Machine learning methods for propensity and disease risk score estimation in high-dimensional data: a plasmode simulation and real-world data cohort analysis

Introduction: Machine learning (ML) methods are promising and scalable alternatives for propensity score (PS) estimation, but their comparative performance in disease risk score (DRS) estimation remains unexplored.

Methods: We used real-world data comparing antihypertensive users to non-users with 69 negative control outcomes, and plasmode simulations to study the performance of ML methods in PS and DRS estimation. We conducted a cohort study using UK primary care records. Further, we conducted a plasmode simulation with synthetic treatment and outcome mimicking empirical data distributions. We compared four PS and DRS estimation methods: 1. Reference: Logistic regression including clinically chosen confounders. 2. Logistic regression with L1 regularisation (LASSO). 3. Multi-layer perceptron (MLP). 4. Extreme Gradient Boosting (XgBoost). Covariate balance, coverage of the null effect of negative control outcomes (real-world data) and bias based on the absolute difference between observed and true effects (for plasmode) were estimated. 632,201 antihypertensive users and nonusers were included.

Results: ML methods outperformed the reference method for PS estimation in some scenarios, both in terms of covariate balance and coverage/bias. Specifically, XgBoost achieved the best performance. DRS-based methods performed worse than PS in all tested scenarios.

Discussion: We found that ML methods could be reliable alternatives for PS estimation. ML-based DRS methods performed worse than PS ones, likely given the rarity of outcomes.