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An Improved Scatter Search Algorithm for Parameter Estimation in Large-Scale Kinetic Models of Biochemical Systems

[ Vol. 16 , Issue. 5 ]

Author(s):

Muhammad Akmal Remli, Mohd Saberi Mohamad*, Safaai Deris, Richard Sinnott and Suhaimi Napis   Pages 425 - 436 ( 12 )

Abstract:


Background: Mathematical models play a central role in facilitating researchers to better understand and comprehensively analyze various processes in biochemical systems. Their usage is beneficial in metabolic engineering as they help predict and improve desired products. However, one of the primary challenges in model building is parameter estimation. It is the process to find nearoptimal values of kinetic parameters which may culminate in the best fit of model prediction to experimental data.

Methods: This paper proposes an improved scatter search algorithm to address the challenging parameter estimation problem. The improved algorithm is based on hybridization of quasi oppositionbased learning in enhanced scatter search (QOBLESS) method. The algorithm is tested using a largescale metabolic model of Chinese Hamster Ovary (CHO) cells.

Results: The experiment result shows that the proposed algorithm performs better than other algorithms in terms of convergence speed and the minimum value of the objective function (loglikelihood). The estimated parameters from the experiment produce a better model by means of obtaining a reasonable good fit of model prediction to the experimental data

Conclusion: The kinetic parameters’ value obtained from our work was able to result in a reasonable best fit of model prediction to the experimental data, which contributes to a better understanding and produced more accurate model. Based on the results, the QOBLESS method can be used as an efficient parameter estimation method in large-scale kinetic model building.

Keywords:

Systems biology, scatter search, opposition-based learning, bioinformatics, artificial intelligence, metabolic engineering.

Affiliation:

Faculty of Computer Systems & Software Engineering, Universiti Malaysia Pahang, Kuantan, Pahang 26300, , Institute For Artificial Intelligence and Big Data, Universiti Malaysia Kelantan, City Campus, Pengkalan Chepa, 16100 Kota Bharu, Kelantan, , Faculty of Bioengineering and Technology, Universiti Malaysia Kelantan, Jeli Campus, Lock Bag 100, 17600 Jeli, Kelantan,, Department of Computing and Information Systems, University of Melbourne, Victoria, 3010, , Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor



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