Closed simon-anders closed 2 weeks ago
you don't need to do that explicitly. it is binarized before feeding into the model. https://github.com/calico/scBasset/blob/d31138b1d28adaa427444a54f41494fe74e4be3a/scbasset/utils.py#L346
Thanks a lot for the very fast reply. And thanks even more for pointing out the code position. I've been looking through the code for it but missed generator.call
.
I'm currently working through your tutorial scripts. I've downloaded your AnnData object of the Buenrostro2018 data, as found here and trained the model with it. I noticed that the
X
matrix in the AnnData object contains read counts, but if I understand the paper right, you use binarized data.Should I hence clip all data to {0,1}, i.e., replace any non-zero count with a one?
I see no mention of this in the tutorial code, but the binary cross entropy loss would not make sense without that, or would it?
Thanks in advance for your help.