pyPESTO: a modular and scalable tool for parameter estimation for dynamic models
Yannik Schälte, Fabian Fröhlich, Paul Jonas Jost, Jakob Vanhoefer, Dilan Pathirana, Paul Stapor, Polina Lakrisenko, Dantong Wang, Elba Raimúndez, Simon Merkt, Leonard Schmiester, Philipp Städter, Stephan Grein, Erika Dudkin, Domagoj Dorešić, Daniel Weindl, Jan Hasenauer
Abstract
SUMMARY: Mechanistic models are important tools to describe and understand biological processes. However, they typically rely on unknown parameters, the estimation of which can be challenging for large and complex systems. pyPESTO is a modular framework for systematic parameter estimation, with scalable algorithms for optimization and uncertainty quantification. While tailored to ordinary differential equation problems, pyPESTO is broadly applicable to black-box parameter estimation problems. Besides own implementations, it provides a unified interface to various popular simulation and inference methods. AVAILABILITY AND IMPLEMENTATION: pyPESTO is implemented in Python, open-source under a 3-Clause BSD license. Code and documentation are available on GitHub (https://github.com/icb-dcm/pypesto).