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Continuously indexed Gaussian fields (GFs) are the most important ingredient in spatial statistical modelling and geostatistics. The specification through the covariance function gives an intuitive interpretation of the field properties. On the computational side, GFs are hampered with the big n problem, since the cost of factorizing dense matrices is cubic in the dimension. Although computational power today is at an all time high, this fact seems still to be a computational bottleneck in many applications. Along with GFs, there is the class of Gaussian Markov random fields (GMRFs) which are discretely indexed. The Markov property makes the precision matrix involved sparse, which enables the use of numerical algorithms for sparse matrices, that for fields in only use the square root of the time required by general algorithms. The specification of a GMRF is through its full conditional distributions but its marginal properties are not transparent in such a parameterization. We show that, using an approximate stochastic weak solution to (linear) stochastic partial differential equations, we can, for some GFs in the Matérn class, provide an explicit link, for any triangulation of , between GFs and GMRFs, formulated as a basis function representation. The consequence is that we can take the best from the two worlds and do the modelling by using GFs but do the computations by using GMRFs. Perhaps more importantly, our approach generalizes to other covariance functions generated by SPDEs, including oscillating and non-stationary GFs, as well as GFs on manifolds. We illustrate our approach by analysing global temperature data with a non-stationary model defined on a sphere.

Structured additive regression models are perhaps the most commonly used class of models in statistical applications. It includes, among others, (generalized) linear models, (generalized) additive models, smoothing spline models, state space models, semiparametric regression, spatial and spatiotemporal models, log-Gaussian Cox processes and geostatistical and geoadditive models. We consider approximate Bayesian inference in a popular subset of structured additive regression models, latent Gaussian models, where the latent field is Gaussian, controlled by a few hyperparameters and with non-Gaussian response variables. The posterior marginals are not available in closed form owing to the non-Gaussian response variables. For such models, Markov chain Monte Carlo methods can be implemented, but they are not without problems, in terms of both convergence and computational time. In some practical applications, the extent of these problems is such that Markov chain Monte Carlo sampling is simply not an appropriate tool for routine analysis. We show that, by using an integrated nested Laplace approximation and its simplified version, we can directly compute very accurate approximations to the posterior marginals. The main benefit of these approximations is computational: where Markov chain Monte Carlo algorithms need hours or days to run, our approximations provide more precise estimates in seconds or minutes. Another advantage with our approach is its generality, which makes it possible to perform Bayesian analysis in an automatic, streamlined way, and to compute model comparison criteria and various predictive measures so that models can be compared and the model under study can be challenged.

Gaussian random fields (GRFs) play an important part in spatial modelling, but can be computationally infeasible for general covariance structures. An efficient approach is to specify GRFs via stochastic partial differential equations (SPDEs) and derive Gaussian Markov random field (GMRF) approximations of the solutions. We consider the construction of a class of non-stationary GRFs with varying local anisotropy, where the local anisotropy is introduced by allowing the coefficients in the SPDE to vary with position. This is done by using a form of diffusion equation driven by Gaussian white noise with a spatially varying diffusion matrix. This allows for the introduction of parameters that control the GRF by parametrizing the diffusion matrix. These parameters and the GRF may be considered to be part of a hierarchical model and the parameters estimated in a Bayesian framework. The results show that the use of an SPDE with non-constant coefficients is a promising way of creating non-stationary spatial GMRFs that allow for physical interpretability of the parameters, although there are several remaining challenges that would need to be solved before these models can be put to general practical use.

This paper lays the foundation for employing Gaussian Markov random fields (GMRFs) for discrete decision–variable optimization via simulation; that is, optimizing the performance of a simulated system. Gaussian processes have gained popularity for inferential optimization, which iteratively updates a model of the simulated solutions and selects the next solution to simulate by relying on statistical inference from that model. We show that, for a discrete problem, GMRFs, a type of Gaussian process defined on a graph, provides better inference on the remaining optimality gap than the typical choice of continuous Gaussian process and thereby enables the algorithm to search efficiently and stop correctly when the remaining optimality gap is below a predefined threshold. We also introduce the concept of multiresolution GMRFs for large-scale problems, with which GMRFs of different resolutions interact to efficiently focus the search on promising regions of solutions. We consider optimizing the expected value of some performance measure of a dynamic stochastic simulation with a statistical guarantee for optimality when the decision variables are discrete , in particular, integer-ordered; the number of feasible solutions is large; and the model execution is too slow to simulate even a substantial fraction of them. Our goal is to create algorithms that stop searching when they can provide inference about the remaining optimality gap similar to the correct-selection guarantee of ranking and selection when it simulates all solutions. Further, our algorithm remains competitive with fixed-budget algorithms that search efficiently but do not provide such inference. To accomplish this we learn and exploit spatial relationships among the decision variables and objective function values using a Gaussian Markov random field (GMRF). Gaussian random fields on continuous domains are already used in deterministic and stochastic optimization because they facilitate the computation of measures, such as expected improvement, that balance exploration and exploitation. We show that GMRFs are particularly well suited to the discrete decision–variable problem, from both a modeling and a computational perspective. Specifically, GMRFs permit the definition of a sensible neighborhood structure, and they are defined by their precision matrices, which can be constructed to be sparse. Using this framework, we create both single and multiresolution algorithms, prove the asymptotic convergence of both, and evaluate their finite-time performance empirically. The e-companion is available at https://doi.org/10.1287/opre.2018.1778 .

We analyze the problem of maximum likelihood estimation for Gaussian distributions that are multivariate totally positive of order two (MTP₂). By exploiting connections to phylogenetics and single-linkage clustering, we give a simple proof that the maximum likelihood estimator (MLE) for such distributions exists based on n ≥ 2 observations, irrespective of the underlying dimension. Slawski and Hein [Linear Algebra Appl. 473 (2015) 145–179], who first proved this result, also provided empirical evidence showing that the MTP₂ constraint serves as an implicit regularizer and leads to sparsity in the estimated inverse covariance matrix, determining what we name the ML graph. We show that we can find an upper bound for the ML graph by adding edges corresponding to correlations in excess of those explained by the maximum weight spanning forest of the correlation matrix. Moreover, we provide globally convergent coordinate descent algorithms for calculating the MLE under the MTP₂ constraint which are structurally similar to iterative proportional scaling. We conclude the paper with a discussion of signed MTP₂ distributions.

Kingman's coalescent process opens the door for estimation of population genetics model parameters from molecular sequences. One paramount parameter of interest is the effective population size. Temporal variation of this quantity characterizes the demographic history of a population. Because researchers are rarely able to choose a priori a deterministic model describing effective population size dynamics for data at hand, nonparametric curve-fitting methods based on multiple change-point (MCP) models have been developed. We propose an alternative to change-point modeling that exploits Gaussian Markov random fields to achieve temporal smoothing of the effective population size in a Bayesian framework. The main advantage of our approach is that, in contrast to MCP models, the explicit temporal smoothing does not require strong prior decisions. To approximate the posterior distribution of the population dynamics, we use efficient, fast mixing Markov chain Monte Carlo algorithms designed for highly structured Gaussian models. In a simulation study, we demonstrate that the proposed temporal smoothing method, named Bayesian skyride, successfully recovers \"true\" population size trajectories in all simulation scenarios and competes well with the MCP approaches without evoking strong prior assumptions. We apply our Bayesian skyride method to 2 real data sets. We analyze sequences of hepatitis C virus contemporaneously sampled in Egypt, reproducing all key known aspects of the viral population dynamics. Next, we estimate the demographic histories of human influenza A hemagglutinin sequences, serially sampled throughout 3 flu seasons. [PUBLICATION ABSTRACT]

Species distribution models (SDMs) are widely used to standardize spatially unbalanced data, project climate impacts and identify habitat for conservation. SDMs typically estimate the impact of local environmental conditions by estimating a dome‐shaped or non‐parametric ‘environmental response function’. However, ecological responses often integrate across local habitat conditions, such that species density depends on habitat at the location of sampling but also at nearby locations. To address this, we extend methods from the stochastic partial differential equation (SPDE) method that is widely used in INLA, which approximates spatial correlations based on local diffusion over a finite‐element mesh (FEM). We specifically introduce the sparse inverse‐diffusion operator on a FEM and apply this operator to covariates to efficiently calculate a spatially weighted average of local habitat that is then passed through pointwise basis expansion to predict species densities. We show that this operator has several useful properties, that is conservation of mass, efficient scaling of computational time with spatial resolution, and invariance to linear (scale and offset) transformations of covariates. We test this covariate‐diffusion method using a simulation experiment and show that it can correctly recover a non‐local environmental response while collapsing to a local (pointwise) response when warranted. We apply it to monitoring data for 25 bottom‐associated fishes in the eastern Bering Sea and 20 bird species in the western United States. This application confirms that non‐local responses in the eastern Bering Sea case study are parsimonious for 26 species–maturity combinations, while 18 collapse to the pointwise method. Estimates suggest that some species–maturity combinations avoid proximity to the continental slope, beyond what is predicted by local bathymetry in isolation. By contrast, in four of the 20 bird species the diffused human population density covariate is more parsimonious than the original covariate. The covariate‐diffusion method introduced here constitutes a fast and efficient approach to modelling non‐local covariate effects. This flexible method may be useful in cases when covariates influence nearby population densities, for instance due to movement of the sampled species or its important biological or physical drivers.

Spatial whole-brain Bayesian modeling of task-related functional magnetic resonance imaging (fMRI) is a great computational challenge. Most of the currently proposed methods therefore do inference in subregions of the brain separately or do approximate inference without comparison to the true posterior distribution. A popular such method, which is now the standard method for Bayesian single subject analysis in the SPM software, is introduced in Penny et al. (2005b). The method processes the data slice-by-slice and uses an approximate variational Bayes (VB) estimation algorithm that enforces posterior independence between activity coefficients in different voxels. We introduce a fast and practical Markov chain Monte Carlo (MCMC) scheme for exact inference in the same model, both slice-wise and for the whole brain using a 3D prior on activity coefficients. The algorithm exploits sparsity and uses modern techniques for efficient sampling from high-dimensional Gaussian distributions, leading to speed-ups without which MCMC would not be a practical option. Using MCMC, we are for the first time able to evaluate the approximate VB posterior against the exact MCMC posterior, and show that VB can lead to spurious activation. In addition, we develop an improved VB method that drops the assumption of independent voxels a posteriori. This algorithm is shown to be much faster than both MCMC and the original VB for large datasets, with negligible error compared to the MCMC posterior. •A fast method for Bayesian inference in task-fMRI with spatial 3D priors is proposed.•Sparse techniques for high-dimensional Gaussian sampling give great speed-ups.•Using exact inference shows that SPM's variational Bayes can lead to false activity.•An improved variational Bayesian method shows increased speed and accuracy.

Autonomous exploration of environmental fields is one of the most promising tasks to be performed by fleets of mobile underwater robots. The goal is to maximize the information gain during the exploration process by integrating an information-metric into the path-planning and control step. Therefore, the system maintains an internal belief representation of the environmental field which incorporates previously collected measurements from the real field. In contrast to surface robots, mobile underwater systems are forced to run all computations on-board due to the limited communication bandwidth in underwater domains. Thus, reducing the computational cost of field exploration algorithms constitutes a key challenge for in-field implementations on micro underwater robot teams. In this work, we present a computationally efficient exploration algorithm which utilizes field belief models based on Gaussian Processes, such as Gaussian Markov random fields or Kalman regression, to enable field estimation with constant computational cost over time. We extend the belief models by the use of weighted shape functions to directly incorporate spatially continuous field observations. The developed belief models function as information-theoretic value functions to enable path planning through stochastic optimal control with path integrals. We demonstrate the efficiency of our exploration algorithm in a series of simulations including the case of a stationary spatio-temporal field.

We provide methods that can be used to obtain more accurate environmental exposure assessment. In particular, we propose two modeling approaches to combine monitoring data at point level with numerical model output at grid cell level, yielding improved prediction of ambient exposure at point level. Extending our earlier downscaler model (Berrocal, V. J., Gelfand, A. E., and Holland, D. M. (2010b). A spatio‐temporal downscaler for outputs from numerical models. Journal of Agricultural, Biological and Environmental Statistics 15, 176–197), these new models are intended to address two potential concerns with the model output. One recognizes that there may be useful information in the outputs for grid cells that are neighbors of the one in which the location lies. The second acknowledges potential spatial misalignment between a station and its putatively associated grid cell. The first model is a Gaussian Markov random field smoothed downscaler that relates monitoring station data and computer model output via the introduction of a latent Gaussian Markov random field linked to both sources of data. The second model is a smoothed downscaler with spatially varying random weights defined through a latent Gaussian process and an exponential kernel function, that yields, at each site, a new variable on which the monitoring station data is regressed with a spatial linear model. We applied both methods to daily ozone concentration data for the Eastern US during the summer months of June, July and August 2001, obtaining, respectively, a 5% and a 15% predictive gain in overall predictive mean square error over our earlier downscaler model (Berrocal et al., 2010b). Perhaps more importantly, the predictive gain is greater at hold‐out sites that are far from monitoring sites.