Probabilistic Prediction in Scikit-Learn

Adding confidence measures to predictive models should increase the trustworthiness, but only if the models are well-calibrated. Historically, some algorithms like logistic regression, but also neural networks, have been considered to produce well-calibrated probability estimates off-the-shelf. Other techniques, like decision trees and Naive Bayes, on the other hand, are infamous for being significantly overconfident in their probabilistic predictions. In this paper, a large experimental study is conducted to investigate how well-calibrated models produced by a number of algorithms in the scikit-learn library are out-of-the-box, but also if either the built-in calibration techniques Platt scaling and isotonic regression, or Venn-Abers, can be used to improve the calibration. The results show that of the seven algorithms evaluated, the only one obtaining well-calibrated models without the external calibration is logistic regression. All other algorithms, i.e., decision trees, adaboost, gradient boosting, kNN, naive Bayes and random forest benefit from using any of the calibration techniques. In particular, decision trees, Naive Bayes and the boosted models are substantially improved using external calibration. From a practitioner’s perspective, the obvious recommendation becomes to incorporate calibration when using probabilistic prediction. Comparing the different calibration techniques, Platt scaling and VennAbers generally outperform isotonic regression, on these rather small datasets. Finally, the unique ability of Venn-Abers to output not only well-calibrated probability estimates, but also the confidence in these estimates is demonstrated.This research is partly funded by the Swedish Knowledge Foundation through the industrial graduate school INSIDR.