/MARS

MARS: Markov Molecular Sampling for Multi-objective Drug Discovery (ICLR 2021)

Primary LanguagePythonGNU General Public License v3.0GPL-3.0

MARS: Markov Molecular Sampling for Multi-objective Drug Discovery

Thanks for your interest! This is the code repository for our ICLR 2021 paper MARS: Markov Molecular Sampling for Multi-objective Drug Discovery.

Dependencies

The conda environment is exported as environment.yml. You can also manually install these packages:

conda install -c conda-forge rdkit
conda install tqdm tensorboard scikit-learn
conda install pytorch cudatoolkit=11.1 -c pytorch -c conda-forge
conda install -c dglteam dgl-cuda11.1

# for cpu only
conda install pytorch cpuonly -c pytorch
conda install -c dglteam dgl

Run

Note: Run the commands outside the MARS directory.

To extract molecular fragments from a database:

python -m MARS.datasets.prepro_vocab

To sample molecules:

python -m MARS.main --train --run_dir runs/RUN_DIR

Citation

@inproceedings{
    xie2021mars,
    title={{\{}MARS{\}}: Markov Molecular Sampling for Multi-objective Drug Discovery},
    author={Yutong Xie and Chence Shi and Hao Zhou and Yuwei Yang and Weinan Zhang and Yong Yu and Lei Li},
    booktitle={International Conference on Learning Representations},
    year={2021},
    url={https://openreview.net/forum?id=kHSu4ebxFXY}
}