Multiple graph edit distance - Simultaneous topological alignment of multiple protein-protein interaction networks with an evolutionary algorithm

Rashid Ibragimov, Maximilian Malek, Jan Baumbach, Jiong Guo

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

24 Scopus citations

Abstract

Motivation: We address the problem of multiple proteinprotein interaction (PPI) network alignment. Given a set of such networks for different species we might ask how much the network topology is conserved throughout evolution. Solving this problem will help to derive a subset of interactions that is conserved over multiple species thus forming a 'core interactome'. Methods: We model the problem as Topological Multiple one-to-one Network Alignment (TMNA), where we aim to minimize the total Graph Edit Distance (GED) between pairs of the input networks. Here, the GED between two graphs is the number of deleted and inserted edges that are required to make one graph isomorphic to another. By minimizing the GED we indirectly maximize the number of edges that are aligned in multiple networks simultaneously. However, computing an optimal GED value is computationally intractable. We thus propose an evolutionary algorithm and developed a software tool, GEDEVO-M, which is able to align multiple PPI networks using topological information only. We demonstrate the power of our approach by computing a maximal common subnetwork for a set of bacterial and eukaryotic PPI networks. GEDEVO-M thus provides great potential for computing the 'core interactome' of different species. Availability: http://gedevo.mpi- inf.mpg.de/multiple-network-alignment/.

Original languageEnglish
Title of host publicationGECCO 2014 - Proceedings of the 2014 Genetic and Evolutionary Computation Conference
PublisherAssociation for Computing Machinery
Pages277-283
Number of pages7
ISBN (Print)9781450326629
DOIs
StatePublished - 2014
Externally publishedYes
Event16th Genetic and Evolutionary Computation Conference, GECCO 2014 - Vancouver, BC, Canada
Duration: 12 Jul 201416 Jul 2014

Publication series

NameGECCO 2014 - Proceedings of the 2014 Genetic and Evolutionary Computation Conference

Conference

Conference16th Genetic and Evolutionary Computation Conference, GECCO 2014
Country/TerritoryCanada
CityVancouver, BC
Period12/07/1416/07/14

Keywords

  • Evolutionary algorithm
  • Graph edit distance
  • Multiple network alignment
  • Protein-protein interaction networks

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