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 --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}
}