https://github.com/awslabs/dgl-lifesci
Python package for graph neural networks in chemistry and biology
Science Score: 10.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
3 of 22 committers (13.6%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.2%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
Python package for graph neural networks in chemistry and biology
Basic Info
Statistics
- Stars: 770
- Watchers: 15
- Forks: 160
- Open Issues: 32
- Releases: 8
Topics
Metadata Files
README.md
DGL-LifeSci
Documentation | Discussion Forum
We also have a slack channel for real-time discussion. If you want to join the channel, contact mufeili1996@gmail.com.
Table of Contents
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+.
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
```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.
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}
}
Owner
- Name: Amazon Web Services - Labs
- Login: awslabs
- Kind: organization
- Location: Seattle, WA
- Website: http://amazon.com/aws/
- Repositories: 914
- Profile: https://github.com/awslabs
AWS Labs
GitHub Events
Total
- Issues event: 1
- Watch event: 45
- Fork event: 13
Last Year
- Issues event: 1
- Watch event: 45
- Fork event: 13
Committers
Last synced: 12 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Mufei Li | m****6@g****m | 199 |
| Yangkang Zhang | 4****8 | 4 |
| autodataming | 1****4@q****m | 3 |
| Martin Volk | m****k@g****t | 3 |
| Krishna Sirumalla | s****s@h****u | 2 |
| Vignesh Venkataraman | m****n@p****n | 2 |
| Andrew Stolman | a****n@k****m | 1 |
| Amazon GitHub Automation | 5****o | 1 |
| Eric O. Korman | e****n@g****m | 1 |
| In-Ho Yi | c****h@g****m | 1 |
| Jinjing Zhou | V****n | 1 |
| Joe | j****e@p****p | 1 |
| JoshuaMeyers | j****s@r****m | 1 |
| Marcos Leal | m****4@y****r | 1 |
| Pavol Drotar | p****1@c****k | 1 |
| Philipp A | f****p@w****e | 1 |
| Raymond Gasper | 1****r | 1 |
| Sooheon Kim | s****n@f****i | 1 |
| Wenxuan Fan | 4****0 | 1 |
| YueZhong | 3****o | 1 |
| cyhFlight | 3****t | 1 |
| xnouhz | x****z@1****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 62
- Total pull requests: 46
- Average time to close issues: about 1 month
- Average time to close pull requests: about 1 month
- Total issue authors: 50
- Total pull request authors: 15
- Average comments per issue: 3.19
- Average comments per pull request: 1.0
- Merged pull requests: 40
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 2
- Pull request authors: 0
- Average comments per issue: 1.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- andt88 (3)
- ph-mehdi (3)
- mar-volk (3)
- nbrosse (3)
- kangqiyue (2)
- VIGNESHinZONE (2)
- dywlkji (2)
- maryamag85 (2)
- lvkd84 (1)
- rajarshiche (1)
- ndickson-nvidia (1)
- amblee0306 (1)
- GattiMh (1)
- kexinhuang12345 (1)
- jadolfbr (1)
Pull Request Authors
- mufeili (26)
- mar-volk (3)
- astolman (2)
- chajath (2)
- marcossilva (2)
- VIGNESHinZONE (2)
- xnuohz (1)
- ekorman (1)
- flying-sheep (1)
- wenx00 (1)
- yxgu2353 (1)
- rgasper (1)
- jacobumland (1)
- cyhFlight (1)
- xuzijian629 (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 3
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Total downloads:
- pypi 13,460 last-month
- Total docker downloads: 74
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Total dependent packages: 8
(may contain duplicates) -
Total dependent repositories: 36
(may contain duplicates) - Total versions: 26
- Total maintainers: 1
pypi.org: dgllife
DGL-based package for Life Science
- Homepage: https://github.com/awslabs/dgl-lifesci
- Documentation: https://dgllife.readthedocs.io/
- License: APACHE
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Latest release: 0.3.2
published about 3 years ago
Rankings
Maintainers (1)
proxy.golang.org: github.com/awslabs/dgl-lifesci
- Documentation: https://pkg.go.dev/github.com/awslabs/dgl-lifesci#section-documentation
- License: apache-2.0
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Latest release: v0.3.2
published about 3 years ago
Rankings
conda-forge.org: dgllife
- Homepage: https://github.com/awslabs/dgl-lifesci
- License: Apache-2.0
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Latest release: 0.3.0
published over 3 years ago
Rankings
Dependencies
- hyperopt *
- joblib *
- networkx >=2.1
- numpy >=1.14.0
- pandas *
- requests >=2.22.0
- scikit-learn >=0.22.2,
- scipy >=1.1.0
- tqdm *