How to get gene embeddings

Thank you very much for providing the UCE model! It has been a great help to me.
I noticed that the program only provides cell embeddings for different cells in the dataset. Is there a way to also easily obtain gene embeddings corresponding to the cells?

You could use the ESM2 embedding files directly.

You can also load the model in python and then apply the gene_embedding_layer to those protein embeddings to get the modified smaller dimensional version that is fed into the model.

Thank you for your reply. Additionally, the README mentions a documentation file, and where can I find it?

Sorry for the confusion-- by that we meant the docstrings in the code / scripts themselves, such as

UCE/eval_single_anndata.py

Line 1 in 7b31528

"""