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OpenBioML / protein-lm-scaling

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Add contact predictions to evaluation framework #19

Closed pascalnotin closed 12 months ago

csjackson0 commented 1 year ago
  1. Create new "contact_prediction.ipynb" that modifies BERT_esm1b.ipynb to use APT model outputs for contact prediction.
  2. Create "utils.py" file and add functions from https://github.com/sokrypton/algosb_2021/blob/main/utils.py and esm.
  3. Add modified "contact_prediction.ipynb" and "utils.py" under evaluation/scripts dir.
csjackson0 commented 1 year ago

/take

Muedi commented 1 year ago

Hi I just wanted to add, that at the moment the eval script just uses esm-fair's pip install, so you could also rely on that and there would be no need for esm functions in a utils.py script, except you plan changes of course :)

pascalnotin commented 12 months ago

Closing this issue as it was addressed by PR#54. Thanks again @csjackson0 !