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

Ko Wei Huang, Jui Le Chen, Chu Sing Yang

Research output: Contribution to conferencePaperpeer-review

5 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages223-228
Number of pages6
DOIs
Publication statusPublished - 2012 Dec 12
Event3rd International Conference on Innovations in Bio-Inspired Computing and Applications, IBICA 2012 - Kaohsiung City, Taiwan
Duration: 2012 Sep 262012 Sep 28

Other

Other3rd International Conference on Innovations in Bio-Inspired Computing and Applications, IBICA 2012
CountryTaiwan
CityKaohsiung City
Period12-09-2612-09-28

All Science Journal Classification (ASJC) codes

  • Bioengineering
  • Software

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