Chained regularization for identifying brain patterns specific to HIV infection

&NA; Human Immunodeficiency Virus (HIV) infection continues to have major adverse public health and clinical consequences despite the effectiveness of combination Antiretroviral Therapy (cART) in reducing HIV viral load and improving immune function. As successfully treated individuals with HIV infection age, their cognition declines faster than reported for normal aging. This phenomenon underlines the importance of improving long‐term care, which requires a better understanding of the impact of HIV on the brain. In this paper, automated identification of patients and brain regions affected by HIV infection are modeled as a classification problem, whose solution is determined in two steps within our proposed Chained‐Regularization framework. The first step focuses on selecting the HIV pattern (i.e., the most informative constellation of brain region measurements for distinguishing HIV infected subjects from healthy controls) by constraining the search for the optimal parameter setting of the classifier via group sparsity (Symbol‐norm). The second step improves classification accuracy by constraining the parameterization with respect to the selected measurements and the Euclidean regularization (Symbol‐norm). When applied to the cortical and subcortical structural Magnetic Resonance Images (MRI) measurements of 65 controls and 65 HIV infected individuals, this approach is more accurate in distinguishing the two cohorts than more common models. Finally, the brain regions of the identified HIV pattern concur with the HIV literature that uses traditional group analysis models. Symbol. No caption available. Symbol. No caption available.

[1]  Olga Meulenbroek,et al.  Cognitive functioning, wellbeing and brain correlates in HIV-1 infected patients on long-term combination antiretroviral therapy , 2015, AIDS (London).

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

[3]  Zhenchao Tang,et al.  Gray and white matter alterations in early HIV‐infected patients: Combined voxel‐based morphometry and tract‐based spatial statistics , 2016, Journal of magnetic resonance imaging : JMRI.

[4]  M W Weiner,et al.  Brain atrophy in HIV infection is more strongly associated with CDC clinical stage than with cognitive impairment , 1997, Journal of the International Neuropsychological Society.

[5]  Brian B. Avants,et al.  N4ITK: Improved N3 Bias Correction , 2010, IEEE Transactions on Medical Imaging.

[6]  Nina Ventura,et al.  Diffusion tensor MRI evaluation of the corona radiata, cingulate gyri, and corpus callosum in HIV patients , 2013, Journal of magnetic resonance imaging : JMRI.

[7]  Adolf Pfefferbaum,et al.  The SRI24 multichannel atlas of normal adult human brain structure , 2009, Human brain mapping.

[8]  M. Castillo,et al.  Diffusion-tensor MR imaging of the brain in human immunodeficiency virus-positive patients. , 2005, AJNR. American journal of neuroradiology.

[9]  Ethem Alpaydin,et al.  Multiple Kernel Learning Algorithms , 2011, J. Mach. Learn. Res..

[10]  Henrik Madsen,et al.  Introduction to General and Generalized Linear Models , 2010 .

[11]  David J. Sharp,et al.  Increased brain-predicted aging in treated HIV disease , 2017, Neurology.

[12]  Dieter J Meyerhoff,et al.  Fat may affect magnetic resonance signal intensity and brain tissue volumes. , 2016, Obesity research & clinical practice.

[13]  Torsten Rohlfing,et al.  Regional Brain Structural Dysmorphology in Human Immunodeficiency Virus Infection: Effects of Acquired Immune Deficiency Syndrome, Alcoholism, and Age , 2012, Biological Psychiatry.

[14]  Atul Kumar,et al.  Mapping the brain in younger and older asymptomatic HIV-1 men: Frontal volume changes in the absence of other cortical or diffusion tensor abnormalities , 2012, Cortex.

[15]  Torsten Rohlfing,et al.  Pontocerebellar contribution to postural instability and psychomotor slowing in HIV infection without dementia , 2011, Brain Imaging and Behavior.

[17]  Torsten Rohlfing,et al.  Thalamic volume deficit contributes to procedural and explicit memory impairment in HIV infection with primary alcoholism comorbidity , 2014, Brain Imaging and Behavior.

[18]  A. S. Rodionov,et al.  Comparison of linear, nonlinear and feature selection methods for EEG signal classification , 2004, International Conference on Actual Problems of Electron Devices Engineering, 2004. APEDE 2004..

[19]  L. Chang,et al.  Cerebral metabolite abnormalities correlate with clinical severity of HIV-1 cognitive motor complex , 1999, Neurology.

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

[21]  Michael W. L. Chee,et al.  Skull stripping using graph cuts , 2010, NeuroImage.

[22]  Manik Varma,et al.  More generality in efficient multiple kernel learning , 2009, ICML '09.

[23]  Torsten Rohlfing,et al.  Accelerated aging of selective brain structures in human immunodeficiency virus infection: a controlled, longitudinal magnetic resonance imaging study , 2014, Neurobiology of Aging.

[24]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[25]  Kiralee M. Hayashi,et al.  Thinning of the cerebral cortex visualized in HIV/AIDS reflects CD4+ T lymphocyte decline , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Bruce Fischl,et al.  Within-subject template estimation for unbiased longitudinal image analysis , 2012, NeuroImage.

[27]  Fuhui Long,et al.  Feature selection based on mutual information criteria of max-dependency, max-relevance, and min-redundancy , 2003, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[28]  Kim-Han Thung,et al.  Robust Feature-Sample Linear Discriminant Analysis for Brain Disorders Diagnosis , 2015, NIPS.

[29]  Jing Zhao,et al.  Structural gray matter change early in male patients with HIV. , 2014, International journal of clinical and experimental medicine.

[30]  Bernhard Schölkopf,et al.  Comparing support vector machines with Gaussian kernels to radial basis function classifiers , 1997, IEEE Trans. Signal Process..

[31]  Wotao Yin,et al.  A Block Coordinate Descent Method for Regularized Multiconvex Optimization with Applications to Nonnegative Tensor Factorization and Completion , 2013, SIAM J. Imaging Sci..

[32]  Thomas Doring,et al.  Longitudinal assessment of subcortical gray matter volume, cortical thickness, and white matter integrity in HIV‐positive patients , 2016, Journal of magnetic resonance imaging : JMRI.

[33]  C. O’Brien Statistical Learning with Sparsity: The Lasso and Generalizations , 2016 .

[34]  C. Hinkin,et al.  Emerging issues in the neuropsychology of HIV infection , 2008, Current HIV/AIDS reports.

[35]  D. Karnofsky The clinical evaluation of chemotherapeutic agents in cancer , 1949 .

[36]  Pamela C. Cosman,et al.  Evaluating quality of compressed medical images: SNR, subjective rating, and diagnostic accuracy , 1994, Proc. IEEE.

[37]  M Tagliati,et al.  Cerebellar degeneration associated with human immunodeficiency virus infection , 1998, Neurology.

[38]  Monica Zilbovicius,et al.  Cognitive Functioning in , 1995 .

[39]  John Shawe-Taylor,et al.  SCoRS—A Method Based on Stability for Feature Selection and Mapping in Neuroimaging , 2014, IEEE Transactions on Medical Imaging.

[40]  Stefan Bauer,et al.  Fully Automatic Segmentation of Brain Tumor Images Using Support Vector Machine Classification in Combination with Hierarchical Conditional Random Field Regularization , 2011, MICCAI.

[41]  Thomas M. Doring,et al.  Diffusion tensor MR imaging of white matter integrity in HIV-positive patients with planning deficit , 2015, Neuroradiology.

[42]  Glyn Johnson,et al.  White matter abnormalities in HIV-1 infection: A diffusion tensor imaging study , 2001, Psychiatry Research: Neuroimaging.

[43]  Ann B. Ragin,et al.  Matrix metalloproteinase levels in early HIV infection and relation to in vivo brain status , 2013, Journal of NeuroVirology.

[44]  Benson Mwangi,et al.  A Review of Feature Reduction Techniques in Neuroimaging , 2013, Neuroinformatics.

[45]  Heikki Huttunen,et al.  Comparison of Feature Selection Techniques in Machine Learning for Anatomical Brain MRI in Dementia , 2016, Neuroinformatics.

[46]  M. Moseley,et al.  HIV-Associated Alterations in Normal-Appearing White Matter: A Voxel-Wise Diffusion Tensor Imaging Study , 2007, Journal of acquired immune deficiency syndromes.

[47]  G. D. Pearlson,et al.  Reduced basal ganglia volume in HIV‐1‐associated dementia , 1993, Neurology.

[48]  Stefan Klein,et al.  Feature Selection Based on SVM Significance Maps for Classification of Dementia , 2014, MLMI.

[49]  E. DeLong,et al.  Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach. , 1988, Biometrics.

[50]  Olivier Chapelle,et al.  Training a Support Vector Machine in the Primal , 2007, Neural Computation.

[51]  John Shawe-Taylor,et al.  Sparse Network-Based Models for Patient Classification Using fMRI , 2013, PRNI.

[52]  Dennis G. Zill,et al.  Advanced Engineering Mathematics , 2021, Technometrics.

[53]  Linda Chang,et al.  Altered Associations between Pain Symptoms and Brain Morphometry in the Pain Matrix of HIV-Seropositive Individuals , 2018, Journal of Neuroimmune Pharmacology.

[54]  Anil K. Jain,et al.  Small Sample Size Effects in Statistical Pattern Recognition: Recommendations for Practitioners , 1991, IEEE Trans. Pattern Anal. Mach. Intell..

[55]  James T. Becker,et al.  Factors affecting brain structure in men with HIV disease in the post-HAART era , 2012, Neuroradiology.

[56]  Jianping Yin,et al.  Multiple Kernel Learning in the Primal for Multimodal Alzheimer’s Disease Classification , 2013, IEEE Journal of Biomedical and Health Informatics.

[57]  A. Ng Feature selection, L1 vs. L2 regularization, and rotational invariance , 2004, Twenty-first international conference on Machine learning - ICML '04.

[58]  C. Stern,et al.  Altered hippocampal-prefrontal activation in HIV patients during episodic memory encoding , 2006, Neurology.

[59]  Paul M. Thompson,et al.  Subcortical shape and volume abnormalities in an elderly HIV+ cohort , 2015, Medical Imaging.

[60]  Bensheng Qiu,et al.  Motor-related brain abnormalities in HIV-infected patients: a multimodal MRI study , 2017, Neuroradiology.

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

[62]  Ying Wu,et al.  Structural brain alterations can be detected early in HIV infection , 2012, Neurology.

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

[64]  Allen Y. Yang,et al.  Robust Face Recognition via Sparse Representation , 2009, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[65]  Mert R. Sabuncu A Universal and Efficient Method to Compute Maps from Image-Based Prediction Models , 2014, MICCAI.

[66]  Torsten Rohlfing,et al.  Contribution of alcoholism to brain dysmorphology in HIV infection: Effects on the ventricles and corpus callosum , 2006, NeuroImage.

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

[68]  Gunnar Rätsch,et al.  Large Scale Multiple Kernel Learning , 2006, J. Mach. Learn. Res..

[69]  René Vidal,et al.  Robust classification using structured sparse representation , 2011, CVPR 2011.

[70]  David F. Tate,et al.  Reliability and validity of MRI-based automated volumetry software relative to auto-assisted manual measurement of subcortical structures in HIV-infected patients from a multisite study , 2010, NeuroImage.

[71]  Robert Leech,et al.  Gray and White Matter Abnormalities in Treated Human Immunodeficiency Virus Disease and Their Relationship to Cognitive Function , 2017, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[72]  อนิรุธ สืบสิงห์,et al.  Data Mining Practical Machine Learning Tools and Techniques , 2014 .

[73]  Ivor W. Tsang,et al.  Learning Sparse SVM for Feature Selection on Very High Dimensional Datasets , 2010, ICML.

[74]  Paul M. Thompson,et al.  Robust Brain Extraction Across Datasets and Comparison With Publicly Available Methods , 2011, IEEE Transactions on Medical Imaging.

[75]  Adolf Pfefferbaum,et al.  Impairments in Component Processes of Executive Function and Episodic Memory in Alcoholism, HIV Infection, and HIV Infection with Alcoholism Comorbidity. , 2016, Alcoholism, clinical and experimental research.

[76]  Gregory R. Kirk,et al.  Peripheral blood HIV DNA is associated with atrophy of cerebellar and subcortical gray matter , 2013, Neurology.

[77]  D. Clifford,et al.  HIV-associated neurocognitive disorder , 2016, Current opinion in infectious diseases.

[78]  Pierrick Coupé,et al.  An Optimized Blockwise Nonlocal Means Denoising Filter for 3-D Magnetic Resonance Images , 2008, IEEE Transactions on Medical Imaging.

[79]  Thomas Hofmann,et al.  Support Vector Machines for Multiple-Instance Learning , 2002, NIPS.

[80]  Stephen M Smith,et al.  Fast robust automated brain extraction , 2002, Human brain mapping.

[81]  Dinggang Shen,et al.  Maximum Mean Discrepancy Based Multiple Kernel Learning for Incomplete Multimodality Neuroimaging Data , 2017, MICCAI.

[82]  Torsten Rohlfing,et al.  Performance-based classifier combination in atlas-based image segmentation using expectation-maximization parameter estimation , 2004, IEEE Transactions on Medical Imaging.

[83]  Kilian M. Pohl,et al.  Extracting patterns of morphometry distinguishing HIV associated neurodegeneration from mild cognitive impairment via group cardinality constrained classification , 2016, Human brain mapping.

[84]  Tony W Wilson,et al.  Multimodal neuroimaging evidence of alterations in cortical structure and function in HIV‐infected older adults , 2015, Human brain mapping.

[85]  Pedro Larrañaga,et al.  A review of feature selection techniques in bioinformatics , 2007, Bioinform..

[86]  A. Uluğ,et al.  Diffusion tensor imaging of patients with HIV and normal-appearing white matter on MR images of the brain. , 2001, AJNR. American journal of neuroradiology.

[87]  Gregory R. Kirk,et al.  Regional cortical thinning associated with detectable levels of HIV DNA. , 2012, Cerebral cortex.

[88]  Ehsan Adeli,et al.  Kernel-based Joint Feature Selection and Max-Margin Classification for Early Diagnosis of Parkinson’s Disease , 2017, Scientific Reports.

[89]  Terry L. Jernigan,et al.  HIV-associated neurocognitive disorders before and during the era of combination antiretroviral therapy: differences in rates, nature, and predictors , 2010, Journal of NeuroVirology.

[90]  T. Jernigan,et al.  Progressive cerebral volume loss in human immunodeficiency virus infection: a longitudinal volumetric magnetic resonance imaging study. HIV Neurobehavioral Research Center Group. , 1998, Archives of neurology.

[91]  Mehryar Mohri,et al.  L2 Regularization for Learning Kernels , 2009, UAI.

[92]  R W Cox,et al.  AFNI: software for analysis and visualization of functional magnetic resonance neuroimages. , 1996, Computers and biomedical research, an international journal.

[93]  Stefan Klein,et al.  Feature Selection Based on the SVM Weight Vector for Classification of Dementia , 2015, IEEE Journal of Biomedical and Health Informatics.

[94]  Subhransu Maji,et al.  Classification using intersection kernel support vector machines is efficient , 2008, 2008 IEEE Conference on Computer Vision and Pattern Recognition.

[95]  D Louis Collins,et al.  Regionally Specific Brain Volumetric and Cortical Thickness Changes in HIV-Infected Patients in the HAART Era , 2017, Journal of acquired immune deficiency syndromes.

[96]  Brian B. Avants,et al.  Symmetric diffeomorphic image registration with cross-correlation: Evaluating automated labeling of elderly and neurodegenerative brain , 2008, Medical Image Anal..

[97]  G D Pearlson,et al.  Magnetic resonance imaging measurement of gray matter volume reductions in HIV dementia. , 1995, The American journal of psychiatry.

[98]  R. Fisher,et al.  The Logic of Inductive Inference , 1935 .

[99]  Torsten Rohlfing,et al.  Variation in longitudinal trajectories of regional brain volumes of healthy men and women (ages 10 to 85years) measured with atlas-based parcellation of MRI , 2013, NeuroImage.

[100]  Ronald A. Cohen,et al.  Facial emotion recognition impairments are associated with brain volume abnormalities in individuals with HIV , 2015, Neuropsychologia.

[101]  Alex Smola,et al.  Kernel methods in machine learning , 2007, math/0701907.

[102]  Paul H. Calamai,et al.  Projected gradient methods for linearly constrained problems , 1987, Math. Program..

[103]  Dan J Stein,et al.  Neuroimaging markers of human immunodeficiency virus infection in South Africa , 2012, Journal of NeuroVirology.

[104]  Sylvain Arlot,et al.  A survey of cross-validation procedures for model selection , 2009, 0907.4728.

[105]  Feiping Nie,et al.  Efficient and Robust Feature Selection via Joint ℓ2, 1-Norms Minimization , 2010, NIPS.

[106]  Matthijs Vink,et al.  Prefrontal cortical thinning in HIV infection is associated with impaired striatal functioning , 2016, Journal of Neural Transmission.

[107]  Yukitaka Minesaki,et al.  AN EFFICIENT CONSERVATIVE INTEGRATOR WITH A CHAIN REGULARIZATION FOR THE FEW-BODY PROBLEM , 2015 .

[108]  Isabelle Guyon,et al.  An Introduction to Variable and Feature Selection , 2003, J. Mach. Learn. Res..

[109]  Tong Zhu,et al.  Patterns of white matter injury in HIV infection after partial immune reconstitution: a DTI tract-based spatial statistics study , 2012, Journal of NeuroVirology.

[110]  A. Berlinet,et al.  Reproducing kernel Hilbert spaces in probability and statistics , 2004 .

[111]  Kewei Cheng,et al.  Feature Selection , 2016, ACM Comput. Surv..