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.
|Title of host publication
|Algorithms in Bioinformatics - 10th International Workshop, WABI 2010, Proceedings
|Number of pages
|Published - 2010
|10th International Workshop on Algorithms in Bioinformatics, WABI 2010 - Liverpool, United Kingdom
Duration: 6 Sep 2010 → 8 Sep 2010
|Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
|10th International Workshop on Algorithms in Bioinformatics, WABI 2010
|6/09/10 → 8/09/10
Bibliographical noteFunding Information:
We thank Yael Silberberg for her help in gathering statistics on the KEGG pathways. I.G. was supported by the Israel Science Foundation, by the European Commission under the Integrated Project QAP funded by the IST directorate as Contract Number 015848, by a European Research Council (ERC) Starting Grant, and by the Wolfson Family Charitable Trust. R.S. was supported by a research grant from the Israel Science Foundation (grant no. 385/06).
ASJC Scopus subject areas
- Theoretical Computer Science
- General Computer Science