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Computational Biology and Chemistry
Volume 30, Issue 1, February 2006, Pages 63-71
 
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doi:10.1016/j.compbiolchem.2005.10.008    How to Cite or Link Using DOI (Opens New Window)
Copyright © 2005 Elsevier Ltd All rights reserved.

Brief communication

Reducing multiclass cancer classification to binary by output coding and SVM

Li ShenCorresponding Author Contact Information, E-mail The Corresponding Author and Eng Chong Tan

School of Computer Engineering, Nanyang Technological University, Nanyang Avenue, Singapore 639798, Singapore

Received 20 July 2005; 
revised 11 October 2005; 
accepted 11 October 2005. 
Available online 29 November 2005.

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Abstract

Multiclass cancer classification based on microarray data is presented. The binary classifiers used combine support vector machines with a generalized output-coding scheme. Different coding strategies, decoding functions and feature selection methods are incorporated and validated on two cancer datasets: GCM and ALL. Using random coding strategy and recursive feature elimination, the testing accuracy achieved is as high as 83% on GCM data with 14 classes. Comparing with other classification methods, our method is superior in classificatory performance.

Keywords: Multiclass; Cancer classification; Microarrays; Output coding; Support vector machine

Article Outline

1. Introduction
2. Methods
2.1. Output coding for multiclass classification
2.2. Coding matrix
2.2.1. Random coding
2.2.2. Exhaustive coding
2.3. Decoding function
2.4. Classification methods
2.4.1. Support vector machine
2.4.2. K-nearest neighbor
2.4.3. C4.5 decision tree
2.4.4. Backpropagation neural network
2.4.5. Parameters for classification methods
2.5. Feature selection
2.5.1. Gene ranking
2.5.2. Dimension reduction
2.5.3. Recursive feature elimination
3. Results
3.1. Datasets and experimental setup
3.2. Testing on output coding and SVM
3.3. Comparison of classification accuracies with other classification methods
4. Conclusions and future work
References




 
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