What are the versions of PyTorch?

[YeojinKim220]

Hi, Thank you for this work.
I have two questions about the code.

I am wondering what the version of PyTorch for this project is.
I could not find information about the version on the environment.yml file.

Could you explain what "prot_[data_type]_inter_exist.npy" file is for?
prot_train_inter_exist = np.load(data_processed_dir+'prot_train_inter_exist.npy')
It seems related to calculating loss for interaction but I could not find information in the paper.

Thanks in advance.

[yyou1996]

Hi @YeojinKim220,

1. We did not have special requirements for the PyTorch version. Generally, I believe >=1.6.0 would work.
2. inter_exist is the normalized factor for contacts, since in the repo the supervision objective of the contact prediction is via regression, we follow https://pubs.acs.org/doi/full/10.1021/acs.jcim.0c00866 for such normalization which helps performance (

   CPAC/cross_modality_keras/nets.py

   Line 380 in 243a899

   real = tf.einsum('b,bij->bij',real_exist,real)

   ).

[ZzzzzzzSkyward]

Actually newer version of Pytorch will fail because of an inplace operation x+=x0.