Improving Sparsity and Modularity of High-Order Functional Connectivity Networks for MCI and ASD Identification

Neighborhood structure-guided brain functional networks estimation for mild cognitive impairment identification

The adoption and growth of functional magnetic resonance imaging (fMRI) technology, especially through the use of Pearson's correlation (PC) for constructing brain functional networks (BFN), has significantly advanced brain disease diagnostics by uncovering the brain's operational mechanisms and offering biomarkers for early detection. However, the PC always tends to make for a dense BFN, which violates the biological prior. Therefore, in practice, researchers use hard-threshold to remove weak connection edges or introduce l 1-norm as a regularization term to obtain sparse BFNs. However, these approaches neglect the spatial neighborhood information between regions of interest (ROIs), and ROI with closer distances has higher connectivity prospects than ROI with farther distances due to the principle of simple wiring costs in resent studies. Thus, we propose a neighborhood structure-guided BFN estimation method in this article. In detail, we figure the ROIs' Euclidean distances and sort them. Then, we apply the K-nearest neighbor (KNN) to find out the top K neighbors closest to the current ROIs, where each ROI's K neighbors are independent of each other. We establish the connection relationship between the ROIs and these K neighbors and construct the global topology adjacency matrix according to the binary network. Connect ROI nodes with k nearest neighbors using edges to generate an adjacency graph, forming an adjacency matrix. Based on adjacency matrix, PC calculates the correlation coefficient between ROIs connected by edges, and generates the BFN. With the purpose of evaluating the performance of the introduced method, we utilize the estimated BFN for distinguishing individuals with mild cognitive impairment (MCI) from the healthy ones. Experimental outcomes imply this method attains better classification performance than the baselines. Additionally, we compared it with the most commonly used time series methods in deep learning. Results of the performance of K-nearest neighbor-Pearson's correlation (K-PC) has some advantage over deep learning.

Accurate module induced brain network construction for mild cognitive impairment identification with functional MRI

Introduction

Functional brain networks (FBNs) estimated from functional magnetic resonance imaging (fMRI) data has become a potentially useful way for computer-aided diagnosis of neurological disorders, such as mild cognitive impairment (MCI), a prodromal stage of Alzheimer's Disease (AD). Currently, Pearson's correlation (PC) is the most widely-used method for constructing FBNs. Despite its popularity and simplicity, the conventional PC-based method usually results in dense networks where regions-of-interest (ROIs) are densely connected. This is not accordance with the biological prior that ROIs may be sparsely connected in the brain. To address this issue, previous studies proposed to employ a threshold or l_1-regularizer to construct sparse FBNs. However, these methods usually ignore rich topology structures, such as modularity that has been proven to be an important property for improving the information processing ability of the brain.

Methods

To this end, in this paper, we propose an accurate module induced PC (AM-PC) model to estimate FBNs with a clear modular structure, by including sparse and low-rank constraints on the Laplacian matrix of the network. Based on the property that zero eigenvalues of graph Laplacian matrix indicate the connected components, the proposed method can reduce the rank of the Laplacian matrix to a pre-defined number and obtain FBNs with an accurate number of modules.

Results

To validate the effectiveness of the proposed method, we use the estimated FBNs to classify subjects with MCI from healthy controls. Experimental results on 143 subjects from Alzheimer's Disease Neuroimaging Initiative (ADNI) with resting-state functional MRIs show that the proposed method achieves better classification performance than previous methods.

Multiple measurement analysis of resting-state fMRI for ADHD classification in adolescent brain from the ABCD study

Attention deficit hyperactivity disorder (ADHD) is one of the most common psychiatric disorders in school-aged children. Its accurate diagnosis looks after patients' interests well with effective treatment, which is important to them and their family. Resting-state functional magnetic resonance imaging (rsfMRI) has been widely used to characterize the abnormal brain function by computing the voxel-wise measures and Pearson's correlation (PC)-based functional connectivity (FC) for ADHD diagnosis. However, exploring the powerful measures of rsfMRI to improve ADHD diagnosis remains a particular challenge. To this end, this paper proposes an automated ADHD classification framework by fusion of multiple measures of rsfMRI in adolescent brain. First, we extract the voxel-wise measures and ROI-wise time series from the brain regions of rsfMRI after preprocessing. Then, to extract the multiple functional connectivities, we compute the PC-derived FCs including the topographical information-based high-order FC (tHOFC) and dynamics-based high-order FC (dHOFC), the sparse representation (SR)-derived FCs including the group SR (GSR), the strength and similarity guided GSR (SSGSR), and sparse low-rank (SLR). Finally, these measures are combined with multiple kernel learning (MKL) model for ADHD classification. The proposed method is applied to the Adolescent Brain and Cognitive Development (ABCD) dataset. The results show that the FCs of dHOFC and SLR perform better than the others. Fusing multiple measures achieves the best classification performance (AUC = 0.740, accuracy = 0.6916), superior to those from the single measure and the previous studies. We have identified the most discriminative FCs and brain regions for ADHD diagnosis, which are consistent with those of published literature.

Constructing brain functional network by Adversarial Temporal-Spatial Aligned Transformer for early AD analysis

Introduction

The brain functional network can describe the spontaneous activity of nerve cells and reveal the subtle abnormal changes associated with brain disease. It has been widely used for analyzing early Alzheimer's disease (AD) and exploring pathological mechanisms. However, the current methods of constructing functional connectivity networks from functional magnetic resonance imaging (fMRI) heavily depend on the software toolboxes, which may lead to errors in connection strength estimation and bad performance in disease analysis because of many subjective settings.

Methods

To solve this problem, in this paper, a novel Adversarial Temporal-Spatial Aligned Transformer (ATAT) model is proposed to automatically map 4D fMRI into functional connectivity network for early AD analysis. By incorporating the volume and location of anatomical brain regions, the region-guided feature learning network can roughly focus on local features for each brain region. Also, the spatial-temporal aligned transformer network is developed to adaptively adjust boundary features of adjacent regions and capture global functional connectivity patterns of distant regions. Furthermore, a multi-channel temporal discriminator is devised to distinguish the joint distributions of the multi-region time series from the generator and the real sample.

Results

Experimental results on the Alzheimer's Disease Neuroimaging Initiative (ADNI) proved the effectiveness and superior performance of the proposed model in early AD prediction and progression analysis.

Discussion

To verify the reliability of the proposed model, the detected important ROIs are compared with clinical studies and show partial consistency. Furthermore, the most significant altered connectivity reflects the main characteristics associated with AD.

Conclusion

Generally, the proposed ATAT provides a new perspective in constructing functional connectivity networks and is able to evaluate the disease-related changing characteristics at different stages for neuroscience exploration and clinical disease analysis.

Multi-View Feature Enhancement Based on Self-Attention Mechanism Graph Convolutional Network for Autism Spectrum Disorder Diagnosis

Functional connectivity (FC) network based on resting-state functional magnetic resonance imaging (rs-fMRI) has become an important tool to explore and understand the brain, which can provide objective basis for the diagnosis of neurodegenerative diseases, such as autism spectrum disorder (ASD). However, most functional connectivity (FC) networks only consider the unilateral features of nodes or edges, and the interaction between them is ignored. In fact, their integration can provide more comprehensive and crucial information in the diagnosis. To address this issue, a new multi-view brain network feature enhancement method based on self-attention mechanism graph convolutional network (SA-GCN) is proposed in this article, which can enhance node features through the connection relationship among different nodes, and then extract deep-seated and more discriminative features. Specifically, we first plug the pooling operation of self-attention mechanism into graph convolutional network (GCN), which can consider the node features and topology of graph network at the same time and then capture more discriminative features. In addition, the sample size is augmented by a "sliding window" strategy, which is beneficial to avoid overfitting and enhance the generalization ability. Furthermore, to fully explore the complex connection relationship among brain regions, we constructed the low-order functional graph network (Lo-FGN) and the high-order functional graph network (Ho-FGN) and enhance the features of the two functional graph networks (FGNs) based on SA-GCN. The experimental results on benchmark datasets show that: (1) SA-GCN can play a role in feature enhancement and can effectively extract more discriminative features, and (2) the integration of Lo-FGN and Ho-FGN can achieve the best ASD classification accuracy (79.9%), which reveals the information complementarity between them.

Estimating High-Order Brain Functional Networks in Bayesian View for Autism Spectrum Disorder Identification

Brain functional network (BFN) has become an increasingly important tool to understand the inherent organization of the brain and explore informative biomarkers of neurological disorders. Pearson’s correlation (PC) is the most widely accepted method for constructing BFNs and provides a basis for designing new BFN estimation schemes. Particularly, a recent study proposes to use two sequential PC operations, namely, correlation’s correlation (CC), for constructing the high-order BFN. Despite its empirical effectiveness in identifying neurological disorders and detecting subtle changes of connections in different subject groups, CC is defined intuitively without a solid and sustainable theoretical foundation. For understanding CC more rigorously and providing a systematic BFN learning framework, in this paper, we reformulate it in the Bayesian view with a prior of matrix-variate normal distribution. As a result, we obtain a probabilistic explanation of CC. In addition, we develop a Bayesian high-order method (BHM) to automatically and simultaneously estimate the high- and low-order BFN based on the probabilistic framework. An efficient optimization algorithm is also proposed. Finally, we evaluate BHM in identifying subjects with autism spectrum disorder (ASD) from typical controls based on the estimated BFNs. Experimental results suggest that the automatically learned high- and low-order BFNs yield a superior performance over the artificially defined BFNs via conventional CC and PC.

Hierarchical Synchronization Estimation of Low- and High-Order Functional Connectivity Based on Sub-Network Division for the Diagnosis of Autism Spectrum Disorder

Functional connectivity network (FCN) calculated by resting-state functional magnetic resonance imaging (rs-fMRI) plays an increasingly important role in the exploration of neurologic and mental diseases. Among the presented researches, the method of constructing FCN based on Matrix Variate Normal Distribution (MVND) theory provides a novel perspective, which can capture both low- and high-order correlations simultaneously with a clear mathematical interpretability. However, when fitting MVND model, the dimension of the parameters (i.e., population mean and population covariance) to be estimated is too high, but the number of samples is relatively quite small, which is insufficient to achieve accurate fitting. To address the issue, we divide the brain network into several sub-networks, and then the MVND based FCN construction algorithm is implemented in each sub-network, thus the spatial dimension of MVND is reduced and more accurate estimates of low- and high-order FCNs is obtained. Furthermore, for making up the functional connectivity which is lost because of the sub-network division, the rs-fMRI mean series of all sub-networks are calculated, and the low- and high-order FCN across sub-networks are estimated with the MVND based FCN construction method. In order to prove the superiority and effectiveness of this method, we design and conduct classification experiments on ASD patients and normal controls. The experimental results show that the classification accuracy of “hierarchical sub-network method” is greatly improved, and the sub-network found most related to ASD in our experiment is consistent with other related medical researches.

Cross-task Cognitive Workload Recognition Based on EEG and Domain Adaptation

Cognitive workload recognition is pivotal to maintain the operator's health and prevent accidents in the human-robot interaction condition. So far, the focus of workload research is mostly restricted to a single task, yet cross-task cognitive workload recognition has remained a challenge. Furthermore, when extending to a new workload condition, the discrepancy of electroencephalogram (EEG) signals across various cognitive tasks limits the generalization of the existed model. To tackle this problem, we propose to construct the EEG-based cross-task cognitive workload recognition models using domain adaptation methods in a leave-one-task-out cross-validation setting, where we view any task of each subject as a domain. Specifically, we first design a fine-grained workload paradigm including working memory and mathematic addition tasks. Then, we explore four domain adaptation methods to bridge the discrepancy between the two different tasks. Finally, based on the supporting vector machine classifier, we conduct experiments to classify the low and high workload levels on a private EEG dataset. Experimental results demonstrate that our proposed task transfer framework outperforms the non-transfer classifier with improvements of 3% to 8% in terms of mean accuracy, and the transfer joint matching (TJM) consistently achieves the best performance.

Multi-Band Brain Network Analysis for Functional Neuroimaging Biomarker Identification

The functional connectomic profile is one of the non-invasive imaging biomarkers in the computer-assisted diagnostic system for many neuro-diseases. However, the diagnostic power of functional connectivity is challenged by mixed frequency-specific neuronal oscillations in the brain, which makes the single Functional Connectivity Network (FCN) often underpowered to capture the disease-related functional patterns. To address this challenge, we propose a novel functional connectivity analysis framework to conduct joint feature learning and personalized disease diagnosis, in a semi-supervised manner, aiming at focusing on putative multi-band functional connectivity biomarkers from functional neuroimaging data. Specifically, we first decompose the Blood Oxygenation Level Dependent (BOLD) signals into multiple frequency bands by the discrete wavelet transform, and then cast the alignment of all fully-connected FCNs derived from multiple frequency bands into a parameter-free multi-band fusion model. The proposed fusion model fuses all fully-connected FCNs to obtain a sparsely-connected FCN (sparse FCN for short) for each individual subject, as well as lets each sparse FCN be close to its neighbored sparse FCNs and be far away from its furthest sparse FCNs. Furthermore, we employ the l1 -SVM to conduct joint brain region selection and disease diagnosis. Finally, we evaluate the effectiveness of our proposed framework on various neuro-diseases, i.e., Fronto-Temporal Dementia (FTD), Obsessive-Compulsive Disorder (OCD), and Alzheimer's Disease (AD), and the experimental results demonstrate that our framework shows more reasonable results, compared to state-of-the-art methods, in terms of classification performance and the selected brain regions. The source code can be visited by the url https://github.com/reynard-hu/mbbna.

Multi-Class ASD Classification via Label Distribution Learning with Class-Shared and Class-Specific Decomposition

The behavioral and cognitive deficits in autism spectrum disorder (ASD) patients are associated with abnormal brain function. The resting-state functional magnetic resonance imaging (rs-fMRI) is an effective non-invasive tool for revealing the brain dysfunction for ASD patients. However, most rs-fMRI based ASD diagnosis methods are developed for simple binary classification, instead of classification of multiple sub-types in ASD. Besides, they assume that the class boundary in ASD classification is crisp, whereas the symptoms of ASD sub-types are a continuum from mild to severe impairments in both social communication and restrictive repetitive behaviors/interests, and do not have crisp boundary between each other. To this end, we introduce label distribution learning (LDL) into multi-class ASD classification and propose LDL-CSCS under the LDL framework. Specifically, the label distribution is introduced to describe how individual disease labels correlate with the subject. In the learning crierion of LDL-CSCS, the label distribution is decomposed into the class-shared and class-specific components, in which the class-shared component records the common knowledge across all persons and the class-specific component records the specific information in each ASD sub-type. Low-rank constraint is imposed on the class-shared component whereas the group sparse constraint is imposed on the class-specific component, respectively. An Augmented Lagrange Method (ALM) is developed to find the optimal solution. The experimental results show that the proposed method for ASD diagnosis has superior classification performance, compared with some existing algorithms.

Modularity-Guided Functional Brain Network Analysis for Early-Stage Dementia Identification

Function brain network (FBN) analysis has shown great potential in identifying brain diseases, such as Alzheimer's disease (AD) and its prodromal stage, namely mild cognitive impairment (MCI). It is essential to identify discriminative and interpretable features from function brain networks, so as to improve classification performance and help us understand the pathological mechanism of AD-related brain disorders. Previous studies usually extract node statistics or edge weights from FBNs to represent each subject. However, these methods generally ignore the topological structure (such as modularity) of FBNs. To address this issue, we propose a modular-LASSO feature selection (MLFS) framework that can explicitly model the modularity information to identify discriminative and interpretable features from FBNs for automated AD/MCI classification. Specifically, the proposed MLFS method first searches the modular structure of FBNs through a signed spectral clustering algorithm, and then selects discriminative features via a modularity-induced group LASSO method, followed by a support vector machine (SVM) for classification. To evaluate the effectiveness of the proposed method, extensive experiments are performed on 563 resting-state functional MRI scans from the public ADNI database to identify subjects with AD/MCI from normal controls and predict the future progress of MCI subjects. Experimental results demonstrate that our method is superior to previous methods in both tasks of AD/MCI identification and MCI conversion prediction, and also helps discover discriminative brain regions and functional connectivities associated with AD.

A Novel Unit-Based Personalized Fingerprint Feature Selection Strategy for Dynamic Functional Connectivity Networks

The sliding-window-based dynamic functional connectivity networks (SW-D-FCN) derive from resting-state functional Magnetic Resonance Imaging has become an increasingly useful tool in the diagnosis of various neurodegenerative diseases. However, it is still challenging to learn how to extract and select the most discriminative features from SW-D-FCN. Conventionally, existing methods opt to select a single discriminative feature set or concatenate a few more from the SW-D-FCN. However, such reductionist strategies may fail to fully capture the personalized discriminative characteristics contained in each functional connectivity (FC) sequence of the SW-D-FCN. To address this issue, we propose a unit-based personalized fingerprint feature selection (UPFFS) strategy to better capture the most discriminative feature associated with a target disease for each unit. Specifically, we regard the FC sequence between any pair of brain regions of interest (ROIs) is regarded as a unit. For each unit, the most discriminative feature is identified by a specific feature evaluation method and all the most discriminative features are then concatenated together as a feature set for the subsequent classification task. In such a way, the personalized fingerprint feature derived from each FC sequence can be fully mined and utilized in classification decision. To illustrate the effectiveness of the proposed strategy, we conduct experiments to distinguish subjects diagnosed with autism spectrum disorder from normal controls. Experimental results show that the proposed strategy can select relevant discriminative features and achieve superior performance to benchmark methods.

Estimating sparse functional connectivity networks via hyperparameter-free learning model

Functional connectivity networks (FCNs) provide a potential way for understanding the brain organizational patterns and diagnosing neurological diseases. Currently, researchers have proposed many methods for FCN construction, among which the most classic example is Pearson's correlation (PC). Despite its simplicity and popularity, PC always results in dense FCNs, and thus a thresholding strategy is usually needed in practice to sparsify the estimated FCNs prior to the network analysis, which undoubtedly causes the problem of threshold parameter selection. As an alternative to PC, sparse representation (SR) can directly generate sparse FCNs due to the l₁ regularizer in the estimation model. However, similar to the thresholding scheme used in PC, it is also challenging to determine suitable values for the regularization parameter in SR. To circumvent the difficulty of parameter selection involved in these traditional methods, we propose a hyperparameter-free method for FCN construction based on the global representation among fMRI time courses. Interestingly, the proposed method can automatically generate sparse FCNs, without any thresholding or regularization parameters. To verify the effectiveness of the proposed method, we conduct experiments to identify subjects with mild cognitive impairment (MCI) and Autism spectrum disorder (ASD) from normal controls (NCs) based on the estimated FCNs. Experimental results on two benchmark databases demonstrate that the achieved classification performance of our proposed scheme is comparable to four conventional methods.

A toolbox for brain network construction and classification (BrainNetClass)

Brain functional network has been increasingly used in understanding brain functions and diseases. While many network construction methods have been proposed, the progress in the field still largely relies on static pairwise Pearson's correlation-based functional network and group-level comparisons. We introduce a "Brain Network Construction and Classification (BrainNetClass)" toolbox to promote more advanced brain network construction methods to the filed, including some state-of-the-art methods that were recently developed to capture complex and high-order interactions among brain regions. The toolbox also integrates a well-accepted and rigorous classification framework based on brain connectome features toward individualized disease diagnosis in a hope that the advanced network modeling could boost the subsequent classification. BrainNetClass is a MATLAB-based, open-source, cross-platform toolbox with both graphical user-friendly interfaces and a command line mode targeting cognitive neuroscientists and clinicians for promoting reliability, reproducibility, and interpretability of connectome-based, computer-aided diagnosis. It generates abundant classification-related results from network presentations to contributing features that have been largely ignored by most studies to grant users the ability of evaluating the disease diagnostic model and its robustness and generalizability. We demonstrate the effectiveness of the toolbox on real resting-state functional MRI datasets. BrainNetClass (v1.0) is available at https://github.com/zzstefan/BrainNetClass.