iq-scm / dgl-lifesci

Python package for graph neural networks in chemistry and biology

DGL-LifeSci

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We also have a slack channel for real-time discussion. If you want to join the channel, contact [email protected].

Table of Contents

• Introduction
• Installation
  • Requirements
  • Pip installation for DGL-LifeSci
  • Installation from source
  • Verifying successful installation
• Command Line Interface
• Examples
• Cite

Introduction

Deep learning on graphs has been an arising trend in the past few years. There are a lot of graphs in life science such as molecular graphs and biological networks, making it an import area for applying deep learning on graphs. DGL-LifeSci is a DGL-based package for various applications in life science with graph neural networks.

We provide various functionalities, including but not limited to methods for graph construction, featurization, and evaluation, model architectures, training scripts and pre-trained models.

For a list of community contributors, see here.

Installation

Requirements

DGL-LifeSci should work on

• all Linux distributions no earlier than Ubuntu 16.04
• macOS X
• Windows 10

It is recommended to create a conda environment for DGL-LifeSci with for example

conda create -n dgllife python=3.6

DGL-LifeSci requires python 3.6+, DGL 0.7.0+ and PyTorch 1.5.0+.

Install pytorch

Install dgl

Additionally, we require RDKit. The easiest way to install RDKit is

pip install rdkit

If you need to work on the example of JTVAE, then you need RDKit 2018.09.3. We recommend installing it with

conda install -c rdkit rdkit==2018.09.3

For other installation recipes for RDKit, see the official documentation.

Pip installation for DGL-LifeSci

pip install dgllife

Installation from source

If you want to try experimental features, you can install from source as follows:

git clone https://github.com/awslabs/dgl-lifesci.git
cd dgl-lifesci/python
python setup.py install

Verifying successful installation

Once you have installed the package, you can verify the success of installation with

import dgllife

print(dgllife.__version__)
# 0.3.2

Command Line Interface

DGL-LifeSci provides command line interfaces that allow users to perform modeling without any background in programming and deep learning. You will need to first clone the github repo.

• Molecular Property Prediction
• Reaction Prediction

Examples

For a full list of work implemented in DGL-LifeSci, see here.

Cite

If you use DGL-LifeSci in a scientific publication, we would appreciate citations to the following paper:

@article{dgllife,
    title={DGL-LifeSci: An Open-Source Toolkit for Deep Learning on Graphs in Life Science},
    author={Mufei Li and Jinjing Zhou and Jiajing Hu and Wenxuan Fan and Yangkang Zhang and Yaxin Gu and George Karypis},
    year={2021},
    journal = {ACS Omega}
}