GCLmf

GCLmf: A novel molecular graph contrastive learning framework based on hard negatives and application in toxicity prediction

Requirements

• python 3.7

install requirements

pip install torch==1.7.1+cu101 torchvision==0.8.2+cu101 -f https://download.pytorch.org/whl/torch_stable.html  
pip install torch-geometric==1.6.3 torch-sparse==0.6.9 torch-scatter==2.0.6 -f https://pytorch-geometric.com/whl/torch-1.7.0+cu101.html
pip install PyYAML
conda install -c conda-forge rdkit=2020.09.1.0

Dataset

pre-training data

You can download the pre-training data and benchmarks used in the paper here and extract the file under ./github/data folder.

fine-tuning data

All the databases for fine-tuning are saved in ./github/data

Pre-training

To train the GCLmf, where the configurations and detailed explaination for each variable can be found in config_pretrain.yaml
python GCLmf_pre.py

Fine-tuning

molecular property benchmarks

python GCLmf_ft_property.py

toxicity data sets

python GCLmf_ft_tox.py