Prototype branch#2

Merged

AlejandroTL merged 37 commits into

mainfrom

prototype_branch

Sep 19, 2025

Commits on Jun 2, 2025

borzoi embeddings
grpinto
committed

Commits on Jun 8, 2025

Commits on Jun 9, 2025

pseudo tested chemberta, more verifications are required
grpinto
committed

Commits on Jun 10, 2025

checked embed batch from enformer and borzoi and it works, fixed a bug in enformer
grpinto
committed

Commits on Jun 24, 2025

Fixed gene_resolver and I can now get protein sequences and fasta sequences as well as gene info from MyGene.info
grpinto
committed

Commits on Jun 25, 2025

mage gene embeddings.py operational
grpinto
committed

Commits on Jun 26, 2025

Commits on Jul 2, 2025

code to run in the cluster
grpinto
committed

Commits on Jul 3, 2025

changed the gene_embeddings to deal with borzoi, should be a temporary change
Goncalo Pinto
committed

Commits on Jul 10, 2025

this is to be able to merge
grpinto
committed

Commits on Jul 11, 2025

Commits on Jul 13, 2025

Commits on Jul 24, 2025

Commits on Jul 25, 2025

STRING embeddings added and verified manually
grpinto
committed

Commits on Jul 26, 2025

Added Enformer Test, now we just need to add a sequence from a pretrained enformer model to complete the test
grpinto
committed

Commits on Aug 1, 2025

Test to check if it is center or not
grpinto
committed

Commits on Aug 4, 2025

Commits on Sep 16, 2025

chemical embeddings generated
grpinto
committed