No imputation without representation

By filling in missing values in datasets, imputation allows these datasets to be used with algorithms that cannot handle missing values by themselves. However, missing values may in principle contribute useful information that is lost through imputation. The missing-indicator approach can be used in combination with imputation to instead represent this information as a part of the dataset. There are several theoretical considerations why missing-indicators may or may not be beneficial, but there has not been any large-scale practical experiment on real-life datasets to test this question for machine learning predictions. We perform this experiment for three imputation strategies and a range of different classification algorithms, on the basis of twenty real-life datasets. We find that on these datasets, missing-indicators generally increase classification performance. In addition, we find no evidence for most algorithms that nearest neighbour and iterative imputation lead to better performance than simple mean/mode imputation. Therefore, we recommend the use of missing-indicators with mean/mode imputation as a safe default, with the caveat that for decision trees, pruning is necessary to prevent overfitting. In a follow-up experiment, we determine attribute-specific missingness thresholds for each classifier above which missing-indicators are more likely than not to increase classification performance, and observe that these thresholds are much lower for categorical than for numerical attributes. Finally, we argue that mean imputation of numerical attributes may preserve some of the information from missing values, and we show that in the absence of missing-indicators, it can similarly be useful to apply mean imputation to one-hot encoded categorical attributes instead of mode imputation.