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Patch SCANVI classifier logits bug #2301

Merged
merged 22 commits into from Nov 20, 2023
Merged

Patch SCANVI classifier logits bug #2301

merged 22 commits into from Nov 20, 2023

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martinkim0
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@martinkim0 martinkim0 commented Oct 25, 2023

As pointed out in offline discussions, SCANVI currently has a critical bug in its classifier code where the output of the classifier is incorrectly treated as logits (for example). By default, the classifier outputs probabilities as seen here. The effect is unknown but likely undesirable.

  • Add tests for backwards compat loading and training
  • Add release note
  • Run small benchmark with tutorial data
  • Run benchmark, possibly with OpenProblems

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codecov bot commented Oct 25, 2023

Codecov Report

Attention: 1 lines in your changes are missing coverage. Please review.

Comparison is base (ed768ab) 89.29% compared to head (8f0ba22) 89.30%.

Files Patch % Lines
scvi/module/_scanvae.py 93.33% 1 Missing ⚠️
Additional details and impacted files
@@           Coverage Diff           @@
##             main    #2301   +/-   ##
=======================================
  Coverage   89.29%   89.30%           
=======================================
  Files         145      145           
  Lines       11872    11889   +17     
=======================================
+ Hits        10601    10617   +16     
- Misses       1271     1272    +1     

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@martinkim0 martinkim0 merged commit aaad33c into main Nov 20, 2023
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@martinkim0 martinkim0 deleted the fix-scanvi branch November 20, 2023 22:41
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