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Mixed usage of `n_samples_overall` in `get_normalized_expression`

Open martinkim0 opened this issue 1 year ago • 2 comments

In TOTALVI.get_normalized_expression, MULTIVI.get_normalized_expression, and ContrastiveVI.get_normalized_expression, n_samples_overall just downsamples indices, while in RNASeqMixin.get_normalized_expression, it's used for the number of MC inference samples. This might be confusing for users who expect the argument to mean and do the same thing across methods.

martinkim0 avatar Apr 01 '24 23:04 martinkim0

@PierreBoyeau Currently this means that these other function don't use importance weighting? I assume it would make sense to add it to these models as well?

canergen avatar Aug 08 '24 18:08 canergen

I think we can improve the naming as well (but that's styling and I would stick to n_samples_overall for number of mc_samples and n_samples to number of samples for a single input cell in a forward pass.

canergen avatar Aug 08 '24 18:08 canergen