Parameter estimation of essential amino acids in Arabidopsis thaliana using hybrid of bees algorithm and harmony search

Mei Yee Aw; Mohd Saberi Mohamad; Chuii Khim Chong; Safaai Deris; Muhammad Akmal Remli; Mohd Arfian Ismail; Juan Manuel Corchado; Sigeru Omatu

doi:10.1007/978-3-319-98702-6_2

Parameter estimation of essential amino acids in Arabidopsis thaliana using hybrid of bees algorithm and harmony search

Mei Yee Aw, Mohd Saberi Mohamad, Chuii Khim Chong, Safaai Deris, Muhammad Akmal Remli, Mohd Arfian Ismail, Juan Manuel Corchado, Sigeru Omatu

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

2 Citations (Scopus)

Abstract

Mathematical models of metabolic processes are the cornerstone of computational systems biology. In model building, the task of parameter estimation is difficult due to the huge numbers of kinetics parameters involved. The common way of estimating the parameters is to formulate it as an optimization problem. Global optimization methods can be applied by minimizing the distance between experimental data and predicted models. This paper proposes the Hybrid of Bees Algorithm and Harmony Search (BAHS) to estimate the kinetics parameters of essential amino acid production in the aspartate metabolism for Arabidopsis thaliana. The performance of the BAHS is evaluated and compared with other algorithms. The results show that BAHS performed better as it improved the performance of the original BA by 60%. Meanwhile, it takes less computational time to estimate the kinetics parameters of essential amino acid production for Arabidopsis thaliana.

Original language	English
Title of host publication	Practical Applications of Computational Biology and Bioinformatics, 12th International Conference
Editors	Miguel Rocha, Mohd Saberi Mohamad, Juan F. De Paz, Florentino Fdez-Riverola, Pascual Gonzalez
Publisher	Springer Verlag
Pages	9-16
Number of pages	8
ISBN (Print)	9783319987019
DOIs	https://doi.org/10.1007/978-3-319-98702-6_2
Publication status	Published - 2019
Externally published	Yes
Event	12th International Conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2018 - Toledo, Spain Duration: Jun 20 2018 → Jun 22 2018

Publication series

Name	Advances in Intelligent Systems and Computing
Volume	803
ISSN (Print)	2194-5357

Other

Other	12th International Conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2018
Country/Territory	Spain
City	Toledo
Period	6/20/18 → 6/22/18

Keywords

Arabidopsis thaliana
Bees algorithm
Computational intelligence
Harmony search
Parameter estimation
Systems biology

ASJC Scopus subject areas

Control and Systems Engineering
General Computer Science

Access to Document

10.1007/978-3-319-98702-6_2

Cite this

Aw, M. Y., Mohamad, M. S., Chong, C. K., Deris, S., Remli, M. A., Ismail, M. A., Corchado, J. M., & Omatu, S. (2019). Parameter estimation of essential amino acids in Arabidopsis thaliana using hybrid of bees algorithm and harmony search. In M. Rocha, M. S. Mohamad, J. F. De Paz, F. Fdez-Riverola, & P. Gonzalez (Eds.), Practical Applications of Computational Biology and Bioinformatics, 12th International Conference (pp. 9-16). (Advances in Intelligent Systems and Computing; Vol. 803). Springer Verlag. https://doi.org/10.1007/978-3-319-98702-6_2

Parameter estimation of essential amino acids in Arabidopsis thaliana using hybrid of bees algorithm and harmony search. / Aw, Mei Yee; Mohamad, Mohd Saberi; Chong, Chuii Khim et al.
Practical Applications of Computational Biology and Bioinformatics, 12th International Conference. ed. / Miguel Rocha; Mohd Saberi Mohamad; Juan F. De Paz; Florentino Fdez-Riverola; Pascual Gonzalez. Springer Verlag, 2019. p. 9-16 (Advances in Intelligent Systems and Computing; Vol. 803).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Aw, MY, Mohamad, MS, Chong, CK, Deris, S, Remli, MA, Ismail, MA, Corchado, JM & Omatu, S 2019, Parameter estimation of essential amino acids in Arabidopsis thaliana using hybrid of bees algorithm and harmony search. in M Rocha, MS Mohamad, JF De Paz, F Fdez-Riverola & P Gonzalez (eds), Practical Applications of Computational Biology and Bioinformatics, 12th International Conference. Advances in Intelligent Systems and Computing, vol. 803, Springer Verlag, pp. 9-16, 12th International Conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2018, Toledo, Spain, 6/20/18. https://doi.org/10.1007/978-3-319-98702-6_2

Aw MY, Mohamad MS, Chong CK, Deris S, Remli MA, Ismail MA et al. Parameter estimation of essential amino acids in Arabidopsis thaliana using hybrid of bees algorithm and harmony search. In Rocha M, Mohamad MS, De Paz JF, Fdez-Riverola F, Gonzalez P, editors, Practical Applications of Computational Biology and Bioinformatics, 12th International Conference. Springer Verlag. 2019. p. 9-16. (Advances in Intelligent Systems and Computing). doi: 10.1007/978-3-319-98702-6_2

Aw, Mei Yee ; Mohamad, Mohd Saberi ; Chong, Chuii Khim et al. / Parameter estimation of essential amino acids in Arabidopsis thaliana using hybrid of bees algorithm and harmony search. Practical Applications of Computational Biology and Bioinformatics, 12th International Conference. editor / Miguel Rocha ; Mohd Saberi Mohamad ; Juan F. De Paz ; Florentino Fdez-Riverola ; Pascual Gonzalez. Springer Verlag, 2019. pp. 9-16 (Advances in Intelligent Systems and Computing).

@inproceedings{ba6eb9ed09cc456db580747385354cdb,

title = "Parameter estimation of essential amino acids in Arabidopsis thaliana using hybrid of bees algorithm and harmony search",

abstract = "Mathematical models of metabolic processes are the cornerstone of computational systems biology. In model building, the task of parameter estimation is difficult due to the huge numbers of kinetics parameters involved. The common way of estimating the parameters is to formulate it as an optimization problem. Global optimization methods can be applied by minimizing the distance between experimental data and predicted models. This paper proposes the Hybrid of Bees Algorithm and Harmony Search (BAHS) to estimate the kinetics parameters of essential amino acid production in the aspartate metabolism for Arabidopsis thaliana. The performance of the BAHS is evaluated and compared with other algorithms. The results show that BAHS performed better as it improved the performance of the original BA by 60%. Meanwhile, it takes less computational time to estimate the kinetics parameters of essential amino acid production for Arabidopsis thaliana.",

keywords = "Arabidopsis thaliana, Bees algorithm, Computational intelligence, Harmony search, Parameter estimation, Systems biology",

author = "Aw, {Mei Yee} and Mohamad, {Mohd Saberi} and Chong, {Chuii Khim} and Safaai Deris and Remli, {Muhammad Akmal} and Ismail, {Mohd Arfian} and Corchado, {Juan Manuel} and Sigeru Omatu",

note = "Publisher Copyright: {\textcopyright} Springer Nature Switzerland AG 2019.; 12th International Conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2018 ; Conference date: 20-06-2018 Through 22-06-2018",

year = "2019",

doi = "10.1007/978-3-319-98702-6_2",

language = "English",

isbn = "9783319987019",

series = "Advances in Intelligent Systems and Computing",

publisher = "Springer Verlag",

pages = "9--16",

editor = "Miguel Rocha and Mohamad, {Mohd Saberi} and {De Paz}, {Juan F.} and Florentino Fdez-Riverola and Pascual Gonzalez",

booktitle = "Practical Applications of Computational Biology and Bioinformatics, 12th International Conference",

}

TY - GEN

T1 - Parameter estimation of essential amino acids in Arabidopsis thaliana using hybrid of bees algorithm and harmony search

AU - Aw, Mei Yee

AU - Mohamad, Mohd Saberi

AU - Chong, Chuii Khim

AU - Deris, Safaai

AU - Remli, Muhammad Akmal

AU - Ismail, Mohd Arfian

AU - Corchado, Juan Manuel

AU - Omatu, Sigeru

N1 - Publisher Copyright: © Springer Nature Switzerland AG 2019.

PY - 2019

Y1 - 2019

N2 - Mathematical models of metabolic processes are the cornerstone of computational systems biology. In model building, the task of parameter estimation is difficult due to the huge numbers of kinetics parameters involved. The common way of estimating the parameters is to formulate it as an optimization problem. Global optimization methods can be applied by minimizing the distance between experimental data and predicted models. This paper proposes the Hybrid of Bees Algorithm and Harmony Search (BAHS) to estimate the kinetics parameters of essential amino acid production in the aspartate metabolism for Arabidopsis thaliana. The performance of the BAHS is evaluated and compared with other algorithms. The results show that BAHS performed better as it improved the performance of the original BA by 60%. Meanwhile, it takes less computational time to estimate the kinetics parameters of essential amino acid production for Arabidopsis thaliana.

AB - Mathematical models of metabolic processes are the cornerstone of computational systems biology. In model building, the task of parameter estimation is difficult due to the huge numbers of kinetics parameters involved. The common way of estimating the parameters is to formulate it as an optimization problem. Global optimization methods can be applied by minimizing the distance between experimental data and predicted models. This paper proposes the Hybrid of Bees Algorithm and Harmony Search (BAHS) to estimate the kinetics parameters of essential amino acid production in the aspartate metabolism for Arabidopsis thaliana. The performance of the BAHS is evaluated and compared with other algorithms. The results show that BAHS performed better as it improved the performance of the original BA by 60%. Meanwhile, it takes less computational time to estimate the kinetics parameters of essential amino acid production for Arabidopsis thaliana.

KW - Arabidopsis thaliana

KW - Bees algorithm

KW - Computational intelligence

KW - Harmony search

KW - Parameter estimation

KW - Systems biology

UR - http://www.scopus.com/inward/record.url?scp=85052912250&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85052912250&partnerID=8YFLogxK

U2 - 10.1007/978-3-319-98702-6_2

DO - 10.1007/978-3-319-98702-6_2

M3 - Conference contribution

AN - SCOPUS:85052912250

SN - 9783319987019

T3 - Advances in Intelligent Systems and Computing

SP - 9

EP - 16

BT - Practical Applications of Computational Biology and Bioinformatics, 12th International Conference

A2 - Rocha, Miguel

A2 - Mohamad, Mohd Saberi

A2 - De Paz, Juan F.

A2 - Fdez-Riverola, Florentino

A2 - Gonzalez, Pascual

PB - Springer Verlag

T2 - 12th International Conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2018

Y2 - 20 June 2018 through 22 June 2018

ER -

Parameter estimation of essential amino acids in Arabidopsis thaliana using hybrid of bees algorithm and harmony search

Abstract

Publication series

Other

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this