A novel clustering based niching EDA for protein folding

Benhui Chen, Takayuki Furuzuki

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Citations (Scopus)

Abstract

Protein structure prediction (PSP) is one of the most important problems in computational biology. And it also is a very difficult optimization task, especially for long sequence instances. This paper proposes a novel clustering based niching EDA for HP model folding problem. The EDA individuals are clustered by the affinity propagation clustering method before submitting them to niching clearing. A cluster can be seen as a niche in clearing procedure. The niche clearing radius can be adaptively determined by clustering. And an approach based on Boltzmann scheme is proposed to determine the niche capacity according to the adaptive clearing radius and niche fitness. Experimental results demonstrate that the proposed method outperforms the basic EDAs method. At the same time, it is very competitive with other existing algorithms for the PSP problem on lattice HP models.

Original languageEnglish
Title of host publication2009 World Congress on Nature and Biologically Inspired Computing, NABIC 2009 - Proceedings
Pages748-753
Number of pages6
DOIs
Publication statusPublished - 2009
Event2009 World Congress on Nature and Biologically Inspired Computing, NABIC 2009 - Coimbatore
Duration: 2009 Dec 92009 Dec 11

Other

Other2009 World Congress on Nature and Biologically Inspired Computing, NABIC 2009
CityCoimbatore
Period09/12/909/12/11

Fingerprint

Protein folding
Proteins

ASJC Scopus subject areas

  • Artificial Intelligence
  • Computer Science Applications
  • Software

Cite this

Chen, B., & Furuzuki, T. (2009). A novel clustering based niching EDA for protein folding. In 2009 World Congress on Nature and Biologically Inspired Computing, NABIC 2009 - Proceedings (pp. 748-753). [5393870] https://doi.org/10.1109/NABIC.2009.5393870

A novel clustering based niching EDA for protein folding. / Chen, Benhui; Furuzuki, Takayuki.

2009 World Congress on Nature and Biologically Inspired Computing, NABIC 2009 - Proceedings. 2009. p. 748-753 5393870.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Chen, B & Furuzuki, T 2009, A novel clustering based niching EDA for protein folding. in 2009 World Congress on Nature and Biologically Inspired Computing, NABIC 2009 - Proceedings., 5393870, pp. 748-753, 2009 World Congress on Nature and Biologically Inspired Computing, NABIC 2009, Coimbatore, 09/12/9. https://doi.org/10.1109/NABIC.2009.5393870
Chen B, Furuzuki T. A novel clustering based niching EDA for protein folding. In 2009 World Congress on Nature and Biologically Inspired Computing, NABIC 2009 - Proceedings. 2009. p. 748-753. 5393870 https://doi.org/10.1109/NABIC.2009.5393870
Chen, Benhui ; Furuzuki, Takayuki. / A novel clustering based niching EDA for protein folding. 2009 World Congress on Nature and Biologically Inspired Computing, NABIC 2009 - Proceedings. 2009. pp. 748-753
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