Imputation of Data Missing Not at Random: artificial generationand benchmark analysis

Abstract

Experimental assessment of different missing data imputation methods often compute error rates between the original values and the estimated ones. This experimental setup relies on complete datasets that are injected with missing values. The injection process is straightforward for the Missing Completely At Random and Missing At Random mechanisms; however, the Missing Not At Random mechanism poses a major challenge, since the available artificial generation strategies are limited. Furthermore, the studies focused on this latter mechanism tend to disregard a comprehensive baseline of state-of-the-art imputation methods. In this work, both challenges are addressed: four new Missing Not At Random generation strategies are introduced and a benchmark study is conducted to compare six imputation methods in an experimental setup that covers 10 datasets and five missingness levels (10% to 80%). The overall findings are that, for most missing rates and datasets, the best imputation method to deal with Missing Not At Random values is the Multiple Imputation by Chained Equations, whereas for higher missingness rates autoencoders show promising results.