An algorithm for orienting graphs based on cause-effect pairs and its applications to orienting protein networks

Alexander Medvedovsky*, Vineet Bafna, Uri Zwick, Roded Sharan

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

34 Scopus citations

Abstract

We consider a graph orientation problem arising in the study of biological networks. Given an undirected graph and a list of ordered source-target pairs, the goal is to orient the graph so that a maximum number of pairs will admit a directed path from the source to the target. We show that the problem is NP-hard and hard to approximate to within a constant ratio. We then study restrictions of the problem to various graph classes, and provide an O(logn) approximation algorithm for the general case. We show that this algorithm achieves very tight approximation ratios in practice and is able to infer edge directions with high accuracy on both simulated and real network data.

Original languageEnglish
Title of host publicationAlgorithms in Bioinformatics - 8th International Workshop, WABI 2008, Proceedings
Pages222-232
Number of pages11
DOIs
StatePublished - 2008
Event8th International Workshop on Algorithms in Bioinformatics, WABI 2008 - Karlsruhe, Germany
Duration: 15 Sep 200819 Sep 2008

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5251 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference8th International Workshop on Algorithms in Bioinformatics, WABI 2008
Country/TerritoryGermany
CityKarlsruhe
Period15/09/0819/09/08

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