Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs

N. Kashtan, S. Itzkovitz, R. Milo, Uri Alon*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

426 Scopus citations

Abstract

Summary: Biological and engineered networks have recently been shown to display network motifs: a small set of characteristic patterns that occur much more frequently than in randomized networks with the same degree sequence. Network motifs were demonstrated to play key information processing roles in biological regulation networks. Existing algorithms for detecting network motifs act by exhaustively enumerating all subgraphs with a given number of nodes in the network. The runtime of such algorithms increases strongly with network size. Here, we present a novel algorithm that allows estimation of subgraph concentrations and detection of network motifs at a runtime that is asymptotically independent of the network size. This algorithm is based on random sampling of subgraphs. Network motifs are detected with a surprisingly small number of samples in a wide variety of networks. Our method can be applied to estimate the concentrations of larger subgraphs in larger networks than was previously possible with exhaustive enumeration algorithms. We present results for high-order motifs in several biological networks.

Original languageAmerican English
Pages (from-to)1746-1758
Number of pages13
JournalBioinformatics
Volume20
Issue number11
DOIs
StatePublished - 22 Jul 2004
Externally publishedYes

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