Detecting Inconsistencies in Large Biological Networks with Answer Set Programming

DOI10.1007/978-3-540-89982-2_19MaRDI QIDQ5504653zbMATH OpenOpenAlexWikidataFDO

Authors Martin Gebser, Torsten Schaub, Sven Thiele, Björn Usadel, Philippe Veber

Publication date 22 January 2009

Published in Logic Programming (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1007.0134

Mathematics Subject Classification ID

Logic programming (68N17) Systems biology, networks (92C42)

Abstract: We introduce an approach to detecting inconsistencies in large biological networks by using Answer Set Programming (ASP). To this end, we build upon a recently proposed notion of consistency between biochemical/genetic reactions and high-throughput profiles of cell activity. We then present an approach based on ASP to check the consistency of large-scale data sets. Moreover, we extend this methodology to provide explanations for inconsistencies by determining minimal representations of conflicts. In practice, this can be used to identify unreliable data or to indicate missing reactions.

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Cites work

• A Scalable Algorithm for Minimal Unsatisfiable Core Extraction
• Answer set programming based on propositional satisfiability
• Extending and implementing the stable model semantics
• Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework
• scientific article; zbMATH DE number 3150484 (Why is no real title available?)
• scientific article; zbMATH DE number 140388 (Why is no real title available?)
• scientific article; zbMATH DE number 3639144 (Why is no real title available?)
• scientific article; zbMATH DE number 1368933 (Why is no real title available?)
• Knowledge Representation, Reasoning and Declarative Problem Solving
• Logic programs with stable model semantics as a constraint programming paradigm
• Necessary conditions for multistationarity in discrete dynamical systems
• On the computational cost of disjunctive logic programming: Propositional case
• Propositional semantics for disjunctive logic programs
• The complexity of facets (and some facets of complexity)
• The DLV system for knowledge representation and reasoning
• Unfolding partiality and disjunctions in stable model semantics

Cited in

(7)

• Detecting inconsistencies in large biological networks with answer set programming
• Measuring instability in normal residuated logic programs: discarding information
• scientific article; zbMATH DE number 1950564 (Why is no real title available?)
• Constraint Answer Set Solving
• Repairing inconsistent answer set programs using rules of thumb: a gene regulatory networks case study
• Constrained community-based gene regulatory network inference
• Artificial intelligence in biological modelling

Describes a project that uses

Uses Software

• clasp
• Gringo
• Lparse
• zChaff
• Potassco
• Cmodels

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