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Data Discretization for Dynamic Bayesian Network Based Modeling of Genetic Networks

  • Nguyen Xuan Vinh
  • Madhu Chetty
  • Ross Coppel
  • Pramod P. Wangikar
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7664)

Abstract

Dynamic Bayesian networks (DBN) are widely applied in Systems biology for modeling various biological networks, including gene regulatory networks and metabolic networks. The application of DBN models often requires data discretization. Although various discretization techniques exist, currently there is no consensus on which approach is most suitable. Popular discretization strategies within the bioinformatics community, such as interval and quantile discretization, are likely not optimal. In this paper, we propose a novel approach for data discretization for mutual information based learning of DBN. In this approach, the data are discretized so that the mutual information between parent and child nodes is maximized, subject to a suitable penalty put on the complexity of the discretization. A dynamic programming approach is used to find the optimal discretization threshold for each individual variable. Our approach iteratively learns both the network and the discretization scheme until a locally optimal solution is reached. Tests on real genetic networks confirm the effectiveness of the proposed method.

Keywords

Dynamic Bayesian network Gene regulatory network Discretization Mutual information Microarray 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Nguyen Xuan Vinh
    • 1
  • Madhu Chetty
    • 1
  • Ross Coppel
    • 2
  • Pramod P. Wangikar
    • 3
  1. 1.Gippsland School of Information TechnologyMonash UniversityAustralia
  2. 2.Department of MicrobiologyMonash UniversityAustralia
  3. 3.Chemical Engineering DepartmentIndian Institute of TechnologyMumbaiIndia

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