Fitting large-scale structured additive regression models using Krylov subspace methods

Fitting regression models can be challenging when regression coefficients are high-dimensional. Especially when large spatial or temporal effects need to be taken into account the limits of computational capacities of normal working stations are reached quickly. The analysis of images with several million pixels, where each pixel value can be seen as an observation on a new spatial location, represent such a situation. A Markov chain Monte Carlo (MCMC) framework for the applied statistician is presented that allows to fit models with millions of parameters with only low to moderate computational requirements. The method combines a modified sampling scheme with novel accomplishments in iterative methods for sparse linear systems. This way a solution is given that eliminates potential computational burdens such as calculating the log-determinant of massive precision matrices and sampling from high-dimensional Gaussian distributions. In an extensive simulation study with models of moderate size it is shown that this approach gives results that are in perfect agreement with state-of-the-art methods for fitting structured additive regression models. Furthermore, the method is applied to two real world examples from the field of medical imaging.

[1]  Karl J. Friston,et al.  Voxel-Based Morphometry—The Methods , 2000, NeuroImage.

[2]  Sw. Banerjee,et al.  Hierarchical Modeling and Analysis for Spatial Data , 2003 .

[3]  L. Knorr‐Held Conditional Prior Proposals in Dynamic Models , 1999 .

[4]  C Gössl,et al.  Bayesian Spatiotemporal Inference in Functional Magnetic Resonance Imaging , 2001, Biometrics.

[5]  Karl J. Friston,et al.  Bayesian fMRI time series analysis with spatial priors , 2005, NeuroImage.

[6]  Jo Eidsvik,et al.  Norges Teknisk-naturvitenskapelige Universitet Iterative Numerical Methods for Sampling from High Dimensional Gaussian Distributions Iterative Numerical Methods for Sampling from High Dimensional Gaussian Distributions , 2022 .

[7]  A. Pettitt,et al.  Scalable iterative methods for sampling from massive Gaussian random vectors , 2013, 1312.1476.

[8]  Nick C. Fox,et al.  Global and local gray matter loss in mild cognitive impairment and Alzheimer's disease , 2004, NeuroImage.

[9]  L. Fahrmeir,et al.  PENALIZED STRUCTURED ADDITIVE REGRESSION FOR SPACE-TIME DATA: A BAYESIAN PERSPECTIVE , 2004 .

[10]  A. Kouzani,et al.  Segmentation of multiple sclerosis lesions in MR images: a review , 2011, Neuroradiology.

[11]  J. Cullum,et al.  A survey of Lanczos procedures for very large real ‘symmetric’ eigenvalue problems , 1985 .

[12]  Vo Anh,et al.  A Numerical Solution Using an Adaptively Preconditioned Lanczos Method for a Class of Linear Systems Related with the Fractional Poisson Equation , 2008 .

[13]  H. Rue,et al.  On Block Updating in Markov Random Field Models for Disease Mapping , 2002 .

[14]  L. Fahrmeir,et al.  Bayesian inference for generalized additive mixed models based on Markov random field priors , 2001 .

[15]  David B. Dunson,et al.  Bayesian Data Analysis , 2010 .

[16]  Edmond Chow,et al.  Preconditioned Krylov Subspace Methods for Sampling Multivariate Gaussian Distributions , 2014, SIAM J. Sci. Comput..

[17]  H. Rue Fast sampling of Gaussian Markov random fields , 2000 .

[18]  D. Rubin,et al.  Inference from Iterative Simulation Using Multiple Sequences , 1992 .

[19]  A. Gelfand,et al.  Gaussian predictive process models for large spatial data sets , 2008, Journal of the Royal Statistical Society. Series B, Statistical methodology.

[20]  Ludwig Fahrmeir,et al.  Bayesian smoothing and regression for longitudinal, spatial and event history data / Ludwig Fahrmeir , 2011 .

[21]  B. Welford Note on a Method for Calculating Corrected Sums of Squares and Products , 1962 .

[22]  Bernhard Hemmer,et al.  An automated tool for detection of FLAIR-hyperintense white-matter lesions in Multiple Sclerosis , 2012, NeuroImage.

[23]  Andreas Brezger,et al.  Generalized structured additive regression based on Bayesian P-splines , 2006, Comput. Stat. Data Anal..

[24]  Karl J. Friston,et al.  Statistical parametric maps in functional imaging: A general linear approach , 1994 .

[25]  Gerhard Winkler,et al.  Image Analysis, Random Fields and Markov Chain Monte Carlo Methods: A Mathematical Introduction , 2002 .

[26]  J. Besag,et al.  Bayesian analysis of agricultural field experiments , 1999 .

[27]  Andrew O. Finley,et al.  Norges Teknisk-naturvitenskapelige Universitet Approximate Bayesian Inference for Large Spatial Datasets Using Predictive Process Models Approximate Bayesian Inference for Large Spatial Datasets Using Predictive Process Models , 2022 .

[28]  H. Rue,et al.  Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations , 2009 .

[29]  S. Wood,et al.  Generalized additive models for large data sets , 2015 .

[30]  Guang-Zhong Yang,et al.  Bayesian Methods for Pharmacokinetic Models in Dynamic Contrast-Enhanced Magnetic Resonance Imaging , 2006, IEEE Transactions on Medical Imaging.

[31]  A. V. Vecchia Estimation and model identification for continuous spatial processes , 1988 .

[32]  James P. LeSage,et al.  Chebyshev approximation of log-determinants of spatial weight matrices , 2004, Comput. Stat. Data Anal..

[33]  Johnathan M. Bardsley,et al.  MCMC-Based Image Reconstruction with Uncertainty Quantification , 2012, SIAM J. Sci. Comput..

[34]  Jeffrey A. Cohen,et al.  Diagnostic criteria for multiple sclerosis: 2010 Revisions to the McDonald criteria , 2011, Annals of neurology.

[35]  C Gössl,et al.  Dynamic models in fMRI , 2000, Magnetic resonance in medicine.

[36]  S. Lang,et al.  Bayesian P-Splines , 2004 .

[37]  L. Fahrmeir,et al.  Multivariate statistical modelling based on generalized linear models , 1994 .

[38]  Andrew M. Stuart,et al.  Analysis of the Gibbs Sampler for Hierarchical Inverse Problems , 2013, SIAM/ASA J. Uncertain. Quantification.

[39]  I. Turner,et al.  A restarted Lanczos approximation to functions of a symmetric matrix , 2010 .

[40]  C. Paige Computational variants of the Lanczos method for the eigenproblem , 1972 .

[41]  Jo Eidsvik,et al.  Parameter estimation in high dimensional Gaussian distributions , 2011, Stat. Comput..

[42]  Yousef Saad,et al.  Iterative methods for sparse linear systems , 2003 .

[43]  Mark W. Woolrich,et al.  Constrained linear basis sets for HRF modelling using Variational Bayes , 2004, NeuroImage.

[44]  M. Fuentes Approximate Likelihood for Large Irregularly Spaced Spatial Data , 2007, Journal of the American Statistical Association.

[45]  Z. Strakos,et al.  Krylov Subspace Methods: Principles and Analysis , 2012 .

[46]  Karsten Tabelow,et al.  Image analysis and statistical inference in neuroimaging with R , 2011, NeuroImage.

[47]  G. Roberts,et al.  Updating Schemes, Correlation Structure, Blocking and Parameterization for the Gibbs Sampler , 1997 .

[48]  Leonhard Held,et al.  Gaussian Markov Random Fields: Theory and Applications , 2005 .

[49]  A. Thompson,et al.  Disability and T2 MRI lesions: a 20-year follow-up of patients with relapse onset of multiple sclerosis. , 2008, Brain : a journal of neurology.

[50]  Karl J. Friston,et al.  Posterior probability maps and SPMs , 2003, NeuroImage.

[51]  Achim Zeileis,et al.  Structured Additive Regression Models: An R Interface to BayesX , 2015 .

[52]  Debashis Mondal,et al.  First-order intrinsic autoregressions and the de Wijs process , 2005 .

[53]  T. Kneib,et al.  BayesX: Analyzing Bayesian Structural Additive Regression Models , 2005 .

[54]  Volker J Schmid,et al.  Fully Bayesian Inference for Structural MRI: Application to Segmentation and Statistical Analysis of T2-Hypointensities , 2013, PloS one.

[55]  Y. Saad,et al.  Numerical Methods for Large Eigenvalue Problems , 2011 .

[56]  Zhiyi Chi,et al.  Approximating likelihoods for large spatial data sets , 2004 .