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Decoding Gene Embeddings

#502
by cstansbu - opened
Discussion
cstansbu

Hello!

I'm wondering if there is a way to decode GeneFormer gene embeddings? Given a single vector (gene embedding), can I obtain a token id?

Thanks!

Cooper

ctheodoris
 Owner

Thanks for your question. Others have trained decoders to accomplish this, but it’s not a method provided in this repository. We generally are more interested in learning whether a perturbation moves to a specified state though so the exact rank value encoding is not necessary for that as the analysis can be done within the embedding space.

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