Use 2015 data & remove holdout set #5
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d33bs
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Dec 7, 2022
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Nice job! I left a few comments and suggestions with this review. Please don't hesitate to let me know if you have any questions or if I may clarify at all.
I also wanted to follow up with a general question:
- I noticed that notebook files
2.train_model/train_model.ipynband4.interpret_model/interpret_model.ipynbdid not have nbconverted.pypair files. Should those be included with this PR?
Co-authored-by: Dave Bunten <ekgto445@gmail.com>
…iling_model into use-2015-data
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Thank you for the review @d33bs! Notebook files |
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Accidentally merged this PR without approval, but @d33bs and I discussed that everything was good to merge. |
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Dec 12, 2022
* Use 2015 data & remove holdout set (#5) * finish download module changes * download notebook * rerun split data module * rerun download module * rerun train_model * rerun evaluation module * rerun interpretation module * combine datasets * combine datasets * split changes * update format * format update * format * finish split data * combine datasets, remove holdout * formatting * rerun pipelines * remove folded class * rerun pipeline * Update utils/download_utils.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * PR fixes * module docstrings Co-authored-by: Dave Bunten <ekgto445@gmail.com> * add PR curves * get PR curves/data * update docs, recreate py files * greg recommendations Co-authored-by: Dave Bunten <ekgto445@gmail.com>
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* Use 2015 data & remove holdout set (#5) * finish download module changes * download notebook * rerun split data module * rerun download module * rerun train_model * rerun evaluation module * rerun interpretation module * combine datasets * combine datasets * split changes * update format * format update * format * finish split data * combine datasets, remove holdout * formatting * rerun pipelines * remove folded class * rerun pipeline * Update utils/download_utils.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * PR fixes * module docstrings Co-authored-by: Dave Bunten <ekgto445@gmail.com> * validation module * correlation matrix * reviz * reformat * pearson correlation * spearman correlation * documentation * documentation * docs * docs, rerun * docs * docs * Update 5.validate_model/validate_model.sh Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update utils/validate_utils.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * raw link clarification * Update utils/validate_utils.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update utils/validate_utils.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * Update utils/validate_utils.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * conditional to remove x, y columns * clarify perturbation rename * black formatting Co-authored-by: Dave Bunten <ekgto445@gmail.com>
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* Use 2015 data & remove holdout set (#5) * finish download module changes * download notebook * rerun split data module * rerun download module * rerun train_model * rerun evaluation module * rerun interpretation module * combine datasets * combine datasets * split changes * update format * format update * format * finish split data * combine datasets, remove holdout * formatting * rerun pipelines * remove folded class * rerun pipeline * Update utils/download_utils.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * PR fixes * module docstrings Co-authored-by: Dave Bunten <ekgto445@gmail.com> * move class PR curves * use typing tuple return hint * use tuple * confusion matrix evaluation * rename cm files * update documentation * code documentation * get model scores * undo last commit * update documentation * use correct env * dave suggestions --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com>
roshankern
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* Use 2015 data & remove holdout set (#5) * finish download module changes * download notebook * rerun split data module * rerun download module * rerun train_model * rerun evaluation module * rerun interpretation module * combine datasets * combine datasets * split changes * update format * format update * format * finish split data * combine datasets, remove holdout * formatting * rerun pipelines * remove folded class * rerun pipeline * Update utils/download_utils.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * PR fixes * module docstrings Co-authored-by: Dave Bunten <ekgto445@gmail.com> * add score util * add/run notebook * update documentation/formatting * update documentation * black formatting * rename function * compile tidy data * update documentation, dave suggestions --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com>
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* Use 2015 data & remove holdout set (#5) * finish download module changes * download notebook * rerun split data module * rerun download module * rerun train_model * rerun evaluation module * rerun interpretation module * combine datasets * combine datasets * split changes * update format * format update * format * finish split data * combine datasets, remove holdout * formatting * rerun pipelines * remove folded class * rerun pipeline * Update utils/download_utils.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * PR fixes * module docstrings Co-authored-by: Dave Bunten <ekgto445@gmail.com> * create single cell images module * rename_module * finish module * remove sample images from PR * Co-authored-by: Jenna Tomkinson <jenna.tomkinson@ucdenver.edu> * documentation * documentation * dave suggestions * Update utils/single_cell_utils.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com>
roshankern
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* Use 2015 data & remove holdout set (#5) * finish download module changes * download notebook * rerun split data module * rerun download module * rerun train_model * rerun evaluation module * rerun interpretation module * combine datasets * combine datasets * split changes * update format * format update * format * finish split data * combine datasets, remove holdout * formatting * rerun pipelines * remove folded class * rerun pipeline * Update utils/download_utils.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * PR fixes * module docstrings Co-authored-by: Dave Bunten <ekgto445@gmail.com> * upload files --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com>
roshankern
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Feb 13, 2023
* Use 2015 data & remove holdout set (#5) * finish download module changes * download notebook * rerun split data module * rerun download module * rerun train_model * rerun evaluation module * rerun interpretation module * combine datasets * combine datasets * split changes * update format * format update * format * finish split data * combine datasets, remove holdout * formatting * rerun pipelines * remove folded class * rerun pipeline * Update utils/download_utils.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * PR fixes * module docstrings Co-authored-by: Dave Bunten <ekgto445@gmail.com> * save interpretations * docs, recreate py file * fix typo * PR suggestions --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com>
roshankern
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* Use 2015 data & remove holdout set (#5) * finish download module changes * download notebook * rerun split data module * rerun download module * rerun train_model * rerun evaluation module * rerun interpretation module * combine datasets * combine datasets * split changes * update format * format update * format * finish split data * combine datasets, remove holdout * formatting * rerun pipelines * remove folded class * rerun pipeline * Update utils/download_utils.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * PR fixes * module docstrings Co-authored-by: Dave Bunten <ekgto445@gmail.com> * get predictions * delete unused file, compiled predictions * rerun evaluate module * docs * dave suggestions --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com>
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* Use 2015 data & remove holdout set (#5) * finish download module changes * download notebook * rerun split data module * rerun download module * rerun train_model * rerun evaluation module * rerun interpretation module * combine datasets * combine datasets * split changes * update format * format update * format * finish split data * combine datasets, remove holdout * formatting * rerun pipelines * remove folded class * rerun pipeline * Update utils/download_utils.py Co-authored-by: Dave Bunten <ekgto445@gmail.com> * PR fixes * module docstrings Co-authored-by: Dave Bunten <ekgto445@gmail.com> * restructure PR curves notebook * dave suggestions --------- Co-authored-by: Dave Bunten <ekgto445@gmail.com>
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This PR is ready for review! This PR incorporates a newer version of mitocheck_data, downloading the 2015 MitoCheck dataset and merging it with the older dataset. The pipeline is then rerun with this expanded dataset.
The "holdout" dataset is also removed, leaving only the training and testing data subsets. Our logic here is that the application of the final phenotypic profiling model to other datasets (ex Cell Health) will validate the model in the same way a holdout dataset would.