Training details of basic GearNet on Fold prediction task about gearnet HOT 7 CLOSED

Yes, I use a 3-layer MLP for prediction as defined here. You can find the implementation in torchdrug.tasks.PropertyPrediction.

from gearnet.

Hi, you're right. This is the config for running GearNet on Fold3D. In this config, we turn off the use_ieconv option to use a vanilla GearNet.

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Thanks! Did you finally use an additional linear layer to convert the graph representation as the output of the model into 1195 (num_classes) classes?

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I want to reproduce your work using python script/downstream.py -c config/downstream/Fold3D/gearnet.yaml --gpus [0], but it returns an error:

  File "script/downstream.py", line 17, in <module>
    from gearnet import dataset, model
  File "/lustre07/scratch/liusheng/GearNet/GearNet_test/GearNet/gearnet/dataset.py", line 17, in <module>
    class Fold3D(data.ProteinDataset):
AttributeError: module 'torchdrug.data' has no attribute 'ProteinDataset'

I believe I have torchdrug installed.

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Hi, could you provide the version of your torchdrug? For Fold3D, you need to install torchdrug from source.

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Get it. I used git clone to clone the torchdrug repo.

By the way, how did you train your GearNet_IEConv with hidden size [512, 512, 512, 512, 512, 512] as described in your config? I always encountered the "cuda out of memory error".

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I use 40GB A100 for training. If you don't have large enough gpu memory, maybe consider a smaller batch size or smaller mdoel.

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