README.md

Learning Invariant Molecular Representation in Latent Discrete Space

This repository is the official implementation of our paper:

Learning Invariant Molecular Representation in Latent Discrete Space

Xiang Zhuang, Qiang Zhang*, Keyan Ding, Yatao Bian, Xiao Wang, Jingsong Lv, Hongyang Chen, Huajun Chen* (* denotes correspondence)

Advances in Neural Information Processing Systems (NeurIPS) 2023

Environment

To run the code successfully, the following dependencies need to be installed:

Python                     3.8      
torch                      1.10.1
torch_geometric            2.0.4
torch_scatter              2.0.9
torch_cluster              1.6.0
torch_sparse               0.6.13
torch_spline_conv          1.2.1
rdkit_pypi                 2022.9.5
vector_quantize_pytorch    1.0.7
ogb                        1.3.6

This repo is also depended on GOOD and DrugOOD, please follow the installation methods provided for each package:

• GOOD (Version 1.1.1)
  • Repository: https://github.com/divelab/GOOD/
  • Installation: Please follow the instructions provided in the repository to install.
• DrugOOD (Version 0.0.1)
  • Repository: https://github.com/tencent-ailab/DrugOOD
  • Installation: Please follow the instructions provided in the repository to install.

Data

The data used in the experiments can be downloaded from the following sources:

1. GOOD
   • GOODPCBA
   • GOODHIV
   • GOODZINC
   • Extract the downloaded files and save the contents in the data directory.
2. DrugOOD
   • download from link.
   • Extract the downloaded file and save the contents in the drugood-data-chembl30 directory.

An example of the folder hierarchy after adding the data files:

├── data
│   ├── GOODHIV
│   ├── GOODPCBA
│   ├── GOODZINC
├── drugood-data-chembl30
│   ├── lbap_core_ec50_assay.json
│   └── ...
├── models
│   ├── model.py
│   └── ...
├── run.py
└── README.md

Running Script

Training

python run.py --dataset GOODZINC --domain scaffold --shift concept --num_e 4000 --bs 256 --gamma 0.5 --inv_w 0.01 --reg_w 0.5 --gpu 0 --exp_name ZINC --exp_id scaffold-concept

Running parameters and descriptions are as follows:

Parameter	Description	Choices
dataset	name of dataset	GOODHIV, GOODZINC, GOODPCBA, ic50_assay, ic50_scaffold, ic50_size, ec50_assay, ec50_scaffold, ec50_size.
domain	environment-splitting strategy	scaffold, size. Only need to be specified for datasets in GOOD.
shift	type of distribution shift	covariate, concept. Only need to be specified for datasets in GOOD.
num_e	code book size	-
bs	batch size	-
gamma	threshold $\gamma$	-
inv_w	$\lambda_1$	-
reg_w	$\lambda_2$	-
gpu	which GPU to use	-
exp_name	experiment name	-
exp_id	experiment ID	-

Evaluation

We provide the hyperparameters for the training of each dataset in the Appendix, and provide the corresponding checkpoints in the release page.

python eval.py --dataset GOODZINC --domain scaffold --shift concept --load_path checkpoint/GOODZINC-scaffold-concept.pkl

The load_path parameter specifies the path to load the checkpoint.

Citation

If you use or extend our work, please cite the paper as follows:

@InProceedings{zhuang2023learning,
  title={Learning Invariant Molecular Representation in Latent Discrete Space},
  author={Xiang Zhuang and Qiang Zhang and Keyan Ding and Yatao Bian and Xiao Wang and Jingsong Lv and Hongyang Chen and Huajun Chen},
  booktile={Advances in Neural Information Processing Systems},
  year={2023}
}