A flexible approach for causal inference with multiple treatments and clustered survival outcomes

Leveraging machine learning: Covariate-adjusted Bayesian adaptive randomization and subgroup discovery in multi-arm survival trials

Clinical trials evaluate the safety and efficacy of treatments for specific diseases. Ensuring these studies are well-powered is crucial for identifying superior treatments. With the rise of personalized medicine, treatment efficacy may vary based on biomarker profiles. However, researchers often lack prior knowledge about which biomarkers are linked to varied treatment effects. Fixed or response-adaptive designs may not sufficiently account for heterogeneous patient characteristics, such as genetic diversity, potentially reducing the chance of selecting the optimal treatment for individuals. Recent advances in Bayesian nonparametric modeling pave the way for innovative trial designs that not only maintain robust power but also offer the flexibility to identify subgroups deriving greater benefits from specific treatments. Building on this inspiration, we introduce a Bayesian adaptive design for multi-arm trials focusing on time-to-event endpoints. We introduce a covariate-adjusted response adaptive randomization, updating treatment allocation probabilities grounded on causal effect estimates using a random intercept accelerated failure time BART model. After the trial concludes, we suggest employing a multi-response decision tree to pinpoint subgroups with varying treatment impacts. The performance of our design is then assessed via comprehensive simulations.

A new method for clustered survival data: Estimation of treatment effect heterogeneity and variable selection

We recently developed a new method random-intercept accelerated failure time model with Bayesian additive regression trees (riAFT-BART) to draw causal inferences about population treatment effect on patient survival from clustered and censored survival data while accounting for the multilevel data structure. The practical utility of this method goes beyond the estimation of population average treatment effect. In this work, we exposit how riAFT-BART can be used to solve two important statistical questions with clustered survival data: estimating the treatment effect heterogeneity and variable selection. Leveraging the likelihood-based machine learning, we describe a way in which we can draw posterior samples of the individual survival treatment effect from riAFT-BART model runs, and use the drawn posterior samples to perform an exploratory treatment effect heterogeneity analysis to identify subpopulations who may experience differential treatment effects than population average effects. There is sparse literature on methods for variable selection among clustered and censored survival data, particularly ones using flexible modeling techniques. We propose a permutation-based approach using the predictor's variable inclusion proportion supplied by the riAFT-BART model for variable selection. To address the missing data issue frequently encountered in health databases, we propose a strategy to combine bootstrap imputation and riAFT-BART for variable selection among incomplete clustered survival data. We conduct an expansive simulation study to examine the practical operating characteristics of our proposed methods, and provide empirical evidence that our proposed methods perform better than several existing methods across a wide range of data scenarios. Finally, we demonstrate the methods via a case study of predictors for in-hospital mortality among severe COVID-19 patients and estimating the heterogeneous treatment effects of three COVID-specific medications. The methods developed in this work are readily available in the R ${\textsf {R}}$ package riAFTBART $\textsf {riAFTBART}$ .

Using Tree-Based Machine Learning for Health Studies: Literature Review and Case Series

Tree-based machine learning methods have gained traction in the statistical and data science fields. They have been shown to provide better solutions to various research questions than traditional analysis approaches. To encourage the uptake of tree-based methods in health research, we review the methodological fundamentals of three key tree-based machine learning methods: random forests, extreme gradient boosting and Bayesian additive regression trees. We further conduct a series of case studies to illustrate how these methods can be properly used to solve important health research problems in four domains: variable selection, estimation of causal effects, propensity score weighting and missing data. We exposit that the central idea of using ensemble tree methods for these research questions is accurate prediction via flexible modeling. We applied ensemble trees methods to select important predictors for the presence of postoperative respiratory complication among early stage lung cancer patients with resectable tumors. We then demonstrated how to use these methods to estimate the causal effects of popular surgical approaches on postoperative respiratory complications among lung cancer patients. Using the same data, we further implemented the methods to accurately estimate the inverse probability weights for a propensity score analysis of the comparative effectiveness of the surgical approaches. Finally, we demonstrated how random forests can be used to impute missing data using the Study of Women's Health Across the Nation data set. To conclude, the tree-based methods are a flexible tool and should be properly used for health investigations.

A Flexible Approach for Assessing Heterogeneity of Causal Treatment Effects on Patient Survival Using Large Datasets with Clustered Observations

Personalized medicine requires an understanding of treatment effect heterogeneity. Evolving toward causal evidence for scenarios not studied in randomized trials necessitates a methodology using real-world evidence. Herein, we demonstrate a methodology that generates causal effects, assesses the heterogeneity of the effects and adjusts for the clustered nature of the data. This study uses a state-of-the-art machine learning survival model, riAFT-BART, to draw causal inferences about individual survival treatment effects, while accounting for the variability in institutional effects; further, it proposes a data-driven approach to agnostically (as opposed to a priori hypotheses) ascertain which subgroups exhibit an enhanced treatment effect from which intervention, relative to global evidence-average treatment effects measured at the population level. Comprehensive simulations show the advantages of the proposed method in terms of bias, efficiency and precision in estimating heterogeneous causal effects. The empirically validated method was then used to analyze the National Cancer Database.