hopsy — a methods marketplace for convex polytope sampling in Python

Bioinformatics, vol. 40

Abstract

SUMMARY: Effective collaboration between developers of Bayesian inference methods and users is key to advance our quantitative understanding of biosystems. We here present hopsy, a versatile open-source platform designed to provide convenient access to powerful Markov chain Monte Carlo sampling algorithms tailored to models defined on convex polytopes (CP). Based on the high-performance C++ sampling library HOPS, hopsy inherits its strengths and extends its functionalities with the accessibility of the Python programming language. A versatile plugin-mechanism enables seamless integration with domain-specific models, providing method developers with a framework for testing, benchmarking, and distributing CP samplers to approach real-world inference tasks. We showcase hopsy by solving common and newly composed domain-specific sampling problems, highlighting important design choices. By likening hopsy to a marketplace, we emphasize its role in bringing together users and developers, where users get access to state-of-the-art methods, and developers contribute their own innovative solutions for challenging domain-specific inference problems. AVAILABILITY AND IMPLEMENTATION: Sources, documentation and a continuously updated list of sampling algorithms are available at https://jugit.fz-juelich.de/IBG-1/ModSim/hopsy, with Linux, Windows and MacOS binaries at https://pypi.org/project/hopsy/.

Authors 5

1. Richard Dominik Paul

   Forschungszentrum Jülich

   Affiliation as printed

   Institute of Advanced Simulations, IAS-8: Data Analytics and Machine Learning, Forschungszentrum Jülich , 52428 Jülich, Germany

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich , 52428 Jülich, Germany

2. Johann F. Jadebeck Aachen Computational Systems Biotechnology

   Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University , 52074 Aachen, Germany

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich , 52428 Jülich, Germany

3. Anton Stratmann Aachen Computational Systems Biotechnology

   Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University , 52074 Aachen, Germany

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich , 52428 Jülich, Germany

4. Wolfgang Wiechert Aachen Computational Systems Biotechnology

   Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University , 52074 Aachen, Germany

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich , 52428 Jülich, Germany

5. Katharina Nöh corresponding

   Forschungszentrum Jülich

   Affiliation as printed

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich , 52428 Jülich, Germany