A hybrid PSO-based algorithm for solving DNA fragment assembly problem

Ko Wei Huang, Jui Le Chen, Chu Sing Yang

研究成果: Paper

2 引文 (Scopus)

摘要

In this paper, a hybrid particle swarm optimization algorithm (HPSO) is proposed for the DNA fragment assembly (DFA) problem by maximizing the overlapping-score measurement. The smallest position value (SPV) rule is used for encoding the particles to enable PSO to be suitable for DFA, and the Tabu search algorithms are used to initialize the particles. Additionally, a simulated annealing (SA) algorithm-based local search is utilized for local search to improve the best solution after the PSO search process. Finally, the results show that HPSO can significantly get better overlap score than other PSO-based algorithms with different-sized benchmarks.

原文English
頁面223-228
頁數6
DOIs
出版狀態Published - 2012 十二月 12
事件3rd International Conference on Innovations in Bio-Inspired Computing and Applications, IBICA 2012 - Kaohsiung City, Taiwan
持續時間: 2012 九月 262012 九月 28

Other

Other3rd International Conference on Innovations in Bio-Inspired Computing and Applications, IBICA 2012
國家Taiwan
城市Kaohsiung City
期間12-09-2612-09-28

指紋

Particle swarm optimization (PSO)
DNA
Tabu search
Simulated annealing

All Science Journal Classification (ASJC) codes

  • Bioengineering
  • Software

引用此文

Huang, K. W., Chen, J. L., & Yang, C. S. (2012). A hybrid PSO-based algorithm for solving DNA fragment assembly problem. 223-228. 論文發表於 3rd International Conference on Innovations in Bio-Inspired Computing and Applications, IBICA 2012, Kaohsiung City, Taiwan. https://doi.org/10.1109/IBICA.2012.8
Huang, Ko Wei ; Chen, Jui Le ; Yang, Chu Sing. / A hybrid PSO-based algorithm for solving DNA fragment assembly problem. 論文發表於 3rd International Conference on Innovations in Bio-Inspired Computing and Applications, IBICA 2012, Kaohsiung City, Taiwan.6 p.
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Huang, KW, Chen, JL & Yang, CS 2012, 'A hybrid PSO-based algorithm for solving DNA fragment assembly problem' 論文發表於 3rd International Conference on Innovations in Bio-Inspired Computing and Applications, IBICA 2012, Kaohsiung City, Taiwan, 12-09-26 - 12-09-28, 頁 223-228. https://doi.org/10.1109/IBICA.2012.8

A hybrid PSO-based algorithm for solving DNA fragment assembly problem. / Huang, Ko Wei; Chen, Jui Le; Yang, Chu Sing.

2012. 223-228 論文發表於 3rd International Conference on Innovations in Bio-Inspired Computing and Applications, IBICA 2012, Kaohsiung City, Taiwan.

研究成果: Paper

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AB - In this paper, a hybrid particle swarm optimization algorithm (HPSO) is proposed for the DNA fragment assembly (DFA) problem by maximizing the overlapping-score measurement. The smallest position value (SPV) rule is used for encoding the particles to enable PSO to be suitable for DFA, and the Tabu search algorithms are used to initialize the particles. Additionally, a simulated annealing (SA) algorithm-based local search is utilized for local search to improve the best solution after the PSO search process. Finally, the results show that HPSO can significantly get better overlap score than other PSO-based algorithms with different-sized benchmarks.

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Huang KW, Chen JL, Yang CS. A hybrid PSO-based algorithm for solving DNA fragment assembly problem. 2012. 論文發表於 3rd International Conference on Innovations in Bio-Inspired Computing and Applications, IBICA 2012, Kaohsiung City, Taiwan. https://doi.org/10.1109/IBICA.2012.8