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An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and Its Applications to Orienting Protein Networks
[chapter]
Lecture Notes in Computer Science
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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 then study restrictions of the problem to various graph classes, and provide an O(log n) approximation algorithm for the general case. ...
Acknowledgments We thank Richard Karp, Eran Halperin, Tomer Shlomi and Eytan Ruppin for stimulating discussions about the orientation problem. ...
doi:10.1007/978-3-540-87361-7_19
fatcat:vhlztajbcngldiyls7swfzwycy
Optimally Orienting Physical Networks
[chapter]
2011
Lecture Notes in Computer Science
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This problem is NP-complete and no approximation algorithms are known for it. It arises in the context of analyzing physical networks of protein-protein and protein-DNA interactions. ...
Assuming that each cause-effect pair should be connected by a directed pathway in the physical network, one can predict an orientation (direction assignments) to the undirected part of the network that ...
In Section 3 we present an ILP-based algorithm to solve the orientation problem on mixed graphs. ...
doi:10.1007/978-3-642-20036-6_39
fatcat:occm7yjcenczrps2ddka7p452y
Optimally Orienting Physical Networks
2011
Journal of Computational Biology
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This problem is NP-complete and no approximation algorithms are known for it. It arises in the context of analyzing physical networks of protein-protein and protein-DNA interactions. ...
Assuming that each cause-effect pair should be connected by a directed pathway in the physical network, one can predict an orientation (direction assignments) to the undirected part of the network that ...
In Section 3 we present an ILP-based algorithm to solve the orientation problem on mixed graphs. ...
doi:10.1089/cmb.2011.0163
pmid:21999286
fatcat:ykdvlozy75ekrjfrenajryq764
A note on the parameterized complexity of unordered maximum tree orientation
2012
Discrete Applied Mathematics
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In the Unordered Maximum Tree Orientation problem, a set P of paths in a tree and a parameter k is given, and we want to orient the edges in the tree such that all but at most k paths in P become directed ...
We show that the parameterized complexity of the unordered version is between Edge Bipartization and Vertex Bipartization, and we give a characterization of orientable path sets in trees by forbidden substructures ...
We are indebted to Falk Hüffner and Rolf Niedermeier for drawing our attention to their paper [3] and pointing out a mishap in an early draft. ...
doi:10.1016/j.dam.2012.02.017
fatcat:dcimedm6lvdlxnrjpvfojjdfge
Network orientation via shortest paths
2014
Bioinformatics
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We apply our algorithm to orient protein-protein interaction networks in yeast and compare it with two state-of-the-art algorithms. ...
The graph orientation problem calls for orienting the edges of a graph so as to maximize the number of pre-specified source-target vertex pairs that admit a directed path from the source to the target. ...
ACKNOWLEDGEMENTS The authors would like to thank Dr. Anthony Gitter for his help in the comparison to Gitter et al. (2011) . ...
doi:10.1093/bioinformatics/btu043
pmid:24470573
fatcat:myg3wdhm5rbarkcepubpj6polu
Approximation algorithms for orienting mixed graphs
2013
Theoretical Computer Science
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Given a graph and a list of ordered source-target vertex pairs, it calls for assigning directions to the edges of the graph so as to maximize the number of pairs that admit a directed source-to-target ...
Graph orientation is a fundamental problem in graph theory that has recently arisen in the study of signaling-regulatory pathways in protein networks. ...
motivated by applications in street network design, showed that an undirected graph has a strongly connected orientation if and only if it has no bridge edge. ...
doi:10.1016/j.tcs.2012.03.044
fatcat:xnlp26mjlnaermoav5xzh3wl4i
Approximation Algorithms for Orienting Mixed Graphs
[chapter]
2011
Lecture Notes in Computer Science
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Given a graph and a list of ordered source-target vertex pairs, it calls for assigning directions to the edges of the graph so as to maximize the number of pairs that admit a directed source-to-target ...
Graph orientation is a fundamental problem in graph theory that has recently arisen in the study of signaling-regulatory pathways in protein networks. ...
motivated by applications in street network design, showed that an undirected graph has a strongly connected orientation if and only if it has no bridge edge. ...
doi:10.1007/978-3-642-21458-5_35
fatcat:oefqitkwnrfcfc5cuzvzbbwivu
Inferring protein-protein interaction and protein-DNA interaction directions based on cause-effect pairs in undirected and mixed networks
[article]
2017
arXiv
pre-print
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This is called maximum graph orientation problem, and has applications in understanding interactions in protein-protein interaction networks and protein-DNA interaction networks. ...
In the mixed case, we present polynomial-time algorithms for the problem on paths and cycles, and an FPT-algorithm based on the combined parameter the number of arcs and the number of pairs on general ...
We present polynomial-time algorithms for paths and cycles, and an FPTalgorithm based on the combined parameter the number of arcs and the number of pairs for general graphs. ...
arXiv:1706.00911v1
fatcat:ozt5w7satfajjpza44g2r6fr64
Discovering pathways by orienting edges in protein interaction networks
2010
Nucleic Acids Research
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We formalize the orientation problem in weighted protein interaction graphs as an optimization problem and present three approximation algorithms based on either weighted Boolean satisfiability solvers ...
However, when attempting to reconstruct the signaling networks and pathways between these sources and targets, one faces a substantial challenge. ...
ACKNOWLEDGEMENTS We would like to express our gratitude to Itamar Simon for his assistance in analyzing the cell-cycle predictions. ...
doi:10.1093/nar/gkq1207
pmid:21109539
pmcid:PMC3045580
fatcat:tjmcmwadujg4fhyj6u57k6vwgu
Exploiting bounded signal flow for graph orientation based on cause-effect pairs
2011
Algorithms for Molecular Biology
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This problem has applications in understanding protein interaction based cell regulation mechanisms. ...
We consider the following problem: Given an undirected network and a set of sender-receiver pairs, direct all edges such that the maximum number of "signal flows" defined by the pairs can be routed respecting ...
Acknowledgements A preliminary version of this work appeared in the proceedings of the 1st International ICST Conference on Theory and Practice of Algorithms in (Computer) Systems (TAPAS '11), volume 6595 ...
doi:10.1186/1748-7188-6-21
pmid:21867496
pmcid:PMC3189099
fatcat:fbe65r4f7bcifgit6zsbcdrcfy
Exploiting Bounded Signal Flow for Graph Orientation Based on Cause–Effect Pairs
[chapter]
2011
Lecture Notes in Computer Science
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This problem has applications in understanding protein interaction based cell regulation mechanisms. ...
We consider the following problem: Given an undirected network and a set of sender-receiver pairs, direct all edges such that the maximum number of "signal flows" defined by the pairs can be routed respecting ...
Acknowledgements A preliminary version of this work appeared in the proceedings of the 1st International ICST Conference on Theory and Practice of Algorithms in (Computer) Systems (TAPAS '11), volume 6595 ...
doi:10.1007/978-3-642-19754-3_12
fatcat:rrnprkzn4nhnzgiseijnvkhy6y
Learning biological network using mutual information and conditional independence
2010
BMC Bioinformatics
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Results: To discover the signaling pathway responsive to RPPM, a new structure learning algorithm of Bayesian networks is developed based on mutual Information, conditional independence, and graph immorality ...
Conclusions: By using a new protein microarray technology in combination with a new computational framework, we demonstrate an application of the methodology to the study of biological networks of ATM ...
Since an edge in a discovered network means a cause and effect relationship and may not be direct interactions , additional components may exist between the two nodes that the edge connects. ...
doi:10.1186/1471-2105-11-s3-s9
pmid:20438656
pmcid:PMC2863068
fatcat:xzah3txtw5enxl67rj7inrm6xm
Prediction of signaling networks by information propagation on protein-protein interaction networks integrated with GO annotations
2013
2013 IEEE International Conference on Bioinformatics and Biomedicine
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We adopt an advanced semantic similarity metric for weighting PPIs, and an information propagation algorithm that runs on a weighted PPI network. ...
High efficiency of this approach would facilitate development of a web-based application tool to discover potential signaling networks. ...
Second, the results of edge recall and directed edge recall are identical. It indicates that our approach correctly assigned orientations for all selected protein pairs to build signaling networks. ...
doi:10.1109/bibm.2013.6732475
dblp:conf/bibm/ChoJ13
fatcat:fkwbnv2slzbillxkvhzk3wodii
An algorithm for score aggregation over causal biological networks based on random walk sampling
2014
BMC Research Notes
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Since the SST algorithm is based on general graph-theoretical considerations, it is scalable to arbitrary graph sizes and can potentially be used for performing quantitative analyses in any context involving ...
The SST algorithm is based on spanning trees, which are a particular class of subgraphs used in graph theory, and on a sampling procedure leveraging the properties of specific random walks on the graph ...
Acknowledgements The authors would like to thank Sylvain Gubian, Jason Sroka, and Gregory Vuillaume for their comments on the manuscript. ...
doi:10.1186/1756-0500-7-516
pmid:25113603
pmcid:PMC4266947
fatcat:fkuttdiawjc53fp2u4hlnut234
Improved Orientations of Physical Networks
[chapter]
2010
Lecture Notes in Computer Science
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One manifestation of this computational task is as a maximum graph orientation problem, where given an undirected graph with n vertices and a collection of vertex pairs, the goal is to orient the edges ...
We develop an approximation algorithm for this problem with a performance guarantee of O(log n/ log log n). This result improves on a previous logarithmic approximation, due to Medvedovsky et al. ...
Acknowledgments: The authors would like to thank Yael Silberberg for her help in gathering statistics on the KEGG pathways. ...
doi:10.1007/978-3-642-15294-8_18
fatcat:zzqmck6bgng25kiffniy5gjwlu
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