bitbol-lab/protmamba-ssm

ProtMamba: a homology-aware but alignment-free protein state space model

protmamba-ssm's Issues

mamba_ssm code version

Hi,

As the ProtMamba_ssm/ is missing the mamba_ssm code in the distribution, can you please point me to the right version of mamba_ssm code you used for ProtMamba or add that to the ProtMamba_ssm/?

Thank you

Test Set Creation

Hi thank you for your work and the nice codebase. I have a question regarding the creation of the held out test set, referenced by "encoded_MSAs_test.pkl". In core.py training and validation are split on the fly with seed=0 and eval_size=193. Am I correct that the test set is sampled similarly, i.e. from the full training set (without replacement), with the same seed, and consisting of 500 clusters as described in section 2.3 in the paper?

Thank you!