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Minimal intervention strategies in logical signaling networks with ASP

Published online by Cambridge University Press:  25 September 2013

ROLAND KAMINSKI ,
TORSTEN SCHAUB ,
ANNE SIEGEL  and
SANTIAGO VIDELA
ROLAND KAMINSKI
Affiliation:
University of Potsdam
TORSTEN SCHAUB
Affiliation:
University of Potsdam
ANNE SIEGEL
Affiliation:
CNRS - IRISA, Rennes INRIA - Dyliss, Rennes
SANTIAGO VIDELA
Affiliation:
CNRS - IRISA, Rennes INRIA - Dyliss, Rennes University of Potsdam
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Abstract

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.

Type
Regular Papers
Information
Theory and Practice of Logic Programming , Volume 13 , Issue 4-5: 29th International Conference on Logic Programming , July 2013 , pp. 675 - 690
Copyright
Copyright © 2013 [ROLAND KAMINSKI, TORSTEN SCHAUB, ANNE SIEGEL and SANTIAGO VIDELA] 

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