v1.0 - Manuscript Submission

Full version release of analysis code for training, evaluating, and validating machine learning models to predict phenotype from single-cell morphology representations.

We will submit this version as a preprint and to peer-reviewed journals.

What's Changed

• Format data by @roshankern in #1
• Add ml model by @roshankern in #2
• Add analysis module by @roshankern in #3
• Use new mitocheck data by @roshankern in #4
• Use 2015 data & remove holdout set by @roshankern in #5
• Add class pr curves by @roshankern in #6
• Create validation module by @roshankern in #7
• Add confusion matrix notebook by @roshankern in #8
• Add F1 scores notebook by @roshankern in #9
• Add single cell sample images module by @roshankern in #10
• Add single cell images by @roshankern in #11
• Save interpretations by @roshankern in #12
• Get model predictions by @roshankern in #14
• Restructure pr curves notebook by @roshankern in #15
• Add PR curve figure for DeepProfiler multiclass model by @gwaybio in #16
• Cp feature refactor by @roshankern in #35
• Update readmes by @roshankern in #36
• Update docs by @roshankern in #37
• Adding several publication ready figures [Figure 2, Supplementary Figs 2 and 3] by @gwaybio in #38
• Adding figure 3 and associated notebook by @gwaybio in #39
• Adding single-class model evaluation [Supplementary Figure] by @gwaybio in #41
• Add training/models of Zernike and AreaShape feature space only by @gwaybio in #44
• Adding Figure 4 - Leave One Image Out Analysis by @gwaybio in #40
• Visualize performance for subset featurespaces by @gwaybio in #43
• Add JUMP Mitocheck feature analysis comparison with KS tests by @gwaybio in #42
• Updating LOIO analysis to include all features spaces by @gwaybio in #46
• Add models with no-ic [training and LOIO] by @gwaybio in #51
• Updating LOIO visualization by @gwaybio in #47
• Adding supplementary LOIO figure by @gwaybio in #53
• Adding feature importance visualizations by @gwaybio in #48
• Add Figure 1 by @jenna-tomkinson in #57
• Process jump single cell data by @gwaybio in #56
• Add enrichment and introductory notes to readme by @gwaybio in #61
• Repo cleanup by @roshankern in #62
• Add details to Readme by @gwaybio in #64
• Minor tweaks to sup fig 7 by @gwaybio in #58
• Minor tweaks to Sup Figure 8 by @gwaybio in #59
• Add JUMP analysis figure by @gwaybio in #55
• update download path by @roshankern in #65
• Switch to top 100 enriched treatments in JUMP (new sup table) by @gwaybio in #60
• Increase font size and fix arrangement of figure 4 by @gwaybio in #66

New Contributors

• @jenna-tomkinson made their first contribution in #57

Full Changelog: https://github.com/WayScience/phenotypic_profiling/commits/v1.0