In plain words: They tested three label-free cleanup steps—dropping low-variance features, merging rare categories, and rescaling—done before the usual held-out test of a regression model's accuracy. Even without using the outcomes, these steps can skew that accuracy estimate up or down and lead to picking a worse model.
Abstract · On the cross-validation bias due to unsupervised pre-processing
Cross-validation is the de facto standard for predictive model evaluation and selection. In proper use, it provides an unbiased estimate of a model's predictive performance. However, data sets often undergo various forms of data-dependent preprocessing, such as mean-centering, rescaling, dimensionality reduction, and outlier removal. It is often believed that such preprocessing stages, if done in an unsupervised manner (that does not incorporate the class labels or response values) are generally safe to do prior to cross-validation. In this paper, we study three commonly-practiced preprocessing procedures prior to a regression analysis: (i) variance-based feature selection; (ii) grouping of rare categorical features; and (iii) feature rescaling. We demonstrate that unsupervised preprocessing can, in fact, introduce a substantial bias into cross-validation estimates and potentially hurt model selection. This bias may be either positive or negative and its exact magnitude depends on all the parameters of the problem in an intricate manner. Further research is needed to understand the real-world impact of this bias across different application domains, particularly when dealing with small sample sizes and high-dimensional data.
Amit Moscovich, Saharon Rosset
arXiv:1901.08974 · stat.ME, cs.LG, stat.ML · submitted Jan 25, 2019 · updated May 27, 2021
abstract · pdf · html · 31 pages, 6 figures, 1 table. New sections: (4.2.) Experiments on a real dataset; (6.) Potential impact on model selection; (7.1.) Upper bounds based on stability arguments. Updated Fig. 1. with larger sample sizes