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Xue Y, Xue H, Fang P, Zhu S, Qiao L, An Y. Dynamic functional connections analysis with spectral learning for brain disorder detection. Artif Intell Med 2024; 157:102984. [PMID: 39298922 DOI: 10.1016/j.artmed.2024.102984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 09/04/2024] [Accepted: 09/13/2024] [Indexed: 09/22/2024]
Abstract
Dynamic functional connections (dFCs), can reveal neural activities, which provides an insightful way of mining the temporal patterns within the human brain and further detecting brain disorders. However, most existing studies focus on the dFCs estimation to identify brain disorders by shallow temporal features and methods, which cannot capture the inherent temporal patterns of dFCs effectively. To address this problem, this study proposes a novel method, named dynamic functional connections analysis with spectral learning (dCSL), to explore inherently temporal patterns of dFCs and further detect the brain disorders. Concretely, dCSL includes two components, dFCs estimation module and dFCs analysis module. In the former, dFCs are estimated via the sliding window technique. In the latter, the spectral kernel mapping is first constructed by combining the Fourier transform with the non-stationary kernel. Subsequently, the spectral kernel mapping is stacked into a deep kernel network to explore higher-order temporal patterns of dFCs through spectral learning. The proposed dCSL, sharing the benefits of deep architecture and non-stationary kernel, can not only calculate the long-range relationship but also explore the higher-order temporal patterns of dFCs. To evaluate the proposed method, a set of brain disorder classification tasks are conducted on several public datasets. As a result, the proposed dCSL achieves 5% accuracy improvement compared with the widely used approaches for analyzing sequence data, 1.3% accuracy improvement compared with the state-of-the-art methods for dFCs. In addition, the discriminative brain regions are explored in the ASD detection task. The findings in this study are consistent with the clinical performance in ASD.
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Affiliation(s)
- Yanfang Xue
- School of Computer Science and Engineering, Southeast University, Nanjing, 210096, China; Key Laboratory of New Generation Artificial Intelligence Technology and Its Interdisciplinary Applications (Southeast University), Nanjing, 210096, China
| | - Hui Xue
- School of Computer Science and Engineering, Southeast University, Nanjing, 210096, China; Key Laboratory of New Generation Artificial Intelligence Technology and Its Interdisciplinary Applications (Southeast University), Nanjing, 210096, China.
| | - Pengfei Fang
- School of Computer Science and Engineering, Southeast University, Nanjing, 210096, China; Key Laboratory of New Generation Artificial Intelligence Technology and Its Interdisciplinary Applications (Southeast University), Nanjing, 210096, China
| | - Shipeng Zhu
- School of Computer Science and Engineering, Southeast University, Nanjing, 210096, China; Key Laboratory of New Generation Artificial Intelligence Technology and Its Interdisciplinary Applications (Southeast University), Nanjing, 210096, China
| | - Lishan Qiao
- School of Mathematical Science, Liaocheng University, Liaocheng, 252000, China
| | - Yuexuan An
- School of Computer Science and Engineering, Southeast University, Nanjing, 210096, China; Key Laboratory of New Generation Artificial Intelligence Technology and Its Interdisciplinary Applications (Southeast University), Nanjing, 210096, China
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Cai P, Li B, Sun G, Yang B, Wang X, Lv C, Yan J. DEAF-Net: Detail-Enhanced Attention Feature Fusion Network for Retinal Vessel Segmentation. JOURNAL OF IMAGING INFORMATICS IN MEDICINE 2024:10.1007/s10278-024-01207-6. [PMID: 39103564 DOI: 10.1007/s10278-024-01207-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/25/2024] [Accepted: 07/08/2024] [Indexed: 08/07/2024]
Abstract
Retinal vessel segmentation is crucial for the diagnosis of ophthalmic and cardiovascular diseases. However, retinal vessels are densely and irregularly distributed, with many capillaries blending into the background, and exhibit low contrast. Moreover, the encoder-decoder-based network for retinal vessel segmentation suffers from irreversible loss of detailed features due to multiple encoding and decoding, leading to incorrect segmentation of the vessels. Meanwhile, the single-dimensional attention mechanisms possess limitations, neglecting the importance of multidimensional features. To solve these issues, in this paper, we propose a detail-enhanced attention feature fusion network (DEAF-Net) for retinal vessel segmentation. First, the detail-enhanced residual block (DERB) module is proposed to strengthen the capacity for detailed representation, ensuring that intricate features are efficiently maintained during the segmentation of delicate vessels. Second, the multidimensional collaborative attention encoder (MCAE) module is proposed to optimize the extraction of multidimensional information. Then, the dynamic decoder (DYD) module is introduced to preserve spatial information during the decoding process and reduce the information loss caused by upsampling operations. Finally, the proposed detail-enhanced feature fusion (DEFF) module composed of DERB, MCAE and DYD modules fuses feature maps from both encoding and decoding and achieves effective aggregation of multi-scale contextual information. The experiments conducted on the datasets of DRIVE, CHASEDB1, and STARE, achieving Sen of 0.8305, 0.8784, and 0.8654, and AUC of 0.9886, 0.9913, and 0.9911 on DRIVE, CHASEDB1, and STARE, respectively, demonstrate the performance of our proposed network, particularly in the segmentation of fine retinal vessels.
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Affiliation(s)
- Pengfei Cai
- School of Electronic Engineering, Tianjin University of Technology and Education, Tianjin, 300222, China
| | - Biyuan Li
- School of Electronic Engineering, Tianjin University of Technology and Education, Tianjin, 300222, China.
- Tianjin Development Zone Jingnuohanhai Data Technology Co., Ltd, Tianjin, China.
| | - Gaowei Sun
- School of Electronic Engineering, Tianjin University of Technology and Education, Tianjin, 300222, China
| | - Bo Yang
- School of Electronic Engineering, Tianjin University of Technology and Education, Tianjin, 300222, China
| | - Xiuwei Wang
- School of Electronic Engineering, Tianjin University of Technology and Education, Tianjin, 300222, China
| | - Chunjie Lv
- School of Electronic Engineering, Tianjin University of Technology and Education, Tianjin, 300222, China
| | - Jun Yan
- School of Mathematics, Tianjin University, Tianjin, 300072, China
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Ji CH, Shin DH, Son YH, Kam TE. Sparse Graph Representation Learning Based on Reinforcement Learning for Personalized Mild Cognitive Impairment (MCI) Diagnosis. IEEE J Biomed Health Inform 2024; 28:4842-4853. [PMID: 38683720 DOI: 10.1109/jbhi.2024.3393625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Resting-state functional magnetic resonance imaging (rs-fMRI) has gained attention as a reliable technique for investigating the intrinsic function patterns of the brain. It facilitates the extraction of functional connectivity networks (FCNs) that capture synchronized activity patterns among regions of interest (ROIs). Analyzing FCNs enables the identification of distinctive connectivity patterns associated with mild cognitive impairment (MCI). For MCI diagnosis, various sparse representation techniques have been introduced, including statistical- and deep learning-based methods. However, these methods face limitations due to their reliance on supervised learning schemes, which restrict the exploration necessary for probing novel solutions. To overcome such limitation, prior work has incorporated reinforcement learning (RL) to dynamically select ROIs, but effective exploration remains challenging due to the vast search space during training. To tackle this issue, in this study, we propose an advanced RL-based framework that utilizes a divide-and-conquer approach to decompose the FCN construction task into smaller sub-problems in a subject-specific manner, enabling efficient exploration under each sub-problem condition. Additionally, we leverage the learned value function to determine the sparsity level of FCNs, considering individual characteristics of FCNs. We validate the effectiveness of our proposed framework by demonstrating its superior performance in MCI diagnosis on publicly available cohort datasets.
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Liu J, Han L, Ji J. MCAN: Multimodal Causal Adversarial Networks for Dynamic Effective Connectivity Learning From fMRI and EEG Data. IEEE TRANSACTIONS ON MEDICAL IMAGING 2024; 43:2913-2923. [PMID: 38526887 DOI: 10.1109/tmi.2024.3381670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Dynamic effective connectivity (DEC) is the accumulation of effective connectivity in the time dimension, which can describe the continuous neural activities in the brain. Recently, learning DEC from functional magnetic resonance imaging (fMRI) and electroencephalography (EEG) data has attracted the attention of neuroinformatics researchers. However, the current methods fail to consider the gap between the fMRI and EEG modality, which can not precisely learn the DEC network from multimodal data. In this paper, we propose a multimodal causal adversarial network for DEC learning, named MCAN. The MCAN contains two modules: multimodal causal generator and multimodal causal discriminator. First, MCAN employs a multimodal causal generator with an attention-guided layer to produce a posterior signal and output a set of DEC networks. Then, the proposed method uses a multimodal causal discriminator to unsupervised calculate the joint gradient, which directs the update of the whole network. The experimental results on simulated data sets show that MCAN is superior to other state-of-the-art methods in learning the network structure of DEC and can effectively estimate the brain states. The experimental results on real data sets show that MCAN can better reveal abnormal patterns of brain activity and has good application potential in brain network analysis.
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Dong Q, Cai H, Li Z, Liu J, Hu B. A Multiview Brain Network Transformer Fusing Individualized Information for Autism Spectrum Disorder Diagnosis. IEEE J Biomed Health Inform 2024; 28:4854-4865. [PMID: 38700974 DOI: 10.1109/jbhi.2024.3396457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Functional connectivity (FC) networks, built from analyses of resting-state magnetic resonance imaging (rs-fMRI), serve as efficacious biomarkers for identifying Autism Spectrum Disorders (ASD) patients. Given the neurobiological heterogeneity across individuals and the unique presentation of ASD symptoms, the fusion of individualized information into diagnosis becomes essential. However, this aspect is overlooked in most methods. Furthermore, the existing methods typically focus on studying direct pairwise connections between brain ROIs, while disregarding interactions between indirectly connected neighbors. To overcome above challenges, we build common FC and individualized FC by tangent pearson embedding (TP) and common orthogonal basis extraction (COBE) respectively, and present a novel multiview brain transformer (MBT) aimed at effectively fusing common and indivinformation of subjects. MBT is mainly constructed by transformer layers with diffusion kernel (DK), fusion quality-inspired weighting module (FQW), similarity loss and orthonormal clustering fusion readout module (OCFRead). DK transformer can incorporate higher-order random walk methods to capture wider interactions among indirectly connected brain regions. FQW promotes adaptive fusion of features between views, and similarity loss and OCFRead are placed on the last layer to accomplish the ultimate integration of information. In our method, TP, DK and FQW modules all help to model wider connectivity in the brain that make up for the shortcomings of traditional methods. We conducted experiments on the public ABIDE dataset based on AAL and CC200 respectively. Our framework has shown promising results, outperforming state-of-the-art methods on both templates. This suggests its potential as a valuable approach for clinical ASD diagnosis.
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Jiang M, Chen Y, Yan J, Xiao Z, Mao W, Zhao B, Yang S, Zhao Z, Zhang T, Guo L, Becker B, Yao D, Kendrick KM, Jiang X. Anatomy-Guided Spatio-Temporal Graph Convolutional Networks (AG-STGCNs) for Modeling Functional Connectivity Between Gyri and Sulci Across Multiple Task Domains. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2024; 35:7435-7445. [PMID: 35930515 DOI: 10.1109/tnnls.2022.3194733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The cerebral cortex is folded as gyri and sulci, which provide the foundation to unveil anatomo-functional relationship of brain. Previous studies have extensively demonstrated that gyri and sulci exhibit intrinsic functional difference, which is further supported by morphological, genetic, and structural evidences. Therefore, systematically investigating the gyro-sulcal (G-S) functional difference can help deeply understand the functional mechanism of brain. By integrating functional magnetic resonance imaging (fMRI) with advanced deep learning models, recent studies have unveiled the temporal difference in functional activity between gyri and sulci. However, the potential difference of functional connectivity, which represents functional dependency between gyri and sulci, is much unknown. Moreover, the regularity and variability of the G-S functional connectivity difference across multiple task domains remains to be explored. To address the two concerns, this study developed new anatomy-guided spatio-temporal graph convolutional networks (AG-STGCNs) to investigate the regularity and variability of functional connectivity differences between gyri and sulci across multiple task domains. Based on 830 subjects with seven different task-based and one resting state fMRI (rs-fMRI) datasets from the public Human Connectome Project (HCP), we consistently found that there are significant differences of functional connectivity between gyral and sulcal regions within task domains compared with resting state (RS). Furthermore, there is considerable variability of such functional connectivity and information flow between gyri and sulci across different task domains, which are correlated with individual cognitive behaviors. Our study helps better understand the functional segregation of gyri and sulci within task domains as well as the anatomo-functional-behavioral relationship of the human brain.
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Wang F, Ren J, Cui W, Zhou Y, Yao P, Lai X, Pang Y, Chen Z, Lin Y, Liu H. Verbal memory network mapping in individual patients predicts postoperative functional impairments. Hum Brain Mapp 2024; 45:e26691. [PMID: 38703114 PMCID: PMC11069337 DOI: 10.1002/hbm.26691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/15/2024] [Accepted: 04/08/2024] [Indexed: 05/06/2024] Open
Abstract
Verbal memory decline is a significant concern following temporal lobe surgeries in patients with epilepsy, emphasizing the need for precision presurgical verbal memory mapping to optimize functional outcomes. However, the inter-individual variability in functional networks and brain function-structural dissociations pose challenges when relying solely on group-level atlases or anatomical landmarks for surgical guidance. Here, we aimed to develop and validate a personalized functional mapping technique for verbal memory using precision resting-state functional MRI (rs-fMRI) and neurosurgery. A total of 38 patients with refractory epilepsy scheduled for surgical interventions were enrolled and 28 patients were analyzed in the study. Baseline 30-min rs-fMRI scanning, verbal memory and language assessments were collected for each patient before surgery. Personalized verbal memory networks (PVMN) were delineated based on preoperative rs-fMRI data for each patient. The accuracy of PVMN was assessed by comparing post-operative functional impairments and the overlapping extent between PVMN and surgical lesions. A total of 14 out of 28 patients experienced clinically meaningful declines in verbal memory after surgery. The personalized network and the group-level atlas exhibited 100% and 75.0% accuracy in predicting postoperative verbal memory declines, respectively. Moreover, six patients with extra-temporal lesions that overlapped with PVMN showed selective impairments in verbal memory. Furthermore, the lesioned ratio of the personalized network rather than the group-level atlas was significantly correlated with postoperative declines in verbal memory (personalized networks: r = -0.39, p = .038; group-level atlas: r = -0.19, p = .332). In conclusion, our personalized functional mapping technique, using precision rs-fMRI, offers valuable insights into individual variability in the verbal memory network and holds promise in precision verbal memory network mapping in individuals.
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Affiliation(s)
- Feng Wang
- Department of Neurosurgery, Neurosurgery Research InstituteThe First Affiliated Hospital of Fujian Medical UniversityFuzhouChina
| | | | | | | | - Peisen Yao
- Department of Neurosurgery, Neurosurgery Research InstituteThe First Affiliated Hospital of Fujian Medical UniversityFuzhouChina
- Department of Neurosurgery, Binhai Branch of National Regional Medical CenterThe First Affiliated Hospital of Fujian Medical UniversityFuzhouChina
- Fujian Provincial Institutes of Brain Disorders and Brain SciencesThe First Affiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Xuemiao Lai
- Department of Neurosurgery, Neurosurgery Research InstituteThe First Affiliated Hospital of Fujian Medical UniversityFuzhouChina
- Department of Neurosurgery, Binhai Branch of National Regional Medical CenterThe First Affiliated Hospital of Fujian Medical UniversityFuzhouChina
- Fujian Provincial Institutes of Brain Disorders and Brain SciencesThe First Affiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Yue Pang
- Department of Neurosurgery, Neurosurgery Research InstituteThe First Affiliated Hospital of Fujian Medical UniversityFuzhouChina
- Department of Neurosurgery, Binhai Branch of National Regional Medical CenterThe First Affiliated Hospital of Fujian Medical UniversityFuzhouChina
- Fujian Provincial Institutes of Brain Disorders and Brain SciencesThe First Affiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Zhili Chen
- Department of Neurosurgery, Neurosurgery Research InstituteThe First Affiliated Hospital of Fujian Medical UniversityFuzhouChina
- Department of Neurosurgery, Binhai Branch of National Regional Medical CenterThe First Affiliated Hospital of Fujian Medical UniversityFuzhouChina
- Fujian Provincial Institutes of Brain Disorders and Brain SciencesThe First Affiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Yuanxiang Lin
- Department of Neurosurgery, Neurosurgery Research InstituteThe First Affiliated Hospital of Fujian Medical UniversityFuzhouChina
- Department of Neurosurgery, Binhai Branch of National Regional Medical CenterThe First Affiliated Hospital of Fujian Medical UniversityFuzhouChina
- Fujian Provincial Institutes of Brain Disorders and Brain SciencesThe First Affiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Hesheng Liu
- Changping LaboratoryBeijingChina
- Biomedical Pioneering Innovation Center (BIOPIC)Peking UniversityBeijingChina
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Kang E, Heo DW, Lee J, Suk HI. A Learnable Counter-Condition Analysis Framework for Functional Connectivity-Based Neurological Disorder Diagnosis. IEEE TRANSACTIONS ON MEDICAL IMAGING 2024; 43:1377-1387. [PMID: 38019623 DOI: 10.1109/tmi.2023.3337074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
To understand the biological characteristics of neurological disorders with functional connectivity (FC), recent studies have widely utilized deep learning-based models to identify the disease and conducted post-hoc analyses via explainable models to discover disease-related biomarkers. Most existing frameworks consist of three stages, namely, feature selection, feature extraction for classification, and analysis, where each stage is implemented separately. However, if the results at each stage lack reliability, it can cause misdiagnosis and incorrect analysis in afterward stages. In this study, we propose a novel unified framework that systemically integrates diagnoses (i.e., feature selection and feature extraction) and explanations. Notably, we devised an adaptive attention network as a feature selection approach to identify individual-specific disease-related connections. We also propose a functional network relational encoder that summarizes the global topological properties of FC by learning the inter-network relations without pre-defined edges between functional networks. Last but not least, our framework provides a novel explanatory power for neuroscientific interpretation, also termed counter-condition analysis. We simulated the FC that reverses the diagnostic information (i.e., counter-condition FC): converting a normal brain to be abnormal and vice versa. We validated the effectiveness of our framework by using two large resting-state functional magnetic resonance imaging (fMRI) datasets, Autism Brain Imaging Data Exchange (ABIDE) and REST-meta-MDD, and demonstrated that our framework outperforms other competing methods for disease identification. Furthermore, we analyzed the disease-related neurological patterns based on counter-condition analysis.
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Liu J, Yang W, Ma Y, Dong Q, Li Y, Hu B. Effective hyper-connectivity network construction and learning: Application to major depressive disorder identification. Comput Biol Med 2024; 171:108069. [PMID: 38394798 DOI: 10.1016/j.compbiomed.2024.108069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 01/08/2024] [Accepted: 01/27/2024] [Indexed: 02/25/2024]
Abstract
Functional connectivity (FC) derived from resting-state fMRI (rs-fMRI) is a primary approach for identifying brain diseases, but it is limited to capturing the pairwise correlation between regions-of-interest (ROIs) in the brain. Thus, hyper-connectivity which describes the higher-order relationship among multiple ROIs is receiving increasing attention. However, most hyper-connectivity methods overlook the directionality of connections. The direction of information flow constitutes a pivotal factor in shaping brain activity and cognitive processes. Neglecting this directional aspect can lead to an incomplete understanding of high-order interactions within the brain. To this end, we propose a novel effective hyper-connectivity (EHC) network that integrates direction detection and hyper-connectivity modeling. It characterizes the high-order directional information flow among multiple ROIs, providing a more comprehensive understanding of brain activity. Then, we develop a directed hypergraph convolutional network (DHGCN) to acquire deep representations from EHC network and functional indicators of ROIs. In contrast to conventional hypergraph convolutional networks designed for undirected hypergraphs, DHGCN is specifically tailored to handle directed hypergraph data structures. Moreover, unlike existing methods that primarily focus on fMRI time series, our proposed DHGCN model also incorporates multiple functional indicators, providing a robust framework for feature learning. Finally, deep representations generated via DHGCN, combined with demographic factors, are used for major depressive disorder (MDD) identification. Experimental results demonstrate that the proposed framework outperforms both FC and undirected hyper-connectivity models, as well as surpassing other state-of-the-art methods. The identification of EHC abnormalities through our framework can enhance the analysis of brain function in individuals with MDD.
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Affiliation(s)
- Jingyu Liu
- Key Laboratory of Brain Health Intelligent Evaluation and Intervention, Ministry of Education, and the School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, China
| | - Wenxin Yang
- School of Information Science and Engineering, Lanzhou University, 730000, Lanzhou, China
| | - Yulan Ma
- School of Automation Science and Electrical Engineering, State Key Laboratory of Virtual Reality Technology and Systems, Beihang University, Beijing, 100191, China
| | - Qunxi Dong
- Key Laboratory of Brain Health Intelligent Evaluation and Intervention, Ministry of Education, and the School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, China.
| | - Yang Li
- School of Automation Science and Electrical Engineering, State Key Laboratory of Virtual Reality Technology and Systems, Beihang University, Beijing, 100191, China.
| | - Bin Hu
- Key Laboratory of Brain Health Intelligent Evaluation and Intervention, Ministry of Education, and the School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, China.
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Lei D, Zhang T, Wu Y, Li W, Li X. Autism spectrum disorder diagnosis based on deep unrolling-based spatial constraint representation. Med Biol Eng Comput 2023; 61:2829-2842. [PMID: 37486440 DOI: 10.1007/s11517-023-02859-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/25/2023] [Indexed: 07/25/2023]
Abstract
Accurate diagnosis of autism spectrum disorder (ASD) is crucial for effective treatment and prognosis. Functional brain networks (FBNs) constructed from functional magnetic resonance imaging (fMRI) have become a popular tool for ASD diagnosis. However, existing model-driven approaches used to construct FBNs lack the ability to capture potential non-linear relationships between data and labels. Moreover, most existing studies treat the FBNs construction and disease classification as separate steps, leading to large inter-subject variability in the estimated FBNs and reducing the statistical power of subsequent group comparison. To address these limitations, we propose a new approach to FBNs construction called the deep unrolling-based spatial constraint representation (DUSCR) model and integrate it with a convolutional classifier to create an end-to-end framework for ASD recognition. Specifically, the model spatial constraint representation (SCR) is solved using a proximal gradient descent algorithm, and we unroll it into deep networks using the deep unrolling algorithm. Classification is then performed using a convolutional prototype learning model. We evaluated the effectiveness of the proposed method on the ABIDE I dataset and observed a significant improvement in model performance and classification accuracy. The resting state fMRI images are preprocessed into time series data and 3D coordinates of each region of interest. The data are fed into the DUSCR model, a model for building functional brain networks using deep learning instead of traditional models, that we propose, and then the outputs are fed into the convolutional classifier with prototype learning to determine whether the patient has ASD disease.
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Affiliation(s)
- Dajiang Lei
- School of Computer Science and Technology, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Tao Zhang
- School of Computer Science and Technology, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Yue Wu
- School of Computer Science and Technology, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Weisheng Li
- School of Computer Science and Technology, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Xinwei Li
- School of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, China.
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Zhang Z, Gao L, Li P, Jin G, Wang J. DAUF: A disease-related attentional UNet framework for progressive and stable mild cognitive impairment identification. Comput Biol Med 2023; 165:107401. [PMID: 37678136 DOI: 10.1016/j.compbiomed.2023.107401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 08/02/2023] [Accepted: 08/26/2023] [Indexed: 09/09/2023]
Abstract
Identifying progressive mild cognitive impairment (pMCI) and stable mild cognitive impairment (sMCI) plays a significant role in early Alzheimer's disease (AD) diagnosis, which can effectively boost the life quality of patients. Recently, convolutional neural network (CNN)- based methods using structural magnetic resonance imaging (sMRI) images have shown effective for AD identification. However, these CNN-based methods fail to effectively explore the feature extraction of disease-related multi-scale tissues, such as ventricles, hippocampi and cerebral cortex. To address this issue, we propose an end-to-end disease-related attentional UNet framework (DAUF) for identifying pMCI and sMCI, by embedding a devised dual disease-related attention module (D2AM) and a novel tree-structured feature fusion classifier (TFFC). Specifically, D2AM leverages the complementarity between feature maps and attention maps and the complementary features from the encoder and decoder, so as to highlight discriminative semantic and detailed features. Additionally, TFFC is a powerfully joint multi-scale feature fusion and classification head, by employing the homogeneity among multi-scale features, so that the discriminative features of the multi-scale tissues are adequately fused for enhancing classification performance. Finally, extensive experiments demonstrate the superior performance of DAUF, with the effectiveness of D2AM and TFFC on identifying pMCI and sMCI subjects.
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Affiliation(s)
- Zhehao Zhang
- First Affiliated Hospital of Ningbo University, Ningbo, 315020, China; Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo 315210, China
| | - Linlin Gao
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo 315210, China; Zhejiang Key Laboratory of Mobile Network Application Technology, Ningbo University, Ningbo 315210, China; Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo 315210, China.
| | - Pengyuan Li
- IBM Research-Almaden, San Jose, CA 95120, USA
| | - Guang Jin
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo 315210, China
| | - Jianhua Wang
- First Affiliated Hospital of Ningbo University, Ningbo, 315020, China.
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Zhang X, Li Z, Zhang Q, Yin Z, Lu Z, Li Y. A new weakly supervised deep neural network for recognizing Alzheimer's disease. Comput Biol Med 2023; 163:107079. [PMID: 37321100 DOI: 10.1016/j.compbiomed.2023.107079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/15/2023] [Accepted: 05/27/2023] [Indexed: 06/17/2023]
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative disease that mainly affects older adults, causing memory loss and decline in thinking skills. In recent years, many traditional machine learning and deep learning methods have been used to assist in the diagnosis of AD, and most existing methods focus on early prediction of disease on a supervised basis. In reality, there is a massive amount of medical data available. However, some of those data have problems with the low-quality or lack of labels, and the cost of labeling them will be too high. To solve above problem, a new Weakly Supervised Deep Learning model (WSDL) is proposed, which adds attention mechanisms and consistency regularization to the EfficientNet framework and uses data augmentation techniques on the original data that can take full advantage of this unlabeled data. Validation of the proposed WSDL method on the brain MRI datasets of the Alzheimer's Disease Neuroimaging Program by setting five different unlabeled ratios to complete weakly supervised training showed better performance according to the compared experimental results with others baselines.
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Affiliation(s)
- Xiaobo Zhang
- School of Computing and Artificial Intelligence, SouthWest JiaoTong University, Chengdu 611756, China; Engineering Research Center of Sustainable Urban Intelligent Transportation, Ministry of Education, Chengdu 611756, China; National Engineering Laboratory of Integrated Transportation Big Data Application Technology, Southwest Jiaotong University, Chengdu 611756, China
| | - Zhimin Li
- School of Computing and Artificial Intelligence, SouthWest JiaoTong University, Chengdu 611756, China
| | - Qian Zhang
- School of Economics and Management, Chengdu Textile College, Chengdu 611731, China.
| | - Zegang Yin
- Department of Neurology, The General Hospital of Western Theater Command, Chengdu 610083, China
| | - Zhijie Lu
- Department of Neurology, The General Hospital of Western Theater Command, Chengdu 610083, China
| | - Yang Li
- School of Automation Science and Electrical Engineering, Beijing University of Aeronautics and Astronautics, Beijing 100191, China
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Li Y, Zhang Y, Liu JY, Wang K, Zhang K, Zhang GS, Liao XF, Yang G. Global Transformer and Dual Local Attention Network via Deep-Shallow Hierarchical Feature Fusion for Retinal Vessel Segmentation. IEEE TRANSACTIONS ON CYBERNETICS 2023; 53:5826-5839. [PMID: 35984806 DOI: 10.1109/tcyb.2022.3194099] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Clinically, retinal vessel segmentation is a significant step in the diagnosis of fundus diseases. However, recent methods generally neglect the difference of semantic information between deep and shallow features, which fail to capture the global and local characterizations in fundus images simultaneously, resulting in the limited segmentation performance for fine vessels. In this article, a global transformer (GT) and dual local attention (DLA) network via deep-shallow hierarchical feature fusion (GT-DLA-dsHFF) are investigated to solve the above limitations. First, the GT is developed to integrate the global information in the retinal image, which effectively captures the long-distance dependence between pixels, alleviating the discontinuity of blood vessels in the segmentation results. Second, DLA, which is constructed using dilated convolutions with varied dilation rates, unsupervised edge detection, and squeeze-excitation block, is proposed to extract local vessel information, consolidating the edge details in the segmentation result. Finally, a novel deep-shallow hierarchical feature fusion (dsHFF) algorithm is studied to fuse the features in different scales in the deep learning framework, respectively, which can mitigate the attenuation of valid information in the process of feature fusion. We verified the GT-DLA-dsHFF on four typical fundus image datasets. The experimental results demonstrate our GT-DLA-dsHFF achieves superior performance against the current methods and detailed discussions verify the efficacy of the proposed three modules. Segmentation results of diseased images show the robustness of our proposed GT-DLA-dsHFF. Implementation codes will be available on https://github.com/YangLibuaa/GT-DLA-dsHFF.
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Cui W, Du J, Sun M, Zhu S, Zhao S, Peng Z, Tan L, Li Y. Dynamic multi-site graph convolutional network for autism spectrum disorder identification. Comput Biol Med 2023; 157:106749. [PMID: 36921455 DOI: 10.1016/j.compbiomed.2023.106749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/13/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023]
Abstract
Multi-site learning has attracted increasing interests in autism spectrum disorder (ASD) identification tasks by its efficacy on capturing data heterogeneity of neuroimaging taken from different medical sites. However, existing multi-site graph convolutional network (MSGCN) often ignores the correlations between different sites, and may obtain suboptimal identification results. Moreover, current feature extraction methods characterizing temporal variations of functional magnetic resonance imaging (fMRI) signals require the time series to be of the same length and cannot be directly applied to multi-site fMRI datasets. To address these problems, we propose a dual graph based dynamic multi-site graph convolutional network (DG-DMSGCN) for multi-site ASD identification. First, a sliding-window dual-graph convolutional network (SW-DGCN) is introduced for feature extraction, simultaneously capturing temporal and spatial features of fMRI data with different series lengths. Then we aggregate the features extracted from multiple medical sites through a novel dynamic multi-site graph convolutional network (DMSGCN), which effectively considers the correlations between different sites and is beneficial to improve identification performance. We evaluate the proposed DG-DMSGCN on public ABIDE I dataset containing data from 17 medical sites. The promising results obtained by our framework outperforms the state-of-the-art methods with increase in identification accuracy, indicating that it has a potential clinical prospect for practical ASD diagnosis. Our codes are available on https://github.com/Junling-Du/DG-DMSGCN.
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Affiliation(s)
- Weigang Cui
- School of Engineering Medicine, Beihang University, Beijing, 100191, China.
| | - Junling Du
- Department of Automation Science and Electrical Engineering, Beihang University, Beijing, 100191, China.
| | - Mingyi Sun
- Department of Automation Science and Electrical Engineering, Beihang University, Beijing, 100191, China.
| | - Shimao Zhu
- South China Hospital of Shenzhen University, Shenzhen University, Shenzhen, 518111, China.
| | - Shijie Zhao
- School of Automation, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, China.
| | - Ziwen Peng
- Department of Child Psychiatry, Shenzhen Kangning Hospital, Shenzhen University School of Medicine, Shenzhen, 518020, China.
| | - Li Tan
- School of Computer Science and Engineering, Beijing Technology and Business Universtiy, Beijing, 100048, China.
| | - Yang Li
- Department of Automation Science and Electrical Engineering, Beihang University, Beijing, 100191, China; State Key Laboratory of Virtual Reality Technology and Systems, Beihang University, Beijing, 100191, China.
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Song X, Zhou F, Frangi AF, Cao J, Xiao X, Lei Y, Wang T, Lei B. Multicenter and Multichannel Pooling GCN for Early AD Diagnosis Based on Dual-Modality Fused Brain Network. IEEE TRANSACTIONS ON MEDICAL IMAGING 2023; 42:354-367. [PMID: 35767511 DOI: 10.1109/tmi.2022.3187141] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
For significant memory concern (SMC) and mild cognitive impairment (MCI), their classification performance is limited by confounding features, diverse imaging protocols, and limited sample size. To address the above limitations, we introduce a dual-modality fused brain connectivity network combining resting-state functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI), and propose three mechanisms in the current graph convolutional network (GCN) to improve classifier performance. First, we introduce a DTI-strength penalty term for constructing functional connectivity networks. Stronger structural connectivity and bigger structural strength diversity between groups provide a higher opportunity for retaining connectivity information. Second, a multi-center attention graph with each node representing a subject is proposed to consider the influence of data source, gender, acquisition equipment, and disease status of those training samples in GCN. The attention mechanism captures their different impacts on edge weights. Third, we propose a multi-channel mechanism to improve filter performance, assigning different filters to features based on feature statistics. Applying those nodes with low-quality features to perform convolution would also deteriorate filter performance. Therefore, we further propose a pooling mechanism, which introduces the disease status information of those training samples to evaluate the quality of nodes. Finally, we obtain the final classification results by inputting the multi-center attention graph into the multi-channel pooling GCN. The proposed method is tested on three datasets (i.e., an ADNI 2 dataset, an ADNI 3 dataset, and an in-house dataset). Experimental results indicate that the proposed method is effective and superior to other related algorithms, with a mean classification accuracy of 93.05% in our binary classification tasks. Our code is available at: https://github.com/Xuegang-S.
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Hao X, An Q, Li J, Min H, Guo Y, Yu M, Qin J. Exploring high-order correlations with deep-broad learning for autism spectrum disorder diagnosis. Front Neurosci 2022; 16:1046268. [PMID: 36483179 PMCID: PMC9723136 DOI: 10.3389/fnins.2022.1046268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/02/2022] [Indexed: 01/25/2023] Open
Abstract
Recently, a lot of research has been conducted on diagnosing neurological disorders, such as autism spectrum disorder (ASD). Functional magnetic resonance imaging (fMRI) is the commonly used technique to assist in the diagnosis of ASD. In the past years, some conventional methods have been proposed to extract the low-order functional connectivity network features for ASD diagnosis, which ignore the complexity and global features of the brain network. Most deep learning-based methods generally have a large number of parameters that need to be adjusted during the learning process. To overcome the limitations mentioned above, we propose a novel deep-broad learning method for learning the higher-order brain functional connectivity network features to assist in ASD diagnosis. Specifically, we first construct the high-order functional connectivity network that describes global correlations of the brain regions based on hypergraph, and then we use the deep-broad learning method to extract the high-dimensional feature representations for brain networks sequentially. The evaluation of the proposed method is conducted on Autism Brain Imaging Data Exchange (ABIDE) dataset. The results show that our proposed method can achieve 71.8% accuracy on the multi-center dataset and 70.6% average accuracy on 17 single-center datasets, which are the best results compared with the state-of-the-art methods. Experimental results demonstrate that our method can describe the global features of the brain regions and get rich discriminative information for the classification task.
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Affiliation(s)
- Xiaoke Hao
- School of Artificial Intelligence, Hebei University of Technology, Tianjin, China
| | - Qijin An
- School of Artificial Intelligence, Hebei University of Technology, Tianjin, China
| | - Jiayang Li
- School of Artificial Intelligence, Hebei University of Technology, Tianjin, China
| | - Hongjie Min
- School of Artificial Intelligence, Hebei University of Technology, Tianjin, China
| | - Yingchun Guo
- School of Artificial Intelligence, Hebei University of Technology, Tianjin, China
| | - Ming Yu
- School of Artificial Intelligence, Hebei University of Technology, Tianjin, China
| | - Jing Qin
- School of Nursing, Centre for Smart Health, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China
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Huang H, Liu Q, Jiang Y, Yang Q, Zhu X, Li Y. Deep Spatio-Temporal Attention-based Recurrent Network from Dynamic Adaptive Functional Connectivity for MCI Identification. IEEE Trans Neural Syst Rehabil Eng 2022; 30:2600-2612. [PMID: 36040940 DOI: 10.1109/tnsre.2022.3202713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Most existing methods of constructing dynamic functional connectivity (dFC) network obtain the connectivity strength via the sliding window correlation (SWC) method, which estimates the connectivity strength at each time segment, rather than at each time point, and thus is difficult to produce accurate dFC network due to the influence of the window type and window width. Furthermore, the deep learning methods may not capture the discriminative spatio-temporal information that is closely related to disease, thus impacting the performance of (mild cognitive impairment) MCI identification. In this paper, a novel spatio-temporal attention-based bidirectional gated recurrent unit (STA-BiGRU) network is proposed to extract inherent spatio-temporal information from a dynamic adaptive functional connectivity (dAFC) network for MCI diagnosis. Specifically, we adopt a group lasso-based Kalman filter algorithm to obtain the dAFC network with more accurate connectivity strength at each time step. Then a spatial attention module with self-attention and a temporal attention module with multiple temporal attention vectors are incorporated into the BiGRU network to extract more discriminative disease-related spatio-temporal information. Finally, the spatio-temporal regularizations are employed to better guide the attention learning of STA-BiGRU network to enhance the robustness of the deep network. Experimental results show that the proposed framework achieves mean accuracies of 90.2%, 90.0%, and 81.5%, respectively, for three MCI classification tasks. This study provides a more effective deep spatio-temporal attention-based recurrent network and obtains good performance and interpretability of deep learning for psychiatry diagnosis research.
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Li Y, Zhang Y, Cui W, Lei B, Kuang X, Zhang T. Dual Encoder-Based Dynamic-Channel Graph Convolutional Network With Edge Enhancement for Retinal Vessel Segmentation. IEEE TRANSACTIONS ON MEDICAL IMAGING 2022; 41:1975-1989. [PMID: 35167444 DOI: 10.1109/tmi.2022.3151666] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Retinal vessel segmentation with deep learning technology is a crucial auxiliary method for clinicians to diagnose fundus diseases. However, the deep learning approaches inevitably lose the edge information, which contains spatial features of vessels while performing down-sampling, leading to the limited segmentation performance of fine blood vessels. Furthermore, the existing methods ignore the dynamic topological correlations among feature maps in the deep learning framework, resulting in the inefficient capture of the channel characterization. To address these limitations, we propose a novel dual encoder-based dynamic-channel graph convolutional network with edge enhancement (DE-DCGCN-EE) for retinal vessel segmentation. Specifically, we first design an edge detection-based dual encoder to preserve the edge of vessels in down-sampling. Secondly, we investigate a dynamic-channel graph convolutional network to map the image channels to the topological space and synthesize the features of each channel on the topological map, which solves the limitation of insufficient channel information utilization. Finally, we study an edge enhancement block, aiming to fuse the edge and spatial features in the dual encoder, which is beneficial to improve the accuracy of fine blood vessel segmentation. Competitive experimental results on five retinal image datasets validate the efficacy of the proposed DE-DCGCN-EE, which achieves more remarkable segmentation results against the other state-of-the-art methods, indicating its potential clinical application.
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