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Minimal intervention strategies in logical signaling networks with ASP

  • Proposing relevant perturbations to biological signaling networks is central to many problems in biology and medicine because it allows for enabling or disabling certain biological outcomes. In contrast to quantitative methods that permit fine-grained (kinetic) analysis, qualitative approaches allow for addressing large-scale networks. This is accomplished by more abstract representations such as logical networks. We elaborate upon such a qualitative approach aiming at the computation of minimal interventions in logical signaling networks relying on Kleene's three-valued logic and fixpoint semantics. We address this problem within answer set programming and show that it greatly outperforms previous work using dedicated algorithms.

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Metadaten
Author:Roland Kaminski, Torsten SchaubORCiDGND, Anne SiegelORCiD, Santiago Videla
DOI:https://doi.org/10.1017/S1471068413000422
ISSN:1471-0684 (print)
Parent Title (English):Theory and practice of logic programming
Publisher:Cambridge Univ. Press
Place of publication:New York
Document Type:Article
Language:English
Year of first Publication:2013
Year of Completion:2013
Release Date:2017/03/26
Volume:13
Pagenumber:16
First Page:675
Last Page:690
Funder:DFG grant [SCHA 550/9-1]; [ANR-10-BLANC-0218]
Organizational units:Mathematisch-Naturwissenschaftliche Fakultät / Institut für Informatik und Computational Science
Peer Review:Referiert
Institution name at the time of publication:Mathematisch-Naturwissenschaftliche Fakultät / Institut für Informatik
Notes extern:Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 596