Multi-Class Clustering of Cancer Subtypes through SVM Based Ensemble of Pareto-Optimal Solutions for Gene Marker Identification

Anirban Mukhopadhyay, Sanghamitra Bandyopadhyay and Ujjwal Maulik

PLOS ONE, 2010, vol. 5, issue 11, 1-14

Abstract: With the advancement of microarray technology, it is now possible to study the expression profiles of thousands of genes across different experimental conditions or tissue samples simultaneously. Microarray cancer datasets, organized as samples versus genes fashion, are being used for classification of tissue samples into benign and malignant or their subtypes. They are also useful for identifying potential gene markers for each cancer subtype, which helps in successful diagnosis of particular cancer types. In this article, we have presented an unsupervised cancer classification technique based on multiobjective genetic clustering of the tissue samples. In this regard, a real-coded encoding of the cluster centers is used and cluster compactness and separation are simultaneously optimized. The resultant set of near-Pareto-optimal solutions contains a number of non-dominated solutions. A novel approach to combine the clustering information possessed by the non-dominated solutions through Support Vector Machine (SVM) classifier has been proposed. Final clustering is obtained by consensus among the clusterings yielded by different kernel functions. The performance of the proposed multiobjective clustering method has been compared with that of several other microarray clustering algorithms for three publicly available benchmark cancer datasets. Moreover, statistical significance tests have been conducted to establish the statistical superiority of the proposed clustering method. Furthermore, relevant gene markers have been identified using the clustering result produced by the proposed clustering method and demonstrated visually. Biological relationships among the gene markers are also studied based on gene ontology. The results obtained are found to be promising and can possibly have important impact in the area of unsupervised cancer classification as well as gene marker identification for multiple cancer subtypes.

Date: 2010
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pone00:0013803

DOI: 10.1371/journal.pone.0013803

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