Holistic Molecular Representation Leraning via Multi-view Fragmentation (TMLR 2024)

Official Pytorch implementation of "Holistic Molecular Representation Learning via Multi-view Fragmentation" by Seojin Kim, Jaehyun Nam, Junsu Kim, Hankook Lee, Sungsoo Ahn, and Jinwoo Shin.

TL;DR: We propose a molecular contrastive learning framework that utilizies fragment-wise feature of molecules.

TODO: Video description will be uploaded soon.

1. Dataset Preparation

python GEOM_dataset_preparation.py --n_mol 50000 --data_foler ../datasets/path_to_dataset

2. Training

cd scripts_classification/
bash submit_pretraining_holimol_dihedral2.sh

Citation

@article{
kim2024holistic,
title={Holistic Molecular Representation Learning via Multi-view Fragmentation},
author={Seojin Kim and Jaehyun Nam and Junsu Kim and Hankook Lee and Sungsoo Ahn and Jinwoo Shin},
journal={Transactions on Machine Learning Research},
issn={2835-8856},
year={2024},
url={https://openreview.net/forum?id=ufDh55J1ML},
note={}
}