Visual interpretation of kernel-based prediction models

Katja Hansen, David Baehrens, Timon Schroeter, Matthias Rupp, Klaus Robert Müller

Research output: Contribution to journalArticlepeer-review

40 Citations (Scopus)


Statistical models are frequently used to estimate molecular properties, e.g., to establish quantitative structure-activity and structure-property relationships. For such models, interpretability, knowledge of the domain of applicability, and an estimate of confidence in the predictions are essential. We develop and validate a method for the interpretation of kernel-based prediction models. As a consequence of interpretability, the method helps to assess the domain of applicability of a model, to judge the reliability of a prediction, and to determine relevant molecular features. Increased interpretability also facilitates the acceptance of such models. Our method is based on visualization: For each prediction, the most contributing training samples are computed and visualized. We quantitatively show the effectiveness of our approach by conducting a questionnaire study with 71 participants, resulting in significant improvements of the participants' ability to distinguish between correct and incorrect predictions of a Gaussian process model for Ames mutagenicity.

Original languageEnglish
Pages (from-to)817-826
Number of pages10
JournalMolecular Informatics
Issue number9
Publication statusPublished - 2011 Sept


  • Confidence estimation
  • Domain of applicability
  • Kernel-based learning
  • QSAR
  • QSPR

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Medicine
  • Drug Discovery
  • Computer Science Applications
  • Organic Chemistry


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