https://github.com/brainets/hoi

Higher-Order Interactions
https://github.com/brainets/hoi

higher-order-interactions hoi jax network python

Last synced: 2 months ago
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Higher-Order Interactions

• Host: GitHub
• URL: https://github.com/brainets/hoi
• Owner: brainets
• License: bsd-3-clause
• Created: 2023-02-03T09:32:16.000Z (almost 2 years ago)
• Default Branch: main
• Last Pushed: 2024-11-06T15:03:09.000Z (3 months ago)
• Last Synced: 2024-11-06T15:08:07.280Z (3 months ago)
• Topics: higher-order-interactions, hoi, jax, network, python
• Language: Python
• Homepage: https://brainets.github.io/hoi/
• Size: 34.9 MB
• Stars: 23
• Watchers: 3
• Forks: 8
• Open Issues: 2
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

Awesome Lists containing this project

README

        
.. -*- 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)