Bioinformatics Advance Access originally published online on April 15, 2004
Bioinformatics 2004 20(15):2429-2437; doi:10.1093/bioinformatics/bth267
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Bioinformatics 20(15) © Oxford University Press 2004; all rights reserved.
A comparative study of feature selection and multiclass classification methods for tissue classification based on gene expression
Computer Science Department, University of Rochester, Rochester, NY 14627-0226, USA
Received on November 11, 2003; revised on March 31, 2004; accepted on April 4, 2004
Advance Access Publication April 15, 2004
Summary: This paper studies the problem of building multiclass classifiers for tissue classification based on gene expression. The recent development of microarray technologies has enabled biologists to quantify gene expression of tens of thousands of genes in a single experiment. Biologists have begun collecting gene expression for a large number of samples. One of the urgent issues in the use of microarray data is to develop methods for characterizing samples based on their gene expression. The most basic step in the research direction is binary sample classification, which has been studied extensively over the past few years. This paper investigates the next step—multiclass classification of samples based on gene expression. The characteristics of expression data (e.g. large number of genes with small sample size) makes the classification problem more challenging.
The process of building multiclass classifiers is divided into two components: (i) selection of the features (i.e. genes) to be used for training and testing and (ii) selection of the classification method. This paper compares various feature selection methods as well as various state-of-the-art classification methods on various multiclass gene expression datasets.
Our study indicates that multiclass classification problem is much more difficult than the binary one for the gene expression datasets. The difficulty lies in the fact that the data are of high dimensionality and that the sample size is small. The classification accuracy appears to degrade very rapidly as the number of classes increases. In particular, the accuracy was very low regardless of the choices of the methods for large-class datasets (e.g. NCI60 and GCM). While increasing the number of samples is a plausible solution to the problem of accuracy degradation, it is important to develop algorithms that are able to analyze effectively multiple-class expression data for these special datasets.
Contact: ogihara{at}cs.rochester.edu
* To whom correspondence should be addressed.
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