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batch integration baselines are suboptimal #685

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scottgigante-immunai opened this issue Nov 14, 2022 · 6 comments
Closed

batch integration baselines are suboptimal #685

scottgigante-immunai opened this issue Nov 14, 2022 · 6 comments
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@scottgigante-immunai
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isolated label silhouette in batch_integration_embed and ARI in batch_integration_graph have scores much greater than 1. We need to design better baselines that are optimised to perform on these metrics. cc @LuckyMD

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LuckyMD commented Nov 18, 2022

may be solved via #686 . To be closed once results come out

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LuckyMD commented Jan 3, 2023

The iso label ASW baseline improvement was not solved via #686 for the pancreas dataset. It seems that the issue may be related to the isolated label being t cells in that dataset, which only has 7 cells. We should put a filter on n_cells per label in the dataset function to avoid this @danielStrobl. Maybe that could help this situation?

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LuckyMD commented Jan 4, 2023

See also #757

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LuckyMD commented Jan 9, 2023

@scottgigante-immunai... something strange is going on, as the baseline is perfect in scib. See theislab/scib#362

@scottgigante-immunai
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silhouette_batch still not resolved here.

image

@LuckyMD
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LuckyMD commented Feb 7, 2023

Maybe this should go to a different issue, as this issue was for iso label ASW and ARI, which are both addressed.

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