Probabilistic performance estimators for computational chemistry methods: Systematic Improvement Probability and Ranking Probability Matrix. I. Theory

The comparison of benchmark error sets is an essential tool for the evaluation of theories in computational chemistry. The standard ranking of methods by their Mean Unsigned Error is unsatisfactory for several reasons linked to the non-normality of the error distributions and the presence of underlying trends. Complementary statistics have recently been proposed to palliate such deficiencies, such as quantiles of the absolute errors distribution or the mean prediction uncertainty. We introduce here a new score, the systematic improvement probability (SIP), based on the direct system-wise comparison of absolute errors. Independently of the chosen scoring rule, the uncertainty of the statistics due to the incompleteness of the benchmark data sets is also generally overlooked. However, this uncertainty is essential to appreciate the robustness of rankings. In the present article, we develop two indicators based on robust statistics to address this problem: P_{inv}, the inversion probability between two values of a statistic, and \mathbf{P}_{r}, the ranking probability matrix. We demonstrate also the essential contribution of the correlations between error sets in these scores comparisons

Probabilistic performance estimators for computational chemistry methods: the empirical cumulative distribution function of absolute errors

Benchmarking studies in computational chemistry use reference datasets to assess the accuracy of a method through error statistics. The commonly used error statistics, such as the mean signed and mean unsigned errors, do not inform end-users on the expected amplitude of prediction errors attached to these methods. We show that, the distributions of model errors being neither normal nor zero-centered, these error statistics cannot be used to infer prediction error probabilities. To overcome this limitation, we advocate for the use of more informative statistics, based on the empirical cumulative distribution function of unsigned errors, namely (1) the probability for a new calculation to have an absolute error below a chosen threshold, and (2) the maximal amplitude of errors one can expect with a chosen high confidence level. Those statistics are also shown to be well suited for benchmarking and ranking studies. Moreover, the standard error on all benchmarking statistics depends on the size of the reference dataset. Systematic publication of these standard errors would be very helpful to assess the statistical reliability of benchmarking conclusions.Comment: Supplementary material: https://github.com/ppernot/ECDF

Can bin-wise scaling improve consistency and adaptivity of prediction uncertainty for machine learning regression ?

Binwise Variance Scaling (BVS) has recently been proposed as a post hoc recalibration method for prediction uncertainties of machine learning regression problems that is able of more efficient corrections than uniform variance (or temperature) scaling. The original version of BVS uses uncertainty-based binning, which is aimed to improve calibration conditionally on uncertainty, i.e. consistency. I explore here several adaptations of BVS, in particular with alternative loss functions and a binning scheme based on an input-feature (X) in order to improve adaptivity, i.e. calibration conditional on X. The performances of BVS and its proposed variants are tested on a benchmark dataset for the prediction of atomization energies and compared to the results of isotonic regression.Comment: This version corrects an error in the estimation of the Sx scores for the test set, affecting Fig. 2 and Tables I-III of the initial version. The main points of the discussion and the conclusions are unchange

Stratification of uncertainties recalibrated by isotonic regression and its impact on calibration error statistics

Abstract Post hoc recalibration of prediction uncertainties of machine learning regression problems by isotonic regression might present a problem for bin-based calibration error statistics (e.g. ENCE). Isotonic regression often produces stratified uncertainties, i.e. subsets of uncertainties with identical numerical values. Partitioning of the resulting data into equal-sized bins introduces an aleatoric component to the estimation of bin-based calibration statistics. The partitioning of stratified data into bins depends on the order of the data, which is typically an uncontrolled property of calibration test/validation sets. The tie-braking method of the ordering algorithm used for binning might also introduce an aleatoric component. I show on an example how this might significantly affect the calibration diagnostics