Modeling dynamic characteristics of brain functional connectivity networks using resting-state functional MRI

Dynamic network analysis using resting-state functional magnetic resonance imaging (rs-fMRI) provides a great insight into fundamentally dynamic characteristics of human brains, thus providing an efficient solution to automated brain disease identification. Previous studies usually pay less attention to evolution of global network structures over time in each brain's rs-fMRI time series, and also treat network-based feature extraction and classifier training as two separate tasks. To address these issues, we propose a temporal dynamics learning (TDL) method for network-based brain disease identification using rs-fMRI time-series data, through which network feature extraction and classifier training are integrated into the unified framework. Specifically, we first partition rs-fMRI time series into a sequence of segments using overlapping sliding windows, and then construct longitudinally ordered functional connectivity networks. To model the global temporal evolution patterns of these successive networks, we introduce a group-fused Lasso regularizer in our TDL framework, while the specific network architecture is induced by an ℓ1-norm regularizer. Besides, we develop an efficient optimization algorithm to solve the proposed objective function via the Alternating Direction Method of Multipliers (ADMM). Compared with previous studies, the proposed TDL model can not only explicitly model the evolving connectivity patterns of global networks over time, but also capture unique characteristics of each network defined at each segment. We evaluate our TDL on three real autism spectrum disorder (ASD) datasets with rs-fMRI data, achieving superior results in ASD identification compared with several state-of-the-art methods.

[1]  Dinggang Shen,et al.  Identifying Autism Spectrum Disorder With Multi-Site fMRI via Low-Rank Domain Adaptation , 2020, IEEE Transactions on Medical Imaging.

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

[3]  Scott T. Grafton,et al.  Dynamic reconfiguration of human brain networks during learning , 2010, Proceedings of the National Academy of Sciences.

[4]  Philip S. Yu,et al.  Multi-View Multi-Graph Embedding for Brain Network Clustering Analysis , 2018, AAAI.

[5]  Yuji Matsumoto,et al.  An Application of Boosting to Graph Classification , 2004, NIPS.

[6]  R. Tibshirani,et al.  Regression shrinkage and selection via the lasso: a retrospective , 2011 .

[7]  Dinggang Shen,et al.  Integration of temporal and spatial properties of dynamic connectivity networks for automatic diagnosis of brain disease , 2018, Medical Image Anal..

[8]  C. Stam Modern network science of neurological disorders , 2014, Nature Reviews Neuroscience.

[9]  Alvis Cheuk M. Fong,et al.  ASD-DiagNet: A Hybrid Learning Approach for Detection of Autism Spectrum Disorder Using fMRI Data , 2019, Front. Neuroinform..

[10]  Danielle S. Bassett,et al.  Modeling and interpreting mesoscale network dynamics , 2017, NeuroImage.

[11]  Daoqiang Zhang,et al.  Functional Connectivity Network Analysis with Discriminative Hub Detection for Brain Disease Identification , 2019, AAAI.

[12]  Dinggang Shen,et al.  First-year development of modules and hubs in infant brain functional networks , 2019, NeuroImage.

[13]  Jing Li,et al.  Learning Brain Connectivity of Alzheimer's Disease from Neuroimaging Data , 2009, NIPS.

[14]  Dimitri Van De Ville,et al.  The dynamic functional connectome: State-of-the-art and perspectives , 2017, NeuroImage.

[15]  Charles J. Lynch,et al.  The Default Mode Network in Autism. , 2017, Biological psychiatry. Cognitive neuroscience and neuroimaging.

[16]  Huafu Chen,et al.  Dynamic functional connectivity analysis reveals decreased variability of the default‐mode network in developing autistic brain , 2018, Autism research : official journal of the International Society for Autism Research.

[17]  Brian S Caffo,et al.  Modular preprocessing pipelines can reintroduce artifacts into fMRI data , 2018, bioRxiv.

[18]  Daoqiang Zhang,et al.  Identification of MCI individuals using structural and functional connectivity networks , 2012, NeuroImage.

[19]  Hao He,et al.  Assessing dynamic brain graphs of time-varying connectivity in fMRI data: Application to healthy controls and patients with schizophrenia , 2015, NeuroImage.

[20]  Xiang Ji,et al.  Representing and Retrieving Video Shots in Human-Centric Brain Imaging Space , 2013, IEEE Transactions on Image Processing.

[21]  David A. Leopold,et al.  Dynamic functional connectivity: Promise, issues, and interpretations , 2013, NeuroImage.

[22]  M. Bensafi,et al.  Impaired Odor Perception in Autism Spectrum Disorder Is Associated with Decreased Activity in Olfactory Cortex , 2018, Chemical senses.

[23]  N. Tzourio-Mazoyer,et al.  Automated Anatomical Labeling of Activations in SPM Using a Macroscopic Anatomical Parcellation of the MNI MRI Single-Subject Brain , 2002, NeuroImage.

[24]  Canhua Wang,et al.  Identification of Autism Based on SVM-RFE and Stacked Sparse Auto-Encoder , 2019, IEEE Access.

[25]  Stephen P. Boyd,et al.  Proximal Algorithms , 2013, Found. Trends Optim..

[26]  Karl J. Friston,et al.  Autonomic and brain responses associated with empathy deficits in autism spectrum disorder , 2015, Human brain mapping.

[27]  M. Hestenes Multiplier and gradient methods , 1969 .

[28]  Bingsheng He,et al.  Generalized alternating direction method of multipliers: new theoretical insights and applications , 2015, Math. Program. Comput..

[29]  Philip S. Yu,et al.  Mining Brain Networks Using Multiple Side Views for Neurological Disorder Identification , 2015, 2015 IEEE International Conference on Data Mining.

[30]  Larry A. Wasserman,et al.  The Nonparanormal: Semiparametric Estimation of High Dimensional Undirected Graphs , 2009, J. Mach. Learn. Res..

[31]  Daoqiang Zhang,et al.  Spatial-Temporal Dependency Modeling and Network Hub Detection for Functional MRI Analysis via Convolutional-Recurrent Network , 2019, IEEE Transactions on Biomedical Engineering.

[32]  Peter Wonka,et al.  Fused Multiple Graphical Lasso , 2012, SIAM J. Optim..

[33]  Ching Y. Suen,et al.  Application of majority voting to pattern recognition: an analysis of its behavior and performance , 1997, IEEE Trans. Syst. Man Cybern. Part A.

[34]  Jing Li,et al.  Mining brain region connectivity for alzheimer's disease study via sparse inverse covariance estimation , 2009, KDD.

[35]  Jari Saramäki,et al.  Reorganization of functionally connected brain subnetworks in high‐functioning autism , 2015, Human brain mapping.

[36]  A. Kolevzon,et al.  Functional deficits of the attentional networks in autism , 2012, Brain and behavior.

[37]  James D. B. Nelson,et al.  Regularized Estimation of Piecewise Constant Gaussian Graphical Models: The Group-Fused Graphical Lasso , 2015, 1512.06171.

[38]  Daoqiang Zhang,et al.  Integration of Network Topological and Connectivity Properties for Neuroimaging Classification , 2014, IEEE Transactions on Biomedical Engineering.

[39]  Jin Liu,et al.  Improved ASD classification using dynamic functional connectivity and multi-task feature selection , 2020, Pattern Recognit. Lett..

[40]  William H. Thompson,et al.  The frequency dimension of fMRI dynamic connectivity: Network connectivity, functional hubs and integration in the resting brain , 2015, NeuroImage.

[41]  Jingyuan E. Chen,et al.  Methods and Considerations for Dynamic Analysis of Functional MR Imaging Data. , 2017, Neuroimaging clinics of North America.

[42]  Khundrakpam Budhachandra,et al.  The Neuro Bureau Preprocessing Initiative: open sharing of preprocessed neuroimaging data and derivatives , 2013 .

[43]  Kurt Mehlhorn,et al.  Weisfeiler-Lehman Graph Kernels , 2011, J. Mach. Learn. Res..

[44]  Philip S. Yu,et al.  t-BNE: Tensor-based Brain Network Embedding , 2017, SDM.

[45]  Dinggang Shen,et al.  Sparse temporally dynamic resting-state functional connectivity networks for early MCI identification , 2016, Brain Imaging and Behavior.

[46]  Stephen P. Boyd,et al.  Distributed Optimization and Statistical Learning via the Alternating Direction Method of Multipliers , 2011, Found. Trends Mach. Learn..

[47]  Scott Peltier,et al.  Abnormalities of intrinsic functional connectivity in autism spectrum disorders, , 2009, NeuroImage.

[48]  P. K. Vinod,et al.  Atypical Flexibility in Dynamic Functional Connectivity Quantifies the Severity in Autism Spectrum Disorder , 2018, bioRxiv.

[49]  O. Sporns Structure and function of complex brain networks , 2013, Dialogues in clinical neuroscience.

[50]  Daoqiang Zhang,et al.  Sub-Network Kernels for Measuring Similarity of Brain Connectivity Networks in Disease Diagnosis , 2018, IEEE Transactions on Image Processing.

[51]  Albert C. S. Chung,et al.  Edge-variational Graph Convolutional Networks for Uncertainty-aware Disease Prediction , 2020, MICCAI.

[52]  Yuping Wang,et al.  Capturing Dynamic Connectivity From Resting State fMRI Using Time-Varying Graphical Lasso , 2019, IEEE Transactions on Biomedical Engineering.

[53]  Christoforos Anagnostopoulos,et al.  Estimating time-varying brain connectivity networks from functional MRI time series , 2013, NeuroImage.

[54]  Ben Glocker,et al.  Metric learning with spectral graph convolutions on brain connectivity networks , 2018, NeuroImage.

[55]  Hang Joon Jo,et al.  Effective Preprocessing Procedures Virtually Eliminate Distance-Dependent Motion Artifacts in Resting State FMRI , 2013, J. Appl. Math..

[56]  Edward T. Bullmore,et al.  Fundamentals of Brain Network Analysis , 2016 .

[57]  Daoqiang Zhang,et al.  Relationship Induced Multi-Template Learning for Diagnosis of Alzheimer’s Disease and Mild Cognitive Impairment , 2016, IEEE Transactions on Medical Imaging.

[58]  Dimitris Samaras,et al.  Deriving reproducible biomarkers from multi-site resting-state data: An Autism-based example , 2016, NeuroImage.

[59]  Peter Bühlmann Regression shrinkage and selection via the Lasso: a retrospective (Robert Tibshirani): Comments on the presentation , 2011 .

[60]  Mingliang Wang,et al.  A novel node-level structure embedding and alignment representation of structural networks for brain disease analysis , 2020, Medical Image Anal..

[61]  Daniel P. Kennedy,et al.  The Autism Brain Imaging Data Exchange: Towards Large-Scale Evaluation of the Intrinsic Brain Architecture in Autism , 2013, Molecular Psychiatry.

[62]  K. Kendrick,et al.  Neural, electrophysiological and anatomical basis of brain-network variability and its characteristic changes in mental disorders. , 2016, Brain : a journal of neurology.

[63]  Kevin Murphy,et al.  Towards a consensus regarding global signal regression for resting state functional connectivity MRI , 2017, NeuroImage.

[64]  A. Franco,et al.  NeuroImage: Clinical , 2022 .