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An evaluation of experimental design in QSARmodelling utilizing the k-medoid clustering
Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.ORCID iD: 0000-0001-9382-9296
2012 (English)In: Journal of Chemometrics, ISSN 0886-9383, E-ISSN 1099-128X, Vol. 26, no 10, 509-517 p.Article in journal (Refereed) Published
Abstract [en]

A reliable selection of a representative subset of chemical compounds has been reported to be crucial for numeroustasks in computational chemistry and chemoinformatics. We investigated the usability of an approach on the basisof the k-medoid algorithm for this task and in particular for experimental design and the split between training andvalidation set. We therefore compared the performance of models derived from such a selection to that of modelsderived using several other approaches, such as space-filling design and D-optimal design. We validated the performance on four datasets with different endpoints, representing toxicity, physicochemical properties and others.Compared with the models derived from the compounds selected by the other examined approaches, those derivedwith the k-medoid selection show a high reliability for experimental design, as their performance was constantlyamong the best for all examined datasets. Of all the models derived with all examined approaches, those derivedwith the k-medoid approach were the only ones that showed a significantly improved performance compared witha random selection, for all datasets, the whole examined range of selected compounds and for each dimensionalityof the search space.

Place, publisher, year, edition, pages
2012. Vol. 26, no 10, 509-517 p.
National Category
Environmental Sciences
Research subject
Natural Science, Environmental Science
Identifiers
URN: urn:nbn:se:lnu:diva-19540DOI: 10.1002/cem.2459OAI: oai:DiVA.org:lnu-19540DiVA: diva2:531155
Available from: 2012-06-05 Created: 2012-06-05 Last updated: 2016-11-15Bibliographically approved

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Publisher's full texthttp://onlinelibrary.wiley.com/doi/10.1002/cem.2459/abstract

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CiteExportLink to record
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Citation style
  • apa
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  • modern-language-association-8th-edition
  • vancouver
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More styles
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  • de-DE
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  • en-US
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  • Other locale
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