Scripts for Clinical data benchmarks

[YinghuiChen-sky]

Dear ProteinGym team,

I noticed that there is a script named performance_DMS_benchmarks.py for DMS benchmarking in the ProteinGym repository. However, I couldn't find a similar script for Clinical Substitutions/Indels benchmarking.

Would it be possible for you to provide a benchmark script for clinical data as well?

Thank you very much for your help and for sharing this great resource!

[pascalnotin]

Hi @YinghuiChen-sky -- apologies for the delayed response, and thank you for flagging! For the the clinical benchmarks, we first compute gene-specific AUCs, and then take the arithmetic average of these AUC values across all genes to obtain the final aggregate performance. But we will upload a script to clarify that point.
Best,
Pascal