Kernel-Based Data Fusion and Its Application to Protein Function Prediction in Yeast

GRG Lanckriet, M Deng, Nello Cristianini, MI Jordan, WS Noble

Research output: Contribution to journalArticle (Academic Journal)peer-review

229 Citations (Scopus)

Abstract

Kernel methods provide a principled framework in which to represent many types of data, including vectors, strings, trees and graphs. As such, these methods are useful for drawing inferences about biological phenomena. We describe a method for combining multiple kernel representations in an optimal fashion, by formulating the problem as a convex optimization problem that can be solved using semideflnite programming techniques. The method is applied to the problem of predicting yeast protein functional classiflcations using a support vector machine SVM trained on flve types of data. For this problem, the new method performs better than a previously-described Markov random fleld method, and better than the SVM trained on any single type of data.
Translated title of the contributionKernel-Based Data Fusion and Its Application to Protein Function Prediction in Yeast
Original languageEnglish
Pages (from-to)300-311
JournalBiocomputing 2004, Proceedings of the Pacific Symposium, Hawaii, USA
Publication statusPublished - 2004

Bibliographical note

ISBN: 9812385983
Publisher: World Scientific
Name and Venue of Conference: Biocomputing 2004, Proceedings of the Pacific Symposium, Hawaii, USA
Other identifier: 2000790

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