The application of feature selection to the development of Gaussian process models for percutaneous absorption
Article first published online: 10 JUN 2010
© 2010 The Authors Journal compilation © 2010 Royal Pharmaceutical Society of Great Britain
Journal of Pharmacy and Pharmacology
Special Issue: Recent advances in transdermal drug delivery
Volume 62, Issue 6, pages 738–749, June 2010
How to Cite
Lam, L. T., Sun, Y., Davey, N., Adams, R., Prapopoulou, M., Brown, M. B. and Moss, G. P. (2010), The application of feature selection to the development of Gaussian process models for percutaneous absorption. Journal of Pharmacy and Pharmacology, 62: 738–749. doi: 10.1211/jpp.62.06.0010
- Issue published online: 10 JUN 2010
- Article first published online: 10 JUN 2010
- Received November 02, 2009Accepted February 01, 2010
- Gaussian process;
- machine learning methods;
- percutaneous absorption;
- quantitative structure–permeability relationships
Objectives The aim was to employ Gaussian processes to assess mathematically the nature of a skin permeability dataset and to employ these methods, particularly feature selection, to determine the key physicochemical descriptors which exert the most significant influence on percutaneous absorption, and to compare such models with established existing models.
Methods Gaussian processes, including automatic relevance detection (GPRARD) methods, were employed to develop models of percutaneous absorption that identified key physicochemical descriptors of percutaneous absorption. Using MatLab software, the statistical performance of these models was compared with single linear networks (SLN) and quantitative structure–permeability relationships (QSPRs). Feature selection methods were used to examine in more detail the physicochemical parameters used in this study. A range of statistical measures to determine model quality were used.
Key findings The inherently nonlinear nature of the skin data set was confirmed. The Gaussian process regression (GPR) methods yielded predictive models that offered statistically significant improvements over SLN and QSPR models with regard to predictivity (where the rank order was: GPR > SLN > QSPR). Feature selection analysis determined that the best GPR models were those that contained log P, melting point and the number of hydrogen bond donor groups as significant descriptors. Further statistical analysis also found that great synergy existed between certain parameters. It suggested that a number of the descriptors employed were effectively interchangeable, thus questioning the use of models where discrete variables are output, usually in the form of an equation.
Conclusions The use of a nonlinear GPR method produced models with significantly improved predictivity, compared with SLN or QSPR models. Feature selection methods were able to provide important mechanistic information. However, it was also shown that significant synergy existed between certain parameters, and as such it was possible to interchange certain descriptors (i.e. molecular weight and melting point) without incurring a loss of model quality. Such synergy suggested that a model constructed from discrete terms in an equation may not be the most appropriate way of representing mechanistic understandings of skin absorption.