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Using an improved bee memory differential evolution algorithm for parameter estimation to simulate biochemical pathways

Chong, Chuiikhim and Mohamad, Mohd. Saberi and Deris, Safaai and Shamsir, Mohd. Shahir and Chai, Lian En and Choon, Yeewen (2014) Using an improved bee memory differential evolution algorithm for parameter estimation to simulate biochemical pathways. Journal of Biological Systems, 22 (1). pp. 101-121. ISSN 0218-3390

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Official URL: http://dx.doi.org/10.1142/S0218339014500065

Abstract

When analyzing a metabolic pathway in a mathematical model, it is important that the essential parameters are estimated correctly. However, this process often faces few problems like when the number of unknown parameters increase, trapping of data in the local minima, repeated exposure to bad results during the search process and occurrence of noisy data. Thus, this paper intends to present an improved bee memory differential evolution (IBMDE) algorithm to solve the mentioned problems. This is a hybrid algorithm that combines the differential evolution (DE) algorithm, the Kalman filter, artificial bee colony (ABC) algorithm, and a memory feature. The aspartate and threonine biosynthesis pathway, and cell cycle pathway are the metabolic pathways used in this paper. For three production simulation pathways, the IBMDE managed to robustly produce the estimated optimal kinetic parameter values with significantly reduced errors. Besides, it also demonstrated faster convergence time compared to the Nelder-Mead (NM), simulated annealing (SA), the genetic algorithm (GA) and DE, respectively. Most importantly, the kinetic parameters that were generated by the IBMDE have improved the production rates of desired metabolites better than other estimation algorithms. Meanwhile, the results proved that the IBMDE is a reliable estimation algorithm.

Item Type:Article
Uncontrolled Keywords:memory feature, parameter estimation
Subjects:Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Divisions:Computing
ID Code:63185
Deposited By: Siti Nor Hashidah Zakaria
Deposited On:15 Jun 2017 02:28
Last Modified:15 Jun 2017 02:28

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