8000 Scale isolated label ASW by mumichae · Pull Request #371 · theislab/scib · GitHub
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Scale isolated label ASW #371

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Merged
merged 1 commit into from
Feb 2, 2023
Merged

Scale isolated label ASW #371

merged 1 commit into from
Feb 2, 2023

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mumichae
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@mumichae mumichae commented Feb 1, 2023

Isolated label ASW is not scaled, so that the expected output range would be between -1 and +1

scib/scib/metrics/isolated_labels.py

Lines 237 to 249 in 98ee9a2

# AWS score between isolated label vs rest
if "silhouette_temp" not in adata.obs:
adata.obs["silhouette_temp"] = silhouette_samples(
adata.obsm[embed], adata.obs[label_key]
)
# aggregate silhouette scores for isolated label only
score = adata.obs[adata.obs[label_key] == isolated_label].silhouette_temp.mean()
if verbose:
print(f"{isolated_label}: {score}")
return score

Solution: Add scaling option to metric

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codecov bot commented Feb 1, 2023

Codecov Report

Merging #371 (225adf6) into main (98ee9a2) will increase coverage by 0.05%.
The diff coverage is 100.00%.

Additional details and impacted files 
@@            Coverage Diff             @@
##             main     #371      +/-   ##
==========================================
+ Coverage   53.13%   53.18%   +0.05%     
==========================================
  Files          22       22              
  Lines        1850     1852       +2     
==========================================
+ Hits          983      985       +2     
  Misses        867      867
Flag Coverage Δ
unittests 53.18% <100.00%> (+0.05%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
scib/metrics/isolated_labels.py 92.98% <100.00%> (+0.25%) ⬆️

danielStrobl
danielStrobl approved these changes Feb 1, 2023
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Looks good! Was wondering about that test_isolated_labels_silhouette one, it's a duplicate from test_isolated_label_metrics.py, right?

LuckyMD
LuckyMD approved these changes Feb 1, 2023
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Looks good to me. The same scaling as in cell type ASW, and it's scaled per label, so each label has equal weight.

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LuckyMD commented Feb 1, 2023

We'll need a new release and then an open problems PR to pin to that release @danielStrobl

@mumichae mumichae merged commit c42935b into main Feb 2, 2023
@mumichae mumichae deleted the fix/scale_isolated_asw branch February 2, 2023 09:10
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@LuckyMD LuckyMD LuckyMD approved these changes

@danielStrobl danielStrobl danielStrobl approved these changes

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@mumichae @LuckyMD @danielStrobl
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