Multidimensional support vector machines for visualization of gene expression data

Authors:
Daisuke Komura;Hiroshi Nakamura;Shuichi Tsutsumi;Hiroyuki Aburatani;Sigeo Ihara
Affiliations:
The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo, Japan;The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo, Japan;The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo, Japan;The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo, Japan;The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo, Japan
Venue:
Proceedings of the 2004 ACM symposium on Applied computing
Year:
2004

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Abstract

DNA microarray technology has helped us to understand the biological system because of its ability to monitor the expression levels of thousands of genes simultaneously. Since DNA microarray experiments provide us with huge amount of gene expression data, they should be analyzed with statistical methods to extract the meanings of experimental results.For visualization and class prediction of gene expression data, we have developed a new SVM-based method called multidimensional SVMs, that generate multiple orthogonal axes. This method projects high dimensional data into lower dimensional space to exhibit properties of the data clearly and to visualize the distribution of the data roughly. Furthermore, the multiple axes can be used for class prediction. The basic properties of conventional SVMs are retained in our method: solutions of mathematical programming are sparse, the optimal solutions can always be found due to its convexity, and nonlinear classification is implemented implicitly through the use of kernel functions. The application of our method to the experimentally obtained gene expression datasets for patients' samples indicates that our algorithm is efficient and useful for visualization and class prediction.