Leave-One-Out Cross-Validation for Bayesian Model Comparison in Large Data

Recently, new methods for model assessment, based on subsampling and posterior approximations, have been proposed for scaling leave-one-out cross-validation (LOO) to large datasets. Although these methods work well for estimating predictive performance for individual models, they are less powerful in model comparison. We propose an efficient method for estimating differences in predictive performance by combining fast approximate LOO surrogates with exact LOO subsampling using the difference estimator and supply proofs with regards to scaling characteristics. The resulting approach can be orders of magnitude more efficient than previous approaches, as well as being better suited to model comparison

W-kernel and essential subspace for frequencist's evaluation of Bayesian estimators

The posterior covariance matrix W defined by the log-likelihood of each observation plays important roles both in the sensitivity analysis and frequencist's evaluation of the Bayesian estimators. This study focused on the matrix W and its principal space; we term the latter as an essential subspace. First, it is shown that they appear in various statistical settings, such as the evaluation of the posterior sensitivity, assessment of the frequencist's uncertainty from posterior samples, and stochastic expansion of the loss; a key tool to treat frequencist's properties is the recently proposed Bayesian infinitesimal jackknife approximation (Giordano and Broderick (2023)). In the following part, we show that the matrix W can be interpreted as a reproducing kernel; it is named as W-kernel. Using the W-kernel, the essential subspace is expressed as a principal space given by the kernel PCA. A relation to the Fisher kernel and neural tangent kernel is established, which elucidates the connection to the classical asymptotic theory; it also leads to a sort of Bayesian-frequencist's duality. Finally, two applications, selection of a representative set of observations and dimensional reduction in the approximate bootstrap, are discussed. In the former, incomplete Cholesky decomposition is introduced as an efficient method to compute the essential subspace. In the latter, different implementations of the approximate bootstrap for posterior means are compared.Comment: 48 pages, 10 figures. Revised and enlarged version of ISM Research Memorandum No.122

High-dimensional modeling of spatial and spatio-temporal conditional extremes using INLA and the SPDE approach

The conditional extremes framework allows for event-based stochastic modeling of dependent extremes, and has recently been extended to spatial and spatio-temporal settings. After standardizing the marginal distributions and applying an appropriate linear normalization, certain non-stationary Gaussian processes can be used as asymptotically-motivated models for the process conditioned on threshold exceedances at a fixed reference location and time. In this work, we adopt a Bayesian perspective by implementing estimation through the integrated nested Laplace approximation (INLA), allowing for novel and flexible semi-parametric specifications of the Gaussian mean function. By using Gauss-Markov approximations of the Mat\'ern covariance function (known as the Stochastic Partial Differential Equation approach) at a latent stage of the model, likelihood-based inference becomes feasible even with thousands of observed locations. We explain how constraints on the spatial and spatio-temporal Gaussian processes, arising from the conditioning mechanism, can be implemented through the latent variable approach without losing the computationally convenient Markov property. We discuss tools for the comparison of models via their posterior distributions, and illustrate the flexibility of the approach with gridded Red Sea surface temperature data at over 6,000 observed locations. Posterior sampling is exploited to study the probability distribution of cluster functionals of spatial and spatio-temporal extreme episodes

MCMC methods for inference in a mathematical model of pulmonary circulation

This study performs parameter inference in a partial differential equations system of pulmonary circulation. We use a fluid dynamics network model that takes selected parameter values and mimics the behaviour of the pulmonary haemodynamics under normal physiological and pathological conditions. This is of medical interest as it enables tracking the progression of pulmonary hypertension. We show how we make the fluids model tractable by reducing the parameter dimension from a 55D to a 5D problem. The Delayed Rejection Adaptive Metropolis algorithm, coupled with constraint non‐linear optimization, is successfully used to learn the parameter values and quantify the uncertainty in the parameter estimates. To accommodate for different magnitudes of the parameter values, we introduce an improved parameter scaling technique in the Delayed Rejection Adaptive Metropolis algorithm. Formal convergence diagnostics are employed to check for convergence of the Markov chains. Additionally, we perform model selection using different information criteria, including Watanabe Akaike Information Criteria

A flexible Bayesian tool for CoDa mixed models: logistic-normal distribution with Dirichlet covariance

Compositional Data Analysis (CoDa) has gained popularity in recent years. This type of data consists of values from disjoint categories that sum up to a constant. Both Dirichlet regression and logistic-normal regression have become popular as CoDa analysis methods. However, fitting this kind of multivariate models presents challenges, especially when structured random effects are included in the model, such as temporal or spatial effects. To overcome these challenges, we propose the logistic-normal Dirichlet Model (LNDM). We seamlessly incorporate this approach into the R-INLA package, facilitating model fitting and model prediction within the framework of Latent Gaussian Models (LGMs). Moreover, we explore metrics like Deviance Information Criteria (DIC), Watanabe Akaike information criterion (WAIC), and cross-validation measure conditional predictive ordinate (CPO) for model selection in R-INLA for CoDa. Illustrating LNDM through a simple simulated example and with an ecological case study on Arabidopsis thaliana in the Iberian Peninsula, we underscore its potential as an effective tool for managing CoDa and large CoDa databases