Feature selection using Haar wavelet power spectrum.

Full Abstract

BACKGROUND:
Feature selection is an approach to overcome the 'curse of dimensionality' in complex researches like disease classification using microarrays. Statistical methods are utilized more in this domain. Most of them do not fit for a wide range of datasets. The transform oriented signal processing domains are not probed much when other fields like image and video processing utilize them well. Wavelets, one of such techniques, have the potential to be utilized in feature selection method. The aim of this paper is to assess the capability of Haar wavelet power spectrum in the problem of clustering and gene selection based on expression data in the context of disease classification and to propose a method based on Haar wavelet power spectrum.

RESULTS:
Haar wavelet power spectra of genes were analysed and it was observed to be different in different diagnostic categories. This difference in trend and magnitude of the spectrum may be utilized in gene selection. Most of the genes selected by earlier complex methods were selected by the very simple present method. Each earlier works proved only few genes are quite enough to approach the classification problem 1. Hence the present method may be tried in conjunction with other classification methods. The technique was applied without removing the noise in data to validate the robustness of the method against the noise or outliers in the data. No special software or complex implementation is needed. The qualities of the genes selected by the present method were analysed through their gene expression data. Most of them were observed to be related to solve the classification issue since they were dominant in the diagnostic category of the dataset for which they were selected as features.

CONCLUSION:
In the present paper, the problem of feature selection of microarray gene expression data was considered. We analyzed the wavelet power spectrum of genes and proposed a clustering and feature selection method useful for classification based on Haar wavelet power spectrum. Application of this technique in this area is novel, simple, and faster than other methods, fit for a wide range of data types. The results are encouraging and throw light into the possibility of using this technique for problem domains like disease classification, gene network identification and personalized drug design.

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Author information

Author/s: Subramani, Prabakaran (P); Sahu, Rajendra (R); Verma, Shekhar (S);

Affiliation: ABV-Indian Institute of Information Technology and Management, Gwalior, India. pra_spin2(-atsign-)yahoo.com

Journal and publication information

Publication Type: Journal Article

Journal: BMC bioinformatics (BMC Bioinformatics), published in England. (Language: eng)

Reference: 2006-; vol 7 (issue ) : pp 432

Dates: Created 2006/10/20; Completed 2006/12/14; Revised 2008/11/20;

PMID: 17022808, status: MEDLINE (last retrieval date: 12/26/2008)

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MeSH headings (categories)

This article was linked to the MESH Headings shown below.

Gene Expression Profiling - methods
Oligonucleotide Array Sequence Analysis - methods
Pattern Recognition, Automated - methods

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