Searcharxiv⌕ Search
Home/Archive/arXiv

arXiv · 2305.08204

glmmPen: High Dimensional Penalized Generalized Linear Mixed Models

Hillary M. Heiling·Naim U. Rashid·Quefeng Li·Joseph G. Ibrahim
View original source ↗Read source document ↗Export metadata ↓

Abstract

Generalized linear mixed models (GLMMs) are widely used in research for their ability to model correlated outcomes with non-Gaussian conditional distributions. The proper selection of fixed and random effects is a critical part of the modeling process since model misspecification may lead to significant bias. However, the joint selection of fixed and random effects has historically been limited to lower-dimensional GLMMs, largely due to the use of criterion-based model selection strategies. Here we present the R package glmmPen, one of the first to select fixed and random effects in higher dimension using a penalized GLMM modeling framework. Model parameters are estimated using a Monte Carlo Expectation Conditional Minimization (MCECM) algorithm, which leverages Stan and RcppArmadillo for increased computational efficiency. Our package supports the Binomial, Gaussian, and Poisson families and multiple penalty functions. In this manuscript we discuss the modeling procedure, estimation scheme, and software implementation through application to a pancreatic cancer subtyping study. Simulation results show our method has good performance in selecting both the fixed and random effects in high dimensional GLMMs.

Explore related subjects

stat.COstat.ME

Keep this discovery

BibTeXRIS

Hillary M. Heiling, Naim U. Rashid, Quefeng Li, Joseph G. Ibrahim. 2023-05-14. glmmPen: High Dimensional Penalized Generalized Linear Mixed Models. https://arxiv.org/abs/2305.08204

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Estimating Hierarchically Rank Structured Covariance Matrices

We consider the problem of estimating a high-dimensional covariance matrix from a very limited number of samples. This problem is ubiquitous in computational fluid dynamics, where a small number of fluid snapshots must be used to construct a Gramian matrix determining a reduced-order model, as well as in computational geoscience, where a small ensemble of Earth system forecasts must be used to estimate the covariance matrix associated with the forecast uncertainty. It is common practice to regularize the small-sample covariance by imposing a "localization" structure that enforces a physically realistic correlation length scale, imposing a sparsity constraint, "shrinking" towards a prescribed target, or attenuating small correlations. We propose an alternate technique that regularizes the small-sample covariance by imposing hierarchical rank structure. Compared to regularization methods that assume sparsity such as spatial localization, hierarchical rank structure accommodates a wider range of covariance matrices, roughly corresponding to situations where long-range correlations vary more smoothly than short-range ones. It also results in a data-sparse matrix format that permits highly efficient matrix-vector products. We present theory and algorithms which show how to efficiently estimate a high-dimensional, hierarchically rank structured covariance matrix from limited samples. Through an error analysis and numerical experiments with a variety of model problems, we demonstrate that these techniques are effective at reducing sampling errors, and that in many cases they achieve smaller estimation error than conventional techniques.

stat.CO↗
arXiv2026

Optimal Slice-Adaptive Tuning of Hybrid Slice Sampling

Slice sampling is a Markov chain Monte Carlo algorithm that draws its next state uniformly from a "slice"---a super-level set of the target density function---at each iteration, thereby providing automatic local adaptivity to the scale of the target. In practice the exact slice is not known, so general-purpose implementations use an approximate slice that is grown from a starting interval of length $w>0$, with a computational cost that depends on $w$. This work presents an analysis of the average per-iteration number of target density evaluations, as a function of $w$, of hybrid slice sampling with various slice-finding schemes for targets with contiguous slices. The paper uses the results of the analysis to develop automated, slice-adaptive tuning schemes along with suboptimality bounds and asymptotic convergence guarantees. Simulations demonstrate that the tuning schemes reliably yield near-optimal slice-adaptive tuning with essentially no dependence on the initial setting of $w$.

stat.CO↗