeyValueMap; +}; + +export const oneHot = (dataList: PlainObject[], involvedKeys?: string[], uninvolvedKeys?: string[]) => { + // 获取数据中所有的属性/特征及其对应的值 + const allKeyValueMap = getAllKeyValueMap(dataList, involvedKeys, uninvolvedKeys); + const oneHotCode: unknown[][] = []; + if (!Object.keys(allKeyValueMap).length) { + return oneHotCode; + } + + // 获取所有的属性/特征值 + const allValue = Object.values(allKeyValueMap); + // 是否所有属性/特征的值都是数值型 + const isAllNumber = allValue.every((value) => value.every((item) => (typeof(item) === 'number'))); + + // 对数据进行one-hot编码 + dataList.forEach((data, index) => { + let code: unknown[] = []; + Object.keys(allKeyValueMap).forEach((key) => { + const keyValue = data[key]; + const allKeyValue = allKeyValueMap[key]; + const valueIndex = allKeyValue.findIndex((value) => keyValue === value); + const subCode = []; + // 如果属性/特征所有的值都能转成数值型，不满足分箱，则直接用值（todo: 为了收敛更快，需做归一化处理） + if (isAllNumber) { + subCode.push(keyValue); + } else { + // 进行one-hot编码 + for(let i = 0; i < allKeyValue.length; i++) { + if (i === valueIndex) { + subCode.push(1); + } else { + subCode.push(0); + } + } + } + code = code.concat(subCode); + }); + oneHotCode[index] = code; + }); + return oneHotCode; +}; \ No newline at end of file diff --git a/packages/graph/src/vector.ts b/packages/graph/src/vector.ts new file mode 100644 index 0000000..ee65fa9 --- /dev/null +++ b/packages/graph/src/vector.ts @@ -0,0 +1,156 @@ +/** + * 向量运算 + */ +import { clone } from '@antv/util'; + +export class Vector { + arr: number[]; + + constructor(arr: number[]) { + this.arr = arr; + } + + getArr() { + return this.arr || []; + } + + add(otherVector: Vector) { + const otherArr = otherVector.arr; + if (!this.arr?.length) { + return new Vector(otherArr); + } + if (!otherArr?.length) { + return new Vector(this.arr); + } + if (this.arr.length === otherArr.length) { + const res: number[] = []; + for (const index in this.arr) { + res[index] = this.arr[index] + otherArr[index]; + } + return new Vector(res); + } + } + + subtract(otherVector: Vector) { + const otherArr = otherVector.arr; + if (!this.arr?.length) { + return new Vector(otherArr); + } + if (!otherArr?.length) { + return new Vector(this.arr); + } + if (this.arr.length === otherArr.length) { + const res: number[] = []; + for (const index in this.arr) { + res[index] = this.arr[index] - otherArr[index]; + } + return new Vector(res); + } + } + + avg(length: number) { + const res: number[] = []; + if (length !== 0) { + for (const index in this.arr) { + res[index] = this.arr[index] / length; + } + } + return new Vector(res); + } + + negate() { + const res: number[] = []; + for (const index in this.arr) { + res[index] = - this.arr[index]; + } + return new Vector(res); + } + + // 平方欧式距离 + squareEuclideanDistance(otherVector: Vector) { + const otherArr = otherVector.arr; + if (!this.arr?.length || !otherArr?.length) { + return 0; + } + if (this.arr.length === otherArr.length) { + let res = 0; + for (const index in this.arr) { + res += Math.pow(this.arr[index] - otherVector.arr[index], 2); + } + return res; + } + } + + // 欧式距离 + euclideanDistance(otherVector: Vector) { + const otherArr = otherVector.arr; + if (!this.arr?.length || !otherArr?.length) { + return 0; + } + if (this.arr.length === otherArr.length) { + let res = 0; + for (const index in this.arr) { + res += Math.pow(this.arr[index] - otherVector.arr[index], 2); + } + return Math.sqrt(res); + } + console.error('The two vectors are unequal in length.'); + + } + + // 归一化处理 + normalize() { + const res: number[] = []; + const cloneArr = clone(this.arr); + cloneArr.sort((a: number, b: number) => a - b); + const max = cloneArr[cloneArr.length - 1]; + const min = cloneArr[0]; + for (const index in this.arr) { + res[index] = (this.arr[index] - min) / (max - min); + } + return new Vector(res); + } + + // 2范数 or 模长 + norm2() { + if (!this.arr?.length) { + return 0; + } + let res = 0; + for (const index in this.arr) { + res += Math.pow(this.arr[index], 2); + } + return Math.sqrt(res); + } + + // 两个向量的点积 + dot(otherVector: Vector) { + const otherArr = otherVector.arr; + if (!this.arr?.length || !otherArr?.length) { + return 0; + } + if (this.arr.length === otherArr.length) { + let res = 0; + for (const index in this.arr) { + res += this.arr[index] * otherVector.arr[index]; + } + return res; + } + console.error('The two vectors are unequal in length.'); + + } + + // 两个向量比较 + equal(otherVector: Vector) { + const otherArr = otherVector.arr; + if (this.arr?.length !== otherArr?.length) { + return false; + } + for (const index in this.arr) { + if (this.arr[index] !== otherArr[index]) { + return false; + } + } + return true; + } +} diff --git a/site/benchmark/main.ts b/site/benchmark/main.ts index 3a944fd..8d46dc0 100644 --- a/site/benchmark/main.ts +++ b/site/benchmark/main.ts @@ -7,7 +7,7 @@ import { webgpu as webgpuPageRank, wasm as wasmPageRank } from "./page-rank"; -import { graphology as graphologySSSP, webgpu as webgpuSSSP } from "./sssp"; +import { graphology as graphologySSSP, webgpu as webgpuSSSP, wasm as wasmSSSP } from "./sssp"; import { initThreads } from "../../packages/graph-wasm"; const TestsConfig = [ @@ -65,7 +65,7 @@ const initThreadsPool = async () => { name: TestName.GRAPHOLOGY, methods: { pageRank: graphologyPageRank, - // sssp: graphologySSSP, + sssp: graphologySSSP, }, }, { @@ -86,7 +86,7 @@ const initThreadsPool = async () => { name: TestName.ANTV_GRAPH_WASM, methods: { pageRank: wasmPageRank, - // sssp: webgpuSSSP, + sssp: wasmSSSP, }, }, ]; @@ -95,10 +95,10 @@ const initThreadsPool = async () => { const dataset = datasets[$dataset.value]; const algorithmName = $algorithm.value; let options = {}; - // if (algorithmName === "sssp") { - // const graph = dataset[TestName.ANTV_WEBGPU_GRAPH]; - // options = graph.getAllNodes()[1].id; - // } + if (algorithmName === "sssp") { + const graph = dataset[TestName.ANTV_ALGORITHM]; + options = graph.getAllNodes()[1].id; + } await Promise.all( layoutConfig.map(async ({ name, methods }: any, i: number) => { diff --git a/site/benchmark/page-rank.ts b/site/benchmark/page-rank.ts index fc9ff37..fcc9a47 100644 --- a/site/benchmark/page-rank.ts +++ b/site/benchmark/page-rank.ts @@ -3,6 +3,7 @@ import pagerank from "graphology-metrics/centrality/pagerank"; import { pageRank } from "../../packages/graph"; import { WebGPUGraph } from "../../packages/graph-gpu"; import { Threads } from "../../packages/graph-wasm"; +import { graph2Edgelist } from "./util"; function format(records: { id: ID; score: number}[]) { return records.map(({ id, score }) => ({ id, score: score.toFixed(6) })); @@ -73,21 +74,10 @@ export async function wasm( _: any, threads: Threads ): Promise { - const edgelist: [number, number][] = []; - const nodeIdxMap: Record = {}; - const idxNodeMap: Record = {}; - const edges = graph.getAllEdges(); - graph.getAllNodes().forEach((node, i) => { - nodeIdxMap[node.id] = i; - idxNodeMap[i] = node.id; - }); - // convert graph to edgelist - edges.forEach((edge) => { - edgelist.push([nodeIdxMap[edge.source], nodeIdxMap[edge.target]]); - }); + const { edgelist, idxNodeMap } = graph2Edgelist(graph); const ranks = await threads.pageRank({ ...options, - edgelist + edgelist: edgelist as [number, number][] }); const formatted = ranks.map((rank, i) => ({ id: idxNodeMap[i], score: rank })); return format(formatted.sort((a, b) => b.score - a.score).slice(0, 10)); // {id: 'Valjean', score: 0.1} diff --git a/site/benchmark/sssp.ts b/site/benchmark/sssp.ts index 77c7572..06444d8 100644 --- a/site/benchmark/sssp.ts +++ b/site/benchmark/sssp.ts @@ -1,12 +1,20 @@ +import { Graph } from "@antv/graphlib"; import { dijkstra } from "graphology-shortest-path"; -import { WebGPUGraph } from "../../packages/graph-gpu/src"; +import { findShortestPath } from "../../packages/graph"; +import { WebGPUGraph } from "../../packages/graph-gpu"; +import { Threads } from "../../packages/graph-wasm"; +import { graph2Edgelist } from "./util"; export async function graphology(graph: any, source: string) { return dijkstra.singleSource(graph, source, "weight"); } +export async function antv(graph: Graph, source: string) { + // findShortestPath(graph, source) +} + export async function webgpu( - graph: any, + graph: Graph, source: string, webgpuGraph: WebGPUGraph ) { @@ -14,3 +22,19 @@ export async function webgpu( return result.filter((r) => r.distance !== 1000000); } + +export async function wasm( + graph: Graph, + source: string, + _: any, + threads: Threads +): Promise { + const { edgelist, nodeIdxMap, idxNodeMap } = graph2Edgelist(graph, 'weight'); + const paths = await threads.sssp({ + startNode: nodeIdxMap[source], + edgelist: edgelist as [number, number, number][], + }); + console.log(paths); + // const formatted = ranks.map((rank, i) => ({ id: idxNodeMap[i], score: rank })); + // return format(formatted.sort((a, b) => b.score - a.score).slice(0, 10)); // {id: 'Valjean', score: 0.1} +} \ No newline at end of file diff --git a/site/benchmark/util.ts b/site/benchmark/util.ts new file mode 100644 index 0000000..649d594 --- /dev/null +++ b/site/benchmark/util.ts @@ -0,0 +1,20 @@ +import { Graph, ID } from "@antv/graphlib"; + +export function graph2Edgelist(graph: Graph, weightPropertyName?: string) { + const edgelist: number[][] = []; + const nodeIdxMap: Record = {}; + const idxNodeMap: Record = {}; + const edges = graph.getAllEdges(); + graph.getAllNodes().forEach((node, i) => { + nodeIdxMap[node.id] = i; + idxNodeMap[i] = node.id; + }); + edges.forEach((edge) => { + if (weightPropertyName) { + edgelist.push([nodeIdxMap[edge.source], nodeIdxMap[edge.target], edge.data[weightPropertyName] || 1]); + } else { + edgelist.push([nodeIdxMap[edge.source], nodeIdxMap[edge.target]]); + } + }); + return { edgelist, nodeIdxMap, idxNodeMap }; +} \ No newline at end of file diff --git a/tsconfig.json b/tsconfig.json index 03e2ca5..cf11009 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -6,6 +6,7 @@ "jsx": "react", "allowJs": true, "moduleResolution": "node", + "resolveJsonModule": true, "allowSyntheticDefaultImports": true } } From 1b42e9ede8680d0f164c0ee9f1a0531c00f53923 Mon Sep 17 00:00:00 2001 From: "yuqi.pyq" Date: Thu, 13 Jul 2023 15:28:52 +0800 Subject: [PATCH 6/6] feat: rust impl for louvain --- benchmarks/louvain.test.js | 54 ++ benchmarks/util.js | 60 ++ package.json | 5 + packages/graph-rust/Cargo.toml | 1 + .../graph-rust/src/graph_builder/builder.rs | 199 ------ packages/graph-rust/src/lib.rs | 1 + packages/graph-rust/src/louvain.rs | 604 ++++++++++++++++++ packages/graph-rust/src/prelude.rs | 3 +- packages/graph-wasm/Cargo.lock | 7 + packages/graph-wasm/rust-src/lib.rs | 15 + packages/graph-wasm/src/interface.ts | 7 +- packages/graph-wasm/src/wasm-worker.js | 17 +- packages/graph/src/louvain.ts | 4 +- pnpm-lock.yaml | 42 ++ site/benchmark/index.html | 2 + site/benchmark/louvain.ts | 44 ++ site/benchmark/main.ts | 50 +- site/benchmark/sssp.ts | 19 +- site/data/undirected1000.json | 1 + site/data/undirected500.json | 1 + site/datasets.ts | 28 +- 21 files changed, 927 insertions(+), 237 deletions(-) create mode 100644 benchmarks/louvain.test.js create mode 100644 benchmarks/util.js create mode 100644 packages/graph-rust/src/louvain.rs create mode 100644 site/benchmark/louvain.ts create mode 100644 site/data/undirected1000.json create mode 100644 site/data/undirected500.json diff --git a/benchmarks/louvain.test.js b/benchmarks/louvain.test.js new file mode 100644 index 0000000..28ae2bf --- /dev/null +++ b/benchmarks/louvain.test.js @@ -0,0 +1,54 @@ +var Benchmark = require("benchmark"); +var suite = new Benchmark.Suite(); + +/** + * Graphology + */ +var Graph = require("graphology"); +var louvain = require('graphology-communities-louvain'); +var { louvain: AntvLouvain } = require("../packages/graph"); +var randomClusters = require("graphology-generators/random/clusters"); +var seedrandom = require("seedrandom"); +var rng = function () { + return seedrandom("bench"); +}; +const { graphology2antv } = require("./util"); + +const NODE_NUM = 10; +const EDGE_NUM = 30; +var graph = randomClusters(Graph, { + order: NODE_NUM, + size: EDGE_NUM, + clusters: 5, + rng: rng(), +}); +graph.edges().forEach(function (edge, i) { + graph.setEdgeAttribute(edge, "weight", 1); +}); +// graph.nodes().forEach(function (node) { +// graph.setNodeAttribute(node, "x", Math.random() * CANVAS_SIZE); +// graph.setNodeAttribute(node, "y", Math.random() * CANVAS_SIZE); +// }); +const antvgraph = graphology2antv(graph); + +// add tests +suite + .add("Graphology", async function () { + louvain(graph); + }) + .add("@antv/layout", async function () { + AntvLouvain(antvgraph); + }) + // add listeners + .on("cycle", function (event) { + console.log(String(event.target)); + }) + .on("complete", function () { + console.log("Fastest is " + this.filter("fastest").map("name")); + }) + .run({ async: true }); + +// logs: +// Graphology x 154,854 ops/sec ±0.38% (98 runs sampled) +// @antv/layout x 1,163 ops/sec ±0.47% (97 runs sampled) +// Fastest is Graphology diff --git a/benchmarks/util.js b/benchmarks/util.js new file mode 100644 index 0000000..c0816cf --- /dev/null +++ b/benchmarks/util.js @@ -0,0 +1,60 @@ +var { Graph } = require("@antv/graphlib"); + +const graphology2antv = (graph) => { + return new Graph({ + nodes: graph.nodes().map((id) => ({ + id, + data: { + x: graph.getNodeAttribute(id, "x"), + y: graph.getNodeAttribute(id, "y"), + }, + })), + edges: graph.edges().map((id) => ({ + id, + source: graph.source(id), + target: graph.target(id), + data: { + weight: graph.getEdgeAttribute(id, "weight"), + }, + })), + }); +}; + +const graphology2antv_wasm = (graph) => { + const nodes = []; + const masses = []; + const edges = []; + const weights = []; + const nodeIdxMap = {}; + graph.nodes().forEach((id, i) => { + nodeIdxMap[id] = i; + nodes.push( + graph.getNodeAttribute(id, "x"), + graph.getNodeAttribute(id, "y") + ); + masses.push(1); + }); + graph.edges().forEach((id) => { + const weight = graph.getEdgeAttribute(id, "weight"); + const source = nodeIdxMap[graph.source(id)]; + const target = nodeIdxMap[graph.target(id)]; + + if (source !== undefined && target !== undefined) { + // n1 <- n2 + edges.push([target, source]); + weights.push(weight); + // @see https://github.com/graphology/graphology/blob/master/src/layout-forceatlas2/helpers.js#L156-L158 + masses[source] += weight; + masses[target] += weight; + } + }); + + return { + nodes, + masses, + edges, + weights, + }; +}; + +module.exports = { graphology2antv, graphology2antv_wasm }; diff --git a/package.json b/package.json index 439a852..cb0ec1a 100644 --- a/package.json +++ b/package.json @@ -10,6 +10,8 @@ }, "license": "MIT", "scripts": { + "benchmarks": "run-p benchmarks:*", + "benchmarks:louvain": "node benchmarks/louvain.test.js", "dev": "vite", "lint:es": "eslint --ext .js --fix", "lint:ts": "tslint -c tslint.json -p packages/graph/tsconfig.json --fix", @@ -36,6 +38,7 @@ "@antv/graphlib": "^2.0.0", "@changesets/cli": "^2.26.1", "@types/jest": "latest", + "benchmark": "^2.1.4", "cross-env": "^7.0.3", "eslint": "^7.32.0", "eslint-config-airbnb-base": "^14.2.1", @@ -43,6 +46,7 @@ "eslint-plugin-import": "^2.27.5", "gh-pages": "^5.0.0", "graphology": "^0.25.1", + "graphology-communities-louvain": "latest", "graphology-generators": "^0.11.2", "graphology-types": "^0.24.7", "graphology-metrics": "^2.1.0", @@ -53,6 +57,7 @@ "lint-staged": "^10.5.4", "npm-run-all": "^4.1.5", "rimraf": "^3.0.2", + "seedrandom": "^3.0.5", "ts-jest": "^29.1.0", "ts-loader": "^8.4.0", "tslint": "^6.1.3", diff --git a/packages/graph-rust/Cargo.toml b/packages/graph-rust/Cargo.toml index 7f4302c..948423c 100644 --- a/packages/graph-rust/Cargo.toml +++ b/packages/graph-rust/Cargo.toml @@ -28,6 +28,7 @@ fxhash = "0.2.1" gdl = { version = "0.2.7", optional = true} rayon = "1.5.1" serde = { optional = true } +slotmap = {version = "0.4"} [dependencies.linereader] version = "0.4.0" diff --git a/packages/graph-rust/src/graph_builder/builder.rs b/packages/graph-rust/src/graph_builder/builder.rs index 727273f..46be7cd 100644 --- a/packages/graph-rust/src/graph_builder/builder.rs +++ b/packages/graph-rust/src/graph_builder/builder.rs @@ -42,28 +42,6 @@ where _node: PhantomData, } -#[cfg(feature = "gdl")] -#[cfg_attr(all(feature = "gdl", has_doc_cfg), doc(cfg(feature = "gdl")))] -pub struct FromGdlString -where - NI: Idx, -{ - csr_layout: CsrLayout, - gdl: String, - _node: PhantomData, -} - -#[cfg(feature = "gdl")] -#[cfg_attr(all(feature = "gdl", has_doc_cfg), doc(cfg(feature = "gdl")))] -pub struct FromGdlGraph<'a, NI> -where - NI: Idx, -{ - csr_layout: CsrLayout, - gdl_graph: &'a gdl::Graph, - _node: PhantomData, -} - pub struct FromInput where P: AsRef, @@ -233,151 +211,6 @@ impl GraphBuilder { }, } } - - /// Creates a graph using Graph Definition Language (GDL). - /// - /// Creating graphs from GDL is recommended for small graphs only, e.g., - /// during testing. The graph construction is **not** parallelized. - /// - /// See [GDL on crates.io](https://crates.io/crates/gdl) for more - /// information on how to define graphs using GDL. - /// - /// # Example - /// - /// ``` - /// use graph_builder::prelude::*; - /// - /// let g: UndirectedCsrGraph = GraphBuilder::new() - /// .gdl_str::("(a)-->(),(a)-->()") - /// .build() - /// .unwrap(); - /// - /// assert_eq!(g.node_count(), 3); - /// assert_eq!(g.edge_count(), 2); - /// ``` - /// - /// One can also create weighted graphs using GDL. There needs to be exactly - /// one edge property with the same type as specified for the edge value. - /// The property key is not relevant. - /// - /// ``` - /// use graph_builder::prelude::*; - /// - /// let g: UndirectedCsrGraph = GraphBuilder::new() - /// .csr_layout(CsrLayout::Sorted) - /// .gdl_str::("(a)-[{f: 0.42}]->(),(a)-[{f: 13.37}]->()") - /// .build() - /// .unwrap(); - /// - /// assert_eq!(g.node_count(), 3); - /// assert_eq!(g.edge_count(), 2); - /// - /// let mut neighbors = g.neighbors_with_values(0); - /// assert_eq!(neighbors.next(), Some(&Target::new(1, 0.42))); - /// assert_eq!(neighbors.next(), Some(&Target::new(2, 13.37))); - /// assert_eq!(neighbors.next(), None); - /// ``` - #[cfg(feature = "gdl")] - #[cfg_attr(all(feature = "gdl", has_doc_cfg), doc(cfg(feature = "gdl")))] - pub fn gdl_str(self, gdl: S) -> GraphBuilder> - where - NI: Idx, - S: Into, - { - GraphBuilder { - state: FromGdlString { - csr_layout: self.state.csr_layout, - gdl: gdl.into(), - _node: PhantomData, - }, - } - } - - /// Creates a graph from an already constructed GDL graph. - /// - /// Creating graphs from GDL is recommended for small graphs only, e.g., - /// during testing. The graph construction is **not** parallelized. - /// - /// See [GDL on crates.io](https://crates.io/crates/gdl) for more - /// information on how to define graphs using GDL. - /// - /// # Example - /// - /// ``` - /// use graph_builder::prelude::*; - /// - /// let gdl_graph = "(a)-->(),(a)-->()".parse::<::gdl::Graph>().unwrap(); - /// - /// let g: DirectedCsrGraph = GraphBuilder::new() - /// .gdl_graph::(&gdl_graph) - /// .build() - /// .unwrap(); - /// - /// assert_eq!(g.node_count(), 3); - /// assert_eq!(g.edge_count(), 2); - /// - /// let id_a = gdl_graph.get_node("a").unwrap().id(); - /// - /// assert_eq!(g.out_neighbors(id_a).len(), 2); - /// ``` - #[cfg(feature = "gdl")] - #[cfg_attr(all(feature = "gdl", has_doc_cfg), doc(cfg(feature = "gdl")))] - pub fn gdl_graph(self, gdl_graph: &::gdl::Graph) -> GraphBuilder> - where - NI: Idx, - { - GraphBuilder { - state: FromGdlGraph { - csr_layout: self.state.csr_layout, - gdl_graph, - _node: PhantomData, - }, - } - } - - /// Creates a graph by reading it from the given file format. - /// - /// # Examples - /// - /// Read a directed graph from an edge list file: - /// - /// ``` - /// use std::path::PathBuf; - /// - /// use graph_builder::prelude::*; - /// - /// let path = [env!("CARGO_MANIFEST_DIR"), "resources", "example.el"] - /// .iter() - /// .collect::(); - /// - /// let graph: DirectedCsrGraph = GraphBuilder::new() - /// .file_format(EdgeListInput::default()) - /// .path(path) - /// .build() - /// .expect("loading failed"); - /// - /// assert_eq!(graph.node_count(), 4); - /// assert_eq!(graph.edge_count(), 5); - /// ``` - pub fn file_format( - self, - _format: Format, - ) -> GraphBuilder> - where - Path: AsRef, - NI: Idx, - Format: InputCapabilities, - Format::GraphInput: TryFrom>, - { - GraphBuilder { - state: FromInput { - csr_layout: self.state.csr_layout, - _idx: PhantomData, - _path: PhantomData, - _format: PhantomData, - }, - } - } } impl GraphBuilder> @@ -466,38 +299,6 @@ impl GraphBuilder> { } } -#[cfg(feature = "gdl")] -#[cfg_attr(all(feature = "gdl", has_doc_cfg), doc(cfg(feature = "gdl")))] -impl GraphBuilder> -where - NI: Idx, -{ - /// Builds the graph from the given GDL string. - pub fn build(self) -> Result - where - Graph: From<(gdl::Graph, CsrLayout)>, - { - let gdl_graph = self.state.gdl.parse::()?; - let graph = Graph::from((gdl_graph, self.state.csr_layout)); - Ok(graph) - } -} - -#[cfg(feature = "gdl")] -#[cfg_attr(all(feature = "gdl", has_doc_cfg), doc(cfg(feature = "gdl")))] -impl<'a, NI> GraphBuilder> -where - NI: Idx, -{ - /// Build the graph from the given GDL graph. - pub fn build(self) -> Result - where - Graph: From<(&'a gdl::Graph, CsrLayout)>, - { - Ok(Graph::from((self.state.gdl_graph, self.state.csr_layout))) - } -} - impl GraphBuilder> where Path: AsRef, diff --git a/packages/graph-rust/src/lib.rs b/packages/graph-rust/src/lib.rs index e18da0b..e8b9db8 100644 --- a/packages/graph-rust/src/lib.rs +++ b/packages/graph-rust/src/lib.rs @@ -1,6 +1,7 @@ pub mod page_rank; pub mod prelude; pub mod sssp; +pub mod louvain; pub mod utils; pub mod graph_builder; diff --git a/packages/graph-rust/src/louvain.rs b/packages/graph-rust/src/louvain.rs new file mode 100644 index 0000000..767f863 --- /dev/null +++ b/packages/graph-rust/src/louvain.rs @@ -0,0 +1,604 @@ +#![allow(non_snake_case)] // FIXME: Good while porting + +use super::graph_builder::{prelude::*}; +use std::collections::{BTreeMap}; +use std::cell::{RefCell}; +use std::ops::{AddAssign}; +use slotmap::DenseSlotMap; +use std::f32; + +#[derive(Debug, PartialEq)] +pub struct ModEdge { + source: usize, + target: usize, + weight: f32, +} + +type CommunityId = slotmap::DefaultKey; + +#[derive(Debug, Default, PartialEq)] +pub struct Community { + id: CommunityId, + weightSum: f64, + nodes: Vec, + connectionsWeight: RefCell>, + connectionsCount: RefCell>, +} + +impl Community { + + fn new(id: CommunityId) -> Community { + Community { id, ..Default::default() } + } + + fn size(&self) -> usize { + self.nodes.len() + } + + fn seed(&mut self, node: usize, cs: & CommunityStructure) { + self.nodes.push(node); + self.weightSum += cs.weights[node] as f64; + } + + fn add(&mut self, node: usize, cs: & CommunityStructure) -> bool { + self.nodes.push(node); + self.weightSum += cs.weights[node] as f64; + true + } + + fn remove(&mut self, node: usize, cs: &mut CommunityStructure) -> bool { + self.nodes.retain(|&n| n != node); + self.weightSum -= cs.weights[node] as f64; + if self.nodes.is_empty() { + cs.communities.retain(|&c| c != self.id); // FIXME: Maybe remove from cc too + } + true + } +} + + +#[derive(Default, Debug)] +pub struct CommunityCatalog { + map: DenseSlotMap +} + +impl CommunityCatalog { + pub fn createNew(&mut self) -> CommunityId { + self.map.insert_with_key(|id| Community::new(id)) + } + + #[inline] + pub fn get(&self, key: &CommunityId) -> Option<&Community> { + self.map.get(*key) + } + + #[inline] + pub fn get_mut(&mut self, key: &CommunityId) -> Option<&mut Community> { + self.map.get_mut(*key) + } + + #[inline] + pub fn remove(&mut self, key: &CommunityId) { + self.map.remove(*key); + } +} + + +#[derive(Debug, Default, PartialEq)] +pub struct CommunityStructure { + N: usize, // Number of nodes / communities + communities: Vec, // Direct communities + nodeConnectionsWeight: Vec>, + nodeConnectionsCount: Vec>, + nodeCommunities: Vec, + weights: Vec, // One per node + topology: Vec>, // One per node + invMap: BTreeMap, + graphWeightSum: f64, +} + +impl CommunityStructure { + + pub fn new(graph: &G, modularity: &mut Modularity) -> CommunityStructure where + NI: Idx, + G: Graph + DirectedDegrees + DirectedNeighborsWithValues + Sync { + let N = graph.node_count().index(); + let cc = &mut modularity.cc; + let mut cs = CommunityStructure { + N, + communities: Vec::new(), + nodeConnectionsWeight: Vec::with_capacity(N), + nodeConnectionsCount: Vec::with_capacity(N), + nodeCommunities: Vec::with_capacity(N), + weights: Vec::with_capacity(N), + topology: Vec::with_capacity(N), + //map: BTreeMap::default(), + invMap: BTreeMap::default(), + graphWeightSum: 0.0, + }; + + // Create one community and one inverse community per node + // All weights to 0.0 + (0..N).into_iter().enumerate().for_each(|(_, index)| { + //cs.map.insert(node.clone(), index); + cs.nodeCommunities.push( cc.createNew() ); + + cs.nodeConnectionsWeight.push(BTreeMap::default()); + cs.nodeConnectionsCount.push(BTreeMap::default()); + cs.weights.push(0.0); + cc.get_mut(& cs.nodeCommunities[index]).unwrap().seed(index, & cs); + + // New hidden community + let hidden = cc.createNew(); + cc.get_mut(& hidden).unwrap().nodes.push(index); + cs.invMap.insert(index, hidden); + + cs.communities.push(cs.nodeCommunities[index]); + }); + + (0..N) + .into_iter() + .map(NI::new) + .for_each(|node| { + cs.topology.push(Vec::new()); + + for Target { target, value } in graph.out_neighbors_with_values(node) { + let neighbor = target; + if node == *neighbor { continue } + + // Assume there is no parallel edges: + let weight: f32 = *value; + + //Finally add a single edge with the summed weight of all parallel edges: + cs.weights[node.index()] += weight as f64; + let modularity_edge = ModEdge { source: node.index(), target: neighbor.index(), weight }; + cs.topology[node.index()].push(modularity_edge); + let adjCom = cc.get(&cs.nodeCommunities[neighbor.index()]).unwrap(); + + cs.nodeConnectionsWeight[node.index()].insert(adjCom.id, weight); + cs.nodeConnectionsCount[node.index()].insert(adjCom.id, 1); + + let nodeCom = cc.get(&cs.nodeCommunities[node.index()]).unwrap(); + nodeCom.connectionsWeight.borrow_mut().insert(adjCom.id, weight); + nodeCom.connectionsCount.borrow_mut().insert(adjCom.id, 1); + + cs.nodeConnectionsWeight[neighbor.index()].insert(nodeCom.id, weight); + cs.nodeConnectionsCount[neighbor.index()].insert(nodeCom.id, 1); + + adjCom.connectionsWeight.borrow_mut().insert(nodeCom.id, weight); + adjCom.connectionsCount.borrow_mut().insert(nodeCom.id, 1); + + cs.graphWeightSum += weight as f64; + } + }); + + cs.graphWeightSum /= 2.0; + cs + } + + fn addNodeTo(&mut self, node : usize, com_id: CommunityId, cc: &mut CommunityCatalog) { + + #[inline] + fn add_node >(map : &mut BTreeMap, key: CommunityId, weight: V) { + let w = map.entry(key).or_insert(V::from(0)); + *w += weight; + } + + self.nodeCommunities[node] = com_id; + + { + let com = cc.get_mut(& com_id).unwrap(); + com.add(node, self); + } + + for e in &self.topology[node] { + let neighbor = &e.target; + + add_node(&mut self.nodeConnectionsWeight[*neighbor], com_id, e.weight); + add_node(&mut self.nodeConnectionsCount[*neighbor], com_id, 1); + + let adjCom = cc.get(& self.nodeCommunities[*neighbor]).unwrap(); + + add_node(&mut adjCom.connectionsWeight.borrow_mut(), com_id, e.weight); + add_node(&mut adjCom.connectionsCount.borrow_mut(), com_id, 1); + + add_node(&mut self.nodeConnectionsWeight[node], adjCom.id, e.weight); + add_node(&mut self.nodeConnectionsCount[node], adjCom.id, 1); + + if com_id != adjCom.id { + let com = cc.get(& com_id).unwrap(); + add_node(&mut com.connectionsWeight.borrow_mut(), adjCom.id, e.weight); + add_node(&mut com.connectionsCount.borrow_mut(), adjCom.id, 1); + } + + } + + + } + + + pub fn removeNodeFromItsCommunity(&mut self, node: usize, cc: &mut CommunityCatalog) { + + #[inline] + fn remove_node( weights_map : &mut BTreeMap, + count_map : &mut BTreeMap, + key: CommunityId, weight: f32 + ) + { + + // println!("*** remove community {} from {:?}", key, count_map); + let count = count_map.get(&key).unwrap().clone(); + + if count -1 == 0 { + weights_map.remove(&key); + count_map.remove(&key); + } else { + let count = count_map.get_mut(&key).unwrap(); + *count -= 1; + let w = weights_map.get_mut(&key).unwrap(); + *w -= weight; + } + } + + { + let community = cc.get(& self.nodeCommunities[node]).unwrap(); + + for e in &self.topology[node] { + let neighbor = &e.target; + + //////// + //Remove Node Connection to this community + remove_node( &mut self.nodeConnectionsWeight[*neighbor], + &mut self.nodeConnectionsCount[*neighbor], + community.id.clone(), e.weight ); + + /////////////////// + //Remove Adjacency Community's connection to this community + let adjCom = cc.get(& self.nodeCommunities[*neighbor]).unwrap(); + remove_node( &mut adjCom.connectionsWeight.borrow_mut(), + &mut adjCom.connectionsCount.borrow_mut(), + community.id.clone(), e.weight ); + + if node == *neighbor { + continue; + } + + if adjCom.id != community.id { + remove_node( &mut community.connectionsWeight.borrow_mut(), + &mut community.connectionsCount.borrow_mut(), + adjCom.id, e.weight); + } + + remove_node( &mut self.nodeConnectionsWeight[node], + &mut self.nodeConnectionsCount[node], + adjCom.id, e.weight ); + } + } + { + let community = cc.get_mut(& self.nodeCommunities[node]).unwrap(); + community.remove(node, self); + } + } + + + fn moveNodeTo(&mut self, node: usize, to: CommunityId, cc: &mut CommunityCatalog) { + self.removeNodeFromItsCommunity(node, cc); + self.addNodeTo(node, to, cc); + } + + fn zoomOut(&mut self, cc: &mut CommunityCatalog) { + let M = self.communities.len(); + self.communities.sort(); + let mut newTopology: Vec> = Vec::with_capacity(M); + let mut index : usize = 0; + let mut nodeCommunities: Vec = Vec::with_capacity(M); + let mut nodeConnectionsWeight: Vec> = Vec::with_capacity(M); + let mut nodeConnectionsCount: Vec> = Vec::with_capacity(M); + let mut newInvMap: BTreeMap = BTreeMap::default(); + + for com_id in & self.communities { + nodeConnectionsWeight.push(BTreeMap::default()); + nodeConnectionsCount.push(BTreeMap::default()); + + newTopology.push( Vec::new() ); + nodeCommunities.push(cc.createNew()); + + let mut weightSum : f32 = 0.0; + let hidden_id = cc.createNew(); + + /* + * FIXME: two unnecessary clones of node vectors to content the Borrow Checker + */ + let nodes = cc.get(com_id).unwrap().nodes.clone(); + for nodeInt in nodes { + let oldHiddenNodes = { + let oldHidden = cc.get(& self.invMap.get(&nodeInt).unwrap()).unwrap(); + oldHidden.nodes.clone() + }; + let hidden = cc.get_mut(& hidden_id).unwrap(); + hidden.nodes.extend(oldHiddenNodes); + } + + newInvMap.insert(index, hidden_id); + { + let com = cc.get(com_id).unwrap(); + for adjCom_id in com.connectionsWeight.borrow().keys() { + let target = self.communities.binary_search(adjCom_id).unwrap(); + let weight = com.connectionsWeight.borrow().get(adjCom_id).unwrap().clone(); + weightSum += if target == index { 2.0 * weight} else { weight }; + + let e = ModEdge {source: index, target: target, weight: weight}; + newTopology[index].push(e); + } + } + self.weights[index] = weightSum as f64; + let com = cc.get_mut(& nodeCommunities[index]).unwrap(); + com.seed(index, & self); + + index += 1; + } + + for com_id in & self.communities { cc.remove(com_id); } + self.communities.clear(); + + for i in 0..M { + let com = cc.get(& nodeCommunities[i]).unwrap(); + self.communities.push(com.id); + for e in & newTopology[i] { + nodeConnectionsWeight[i].insert(nodeCommunities[e.target], e.weight); + nodeConnectionsCount[i].insert(nodeCommunities[e.target], 1); + com.connectionsWeight.borrow_mut().insert(nodeCommunities[e.target], e.weight); + com.connectionsCount.borrow_mut().insert(nodeCommunities[e.target], 1); + } + } + + self.N = M; + self.topology = newTopology; + self.invMap = newInvMap; + self.nodeCommunities = nodeCommunities; + self.nodeConnectionsWeight = nodeConnectionsWeight; + self.nodeConnectionsCount = nodeConnectionsCount; + } + +} + + +pub struct Modularity { + modularity: f64, + modularityResolution: f64, + // isRandomized: bool, + useWeight: bool, + resolution: f64, + noise: u32, + cc : CommunityCatalog, + pub communityByNode: Vec, +} + +impl Modularity { + + /// + /// resolution: 1.0 More resolution produce less Clusters + /// noise: 0 clusters with number_of_nodes <= noise are considered noise (-1 tag) + /// + pub fn new(resolution: f64, noise: u32) -> Modularity { + Modularity { + modularity: 0.0, + modularityResolution: 0.0, + // isRandomized: false, + useWeight: true, + resolution, + noise, + cc: Default::default(), + communityByNode: Default::default() + } + } + + pub fn execute(&mut self, graph: & G) + -> (f64, f64) where + NI: Idx, + G: Graph + DirectedDegrees + DirectedNeighborsWithValues + Sync { + + let mut structure = CommunityStructure::new(graph, self); + let mut communities : Vec= vec![0; graph.node_count().index()]; + + if graph.node_count().index() > 0 { + let (modularity, modularityResolution) = self.computeModularity(graph, &mut structure, &mut communities); + self.modularity = modularity; + self.modularityResolution = modularityResolution; + } else { + self.modularity = 0.0; + self.modularityResolution = 0.0; + } + // saveValues(comStructure, graph, structure); + self.communityByNode = communities; + + (self.modularity, self.modularityResolution) + } + + fn computeModularity(&mut self, graph: & G, cs : &mut CommunityStructure, communities: &mut Vec) -> (f64, f64) where + NI: Idx, + G: Graph + DirectedDegrees + DirectedNeighborsWithValues + Sync { + + let nodeDegrees = cs.weights.clone(); + let totalWeight = cs.graphWeightSum; + + let mut someChange = true; + while someChange { + someChange = false; + let mut localChange = true; + let mut movedNodes: u32 = 0; + while localChange { + localChange = false; + let start: usize = 0; + // if self.isRandomized { + // let mut rng = thread_rng(); + // start = seq::sample_iter(&mut rng, 1..cs.N, 1).unwrap()[0]; + // } + for step in 0..cs.N { + let i = (step + start) % cs.N; + if let Some(bestCommunity) = self.updateBestCommunity(cs, i, self.resolution) { + if cs.nodeCommunities[i] != bestCommunity { + cs.moveNodeTo(i, bestCommunity, &mut self.cc); + localChange = true; + movedNodes += 1; + } + } + if (step % 10000) == 0 { + println!("Step {} of {} -> moved nodes: {}", step, cs.N, movedNodes); + } + } + someChange = localChange || someChange; + println!("Node Pass Ended -> moved nodes: {}", movedNodes); + } + if someChange { + cs.zoomOut(&mut self.cc); + println!("Zooming Out: {} communities left", cs.N); + } + } + let mut comStructure : Vec= vec![0; graph.node_count().index()]; + let noiseMap = self.fillComStructure(cs, &mut comStructure); + let degreeCount = self.fillDegreeCount(graph, cs, &mut comStructure, & nodeDegrees); + + let computedModularity = self.finalQ(&mut comStructure, & degreeCount, graph, totalWeight, 1.); + let computedModularityResolution = self.finalQ(&mut comStructure, & degreeCount, graph, totalWeight, self.resolution); + + for i in 0..communities.len() { + communities[i] = if noiseMap[i] { -1 } else { comStructure[i] as i32 } + } + // let communities: Vec<&Community> = cs.communities.iter().map(|c| self.cc.get(c).unwrap()).collect(); + // println!("{:?}", comStructure); + + (computedModularity, computedModularityResolution) + } + + fn fillComStructure(&self, cs : & CommunityStructure, comStructure: &mut Vec) -> Vec { + let mut noiseMap: Vec = vec![false; comStructure.len()]; + for (count, com_id) in cs.communities.iter().enumerate() { + let com = self.cc.get(com_id).unwrap(); + for node in & com.nodes { + let hidden_id = cs.invMap.get(node).unwrap(); + let hidden = self.cc.get(hidden_id).unwrap(); + let isNoise = hidden.nodes.len() as u32 <= self.noise; + for nodeInt in & hidden.nodes { + comStructure[* nodeInt] = count; + noiseMap[* nodeInt] = isNoise; + } + } + } + noiseMap + } + + fn fillDegreeCount(&self, graph: & G, cs : & CommunityStructure, + comStructure: & Vec, nodeDegrees: & Vec) -> Vec where + NI: Idx, + G: Graph + DirectedDegrees + DirectedNeighborsWithValues + Sync { + + let mut degreeCount : Vec = vec![0.0; cs.communities.len()]; + let N = graph.node_count().index(); + + (0..N) + .into_iter() + .map(NI::new) + .for_each(|node| { + if self.useWeight { + degreeCount[comStructure[node.index()]] += nodeDegrees[node.index()]; + } else { + degreeCount[comStructure[node.index()]] += graph.out_degree(node).index() as f64; + } + }); + degreeCount + } + + fn updateBestCommunity(&mut self, cs: & CommunityStructure, node_id: usize, currentResolution: f64) -> Option { + let mut best = 0.0; + let mut bestCommunity: Option = None; + // println!("{:?} !!!!{:?}", node_id, cs.nodeConnectionsWeight[node_id]); + for com_id in cs.nodeConnectionsWeight[node_id].keys() { + let qValue = self.q(node_id, com_id, cs, currentResolution); + if qValue > best { + best = qValue; + bestCommunity = Some(*com_id); + } + } + bestCommunity + } + + fn q(& self, + node: usize, + com_id: & CommunityId, + cs: & CommunityStructure, + currentResolution: f64 + ) -> f64 + { + let mut edgesTo: f64 = 0.0; + if let Some(edgesToFloat) = cs.nodeConnectionsWeight[node].get(com_id) { + edgesTo = *edgesToFloat as f64; + } + let weightSum: f64 = self.cc.get(com_id).unwrap().weightSum; + let nodeWeight: f64 = cs.weights[node]; + let mut qValue : f64 = currentResolution * edgesTo - (nodeWeight * weightSum) / (2.0 * cs.graphWeightSum); + + let nodeCommunities_len = self.cc.get(& cs.nodeCommunities[node]).unwrap().size(); + if (cs.nodeCommunities[node] == *com_id) && (nodeCommunities_len > 1) { + qValue = currentResolution * edgesTo - (nodeWeight * (weightSum - nodeWeight)) / (2.0 * cs.graphWeightSum); + } + if (cs.nodeCommunities[node] == *com_id) && (nodeCommunities_len == 1) { + qValue = 0.0; + } + qValue + } + + fn finalQ(&self, comStructure: & Vec, degrees: & Vec, graph: & G, totalWeight: f64, usedResolution: f64) -> f64 where + NI: Idx, + G: Graph + DirectedNeighborsWithValues + Sync { + + let mut res: f64 = 0.0; + let mut internal: Vec = vec![0.0; degrees.len()]; + + let N = graph.node_count().index(); + + (0..N) + .into_iter() + .map(NI::new) + .for_each(|node| { + for Target { target, value } in graph.out_neighbors_with_values(node) { + let neighbor = target.index(); + if node == *target { + continue; + } + + if comStructure[neighbor] == comStructure[node.index() as usize] as usize { + if self.useWeight { + internal[comStructure[neighbor]] += *value as f64; + } else { + internal[comStructure[neighbor]] += 1.0; + } + } + } + }); + + for i in 0..degrees.len() { + internal[i] /= 2.0; + res += usedResolution * (internal[i] / totalWeight) - (degrees[i] / (2.0 * totalWeight)).powi(2); + } + res + } + +} + +// AUX functions + +#[allow(dead_code)] +fn check_weights(cc: &CommunityCatalog, cs: &CommunityStructure) -> bool { + for i in 0..cs.nodeCommunities.len() - 1 { + let com0 = cc.get(&cs.nodeCommunities[i]).unwrap(); + if let Some(w0_1) = com0.connectionsWeight.borrow().get(&cs.nodeCommunities[i+1]) { + let nw0_1 = cs.nodeConnectionsWeight[i].get(&cs.nodeCommunities[i+1]).unwrap(); + // println!("{}: {:?} = {:?} --> {:?}", i, w0_1, nw0_1, f32::abs(w0_1 - nw0_1) < f32::EPSILON ); + if f32::abs(w0_1 - nw0_1) > f32::EPSILON { + return false; + } + } + } + true +} \ No newline at end of file diff --git a/packages/graph-rust/src/prelude.rs b/packages/graph-rust/src/prelude.rs index 541de1d..4c33f9f 100644 --- a/packages/graph-rust/src/prelude.rs +++ b/packages/graph-rust/src/prelude.rs @@ -1,5 +1,6 @@ pub use crate::page_rank::*; pub use crate::sssp::*; +pub use crate::louvain::*; pub use crate::utils::*; -pub use super::graph_builder::prelude::*; +pub use crate::graph_builder::prelude::*; diff --git a/packages/graph-wasm/Cargo.lock b/packages/graph-wasm/Cargo.lock index b3a6368..8441b58 100644 --- a/packages/graph-wasm/Cargo.lock +++ b/packages/graph-wasm/Cargo.lock @@ -24,6 +24,7 @@ dependencies = [ "parking_lot", "rayon", "serde", + "slotmap", "thiserror", ] @@ -552,6 +553,12 @@ dependencies = [ "serde", ] +[[package]] +name = "slotmap" +version = "0.4.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "6bf34684c5767b87de9119790e92e9a1d60056be2ceeaf16a8e6ef13082aeab1" + [[package]] name = "smallvec" version = "1.11.0" diff --git a/packages/graph-wasm/rust-src/lib.rs b/packages/graph-wasm/rust-src/lib.rs index 62d7ca1..d79008f 100644 --- a/packages/graph-wasm/rust-src/lib.rs +++ b/packages/graph-wasm/rust-src/lib.rs @@ -63,3 +63,18 @@ pub fn sssp(val: JsValue) -> Array { .collect(); result.into_iter().map(JsValue::from).collect() } + + +#[derive(Serialize, Deserialize)] +pub struct LouvainParams { + pub edgelist: Vec<(usize, usize, f32)>, +} +#[wasm_bindgen(js_name = "louvain")] +pub fn louvain(val: JsValue) -> Array { + let options: LouvainParams = serde_wasm_bindgen::from_value(val).unwrap(); + let graph: DirectedCsrGraph = GraphBuilder::new().edges_with_values(options.edgelist).build(); + + let mut modularity = Modularity::new(1.0, 1); + let results = modularity.execute(& graph); + vec![results.0, results.1].into_iter().map(JsValue::from).collect() +} \ No newline at end of file diff --git a/packages/graph-wasm/src/interface.ts b/packages/graph-wasm/src/interface.ts index 960ce97..8974be0 100644 --- a/packages/graph-wasm/src/interface.ts +++ b/packages/graph-wasm/src/interface.ts @@ -17,7 +17,12 @@ export interface SSSPParams { edgelist: [number, number, number][]; } +export interface LouvainParams { + edgelist: [number, number, number][]; +} + export interface Threads { pageRank: (options: PageRankParams) => Promise; - sssp: (options: SSSPParams) => Promise<{ ranks: number[] }>; + sssp: (options: SSSPParams) => Promise; + louvain: (options: LouvainParams) => Promise; } diff --git a/packages/graph-wasm/src/wasm-worker.js b/packages/graph-wasm/src/wasm-worker.js index fc3e785..5668e05 100644 --- a/packages/graph-wasm/src/wasm-worker.js +++ b/packages/graph-wasm/src/wasm-worker.js @@ -19,7 +19,7 @@ const wrapTransferSSSP = sssp => { return options => { const params = { start_node: options.startNode || 0, - delta: options.delta || 3, + delta: options.delta || 1, edgelist: options.edgelist }; @@ -29,11 +29,24 @@ const wrapTransferSSSP = sssp => { }; }; +const wrapTransferLouvain = louvain => { + return options => { + const params = { + edgelist: options.edgelist + }; + + const ranks = louvain(params); + + return Comlink.transfer(ranks, []); + }; +}; + // Wrap wasm-bindgen exports (the `generate` function) to add time measurement. -function wrapExports({ pageRank, sssp }) { +function wrapExports({ pageRank, sssp, louvain }) { return { pageRank: wrapTransferPageRank(pageRank), sssp: wrapTransferSSSP(sssp), + louvain: wrapTransferLouvain(louvain) }; } diff --git a/packages/graph/src/louvain.ts b/packages/graph/src/louvain.ts index dfb477c..f37ba6d 100644 --- a/packages/graph/src/louvain.ts +++ b/packages/graph/src/louvain.ts @@ -257,7 +257,7 @@ export function louvain( propertiesWeightRemove[index] = allPropertiesWeight[nodeRemove.data.originIndex as number]; }); // the inertialModularity for **removing** the node i from the origin cluster of node i - const removeInertialModularity = getInertialModularity(selfClusterNodesAfterRemove, allPropertiesWeight) * inertialWeight; + const removeInertialModularity = inertialModularity ? getInertialModularity(selfClusterNodesAfterRemove, allPropertiesWeight) * inertialWeight : 0; // the neightbors of the node const nodeNeighborIds = neighbors[node.id]; @@ -289,7 +289,7 @@ export function louvain( propertiesWeightAdd[index] = allPropertiesWeight[nodeAdd.data.originIndex as number]; }); // the inertialModularity for **adding** node i into this neighbor cluster - const addInertialModularity = getInertialModularity(clusterNodesAfterAdd, allPropertiesWeight) * inertialWeight; + const addInertialModularity = inertialModularity ? getInertialModularity(clusterNodesAfterAdd, allPropertiesWeight) * inertialWeight : 0; // the increase modurarity is the difference between addModurarity and removeModurarity let increase = addModurarity - removeModurarity; diff --git a/pnpm-lock.yaml b/pnpm-lock.yaml index 3935168..ec32dfd 100644 --- a/pnpm-lock.yaml +++ b/pnpm-lock.yaml @@ -13,6 +13,9 @@ importers: '@types/jest': specifier: latest version: 29.5.2 + benchmark: + specifier: ^2.1.4 + version: 2.1.4 cross-env: specifier: ^7.0.3 version: 7.0.3 @@ -34,6 +37,9 @@ importers: graphology: specifier: ^0.25.1 version: 0.25.1(graphology-types@0.24.7) + graphology-communities-louvain: + specifier: latest + version: 2.0.1(graphology-types@0.24.7) graphology-generators: specifier: ^0.11.2 version: 0.11.2(graphology-types@0.24.7) @@ -64,6 +70,9 @@ importers: rimraf: specifier: ^3.0.2 version: 3.0.2 + seedrandom: + specifier: ^3.0.5 + version: 3.0.5 ts-jest: specifier: ^29.1.0 version: 29.1.0(@babel/core@7.22.1)(jest@29.5.0)(typescript@4.9.5) @@ -3010,6 +3019,13 @@ packages: resolution: {integrity: sha512-3oSeUO0TMV67hN1AmbXsK4yaqU7tjiHlbxRDZOpH0KW9+CeX4bRAaX0Anxt0tx2MrpRpWwQaPwIlISEJhYU5Pw==} dev: true + /benchmark@2.1.4: + resolution: {integrity: sha512-l9MlfN4M1K/H2fbhfMy3B7vJd6AGKJVQn2h6Sg/Yx+KckoUA7ewS5Vv6TjSq18ooE1kS9hhAlQRH3AkXIh/aOQ==} + dependencies: + lodash: 4.17.21 + platform: 1.3.6 + dev: true + /better-path-resolve@1.0.0: resolution: {integrity: sha512-pbnl5XzGBdrFU/wT4jqmJVPn2B6UHPBOhzMQkY/SPUPB6QtUXtmBHBIwCbXJol93mOpGMnQyP/+BB19q04xj7g==} engines: {node: '>=4'} @@ -4338,6 +4354,18 @@ packages: resolution: {integrity: sha512-bzh50DW9kTPM00T8y4o8vQg89Di9oLJVLW/KaOGIXJWP/iqCN6WKYkbNOF04vFLJhwcpYUh9ydh/+5vpOqV4YQ==} dev: true + /graphology-communities-louvain@2.0.1(graphology-types@0.24.7): + resolution: {integrity: sha512-JxEH8uxao6FcWp3UXNDJIRjU3pamzp9aqIWgpfAqWE66aPwHeBIB39YnqTgbe4baUJRdpbcp1u8jJiYvojHGIQ==} + peerDependencies: + graphology-types: '>=0.19.0' + dependencies: + graphology-indices: 0.17.0(graphology-types@0.24.7) + graphology-types: 0.24.7 + graphology-utils: 2.5.2(graphology-types@0.24.7) + mnemonist: 0.39.5 + pandemonium: 2.4.1 + dev: true + /graphology-generators@0.11.2(graphology-types@0.24.7): resolution: {integrity: sha512-hx+F0OZRkVdoQ0B1tWrpxoakmHZNex0c6RAoR0PrqJ+6fz/gz6CQ88Qlw78C6yD9nlZVRgepIoDYhRTFV+bEHg==} peerDependencies: @@ -5926,6 +5954,12 @@ packages: engines: {node: '>=6'} dev: true + /pandemonium@2.4.1: + resolution: {integrity: sha512-wRqjisUyiUfXowgm7MFH2rwJzKIr20rca5FsHXCMNm1W5YPP1hCtrZfgmQ62kP7OZ7Xt+cR858aB28lu5NX55g==} + dependencies: + mnemonist: 0.39.5 + dev: true + /parent-module@1.0.1: resolution: {integrity: sha512-GQ2EWRpQV8/o+Aw8YqtfZZPfNRWZYkbidE9k5rpl/hC3vtHHBfGm2Ifi6qWV+coDGkrUKZAxE3Lot5kcsRlh+g==} engines: {node: '>=6'} @@ -6047,6 +6081,10 @@ packages: find-up: 4.1.0 dev: true + /platform@1.3.6: + resolution: {integrity: sha512-fnWVljUchTro6RiCFvCXBbNhJc2NijN7oIQxbwsyL0buWJPG85v81ehlHI9fXrJsMNgTofEoWIQeClKpgxFLrg==} + dev: true + /please-upgrade-node@3.2.0: resolution: {integrity: sha512-gQR3WpIgNIKwBMVLkpMUeR3e1/E1y42bqDQZfql+kDeXd8COYfM8PQA4X6y7a8u9Ua9FHmsrrmirW2vHs45hWg==} dependencies: @@ -6435,6 +6473,10 @@ packages: ajv-keywords: 3.5.2(ajv@6.12.6) dev: true + /seedrandom@3.0.5: + resolution: {integrity: sha512-8OwmbklUNzwezjGInmZ+2clQmExQPvomqjL7LFqOYqtmuxRgQYqOD3mHaU+MvZn5FLUeVxVfQjwLZW/n/JFuqg==} + dev: true + /semver-compare@1.0.0: resolution: {integrity: sha512-YM3/ITh2MJ5MtzaM429anh+x2jiLVjqILF4m4oyQB18W7Ggea7BfqdH/wGMK7dDiMghv/6WG7znWMwUDzJiXow==} dev: true diff --git a/site/benchmark/index.html b/site/benchmark/index.html index 30b377d..fde6813 100644 --- a/site/benchmark/index.html +++ b/site/benchmark/index.html @@ -140,6 +140,7 @@
    Choose a dataset: +
    diff --git a/site/benchmark/louvain.ts b/site/benchmark/louvain.ts new file mode 100644 index 0000000..70ac41d --- /dev/null +++ b/site/benchmark/louvain.ts @@ -0,0 +1,44 @@ +import { Graph, ID } from "@antv/graphlib"; +import louvain from 'graphology-communities-louvain'; +import { louvain as antvLouvain } from "../../packages/graph"; +import { Threads } from "../../packages/graph-wasm"; +import { graph2Edgelist } from "./util"; + +/** + * @see https://graphology.github.io/standard-library/communities-louvain.html + */ +export async function graphology(graph: any) { + const mapping = louvain(graph); + const clusters: { id: number; count: number }[] = []; + Object.keys(mapping).forEach((id) => { + const clusterIdx = mapping[id]; + if (!clusters[clusterIdx]) { + clusters[clusterIdx] = { id: clusterIdx, count: 0 }; + } + clusters[clusterIdx].count++; + }); + return clusters; +} + +export async function antv( + graph: Graph, +) { + const { clusters } = antvLouvain(graph, false, 'weight'); + return clusters.map(({ id, nodes }) => ({ id, count: nodes.length })); +} + +export async function wasm( + graph: Graph, + _: any, + _2: any, + threads: Threads +): Promise { + const { edgelist, idxNodeMap } = graph2Edgelist(graph, 'weight'); + const ranks = await threads.louvain({ + edgelist: edgelist as [number, number, number][] + }); + console.log(ranks); + return ranks; + // const formatted = ranks.map((rank, i) => ({ id: idxNodeMap[i], score: rank })); + // return format(formatted.sort((a, b) => b.score - a.score).slice(0, 10)); // {id: 'Valjean', score: 0.1} +} \ No newline at end of file diff --git a/site/benchmark/main.ts b/site/benchmark/main.ts index 8d46dc0..e4748ec 100644 --- a/site/benchmark/main.ts +++ b/site/benchmark/main.ts @@ -7,7 +7,8 @@ import { webgpu as webgpuPageRank, wasm as wasmPageRank } from "./page-rank"; -import { graphology as graphologySSSP, webgpu as webgpuSSSP, wasm as wasmSSSP } from "./sssp"; +import { graphology as graphologySSSP, antv as antvSSSP, webgpu as webgpuSSSP, wasm as wasmSSSP } from "./sssp"; +import { graphology as graphologyLouvain, antv as antvLouvain, wasm as wasmLouvain } from "./louvain"; import { initThreads } from "../../packages/graph-wasm"; const TestsConfig = [ @@ -66,20 +67,22 @@ const initThreadsPool = async () => { methods: { pageRank: graphologyPageRank, sssp: graphologySSSP, + louvain: graphologyLouvain, }, }, { name: TestName.ANTV_ALGORITHM, methods: { pageRank: antvPageRank, - // sssp: graphologyFruchterman, + sssp: antvSSSP, + louvain: antvLouvain, }, }, { name: TestName.ANTV_GRAPH_GPU, methods: { // pageRank: webgpuPageRank, - // sssp: webgpuSSSP, + sssp: webgpuSSSP, }, }, { @@ -87,11 +90,12 @@ const initThreadsPool = async () => { methods: { pageRank: wasmPageRank, sssp: wasmSSSP, + louvain: wasmLouvain, }, }, ]; - $run.onclick = async () => { + $run.onclick = () => { const dataset = datasets[$dataset.value]; const algorithmName = $algorithm.value; let options = {}; @@ -100,26 +104,24 @@ const initThreadsPool = async () => { options = graph.getAllNodes()[1].id; } - await Promise.all( - layoutConfig.map(async ({ name, methods }: any, i: number) => { - if (methods[algorithmName]) { - const start = performance.now(); - const result = await methods[algorithmName]( - dataset[name], - options, - graph, - forceMultiThreads - ); - $results[i][1].innerHTML = `${(performance.now() - start).toFixed( - 2 - )}ms`; + layoutConfig.map(async ({ name, methods }: any, i: number) => { + if (methods[algorithmName]) { + const start = performance.now(); + const result = await methods[algorithmName]( + dataset[name], + options, + graph, + forceMultiThreads + ); + $results[i][1].innerHTML = `${(performance.now() - start).toFixed( + 2 + )}ms`; - $results[i][0].innerHTML = JSON.stringify(result); - } else { - $results[i][0].innerHTML = ""; - $results[i][1].innerHTML = "-"; - } - }) - ); + $results[i][0].innerHTML = JSON.stringify(result); + } else { + $results[i][0].innerHTML = ""; + $results[i][1].innerHTML = "-"; + } + }) }; })(); diff --git a/site/benchmark/sssp.ts b/site/benchmark/sssp.ts index 06444d8..088b3e2 100644 --- a/site/benchmark/sssp.ts +++ b/site/benchmark/sssp.ts @@ -6,11 +6,20 @@ import { Threads } from "../../packages/graph-wasm"; import { graph2Edgelist } from "./util"; export async function graphology(graph: any, source: string) { - return dijkstra.singleSource(graph, source, "weight"); + const result = dijkstra.singleSource(graph, source, "weight"); + return Object.keys(result).map((key) => ({ key, path: result[key] })) + .filter(({ path }) => path.length > 0) + .slice(0, 3); } export async function antv(graph: Graph, source: string) { - // findShortestPath(graph, source) + const nodes = graph.getAllNodes(); + const paths: any[] = []; + nodes.forEach((node) => { + const p = findShortestPath(graph, source, node.id); + paths.push(p); + }); + return paths.slice(0, 3); } export async function webgpu( @@ -20,7 +29,7 @@ export async function webgpu( ) { const result = await webgpuGraph.sssp(graph, source, "weight"); - return result.filter((r) => r.distance !== 1000000); + return result.filter((r) => r.distance !== 1000000).slice(0, 3); } export async function wasm( @@ -34,7 +43,5 @@ export async function wasm( startNode: nodeIdxMap[source], edgelist: edgelist as [number, number, number][], }); - console.log(paths); - // const formatted = ranks.map((rank, i) => ({ id: idxNodeMap[i], score: rank })); - // return format(formatted.sort((a, b) => b.score - a.score).slice(0, 10)); // {id: 'Valjean', score: 0.1} + return paths.slice(0, 3); } \ No newline at end of file diff --git a/site/data/undirected1000.json b/site/data/undirected1000.json new file mode 100644 index 0000000..c9f8717 --- /dev/null +++ b/site/data/undirected1000.json @@ -0,0 +1 @@ +{"nodes":[{"label":"471","x":317.35546875,"y":12.529082298278809,"id":"471","attributes":{"Modularity Class":"2"},"color":"rgb(255,85,132)","size":4.0},{"label":"488","x":37.71865463256836,"y":334.5827331542969,"id":"488","attributes":{"Modularity Class":"7"},"color":"rgb(76,70,62)","size":4.0},{"label":"267","x":-181.7259521484375,"y":278.5659484863281,"id":"267","attributes":{"Modularity Class":"5"},"color":"rgb(0,196,255)","size":4.0},{"label":"193","x":241.61814880371094,"y":13.578747749328613,"id":"193","attributes":{"Modularity Class":"0"},"color":"rgb(223,137,255)","size":4.0},{"label":"606","x":-48.633995056152344,"y":248.1951446533203,"id":"606","attributes":{"Modularity Class":"7"},"color":"rgb(76,70,62)","size":4.0},{"label":"465","x":-105.6462631225586,"y":319.88299560546875,"id":"465","attributes":{"Modularity Class":"7"},"color":"rgb(76,70,62)","size":4.0},{"label":"333","x":-143.01101684570312,"y":168.4177703857422,"id":"333","attributes":{"Modularity Class":"5"},"color":"rgb(0,196,255)","size":4.0},{"label":"882","x":-144.01536560058594,"y":19.3790283203125,"id":"882","attributes":{"Modularity Class":"5"},"color":"rgb(0,196,255)","size":4.0},{"label":"837","x":60.58860397338867,"y":-32.317623138427734,"id":"837","attributes":{"Modularity Class":"0"},"color":"rgb(223,137,255)","size":4.0},{"label":"902","x":-67.84288024902344,"y":-60.66090774536133,"id":"902","attributes":{"Modularity Class":"4"},"color":"rgb(115,192,0)","size":4.0},{"label":"607","x":22.31706428527832,"y":296.8169860839844,"id":"607","attributes":{"Modularity Class":"7"},"color":"rgb(76,70,62)","size":4.0},{"label":"568","x":-208.78225708007812,"y":80.68643951416016,"id":"568","attributes":{"Modularity Class":"5"},"color":"rgb(0,196,255)","size":4.0},{"label":"454","x":3.8920764923095703,"y":299.0199890136719,"id":"454","attributes":{"Modularity 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\ No newline at end of file diff --git a/site/datasets.ts b/site/datasets.ts index 0203d3a..e513f70 100644 --- a/site/datasets.ts +++ b/site/datasets.ts @@ -1,11 +1,32 @@ -import Graph from "graphology"; +import Graph, { UndirectedGraph } from "graphology"; import { Graph as AntvGraph } from "@antv/graphlib"; import { clusters } from "graphology-generators/random"; import { TestName } from "./types"; - export const loadDatasets = async () => { const datasets: Record = {}; + const loadUndirected500 = async () => { + const result = await fetch("https://raw.githubusercontent.com/graphology/graphology/master/src/communities-louvain/test/datasets/undirected1000.json") + const undirected1000Data = await result.json(); + const graph = new UndirectedGraph(); + undirected1000Data.nodes.forEach((d: any) => { + graph.addNode(d.id, d); + }); + undirected1000Data.edges.forEach((d: any) => { + graph.addEdge(d.source, d.target); + }); + + const antvgraph = graphology2antv(graph); + return { + desc: + "Creates a undirected graph with 500 nodes.", + [TestName.GRAPHOLOGY]: graph, + [TestName.ANTV_ALGORITHM]: antvgraph, + [TestName.ANTV_GRAPH_GPU]: antvgraph, + [TestName.ANTV_GRAPH_WASM]: antvgraph, + }; + }; + const loadRandomClusters = () => { const NODES = 1000; const EDGES = 2000; @@ -93,12 +114,14 @@ export const loadDatasets = async () => { }; const [ + undirected500, randomClusters, relations, netscience, eva, regions, ] = await Promise.all([ + loadUndirected500(), loadRandomClusters(), loadG6JSON( "https://gw.alipayobjects.com/os/antvdemo/assets/data/relations.json", @@ -118,6 +141,7 @@ export const loadDatasets = async () => { )(), ]); + datasets.undirected500 = undirected500; datasets["random-clusters"] = randomClusters; datasets.relations = relations; datasets.netscience = netscience;