Improved orientations of physical networks

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

Abstract

The orientation of physical networks is a prime task in deciphering the signaling-regulatory circuitry of the cell. One manifestation of this computational task is as a maximum graph orientation problem, where given an undirected graph on n vertices and a collection of vertex pairs, the goal is to orient the edges of the graph so that a maximum number of pairs are connected by a directed path. We develop a novel approximation algorithm for this problem with a performance guarantee of O(logn / loglogn), improving on the current logarithmic approximation. In addition, motivated by interactions whose direction is pre-set, such as protein-DNA interactions, we extend our algorithm to handle mixed graphs, a major open problem posed by earlier work. In this setting, we show that a polylogarithmic approximation ratio is achievable under biologically-motivated assumptions on the sought paths.

Original languageEnglish
Title of host publicationAlgorithms in Bioinformatics - 10th International Workshop, WABI 2010, Proceedings
Pages215-225
Number of pages11
DOIs
StatePublished - 2010
Event10th International Workshop on Algorithms in Bioinformatics, WABI 2010 - Liverpool, United Kingdom
Duration: 6 Sep 20108 Sep 2010

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6293 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference10th International Workshop on Algorithms in Bioinformatics, WABI 2010
Country/TerritoryUnited Kingdom
CityLiverpool
Period6/09/108/09/10

Fingerprint

Dive into the research topics of 'Improved orientations of physical networks'. Together they form a unique fingerprint.

Cite this