Christine B. Peterson

Kevin McCoy, Zachary Wooten, Katarzyna Tomczak et al.

Clustered data, which arise when observations are nested within groups, are incredibly common in clinical, education, and social science research. Traditionally, a linear mixed model, which includes random effects to account for within-group correlation, would be used to model the observed data and make new predictions on unseen data. Some work has been done to extend the mixed model approach beyond linear regression into more complex and non-parametric models, such as decision trees and random forests. However, existing methods are limited to using the global fixed effects for prediction on data from out-of-sample groups, effectively assuming that all clusters share a common outcome model. We propose a lightweight sum-of-trees model in which we learn a decision tree for each sample group. We combine the predictions from these trees using weights so that out-of-sample group predictions are more closely aligned with the most similar groups in the training data. This strategy also allows for inference on the similarity across groups in the outcome prediction model, as the unique tree structures and variable importances for each group can be directly compared. We show our model outperforms traditional decision trees and random forests in a variety of simulation settings. Finally, we showcase our method on real-world data from the sarcoma cohort of The Cancer Genome Atlas, where patient samples are grouped by sarcoma subtype.

Kevin McCoy, Zachary Wooten, Christine B. Peterson

Measurement error is prevalent across all domains of scientific research where only imprecise observations, rather than the true underlying values, can be obtained. For example, estimates of human microbiome diversity are based on small samples from a much larger, generally unobserved system and reflect both sampling error and technical variation. In high-noise settings like these, it becomes difficult to make accurate predictions and to summarize uncertainty. Methods have previously been proposed to accommodate measurement error in classic predictive models, such as linear regression. However, relatively little work has been done to address measurement error in more complex and flexible models. Bayesian additive regression trees (BART), a Bayesian nonparametric model that sums the output of many decision trees, offers robust predictions with built-in uncertainty quantification. In this work, we propose measurement error BART (meBART), a novel extension to the BART model that directly incorporates measurement error in the independent variable(s). Through simulation studies, we show that in the presence of measurement error, our model enables more accurate parameter estimation, more robust uncertainty quantification, and superior predictive performance. We illustrate the utility of our proposed approach through two biomedical applications where the predictors of interest are subject to measurement error.

Nathan Osborne, Christine B. Peterson, Marina Vannucci

Network estimation and variable selection have been extensively studied in the statistical literature, but only recently have those two challenges been addressed simultaneously. In this paper, we seek to develop a novel method to simultaneously estimate network interactions and associations to relevant covariates for count data, and specifically for compositional data, which have a fixed sum constraint. We use a hierarchical Bayesian model with latent layers and employ spike-and-slab priors for both edge and covariate selection. For posterior inference, we develop a novel variational inference scheme with an expectation maximization step, to enable efficient estimation. Through simulation studies, we demonstrate that the proposed model outperforms existing methods in its accuracy of network recovery. We show the practical utility of our model via an application to microbiome data. The human microbiome has been shown to contribute to many of the functions of the human body, and also to be linked with a number of diseases. In our application, we seek to better understand the interaction between microbes and relevant covariates, as well as the interaction of microbes with each other. We provide a Python implementation of our algorithm, called SINC (Simultaneous Inference for Networks and Covariates), available online.