hopsy - a methods marketplace for convex polytope sampling in Python.

Abstract

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. 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/.