Dependencies & Dataset

Please refer to https://github.com/snap-stanford/pretrain-gnns#installation for environment setup and https://github.com/snap-stanford/pretrain-gnns#dataset-download to download dataset.

Training & Evaluation

Step 1: Pre-training:

cd ./bio
python pretrain_simgrace.py --eta 0.1
cd ./chem
python pretrain_simgrace.py --eta 0.1

Step 2: Finetuning:

cd ./bio
./finetune.sh
cd ./chem
./run.sh

Results will be recorded in result.log.

Acknowledgements

• https://github.com/snap-stanford/pretrain-gnns.
• https://github.com/Shen-Lab/GraphCL/tree/master/transferLearning_MoleculeNet_PPI.