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https://github.com/awslabs/dgl-lifesci
Python package for graph neural networks in chemistry and biology
https://github.com/awslabs/dgl-lifesci
bioinformatics cheminformatics deep-learning dgl drug-discovery geometric-deep-learning graph-neural-networks molecule
Last synced: about 22 hours ago
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Python package for graph neural networks in chemistry and biology
- Host: GitHub
- URL: https://github.com/awslabs/dgl-lifesci
- Owner: awslabs
- License: apache-2.0
- Created: 2020-04-23T07:14:21.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2023-11-01T19:32:07.000Z (over 1 year ago)
- Last Synced: 2025-01-24T20:08:20.943Z (8 days ago)
- Topics: bioinformatics, cheminformatics, deep-learning, dgl, drug-discovery, geometric-deep-learning, graph-neural-networks, molecule
- Language: Python
- Homepage:
- Size: 963 KB
- Stars: 740
- Watchers: 17
- Forks: 155
- Open Issues: 31
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
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README
# DGL-LifeSci
[Documentation](https://lifesci.dgl.ai/index.html) | [Discussion Forum](https://discuss.dgl.ai)
We also have a **slack channel** for real-time discussion. If you want to join the channel, contact [email protected].
## Table of Contents
- [Introduction](#introduction)
- [Installation](#installation)
* [Requirements](#requirements)
* [Pip installation for DGL-LifeSci](#pip-installation-for-dgl-lifesci)
* [Installation from source](#installation-from-source)
* [Verifying successful installation](#verifying-successful-installation)
- [Command Line Interface](#command-line-interface)
- [Examples](#examples)
- [Cite](#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](CONTRIBUTORS.md).
## 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](https://pytorch.org/get-started/locally/)
[Install dgl](https://www.dgl.ai/pages/start.html)
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](https://www.rdkit.org/docs/Install.html).
### 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
```python
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](examples/property_prediction/csv_data_configuration/)
- [Reaction Prediction](examples/reaction_prediction/rexgen_direct/)
## Examples
For a full list of work implemented in DGL-LifeSci, see [here](examples/README.md).
## 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}
}
```