Inference of genetic networks using S-system: information criteria for model selection

ABSTRACT

In this paper we present an evolutionary approach for inferring the structure and dynamics in gene circuits from observed expression kinetics. For representing the regulatory interactions in a genetic network the decoupled S-system formalism has been used. We proposed an Information Criteria based fitness evaluation for model selection instead of the traditional Mean Squared Error (MSE) based fitness evaluation. A hill climbing local search method has been incorporated in our evolutionary algorithm for attaining the skeletal architecture which is most frequently observed in biological networks. Using small and medium-scale artificial networks we verified the implementation. The reconstruction method identified the correct network topology and predicted the kinetic parameters with high accuracy.

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INDEX TERMS

Primary Classification:
  J. Computer Applications
  J.3 LIFE AND MEDICAL SCIENCES
      Subjects: Biology and genetics

Additional Classification:
  I. Computing Methodologies
  I.2 ARTIFICIAL INTELLIGENCE
      I.2.8 Problem Solving, Control Methods, and Search
          Subjects: Heuristic methods

General Terms:
Algorithms, Design, Performance

Keywords:
S-system, genetic network, information criteria, reverse engineering