HOPS: high-performance library for (non-)uniform sampling of convex-constrained models

Bioinformatics, vol. 37, pp. 1776–1777

Abstract

SUMMARY: The C++ library Highly Optimized Polytope Sampling (HOPS) provides implementations of efficient and scalable algorithms for sampling convex-constrained models that are equipped with arbitrary target functions. For uniform sampling, substantial performance gains were achieved compared to the state-of-the-art. The ease of integration and utility of non-uniform sampling is showcased in a Bayesian inference setting, demonstrating how HOPS interoperates with third-party software. AVAILABILITY AND IMPLEMENTATION: Source code is available at https://github.com/modsim/hops/, tested on Linux and MS Windows, includes unit tests, detailed documentation, example applications and a Dockerfile. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Authors 4

1. Johann F. Jadebeck Aachen Computational Systems Biotechnology

   Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University , 52062 Aachen, Germany

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH , 52425 Jülich, Germany

2. Axel Theorell

   Forschungszentrum Jülich

   Affiliation as printed

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH , 52425 Jülich, Germany

3. Samuel Leweke

   Forschungszentrum Jülich

   Affiliation as printed

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH , 52425 Jülich, Germany

4. Katharina Nöh corresponding

   Forschungszentrum Jülich

   Affiliation as printed

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH , 52425 Jülich, Germany