Machine Learning

, Volume 52, Issue 1, pp 147–167

On Learning Gene Regulatory Networks Under the Boolean Network Model

  • Harri Lähdesmäki
  • Ilya Shmulevich
  • Olli Yli-Harja
Article

DOI: 10.1023/A:1023905711304

Cite this article as:
Lähdesmäki, H., Shmulevich, I. & Yli-Harja, O. Machine Learning (2003) 52: 147. doi:10.1023/A:1023905711304

Abstract

Boolean networks are a popular model class for capturing the interactions of genes and global dynamical behavior of genetic regulatory networks. Recently, a significant amount of attention has been focused on the inference or identification of the model structure from gene expression data. We consider the Consistency as well as Best-Fit Extension problems in the context of inferring the networks from data. The latter approach is especially useful in situations when gene expression measurements are noisy and may lead to inconsistent observations. We propose simple efficient algorithms that can be used to answer the Consistency Problem and find one or all consistent Boolean networks relative to the given examples. The same method is extended to learning gene regulatory networks under the Best-Fit Extension paradigm. We also introduce a simple and fast way of finding all Boolean networks having limited error size in the Best-Fit Extension Problem setting. We apply the inference methods to a real gene expression data set and present the results for a selected set of genes.

gene regulatory networks network inference Consistency Problem Best-Fit Extension paradigm 
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Copyright information

© Kluwer Academic Publishers 2003

Authors and Affiliations

  • Harri Lähdesmäki
    • 1
  • Ilya Shmulevich
    • 2
  • Olli Yli-Harja
    • 1
  1. 1.Institute of Signal Processing, Digital Media InstituteTampere University of TechnologyTampereFinland
  2. 2.Cancer Genomics LaboratoryUniversity of Texas M.D. Anderson Cancer CenterHoustonUSA

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