NABEECO: Biological network alignment with bee colony optimization algorithm

Rashid Ibragimov, Jan Martens, Jiong Guo, Jan Baumbach

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

10 Scopus citations

Abstract

Motivation: A growing number of biological networks of ever increasing sizes are becoming available nowadays, making the ability to solve Network Alignment of primer importance. However, computationally the problem is hard for data sets of real-world sizes. Results: we developed NABEECO, a novel and robust Network Alignment heuristic based on Bee Colony Optimization. We use the so-called Graph Edit Distance (GED) as optimization criterion, which is defined as the minimal amount of edge and node modifications necessary to transform one graph into another. We compare NABEECO on a set of protein-protein interaction networks to the current state of the art tool for biological networks, MI-GRAAL. Conclusion: We present the first Bee Colony Optimization algorithm for biological Network Alignment. NABEECO, in contrast to many other tools, can be applied to all kinds of networks and allows incorporating prior knowledge about node/edge similarity, though this is not required a priori. NABEECO together with a more detailed description and all data sets used are publicly available at http://nabeeco.mpi- inf.mpg.de.

Original languageEnglish
Title of host publicationGECCO 2013 - Proceedings of the 2013 Genetic and Evolutionary Computation Conference Companion
Pages43-44
Number of pages2
DOIs
StatePublished - 2013
Externally publishedYes
Event15th Annual Conference on Genetic and Evolutionary Computation, GECCO 2013 - Amsterdam, Netherlands
Duration: 6 Jul 201310 Jul 2013

Publication series

NameGECCO 2013 - Proceedings of the 2013 Genetic and Evolutionary Computation Conference Companion

Conference

Conference15th Annual Conference on Genetic and Evolutionary Computation, GECCO 2013
Country/TerritoryNetherlands
CityAmsterdam
Period6/07/1310/07/13

Keywords

  • Bee colony optimization
  • Graph edit distance
  • Network alignment
  • Protein-protein interaction networks

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