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Bioinformatics Advance Access published online on May 5, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm234
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Incorporating prior knowledge of predictors into penalized classifiers with multiple penalty terms

Feng Tai and Wei Pan *

Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building (MMC 303), Minneapolis, MN 55455-0378,USA

*To whom correspondence should be addressed. Dr. Wei Pan, E-mail: weip{at}biostat.umn.edu


  Abstract

Motivation: In the context of sample (e.g. tumor) classifications with microarray gene expression data, many methods have been proposed. However, almost all the methods ignore existing biological knowledge and treat all the genes equally a priori. On the other hand, because some genes have been identified by previous studies to have biological functions or to be involved in pathways related to the outcome (e.g. cancer), incorporating this type of prior knowledge into a classifier can potentially improve both the predictive performance and interpretability of the resulting model.

Results: We propose a simple and general framework to incorporate such prior knowledge into building a penalized classifier. As two concrete examples, we apply the idea to two penalized classifiers, nearest shrunken centroids (also called PAM) and penalized partial least squares (PPLS). Instead of treating all the genes equally a priori as in standard penalized methods, we group the genes according to their functional associations based on existing biological knowledge or data, and adopt group-specific penalty terms and penalization parameters. Simulated and real data examples demonstrate that, if prior knowledge on gene grouping is indeed informative, our new methods perform better than the two standard penalized methods, yielding higher predictive accuracy and screening out more irrelevant genes.

Associate Editor: Dr. Olga Troyanskaya

Received on January 5, 2007; revised on April 4, 2007; accepted on April 26, 2007

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F. Tai and W. Pan
Incorporating prior knowledge of gene functional groups into regularized discriminant analysis of microarray data
Bioinformatics, December 1, 2007; 23(23): 3170 - 3177.
[Abstract] [Full Text] [PDF]


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