Embeddings

[grpinto]

Hi,

Thank you so much for your work, this looks amazing. Is there an easy way to get embeddings of the model, the same way Enformer has ?

Thanks and keep up the good work,
Best wishes,
Gonçalo Rei Pinto

[davek44]

I haven't tried it yet, but I think this script with this option will do it: https://github.com/calico/baskerville/blob/main/src/baskerville/scripts/hound_predbed.py#L51C12-L51C23

I've also found in the past that you can do pretty well by generating the full predictions vector and computing a matrix factorization back down to whatever size embedding you'd like.