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One important application of gene expression analysis is to classify tissue samples according to their gene expression levels. Gene expression data are typically characterized by high dimensionality and small sample size, which makes the classification task quite challenging. In this paper, we present a data-dependent kernel for microarray data classification. This kernel function is engineered so that the class separability of the training data is maximized. A bootstrapping-based resampling scheme is introduced to reduce the possible training bias. The effectiveness of this adaptive kernel for microarray data classification is illustrated with a k-Nearest Neighbor (KNN) classifier. Our experimental study shows that the data-dependent kernel leads to a significant improvement in the accuracy of KNN classifiers. Furthermore, this kernel-based KNN scheme has been demonstrated to be competitive to, if not better than, more sophisticated classifiers such as Support Vector Machines (SVMs) and the Uncorrelated Linear Discriminant Analysis (ULDA) for classifying gene expression data.
Microarray data analysis, cancer classification, kernel machines, kernel optimization, bootstrapping resampling

X. Chen, H. Xiong and Y. Zhang, "Data-Dependent Kernel Machines for Microarray Data Classification," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 4, no. , pp. 583-595, 2007.
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