Molecular Classification of Multiple Tumor Types

Bioinformatics 17(Suppl. 1):S316-S322. 2001. Published: 2001.07.20

Chen-Hsiang Yeang, Sridhar Ramaswamy, Pablo Tamayo, Sayan Mukherjee, Ryan M. Rifkin, Michael Angelo, Michael Reich, Eric Lander, Jill P. Mesirov, and Todd Golub

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Abstract

Using gene expression data to classify tumor types is a very promising tool in cancer diagnosis. Previous works show several pairs of tumor types can be successfully distinguished by their gene expression patterns. However, the simultaneous classification across a heterogeneous set of tumor types has not been well studied yet. We obtained 190 samples from 14 tumor classes and generated a combined expression dataset containing 16063 genes for each of those samples. We performed multi-class classification by combining the outputs of binary classifiers. Three binary classifiers (k-nearest neighbors, weighted voting, and support vector machines) were applied in conjunction with three combination scenarios (one-vs-all, all-pairs, hierarchical partitioning). We achieved the best cross validation error rate of 18.75% and the best test error rate of 21.74% by using the one-vs-all support vector machine algorithm. The results demonstrate the feasibility of performing clinically useful classification from samples of multiple tumor types.

Keywords: Cancer classification cancer genomics molecular classification molecular pattern recognition

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Paper (PDF) Bioinformatics_200107.pdf
Same datasets as this paper http://www-genome.wi.mit.edu/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=61