Cp feature refactor #35
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* refactor module * remove training data file * Update 0.download_data/scripts/nbconverted/download_data.py Co-authored-by: Erik Serrano <[email protected]> * eric suggestions --------- Co-authored-by: Erik Serrano <[email protected]>
* refactor module * greg suggestions
* refactor format module * use straify function * rerun train module * black formatting * docs, nbconvert * nbconvert * rerun pipeline, rename model * fix typo * Update 2.train_model/README.md Co-authored-by: Gregory Way <[email protected]> * Update 2.train_model/README.md Co-authored-by: Gregory Way <[email protected]> * Update 2.train_model/README.md Co-authored-by: Gregory Way <[email protected]> * notebook run --------- Co-authored-by: Gregory Way <[email protected]>
* refactor clas pr curves * refactor confusion matrix * refactor F1 scores * refactor model predictions * documentation * dave suggestions * erik suggestions, reconvert
* refactor interpret notebook * docs, reconvert script * greg suggestions
* add LOIO notebook * LOIO notebook * update notebook * download and split data with cell UUIDs * move LOIO * finish LOIO * black formatting * rerun notebook * rerun notebook, dave suggestions * greg comment
* move multiclass models * rename files, fix sh * single class models notebook * run notebook * binarize labels * train single class models * reconvert notebooks * update readme * rename sh file * remove models * eric readme suggestions * rerun notebook, eric suggestions
* get SCM PR curves * shuffled baseline * retrain single class models with correct kernel * rerun pr curves notebook * remove nones * rerun multiclass model * rerun notebook * move file * docs, black formatting * format notebook * Update 3.evaluate_model/README.md Co-authored-by: Dave Bunten <[email protected]> * dave suggestions * reconvert notebook --------- Co-authored-by: Dave Bunten <[email protected]>
* get SCM PR curves * shuffled baseline * retrain single class models with correct kernel * rerun pr curves notebook * remove nones * rerun multiclass model * rerun notebook * move file * create SCM confusion matrix * rerun notebook * add changes from last PR * rerun notebook * add SCM F1, update SCM confusion matrices * documentation * rerun notebook * Update utils/evaluate_utils.py Co-authored-by: Dave Bunten <[email protected]> * Update utils/evaluate_utils.py Co-authored-by: Dave Bunten <[email protected]> * Update 3.evaluate_model/scripts/nbconverted/F1_scores.py Co-authored-by: Dave Bunten <[email protected]> * dave suggestions --------- Co-authored-by: Dave Bunten <[email protected]>
* get SCM LOIO probas * reconvert notebook * get model predictions * rerun LOIO * reconvert notebook * save and reconvert notebook * eric suggestions
* add scm coefficients * rerun interpret multi-class model * compare model coefficients * nbconvert * readme * make all correlations negative * rerun training * rerun evaluate * rerun interpret * docs * newline * rerun LOIO
* rerun download/split modules * rerun multicalss models * rerun single class model * rerun evaluate module * get LOIO probas * rerun interpret module * rerun download data
* set colors for model types * visualize precision recall with CP and DP+CP * add F1 score barchart visualization * minor tweak of f1 score print * ignore mac files * merge main and rerun viz * change color scheme for increased contrast * add f1 score of the top model, and rerun with updated colors * nrow = 3 in facet * change name of weighted f1 score
* update validate module * refactor validation * get correlations * convert notebook * update readme * formatting, documentation * reset index * vadd view notebook * docs, black formatting * ccc credit * show all correlations * add notebook * remove preview notebook * convert notebook * add differences heatmaps * preview correlation differences * add docs * black formatting
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gwaybio
approved these changes
Jul 6, 2023
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All other PRs were approved, let's get this into main. Congrats and well done @roshankern !
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This PR is ready for review!
In this PR, this repo is refactored to include the extraction and processing of CP features. Every change has already been reviewed, just need a comprehensive review to merge to main!