arXiv subjects

Brian J. Reich

Publications and source records attributed to Brian J. Reich.

At least 37 records · Page 2Linked to original sources

arXiv2024

Stochastic Gradient MCMC for Massive Geostatistical Data

Gaussian processes (GPs) are commonly used for prediction and inference for spatial data analyses. However, since estimation and prediction tasks have cubic time and quadratic memory complexity in number of locations, GPs are difficult to scale to large spatial datasets. The Vecchia approximation induces sparsity in the dependence structure and is one of several methods proposed to scale GP inference. Our work adds to the substantial research in this area by developing a stochastic gradient Markov chain Monte Carlo (SGMCMC) framework for efficient computation in GPs. At each step, the algorithm subsamples a minibatch of locations and subsequently updates process parameters through a Vecchia-approximated GP likelihood. Since the Vecchia-approximated GP has a time complexity that is linear in the number of locations, this results in scalable estimation in GPs. Through simulation studies, we demonstrate that SGMCMC is competitive with state-of-the-art scalable GP algorithms in terms of computational time and parameter estimation. An application of our method is also provided using the Argo dataset of ocean temperature measurements.

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arXiv2024

Distributed model building and recursive integration for big spatial data modeling

Motivated by the need for computationally tractable spatial methods in neuroimaging studies, we develop a distributed and integrated framework for estimation and inference of Gaussian process model parameters with ultra-high-dimensional likelihoods. We propose a shift in viewpoint from whole to local data perspectives that is rooted in distributed model building and integrated estimation and inference. The framework's backbone is a computationally and statistically efficient integration procedure that simultaneously incorporates dependence within and between spatial resolutions in a recursively partitioned spatial domain. Statistical and computational properties of our distributed approach are investigated theoretically and in simulations. The proposed approach is used to extract new insights on autism spectrum disorder from the Autism Brain Imaging Data Exchange.

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arXiv2024

The R2D2 Prior for Generalized Linear Mixed Models

In Bayesian analysis, the selection of a prior distribution is typically done by considering each parameter in the model. While this can be convenient, in many scenarios it may be desirable to place a prior on a summary measure of the model instead. In this work, we propose a prior on the model fit, as measured by a Bayesian coefficient of determination ($R^2)$, which then induces a prior on the individual parameters. We achieve this by placing a beta prior on $R^2$ and then deriving the induced prior on the global variance parameter for generalized linear mixed models. We derive closed-form expressions in many scenarios and present several approximation strategies when an analytic form is not possible and/or to allow for easier computation. In these situations, we suggest approximating the prior by using a generalized beta prime distribution and provide a simple default prior construction scheme. This approach is quite flexible and can be easily implemented in standard Bayesian software. Lastly, we demonstrate the performance of the method on simulated and real-world data, where the method particularly shines in high-dimensional settings, as well as modeling random effects.

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arXiv2023

Modeling Extremal Streamflow using Deep Learning Approximations and a Flexible Spatial Process

Quantifying changes in the probability and magnitude of extreme flooding events is key to mitigating their impacts. While hydrodynamic data are inherently spatially dependent, traditional spatial models such as Gaussian processes are poorly suited for modeling extreme events. Spatial extreme value models with more realistic tail dependence characteristics are under active development. They are theoretically justified, but give intractable likelihoods, making computation challenging for small datasets and prohibitive for continental-scale studies. We propose a process mixture model (PMM) which specifies spatial dependence in extreme values as a convex combination of a Gaussian process and a max-stable process, yielding desirable tail dependence properties but intractable likelihoods. To address this, we employ a unique computational strategy where a feed-forward neural network is embedded in a density regression model to approximate the conditional distribution at one spatial location given a set of neighbors. We then use this univariate density function to approximate the joint likelihood for all locations by way of a Vecchia approximation. The PMM is used to analyze changes in annual maximum streamflow within the US over the last 50 years, and is able to detect areas which show increases in extreme streamflow over time.

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arXiv2023

Spatial regression modeling via the R2D2 framework

Spatially dependent data arises in many applications, and Gaussian processes are a popular modelling choice for these scenarios. While Bayesian analyses of these problems have proven to be successful, selecting prior distributions for these complex models remains a difficult task. In this work, we propose a principled approach for setting prior distributions on model variance components by placing a prior distribution on a measure of model fit. In particular, we derive the distribution of the prior coefficient of determination. Placing a beta prior distribution on this measure induces a generalized beta prime prior distribution on the global variance of the linear predictor in the model. This method can also be thought of as shrinking the fit towards the intercept-only (null) model. We derive an efficient Gibbs sampler for the majority of the parameters and use Metropolis-Hasting updates for the others. Finally, the method is applied to a marine protection area data set. We estimate the effect of marine policies on biodiversity and conclude that no-take restrictions lead to a slight increase in biodiversity and that the majority of the variance in the linear predictor comes from the spatial effect.\vspace{12pt}

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arXiv2022

A Bayesian Semiparametric Method For Estimating Causal Quantile Effects

Standard causal inference characterizes treatment effect through averages, but the counterfactual distributions could be different in not only the central tendency but also spread and shape. To provide a comprehensive evaluation of treatment effects, we focus on estimating quantile treatment effects (QTEs). Existing methods that invert a nonsmooth estimator of the cumulative distribution functions forbid inference on probability density functions (PDFs), but PDFs can reveal more nuanced characteristics of the counterfactual distributions. We adopt a semiparametric conditional distribution regression model that allows inference on any functionals of counterfactual distributions, including PDFs and multiple QTEs. To account for the observational nature of the data and ensure an efficient model, we adjust for a double balancing score that augments the propensity score with individual covariates. We provide a Bayesian estimation framework that appropriately propagates modeling uncertainty. We show via simulations that the use of double balancing score for confounding adjustment improves performance over adjusting for any single score alone, and the proposed semiparametric model estimates QTEs more accurately than other semiparametric methods. We apply the proposed method to the North Carolina birth weight dataset to analyze the effect of maternal smoking on infant's birth weight.

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arXiv2022

SPQR: An R Package for Semi-Parametric Density and Quantile Regression

We develop an R package SPQR that implements the semi-parametric quantile regression (SPQR) method in Xu and Reich (2021). The method begins by fitting a flexible density regression model using monotonic splines whose weights are modeled as data-dependent functions using artificial neural networks. Subsequently, estimates of conditional density and quantile process can all be obtained. Unlike many approaches to quantile regression that assume a linear model, SPQR allows for virtually any relationship between the covariates and the response distribution including non-linear effects and different effects on different quantile levels. To increase the interpretability and transparency of SPQR, model-agnostic statistics developed by Apley and Zhu (2020) are used to estimate and visualize the covariate effects and their relative importance on the quantile function. In this article, we detail how this framework is implemented in SPQR and illustrate how this package should be used in practice through simulated and real data examples.

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arXiv2022

A Gaussian-process approximation to a spatial SIR process using moment closures and emulators

The dynamics that govern disease spread are hard to model because infections are functions of both the underlying pathogen as well as human or animal behavior. This challenge is increased when modeling how diseases spread between different spatial locations. Many proposed spatial epidemiological models require trade-offs to fit, either by abstracting away theoretical spread dynamics, fitting a deterministic model, or by requiring large computational resources for many simulations. We propose an approach that approximates the complex spatial spread dynamics with a Gaussian process. We first propose a flexible spatial extension to the well-known SIR stochastic process, and then we derive a moment-closure approximation to this stochastic process. This moment-closure approximation yields ordinary differential equations for the evolution of the means and covariances of the susceptibles and infectious through time. Because these ODEs are a bottleneck to fitting our model by MCMC, we approximate them using a low-rank emulator. This approximation serves as the basis for our hierarchical model for noisy, underreported counts of new infections by spatial location and time. We demonstrate using our model to conduct inference on simulated infections from the underlying, true spatial SIR jump process. We then apply our method to model counts of new Zika infections in Brazil from late 2015 through early 2016.

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arXiv2022

Distributed Inference for Spatial Extremes Modeling in High Dimensions

Extreme environmental events frequently exhibit spatial and temporal dependence. These data are often modeled using max stable processes (MSPs). MSPs are computationally prohibitive to fit for as few as a dozen observations, with supposed computationally-efficient approaches like the composite likelihood remaining computationally burdensome with a few hundred observations. In this paper, we propose a spatial partitioning approach based on local modeling of subsets of the spatial domain that delivers computationally and statistically efficient inference. Marginal and dependence parameters of the MSP are estimated locally on subsets of observations using censored pairwise composite likelihood, and combined using a modified generalized method of moments procedure. The proposed distributed approach is extended to estimate spatially varying coefficient models to deliver computationally efficient modeling of spatial variation in marginal parameters. We demonstrate consistency and asymptotic normality of estimators, and show empirically that our approach leads to a surprising reduction in bias of parameter estimates over a full data approach. We illustrate the flexibility and practicability of our approach through simulations and the analysis of streamflow data from the U.S. Geological Survey.

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arXiv2021

Monitoring Deforestation Using Multivariate Bayesian Online Changepoint Detection with Outliers

Near real time change detection is important for a variety of Earth monitoring applications and remains a high priority for remote sensing science. Data sparsity, subtle changes, seasonal trends, and the presence of outliers make detecting actual landscape changes challenging. Adams and MacKay (2007) introduced Bayesian Online Changepoint Detection (BOCPD), a computationally efficient, exact Bayesian method for change detection. Incorporation of prior information allows for relaxed dependence on dense data and an extensive stable period, making this method applicable to relatively short time series and multiple changepoint detection. In this paper we conduct BOCPD with a multivariate linear regression framework that supports seasonal trends. We introduce a mechanism to make BOCPD robust against occasional outliers without compromising the computational efficiency of an exact posterior change distribution nor the detection latency. We show via simulations that the method effectively detects change in the presence of outliers. The method is then applied to monitor deforestation in Myanmar where we show superior performance compared to current online changepoint detection methods.

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arXiv2021

Selecting Diverse Models for Scientific Insight

Model selection often aims to choose a single model, assuming that the form of the model is correct. However, there may be multiple possible underlying explanatory patterns in a set of predictors that could explain a response. Model selection without regard for model uncertainty can fail to bring these patterns to light. We explore multi-model penalized regression (MMPR) to acknowledge model uncertainty in the context of penalized regression. We examine how different penalty settings can promote either shrinkage or sparsity of coefficients in separate models. The method is tuned to explicitly limit model similarity. A choice of penalty form that enforces variable selection is applied to predict stacking fault energy (SFE) from steel alloy composition. The aim is to identify multiple models with different subsets of covariates that explain a single type of response.

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arXiv2021

Kryging: Geostatistical analysis of large-scale datasets using Krylov subspace methods

Analyzing massive spatial datasets using Gaussian process model poses computational challenges. This is a problem prevailing heavily in applications such as environmental modeling, ecology, forestry and environmental heath. We present a novel approximate inference methodology that uses profile likelihood and Krylov subspace methods to estimate the spatial covariance parameters and makes spatial predictions with uncertainty quantification. The proposed method, Kryging, applies for both observations on regular grid and irregularly-spaced observations, and for any Gaussian process with a stationary covariance function, including the popular $\Matern$ covariance family. We make use of the block Toeplitz structure with Toeplitz blocks of the covariance matrix and use fast Fourier transform methods to alleviate the computational and memory bottlenecks. We perform extensive simulation studies to show the effectiveness of our model by varying sample sizes, spatial parameter values and sampling designs. A real data application is also performed on a dataset consisting of land surface temperature readings taken by the MODIS satellite. Compared to existing methods, the proposed method performs satisfactorily with much less computation time and better scalability.

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arXiv2021

Bayesian Non-parametric Quantile Process Regression and Estimation of Marginal Quantile Effects

Flexible estimation of multiple conditional quantiles is of interest in numerous applications, such as studying the effect of pregnancy-related factors on low and high birth weight. We propose a Bayesian non-parametric method to simultaneously estimate non-crossing, non-linear quantile curves. We expand the conditional distribution function of the response in I-spline basis functions where the covariate-dependent coefficients are modeled using neural networks. By leveraging the approximation power of splines and neural networks, our model can approximate any continuous quantile function. Compared to existing models, our model estimates all rather than a finite subset of quantiles, scales well to high dimensions, and accounts for estimation uncertainty. While the model is arbitrarily flexible, interpretable marginal quantile effects are estimated using accumulative local effect plots and variable importance measures. A simulation study shows that our model can better recover quantiles of the response distribution when the data is sparse, and an analysis of birth weight data is presented.

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arXiv2021

Estimating Atmospheric Motion Winds from Satellite Image Data using Space-time Drift Models

Geostationary satellites collect high-resolution weather data comprising a series of images which can be used to estimate wind speed and direction at different altitudes. The Derived Motion Winds (DMW) Algorithm is commonly used to process these data and estimate atmospheric winds by tracking features in images taken by the GOES-R series of the NOAA geostationary meteorological satellites. However, the wind estimates from the DMW Algorithm are sparse and do not come with uncertainty measures. This motivates us to statistically model wind motions as a spatial process drifting in time. We propose a covariance function that depends on spatial and temporal lags and a drift parameter to capture the wind speed and wind direction. We estimate the parameters by local maximum likelihood. Our method allows us to compute standard errors of the estimates, enabling spatial smoothing of the estimates using a Gaussian kernel weighted by the inverses of the estimated variances. We conduct extensive simulation studies to determine the situations where our method performs well. The proposed method is applied to the GOES-15 brightness temperature data over Colorado and reduces prediction error of brightness temperature compared to the DMW Algorithm.

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arXiv2021

Estimating intervention effects on infectious disease control: the effect of community mobility reduction on Coronavirus spread

Understanding the effects of interventions, such as restrictions on community and large group gatherings, is critical to controlling the spread of COVID-19. Susceptible-Infectious-Recovered (SIR) models are traditionally used to forecast the infection rates but do not provide insights into the causal effects of interventions. We propose a spatiotemporal model that estimates the causal effect of changes in community mobility (intervention) on infection rates. Using an approximation to the SIR model and incorporating spatiotemporal dependence, the proposed model estimates a direct and indirect (spillover) effect of intervention. Under an interference and treatment ignorability assumption, this model is able to estimate causal intervention effects, and additionally allows for spatial interference between locations. Reductions in community mobility were measured by cell phone movement data. The results suggest that the reductions in mobility decrease Coronavirus cases 4 to 7 weeks after the intervention.

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arXiv2021

Instrumental variables, spatial confounding and interference

Unobserved spatial confounding variables are prevalent in environmental and ecological applications where the system under study is complex and the data are often observational. Instrumental variables (IVs) are a common way to address unobserved confounding; however, the efficacy of using IVs on spatial confounding is largely unknown. This paper explores the effectiveness of IVs in this situation -- with particular attention paid to the spatial scale of the instrument. We show that, in case of spatially-dependent treatments, IVs are most effective when they vary at a finer spatial resolution than the treatment. We investigate IV performance in extensive simulations and apply the model in the example of long term trends in the air pollution and cardiovascular mortality in the United States over 1990-2010. Finally, the IV approach is also extended to the spatial interference setting, in which treatments can affect nearby responses.

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arXiv2020

A semiparametric spatiotemporal Bayesian model for the bulk and extremes of the Fosberg Fire Weather Index

Large wildfires pose a major environmental concern, and precise maps of fire risk can improve disaster relief planning. Fosberg Fire Weather Index (FFWI) is often used to measure wildfire risk; FFWI exhibits non-Gaussian marginal distributions as well as strong spatiotemporal extremal dependence and thus, modeling FFWI using geostatistical models like Gaussian processes is questionable. Extreme value theory (EVT)-driven models like max-stable processes are theoretically appealing but are computationally demanding and applicable only for threshold exceedances or block maxima. Disaster management policies often consider moderate-to-extreme quantiles of climate parameters and hence, joint modeling of the bulk and the tail of the data is required. In this paper, we consider a Dirichlet process mixture of spatial skew-t processes that can flexibly model the bulk as well as the tail. The proposed model has nonstationary mean and covariance structure, and also nonzero spatiotemporal extremal dependence. A simulation study demonstrates that the proposed model has better spatial prediction performance compared to some competing models. We develop spatial maps of FFWI medians and extremes, and discuss the wildfire risk throughout the Santa Ana region of California.

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arXiv2020

Nonparametric Conditional Density Estimation In A Deep Learning Framework For Short-Term Forecasting

Short-term forecasting is an important tool in understanding environmental processes. In this paper, we incorporate machine learning algorithms into a conditional distribution estimator for the purposes of forecasting tropical cyclone intensity. Many machine learning techniques give a single-point prediction of the conditional distribution of the target variable, which does not give a full accounting of the prediction variability. Conditional distribution estimation can provide extra insight on predicted response behavior, which could influence decision-making and policy. We propose a technique that simultaneously estimates the entire conditional distribution and flexibly allows for machine learning techniques to be incorporated. A smooth model is fit over both the target variable and covariates, and a logistic transformation is applied on the model output layer to produce an expression of the conditional density function. We provide two examples of machine learning models that can be used, polynomial regression and deep learning models. To achieve computational efficiency we propose a case-control sampling approximation to the conditional distribution. A simulation study for four different data distributions highlights the effectiveness of our method compared to other machine learning-based conditional distribution estimation techniques. We then demonstrate the utility of our approach for forecasting purposes using tropical cyclone data from the Atlantic Seaboard. This paper gives a proof of concept for the promise of our method, further computational developments can fully unlock its insights in more complex forecasting and other applications.

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