fine-tuning with more protein sequences

[avilella]

Hi, I have a corpus of about 500,000 protein sequences and would like to apply them to existing models like ESM2 or this one for predicting the fitness effect of changing an amino-acid for another.
How could I add my sequences to the models referred in this repo to then use the modified model for such task? Thanks.

[pascalnotin]

Hi @avilella -- do you have property annotations for these 500k sequences? Or just the amino acid sequences w/ no annotation? ProteinNPT is first and foremost a model that learns a joint distribution of sequences and corresponding labels, so it is not the most adapted to your setting if there is no such label/annotation.
If no label, you may be interested in the various zero-shot baselines we have integrated in the ProteinGym benchmark.
Best,
Pascal