A hybrid computational approach for efficient Alzheimer’s disease classification based on heterogeneous data

There is currently a lack of an efficient, objective and systemic approach towards the classification of Alzheimer’s disease (AD), due to its complex etiology and pathogenesis. As AD is inherently dynamic, it is also not clear how the relationships among AD indicators vary over time. To address these issues, we propose a hybrid computational approach for AD classification and evaluate it on the heterogeneous longitudinal AIBL dataset. Specifically, using clinical dementia rating as an index of AD severity, the most important indicators (mini-mental state examination, logical memory recall, grey matter and cerebrospinal volumes from MRI and active voxels from PiB-PET brain scans, ApoE, and age) can be automatically identified from parallel data mining algorithms. In this work, Bayesian network modelling across different time points is used to identify and visualize time-varying relationships among the significant features, and importantly, in an efficient way using only coarse-grained data. Crucially, our approach suggests key data features and their appropriate combinations that are relevant for AD severity classification with high accuracy. Overall, our study provides insights into AD developments and demonstrates the potential of our approach in supporting efficient AD diagnosis.

[1]  Nicola Smania,et al.  Effects of Robot-Assisted Training for the Unaffected Arm in Patients with Hemiparetic Cerebral Palsy: A Proof-of-Concept Pilot Study , 2017, Behavioural neurology.

[2]  Bianca Zadrozny,et al.  A Bayesian network decision model for supporting the diagnosis of dementia, Alzheimer's disease and mild cognitive impairment , 2014, Comput. Biol. Medicine.

[3]  M. Folstein,et al.  Clinical diagnosis of Alzheimer's disease , 1984, Neurology.

[4]  M. Cecchini,et al.  Ultrastructural Characterization of the Lower Motor System in a Mouse Model of Krabbe Disease , 2016, Scientific Reports.

[5]  Thomas Wisniewski,et al.  Apolipoprotein E: A pathological chaperone protein in patients with cerebral and systemic amyloid , 1992, Neuroscience Letters.

[6]  R. Martínez-Tomás,et al.  Diagnosis of Cognitive Impairment Compatible with Early Diagnosis of Alzheimer’s Disease , 2015, Methods of Information in Medicine.

[7]  Sterling C. Johnson,et al.  A semi-mechanism approach based on MRI and proteomics for prediction of conversion from mild cognitive impairment to Alzheimer’s disease , 2016, Scientific Reports.

[8]  Luis M. de Campos,et al.  A Scoring Function for Learning Bayesian Networks based on Mutual Information and Conditional Independence Tests , 2006, J. Mach. Learn. Res..

[9]  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.

[10]  Huilong Duan,et al.  A Hybrid Intelligent Diagnosis Approach for Quick Screening of Alzheimer's Disease Based on Multiple Neuropsychological Rating Scales , 2015, Comput. Math. Methods Medicine.

[11]  L. Maffei,et al.  Environmental enrichment strengthens corticocortical interactions and reduces amyloid-β oligomers in aged mice , 2013, Front. Aging Neurosci..

[12]  John M. Noble,et al.  Bayesian Networks: An Introduction , 2009 .

[13]  Nick C Fox,et al.  The Alzheimer's disease neuroimaging initiative (ADNI): MRI methods , 2008, Journal of magnetic resonance imaging : JMRI.

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

[15]  Graziano Pesole,et al.  Regularized Least Squares Cancer Classifiers from DNA microarray data , 2005, BMC Bioinformatics.

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

[17]  Paul Maruff,et al.  Trajectories of memory decline in preclinical Alzheimer's disease: results from the Australian Imaging, Biomarkers and Lifestyle Flagship Study of Ageing , 2015, Neurobiology of Aging.

[18]  Matthew J. Beal,et al.  The variational Bayesian EM algorithm for incomplete data: with application to scoring graphical model structures , 2003 .

[19]  Christian Salvatore,et al.  Optimizing Neuropsychological Assessments for Cognitive, Behavioral, and Functional Impairment Classification: A Machine Learning Study , 2017, Behavioural neurology.

[20]  A. Hofman,et al.  Prevalence of dementia and major subtypes in Europe: A collaborative study of population-based cohorts. Neurologic Diseases in the Elderly Research Group. , 2000, Neurology.

[21]  ZadroznyBianca,et al.  A Bayesian network decision model for supporting the diagnosis of dementia, Alzheimer's disease and mild cognitive impairment , 2014 .

[22]  J. Duchek,et al.  Reliability of the Washington University Clinical Dementia Rating. , 1988, Archives of neurology.

[23]  Jinglong Wu,et al.  Network-Based Biomarkers in Alzheimer’s Disease: Review and Future Directions , 2014, Front. Aging Neurosci..

[24]  A. King,et al.  The question of familial meningiomas and schwannomas: , 2000, Neurology.

[25]  Zdenka Kuncic,et al.  Unraveling the mechanistic complexity of Alzheimer's disease through systems biology , 2016, Alzheimer's & Dementia.

[26]  Andrea C. Bozoki,et al.  Predicting Progression from Mild Cognitive Impairment to Alzheimer's Dementia Using Clinical, MRI, and Plasma Biomarkers via Probabilistic Pattern Classification , 2016, PloS one.

[27]  Max Kuhn,et al.  Applied Predictive Modeling , 2013 .

[28]  Linda C. van der Gaag,et al.  Probabilistic Graphical Models , 2014, Lecture Notes in Computer Science.

[29]  D. Holtzman,et al.  ApoE Promotes the Proteolytic Degradation of Aβ , 2008, Neuron.

[30]  D. Louis Collins,et al.  Feature-based morphometry: Discovering group-related anatomical patterns , 2010, NeuroImage.

[31]  C. Rowe,et al.  The Australian Imaging, Biomarkers and Lifestyle (AIBL) study of aging: methodology and baseline characteristics of 1112 individuals recruited for a longitudinal study of Alzheimer's disease , 2009, International Psychogeriatrics.

[32]  C. E. SHANNON,et al.  A mathematical theory of communication , 1948, MOCO.

[33]  Sang Joon Kim,et al.  A Mathematical Theory of Communication , 2006 .

[34]  Christian Jutten,et al.  Multimodal Data Fusion: An Overview of Methods, Challenges, and Prospects , 2015, Proceedings of the IEEE.

[35]  Vahab Youssofzadeh,et al.  Multi-Kernel Learning with Dartel Improves Combined MRI-PET Classification of Alzheimer’s Disease in AIBL Data: Group and Individual Analyses , 2017, Front. Hum. Neurosci..

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

[37]  Bruno Vellas,et al.  Rationale for use of the Clinical Dementia Rating Sum of Boxes as a primary outcome measure for Alzheimer’s disease clinical trials , 2013, Alzheimer's & Dementia.

[38]  M. Folstein,et al.  Clinical diagnosis of Alzheimer's disease: Report of the NINCDS—ADRDA Work Group under the auspices of Department of Health and Human Services Task Force on Alzheimer's Disease , 2011, Neurology.

[39]  Gregory F. Cooper,et al.  A Bayesian method for the induction of probabilistic networks from data , 1992, Machine Learning.

[40]  Wiesje M van der Flier,et al.  Progression to dementia in memory clinic patients without dementia , 2013, Neurology.

[41]  Roberto Battiti,et al.  Using mutual information for selecting features in supervised neural net learning , 1994, IEEE Trans. Neural Networks.

[42]  Fong-Chin Su,et al.  Assessing Finger Joint Biomechanics by Applying Equal Force to Flexor Tendons In Vitro Using a Novel Simultaneous Approach , 2016, PloS one.

[43]  A. Dale,et al.  CSF Biomarkers in Prediction of Cerebral and Clinical Change in Mild Cognitive Impairment and Alzheimer's Disease , 2010, The Journal of Neuroscience.

[44]  Paul Maruff,et al.  Longitudinal cognitive decline in the AIBL cohort: The role of APOE ε4 status , 2014, Neuropsychologia.

[45]  Lukasz A. Kurgan,et al.  CAIM discretization algorithm , 2004, IEEE Transactions on Knowledge and Data Engineering.

[46]  Manju Bansal,et al.  A novel method for prokaryotic promoter prediction based on DNA stability , 2005, BMC Bioinformatics.

[47]  R. Mohs,et al.  A 24-week, double-blind, placebo-controlled trial of donepezil in patients with Alzheimer's disease , 1998, Neurology.

[48]  C. Kemner,et al.  Spatial Frequency Training Modulates Neural Face Processing: Learning Transfers from Low- to High-Level Visual Features , 2017, Front. Hum. Neurosci..

[49]  Xiaoxing Liu,et al.  An Entropy-based gene selection method for cancer classification using microarray data , 2005, BMC Bioinformatics.

[50]  Qiang Shen,et al.  Learning Bayesian networks: approaches and issues , 2011, The Knowledge Engineering Review.

[51]  Sid E O'Bryant,et al.  Validation of a latent variable representing the dementing process. , 2012, Journal of Alzheimer's disease : JAD.

[52]  Viswanath Devanarayan,et al.  Big data to smart data in Alzheimer's disease: The brain health modeling initiative to foster actionable knowledge , 2016, Alzheimer's & Dementia.

[53]  Tom Fawcett,et al.  An introduction to ROC analysis , 2006, Pattern Recognit. Lett..

[54]  Francisco Herrera,et al.  A Review on Ensembles for the Class Imbalance Problem: Bagging-, Boosting-, and Hybrid-Based Approaches , 2012, IEEE Transactions on Systems, Man, and Cybernetics, Part C (Applications and Reviews).

[55]  Paul Maruff,et al.  Amyloid-Related Memory Decline in Preclinical Alzheimer’s Disease Is Dependent on APOE ε4 and Is Detectable over 18-Months , 2015, PloS one.

[56]  Nitesh V. Chawla,et al.  SMOTE: Synthetic Minority Over-sampling Technique , 2002, J. Artif. Intell. Res..

[57]  Minsheng You,et al.  Determining putative vectors of the Bogia Coconut Syndrome phytoplasma using loop-mediated isothermal amplification of single-insect feeding media , 2016, Scientific Reports.

[58]  J. Haines,et al.  Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer's disease in late onset families. , 1993, Science.

[59]  Huaxi Xu,et al.  Apolipoprotein E and Alzheimer disease: risk, mechanisms and therapy , 2013, Nature Reviews Neurology.

[60]  Ron Kohavi,et al.  A Study of Cross-Validation and Bootstrap for Accuracy Estimation and Model Selection , 1995, IJCAI.