Adapting tree-based multiple imputation methods for multi-level data? A simulation study

This simulation study evaluates the effectiveness of multiple imputation (MI) techniques for multilevel data. It compares the performance of traditional Multiple Imputation by Chained Equations (MICE) with tree-based methods such as Chained Random Forests with Predictive Mean Matching and Extreme Gradient Boosting. Adapted versions that include dummy variables for cluster membership are also included for the tree-based methods. Methods are evaluated for coefficient estimation bias, statistical power, and type I error rates on simulated hierarchical data with different cluster sizes (25 and 50) and levels of missingness (10\% and 50\%). Coefficients are estimated using random intercept and random slope models. The results show that while MICE is preferred for accurate rejection rates, Extreme Gradient Boosting is advantageous for reducing bias. Furthermore, the study finds that bias levels are similar across different cluster sizes, but rejection rates tend to be less favorable with fewer clusters (lower power, higher type I error). In addition, the inclusion of cluster dummies in tree-based methods improves estimation for Level 1 variables, but is less effective for Level 2 variables. When data become too complex and MICE is too slow, extreme gradient boosting is a good alternative for hierarchical data. Keywords: Multiple imputation; multi-level data; MICE; missRanger; mixgb

Evaluating tree-based imputation methods as an alternative to MICE PMM for drawing inference in empirical studies

Dealing with missing data is an important problem in statistical analysis that is often addressed with imputation procedures. The performance and validity of such methods are of great importance for their application in empirical studies. While the prevailing method of Multiple Imputation by Chained Equations (MICE) with Predictive Mean Matching (PMM) is considered standard in the social science literature, the increase in complex datasets may require more advanced approaches based on machine learning. In particular, tree-based imputation methods have emerged as very competitive approaches. However, the performance and validity are not completely understood, particularly compared to the standard MICE PMM. This is especially true for inference in linear models. In this study, we investigate the impact of various imputation methods on coefficient estimation, Type I error, and power, to gain insights that can help empirical researchers deal with missingness more effectively. We explore MICE PMM alongside different tree-based methods, such as MICE with Random Forest (RF), Chained Random Forests with and without PMM (missRanger), and Extreme Gradient Boosting (MIXGBoost), conducting a realistic simulation study using the German National Educational Panel Study (NEPS) as the original data source. Our results reveal that Random Forest-based imputations, especially MICE RF and missRanger with PMM, consistently perform better in most scenarios. Standard MICE PMM shows partially increased bias and overly conservative test decisions, particularly with non-true zero coefficients. Our results thus underscore the potential advantages of tree-based imputation methods, albeit with a caveat that all methods perform worse with an increased missingness, particularly missRanger.