Soft computing approach to the metabolic modeling

John Yen, Bogju Lee

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

1 Scopus citations

Abstract

The identification of metabolic systems such as metabolic pathways, enzyme actions, and gene regulations is a complex task due to the complexity of the system and limited knowledge about the model. Mathematical equations and ODE's have been used to capture the structure of the model, and the conventional optimization techniques have been used to identify the parameters of the model. In general, however, a pure mathematical formulation of the model is difficult due to parametric uncertainty and incomplete knowledge of mechanisms. In this paper, we propose a modeling approach that (1) uses fuzzy rule-based model to augment algebraic enzyme models that are incomplete, and (2) uses a hybrid genetic algorithm (GA) to identify uncertain parameters in the model. The hybrid GA integrates GA with the simplex method in functional optimization to improve GA's convergence rate. We have applied this approach to modeling the rate of an enzyme reactions in E. coli central metabolism. The proposed modeling strategy allows (1) easy incorporation of qualitative insights into a pure mathematical model and (2) adaptive identification and optimization of key parameters to fit system behaviors observed in biochemical experiments.

Original languageEnglish (US)
Title of host publicationNew Frontiers in Fuzzy Logic and Soft Computing
PublisherIEEE
Pages343-347
Number of pages5
StatePublished - 1996
EventProceedings of the 1996 Biennial Conference of the North American Fuzzy Information Processing Society - NAFIPS - Berkeley, CA, USA
Duration: Jun 19 1996Jun 22 1996

Other

OtherProceedings of the 1996 Biennial Conference of the North American Fuzzy Information Processing Society - NAFIPS
CityBerkeley, CA, USA
Period6/19/966/22/96

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All Science Journal Classification (ASJC) codes

  • Engineering(all)

Cite this

Yen, J., & Lee, B. (1996). Soft computing approach to the metabolic modeling. In New Frontiers in Fuzzy Logic and Soft Computing (pp. 343-347). IEEE.