Propensity score prediction for electronic healthcare databases using super learner and high-dimensional propensity score methods

The optimal learner for prediction modeling varies depending on the underlying data-generating distribution. Super Learner (SL) is a generic ensemble learning algorithm that uses cross-validation to select among a ‘library’ of candidate prediction models. While SL has been widely studied in a number of settings, it has not been thoroughly evaluated in large electronic healthcare databases that are common in pharmacoepidemiology and comparative effectiveness research. In this study, we applied and evaluated the performance of SL in its ability to predict the propensity score (PS), the conditional probability of treatment assignment given baseline covariates, using three electronic healthcare databases. We considered a library of algorithms that consisted of both nonparametric and parametric models. We also proposed a novel strategy for prediction modeling that combines SL with the high-dimensional propensity score (hdPS) variable selection algorithm. Predictive performance was assessed using three metrics: the negative log-likelihood, area under the curve (AUC), and time complexity. Results showed that the best individual algorithm, in terms of predictive performance, varied across datasets. The SL was able to adapt to the given dataset and optimize predictive performance relative to any individual learner. Combining the SL with the hdPS was the most consistent prediction method and may be promising for PS estimation and prediction modeling in electronic healthcare databases.