microarraygeneexpressiondataanalysiswithsvm.docVIP

?Microarray Gene Expression Data Analysis with SVM Suvrajit Maji Department of Computational Biology University of Pittsburgh Pittsburgh, PA 15213 smaji@andrew.cmu.edu 1 Introduction and Motivation Microarrays are capable of determining the expression levels of thousands of genes simultaneously. One important application of gene expression data is classification of samples into categories. In combination with classification methods, this tool can be useful to support clinical management decisions for individual patients, e.g. in oncology. Standard statistic methodologies in classification or prediction do not work well when the number of variables p (genes) far too exceeds the number of samples n which is the case in gene microarray expression data. Several machine learning algorithms have been applied to the analysis of microarray data. Gene expression profiles generated by Microarray experiments can be quite complex since these experiments can involve hypotheses involving entire genomes. So, modification of existing statistical methodologies or development of new methodologies is needed for the analysis of microarray data It is only natural, then, to apply tried and tested machine learning algorithms to analyze this data in a timely, automated and cost effective way. 2 Related Work Recently, with the development of large-scale high-throughput gene expression technology, several studies have been reported on the application of microarray gene expression data analysis for molecular classification of cancer ( [1], [2], [6] ).Also, the work that predicts clinical outcomes in breast cancer ( [10], [11] ) and lymphoma ( [9] ) from gene expression data has been proven to be successful. [7] utilized a nearest-neighbor classifier method for the classification of acute myeloid lymphoma (AML) and acute leukemia lymphoma (ALL) in children. [5] performed a systematic comparison of several discrimination methods for classification of tumors based on microarr