Open Access
December 2011 Efficient, adaptive cross-validation for tuning and comparing models, with application to drug discovery
Hui Shen, William J. Welch, Jacqueline M. Hughes-Oliver
Ann. Appl. Stat. 5(4): 2668-2687 (December 2011). DOI: 10.1214/11-AOAS491


Cross-validation (CV) is widely used for tuning a model with respect to user-selected parameters and for selecting a “best” model. For example, the method of k-nearest neighbors requires the user to choose k, the number of neighbors, and a neural network has several tuning parameters controlling the network complexity. Once such parameters are optimized for a particular data set, the next step is often to compare the various optimized models and choose the method with the best predictive performance. Both tuning and model selection boil down to comparing models, either across different values of the tuning parameters or across different classes of statistical models and/or sets of explanatory variables. For multiple large sets of data, like the PubChem drug discovery cheminformatics data which motivated this work, reliable CV comparisons are computationally demanding, or even infeasible. In this paper we develop an efficient sequential methodology for model comparison based on CV. It also takes into account the randomness in CV. The number of models is reduced via an adaptive, multiplicity-adjusted sequential algorithm, where poor performers are quickly eliminated. By exploiting matching of individual observations, it is sometimes even possible to establish the statistically significant inferiority of some models with just one execution of CV.


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Hui Shen. William J. Welch. Jacqueline M. Hughes-Oliver. "Efficient, adaptive cross-validation for tuning and comparing models, with application to drug discovery." Ann. Appl. Stat. 5 (4) 2668 - 2687, December 2011.


Published: December 2011
First available in Project Euclid: 20 December 2011

zbMATH: 1234.62115
MathSciNet: MR2907131
Digital Object Identifier: 10.1214/11-AOAS491

Keywords: Assay data , cheminformatics , drug discovery , k-nearest neighbors , multiplicity adjustment , neural network , PubChem , randomized-block design , sequential analysis

Rights: Copyright © 2011 Institute of Mathematical Statistics

Vol.5 • No. 4 • December 2011
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