A hybrid approach to modeling metabolic systems using a genetic algorithm and simplex method

John Yen, James C. Liao, Bogju Lee, David Randolph

Research output: Contribution to journalArticle

171 Scopus citations

Abstract

One of the main obstacles in applying genetic algorithms (GA's) to complex problems has been the high computational cost due to their slow convergence rate. We encountered such a difficulty in our attempt to use the classical GA for estimating parameters of a metabolic model. To alleviate this difficulty, we developed a hybrid approach that combines a GA with a stochastic variant of the simplex method in function optimization. Our motivation for developing the stochastic simplex method is to introduce a cost-effective exploration component into the conventional simplex method. In an attempt to make effective use of the simplex operation in a hybrid GA framework, we used an elite-based hybrid architecture that applies one simplex step to a top portion of the ranked population. We compared our approach with five alternative optimization techniques including a simplex-GA hybrid independently developed by Renders-Bersini (R-B) and adaptive simulated annealing (ASA). Our empirical evaluations showed that our hybrid approach for the metabolic modeling problem outperformed all other techniques in terms of accuracy and convergence rate. We used two additional function optimization problems to compare our approach with the five alternative methods. For a sin function maximization problem, our hybrid approach yields the fastest convergence rate without sacrificing the accuracy of the solution found. For De Jong's F5 function minimization problem, our hybrid approach is the second best (next to ASA). Overall, these tests showed that our hybrid approach is an effective and robust optimization technique. We further conducted an empirical study to identify major factors that affect the performance of the hybrid approach. The study indicated that 1) our elite-based hybrid GA architecture contributes significantly to the performance improvement and 2) the probabilistic simplex is more cost-effective for our hybrid architecture than is the conventional simplex. By analyzing the performance of the hybrid approach for the metabolic modeling problem, we hypothesized that the hybrid approach is particularly suitable for solving complex optimization problems the variables of which vary widely in their sensitivity to the objective function.

Original languageEnglish (US)
Pages (from-to)173-191
Number of pages19
JournalIEEE Transactions on Systems, Man, and Cybernetics, Part B: Cybernetics
Volume28
Issue number2
DOIs
StatePublished - Dec 1 1998

All Science Journal Classification (ASJC) codes

  • Control and Systems Engineering
  • Software
  • Information Systems
  • Human-Computer Interaction
  • Computer Science Applications
  • Electrical and Electronic Engineering

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