LR-GLM: High-Dimensional Bayesian Inference Using Low-Rank Data Approximations

The INLA package provides a tool for computationally efficient Bayesian modeling and inference for various widely used models, more formally the class of latent Gaussian models. It is a non-sampling based framework which provides approximate results for Bayesian inference, using sparse matrices. The swift uptake of this framework for Bayesian modeling is rooted in the computational efficiency of the approach and catalyzed by the demand presented by the big data era. In this p...

We develop a Bayesian methodology aimed at simultaneously estimating low-rank and row-sparse matrices in a high-dimensional multiple-response linear regression model. We consider a carefully devised shrinkage prior on the matrix of regression coefficients which obviates the need to specify a prior on the rank, and shrinks the regression matrix towards low-rank and row-sparse structures. We provide theoretical support to the proposed methodology by proving minimax optimality o...

Bayesian variable selection is a powerful tool for data analysis, as it offers a principled method for variable selection that accounts for prior information and uncertainty. However, wider adoption of Bayesian variable selection has been hampered by computational challenges, especially in difficult regimes with a large number of covariates P or non-conjugate likelihoods. To scale to the large P regime we introduce an efficient MCMC scheme whose cost per iteration is sublinea...

Modern biomedical datasets are increasingly high dimensional and exhibit complex correlation structures. Generalized Linear Mixed Models (GLMMs) have long been employed to account for such dependencies. However, proper specification of the fixed and random effects in GLMMs is increasingly difficult in high dimensions, and computational complexity grows with increasing dimension of the random effects. We present a novel reformulation of the GLMM using a factor model decomposit...

The expressive power of a Gaussian process (GP) model comes at a cost of poor scalability in the data size. To improve its scalability, this paper presents a low-rank-cum-Markov approximation (LMA) of the GP model that is novel in leveraging the dual computational advantages stemming from complementing a low-rank approximate representation of the full-rank GP based on a support set of inputs with a Markov approximation of the resulting residual process; the latter approximati...

Generalized linear models (GLMs) arguably represent the standard approach for statistical regression beyond the Gaussian likelihood scenario. When Bayesian formulations are employed, the general absence of a tractable posterior distribution has motivated the development of deterministic approximations, which are generally more scalable than sampling techniques. Among them, expectation propagation (EP) showed extreme accuracy, usually higher than many variational Bayes solutio...

Gaussian and discrete non-Gaussian spatial datasets are prevalent across many fields such as public health, ecology, geosciences, and social sciences. Bayesian spatial generalized linear mixed models (SGLMMs) are a flexible class of models designed for these data, but SGLMMs do not scale well, even to moderately large datasets. State-of-the-art scalable SGLMMs (i.e., basis representations or sparse covariance/precision matrices) require posterior sampling via Markov chain Mon...

We consider Bayesian variable selection in sparse high-dimensional regression, where the number of covariates $p$ may be large relative to the samples size $n$, but at most a moderate number $q$ of covariates are active. Specifically, we treat generalized linear models. For a single fixed sparse model with well-behaved prior distribution, classical theory proves that the Laplace approximation to the marginal likelihood of the model is accurate for sufficiently large sample si...

Discovering interaction effects on a response of interest is a fundamental problem faced in biology, medicine, economics, and many other scientific disciplines. In theory, Bayesian methods for discovering pairwise interactions enjoy many benefits such as coherent uncertainty quantification, the ability to incorporate background knowledge, and desirable shrinkage properties. In practice, however, Bayesian methods are often computationally intractable for even moderate-dimensio...

Light and Widely Applicable (LWA-) MCMC is a novel approximation of the Metropolis-Hastings kernel targeting a posterior distribution defined on a large number of observations. Inspired by Approximate Bayesian Computation, we design a Markov chain whose transition makes use of an unknown but fixed, fraction of the available data, where the random choice of sub-sample is guided by the fidelity of this sub-sample to the observed data, as measured by summary (or sufficient) stat...