Sparse linear mixed model selection via streamlined variational Bayes

Abstract

Linear mixed models are a versatile statistical tool to study data by accounting for fixed effects and random effects from multiple sources of variability. In many situations, a large number of candidate fixed effects is available and it is of interest to select a parsimonious subset of those being effectively relevant for predicting the response variable. Variational approximations facilitate fast approximate Bayesian inference for the parameters of a variety of statistical models, including linear mixed models. However, for models having a high number of fixed or random effects, simple application of standard variational inference principles does not lead to fast approximate inference algorithms, due to the size of model design matrices and inefficient treatment of sparse matrix problems arising from the required approximating density parameters updates. We illustrate how recently developed streamlined variational inference procedures can be generalized to make fast and accurate inference for the parameters of linear mixed models with nested random effects and global-local priors for Bayesian fixed effects selection. Our variational inference algorithms achieve convergence to the same optima of their standard implementations, although with significantly lower computational effort, memory usage and time, especially for large numbers of random effects. Using simulated and real data examples, we assess the quality of automated procedures for fixed effects selection that are free from hyperparameters tuning and only rely upon variational posterior approximations. Moreover, we show high accuracy of variational approximations against model fitting via Markov Chain Monte Carlo sampling.