Brain functional connectivity analysis based on multi-graph fusion

D-MHGCN: An End-to-End Individual Behavioral Prediction Model Using Dual Multi-Hop Graph Convolutional Network

Predicting individual behavior is a crucial area of research in neuroscience. Graph Neural Networks (GNNs), as powerful tools for extracting graph-structured features, are increasingly being utilized in various functional connectivity (FC) based behavioral prediction tasks. However, current predictive models primarily focus on enhancing GNNs' ability to extract features from FC networks while neglecting the importance of upstream individual network construction quality. This oversight results in constructed functional networks that fail to adequately represent individual behavioral capacity, thereby affecting the subsequent prediction accuracy. To address this issue, we proposed a new GNN-based behavioral prediction framework, named Dual Multi-Hop Graph Convolutional Network (D-MHGCN). Through the joint training of two GCNs, this framework integrates individual functional network construction and behavioral prediction into a unified optimization model. It allows the model to dynamically adjust the individual functional cortical parcellation according to the downstream tasks, thus creating task-aware, individual-specific FCNs that largely enhance its ability to predict behavior scores. Additionally, we employed multi-hop graph convolution layers instead of traditional single-hop methods in GCN to capture complex hierarchical connectivity patterns in brain networks. Our experimental evaluations, conducted on the large, public Human Connectome Project dataset, demonstrate that our proposed method outperforms existing methods in various behavioral prediction tasks. Moreover, it produces more functionally homogeneous cortical parcellation, showcasing its practical utility and effectiveness. Our work not only enhances the accuracy of individual behavioral prediction but also provides deeper insights into the neural mechanisms underlying individual differences in behavior.

A novel graph neural network method for Alzheimer's disease classification

Alzheimer's disease (AD) is a chronic neurodegenerative disease. Early diagnosis are very important to timely treatment and delay the progression of the disease. In the past decade, many computer-aided diagnostic (CAD) algorithms have been proposed for classification of AD. In this paper, we propose a novel graph neural network method, termed Brain Graph Attention Network (BGAN) for classification of AD. First, brain graph data are used to model classification of AD as a graph classification task. Second, a local attention layer is designed to capture and aggregate messages of interactions between node neighbors. And, a global attention layer is introduced to obtain the contribution of each node for graph representation. Finally, using the BGAN to implement AD classification. We train and test on two open public databases for AD classification task. Compared to classic models, the experimental results show that our model is superior to six classic models. We demonstrate that BGAN is a powerful classification model for AD. In addition, our model can provide an analysis of brain regions in order to judge which regions are related to AD disease and which regions are related to AD progression.

Leveraging Brain Modularity Prior for Interpretable Representation Learning of fMRI

Resting-state functional magnetic resonance imaging (rs-fMRI) can reflect spontaneous neural activities in the brain and is widely used for brain disorder analysis. Previous studies focus on extracting fMRI representations using machine/deep learning methods, but these features typically lack biological interpretability. The human brain exhibits a remarkable modular structure in spontaneous brain functional networks, with each module comprised of functionally interconnected brain regions-of-interest (ROIs). However, existing learning-based methods cannot adequately utilize such brain modularity prior. In this paper, we propose a brain modularity-constrained dynamic representation learning framework for interpretable fMRI analysis, consisting of dynamic graph construction, dynamic graph learning via a novel modularity-constrained graph neural network (MGNN), and prediction and biomarker detection. The designed MGNN is constrained by three core neurocognitive modules (i.e., salience network, central executive network, and default mode network), encouraging ROIs within the same module to share similar representations. To further enhance discriminative ability of learned features, we encourage the MGNN to preserve network topology of input graphs via a graph topology reconstruction constraint. Experimental results on 534 subjects with rs-fMRI scans from two datasets validate the effectiveness of the proposed method. The identified discriminative brain ROIs and functional connectivities can be regarded as potential fMRI biomarkers to aid in clinical diagnosis.

Inferring brain causal and temporal-lag networks for recognizing abnormal patterns of dementia

Brain functional network analysis has become a popular method to explore the laws of brain organization and identify biomarkers of neurological diseases. However, it is still a challenging task to construct an ideal brain network due to the limited understanding of the human brain. Existing methods often ignore the impact of temporal-lag on the results of brain network modeling, which may lead to some unreliable conclusions. To overcome this issue, we propose a novel brain functional network estimation method, which can simultaneously infer the causal mechanisms and temporal-lag values among brain regions. Specifically, our method converts the lag learning into an instantaneous effect estimation problem, and further embeds the search objectives into a deep neural network model as parameters to be learned. To verify the effectiveness of the proposed estimation method, we perform experiments on the Alzheimer's Disease Neuroimaging Initiative (ADNI) database by comparing the proposed model with several existing methods, including correlation-based and causality-based methods. The experimental results show that our brain networks constructed by the proposed estimation method can not only achieve promising classification performance, but also exhibit some characteristics of physiological mechanisms. Our approach provides a new perspective for understanding the pathogenesis of brain diseases. The source code is released at https://github.com/NJUSTxiazw/CTLN.

Reverse Graph Learning for Graph Neural Network

Graph neural networks (GNNs) conduct feature learning by taking into account the local structure preservation of the data to produce discriminative features, but need to address the following issues, i.e., 1) the initial graph containing faulty and missing edges often affect feature learning and 2) most GNN methods suffer from the issue of out-of-example since their training processes do not directly generate a prediction model to predict unseen data points. In this work, we propose a reverse GNN model to learn the graph from the intrinsic space of the original data points as well as to investigate a new out-of-sample extension method. As a result, the proposed method can output a high-quality graph to improve the quality of feature learning, while the new method of out-of-sample extension makes our reverse GNN method available for conducting supervised learning and semi-supervised learning. Experimental results on real-world datasets show that our method outputs competitive classification performance, compared to state-of-the-art methods, in terms of semi-supervised node classification, out-of-sample extension, random edge attack, link prediction, and image retrieval.

A multi-view convolutional neural network method combining attention mechanism for diagnosing autism spectrum disorder

Autism Spectrum Disorder (ASD) is a neurodevelopmental condition whose current psychiatric diagnostic process is subjective and behavior-based. In contrast, functional magnetic resonance imaging (fMRI) can objectively measure brain activity and is useful for identifying brain disorders. However, the ASD diagnostic models employed to date have not reached satisfactory levels of accuracy. This study proposes the use of MAACNN, a method that utilizes multi-view convolutional neural networks (CNNs) in conjunction with attention mechanisms for identifying ASD in multi-scale fMRI. The proposed algorithm effectively combines unsupervised and supervised learning. In the initial stage, we employ stacked denoising autoencoders, an unsupervised learning method for feature extraction, which provides different nodes to adapt to multi-scale data. In the subsequent stage, we perform supervised learning by employing multi-view CNNs for classification and obtain the final results. Finally, multi-scale data fusion is achieved by using the attention fusion mechanism. The ABIDE dataset is used to evaluate the model we proposed., and the experimental results show that MAACNN achieves superior performance with 75.12% accuracy and 0.79 AUC on ABIDE-I, and 72.88% accuracy and 0.76 AUC on ABIDE-II. The proposed method significantly contributes to the clinical diagnosis of ASD.

Diagnosis of Alzheimer's disease by joining dual attention CNN and MLP based on structural MRIs, clinical and genetic data

Alzheimer's disease (AD) is an irreversible central nervous degenerative disease, while mild cognitive impairment (MCI) is a precursor state of AD. Accurate early diagnosis of AD is conducive to the prevention and early intervention treatment of AD. Although some computational methods have been developed for AD diagnosis, most employ only neuroimaging, ignoring other data (e.g., genetic, clinical) that may have potential disease information. In addition, the results of some methods lack interpretability. In this work, we proposed a novel method (called DANMLP) of joining dual attention convolutional neural network (CNN) and multilayer perceptron (MLP) for computer-aided AD diagnosis by integrating multi-modality data of the structural magnetic resonance imaging (sMRI), clinical data (i.e., demographics, neuropsychology), and APOE genetic data. Our DANMLP consists of four primary components: (1) the Patch-CNN for extracting the image characteristics from each local patch, (2) the position self-attention block for capturing the dependencies between features within a patch, (3) the channel self-attention block for capturing dependencies of inter-patch features, (4) two MLP networks for extracting the clinical features and outputting the AD classification results, respectively. Compared with other state-of-the-art methods in the 5CV test, DANMLP achieves 93% and 82.4% classification accuracy for the AD vs. MCI and MCI vs. NC tasks on the ADNI database, which is 0.2%∼15.2% and 3.4%∼26.8% higher than that of other five methods, respectively. The individualized visualization of focal areas can also help clinicians in the early diagnosis of AD. These results indicate that DANMLP can be effectively used for diagnosing AD and MCI patients.

StrokeNet: An automated approach for segmentation and rupture risk prediction of intracranial aneurysm

Intracranial Aneurysms (IA) present a complex challenge for neurosurgeons as the risks associated with surgical intervention, such as Subarachnoid Hemorrhage (SAH) mortality and morbidity, may outweigh the benefits of aneurysmal occlusion in some cases. Hence, there is a critical need for developing techniques that assist physicians in assessing the risk of aneurysm rupture to determine which aneurysms require treatment. However, a reliable IA rupture risk prediction technique is currently unavailable. To address this issue, this study proposes a novel approach for aneurysm segmentation and multidisciplinary rupture prediction using 2D Digital Subtraction Angiography (DSA) images. The proposed method involves training a fully connected convolutional neural network (CNN) to segment aneurysm regions in DSA images, followed by extracting and fusing different features using a multidisciplinary approach, including deep features, geometrical features, Fourier descriptor, and shear pressure on the aneurysm wall. The proposed method also adopts a fast correlation-based filter approach to drop highly correlated features from the set of fused features. Finally, the selected fused features are passed through a Decision Tree classifier to predict the rupture severity of the associated aneurysm into four classes: Mild, Moderate, Severe, and Critical. The proposed method is evaluated on a newly developed DSA image dataset and on public datasets to assess its generalizability. The system's performance is also evaluated on DSA images annotated by expert neurosurgeons for the rupture risk assessment of the segmented aneurysm. The proposed system outperforms existing state-of-the-art segmentation methods, achieving an 85 % accuracy against annotated DSA images for the risk assessment of aneurysmal rupture.

Learning to Fuse Multiple Brain Functional Networks for Automated Autism Identification

Functional connectivity network (FCN) has become a popular tool to identify potential biomarkers for brain dysfunction, such as autism spectrum disorder (ASD). Due to its importance, researchers have proposed many methods to estimate FCNs from resting-state functional MRI (rs-fMRI) data. However, the existing FCN estimation methods usually only capture a single relationship between brain regions of interest (ROIs), e.g., linear correlation, nonlinear correlation, or higher-order correlation, thus failing to model the complex interaction among ROIs in the brain. Additionally, such traditional methods estimate FCNs in an unsupervised way, and the estimation process is independent of the downstream tasks, which makes it difficult to guarantee the optimal performance for ASD identification. To address these issues, in this paper, we propose a multi-FCN fusion framework for rs-fMRI-based ASD classification. Specifically, for each subject, we first estimate multiple FCNs using different methods to encode rich interactions among ROIs from different perspectives. Then, we use the label information (ASD vs. healthy control (HC)) to learn a set of fusion weights for measuring the importance/discrimination of those estimated FCNs. Finally, we apply the adaptively weighted fused FCN on the ABIDE dataset to identify subjects with ASD from HCs. The proposed FCN fusion framework is straightforward to implement and can significantly improve diagnostic accuracy compared to traditional and state-of-the-art methods.

Fusing Multiview Functional Brain Networks by Joint Embedding for Brain Disease Identification

Background: Functional brain networks (FBNs) derived from resting-state functional MRI (rs-fMRI) have shown great potential in identifying brain disorders, such as autistic spectrum disorder (ASD). Therefore, many FBN estimation methods have been proposed in recent years. Most existing methods only model the functional connections between brain regions of interest (ROIs) from a single view (e.g., by estimating FBNs through a specific strategy), failing to capture the complex interactions among ROIs in the brain. Methods: To address this problem, we propose fusion of multiview FBNs through joint embedding, which can make full use of the common information of multiview FBNs estimated by different strategies. More specifically, we first stack the adjacency matrices of FBNs estimated by different methods into a tensor and use tensor factorization to learn the joint embedding (i.e., a common factor of all FBNs) for each ROI. Then, we use Pearson's correlation to calculate the connections between each embedded ROI in order to reconstruct a new FBN. Results: Experimental results obtained on the public ABIDE dataset with rs-fMRI data reveal that our method is superior to several state-of-the-art methods in automated ASD diagnosis. Moreover, by exploring FBN "features" that contributed most to ASD identification, we discovered potential biomarkers for ASD diagnosis. The proposed framework achieves an accuracy of 74.46%, which is generally better than the compared individual FBN methods. In addition, our method achieves the best performance compared to other multinetwork methods, i.e., an accuracy improvement of at least 2.72%. Conclusions: We present a multiview FBN fusion strategy through joint embedding for fMRI-based ASD identification. The proposed fusion method has an elegant theoretical explanation from the perspective of eigenvector centrality.

Functional magnetic resonance imaging, deep learning, and Alzheimer's disease: A systematic review

Alzheimer's disease (AD) is currently diagnosed using a mixture of psychological tests and clinical observations. However, these diagnoses are not perfect, and additional diagnostic tools (e.g., MRI) can help improve our understanding of AD as well as our ability to detect the disease. Accordingly, a large amount of research has been invested into innovative diagnostic methods for AD. Functional MRI (fMRI) is a form of neuroimaging technology that has been used to diagnose AD; however, fMRI is incredibly noisy, complex, and thus lacks clinical use. Nonetheless, recent innovations in deep learning technology could enable the simplified and streamlined analysis of fMRI. Deep learning is a form of artificial intelligence that uses computer algorithms based on human neural networks to solve complex problems. For example, in fMRI research, deep learning models can automatically denoise images and classify AD by detecting patterns in participants' brain scans. In this systematic review, we investigate how fMRI (specifically resting-state fMRI) and deep learning methods are used to diagnose AD. In turn, we outline the common deep neural network, preprocessing, and classification methods used in the literature. We also discuss the accuracy, strengths, limitations, and future direction of fMRI deep learning methods. In turn, we aim to summarize the current field for new researchers, suggest specific areas for future research, and highlight the potential of fMRI to aid AD diagnoses.

Convolutional Recurrent Neural Network for Dynamic Functional MRI Analysis and Brain Disease Identification

Dynamic functional connectivity (dFC) networks derived from resting-state functional magnetic resonance imaging (rs-fMRI) help us understand fundamental dynamic characteristics of human brains, thereby providing an efficient solution for automated identification of brain diseases, such as Alzheimer's disease (AD) and its prodromal stage. Existing studies have applied deep learning methods to dFC network analysis and achieved good performance compared with traditional machine learning methods. However, they seldom take advantage of sequential information conveyed in dFC networks that could be informative to improve the diagnosis performance. In this paper, we propose a convolutional recurrent neural network (CRNN) for automated brain disease classification with rs-fMRI data. Specifically, we first construct dFC networks from rs-fMRI data using a sliding window strategy. Then, we employ three convolutional layers and long short-term memory (LSTM) layer to extract high-level features of dFC networks and also preserve the sequential information of extracted features, followed by three fully connected layers for brain disease classification. Experimental results on 174 subjects with 563 rs-fMRI scans from the Alzheimer's Disease Neuroimaging Initiative (ADNI) demonstrate the effectiveness of our proposed method in binary and multi-category classification tasks.

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.

Multigraph Fusion for Dynamic Graph Convolutional Network

Graph convolutional network (GCN) outputs powerful representation by considering the structure information of the data to conduct representation learning, but its robustness is sensitive to the quality of both the feature matrix and the initial graph. In this article, we propose a novel multigraph fusion method to produce a high-quality graph and a low-dimensional space of original high-dimensional data for the GCN model. Specifically, the proposed method first extracts the common information and the complementary information among multiple local graphs to obtain a unified local graph, which is then fused with the global graph of the data to obtain the initial graph for the GCN model. As a result, the proposed method conducts the graph fusion process twice to simultaneously learn the low-dimensional space and the intrinsic graph structure of the data in a unified framework. Experimental results on real datasets demonstrated that our method outperformed the comparison methods in terms of classification tasks.

Multi-task multi-modality SVM for early COVID-19 Diagnosis using chest CT data

In the early diagnosis of the Coronavirus disease (COVID-19), it is of great importance for either distinguishing severe cases from mild cases or predicting the conversion time that mild cases would possibly convert to severe cases. This study investigates both of them in a unified framework by exploring the problems such as slight appearance difference between mild cases and severe cases, the interpretability, the High Dimension and Low Sample Size (HDLSS) data, and the class imbalance. To this end, the proposed framework includes three steps: (1) feature extraction which first conducts the hierarchical segmentation on the chest Computed Tomography (CT) image data and then extracts multi-modality handcrafted features for each segment, aiming at capturing the slight appearance difference from different perspectives; (2) data augmentation which employs the over-sampling technique to augment the number of samples corresponding to the minority classes, aiming at investigating the class imbalance problem; and (3) joint construction of classification and regression by proposing a novel Multi-task Multi-modality Support Vector Machine (MM-SVM) method to solve the issue of the HDLSS data and achieve the interpretability. Experimental analysis on two synthetic and one real COVID-19 data set demonstrated that our proposed framework outperformed six state-of-the-art methods in terms of binary classification and regression performance.