Deep Imputation of Missing Values in Time Series Health Data: A Review with Benchmarking

The imputation of missing values in multivariate time series data has been explored using a few recently proposed deep learning methods. The evaluation of these state-of-the-art methods is limited to one or two data sets, low missing rates, and completely random missing value types. These limited experiments do not comprehensively evaluate imputation methods on realistic data scenarios with varying missing rates and not-at-random missing types. This survey takes a data-centric approach to benchmark state-of-the-art deep imputation methods across five time series health data sets and six experimental conditions. Our extensive analysis reveals that no single imputation method outperforms the others on all five data sets. The imputation performance depends on data types, individual variable statistics, missing value rates, and types. In this context, state-of-the-art methods jointly perform cross-sectional (across variables) and longitudinal (across time) imputations of missing values in time series data. However, variables with high cross-correlation can be better imputed by cross-sectional imputation methods alone. In contrast, the ones with time series sensor signals may be better imputed by longitudinal imputation methods alone. The findings of this study emphasize the importance of considering data specifics when choosing a missing value imputation method for multivariate time series data.