arXiv subjects

Quan Vu

Publications and source records attributed to Quan Vu.

7 recordsLinked to original sources

arXiv2025

deepspat: An R package for modeling nonstationary spatial and spatio-temporal Gaussian and extremes data through deep deformations

Nonstationarity in spatial and spatio-temporal processes is ubiquitous in environmental datasets, but is not often addressed in practice, due to a scarcity of statistical software packages that implement nonstationary models. In this article, we introduce the R software package deepspat, which allows for modeling, fitting and prediction with nonstationary spatial and spatio-temporal models applied to Gaussian and extremes data. The nonstationary models in our package are constructed using a deep multi-layered deformation of the original spatial or spatio-temporal domain, and are straightforward to implement. Model parameters are estimated using gradient-based optimization of customized loss functions with tensorflow, which implements automatic differentiation. The functionalities of the package are illustrated through simulation studies and an application to Nepal temperature data.

stat.CO↗

arXiv2025

A Single Index Approach to Integrated Species Distribution Modeling for Fisheries Abundance Data

In fisheries ecology, species abundance data are often collected by multiple surveys, each with unique characteristics. This article is motivated by a dataset of Atlantic sea scallop abundance records along the northeast coast of the United States, collected from two bottom trawl surveys which cover a larger spatial domain but have low catch efficiency, and a dredge survey which is more efficient but more bounded in domain. Over the past decade, integrated species distribution models (ISDMs) that include common environmental effects along with correlated survey-specific spatial fields have been used to incorporate information from multiple surveys. While flexible, ISDMs can be susceptible to overfitting, which can complicate interpretability of the shared environmental effects, and potentially lead to poor predictive performance. To overcome these drawbacks, we introduce a novel single index ISDM, built from a single index (with spatial random effects) that represents a latent measure of the true species distribution, and survey-specific catch efficiency functions which map the single index to the survey-specific expected catch. In this article, these functions are constructed via logistic functions or semiparametric spline-based functions. Simulations and application to the motivating sea scallop abundance data demonstrate that the proposed single index ISDM offers more meaningful interpretations of the environmental effects and survey catch efficiency differences, while achieving similar to or better predictive performance than existing ISDMs.

stat.AP↗

arXiv2024

Random Effects Misspecification and its Consequences for Prediction in Generalized Linear Mixed Models

When fitting generalized linear mixed models (GLMMs), one important decision to make relates to the choice of the random effects distribution. As the random effects are unobserved, misspecification of this distribution is a real possibility. In this article, we investigate the consequences of random effects misspecification for point prediction and prediction inference in GLMMs, a topic on which there is considerably less research compared to consequences for parameter estimation and inference. We use theory, simulation, and a real application to explore the effect of using the common normality assumption for the random effects distribution when the correct specification is a mixture of normal distributions, focusing on the impacts on point prediction, mean squared prediction errors (MSEPs), and prediction intervals. We found that the optimal shrinkage is different under the two random effect distributions, so is impacted by misspecification. The unconditional MSEPs for the random effects are almost always larger under the misspecified normal random effects distribution, especially when cluster sizes are small. Results for the MSEPs conditional on the random effects are more complicated, but they remain generally larger under the misspecified distribution when the true random effect is close to the mean of one of the component distributions in the true mixture distribution. Results for prediction intervals indicate that overall coverage probability is not greatly impacted by misspecification.

stat.ME↗

arXiv2022

Constructing Large Nonstationary Spatio-Temporal Covariance Models via Compositional Warpings

Understanding and predicting environmental phenomena often requires the construction of spatio-temporal statistical models, which are typically Gaussian processes. A common assumption made on Gaussian processes is that of covariance stationarity, which is unrealistic in many geophysical applications. In this article, we introduce a deep-learning-inspired approach to construct descriptive nonstationary spatio-temporal models by modeling stationary processes on warped spatio-temporal domains. The warping functions we use are constructed using several simple injective warping units which, when combined through composition, can induce complex warpings. A stationary spatio-temporal covariance function on the warped domain induces covariance nonstationarity on the original domain. Sparse linear algebraic methods are used to reduce the computational complexity when fitting the model in a big data setting. We show that our proposed nonstationary spatio-temporal model can capture covariance nonstationarity in both space and time, and provide better probabilistic predictions than conventional stationary models in both simulation studies and on a real-world data set.

stat.ME↗

arXiv2021

Warped Gradient-Enhanced Gaussian Process Surrogate Models for Exponential Family Likelihoods with Intractable Normalizing Constants

Markov chain Monte Carlo methods for exponential family models with intractable normalizing constant, such as the exchange algorithm, require simulations of the sufficient statistics at every iteration of the Markov chain, which often result in expensive computations. Surrogate models for the likelihood function have been developed to accelerate inference algorithms in this context. However, these surrogate models tend to be relatively inflexible, and often provide a poor approximation to the true likelihood function. In this article, we propose the use of a warped, gradient-enhanced, Gaussian process surrogate model for the likelihood function, which jointly models the sample means and variances of the sufficient statistics, and uses warping functions to capture covariance nonstationarity in the input parameter space. We show that both the consideration of nonstationarity and the inclusion of gradient information can be leveraged to obtain a surrogate model that outperforms the conventional stationary Gaussian process surrogate model when making inference, particularly in regions where the likelihood function exhibits a phase transition. We also show that the proposed surrogate model can be used to improve the effective sample size per unit time when embedded in exact inferential algorithms. The utility of our approach in speeding up inferential algorithms is demonstrated on simulated and real-world data.

stat.CO↗

arXiv2021

Modeling Nonstationary and Asymmetric Multivariate Spatial Covariances via Deformations

Multivariate spatial-statistical models are often used when modeling environmental and socio-demographic processes. The most commonly used models for multivariate spatial covariances assume both stationarity and symmetry for the cross-covariances, but these assumptions are rarely tenable in practice. In this article we introduce a new and highly flexible class of nonstationary and asymmetric multivariate spatial covariance models that are constructed by modeling the simpler and more familiar stationary and symmetric multivariate covariances on a warped domain. Inspired by recent developments in the univariate case, we propose modeling the warping function as a composition of a number of simple injective warping functions in a deep-learning framework. Importantly, covariance-model validity is guaranteed by construction. We establish the types of warpings that allow for cross-covariance symmetry and asymmetry, and we use likelihood-based methods for inference that are computationally efficient. The utility of this new class of models is shown through two data illustrations: a simulation study on nonstationary data and an application on ocean temperatures at two different depths.

stat.ME↗

arXiv2020

Deep Compositional Spatial Models

Spatial processes with nonstationary and anisotropic covariance structure are often used when modelling, analysing and predicting complex environmental phenomena. Such processes may often be expressed as ones that have stationary and isotropic covariance structure on a warped spatial domain. However, the warping function is generally difficult to fit and not constrained to be injective, often resulting in `space-folding.' Here, we propose modelling an injective warping function through a composition of multiple elemental injective functions in a deep-learning framework. We consider two cases; first, when these functions are known up to some weights that need to be estimated, and, second, when the weights in each layer are random. Inspired by recent methodological and technological advances in deep learning and deep Gaussian processes, we employ approximate Bayesian methods to make inference with these models using graphics processing units. Through simulation studies in one and two dimensions we show that the deep compositional spatial models are quick to fit, and are able to provide better predictions and uncertainty quantification than other deep stochastic models of similar complexity. We also show their remarkable capacity to model nonstationary, anisotropic spatial data using radiances from the MODIS instrument aboard the Aqua satellite.

stat.ME↗