Pierre Boyeau

In addition to having the model, I think this is an opportunity to use cases of exotic data handling approaches. Do you think we should get in touch with their...

Ok let me contact them, I'll cc-you!

It sounds like it would be relevant to include it back. Do you remember why we removed this feature?

Hi Valentine, this is a really useful feature to filter out pathological genes. I am reordering the codebase related to DE to prepare for upcoming changes and included your feature...

Hi, it sounds like [this](https://github.com/scverse/scvi-tools/blob/cc38acc8d72d1b03ef3592cb1699114dcd040438/scvi/model/_scanvi.py#L259) already returns the softmax outputs.

Good Evening Mathias, It still does not work for me but never mind, I tried my best to use another repository to implement a convolutional AAE. My autoencoder works quite...

Thanks so much for raising this point. @NathanAzoL worked on reimplementing scANVI that computes the mentioned kl term [here](https://github.com/NathanAzoL/scvi-tools/pull/1). He observed promising results hinting that this correction could be beneficial...

I'm on it!

I struggle with the same issue

Hi @qiuwch, yes, I use the UE4 plugin. First of all, thanks for your help (once again!) I tried your solution. However, the object masks still don't have expected dimensions...