Modelling non-stationary gene regulatory process with hidden Markov dynamic Bayesian network

Shijiazhu Zhu, Yadong Wang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Dynamic Bayesian Network (DBN) has been widely used to infer gene regulatory network from time series gene expression dataset. The standard assumption underlying DBN is based on stationarity, however, in many cases, the gene regulatory network topology might evolve over time. In this paper, we propose a novel non-stationary DBN based network inference approach. In this model, for each variable, a specific HMM implicitly well handles the transition of the stationary DBNs along timesteps. Furthermore, we present a criterion, named as BWBIC score. This criterion is an approximation to the EM objective term, which can reasonably and easily evaluate hmDBN Towards BWBIC score, a greedy hill climbing based structural EM algorithm is proposed to efficiently infer the hmDBN model. We respectively apply our method on synthetic and real biological data. Compared to the recent proposed methods, we obtained better prediction accuracy on both datasets.

Original languageEnglish (US)
Title of host publicationProceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012
Pages449-452
Number of pages4
DOIs
StatePublished - Dec 1 2012
Externally publishedYes
Event2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM2012 - Philadelphia, PA, United States
Duration: Oct 4 2012Oct 7 2012

Publication series

NameProceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012

Other

Other2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM2012
CountryUnited States
CityPhiladelphia, PA
Period10/4/1210/7/12

Keywords

  • DBN
  • HMM
  • gene regulatory network
  • hmDBN
  • non-stationary DBN

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

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  • Cite this

    Zhu, S., & Wang, Y. (2012). Modelling non-stationary gene regulatory process with hidden Markov dynamic Bayesian network. In Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012 (pp. 449-452). [6392721] (Proceedings - 2012 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2012). https://doi.org/10.1109/BIBM.2012.6392721