{"paper":{"title":"pyPESTO: A modular and scalable tool for parameter estimation for dynamic models","license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","headline":"","cross_cats":["stat.CO"],"primary_cat":"q-bio.QM","authors_text":"Daniel Weindl, Dantong Wang, Dilan Pathirana, Domagoj Doresic, Elba Raim\\'undez, Erika Dudkin, Fabian Fr\\\"ohlich, Jakob Vanhoefer, Jan Hasenauer, Leonard Schmiester, Paul J. Jost, Paul Stapor, Philipp St\\\"adter, Polina Lakrisenko, Simon Merkt, Stephan Grein, Yannik Sch\\\"alte","submitted_at":"2023-05-02T23:09:42Z","abstract_excerpt":"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. We present pyPESTO, 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 inferen"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2305.01821","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2305.01821/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}