research-article

Improving BDD-based Attractor Detection for Synchronous Boolean Networks

Authors:

Andrzej MizeraAuthors Info & Claims

Internetware '15: Proceedings of the 7th Asia-Pacific Symposium on Internetware

Pages 212 - 220

https://doi.org/10.1145/2875913.2875925

Published: 06 November 2015 Publication History

Abstract

Boolean networks are an important formalism for modelling biological systems and have attracted much attention in recent years. An important direction in Boolean networks is to exhaustively find attractors, which represent steady states when a biological network evolves for a long term. In this paper, we propose a new approach to improve the efficiency of BDD-based attractor detection. Our approach includes a monolithic algorithm for small networks, an enumerative strategy to deal with large networks, and two heuristics on ordering BDD variables. We demonstrate the performance of our approach on a number of examples, and compare it with one existing technique in the literature.

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Cited By

Wang YLeite MBen-Tal A(2023)From Boolean networks to linear dynamical systems: a simplified routeJournal of Difference Equations and Applications10.1080/10236198.2023.222081129:5(542-560)Online publication date: 13-Jun-2023
https://doi.org/10.1080/10236198.2023.2220811
Beneš NBrim LKadlecaj JPastva SŠafránek D(2022)Exploring attractor bifurcations in Boolean networksBMC Bioinformatics10.1186/s12859-022-04708-923:1Online publication date: 11-May-2022
https://doi.org/10.1186/s12859-022-04708-9
Ben Abdallah EFolschette MRoux OMagnin M(2017)ASP-based method for the enumeration of attractors in non-deterministic synchronous and asynchronous multi-valued networksAlgorithms for Molecular Biology10.1186/s13015-017-0111-212:1Online publication date: 15-Aug-2017
https://doi.org/10.1186/s13015-017-0111-2

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Improving BDD-based Attractor Detection for Synchronous Boolean Networks

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cover image ACM Other conferences

Internetware '15: Proceedings of the 7th Asia-Pacific Symposium on Internetware

November 2015

247 pages

ISBN:9781450336413

DOI:10.1145/2875913

Copyright © 2015 ACM.

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Key Laboratory of High Confidence Software Technologies: Key Laboratory of High Confidence Software Technologies, Ministry of Education

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New York, NY, United States

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Published: 06 November 2015

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Internetware '15

Internetware '15: The Seventh Asia-Pacific Symposium on Internetware

November 6, 2015

Wuhan, China

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Cited By

Wang YLeite MBen-Tal A(2023)From Boolean networks to linear dynamical systems: a simplified routeJournal of Difference Equations and Applications10.1080/10236198.2023.222081129:5(542-560)Online publication date: 13-Jun-2023
https://doi.org/10.1080/10236198.2023.2220811
Beneš NBrim LKadlecaj JPastva SŠafránek D(2022)Exploring attractor bifurcations in Boolean networksBMC Bioinformatics10.1186/s12859-022-04708-923:1Online publication date: 11-May-2022
https://doi.org/10.1186/s12859-022-04708-9
Ben Abdallah EFolschette MRoux OMagnin M(2017)ASP-based method for the enumeration of attractors in non-deterministic synchronous and asynchronous multi-valued networksAlgorithms for Molecular Biology10.1186/s13015-017-0111-212:1Online publication date: 15-Aug-2017
https://doi.org/10.1186/s13015-017-0111-2

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