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Bioinformatics Advance Access published online on September 16, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti033
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received January 21, 2004
Revised July 29, 2004
Accepted September 10, 2004

Article

A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis

Alexander Statnikov 1*, Constantin F. Aliferis 1, Ioannis Tsamardinos 1, Douglas Hardin 2, and Shawn Levy 1

1 Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
2 Department of Mathematics, Vanderbilt University, Nashville, TN, USA

* To whom correspondence should be addressed. E-mail: alexander.statnikov{at}vanderbilt.edu.


  Abstract

Motivation: Cancer diagnosis is one of the most important emerging clinical applications of gene expression microarray technology. We are seeking to develop a computer system for powerful and reliable cancer diagnostic model creation based on microarray data. To keep a realistic perspective on clinical applications we focus on multicategory diagnosis. In order to equip the system with the optimum combination of classifier, gene selection and cross-validation methods, we performed a systematic and comprehensive evaluation of several major algorithms for multicategory classification, several gene selection methods, multiple ensemble classifier methods, and two cross validation designs using 11 datasets spanning 74 diagnostic categories and 41 cancer types and 12 normal tissue types.

Results: Multicategory Support Vector Machines (MC-SVMs) are the most effective classifiers in performing accurate cancer diagnosis from gene expression data. The MC-SVM techniques by Crammer and Singer, Weston and Watkins, and one-versus-rest were found to be the best methods in this domain. MC-SVMs outperform other popular machine learning algorithms such as K-Nearest Neighbors, Backpropagation and Probabilistic Neural Networks, often to a remarkable degree. Gene selection techniques can significantly improve classification performance of both MC-SVMs and other non-SVM learning algorithms. Ensemble classifiers do not generally improve performance of the best non-ensemble models. These results guided the construction of a software system GEMS (Gene Expression Model Selector) that automates high-quality model construction and enforces sound optimization and performance estimation procedures. This is the first such system to be informed by a rigorous comparative analysis of the available algorithms and datasets.

Availability: The software system GEMS is available for download from http://www.gems-system.org for non-commercial use.


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