Inference of Compartmental Models (ICoMo) Toolbox

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.

• 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.