HLA Pseudosequence generation about pmtnet HOT 3 CLOSED

Hi @Hugh-OBrien ，

Thank you for carefully looking into the code and pointing out the problem! After reviewing the pseudo-seq method in both netMHCpan and MHCflurry, I think you are right that we need to do alignments for HLA sequences before taking pseudo sequences. Even though we had the pseudo-sequences not as same as netMHCpans, the performance is still good compared to netMHCpan. I will comment on this caveat in the code. We are also working on pMTnet version 2.0. We will take this caveat into consideration. Thank you again for looking into this and letting us know!

Tianshi

from pmtnet.

Thank you for the reply. Yes on my quick retraining test I found there was a modest performance hit on the MHC-peptide binding affinity; however, as this is only the encoder branch it may not end up affecting the overall performance of the overall model in a significant way. Would be good to add in a caveat in a comment as it may increase the performance of future work

from pmtnet.

I totally agree with you. Thanks again for your input!

from pmtnet.