Local kernel canonical correlation analysis with application to virtual drug screening

DOI10.1214/11-AOAS472zbMATH Open1228.62072arXiv1202.3302OpenAlexW3103587236WikidataQ35570159 ScholiaQ35570159MaRDI QIDQ652382FDOQ652382

Authors: Daniel Samarov, Christopher Grulke, Alexander Tropsha, J. S. Marron, Yufeng Liu 

Publication date: 14 December 2011

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Abstract: Drug discovery is the process of identifying compounds which have potentially meaningful biological activity. A major challenge that arises is that the number of compounds to search over can be quite large, sometimes numbering in the millions, making experimental testing intractable. For this reason computational methods are employed to filter out those compounds which do not exhibit strong biological activity. This filtering step, also called virtual screening reduces the search space, allowing for the remaining compounds to be experimentally tested. In this paper we propose several novel approaches to the problem of virtual screening based on Canonical Correlation Analysis (CCA) and on a kernel-based extension. Spectral learning ideas motivate our proposed new method called Indefinite Kernel CCA (IKCCA). We show the strong performance of this approach both for a toy problem as well as using real world data with dramatic improvements in predictive accuracy of virtual screening over an existing methodology.

Full work available at URL: https://arxiv.org/abs/1202.3302

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zbMATH Keywords

kernel methodsindefinite kernelsdrug discovery

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Measures of association (correlation, canonical correlation, etc.) (62H20)

Cites Work

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Cited In (3)

• Eigenvector-based sparse canonical correlation analysis: fast computation for estimation of multiple canonical vectors
• The virtual screening of the drug protein with a few crystal structures based on the adaboost-SVM
• Local kernel canonical correlation analysis with application to virtual drug screening

Uses Software

• PMA

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