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An algorithm for motif-based network design

Research output: Contribution to journalArticleScientificpeer-review

Details

Original languageEnglish
Pages (from-to)1181-1186
JournalIEEE - ACM Transactions on Computational Biology and Bioinformatics
Volume14
Issue number5
Early online date7 Jun 2016
DOIs
Publication statusPublished - 2017
Publication typeA1 Journal article-refereed

Abstract

A determinant property of the structure of a biological network is the distribution of local connectivity patterns, i.e. network motifs. In this work, a method for creating directed, unweighted networks while promoting a certain combination of motifs is presented. This motif-based network algorithm starts with an empty graph and randomly connects the nodes by advancing or discouraging the formation of chosen motifs. The in- or out-degree distribution of the generated networks can be explicitly chosen. The algorithm is shown to perform well in producing networks with high occurrences of the targeted motifs, both ones consisting of 3 nodes as well as ones consisting of 4 nodes. Moreover, the algorithm can also be tuned to bring about global network characteristics found in many natural networks, such as small-worldness and modularity.

Keywords

  • Algorithm design and analysis, Biological system modeling, Computers, Heuristic algorithms, Indexes, Prediction algorithms, Signal processing algorithms, graph algorithm, network generation, network motifs, network structure, random attachment

Publication forum classification

Field of science, Statistics Finland