Volume 63, Issue 2

Fast sampling of Gaussian Markov random fields

Håvard Rue

Norwegian University for Science and Technology, Trondheim, Norway

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First published: 06 January 2002
Citations: 170
Håvard Rue Department of Mathematical Sciences, Norwegian University for Science and Technology, N‐7491 Trondheim, Norway. E-mail address: Havard.Rue@math.ntnu.no

Abstract

This paper demonstrates how Gaussian Markov random fields (conditional autoregressions) can be sampled quickly by using numerical techniques for sparse matrices. The algorithm is general and efficient, and expands easily to various forms for conditional simulation and evaluation of normalization constants. We demonstrate its use by constructing efficient block updates in Markov chain Monte Carlo algorithms for disease mapping.

Number of times cited according to CrossRef: 170

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  • Lattice Representations of Spartan Random Fields, Random Fields for Spatial Data Modeling, 10.1007/978-94-024-1918-4_8, (365-392), (2020).
  • Data-Driven Probabilistic Optimal Power Flow With Nonparametric Bayesian Modeling and Inference, IEEE Transactions on Smart Grid, 10.1109/TSG.2019.2931160, 11, 2, (1077-1090), (2020).
  • Hamiltonian Monte Carlo sampling to estimate past population dynamics using the skygrid coalescent model in a Bayesian phylogenetics framework, Wellcome Open Research, 10.12688/wellcomeopenres.15770.1, 5, (53), (2020).
  • Bayesian Generalized Horseshoe Estimation of Generalized Linear Models, Machine Learning and Knowledge Discovery in Databases, 10.1007/978-3-030-46147-8_36, (598-613), (2020).
  • A literature survey of matrix methods for data science, GAMM-Mitteilungen, 10.1002/gamm.202000013, 43, 3, (2020).
  • Stochastic Volatility and GARCH: Do Squared End-of-Day Returns Provide Similar Information?, Journal of Risk and Financial Management, 10.3390/jrfm13090202, 13, 9, (202), (2020).
  • A Bayesian multivariate factor analysis model for evaluating an intervention by using observational time series data on multiple outcomes, Journal of the Royal Statistical Society: Series A (Statistics in Society), 10.1111/rssa.12569, 183, 4, (1437-1459), (2020).
  • Do We Need Stochastic Volatility and Generalised Autoregressive Conditional Heteroscedasticity? Comparing Squared End-Of-Day Returns on FTSE, Risks, 10.3390/risks8010012, 8, 1, (12), (2020).
  • Bayesian Function-on-Scalars Regression for High-Dimensional Data, Journal of Computational and Graphical Statistics, 10.1080/10618600.2019.1710837, (1-10), (2020).
  • Iterative algorithms for non-conditional and conditional simulation of Gaussian random vectors, Stochastic Environmental Research and Risk Assessment, 10.1007/s00477-020-01875-0, (2020).
  • Sovereign Risk Indices and Bayesian Theory Averaging, Econometrics, 10.3390/econometrics8020022, 8, 2, (22), (2020).
  • Identification of Structural Vector Autoregressions by Stochastic Volatility, Journal of Business & Economic Statistics, 10.1080/07350015.2020.1813588, (1-39), (2020).
  • Bayesian estimation of subset threshold autoregressions: short-term forecasting of traffic occupancy, Journal of Applied Statistics, 10.1080/02664763.2020.1801606, (1-32), (2020).
  • Bayesian analysis of spatial generalized linear mixed models with Laplace moving average random fields, Computational Statistics & Data Analysis, 10.1016/j.csda.2019.106861, (106861), (2019).
  • Dynamic shrinkage processes, Journal of the Royal Statistical Society: Series B (Statistical Methodology), 10.1111/rssb.12325, 81, 4, (781-804), (2019).
  • Bayesian Geoadditive Seemingly Unrelated Regression, Computational Statistics, 10.1007/s001800300144, 18, 2, (263-292), (2019).
  • Function estimation with locally adaptive dynamic models, Computational Statistics, 10.1007/s001800200121, 17, 4, (479-499), (2019).
  • A general semiparametric Bayesian discrete-time recurrent events model, Biostatistics, 10.1093/biostatistics/kxz029, (2019).
  • A Hierarchical Spatiotemporal Statistical Model Motivated by Glaciology, Journal of Agricultural, Biological and Environmental Statistics, 10.1007/s13253-019-00367-1, (2019).
  • Sampling Strategies for Fast Updating of Gaussian Markov Random Fields, The American Statistician, 10.1080/00031305.2019.1595144, (1-24), (2019).
  • Bayesian Inference of Local Projections with Roughness Penalty Priors, Computational Economics, 10.1007/s10614-019-09905-y, (2019).
  • Simulating Markov Random Fields With a Conclique-Based Gibbs Sampler, Journal of Computational and Graphical Statistics, 10.1080/10618600.2019.1668800, (1-11), (2019).
  • Approximation and sampling of multivariate probability distributions in the tensor train decomposition, Statistics and Computing, 10.1007/s11222-019-09910-z, (2019).
  • Bayesian sparse multiple regression for simultaneous rank reduction and variable selection, Biometrika, 10.1093/biomet/asz056, (2019).
  • A Bayesian Time-Varying Coefficient Model for Multitype Recurrent Events, Journal of Computational and Graphical Statistics, 10.1080/10618600.2019.1686988, (1-12), (2019).
  • Uncertainty quantification for inverse problems with weak partial-differential-equation constraints, GEOPHYSICS, 10.1190/geo2017-0824.1, 83, 6, (R629-R647), (2018).
  • Large scale random fields generation using localized Karhunen–Loève expansion, Advanced Modeling and Simulation in Engineering Sciences, 10.1186/s40323-018-0114-7, 5, 1, (2018).
  • Detection of spatiotemporally coherent rainfall anomalies using Markov Random Fields, Computers & Geosciences, 10.1016/j.cageo.2018.10.004, (2018).
  • Rejoinder on: Some recent work on multivariate Gaussian Markov random fields, TEST, 10.1007/s11749-018-0608-0, 27, 3, (554-569), (2018).
  • An approximate fractional Gaussian noise model with $$\mathcal {O}(n)$$O(n) computational cost, Statistics and Computing, 10.1007/s11222-018-9843-1, (2018).
  • Unconventional U.S. Monetary Policy: New Tools, Same Channels?, Journal of Risk and Financial Management, 10.3390/jrfm11040071, 11, 4, (71), (2018).
  • Adjacency-Clustering and Its Application for Yield Prediction in Integrated Circuit Manufacturing, Operations Research, 10.1287/opre.2018.1741, (2018).
  • An Auxiliary Variable Method for Markov Chain Monte Carlo Algorithms in High Dimension, Entropy, 10.3390/e20020110, 20, 2, (110), (2018).
  • Efficient Simulation of High Dimensional Gaussian Vectors, Mathematics of Operations Research, 10.1287/moor.2017.0914, (2018).
  • A Bayesian hierarchical model for glacial dynamics based on the shallow ice approximation and its evaluation using analytical solutions, The Cryosphere, 10.5194/tc-12-2229-2018, 12, 7, (2229-2248), (2018).
  • Modified Cholesky Riemann Manifold Hamiltonian Monte Carlo: exploiting sparsity for fast sampling of high-dimensional targets, Statistics and Computing, 10.1007/s11222-017-9763-5, 28, 4, (795-817), (2017).
  • Texture Inpainting Using Efficient Gaussian Conditional Simulation, SIAM Journal on Imaging Sciences, 10.1137/16M1109047, 10, 3, (1446-1474), (2017).
  • Bayesian functional enrichment analysis for the Reactome database, Statistical Theory and Related Fields, 10.1080/24754269.2017.1387444, 1, 2, (185-193), (2017).
  • Fitting large-scale structured additive regression models using Krylov subspace methods, Computational Statistics & Data Analysis, 10.1016/j.csda.2016.07.006, 105, (59-75), (2017).
  • Multiscale Spatial Density Smoothing: An Application to Large-Scale Radiological Survey and Anomaly Detection, Journal of the American Statistical Association, 10.1080/01621459.2016.1276461, 112, 519, (1047-1063), (2017).
  • The Stochastic Volatility in Mean Model With Time-Varying Parameters: An Application to Inflation Modeling, Journal of Business & Economic Statistics, 10.1080/07350015.2015.1052459, 35, 1, (17-28), (2017).
  • Spatiotemporal Modeling of Node Temperatures in Supercomputers, Journal of the American Statistical Association, 10.1080/01621459.2016.1195271, 112, 517, (92-108), (2017).
  • Modeling Spatial Covariance Using the Limiting Distribution of Spatio-Temporal Random Walks, Journal of the American Statistical Association, 10.1080/01621459.2016.1224714, 112, 518, (497-507), (2016).
  • Efficient Simulation of High Dimensional Gaussian Vectors, SSRN Electronic Journal, 10.2139/ssrn.2808355, (2016).
  • Bayesian Robust Regression with the Horseshoe+ Estimator, AI 2016: Advances in Artificial Intelligence, 10.1007/978-3-319-50127-7_37, (429-440), (2016).
  • Fast sampling with Gaussian scale mixture priors in high-dimensional regression, Biometrika, 10.1093/biomet/asw042, 103, 4, (985-991), (2016).
  • A Simple Sampler for the Horseshoe Estimator, IEEE Signal Processing Letters, 10.1109/LSP.2015.2503725, 23, 1, (179-182), (2016).
  • On the Observed-Data Deviance Information Criterion for Volatility Modeling, Journal of Financial Econometrics, 10.1093/jjfinec/nbw002, 14, 4, (772-802), (2016).
  • undefined, SEG Technical Program Expanded Abstracts 2016, 10.1190/segam2016-13879108.1, (1390-1394), (2016).
  • Gradient Scan Gibbs Sampler: An Efficient Algorithm for High-Dimensional Gaussian Distributions, IEEE Journal of Selected Topics in Signal Processing, 10.1109/JSTSP.2015.2510961, 10, 2, (343-352), (2016).
  • undefined, SEG Technical Program Expanded Abstracts 2016, 10.1190/segam2016-fwi2, (1304-1510), (2016).
  • Smoothing of land use maps for trend and change detection in urbanization, Environmental and Ecological Statistics, 10.1007/s10651-016-0354-y, 23, 4, (565-584), (2016).
  • A re-examination of maturity effect of energy futures price from the perspective of stochastic volatility, Energy Economics, 10.1016/j.eneco.2016.03.026, 56, (351-362), (2016).
  • A Survey of Stochastic Simulation and Optimization Methods in Signal Processing, IEEE Journal of Selected Topics in Signal Processing, 10.1109/JSTSP.2015.2496908, 10, 2, (224-241), (2016).
  • undefined, SEG Technical Program Expanded Abstracts 2016, 10.1190/segam2016-full, (1-2769), (2016).
  • Spatial modeling of HIV and HSV-2 among women in Kenya with spatially varying coefficients, BMC Public Health, 10.1186/s12889-016-3022-0, 16, 1, (2016).
  • Towards joint disease mapping, Statistical Methods in Medical Research, 10.1191/0962280205sm389oa, 14, 1, (61-82), (2016).
  • Estimating blood vessel areas in ultrasound images using a deformable template model, Statistical Modelling: An International Journal, 10.1191/1471082X04st074oa, 4, 3, (211-226), (2016).
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  • The Stochastic Volatility in Mean Model with Time-Varying Parameters: An Application to Inflation Modeling, SSRN Electronic Journal, 10.2139/ssrn.2579988, (2015).
  • Recent Bayesian approaches for spatial analysis of 2-D images with application to environmental modelling, Environmental and Ecological Statistics, 10.1007/s10651-015-0311-1, 22, 3, (571-600), (2015).
  • undefined, 2015 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), 10.1109/ICASSP.2015.7178739, (4085-4089), (2015).
  • Efficient Gaussian Sampling for Solving Large-Scale Inverse Problems Using MCMC, IEEE Transactions on Signal Processing, 10.1109/TSP.2014.2367457, 63, 1, (70-80), (2015).
  • Sampling From Gaussian Markov Random Fields Using Stationary and Non-Stationary Subgraph Perturbations, IEEE Transactions on Signal Processing, 10.1109/TSP.2014.2375134, 63, 3, (576-589), (2015).
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  • Modelling Inflation Volatility, SSRN Electronic Journal, 10.2139/ssrn.2400771, (2014).
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  • undefined, 2013 IEEE 13th International Conference on Data Mining, 10.1109/ICDM.2013.149, (61-70), (2013).
  • undefined, 2013 IEEE International Symposium on Information Theory, 10.1109/ISIT.2013.6620676, (2498-2502), (2013).
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  • The HESSIAN method: Highly efficient simulation smoothing, in a nutshell, Journal of Econometrics, 10.1016/j.jeconom.2011.12.003, 168, 2, (189-206), (2012).
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  • Sampling Gaussian Distributions in Krylov Spaces with Conjugate Gradients, SIAM Journal on Scientific Computing, 10.1137/110831404, 34, 3, (B312-B334), (2012).
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  • Exact and Approximate Recursive Calculations for Binary Markov Random Fields Defined on Graphs, Journal of Computational and Graphical Statistics, 10.1080/10618600.2012.632236, 21, 3, (758-780), (2012).
  • Robust Markov chain Monte Carlo Methods for Spatial Generalized Linear Mixed Models, Journal of Computational and Graphical Statistics, 10.1198/106186006X100470, 15, 1, (1-17), (2012).
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  • An explicit link between Gaussian fields and Gaussian Markov random fields: the stochastic partial differential equation approach, Journal of the Royal Statistical Society: Series B (Statistical Methodology), 10.1111/j.1467-9868.2011.00777.x, 73, 4, (423-498), (2011).
  • Bayesian inference for additive mixed quantile regression models, Computational Statistics & Data Analysis, 10.1016/j.csda.2010.05.006, 55, 1, (84-96), (2011).
  • Posterior Exploration for Computationally Intensive Forward Models, Handbook of Markov Chain Monte Carlo, 10.1201/b10905-17, (2011).
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