Search

A multivariate distribution can be described by a triangular transport map from the target distribution to a simple reference distribution. We propose Bayesian nonparametric inference on the transport map by modeling its components using Gaussian processes. This enables regularization and uncertainty quantification of the map estimation, while resulting in a closed-form and invertible posterior map. We then focus on inferring the distribution of a nonstationary spatial field from a small number of replicates. We develop specific transport-map priors that are highly flexible and are motivated by the behavior of a large class of stochastic processes. Our approach is scalable to high-dimensional distributions due to data-dependent sparsity and parallel computations. We also discuss extensions, including Dirichlet process mixtures for flexible marginals. We present numerical results to demonstrate the accuracy, scalability, and usefulness of our methods, including statistical emulation of non-Gaussian climate-model output. for this article are available online. [ABSTRACT FROM AUTHOR]

The constellation of Earth-observing satellites has now produced atmospheric greenhouse gas concentration estimates covering a period of several years. Their global coverage is providing additional information on the global carbon cycle. These products can be combined with complex inversion systems to infer the magnitude of carbon sources and sinks around the globe. Multiple factors, including the atmospheric transport model and satellite product aggregation method, can impact such flux estimates. Analysis of variance (ANOVA) is a well-established statistical framework for estimating common signals while partitioning variability across factors in the analysis of experiments. Functional ANOVA extends this approach with a statistical model that incorporates spatiotemporal correlation for each ANOVA component. The approach is illustrated on inversion experiments with different satellite retrieval aggregation methods and identifies consistent significant patterns in flux increments that span large spatial scales. Functional ANOVA identifies these patterns while accounting for the uncertainty at small spatial scales that is attributed to differences in the aggregation method. Functional ANOVA is also applied to a recent flux model intercomparison project (MIP), and the relative magnitudes of inversion system effects and data source (satellite versus in situ) are similar but exhibit slightly different importance for fluxes over different continents. In all examples, the unexplained residual variability is locally sizable in magnitude but with limited spatial and temporal correlation. These common behaviors across flux inversion experiments demonstrate the diagnostic capability for functional ANOVA to simultaneously distinguish the spatiotemporal coherence of carbon cycle processes and algorithmic factors. [ABSTRACT FROM AUTHOR]

Multivariate spatial fields are of interest in many applications, including climate model emulation. Not only can the marginal spatial fields be subject to nonstationarity, but the dependence structure among the marginal fields and between the fields might also differ substantially. Extending a recently proposed Bayesian approach to describe the distribution of a nonstationary univariate spatial field using a triangular transport map, we cast the inference problem for a multivariate spatial field for a small number of replicates into a series of independent Gaussian process (GP) regression tasks with Gaussian errors. Due to the potential nonlinearity in the conditional means, the joint distribution modeled can be non-Gaussian. The resulting nonparametric Bayesian methodology scales well to high-dimensional spatial fields. It is especially useful when only a few training samples are available, because it employs regularization priors and quantifies uncertainty. Inference is conducted in an empirical Bayes setting by a highly scalable stochastic gradient approach. The implementation benefits from mini-batching and could be accelerated with parallel computing. We illustrate the extended transport-map model by studying hydrological variables from non-Gaussian climate-model output. [ABSTRACT FROM AUTHOR]

The constellation of Earth-observing satellites now produces atmospheric greenhouse gas concentration estimates across multiple years. Their global coverage is providing additional information on the global carbon cycle. These products are combined with complex inversion systems to infer the magnitude of carbon sources and sinks around the globe. Multiple factors, including the atmospheric transport model and satellite product aggregation method, can impact flux estimates. Functional analysis of variance (ANOVA) invokes a spatio-temporal statistical model to efficiently estimate common flux signals across multiple inversions, and partitions variability across the discrete factors considered. The approach is illustrated on inversion experiments with different satellite retrieval aggregation methods and identifies significant flux anomalies in the presence of mode differences across aggregation methods. Functional ANOVA is also applied to a recent flux model intercomparison project (MIP), and the relative magnitudes of transport model effects and data source (satellite versus in situ) are similar but exhibit slightly different importance for inversions over different continents. [ABSTRACT FROM AUTHOR]

Spatio-temporal filtering is a common and challenging task in many environmental applications, where the evolution is often nonlinear and the dimension of the spatial state may be very high. We propose a scalable filtering approach based on a hierarchical sparse Cholesky representation of the filtering covariance matrix. At each time point, we compress the sparse Cholesky factor into a dense matrix with a small number of columns. After applying the evolution to each of these columns, we decompress to obtain a hierarchical sparse Cholesky factor of the forecast covariance, which can then be updated based on newly available data. We illustrate the Cholesky evolution via an equivalent representation in terms of spatial basis functions. We also demonstrate the advantage of our method in numerical comparisons, including using a high-dimensional and nonlinear Lorenz model. [ABSTRACT FROM AUTHOR]

Gaussian processes (GPs) are popular models for functions, time series, and spatial fields, but direct application of GPs is computationally infeasible for large datasets. We propose a multi-scale Vecchia (MSV) approximation of GPs for modeling and analysis of multi-scale phenomena, which are ubiquitous in geophysical and other applications. In the MSV approach, increasingly large sets of variables capture increasingly small scales of spatial variation, to obtain an accurate approximation of the spatial dependence from very large to very fine scales. For a given set of observations, the MSV approach decomposes the data into different scales, which can be visualized to obtain insights into the underlying processes. We explore properties of the MSV approximation and propose an algorithm for automatic choice of the tuning parameters. We provide comparisons to existing approaches based on simulated data and using satellite measurements of land-surface temperature. [ABSTRACT FROM AUTHOR]

Spatio-temporal datasets are rapidly growing in size. For example, environmental variables are measured with increasing resolution by increasing numbers of automated sensors mounted on satellites and aircraft. Using such data, which are typically noisy and incomplete, the goal is to obtain complete maps of the spatio-temporal process, together with uncertainty quantification. We focus here on real-time filtering inference in linear Gaussian state-space models. At each time point, the state is a spatial field evaluated on a very large spatial grid, making exact inference using the Kalman filter computationally infeasible. Instead, we propose a multi-resolution filter (MRF), a highly scalable and fully probabilistic filtering method that resolves spatial features at all scales. We prove that the MRF matrices exhibit a particular block-sparse multi-resolution structure that is preserved under filtering operations through time. We describe connections to existing methods, including hierarchical matrices from numerical mathematics. We also discuss inference on time-varying parameters using an approximate Rao-Blackwellized particle filter, in which the integrated likelihood is computed using the MRF. Using a simulation study and a real satellite-data application, we show that the MRF strongly outperforms competing approaches. include Python code for reproducing the simulations, some detailed properties of the MRF and auxiliary theoretical results. [ABSTRACT FROM AUTHOR]

The ensemble Kalman filter (EnKF) is a popular technique for data assimilation in high-dimensional nonlinear state-space models. The EnKF represents distributions of interest by an ensemble, which is a form of dimension reduction that enables straightforward forecasting even for complicated and expensive evolution operators. However, the EnKF update step involves estimation of the forecast covariance matrix based on the (often small) ensemble, which requires regularization. Many existing regularization techniques rely on spatial localization, which may ignore long-range dependence. Instead, our proposed approach assumes a sparse Cholesky factor of the inverse covariance matrix, and the nonzero Cholesky entries are further regularized. The resulting method is highly flexible and computationally scalable. In our numerical experiments, our approach was more accurate and less sensitive to misspecification of tuning parameters than tapering-based localization. [ABSTRACT FROM AUTHOR]

We propose to compute a sparse approximate inverse Cholesky factor L of a dense covariance matrix \Theta by minimizing the Kullback--Leibler divergence between the Gaussian distributions \scrN (0, \Theta) and \scrN (0,L \top L 1), subject to a sparsity constraint. Surprisingly, this problem has a closed-form solution that can be computed efficiently, recovering the popular Vecchia approximation in spatial statistics. Based on recent results on the approximate sparsity of inverse Cholesky factors of \Theta obtained from pairwise evaluation of Green's functions of elliptic boundary-value problems at points \{xi\} 1\leq i\leq N \subset Rd, we propose an elimination ordering and sparsity pattern that allows us to compute \epsilon -approximate inverse Cholesky factors of such \Theta in computational complexity \scrO (N log(N/\epsilon)d) in space and \scrO (N log(N/\epsilon)2d) in time. To the best of our knowledge, this is the best asymptotic complexity for this class of problems. Furthermore, our method is embarrassingly parallel, automatically exploits low-dimensional structure in the data, and can perform Gaussian-process regression in linear (in N) space complexity. Motivated by its optimality properties, we propose applying our method to the joint covariance of training and prediction points in Gaussian-process regression, greatly improving stability and computational cost. Finally, we show how to apply our method to the important setting of Gaussian processes with additive noise, compromising neither accuracy nor computational complexity. [ABSTRACT FROM AUTHOR]

We propose a new class of filtering and smoothing methods for inference in high-dimensional, nonlinear, non-Gaussian, spatio-temporal state-space models. The main idea is to combine the ensemble Kalman filter and smoother, developed in the geophysics literature, with state-space algorithms from the statistics literature. Our algorithms address a variety of estimation scenarios, including online and off-line state and parameter estimation. We take a Bayesian perspective, for which the goal is to generate samples from the joint posterior distribution of states and parameters. The key benefit of our approach is the use of ensemble Kalman methods for dimension reduction, which allows inference for high-dimensional state vectors. We compare our methods to existing ones, including ensemble Kalman filters, particle filters, and particle MCMC. Using a real data example of cloud motion and data simulated under a number of nonlinear and non-Gaussian scenarios, we show that our approaches outperform these existing methods. for this article are available online. [ABSTRACT FROM AUTHOR]

This paper proposes new methodology for sequential state and parameter estimation within the ensemble Kalman filter. The method is fully Bayesian and propagates the joint posterior distribution of states and parameters over time. To implement the method, the authors consider three representations of the marginal posterior distribution of the parameters: a grid-based approach, a Gaussian approximation, and a sequential importance sampling (SIR) approach with kernel resampling. In contrast to existing online parameter estimation algorithms, the new method explicitly accounts for parameter uncertainty and provides a formal way to combine information about the parameters from data at different time periods. The method is illustrated and compared to existing approaches using simulated and real data. [ABSTRACT FROM AUTHOR]

Automated sensing instruments on satellites and aircraft have enabled the collection of massive amounts of high-resolution observations of spatial fields over large spatial regions. If these datasets can be efficiently exploited, they can provide new insights on a wide variety of issues. However, traditional spatial-statistical techniques such as kriging are not computationally feasible for big datasets. We propose a multi-resolution approximation (M-RA) of Gaussian processes observed at irregular locations in space. TheM-RA process is specified as a linear combination of basis functions at multiple levels of spatial resolution, which can capture spatial structure from very fine to very large scales. The basis functions are automatically chosen to approximate a given covariance function, which can be nonstationary. All computations involving theM-RA, including parameter inference and prediction, are highly scalable for massive datasets. Crucially, the inference algorithms can also be parallelized to take full advantage of large distributed-memory computing environments. In comparisons using simulated data and a large satellite dataset, theM-RA outperforms a related state-of-the-art method. Supplementary materials for this article are available online. [ABSTRACT FROM AUTHOR]

Developing global maps of carbon dioxide (CO2) mole fraction (in units of parts per million) near the Earth’s surface can help identify locations where major amounts of CO2are entering and exiting the atmosphere, thus providing valuable insights into the carbon cycle and mitigating the greenhouse effect of atmospheric CO2. Existing satellite remote sensing data do not provide measurements of the CO2mole fraction near the surface. Japan’s Greenhouse gases Observing SATellite (GOSAT) is sensitive to average CO2over the entire column, and NASA’s Atmospheric InfraRed Sounder (AIRS) is sensitive to CO2in the middle troposphere. One might expect that lower-atmospheric CO2could be inferred by differencing GOSAT column-average and AIRS mid-tropospheric data. However, the two instruments have different footprints, measurement-error characteristics, and data coverages. In addition, the spatio-temporal domains are large, and the AIRS dataset is massive. In this article, we describe a spatio-temporal data-fusion (STDF) methodology based on reduced-dimensional Kalman smoothing. Our STDF is able to combine the complementary GOSAT and AIRS datasets to optimally estimate lower-atmospheric CO2mole fraction over the whole globe. Further, it is designed for massive remote sensing datasets and accounts for differences in instrument footprint, measurement-error characteristics, and data coverages. This article has supplementary material online. [ABSTRACT FROM AUTHOR]

The use of satellite measurements in climate studies promises many new scientific insights if those data can be efficiently exploited. Due to sparseness of daily data sets, there is a need to fill spatial gaps and to borrow strength from adjacent days. Nonetheless, these satellites are typically capable of conducting on the order of 100,000 retrievals per day, which makes it impossible to apply traditional spatio-temporal statistical methods, even in supercomputing environments. To overcome these challenges, we make use of a spatio-temporal mixed-effects model. For each massive daily data set, dimension reduction is achieved by essentially modelling the underlying process as a linear combination of spatial basis functions on the globe. The application of a dynamical autoregressive model in time, over the reduced space, allows rapid sequential computation of optimal smoothing predictions via the Kalman smoother; this is known as Fixed Rank Smoothing (FRS). The dimension-reduced mixed-effects model contains a number of unknown parameters, including covariance and propagator matrices, which describe the spatial and temporal dependence structure in the reduced-dimensional process. We take an empirical-Bayes approach to inference, which involves estimating the parameters and substituting them into the optimal predictors. Method-of-moments (MM) parameter estimation (currently used in FRS) is typically inefficient compared to maximum likelihood (ML) estimation and can result in large sampling variability. Here, we develop ML estimation via an expectation-maximization (EM) algorithm, which offers stable computation of valid estimators and makes efficient use of spatial and temporal dependence in the data. The two parameter-estimation approaches, MM and ML, are compared in a simulation study. We also apply our methodology to global satellite CO measurements: We optimally smooth the sparse daily CO maps obtained by the Atmospheric InfraRed Sounder (AIRS) instrument on the Aqua satellite; then, using FRS with EM-estimated parameters, a complete sequence of the daily global CO fields can be obtained, together with their associated prediction uncertainties. [ABSTRACT FROM AUTHOR]

Modern remote-sensing retrievals often invoke a Bayesian approach to infer atmospheric properties from observed radiances. In this approach, plausible mean states and variability for the quantities of interest are encoded in a prior distribution. Recent developments have devised prior assumptions for the correlation among atmospheric constituents and across observing locations. This work formulates a spatial statistical framework for simultaneous multi-footprint retrievals of carbon dioxide (CO2) with application to the Orbiting Carbon Observatory-2/3 (OCO-2/3). Formally, the retrieval state vector is extended to include atmospheric and surface conditions at many footprints in a small region, and a prior distribution that assumes spatial correlation across these locations is assumed. This spatial prior allows the length-scale, or range, of spatial correlation to vary between different elements of the state vector. Various single- and multi-footprint retrievals are compared in a simulation study. A spatial prior that also includes relatively large prior variances for CO2 results in posterior inferences that most accurately represent the true state and that reduce the correlation in retrieval error across locations. [ABSTRACT FROM AUTHOR]

Remote Visible/Shortwave Infrared (VSWIR) imaging spectroscopy is a powerful tool for measuring the composition of Earth's surface over wide areas. This compositional information is captured by the spectral surface reflectance, where distinct shapes and absorption features indicate the chemical, bio- and geophysical properties of the materials in the scene. Estimating this surface reflectance requires removing the influence of atmospheric distortions caused by water vapor and particles. Traditionally reflectance is estimated by considering one location at a time, disentangling atmospheric and surface effects independently at all locations in a scene. However, this approach does not take advantage of spatial correlations between contiguous pixels. We propose an extension to a common Bayesian approach, Optimal Estimation, by introducing atmospheric correlations into the multivariate Gaussian prior. We show how this approach can be implemented as a small change to the traditional estimation procedure, thus limiting the additional computational burden. We demonstrate a simple version of the technique using simulations and multiple airborne radiance data sets. Our results show that the predicted atmospheric fields are smoother and more realistic than independent inversions given the assumption of spatial correlation and may reduce bias in the surface reflectance retrievals compared to post-process smoothing. [ABSTRACT FROM AUTHOR]

Gaussian processes (GPs) are highly flexible function estimators used for geospatial analysis, nonparametric regression, and machine learning, but they are computationally infeasible for large datasets. Vecchia approximations of GPs have been used to enable fast evaluation of the likelihood for parameter inference. Here, we study Vecchia approximations of spatial predictions at observed and unobserved locations, including obtaining joint predictive distributions at large sets of locations. We consider a general Vecchia framework for GP predictions, which contains some novel and some existing special cases. We study the accuracy and computational properties of these approaches theoretically and numerically, proving that our new methods exhibit linear computational complexity in the total number of spatial locations. We show that certain choices within the framework can have a strong effect on uncertainty quantification and computational cost, which leads to specific recommendations on which methods are most suitable for various settings. We also apply our methods to a satellite dataset of chlorophyll fluorescence, showing that the new methods are faster or more accurate than existing methods and reduce unrealistic artifacts in prediction maps. Supplementary materials accompanying this paper appear on-line. [ABSTRACT FROM AUTHOR]

Rapid developments in satellite remote-sensing technology have enabled the collection of geospatial data on a global scale, hence increasing the need for covariance functions that can capture spatial dependence on spherical domains. We propose a general method of constructing nonstationary, locally anisotropic covariance functions on the sphere based on covariance functions in R 3 . We also provide theorems that specify the conditions under which the resulting correlation function is isotropic or axially symmetric. For large datasets on the sphere commonly seen in modern applications, the Vecchia approximation is used to achieve higher scalability on statistical inference. The importance of flexible covariance structures is demonstrated numerically using simulated data and a precipitation dataset. Supplementary materials accompanying this paper appear online. [ABSTRACT FROM AUTHOR]

People are increasingly concerned with understanding their personal environment, including possible exposure to harmful air pollutants. To make informed decisions on their day-to-day activities, they are interested in real-time information on a localized scale. Publicly available, fine-scale, high-quality air pollution measurements acquired using mobile monitors represent a paradigm shift in measurement technologies. A methodological framework utilizing these increasingly fine-scale measurements to provide real-time air pollution maps and short-term air quality forecasts on a fine-resolution spatial scale could prove to be instrumental in increasing public awareness and understanding. The Google Street View study provides a unique source of data with spatial and temporal complexities, with the potential to provide information about commuter exposure and hot spots within city streets with high traffic. We develop a computationally efficient spatiotemporal model for these data and use the model to make short-term forecasts and high-resolution maps of current air pollution levels. We also show via an experiment that mobile networks can provide more nuanced information than an equally sized fixed-location network. This modeling framework has important real-world implications in understanding citizens' personal environments, as data production and real-time availability continue to be driven by the ongoing development and improvement of mobile measurement technologies. for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement. [ABSTRACT FROM AUTHOR]

High-throughput phenotyping (HTP) has expanded the dimensionality of data in plant research; however, HTP has resulted in few novel biological discoveries to date. Field-based HTP (FHTP), using small unoccupied aerial vehicles (UAVs) equipped with imaging sensors, can be deployed routinely to monitor segregating plant population interactions with the environment under biologically meaningful conditions. Here, flowering dates and plant height, important phenological fitness traits, were collected on 520 segregating maize recombinant inbred lines (RILs) in both irrigated and drought stress trials in 2018. Using UAV phenomic, single nucleotide polymorphism (SNP) genomic, as well as combined data, flowering times were predicted using several scenarios. Untested genotypes were predicted with 0.58, 0.59, and 0.41 prediction ability for anthesis, silking, and terminal plant height, respectively, using genomic data, but prediction ability increased to 0.77, 0.76, and 0.58 when phenomic and genomic data were used together. Using the phenomic data in a genome-wide association study, a heat-related candidate gene (GRMZM2G083810 ; hsp18f) was discovered using temporal reflectance phenotypes belonging to flowering times (both irrigated and drought) trials where heat stress also peaked. Thus, a relationship between plants and abiotic stresses belonging to a specific time of growth was revealed only through use of temporal phenomic data. Overall, this study showed that (i) it is possible to predict complex traits using high dimensional phenomic data between different environments, and (ii) temporal phenomic data can reveal a time-dependent association between genotypes and abiotic stresses, which can help understand mechanisms to develop resilient plants. [ABSTRACT FROM AUTHOR]

Gaussian process (GP) regression is a exible, nonparametric approach to regression that naturally quantifies uncertainty. In many applications, the number of responses and covariates are both large, and a goal is to select covariates that are related to the response. For this setting, we propose a novel, scalable algorithm, coined VGPR, which optimizes a penalized GP log-likelihood based on the Vecchia GP approximation, an ordered conditional approximation from spatial statistics that implies a sparse Cholesky factor of the precision matrix. We traverse the regularization path from strong to weak penalization, sequentially adding candidate covariates based on the gradient of the log-likelihood and deselecting irrelevant covariates via a new quadratic constrained coordinate descent algorithm. We propose Vecchia-based mini-batch subsampling, which provides unbiased gradient estimators. The resulting procedure is scalable to millions of responses and thousands of covariates. Theoretical analysis and numerical studies demonstrate the improved scalability and accuracy relative to existing methods. [ABSTRACT FROM AUTHOR]

The Gaussian process is an indispensable tool for spatial data analysts. The onset of the "big data" era, however, has lead to the traditional Gaussian process being computationally infeasible for modern spatial data. As such, various alternatives to the full Gaussian process that are more amenable to handling big spatial data have been proposed. These modern methods often exploit low-rank structures and/or multi-core and multi-threaded computing environments to facilitate computation. This study provides, first, an introductory overview of several methods for analyzing large spatial data. Second, this study describes the results of a predictive competition among the described methods as implemented by different groups with strong expertise in the methodology. Specifically, each research group was provided with two training datasets (one simulated and one observed) along with a set of prediction locations. Each group then wrote their own implementation of their method to produce predictions at the given location and each was subsequently run on a common computing environment. The methods were then compared in terms of various predictive diagnostics. Supplementary materials regarding implementation details of the methods and code are available for this article online. [ABSTRACT FROM AUTHOR]