Improved Orientations of Physical Networks

11 years 3 months ago
Improved Orientations of Physical Networks
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(log n/ log log n), 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.
Iftah Gamzu, Danny Segev, Roded Sharan
Added 31 Jan 2011
Updated 31 Jan 2011
Type Journal
Year 2010
Where WABI
Authors Iftah Gamzu, Danny Segev, Roded Sharan
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