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

doi:10.1007/978-3-540-87361-7_19

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

School of Computer Science

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

36 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 language	English
Title of host publication	Algorithms in Bioinformatics - 8th International Workshop, WABI 2008, Proceedings
Pages	222-232
Number of pages	11
DOIs	https://doi.org/10.1007/978-3-540-87361-7_19
State	Published - 2008
Event	8th International Workshop on Algorithms in Bioinformatics, WABI 2008 - Karlsruhe, Germany Duration: 15 Sep 2008 → 19 Sep 2008

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	5251 LNBI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	8th International Workshop on Algorithms in Bioinformatics, WABI 2008
Country/Territory	Germany
City	Karlsruhe
Period	15/09/08 → 19/09/08

Access to Document

10.1007/978-3-540-87361-7_19

Cite this

Medvedovsky, A., Bafna, V., Zwick, U., & Sharan, R. (2008). An algorithm for orienting graphs based on cause-effect pairs and its applications to orienting protein networks. In Algorithms in Bioinformatics - 8th International Workshop, WABI 2008, Proceedings (pp. 222-232). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5251 LNBI). https://doi.org/10.1007/978-3-540-87361-7_19

Medvedovsky, Alexander ; Bafna, Vineet ; Zwick, Uri et al. / An algorithm for orienting graphs based on cause-effect pairs and its applications to orienting protein networks. Algorithms in Bioinformatics - 8th International Workshop, WABI 2008, Proceedings. 2008. pp. 222-232 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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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.",

author = "Alexander Medvedovsky and Vineet Bafna and Uri Zwick and Roded Sharan",

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Medvedovsky, A, Bafna, V, Zwick, U & Sharan, R 2008, An algorithm for orienting graphs based on cause-effect pairs and its applications to orienting protein networks. in Algorithms in Bioinformatics - 8th International Workshop, WABI 2008, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 5251 LNBI, pp. 222-232, 8th International Workshop on Algorithms in Bioinformatics, WABI 2008, Karlsruhe, Germany, 15/09/08. https://doi.org/10.1007/978-3-540-87361-7_19

An algorithm for orienting graphs based on cause-effect pairs and its applications to orienting protein networks. / Medvedovsky, Alexander; Bafna, Vineet; Zwick, Uri et al.
Algorithms in Bioinformatics - 8th International Workshop, WABI 2008, Proceedings. 2008. p. 222-232 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5251 LNBI).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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Medvedovsky A, Bafna V, Zwick U , Sharan R. An algorithm for orienting graphs based on cause-effect pairs and its applications to orienting protein networks. In Algorithms in Bioinformatics - 8th International Workshop, WABI 2008, Proceedings. 2008. p. 222-232. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-540-87361-7_19

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

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