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README.md

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This is the official codebase of the paper
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[Protein Representation Learning by Geometric Structure Pretraining](https://arxiv.org/abs/2203.06125)
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**Protein Representation Learning by Geometric Structure Pretraining**, *ICLR'2023*
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[[ArXiv](https://arxiv.org/abs/2203.06125)] [[OpenReview](https://openreview.net/forum?id=to3qCB3tOh9)]
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[Zuobai Zhang](https://oxer11.github.io/), [Minghao Xu](https://chrisallenming.github.io/), [Arian Jamasb](https://jamasb.io/), [Vijil Chenthamarakshan](https://researcher.watson.ibm.com/researcher/view.php?person=us-ecvijil), [Aurelie Lozano](https://researcher.watson.ibm.com/researcher/view.php?person=us-aclozano), [Payel Das](https://researcher.watson.ibm.com/researcher/view.php?person=us-daspa), [Jian Tang](https://jian-tang.com/)
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## News
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- [2023/02/01] Our paper has been accepted by ICLR'2023! We have released the pretrained model weights [here](https://zenodo.org/record/7593637).
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- [2022/11/20] We add the scheduler in the `downstream.py` and provide the config file for training GearNet-Edge with single GPU on EC. Now you can reproduce the results in the paper.
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## Overview
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This codebase is based on PyTorch and [TorchDrug] ([TorchProtein](https://torchprotein.ai)).
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It supports training and inference with multiple GPUs.
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The documentation and implementation of our methods can be found in the [docs](https://torchdrug.ai/docs/) of TorchDrug.
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To adapt our model in your setting, you can follow the step-by-step [tuorials](https://torchprotein.ai/tutorials) in TorchProtein.
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To adapt our model in your setting, you can follow the step-by-step [tutorials](https://torchprotein.ai/tutorials) in TorchProtein.
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[TorchDrug]: https://github.com/DeepGraphLearning/torchdrug
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python script/downstream.py -c config/downstream/EC/gearnet_edge.yaml --gpus [0] --ckpt <path_to_your_model>
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```
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You can find the pretrained model weights [here](https://zenodo.org/record/7593637), including those pretrained with [Multiview Contrast](https://zenodo.org/record/7593637/files/mc_gearnet_edge.pth), [Residue Type Prediction](https://zenodo.org/record/7593637/files/attr_gearnet_edge.pth), [Distance Prediction](https://zenodo.org/record/7593637/files/distance_gearnet_edge.pth), [Angle Prediction](https://zenodo.org/record/7593637/files/angle_gearnet_edge.pth) and [Dihedral Prediction](https://zenodo.org/record/7593637/files/dihedral_gearnet_edge.pth).
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## Results
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Here are the results of GearNet w/ and w/o pretraining on standard benchmark datasets. **All the results are obtained with 4 A100 GPUs (40GB). Note results may be slightly different if the model is trained with 1 GPU and/or a smaller batch size. For EC and GO, the provided config files are for 4 GPUs with batch size 2 on each one. If you run the model on 1 GPU, you should set the batch size as 8.**
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More detailed results are listed in the paper.

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