Conformal prediction of biological activity of chemical compounds

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), high-dimensionality 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.     

Criteria of efficiency for set-valued classification

We study optimal conformity measures for various criteria of efficiency of set-valued classification in an idealised setting. This leads to an important class of criteria of efficiency that we call probabilistic and argue for; it turns out that the most standard criteria of efficiency used in literature on conformal prediction are not probabilistic unless the problem of classification is binary. We consider both unconditional and label-conditional conformal prediction.