Is there a way to obtain embeddings?

Feedback & Feature Requests
1

Hi,

I’m very interested in using AlphaGenome embeddings for downstream analysis. Is there a way to extract embeddings for specific DNA sequences from the api? That would greatly help us in extending the model to specific questions we’re working on.

Thanks!

2

Hi Xiaohui,

On what project are you working ?

3

Hi @Xiaohui_Jiang , could you learn something about how to get embeddings from AlphaGenome? On the official website, I could see how to get predicted regulatory properties, but couldn’t find any option to get the embeddings.

4

Our model code and weights are now available at https://github.com/google-deepmind/alphagenome_research, so you should be able to run the model locally and access the trunk embeddings.