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
Contributors
gwaybio, roshankern, and jenna-tomkinson