Zuobai Zhang

Hi, thanks for your interest in our work! You can follow [this tutorial](https://torchprotein.ai/tutorial_3), which describes how to use TorchDrug to construct data.Protein object and pass it into GearNet. Also, you...

Hi! Thanks for your interest in our work. The config `atom_feature: null` and `bond_feature: null` mean that we want to set `atom_feature=None` and `bond_feature=None` so as to avoid the contruction...

This is weird. Have you faced the same issue when pre-training with GearNet-Edge instead of ESM-GearNet? Could you share the full log file with me? I'm sorry that I haven't...

Hi! I'm sorry that I am not familiar with elastic and don't know the reason for your problem. Maybe you could try to use the typical DDP in torch instead...

Hi, thanks for raising the question. The atom view is set to changing the node features from residue features to atom features. You can find the implementation here: https://github.com/DeepGraphLearning/torchdrug/blob/6066fbd82360abb5f270cba1eca560af01b8cc90/torchdrug/data/protein.py#L113. I...

Hi! To define your custom datasets, you can refer to [this page](https://torchdrug.ai/docs/_modules/torchdrug/datasets/enzyme_commission.html#EnzymeCommission). Basicly, you need to define how to load your dataset with the `data.ProteinDataset. load_pdbs` function and save it...

Hi, I'm now working on revising the ESM-GearNet paper and reorgnizing the repo. It should be released in a few weeks.

Hi, sorry for the late update. You can find the latest update of our paper and code here: https://x.com/Oxer22/status/1717167378067316854?s=20 https://arxiv.org/abs/2303.06275 https://github.com/DeepGraphLearning/ESM-GearNet

Hi! The `NodePropertyPrediction` task is orginally defined for sequence-based models. To adapt it to structure-based models, maybe you just need to add a `graph_construction_model` part following what we do in...

Sorry for the late response. In `data.Protein`, we usually use `node` and `atom` interchangably, while `residue` corresponds to the real residue in proteins. You can use `data.Protein.atom2residue` to learn which...