Joint classifier and feature optimization for comprehensive cancer diagnosis using gene expression data.


Journal Article

Recent research has demonstrated quite convincingly that accurate cancer diagnosis can be achieved by constructing classifiers that are designed to compare the gene expression profile of a tissue of unknown cancer status to a database of stored expression profiles from tissues of known cancer status. This paper introduces the JCFO, a novel algorithm that uses a sparse Bayesian approach to jointly identify both the optimal nonlinear classifier for diagnosis and the optimal set of genes on which to base that diagnosis. We show that the diagnostic classification accuracy of the proposed algorithm is superior to a number of current state-of-the-art methods in a full leave-one-out cross-validation study of five widely used benchmark datasets. In addition to its superior classification accuracy, the algorithm is designed to automatically identify a small subset of genes (typically around twenty in our experiments) that are capable of providing complete discriminatory information for diagnosis. Focusing attention on a small subset of genes is useful not only because it produces a classifier with good generalization capacity, but also because this set of genes may provide insights into the mechanisms responsible for the disease itself. A number of the genes identified by the JCFO in our experiments are already in use as clinical markers for cancer diagnosis; some of the remaining genes may be excellent candidates for further clinical investigation. If it is possible to identify a small set of genes that is indeed capable of providing complete discrimination, inexpensive diagnostic assays might be widely deployable in clinical settings.

Full Text

Duke Authors

Cited Authors

  • Krishnapuram, B; Carin, L; Hartemink, AJ

Published Date

  • January 2004

Published In

Volume / Issue

  • 11 / 2-3

Start / End Page

  • 227 - 242

PubMed ID

  • 15285890

Pubmed Central ID

  • 15285890

Electronic International Standard Serial Number (EISSN)

  • 1557-8666

International Standard Serial Number (ISSN)

  • 1066-5277

Digital Object Identifier (DOI)

  • 10.1089/1066527041410463


  • eng