deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

Science Score: 36.0%

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
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
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Academic publication links
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Committers with academic emails
59 of 257 committers (23.0%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (14.7%) to scientific vocabulary

Keywords

biology deep-learning drug-discovery hacktoberfest materials-science quantum-chemistry

Keywords from Contributors

tensors transformer cryptocurrency hyperparameter-optimization speech-recognition closember autograd cryptography audio bioinformatics

Last synced: 6 months ago · JSON representation

Repository

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

Basic Info

Host: GitHub
Owner: deepchem
License: mit
Language: Python
Default Branch: master
Homepage: https://deepchem.io/
Size: 568 MB

Statistics

Stars: 6,176
Watchers: 144
Forks: 1,917
Open Issues: 816
Releases: 20

Topics

biology deep-learning drug-discovery hacktoberfest materials-science quantum-chemistry

Created over 10 years ago · Last pushed 6 months ago

Metadata Files

Readme Contributing License Code of conduct

DeepChem

DeepChem aims to provide a high quality open-source toolchain that democratizes the use of deep-learning in drug discovery, materials science, quantum chemistry, and biology.

Requirements

DeepChem currently supports Python 3.7 through 3.10 and requires these packages on any condition.

Soft Requirements

DeepChem has a number of "soft" requirements. If you face some errors like ImportError: This class requires XXXX, you may need to install some packages.

Please check the document about soft requirements.

Installation

Stable version

DeepChem stable version can be installed using pip or conda as

bash pip install deepchem or conda install -c conda-forge deepchem

Deepchem provides support for tensorflow, pytorch, jax and each require a individual pip Installation.

For using models with tensorflow dependencies, you install using

bash pip install deepchem[tensorflow] For using models with torch dependencies, you install using

bash pip install deepchem[torch] For using models with jax dependencies, you install using

bash pip install deepchem[jax] If GPU support is required, then make sure CUDA is installed and then install the desired deep learning framework using the links below before installing deepchem

tensorflow - just cuda installed
pytorch - https://pytorch.org/get-started/locally/#start-locally
jax - https://github.com/google/jax#pip-installation-gpu-cuda

In zsh square brackets are used for globbing/pattern matching. This means you need to escape the square brackets in the above installation. You can do so by including the dependencies in quotes like pip install --pre 'deepchem[jax]'

Nightly build version

The nightly version is built by the HEAD of DeepChem. It can be installed using

bash pip install --pre deepchem

Docker

If you want to install deepchem using a docker, you can pull two kinds of images.
DockerHub : https://hub.docker.com/repository/docker/deepchemio/deepchem

deepchemio/deepchem:x.x.x
- Image built by using a conda (x.x.x is a version of deepchem)
- The x.x.x image is built when we push x.x.x. tag
- Dockerfile is put in docker/tag directory
deepchemio/deepchem:latest
- Image built from source codes
- The latest image is built every time we commit to the master branch
- Dockerfile is put in docker/nightly directory

You pull the image like this.

bash docker pull deepchemio/deepchem:2.4.0

If you want to know docker usages with deepchem in more detail, please check the document.

From source

If you try install all soft dependencies at once or contribute to deepchem, we recommend you should install deepchem from source.

Please check this introduction.

Getting Started

The DeepChem project maintains an extensive collection of tutorials. All tutorials are designed to be run on Google colab (or locally if you prefer). Tutorials are arranged in a suggested learning sequence which will take you from beginner to proficient at molecular machine learning and computational biology more broadly.

After working through the tutorials, you can also go through other examples. To apply deepchem to a new problem, try starting from one of the existing examples or tutorials and modifying it step by step to work with your new use-case. If you have questions or comments you can raise them on our gitter.

Supported Integrations

Weights & Biases: Track your DeepChem model's training and evaluation metrics.

Discord

The DeepChem Discord hosts a number of scientists, developers, and enthusiasts interested in deep learning for the life sciences. Probably the easiest place to ask simple questions or float requests for new features.

About Us

DeepChem is managed by a team of open source contributors. Anyone is free to join and contribute!

Citing DeepChem

If you have used DeepChem in the course of your research, we ask that you cite the "Deep Learning for the Life Sciences" book by the DeepChem core team.

To cite this book, please use this bibtex entry:

@book{Ramsundar-et-al-2019, title={Deep Learning for the Life Sciences}, author={Bharath Ramsundar and Peter Eastman and Patrick Walters and Vijay Pande and Karl Leswing and Zhenqin Wu}, publisher={O'Reilly Media}, note={\url{https://www.amazon.com/Deep-Learning-Life-Sciences-Microscopy/dp/1492039837}}, year={2019} }

Owner

Name: deepchem
Login: deepchem
Kind: organization

Repositories: 19
Profile: https://github.com/deepchem

GitHub Events

Total

Issues event: 56
Watch event: 695
Issue comment event: 317
Push event: 75
Pull request review comment event: 476
Pull request event: 411
Pull request review event: 545
Fork event: 248

Last Year

Issues event: 56
Watch event: 695
Issue comment event: 317
Push event: 75
Pull request review comment event: 476
Pull request event: 411
Pull request review event: 545
Fork event: 248

Committers

Last synced: 10 months ago

All Time

Total Commits: 8,232
Total Committers: 257
Avg Commits per committer: 32.031
Development Distribution Score (DDS): 0.903

Past Year

Commits: 141
Committers: 30
Avg Commits per committer: 4.7
Development Distribution Score (DDS): 0.872

Top Committers

Name	Email	Commits
Bharath Ramsundar	b**r@g**m	800
peastman	p**n@s**u	515
nd-02110114	n**8@g**m	496
Tony Davis	a**9@g**m	482
leswing	l**g@g**m	395
GreatRSingh	r**1@g**m	379
Arun	a**9@g**m	337
miaecle	z**u@s**u	320
Bharath Ramsundar	b**h@B**m	318
Shreyas Vinaya	v**s@g**m	292
leswing	K****l	222
Bharath Ramsundar	r**h@s**u	180
Atreya Majumdar	a**j@g**m	154
VIGNESHinZONE	m**n@p**n	153
seyonechithrananda	s**c@g**m	151
Suzukazole	6****e	131
aaronrockmenezes	8****s	112
joegomes	j**s@b**u	112
Advika Vidhyadhiraja	a**s@g**m	110
Vignesh	v**h@s**h	110
Nathan Frey	n**3@g**m	108
shaipranesh2	f**1@p**n	100
alat-rights		92
Riya Singh	r**9@g**m	84
JoseAntonioSiguenza	8****a	82
Anshuman Mishra	s**1@g**m	81
mufeili	m**6@g**m	73
Aneesh Pappu	a**7@g**m	64
ARY2260	a**n@g**m	63
Bharath Ramsundar	b**h@B**l	60
and 227 more...

Committer Domains (Top 20 + Academic)

stanford.edu: 7 sherlock-ln02.stanford.edu: 5 qq.com: 4 berkeley.edu: 3 163.com: 2 pilani.bits-pilani.ac.in: 2 sherlock-ln01.stanford.edu: 2 wisc.edu: 1 reverielabs.com: 1 snu.edu.in: 1 uw.edu: 1 exscientia.co.uk: 1 trenthauck.com: 1 greenkeytech.com: 1 sh-ln01.stanford.edu: 1 nitk.edu.in: 1 ip-172-31-30-148.us-west-2.compute.internal: 1 choderalab.org: 1 bharaths-mbp.townisp.com: 1 ip-172-31-55-121.ec2.internal: 1 soton.ac.uk: 1 umail.leidenuniv.nl: 1 drexel.edu: 1 sherlock-ln04.stanford.edu: 1 .ph.iitr.ac.in: 1 sherlock-ln03.stanford.edu: 1 uniandes.edu.co: 1 student.ethz.ch: 1 ph.iitr.ac.in: 1 dhcp-vl2071-4475.eduroam.cornell.edu: 1 dhcp-vl2041-3461.eduroam.cornell.edu: 1 desktop-duln7k0.stanford.edu: 1 llnl.gov: 1 itbhu.ac.in: 1 iiitd.ac.in: 1 cs.stanford.edu: 1 vsp-compute-38.stanford.edu: 1 fu-berlin.de: 1 sh-ln02.stanford.edu: 1 liberty.stanford.edu: 1 vsp-compute-01.stanford.edu: 1 imperial.ac.uk: 1 titan.stanford.edu: 1 alumni.cmu.edu: 1 ucsc.edu: 1 alumni.carnegiemellon.edu: 1 odu.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 259
Total pull requests: 1,434
Average time to close issues: 10 months
Average time to close pull requests: 24 days
Total issue authors: 161
Total pull request authors: 152
Average comments per issue: 2.22
Average comments per pull request: 0.68
Merged pull requests: 600
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 58
Pull requests: 525
Average time to close issues: 16 days
Average time to close pull requests: 16 days
Issue authors: 45
Pull request authors: 86
Average comments per issue: 0.45
Average comments per pull request: 0.5
Merged pull requests: 137
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

arunppsg (37)
rbharath (25)
gehlhaarPfizer (6)
SoodabehGhaffari (5)
syedzayyan (4)
UNCG-JSNN (4)
shreyasvinaya (4)
ShigrafS (4)
oleeviyababu (3)
Bruce20040502 (3)
yxnyu (3)
Running-z (2)
andresilvapimentel (2)
tonydavis629 (2)
ryansamuel13 (2)

Pull Request Authors

GreatRSingh (210)
shreyasvinaya (98)
KitVB (94)
arunppsg (88)
JoseAntonioSiguenza (59)
TRY-ER (49)
riya-singh28 (42)
Shiva-sankaran (41)
aaronrockmenezes (37)
spellsharp (36)
manas1245agrawal (35)
P-Kelley (34)
shaipranesh2 (31)
NimishaDey (30)
bhuvanmdev (28)

Top Labels

Issue Labels

Contribution Welcome (33) Good First Contribution (26) Good Intermediate Contribution (14) bug (6) help wanted (6) enhancement (4) Deep Learning Project (4) discussion (3) docs (3) maintenance (2) needs-investigation (1) refactor (1) Scientific Knowledge Required (1) build: docker (1) tutorials (1)

Pull Request Labels

Packages

Total packages: 3
Total downloads:
- pypi 54,401 last-month
Total docker downloads: 27

Total dependent packages: 8
(may contain duplicates)
Total dependent repositories: 60
(may contain duplicates)
Total versions: 1,043
Total maintainers: 4

pypi.org: deepchem

Deep learning models for drug discovery, quantum chemistry, and the life sciences.

Homepage: https://github.com/deepchem/deepchem
Documentation: https://deepchem.readthedocs.io/en/latest/
License: MIT
Latest release: 2.8.0
published almost 2 years ago

Versions: 1,005
Dependent Packages: 8
Dependent Repositories: 55
Downloads: 54,357 Last month
Docker Downloads: 27

Rankings

Stargazers count: 1.0%

Forks count: 1.1%

Dependent packages count: 1.4%

Average: 1.7%

Dependent repos count: 2.0%

Downloads: 2.1%

Docker downloads count: 2.4%

Maintainers (4)

lilleswing peastman rbharath atreyamaj

Last synced: about 1 year ago

pypi.org: deepchem-nightly

Deep learning models for drug discovery, quantum chemistry, and the life sciences.

Homepage: https://github.com/deepchem/deepchem
Documentation: https://deepchem.readthedocs.io/en/latest/
License: MIT
Latest release: 2.3.0
published over 5 years ago

Versions: 33
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 44 Last month

Rankings

Stargazers count: 1.0%

Forks count: 1.1%

Dependent packages count: 10.1%

Average: 10.2%

Downloads: 17.1%

Dependent repos count: 21.5%

Maintainers (1)

rbharath

Last synced: 6 months ago

conda-forge.org: deepchem

Homepage: https://github.com/deepchem/deepchem
License: MIT
Latest release: 2.6.1
published about 4 years ago

Versions: 5
Dependent Packages: 0
Dependent Repositories: 4

Rankings

Forks count: 3.9%

Stargazers count: 5.5%

Dependent repos count: 16.2%

Average: 19.3%

Dependent packages count: 51.6%

Last synced: 6 months ago

Dependencies

.github/workflows/build.yml actions

actions/cache v3 composite
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conda-incubator/setup-miniconda v2 composite

.github/workflows/docs.yml actions

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.github/workflows/dqc_install.yml actions

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.github/workflows/formatting.yml actions

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.github/workflows/jax_setup.yml actions

actions/cache v3 composite
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conda-incubator/setup-miniconda v2 composite

.github/workflows/mini_build.yml actions

actions/cache v3 composite
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docker/build-push-action v2 composite
docker/login-action v1 composite
docker/setup-buildx-action master composite
mamba-org/setup-micromamba main composite

.github/workflows/release.yml actions

actions/cache v3 composite
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actions/setup-python v3 composite
docker/build-push-action v2 composite
docker/login-action v1 composite

.github/workflows/tensorflow_setup.yml actions

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.github/workflows/test.yml actions

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.github/workflows/torch_setup.yml actions

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.github/workflows/hf_setup.yml actions

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conda-incubator/setup-miniconda v3 composite

.github/workflows/website_build_dispatch.yml actions

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docker/deepchem/Dockerfile docker

ubuntu 22.04 build

docker/deepchem-tf-cpu/Dockerfile docker

ubuntu 22.04 build

docker/deepchem-tf-gpu/Dockerfile docker

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docker/deepchem-torch-cpu/Dockerfile docker

ubuntu 22.04 build

docker/deepchem-torch-gpu/Dockerfile docker

nvidia/cuda 11.8.0-cudnn8-devel-ubuntu22.04 build

docker/nightly/Dockerfile docker

nvidia/cuda 11.8.0-cudnn8-devel-ubuntu22.04 build

docker/tag/Dockerfile docker

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docs/requirements.txt pypi

PyYAML *
dgl *
dm-haiku ==0.0.13
jax ==0.4.30
lightning *
optax *
pandas *
pydantic *
pysam *
rdkit *
scikit-learn *
sphinx ==7.2.6
sphinx-copybutton *
sphinx_rtd_theme >=1.0
sympy *
tensorflow ==2.15.0
torch_geometric *
transformers >=4.34.1
yamlloader *

setup.py pypi

joblib *
numpy <2
pandas *
rdkit *
scikit-learn *
scipy >=1.10.1
sympy *

deepchem

Science Score: 36.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

DeepChem

Table of contents:

Requirements

Soft Requirements

Installation

Stable version

Nightly build version

Docker

From source

Getting Started

Supported Integrations

Discord

About Us

Citing DeepChem

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: deepchem

Rankings

Maintainers (4)

pypi.org: deepchem-nightly

Rankings

Maintainers (1)

conda-forge.org: deepchem

Rankings

Dependencies