Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Different result when reproducing "Downstream Tasks: Text to Protein Retrieval" #10

Open
Litlelian opened this issue Dec 7, 2023 · 0 comments

Comments

@Litlelian
Copy link

Litlelian commented Dec 7, 2023

Excuse me. I'm trying to reproduce "Downstream Tasks: Text to Protein Retrieval" result you show in paper.
However, I met the problem like the issue:
https://github.com/DeepGraphLearning/ProtST/issues/5
And I roll back TorchDrug version to 0.2.0, but I encounter another problem when loading pretrained esm model.
I found a problem in "pretrained.py" in esm code. In load_model_and_alphabet_core function, it requires model_name and model_data. However, in two different version of TorchDrug (0.2.0 & 0.2.1), these two arguments are different, and only 0.2.1 version can pass this part of code. So I just add two lines:
model_data = model_name
model_name = 'esm1b_t33_650M_UR50S.pt'

And the code (torchdrug==0.2.0) can run! : )
But I found results in get in 't2p_go_mf.txt' seems to be wrong after I check the protein. : (

Could you please check this issue?

Best wishes.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant