PEtab Select: Specification standard and supporting software for automated model selection
10 affiliations
- 1Bonn Center for Mathematical Life Sciences, University of Bonn, Bonn, Germany
- 2Life and Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
- 3BioQUANT, Heidelberg University, Heidelberg, Germany
- 4Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
- 5School of Life Sciences, Technische Universität München, Munich, Germany
- 6Department of Mathematical Sciences, Chalmers University of Technology, and University of Gothenburg, Gothenburg, Sweden
- 7Institute of Medical Biometry and Statistics (IMBI), Medical Faculty and Medical Center, University of Freiburg, Freiburg im Breisgau, Baden-Württemberg, Germany
- 8Institute of Physics, University of Freiburg, Freiburg im Breisgau, Baden-Württemberg, Germany
- 9CIBSS, Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg im Breisgau, Baden-Württemberg, Germany
- 10Freiburg Center for Data Analysis and Modelling, University of Freiburg, Freiburg im Breisgau, Baden-Württemberg, Germany
Abstract
A central question in mathematical modeling of biological systems is determining which processes are most relevant and how they can be described. There are often competing hypotheses, which yield different models. Model comparison requires parameter optimization and sampling methods. Yet, standards for the specification of model selection problems and the swift evaluation of a broad spectrum of approaches are not available. PEtab Select addresses this challenge by providing a concise, standardized specification of model selection and its associated calibration problems through a new file format standard and software package. The standard facilitates the compact representation of even very large model selection problems; in one example, billions of model alternatives. PEtab Select builds on the PEtab standard for the specification of parameter estimation problems, and enables the use of state-of-the-art modelling and calibration workflows utilizing COPASI, Data2Dynamics, PEtab.jl, and pyPESTO. PEtab Select supports common model selection criteria (e.g., Akaike and Bayesian information criteria) and can be easily extended to use others. To ensure flexibility, PEtab Select implements several model space exploration approaches, including basic brute-force, forward, and backward selection, and also advanced, flexible selection methods. PEtab Select introduces the first standardization of model selection tasks, filling a critical gap in existing computational pipelines. It constitutes an essential contribution to FAIR research software in systems biology by promoting interoperability and reusability in model selection. Author summary: Model selection is a crucial step in mathematical modeling, guiding the choice of components to include in a model. PEtab Select automates this process across diverse modeling software frameworks and programming languages via (1) a new interoperable, language-agnostic standard for specifying large-scale model selection problems, and (2) a comprehensive software package that implements these selection methods. Developed through a community effort, PEtab Select has been integrated into multiple modeling frameworks and is accessible to users of COPASI, Julia, MATLAB, and Python.
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BibTeX
@article{pathirana2026petab,
title = {{PEtab Select: Specification standard and supporting software for automated model selection}},
author = {Dilan Pathirana and Frank T. Bergmann and Domagoj Doresic and Polina Lakrisenko and Sebastian Persson and Niklas Neubrand and Jens Timmer and Clemens Kreutz and Harald Binder and Marija Cvijovic and Daniel Weindl and Jan Hasenauer and with the PEtab Select community},
journal = {PLOS Computational Biology},
year = {2026},
month = sep,
doi = {10.1371/journal.pcbi.1014774},
url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1014774},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - PEtab Select: Specification standard and supporting software for automated model selection
AU - Dilan Pathirana
AU - Frank T. Bergmann
AU - Domagoj Doresic
AU - Polina Lakrisenko
AU - Sebastian Persson
AU - Niklas Neubrand
AU - Jens Timmer
AU - Clemens Kreutz
AU - Harald Binder
AU - Marija Cvijovic
AU - Daniel Weindl
AU - Jan Hasenauer
AU - with the PEtab Select community
PY - 2026
DA - 2026/09/30
JO - PLOS Computational Biology
DO - 10.1371/journal.pcbi.1014774
UR - https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1014774
AB - A central question in mathematical modeling of biological systems is determining which processes are most relevant and how they can be described. There are often competing hypotheses, which yield different models. Model comparison requires parameter optimization and sampling methods. Yet, standards for the specification of model selection problems and the swift evaluation of a broad spectrum of approaches are not available. PEtab Select addresses this challenge by providing a concise, standardized specification of model selection and its associated calibration problems through a new file format standard and software package. The standard facilitates the compact representation of even very large model selection problems; in one example, billions of model alternatives. PEtab Select builds on the PEtab standard for the specification of parameter estimation problems, and enables the use of state-of-the-art modelling and calibration workflows utilizing COPASI, Data2Dynamics, PEtab.jl, and pyPESTO. PEtab Select supports common model selection criteria (e.g., Akaike and Bayesian information criteria) and can be easily extended to use others. To ensure flexibility, PEtab Select implements several model space exploration approaches, including basic brute-force, forward, and backward selection, and also advanced, flexible selection methods. PEtab Select introduces the first standardization of model selection tasks, filling a critical gap in existing computational pipelines. It constitutes an essential contribution to FAIR research software in systems biology by promoting interoperability and reusability in model selection. Author summary: Model selection is a crucial step in mathematical modeling, guiding the choice of components to include in a model. PEtab Select automates this process across diverse modeling software frameworks and programming languages via (1) a new interoperable, language-agnostic standard for specifying large-scale model selection problems, and (2) a comprehensive software package that implements these selection methods. Developed through a community effort, PEtab Select has been integrated into multiple modeling frameworks and is accessible to users of COPASI, Julia, MATLAB, and Python.
SN - 1553-7358
ER -