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An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and Its Applications to Orienting Protein Networks [chapter]

Alexander Medvedovsky, Vineet Bafna, Uri Zwick, Roded Sharan
Lecture Notes in Computer Science  
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]

Dana Silverbush, Michael Elberfeld, Roded Sharan
2011 Lecture Notes in Computer Science  
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

Dana Silverbush, Michael Elberfeld, Roded Sharan
2011 Journal of Computational Biology  
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

Sebastian Böcker, Peter Damaschke
2012 Discrete Applied Mathematics  
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

D. Silverbush, R. Sharan
2014 Bioinformatics  
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

Michael Elberfeld, Danny Segev, Colin R. Davidson, Dana Silverbush, Roded Sharan
2013 Theoretical Computer Science  
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]

Michael Elberfeld, Danny Segev, Colin R. Davidson, Dana Silverbush, Roded Sharan
2011 Lecture Notes in Computer Science  
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]

Mehdy Roayaei, MohammadReza Razzazi
2017 arXiv   pre-print
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

Anthony Gitter, Judith Klein-Seetharaman, Anupam Gupta, Ziv Bar-Joseph
2010 Nucleic Acids Research  
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

Britta Dorn, Falk Hüffner, Dominikus Krüger, Rolf Niedermeier, Johannes Uhlmann
2011 Algorithms for Molecular Biology  
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]

Britta Dorn, Falk Hüffner, Dominikus Krüger, Rolf Niedermeier, Johannes Uhlmann
2011 Lecture Notes in Computer Science  
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

Dong-Chul Kim, Xiaoyu Wang, Chin-Rang Yang, Jean Gao
2010 BMC Bioinformatics  
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

Young-Rae Cho, Slavka Jaromerska
2013 2013 IEEE International Conference on Bioinformatics and Biomedicine  
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

Dmitry M Vasilyev, Ty M Thomson, Brian P Frushour, Florian Martin, Alain Sewer
2014 BMC Research Notes  
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]

Iftah Gamzu, Danny Segev, Roded Sharan
2010 Lecture Notes in Computer Science  
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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