Request for the pretrained model and instructions on getting own proteins' embeddings. about gearnet HOT 2 CLOSED

Hi! Thanks for raising these questions!

1.We have a plan for releasing model checkpoint, but it still takes some time for preparation. If it is urgent for you, you can send an email to me ([email protected]) and I'll personally share a (good but not ready) checkpoint with you.
2&3.To define a customized dataset, you can follow the tutorials in TorchDrug and TorchProtein. The Customize Models & Tasks is about how to define a customized module in TorchDrug and Tutorial 3-Structure-based Protein Property Prediction is about how to define a dataset and run the GearNet model on it.

For your case, you can first define your customized dataset following the code of datasets.EnzymeCommission, which will show you how to generate .pkl.gz file with the API in TorchProtein. Then, you can load the task and model as the script in repo and then get the final embedding by calling task.model() (refer to tasks.MultipleBinaryClassification).

from gearnet.

Thank you Zuobai!
I have sent you a request email~

from gearnet.