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Exploiting bounded signal flow for graph orientation based on cause–effect pairs

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Author(s): Dorn Britta | Hüffner Falk | Krüger Dominikus | Niedermeier Rolf | Uhlmann Johannes

Journal: Algorithms for Molecular Biology
ISSN 1748-7188

Volume: 6;
Issue: 1;
Start page: 21;
Date: 2011;
Original page

ABSTRACT
Abstract Background We consider the following problem: Given an undirected network and a set of sender–receiver pairs, direct all edges such that the maximum number of "signal flows" defined by the pairs can be routed respecting edge directions. This problem has applications in understanding protein interaction based cell regulation mechanisms. Since this problem is NP-hard, research so far concentrated on polynomial-time approximation algorithms and tractable special cases. Results We take the viewpoint of parameterized algorithmics and examine several parameters related to the maximum signal flow over vertices or edges. We provide several fixed-parameter tractability results, and in one case a sharp complexity dichotomy between a linear-time solvable case and a slightly more general NP-hard case. We examine the value of these parameters for several real-world network instances. Conclusions Several biologically relevant special cases of the NP-hard problem can be solved to optimality. In this way, parameterized analysis yields both deeper insight into the computational complexity and practical solving strategies.
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