Classification and biomarker identification using gene network modules and support vector machines

<p>Abstract</p> <p>Background</p> <p>Classification using microarray datasets is usually based on a small number of samples for which tens of thousands of gene expression measurements have been obtained. The selection of the genes most significant to the classification problem is a challenging issue in high dimension data analysis and interpretation. A previous study with SVM-RCE (Recursive Cluster Elimination), suggested that classification based on groups of correlated genes sometimes exhibits better performance than classification using single genes. Large databases of gene interaction networks provide an important resource for the analysis of genetic phenomena and for classification studies using interacting genes.</p> <p>We now demonstrate that an algorithm which integrates network information with recursive feature elimination based on SVM exhibits good performance and improves the biological interpretability of the results. We refer to the method as SVM with Recursive Network Elimination (SVM-RNE)</p> <p>Results</p> <p>Initially, one thousand genes selected by t-test from a training set are filtered so that only genes that map to a gene network database remain. The Gene Expression Network Analysis Tool (GXNA) is applied to the remaining genes to form <it>n </it>clusters of genes that are highly connected in the network. Linear SVM is used to classify the samples using these clusters, and a weight is assigned to each cluster based on its importance to the classification. The least informative clusters are removed while retaining the remainder for the next classification step. This process is repeated until an optimal classification is obtained.</p> <p>Conclusion</p> <p>More than 90% accuracy can be obtained in classification of selected microarray datasets by integrating the interaction network information with the gene expression information from the microarrays.</p> <p>The Matlab version of SVM-RNE can be downloaded from <url>http://web.macam.ac.il/~myousef</url></p

Open-Set Classification for Automated Genre Identification

Abstract. Automated Genre Identification (AGI) of web pages is a problem of increasing importance since web genre (e.g. blog, news, e-shops, etc.) information can enhance modern Information Retrieval (IR) systems. The state-of-the-art in this field considers AGI as a closed-set classification problem where a variety of web page representation and machine learning models have intensively studied. In this paper, we study AGI as an open-set classification problem which better formulates the real world conditions of exploiting AGI in practice. Focusing on the use of content information, different text representation methods (words and character n-grams) are tested. Moreover, two classification methods are examined, one-class SVM learners, used as a baseline, and an ensemble of classifiers based on random feature subspacing, originally proposed for author identification. It is demonstrated that very high precision can be achieved in open-set AGI while recall remains relatively high