This repository contains the implementation of non-negative and regularised universal differential equations (UDEs) and supplemental material accompanying the 2024 FOSBE publication "Non-Negative Universal Differential Equations With Applications in Systems Biology" [1]. It builds on the PEtab package for specification of a parameter estimation problem, AMICI for simulation and pyPESTO as an interface for parameter estimation.
The Python environment package versions that we used are stored in environment/requirements.txt, and can be installed with pip install -r environment/requirements.txt. A Python virtual environment is recommended, in case you want to use a fresh environment with the latest package versions later.
Computations were performed on an HPC, with the system packages described in environment/env.sh. These system dependencies are only required by the Python environment packages -- if you can install AMICI [2], you probably don't need to install additional system packages.
We additionally used the package provided in nnUDE. From inside the nnUDE directory where the setup.py file is, this package can be installed with pip install -e ..
The example models from the paper are provided in examples. Some are derived from the PEtab Benchmark Collection [3].
[1] arxiv preprint https://arxiv.org/abs/2406.14246
[2] https://amici.readthedocs.io/en/latest/python_installation.html
[3] https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab