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Mole-BERT: Rethinking Pre-training Graph Neural Networks for Molecules (ICLR 2023)

This is a Pytorch implementation of the Mole-BERT paper:

Installation

We used the following Python packages for core development. We tested on Python 3.7.

pytorch                   1.0.1
torch-cluster             1.2.4              
torch-geometric           1.0.3
torch-scatter             1.1.2 
torch-sparse              0.2.4
torch-spline-conv         1.0.6
rdkit                     2019.03.1.0
tqdm                      4.31.1
tensorboardx              1.6

Dataset download

All the necessary data files can be downloaded from the following links.

For the chemistry dataset, download from chem data (2.5GB), unzip it, and put it under dataset/.

Tokenizer Training

python vqvae.py --output_model_file OUTPUT_MODEL_PATH

This will save the resulting tokenizer to OUTPUT_MODEL_PATH.

Pre-training and fine-tuning

1. Self-supervised pre-training

python pretrain.py --output_model_file OUTPUT_MODEL_PATH

This will save the resulting pre-trained model to OUTPUT_MODEL_PATH.

2. Fine-tuning

python finetune.py --model_file INPUT_MODEL_PATH --dataset DOWNSTREAM_DATASET --filename OUTPUT_FILE_PATH

This will finetune pre-trained model specified in INPUT_MODEL_PATH using dataset DOWNSTREAM_DATASET. The result of fine-tuning will be saved to OUTPUT_FILE_PATH.

Reproducing results in the paper

Our results in the paper can be reproduced using a random seed ranging from 0 to 9 with scaffold splitting.

Useful resources for Chemical Pre-trained Models

• The first comprehensive survey on this topic: A Systematic Survey of Chemical Pre-trained Models (IJCAI 2023)
• A curated list of must-read papers, open-source pretrained models and pretraining datasets.

Acknowledgement

[1] Strategies for Pre-training Graph Neural Networks (Hu et al., ICLR 2020)

Citation

@inproceedings{
xia2023molebert,
title={Mole-{BERT}: Rethinking Pre-training Graph Neural Networks for Molecules},
author={Jun Xia and Chengshuai Zhao and Bozhen Hu and Zhangyang Gao and Cheng Tan and Yue Liu and Siyuan Li and Stan Z. Li},
booktitle={The Eleventh International Conference on Learning Representations },
year={2023},
url={https://openreview.net/forum?id=jevY-DtiZTR}
}