A PyTorch implementation of "[Motif-aware Attribute Masking for Molecular Graph Pre-training]".

• pandas==1.5.2
• python==3.10.4
• rdkit==2022.9.3
• torch==1.13.1
• torch-cluster==1.6.0
• torch-geometric==2.2.0
• torch-scatter==2.1.0
• torch-sparse==0.6.16

To install all dependencies:

pip install -r requirements.txt

To download datasets

wget http://snap.stanford.edu/gnn-pretrain/data/chem_dataset.zip
unzip chem_dataset.zip

To pre-train:

python pretrain.py

To fine-tune and evaluate:

python finetune.py --dataset <dataset_name>