Hi K. Frank,
Thanks for getting back to me.
I think the problem which I have is twofold and class inbance which (as far as I understand) can be addressed by weighting the classes is just one of them, and probably the smaller one. I have tried adding such weights and my network dies (gives me all zeros outputs) after a few epochs. Just like without adding weights. I was thinking if there is a simple way providing a binary mask, where I have labels, which would be included in the loss function?