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Compositional Analysis of Homeostasis of Gene Networks by Clustering Algorithms

  • Sohei ItoEmail author
  • Kenji Osari
  • Shigeki Hagihara
  • Naoki Yonezaki
Conference paper
Part of the Communications in Computer and Information Science book series (CCIS, volume 881)

Abstract

In this work we present a compositional approach to qualitatively analyse homeostasis of gene networks. The problem of analysing homeostasis of gene networks is 2EXPTIME-complete in the sizes of the network specifications. Due to this high complexity of the problem, only small networks consisting of a few genes were successfully analysed. Since the analysis of homeostasis of gene networks is based on the technique of realisability checking of Linear Temporal Logic formulae, we can apply a compositional algorithm devised to mitigate the computational difficulty in realisability problems. For this, we develop a clustering algorithm to divide network specifications in suitable sizes to utilise the compositional algorithm. We report the experimental results of analyses of homeostasis of several gene networks with our proposed method. Our experiments show a fair improvement especially in the analyses of larger networks.

Keywords

Gene regulatory network Systems biology Homeostasis Temporal logic Realisability Formal method 

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Sohei Ito
    • 1
    Email author
  • Kenji Osari
    • 2
  • Shigeki Hagihara
    • 3
  • Naoki Yonezaki
    • 4
  1. 1.National Fisheries UniversityShimonosekiJapan
  2. 2.Yahoo Japan CorporationTokyoJapan
  3. 3.Tohoku University of Community Service and ScienceSakataJapan
  4. 4.Tokyo Denki UniversityInzaiJapan

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