Evolutionary clustering algorithm with knowledge-based evaluation for fuzzy cluster analysis of gene expression profiles

Han Saem Park, Sung Bae Cho

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

Abstract

Clustering method, which groups thousands of genes by their similarities of expression levels, has been used for identifying unknown functions of genes. Fuzzy clustering method that is one category of clustering assigns one sample to multiple groups according to their membership degrees. It is more appropriate than hard clustering algorithms for analyzing gene expression profiles since single gene might involve multiple genetic functions. However, general clustering methods have problems that they are sensitive to initialization and can be trapped into local optima. To solve the problems, we propose an evolutionary fuzzy clustering algorithm with knowledge-based evaluation. It uses a genetic algorithm for clustering and prior knowledge of data for evaluation. Yeast cell-cycle dataset has been used for experiments to show the usefulness of the proposed method.

Original languageEnglish
Title of host publicationPattern Recognition and Machine Intelligence - First International Conference, PReMI 2005, Proceedings
Pages640-644
Number of pages5
Publication statusPublished - 2005 Dec 1
Event1st International Conference on Pattern Recognition and Machine Intelligence, PReMI 2005 - Kolkata, India
Duration: 2005 Dec 202005 Dec 22

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3776 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other1st International Conference on Pattern Recognition and Machine Intelligence, PReMI 2005
CountryIndia
CityKolkata
Period05/12/2005/12/22

Fingerprint

Gene Expression Profile
Cluster analysis
Cluster Analysis
Knowledge-based
Clustering Methods
Transcriptome
Gene expression
Clustering algorithms
Evolutionary algorithms
Clustering Algorithm
Evolutionary Algorithms
Fuzzy clustering
Genes
Fuzzy Clustering
Gene
Evaluation
Clustering
Fuzzy Algorithm
Cell Cycle
Initialization

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Park, H. S., & Cho, S. B. (2005). Evolutionary clustering algorithm with knowledge-based evaluation for fuzzy cluster analysis of gene expression profiles. In Pattern Recognition and Machine Intelligence - First International Conference, PReMI 2005, Proceedings (pp. 640-644). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3776 LNCS).
Park, Han Saem ; Cho, Sung Bae. / Evolutionary clustering algorithm with knowledge-based evaluation for fuzzy cluster analysis of gene expression profiles. Pattern Recognition and Machine Intelligence - First International Conference, PReMI 2005, Proceedings. 2005. pp. 640-644 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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Park, HS & Cho, SB 2005, Evolutionary clustering algorithm with knowledge-based evaluation for fuzzy cluster analysis of gene expression profiles. in Pattern Recognition and Machine Intelligence - First International Conference, PReMI 2005, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 3776 LNCS, pp. 640-644, 1st International Conference on Pattern Recognition and Machine Intelligence, PReMI 2005, Kolkata, India, 05/12/20.

Evolutionary clustering algorithm with knowledge-based evaluation for fuzzy cluster analysis of gene expression profiles. / Park, Han Saem; Cho, Sung Bae.

Pattern Recognition and Machine Intelligence - First International Conference, PReMI 2005, Proceedings. 2005. p. 640-644 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3776 LNCS).

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

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Park HS, Cho SB. Evolutionary clustering algorithm with knowledge-based evaluation for fuzzy cluster analysis of gene expression profiles. In Pattern Recognition and Machine Intelligence - First International Conference, PReMI 2005, Proceedings. 2005. p. 640-644. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).