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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
*

Given

doi:10.1007/978-3-540-87361-7_19
fatcat:vhlztajbcngldiyls7swfzwycy
*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. ...##
###
Optimally Orienting Physical Networks
[chapter]

2011
*
Lecture Notes in Computer Science
*

This problem is NP-complete

doi:10.1007/978-3-642-20036-6_39
fatcat:occm7yjcenczrps2ddka7p452y
*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*. ...##
###
Optimally Orienting Physical Networks

2011
*
Journal of Computational Biology
*

This problem is NP-complete

doi:10.1089/cmb.2011.0163
pmid:21999286
fatcat:ykdvlozy75ekrjfrenajryq764
*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*. ...##
###
A note on the parameterized complexity of unordered maximum tree orientation

2012
*
Discrete Applied Mathematics
*

In the Unordered Maximum Tree

doi:10.1016/j.dam.2012.02.017
fatcat:dcimedm6lvdlxnrjpvfojjdfge
*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. ...##
###
Network orientation via shortest paths

2014
*
Bioinformatics
*

We apply our

doi:10.1093/bioinformatics/btu043
pmid:24470573
fatcat:myg3wdhm5rbarkcepubpj6polu
*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) . ...##
###
Approximation algorithms for orienting mixed graphs

2013
*
Theoretical Computer Science
*

Given a

doi:10.1016/j.tcs.2012.03.044
fatcat:xnlp26mjlnaermoav5xzh3wl4i
*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. ...##
###
Approximation Algorithms for Orienting Mixed Graphs
[chapter]

2011
*
Lecture Notes in Computer Science
*

Given a

doi:10.1007/978-3-642-21458-5_35
fatcat:oefqitkwnrfcfc5cuzvzbbwivu
*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. ...##
###
Inferring protein-protein interaction and protein-DNA interaction directions based on cause-effect pairs in undirected and mixed networks
[article]

2017
*
arXiv
*
pre-print

This is called maximum

arXiv:1706.00911v1
fatcat:ozt5w7satfajjpza44g2r6fr64
*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*. ...##
###
Discovering pathways by orienting edges in protein interaction networks

2010
*
Nucleic Acids Research
*

We formalize the

doi:10.1093/nar/gkq1207
pmid:21109539
pmcid:PMC3045580
fatcat:tjmcmwadujg4fhyj6u57k6vwgu
*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. ...##
###
Exploiting bounded signal flow for graph orientation based on cause-effect pairs

2011
*
Algorithms for Molecular Biology
*

This problem has

doi:10.1186/1748-7188-6-21
pmid:21867496
pmcid:PMC3189099
fatcat:fbe65r4f7bcifgit6zsbcdrcfy
*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 ...##
###
Exploiting Bounded Signal Flow for Graph Orientation Based on Cause–Effect Pairs
[chapter]

2011
*
Lecture Notes in Computer Science
*

This problem has

doi:10.1007/978-3-642-19754-3_12
fatcat:rrnprkzn4nhnzgiseijnvkhy6y
*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 ...##
###
Learning biological network using mutual information and conditional independence

2010
*
BMC Bioinformatics
*

Results:

doi:10.1186/1471-2105-11-s3-s9
pmid:20438656
pmcid:PMC2863068
fatcat:xzah3txtw5enxl67rj7inrm6xm
*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. ...##
###
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
*

We adopt

doi:10.1109/bibm.2013.6732475
dblp:conf/bibm/ChoJ13
fatcat:fkwbnv2slzbillxkvhzk3wodii
*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*. ...##
###
An algorithm for score aggregation over causal biological networks based on random walk sampling

2014
*
BMC Research Notes
*

Since the SST

doi:10.1186/1756-0500-7-516
pmid:25113603
pmcid:PMC4266947
fatcat:fkuttdiawjc53fp2u4hlnut234
*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. ...##
###
Improved Orientations of Physical Networks
[chapter]

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. ...

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