mehta-lab
GMM clustering and fixed compute pca
- [x] added GMMClustering class w/ various methods for GMM clustering using BIC and AIC
- [x] fixed compute_pca so values aren't hardcoded
- [x] example script to run gmm clustering w/ ground truth annotations
- [ ] visualizing Feb + June datasets using UMAPs colored by GMM cluster weights and by predicted cluster labels
getting merge conflict currently w/ new refactoring in representation eval, need to fix this
@alishbaimran @Soorya19Pradeep I am booked with multiple planning and writing projects through the end of the year. I think Soorya is situated to provide a solid review and testing of this code. She implemented GMM clustering over time for infection state discrimination for Fig. 5 of https://academic.oup.com/pnasnexus/article/3/9/pgae323/7731083
@alishbaimran , can you pull the changes from the representation branch into this branch? There seem to be some conflicts with the representation branch.
@alishbaimran , can you pull the changes from the representation branch into this branch? There seem to be some conflicts with the representation branch.
Yes I can do this and then push changes again.
@alishbaimran it looks like you started a branch or merged changes in a way that affected files that are not related to this feature.
You may need to do this:
- start a new branch from
mainafter release 0.3.0. - transfer the relevant files by hand from this branch.
- open a fresh PR and close this PR.
@alishbaimran , as you open the new branch to make the changes Shalin mentioned please keep in mind to clean up the scripts like this inside applications/contrastive_phenotyping/figures folder as these doesn't make sense anymore.
@alishbaimran , as you open the new branch to make the changes Shalin mentioned please keep in mind to clean up the scripts like this inside
applications/contrastive_phenotyping/figuresfolder as these doesn't make sense anymore.
@Soorya19Pradeep I'm not sure if these scripts are even suppose to be included in new branch. I pulled the files that were pushed to this branch and it seems some really old commits were moved here?
@mattersoflight could you clarify if/what to do with these olds commits?
@alishbaimran , I think it is best to close this and start a new branch. Let us do that and then you can add the new scripts for GMM clustering and remove those figure scripts there.