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isolated label scores do not return expected results #367

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danielStrobl opened this issue Jan 26, 2023 · 1 comment
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isolated label scores do not return expected results #367

danielStrobl opened this issue Jan 26, 2023 · 1 comment
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@danielStrobl
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danielStrobl commented Jan 26, 2023

adata.obs[iso_label_key] = adata.obs[label_key] == isolated_label
score = silhouette(adata, iso_label_key, embed)

This function gives the mean over all cells and not only the mean for the cells that are part of the isolated label.
This leads to much lower scores with the baselines as observed here: openproblems-bio/openproblems#685

@mumichae
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should be solved by #370

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