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Support for weighted loss either per-batch or per-cell? #2785

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kamilkrukowski opened this issue May 9, 2024 · 0 comments
Open

Support for weighted loss either per-batch or per-cell? #2785

kamilkrukowski opened this issue May 9, 2024 · 0 comments

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@kamilkrukowski
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kamilkrukowski commented May 9, 2024

Could scVI models support weighed loss and weighing individual cells or batch_key groups?

Some potential uses

  • Downweighing over-represented atlases with low interesting variation.
  • Improving ELBO on poorly represented subsets of interest i.e. rare cell types or small samples.

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To my knowledge, oversampling/undersampling is not a viable solution here because scvi-tools requires in-memory AnnData objects containing the entire dataset. Is there any way to "stream" data loading with meaningful oversampling that does not require holding all oversampled entries in memory for the entirety of training?

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