Inference of S-system models of genetic networks using a genetic local search

In this paper, we propose a new method for the inference of S-system models of large-scale genetic networks. This method employs a technique to decompose the genetic network inference problem into several subproblems, and then applies a genetic local search to each of the subproblems. A local search method utilizing the feature of the S-system model is used as one of the search operators in this genetic local search. Finally, the effectiveness of the proposed method is verified through a genetic network inference problem.

[1]  H. Iba,et al.  Inferring a system of differential equations for a gene regulatory network by using genetic programming , 2001, Proceedings of the 2001 Congress on Evolutionary Computation (IEEE Cat. No.01TH8546).

[2]  Isao Ono,et al.  Development of System Identification Technique Based on Real-Coded Genetic Algorithm , 2002 .

[3]  Ting Chen,et al.  Modeling Gene Expression with Differential Equations , 1998, Pacific Symposium on Biocomputing.

[4]  Masahiro Okamoto,et al.  Efficient Numerical Optimization Algorithm Based on Genetic Algorithm for Inverse Problem , 2000, GECCO.

[5]  Masahiro Okamoto,et al.  Development of a System for the Inference of Large Scale Genetic Networks , 2000, Pacific Symposium on Biocomputing.

[6]  Shuhei Kimura,et al.  High dimensional function optimization using a new genetic local search suitable for parallel computers , 2003, SMC'03 Conference Proceedings. 2003 IEEE International Conference on Systems, Man and Cybernetics. Conference Theme - System Security and Assurance (Cat. No.03CH37483).

[7]  Takanori Ueda,et al.  Inference of Genetic Network Using the Expression Profile Time Course Data of Mouse P19 Cells , 2002 .

[8]  Hiroaki Satoh,et al.  Minimal generation gap model for GAs considering both exploration and exploitation , 1996 .

[9]  Araceli M. Huerta,et al.  From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. , 1998, BioEssays : news and reviews in molecular, cellular and developmental biology.

[10]  W. Cleveland Robust Locally Weighted Regression and Smoothing Scatterplots , 1979 .

[11]  S Miyano,et al.  Algorithms for inferring qualitative models of biological networks. , 2000, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[12]  Shigenobu Kobayashi,et al.  An Extension of UNDX Based on Guidelines for Designing Crossover Operators , 2000 .

[13]  Isao Ono,et al.  A Real Coded Genetic Algorithm for Function Optimization Using Unimodal Normal Distributed Crossover , 1997, ICGA.

[14]  P. Brown,et al.  Exploring the metabolic and genetic control of gene expression on a genomic scale. , 1997, Science.