Inference of Compartmental Models toolbox

Leverage the power of JAX libraries for PyMC models

This toolbox aims to simplify the construction of compartmental models and the inference of their parameters.

The aim isn't to provide a complete package that will build models from A to Z, but rather provide different helper functions examples and guidelines to help leverage modern python packages like JAX, Diffrax and PyMC to build, automatically differentiate and fit compartmental models.

A central part of the toolbox is the possibility to wrap JAX functions to be used in PyMC models (see [here](https://icomo.readthedocs. io/en/stable/api/jax2pytensor.html)), which is used tro wrap the Diffrax ODE solvers, but might be also useful for other projects.

Documentation: https://icomo.readthedocs.io.

Features

Facilitate the construction of compartmental models by only defining flow between compartments, and automatically generating the corresponding ODEs.
Plot the graph of the compartmental model to verify the correctness of the model.
Integrate the ODEs using diffrax, automatically generating the Jacobian of the parameters of the ODE
Fit the parameters using minimization algorithms or build a Bayesian model using PyMC.

Citation

If you use this toolbox in your research, please find the citation information on the right sidebar.

Credits

Logo by Fabian Mikulasch

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Source Distribution

icomo-1.0.4.tar.gz (530.9 kB view details)

Uploaded Aug 27, 2026 Source

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Uploaded Aug 27, 2026 Python 3

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Download URL: icomo-1.0.4.tar.gz
Upload date: Aug 27, 2026
Size: 530.9 kB
Tags: Source
Uploaded using Trusted Publishing? Yes
Uploaded via: twine/7.0.0 CPython/3.13.14

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Provenance

The following attestation bundles were made for icomo-1.0.4.tar.gz:

Publisher: release.yaml on Priesemann-Group/icomo

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Statement:
- Statement type: https://in-toto.io/Statement/v1
- Predicate type: https://docs.pypi.org/attestations/publish/v1
- Subject name: icomo-1.0.4.tar.gz
- Subject digest: ad13b8055a2e79f96949beb0ff72fc7734bd6f23e054109b7a106b4c1d2ef0fb
- Sigstore transparency entry: 2618204919
- Sigstore integration time: Aug 27, 2026
Source repository:
- Permalink: Priesemann-Group/icomo@27704529bef7b29d8e60fc3f3f682aa1195b0e70
- Branch / Tag: refs/tags/1.0.4
- Owner: https://github.com/Priesemann-Group
- Access: public
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- Runner Environment: github-hosted
- Publication workflow: release.yaml@27704529bef7b29d8e60fc3f3f682aa1195b0e70
- Trigger Event: release