The Relevance Voxel Machine (RVoxM): A Self-Tuning Bayesian Model for Informative Image-Based Prediction

This paper presents the relevance voxel machine (RVoxM), a dedicated Bayesian model for making predictions based on medical imaging data. In contrast to the generic machine learning algorithms that have often been used for this purpose, the method is designed to utilize a small number of spatially clustered sets of voxels that are particularly suited for clinical interpretation. RVoxM automatically tunes all its free parameters during the training phase, and offers the additional advantage of producing probabilistic prediction outcomes. We demonstrate RVoxM as a regression model by predicting age from volumetric gray matter segmentations, and as a classification model by distinguishing patients with Alzheimer's disease from healthy controls using surface-based cortical thickness data. Our results indicate that RVoxM yields biologically meaningful models, while providing state-of-the-art predictive accuracy.

[1]  Aapo Hyvärinen,et al.  Icasso: software for investigating the reliability of ICA estimates by clustering and visualization , 2003, 2003 IEEE XIII Workshop on Neural Networks for Signal Processing (IEEE Cat. No.03TH8718).

[2]  Clifford R. Jack,et al.  Alzheimer's disease diagnosis in individual subjects using structural MR images: Validation studies , 2008, NeuroImage.

[3]  Tom M. Mitchell,et al.  Learning to Decode Cognitive States from Brain Images , 2004, Machine Learning.

[4]  A. Smith,et al.  Rapidly progressing atrophy of medial temporal lobe in Alzheimer's disease , 1994, The Lancet.

[5]  Janaina Mourão Miranda,et al.  Classifying brain states and determining the discriminating activation patterns: Support Vector Machine on functional MRI data , 2005, NeuroImage.

[6]  Junzhou Huang,et al.  Learning with structured sparsity , 2009, ICML '09.

[7]  Sean M. Polyn,et al.  Beyond mind-reading: multi-voxel pattern analysis of fMRI data , 2006, Trends in Cognitive Sciences.

[8]  Polina Golland,et al.  Discriminative Direction for Kernel Classifiers , 2001, NIPS.

[9]  Mert R. Sabuncu,et al.  The Relevance Voxel Machine (RVoxM): A Bayesian Method for Image-Based Prediction , 2011, MICCAI.

[10]  David A. Rottenberg,et al.  Spatial SVM for feature selection and fMRI activation detection , 2006, The 2006 IEEE International Joint Conference on Neural Network Proceedings.

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

[12]  John Ashburner,et al.  A fast diffeomorphic image registration algorithm , 2007, NeuroImage.

[13]  A. Dale,et al.  High‐resolution intersubject averaging and a coordinate system for the cortical surface , 1999, Human brain mapping.

[14]  Corinna Cortes,et al.  Support-Vector Networks , 1995, Machine Learning.

[15]  Yuan Qi,et al.  Predictive automatic relevance determination by expectation propagation , 2004, ICML.

[16]  A. Dale,et al.  Thinning of the cerebral cortex in aging. , 2004, Cerebral cortex.

[17]  Denise C. Park,et al.  Toward defining the preclinical stages of Alzheimer's disease: Recommendations from the National Institute on Aging and the Alzheimer's Association workgroup , 2011 .

[18]  A. Dale,et al.  Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System , 1999, NeuroImage.

[19]  John G. Csernansky,et al.  Open Access Series of Imaging Studies (OASIS): Cross-sectional MRI Data in Young, Middle Aged, Nondemented, and Demented Older Adults , 2007, Journal of Cognitive Neuroscience.

[20]  Karl J. Friston,et al.  A Voxel-Based Morphometric Study of Ageing in 465 Normal Adult Human Brains , 2001, NeuroImage.

[21]  Rainer Goebel,et al.  Combining multivariate voxel selection and support vector machines for mapping and classification of fMRI spatial patterns , 2008, NeuroImage.

[22]  Ben Taskar,et al.  Generative-Discriminative Basis Learning for Medical Imaging , 2012, IEEE Transactions on Medical Imaging.

[23]  Ben Taskar,et al.  A General and Unifying Framework for Feature Construction, in Image-Based Pattern Classification , 2009, IPMI.

[24]  Bertrand Thirion,et al.  Multi-scale Mining of fMRI Data with Hierarchical Structured Sparsity , 2011, 2011 International Workshop on Pattern Recognition in NeuroImaging.

[25]  Anders M. Dale,et al.  Cortical Surface-Based Analysis I. Segmentation and Surface Reconstruction , 1999, NeuroImage.

[26]  Karl J. Friston,et al.  Identifying global anatomical differences: Deformation‐based morphometry , 1998 .

[27]  Mert R. Sabuncu,et al.  A Unified Framework for MR Based Disease Classification , 2009, IPMI.

[28]  Didier Dormont,et al.  Spatial Regularization of Svm for the Detection of Diffusion Alterations Associated with Stroke Outcome , 2022 .

[29]  J. Berger Statistical Decision Theory and Bayesian Analysis , 1988 .

[30]  Christos Davatzikos,et al.  Voxel-Based Morphometry Using the RAVENS Maps: Methods and Validation Using Simulated Longitudinal Atrophy , 2001, NeuroImage.

[31]  Bertrand Thirion,et al.  Multiclass Sparse Bayesian Regression for fMRI-Based Prediction , 2011, Int. J. Biomed. Imaging.

[32]  Karl J. Friston,et al.  Unified segmentation , 2005, NeuroImage.

[33]  Dinggang Shen,et al.  Classification of Structural Images via High-Dimensional Image Warping, Robust Feature Extraction, and SVM , 2005, MICCAI.

[34]  Radford M. Neal Pattern Recognition and Machine Learning , 2007, Technometrics.

[35]  S. Resnick,et al.  Detection of prodromal Alzheimer's disease via pattern classification of magnetic resonance imaging , 2008, Neurobiology of Aging.

[36]  Yvan Saeys,et al.  Robust Feature Selection Using Ensemble Feature Selection Techniques , 2008, ECML/PKDD.

[37]  Daniel Rueckert,et al.  Fast Brain-Wide Search of Highly Discriminative Regions in Medical Images: an Application to Alzheimers Disease , 2011, MIUA.

[38]  Benjamin J. Shannon,et al.  Molecular, Structural, and Functional Characterization of Alzheimer's Disease: Evidence for a Relationship between Default Activity, Amyloid, and Memory , 2005, The Journal of Neuroscience.

[39]  Francis R. Bach,et al.  Exploring Large Feature Spaces with Hierarchical Multiple Kernel Learning , 2008, NIPS.

[40]  Jonathan D. Power,et al.  Prediction of Individual Brain Maturity Using fMRI , 2010, Science.

[41]  Glenn Fung,et al.  SVM feature selection for classification of SPECT images of Alzheimer's disease using spatial information , 2005, Fifth IEEE International Conference on Data Mining (ICDM'05).

[42]  H. Zou,et al.  Regularization and variable selection via the elastic net , 2005 .

[43]  Dinggang Shen,et al.  COMPARE: Classification of Morphological Patterns Using Adaptive Regional Elements , 2007, IEEE Transactions on Medical Imaging.

[44]  Peter J. Ramadge,et al.  Boosting with Spatial Regularization , 2009, NIPS.

[45]  Christian Böhm,et al.  Automated detection of brain atrophy patterns based on MRI for the prediction of Alzheimer's disease , 2010, NeuroImage.

[46]  S. Geer,et al.  The Smooth-Lasso and other ℓ1+ℓ2-penalized methods , 2011 .

[47]  R. Tibshirani Regression Shrinkage and Selection via the Lasso , 1996 .

[48]  David J. C. MacKay,et al.  Information Theory, Inference, and Learning Algorithms , 2004, IEEE Transactions on Information Theory.

[49]  Nick C Fox,et al.  Automatic classification of MR scans in Alzheimer's disease. , 2008, Brain : a journal of neurology.

[50]  Ying Wang,et al.  High-dimensional Pattern Regression Using Machine Learning: from Medical Images to Continuous Clinical Variables However, Support Vector Regression Has Some Disadvantages That Become Especially , 2022 .

[51]  Anders M. Dale,et al.  An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest , 2006, NeuroImage.

[52]  A M Dale,et al.  Measuring the thickness of the human cerebral cortex from magnetic resonance images. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[53]  David J. C. MacKay,et al.  Comparison of Approximate Methods for Handling Hyperparameters , 1999, Neural Computation.

[54]  Tom Heskes,et al.  Efficient Bayesian multivariate fMRI analysis using a sparsifying spatio-temporal prior , 2010, NeuroImage.

[55]  Mohamed Hebiri,et al.  The Smooth-Lasso and other $\ell_1+\ell_2$-penalized methods , 2010, 1003.4885.

[56]  Peter M. Williams,et al.  Bayesian Regularization and Pruning Using a Laplace Prior , 1995, Neural Computation.

[57]  George Eastman House,et al.  Sparse Bayesian Learning and the Relevan e Ve tor Ma hine , 2001 .

[58]  Chih-Jen Lin,et al.  LIBSVM: A library for support vector machines , 2011, TIST.

[59]  Denise C. Park,et al.  Toward defining the preclinical stages of Alzheimer’s disease: Recommendations from the National Institute on Aging-Alzheimer's Association workgroups on diagnostic guidelines for Alzheimer's disease , 2011, Alzheimer's & Dementia.

[60]  Marie Chupin,et al.  Spatial and anatomical regularization of SVM for brain image analysis , 2010, NIPS.

[61]  Marie Chupin,et al.  Automatic classi fi cation of patients with Alzheimer ' s disease from structural MRI : A comparison of ten methods using the ADNI database , 2010 .

[62]  Edward R. Dougherty,et al.  Performance of feature-selection methods in the classification of high-dimension data , 2009, Pattern Recognit..

[63]  Geoffrey E. Hinton,et al.  Bayesian Learning for Neural Networks , 1995 .

[64]  Karl J. Friston,et al.  Bayesian decoding of brain images , 2008, NeuroImage.

[65]  D. Harville Maximum Likelihood Approaches to Variance Component Estimation and to Related Problems , 1977 .

[66]  D.,et al.  Regression Models and Life-Tables , 2022 .

[67]  Sohail Asghar,et al.  A REVIEW OF FEATURE SELECTION TECHNIQUES IN STRUCTURE LEARNING , 2013 .

[68]  Francis R. Bach,et al.  Structured Variable Selection with Sparsity-Inducing Norms , 2009, J. Mach. Learn. Res..

[69]  Michael E. Tipping,et al.  Fast Marginal Likelihood Maximisation for Sparse Bayesian Models , 2003 .

[70]  G. Rees,et al.  Neuroimaging: Decoding mental states from brain activity in humans , 2006, Nature Reviews Neuroscience.

[71]  Dinggang Shen,et al.  Morphological classification of brains via high-dimensional shape transformations and machine learning methods , 2004, NeuroImage.

[72]  Gaël Varoquaux,et al.  Small-sample brain mapping: sparse recovery on spatially correlated designs with randomization and clustering , 2012, ICML.

[73]  M. D’Esposito,et al.  The Effect of Normal Aging on the Coupling of Neural Activity to the Bold Hemodynamic Response , 1999, NeuroImage.

[74]  P. Zhao,et al.  The composite absolute penalties family for grouped and hierarchical variable selection , 2009, 0909.0411.

[75]  Gaël Varoquaux,et al.  Total Variation Regularization for fMRI-Based Prediction of Behavior , 2011, IEEE Transactions on Medical Imaging.

[76]  Alan C. Evans,et al.  A Unified Statistical Approach to Deformation-Based Morphometry , 2001, NeuroImage.

[77]  H. Benali,et al.  Support vector machine-based classification of Alzheimer’s disease from whole-brain anatomical MRI , 2009, Neuroradiology.

[78]  Stefan Klöppel,et al.  Estimating the age of healthy subjects from T1-weighted MRI scans using kernel methods: Exploring the influence of various parameters , 2010, NeuroImage.

[79]  Glenn Fung,et al.  SVM Feature Selection for Classification of SPECT Images of Alzheimer's Disease Using Spatial Information , 2005, ICDM.

[80]  M. Yuan,et al.  Model selection and estimation in regression with grouped variables , 2006 .

[81]  Francis R. Bach,et al.  Consistency of the group Lasso and multiple kernel learning , 2007, J. Mach. Learn. Res..

[82]  D. Mackay,et al.  Bayesian methods for adaptive models , 1992 .

[83]  A. McKinney,et al.  Automated MRI measures identify individuals with mild cognitive impairment and Alzheimer's disease , 2010 .

[84]  Yanxi Liu,et al.  Discriminative MR Image Feature Analysis for Automatic Schizophrenia and Alzheimer's Disease Classification , 2004, MICCAI.

[85]  W. Eric L. Grimson,et al.  Detection and analysis of statistical differences in anatomical shape , 2005, Medical Image Anal..

[86]  Karl J. Friston,et al.  Analysis of fMRI Time-Series Revisited—Again , 1995, NeuroImage.

[87]  Masa-aki Sato,et al.  Sparse estimation automatically selects voxels relevant for the decoding of fMRI activity patterns , 2008, NeuroImage.

[88]  David P. Wipf,et al.  A New View of Automatic Relevance Determination , 2007, NIPS.

[89]  A. Ishai,et al.  Distributed and Overlapping Representations of Faces and Objects in Ventral Temporal Cortex , 2001, Science.

[90]  S. Geer,et al.  The Smooth-Lasso and other ℓ1+ℓ2-penalized methods , 2011 .

[91]  Hernando Ombao,et al.  Penalized least squares regression methods and applications to neuroimaging , 2011, NeuroImage.