Conformal prediction of biological activity of chemical compounds

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The paper presents an application of Conformal Predictors to a chemoinformatics problem of predicting the biological activities of chemical compounds. The paper addresses some specific challenges in this domain: a large number of compounds (training examples), highdimensionality of feature space, sparseness and a strong class imbalance. A variant of conformal predictors called Inductive Mondrian Conformal Predictor is applied to deal with these challenges. Results are presented for several non-conformity measures extracted from underlying algorithms and different kernels. A number of performance measures are used in order to demonstrate the flexibility of Inductive Mondrian Conformal Predictors in dealing with such a complex set of data. This approach allowed us to identify the most likely active compounds for a given biological target and present them in a ranking order.
Original languageEnglish
Pages (from-to)105–123
Number of pages19
JournalAnnals of Mathematics and Artificial Intelligence
Early online date16 Jun 2017
Publication statusPublished - Oct 2017


  • Conformal Prediction
  • Confidence Estimation
  • Chemoinformatics
  • Non-Conformity Measure

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