HOI

HOI: A Python toolbox for high-performance estimation of Higher-Order Interactions from multivariate data - Published in JOSS (2024)

https://github.com/brainets/hoi

Science Score: 100.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 4 DOI reference(s) in README and JOSS metadata
✓
Academic publication links
Links to: joss.theoj.org
✓
Committers with academic emails
2 of 10 committers (20.0%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
Published in Journal of Open Source Software

Keywords

higher-order-interactions hoi jax network python

Keywords from Contributors

brainhack brainhack-marseille brainweb cluster-based electrophysiological-data ffx functional-connectivity gaussian-copula group-level information-theory

Last synced: 4 months ago · JSON representation ·

Repository

Higher-Order Interactions

Basic Info

Host: GitHub
Owner: brainets
License: bsd-3-clause
Language: Python
Default Branch: main
Homepage: https://brainets.github.io/hoi/
Size: 35.1 MB

Statistics

Stars: 37
Watchers: 4
Forks: 13
Open Issues: 6
Releases: 6

Topics

higher-order-interactions hoi jax network python

Created almost 3 years ago · Last pushed about 1 year ago

Metadata Files

Readme License Citation

README.rst

.. -*- mode: rst -*-

|Black|_ |Codecov|_ |JOSS|_

.. |Black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
.. _Black: https://github.com/psf/black

.. |Codecov| image:: https://codecov.io/gh/brainets/hoi/graph/badge.svg?token=7PNM2VD994
.. _Codecov: https://codecov.io/gh/brainets/hoi

.. |JOSS| image:: https://joss.theoj.org/papers/10.21105/joss.07360/status.svg
.. _JOSS: https://doi.org/10.21105/joss.07360


.. image:: https://github.com/brainets/hoi/blob/main/docs/_static/hoi-logo.png
  :target: https://brainets.github.io/hoi/

Description
===========

HOI (Higher Order Interactions) is a Python package to go beyond pairwise interactions by quantifying the statistical dependencies between 2 or more units using information-theoretical metrics. The package is built on top of `Jax `_ allowing computations on CPU or GPU.

Installation
============

Dependencies
++++++++++++

HOI requires :

- Python (>= 3.8)
- numpy(>=1.22)
- scipy (>=1.9)
- jax
- pandas
- scikit-learn
- jax-tqdm
- tqdm

User installation
+++++++++++++++++

To install Jax on GPU or CPU-only, please refer to Jax's documentation : https://jax.readthedocs.io/en/latest/installation.html

If you already have a working installation of NumPy, SciPy and Jax,
the easiest way to install hoi is using ``pip``:

.. code-block:: shell

    pip install -U hoi

You can also install the latest version of the software directly from Github :

.. code-block:: shell

    pip install git+https://github.com/brainets/hoi.git


For developers
++++++++++++++

For developers, you can install it in develop mode with the following commands :

.. code-block:: shell

    git clone https://github.com/brainets/hoi.git
    cd hoi
    pip install -e .['full']

The full installation of HOI includes additional packages to test the software and build the documentation :

- pytest
- pytest-cov
- codecov
- xarray
- sphinx!=4.1.0
- sphinx-gallery
- pydata-sphinx-theme
- sphinxcontrib-bibtex
- numpydoc
- matplotlib
- flake8
- pep8-naming
- black


Help and Support
================

Documentation
+++++++++++++

- Link to the documentation: https://brainets.github.io/hoi/
- Overview of the mathematical background : https://brainets.github.io/hoi/theory.html
- List of implemented HOI metrics : https://brainets.github.io/hoi/api/modules.html
- Examples : https://brainets.github.io/hoi/auto_examples/index.html

Communication
+++++++++++++

For questions, please use the following link : https://github.com/brainets/hoi/discussions

Acknowledgments
===============

HOI was mainly developed during the Google Summer of Code 2023 (https://summerofcode.withgoogle.com/archive/2023/projects/z6hGpvLS)

Owner

Name: BraiNets
Login: brainets
Kind: organization

Website: https://brainets.github.io/
Repositories: 4
Profile: https://github.com/brainets

Brain Networks and Learning

JOSS Publication

HOI: A Python toolbox for high-performance estimation of Higher-Order Interactions from multivariate data

Published

November 12, 2024

DOI

10.21105/joss.07360

Volume 9, Issue 103, Page 7360

Authors

Matteo Neri

Institut de Neurosciences de la Timone, Aix Marseille Université, UMR 7289 CNRS, 13005, Marseille, France

Dishie Vinchhi
Veermata Jijabai Technological Institute, Mumbai

Christian Ferreyra
Institut de Neurosciences de la Timone, Aix Marseille Université, UMR 7289 CNRS, 13005, Marseille, France, Laboratoire d’Informatique et des Systèmes, Aix Marseille Université, UMR 7020 CNRS, Marseille, France

Thomas Robiglio
Department of Network and Data Science, Central European University, Vienna, Austria

Onur Ates
Institut de Neurosciences de la Timone, Aix Marseille Université, UMR 7289 CNRS, 13005, Marseille, France

Marlis Ontivero-Ortega

University of Ghent, Ghent, Belgium

Andrea Brovelli

Institut de Neurosciences de la Timone, Aix Marseille Université, UMR 7289 CNRS, 13005, Marseille, France

Daniele Marinazzo

University of Ghent, Ghent, Belgium

Etienne Combrisson

Institut de Neurosciences de la Timone, Aix Marseille Université, UMR 7289 CNRS, 13005, Marseille, France

Editor

Mehmet Hakan Satman

Citation (CITATION.cff)

cff-version: "1.2.0"
authors:
- family-names: Neri
  given-names: Matteo
  orcid: "https://orcid.org/0009-0007-0998-552X"
- family-names: Vinchhi
  given-names: Dishie
- family-names: Ferreyra
  given-names: Christian
- family-names: Robiglio
  given-names: Thomas
- family-names: Ates
  given-names: Onur
- family-names: Ontivero-Ortega
  given-names: Marlis
  orcid: "https://orcid.org/0000-0003-0084-8274"
- family-names: Brovelli
  given-names: Andrea
  orcid: "https://orcid.org/0000-0002-5342-1330"
- family-names: Marinazzo
  given-names: Daniele
  orcid: "https://orcid.org/0000-0002-9803-0122"
- family-names: Combrisson
  given-names: Etienne
  orcid: "https://orcid.org/0000-0002-7362-3247"
doi: 10.5281/zenodo.14046562
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Neri
    given-names: Matteo
    orcid: "https://orcid.org/0009-0007-0998-552X"
  - family-names: Vinchhi
    given-names: Dishie
  - family-names: Ferreyra
    given-names: Christian
  - family-names: Robiglio
    given-names: Thomas
  - family-names: Ates
    given-names: Onur
  - family-names: Ontivero-Ortega
    given-names: Marlis
    orcid: "https://orcid.org/0000-0003-0084-8274"
  - family-names: Brovelli
    given-names: Andrea
    orcid: "https://orcid.org/0000-0002-5342-1330"
  - family-names: Marinazzo
    given-names: Daniele
    orcid: "https://orcid.org/0000-0002-9803-0122"
  - family-names: Combrisson
    given-names: Etienne
    orcid: "https://orcid.org/0000-0002-7362-3247"
  date-published: 2024-11-12
  doi: 10.21105/joss.07360
  issn: 2475-9066
  issue: 103
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7360
  title: "HOI: A Python toolbox for high-performance estimation of
    Higher-Order Interactions from multivariate data"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07360"
  volume: 9
title: "HOI: A Python toolbox for high-performance estimation of
  Higher-Order Interactions from multivariate data"

GitHub Events

Total

Create event: 6
Release event: 3
Issues event: 21
Watch event: 14
Delete event: 3
Issue comment event: 39
Push event: 33
Pull request event: 23
Fork event: 6

Last Year

Create event: 6
Release event: 3
Issues event: 21
Watch event: 14
Delete event: 3
Issue comment event: 39
Push event: 33
Pull request event: 23
Fork event: 6

Committers

Last synced: 5 months ago

All Time

Total Commits: 406
Total Committers: 10
Avg Commits per committer: 40.6
Development Distribution Score (DDS): 0.441

Past Year

Commits: 52
Committers: 5
Avg Commits per committer: 10.4
Development Distribution Score (DDS): 0.423

Top Committers

Name	Email	Commits
EtienneCmb	e**n@g**m	227
Dishie2498	v**e@g**m	66
Mattehub	m**8@g**m	30
Matteo NERI	n**m@B**r	29
dependabot[bot]	4****]	13
chrisferreyra13	c**3@g**m	12
Pietro Monticone	3****e	10
Pierre Robiglio	8****o	10
Onur Ates	o**s@u**r	7
Andrea Brovelli	a**i@u**r	2

Committer Domains (Top 20 + Academic)

univ-amu.fr: 1 unic.cnrs-gif.fr: 1 brain-lid-002.intlocal.univ-amu.fr: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 22
Total pull requests: 58
Average time to close issues: 3 months
Average time to close pull requests: 13 days
Total issue authors: 6
Total pull request authors: 8
Average comments per issue: 2.41
Average comments per pull request: 0.62
Merged pull requests: 54
Bot issues: 0
Bot pull requests: 16

Past Year

Issues: 10
Pull requests: 16
Average time to close issues: 11 days
Average time to close pull requests: 8 days
Issue authors: 3
Pull request authors: 4
Average comments per issue: 3.7
Average comments per pull request: 0.31
Merged pull requests: 13
Bot issues: 0
Bot pull requests: 6

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Top Authors

Issue Authors

EtienneCmb (8)
pitmonticone (7)
ClaudMor (2)
Mattehub (2)
me9hanics (1)
thomasrobiglio (1)
patoorio (1)

Pull Request Authors

dependabot[bot] (27)
Mattehub (23)
pitmonticone (11)
Dishie2498 (9)
chrisferreyra13 (4)
jbytecode (4)
thomasrobiglio (2)
aopy (1)

Top Labels

Issue Labels

bug (4) new feature (3) enhancement (2) documentation (2) opmization (1)

Pull Request Labels

dependencies (27) documentation (2) enhancement (2) opmization (1)

Packages

Total packages: 1
Total downloads:
- pypi 90 last-month

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 6
Total maintainers: 1

pypi.org: hoi

Higher Order Interactions

Homepage: https://github.com/brainets/hoi
Documentation: https://hoi.readthedocs.io/
License: BSD 3-Clause License
Latest release: 0.0.5
published about 1 year ago

Versions: 6
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 90 Last month

Rankings

Dependent packages count: 10.7%

Average: 35.4%

Dependent repos count: 60.2%

Maintainers (1)

EtienneCmb

Last synced: 4 months ago

Dependencies

requirements.txt pypi

frites *

HOI

Science Score: 100.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.rst

Owner

JOSS Publication

HOI: A Python toolbox for high-performance estimation of Higher-Order Interactions from multivariate data

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Editor

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Citation (CITATION.cff)

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