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Model fitting for small skin permeability data sets: Hyperparameter optimisation in Gaussian Process Regression

Lookup NU author(s): Dr Simon Wilkinson


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© 2018 Royal Pharmaceutical Society. Objectives: The aim of this study was to investigate how to improve predictions from Gaussian Process models by optimising the model hyperparameters. Methods: Optimisation methods, including Grid Search, Conjugate Gradient, Random Search, Evolutionary Algorithm and Hyper-prior, were evaluated and applied to previously published data. Data sets were also altered in a structured manner to reduce their size, which retained the range, or 'chemical space' of the key descriptors to assess the effect of the data range on model quality. Key findings: The Hyper-prior Smoothbox kernel results in the best models for the majority of data sets, and they exhibited significantly better performance than benchmark quantitative structure-permeability relationship (QSPR) models. When the data sets were systematically reduced in size, the different optimisation methods generally retained their statistical quality, whereas benchmark QSPR models performed poorly. Conclusions: The design of the data set, and possibly also the approach to validation of the model, is critical in the development of improved models. The size of the data set, if carefully controlled, was not generally a significant factor for these models and that models of excellent statistical quality could be produced from substantially smaller data sets.

Publication metadata

Author(s): Ashrafi P, Sun Y, Davey N, Adams RG, Wilkinson SC, Moss GP

Publication type: Article

Publication status: Published

Journal: Journal of Pharmacy and Pharmacology

Year: 2018

Volume: 70

Issue: 3

Pages: 361-373

Print publication date: 01/03/2018

Online publication date: 17/01/2018

Acceptance date: 22/11/2017

ISSN (print): 0022-3573

ISSN (electronic): 2042-7158

Publisher: John Wiley & Sons Ltd


DOI: 10.1111/jphp.12863


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