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Register a new userLR-GLM: High-Dimensional Bayesian Inference Using Low-Rank Data Approximations
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Due to the ease of modern data collection, applied statisticians often have access to a large set of covariates that they wish to relate to some observed outcome. Generalized linear models (GLMs) offer a particularly interpretable framework for such an analysis. In these high-dimensional problems, the number of covariates is often large relative to the number of observations, so we face non-trivial inferential uncertainty; a Bayesian approach allows coherent quantification of this uncertainty. Unfortunately, existing methods for Bayesian inference in GLMs require running times roughly cubic in parameter dimension, and so are limited to settings with at most tens of thousand parameters. We propose to reduce time and memory costs with a low-rank approximation of the data in an approach we call LR-GLM. When used with the Laplace approximation or Markov chain Monte Carlo, LR-GLM provides a full Bayesian posterior approximation and admits running times reduced by a full factor of the parameter dimension. We rigorously establish the quality of our approximation and show how the choice of rank allows a tunable computational-statistical trade-off. Experiments support our theory and demonstrate the efficacy of LR-GLM on real large-scale datasets.
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Modelling random dynamical systems in continuous time, diffusion processes are a powerful tool in many areas of science. Model parameters can be estimated from time-discretely observed processes using Markov chain Monte Carlo (MCMC) methods that introduce auxiliary data. These methods typically approximate the transition densities of the process numerically, both for calculating the posterior densities and proposing auxiliary data. Here, the Euler-Maruyama scheme is the standard approximation technique. However, the MCMC method is computationally expensive. Using higher-order approximations may accelerate it, but the specific implementation and benefit remain unclear. Hence, we investigate the utilisation and usefulness of higher-order approximations in the example of the Milstein scheme. Our study demonstrates that the MCMC methods based on the Milstein approximation yield good estimation results. However, they are computationally more expensive and can be applied to multidimensional processes only with impractical restrictions. Moreover, the combination of the Milstein approximation and the well-known modified bridge proposal introduces additional numerical challenges.
The R package RegressionFactory provides expander functions for constructing the high-dimensional gradient vector and Hessian matrix of the log-likelihood function for generalized linear models (GLMs), from the lower-dimensional base-distribution derivatives. The software follows a modular implementation using the chain rule of derivatives. Such modularity offers a clear separation of case-specific components (base distribution functional form and link functions) from common steps (e.g., matrix algebra operations needed for expansion) in calculating log-likelihood derivatives. In doing so, RegressionFactory offers several advantages: 1) It provides a fast and convenient method for constructing log-likelihood and its derivatives by requiring only the low-dimensional, base-distribution derivatives, 2) The accompanying definiteness-invariance theorem allows researchers to reason about the negative-definiteness of the log-likelihood Hessian in the much lower-dimensional space of the base distributions, 3) The factorized, abstract view of regression suggests opportunities to generate novel regression models, and 4) Computational techniques for performance optimization can be developed generically in the abstract framework and be readily applicable across all the specific regression instances. We expect RegressionFactory to facilitate research and development on optimization and sampling techniques for GLM log-likelihoods as well as construction of composite models from GLM lego blocks, such as Hierarchical Bayesian models.
Extreme mass ratio inspirals (EMRIs) are thought to be one of the most exciting gravitational wave sources to be detected with LISA. Due to their complicated nature and weak amplitudes the detection and parameter estimation of such sources is a challenging task. In this paper we present a statistical methodology based on Bayesian inference in which the estimation of parameters is carried out by advanced Markov chain Monte Carlo (MCMC) algorithms such as parallel tempering MCMC. We analysed high and medium mass EMRI systems that fall well inside the low frequency range of LISA. In the context of the Mock LISA Data Challenges, our investigation and results are also the first instance in which a fully Markovian algorithm is applied for EMRI searches. Results show that our algorithm worked well in recovering EMRI signals from different (simulated) LISA data sets having single and multiple EMRI sources and holds great promise for posterior computation under more realistic conditions. The search and estimation methods presented in this paper are general in their nature, and can be applied in any other scenario such as AdLIGO, AdVIRGO and Einstein Telescope with their respective response functions.
This paper studies inference in linear models whose parameter of interest is a high-dimensional matrix. We focus on the case where the high-dimensional matrix parameter is well-approximated by a ``spiked low-rank matrix whose rank grows slowly compared to its dimensions and whose nonzero singular values diverge to infinity. We show that this framework covers a broad class of models of latent-variables which can accommodate matrix completion problems, factor models, varying coefficient models, principal components analysis with missing data, and heterogeneous treatment effects. For inference, we propose a new ``rotation-debiasing method for product parameters initially estimated using nuclear norm penalization. We present general high-level results under which our procedure provides asymptotically normal estimators. We then present low-level conditions under which we verify the high-level conditions in a treatment effects example.
It has become increasingly common to collect high-dimensional binary data; for example, with the emergence of new sampling techniques in ecology. In smaller dimensions, multivariate probit (MVP) models are routinely used for inferences. However, algorithms for fitting such models face issues in scaling up to high dimensions due to the intractability of the likelihood, involving an integral over a multivariate normal distribution having no analytic form. Although a variety of algorithms have been proposed to approximate this intractable integral, these approaches are difficult to implement and/or inaccurate in high dimensions. We propose a two-stage Bayesian approach for inference on model parameters while taking care of the uncertainty propagation between the stages. We use the special structure of latent Gaussian models to reduce the highly expensive computation involved in joint parameter estimation to focus inference on marginal distributions of model parameters. This essentially makes the method embarrassingly parallel for both stages. We illustrate performance in simulations and applications to joint species distribution modeling in ecology.
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