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Super Learning: An Application to the Prediction of HIV-1 Drug Resistance

Sinisi Sandra E., Polley Eric C, Petersen Maya L, Rhee Soo-Yon and J. van der Laan Mark
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Sinisi Sandra E.: University of California, Berkeley
Polley Eric C: University of California, Berkeley
Petersen Maya L: University of California, Berkeley
Rhee Soo-Yon: Stanford University
J. van der Laan Mark: Division of Biostatistics, School of Public Health, University of California, Berkeley

Statistical Applications in Genetics and Molecular Biology, 2007, vol. 6, issue 1, 1-26

Abstract: Many alternative data-adaptive algorithms can be used to learn a predictor based on observed data. Examples of such learners include decision trees, neural networks, support vector regression, least angle regression, logic regression, and the Deletion/Substitution/Addition algorithm. The optimal learner for prediction will vary depending on the underlying data-generating distribution. In this article we introduce the "super learner", a prediction algorithm that applies any set of candidate learners and uses cross-validation to select between them. Theory shows that asymptotically the super learner performs essentially as well as or better than any of the candidate learners. In this article we present the theory behind the super learner, and illustrate its performance using simulations. We further apply the super learner to a data example, in which we predict the phenotypic antiretroviral susceptibility of HIV based on viral genotype. Specifically, we apply the super learner to predict susceptibility to a specific protease inhibitor, nelfinavir, using a set of database-derived non-polymorphic treatment-selected mutations.

Date: 2007
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DOI: 10.2202/1544-6115.1240

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