pyABC: distributed, likelihood-free inference

Bioinformatics
Emmanuel KlingerJan Hasenauer

Abstract

Likelihood-free methods are often required for inference in systems biology. While approximate Bayesian computation (ABC) provides a theoretical solution, its practical application has often been challenging due to its high computational demands. To scale likelihood-free inference to computationally demanding stochastic models, we developed pyABC: a distributed and scalable ABC-Sequential Monte Carlo (ABC-SMC) framework. It implements a scalable, runtime-minimizing parallelization strategy for multi-core and distributed environments scaling to thousands of cores. The framework is accessible to non-expert users and also enables advanced users to experiment with and to custom implement many options of ABC-SMC schemes, such as acceptance threshold schedules, transition kernels and distance functions without alteration of pyABC's source code. pyABC includes a web interface to visualize ongoing and finished ABC-SMC runs and exposes an API for data querying and post-processing. pyABC is written in Python 3 and is released under a 3-clause BSD license. The source code is hosted on https://github.com/icb-dcm/pyabc and the documentation on http://pyabc.readthedocs.io. It can be installed from the Python Package Index (PyPI). Supplementa...Continue Reading

References

Feb 1, 2007·Proceedings of the National Academy of Sciences of the United States of America·S A SissonMark M Tanaka
Feb 11, 2009·Journal of the Royal Society, Interface·Tina ToniMichael P H Stumpf
Jul 2, 2010·Bioinformatics·Juliane LiepeMichael P H Stumpf

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Citations

Oct 16, 2018·Bioinformatics·Louis RaynalArnaud Estoup
May 26, 2020·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·C HoustonC D Cantwell
Jul 25, 2020·Bioinformatics·Prashant SinghAndreas Hellander
Jun 26, 2020·Physical Biology·Liam J RuskeLinus J Schumacher
Jan 27, 2021·PLoS Computational Biology·Leonard SchmiesterDaniel Weindl
Nov 20, 2019·Developmental Cell·Hanh Thi-Kim VuJochen Christian Rink
Dec 19, 2020·BMC Bioinformatics·H Jonathan G Lindström, Ran Friedman
Jul 10, 2021·The Journal of Chemical Physics·Adrien CoulierAndreas Hellander
Jul 27, 2021·PLoS Computational Biology·Cliff C KerrDaniel J Klein
Aug 11, 2021·Ecological Applications : a Publication of the Ecological Society of America·Jeffrey M MinucciS Thomas Purucker
Aug 4, 2021·Journal of Theoretical Biology·W WaitesV Danos
Aug 21, 2020··Jakob MackeJan Boelts

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