An Improved Scatter Search Algorithm for Parameter Estimation in Large-Scale Kinetic Models of Biochemical Systems
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...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Bentham Science Publishers
2019
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| Online Access: | http://umpir.ump.edu.my/id/eprint/25105/ http://umpir.ump.edu.my/id/eprint/25105/1/An%20Improved%20Scatter%20Search%20Algorithm%20for%20Parameter%20Estimation1.pdf |
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| author | Muhammad Akmal, Remli Mohd Saberi, Mohamad Safaai, Deris Sinnott, Richard O. Suhaimi, Napis |
| author_facet | Muhammad Akmal, Remli Mohd Saberi, Mohamad Safaai, Deris Sinnott, Richard O. Suhaimi, Napis |
| author_sort | Muhammad Akmal, Remli |
| building | UMP Institutional Repository |
| collection | Online Access |
| description | 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. |
| first_indexed | 2025-11-15T02:37:29Z |
| format | Article |
| id | ump-25105 |
| institution | Universiti Malaysia Pahang |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T02:37:29Z |
| publishDate | 2019 |
| publisher | Bentham Science Publishers |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | ump-251052019-06-18T07:59:58Z http://umpir.ump.edu.my/id/eprint/25105/ An Improved Scatter Search Algorithm for Parameter Estimation in Large-Scale Kinetic Models of Biochemical Systems Muhammad Akmal, Remli Mohd Saberi, Mohamad Safaai, Deris Sinnott, Richard O. Suhaimi, Napis QA75 Electronic computers. Computer science 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. Bentham Science Publishers 2019 Article PeerReviewed pdf en http://umpir.ump.edu.my/id/eprint/25105/1/An%20Improved%20Scatter%20Search%20Algorithm%20for%20Parameter%20Estimation1.pdf Muhammad Akmal, Remli and Mohd Saberi, Mohamad and Safaai, Deris and Sinnott, Richard O. and Suhaimi, Napis (2019) An Improved Scatter Search Algorithm for Parameter Estimation in Large-Scale Kinetic Models of Biochemical Systems. Current Proteomics, 16 (5). pp. 425-436. ISSN 1570-1646. (Published) http://www.eurekaselect.com/171196 https://doi.org/10.2174/1570164616666190401203128 |
| spellingShingle | QA75 Electronic computers. Computer science Muhammad Akmal, Remli Mohd Saberi, Mohamad Safaai, Deris Sinnott, Richard O. Suhaimi, Napis An Improved Scatter Search Algorithm for Parameter Estimation in Large-Scale Kinetic Models of Biochemical Systems |
| title | An Improved Scatter Search Algorithm for Parameter Estimation in Large-Scale Kinetic Models of Biochemical Systems |
| title_full | An Improved Scatter Search Algorithm for Parameter Estimation in Large-Scale Kinetic Models of Biochemical Systems |
| title_fullStr | An Improved Scatter Search Algorithm for Parameter Estimation in Large-Scale Kinetic Models of Biochemical Systems |
| title_full_unstemmed | An Improved Scatter Search Algorithm for Parameter Estimation in Large-Scale Kinetic Models of Biochemical Systems |
| title_short | An Improved Scatter Search Algorithm for Parameter Estimation in Large-Scale Kinetic Models of Biochemical Systems |
| title_sort | improved scatter search algorithm for parameter estimation in large-scale kinetic models of biochemical systems |
| topic | QA75 Electronic computers. Computer science |
| url | http://umpir.ump.edu.my/id/eprint/25105/ http://umpir.ump.edu.my/id/eprint/25105/ http://umpir.ump.edu.my/id/eprint/25105/ http://umpir.ump.edu.my/id/eprint/25105/1/An%20Improved%20Scatter%20Search%20Algorithm%20for%20Parameter%20Estimation1.pdf |