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March 2015 Ensembling classification models based on phalanxes of variables with applications in drug discovery
Jabed H. Tomal, William J. Welch, Ruben H. Zamar
Ann. Appl. Stat. 9(1): 69-93 (March 2015). DOI: 10.1214/14-AOAS778


Statistical detection of a rare class of objects in a two-class classification problem can pose several challenges. Because the class of interest is rare in the training data, there is relatively little information in the known class response labels for model building. At the same time the available explanatory variables are often moderately high dimensional. In the four assays of our drug-discovery application, compounds are active or not against a specific biological target, such as lung cancer tumor cells, and active compounds are rare. Several sets of chemical descriptor variables from computational chemistry are available to classify the active versus inactive class; each can have up to thousands of variables characterizing molecular structure of the compounds. The statistical challenge is to make use of the richness of the explanatory variables in the presence of scant response information. Our algorithm divides the explanatory variables into subsets adaptively and passes each subset to a base classifier. The various base classifiers are then ensembled to produce one model to rank new objects by their estimated probabilities of belonging to the rare class of interest. The essence of the algorithm is to choose the subsets such that variables in the same group work well together; we call such groups phalanxes.


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Jabed H. Tomal. William J. Welch. Ruben H. Zamar. "Ensembling classification models based on phalanxes of variables with applications in drug discovery." Ann. Appl. Stat. 9 (1) 69 - 93, March 2015.


Published: March 2015
First available in Project Euclid: 28 April 2015

zbMATH: 06446561
MathSciNet: MR3341108
Digital Object Identifier: 10.1214/14-AOAS778

Keywords: clustering , Model selection , quantitative structure activity relationship , Random forest , ranking , rare class

Rights: Copyright © 2015 Institute of Mathematical Statistics

Vol.9 • No. 1 • March 2015
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