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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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2
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Chen L, Qiao C, Ren K, Qu G, Calhoun VD, Stephen JM, Wilson TW, Wang YP. Explainable spatio-temporal graph evolution learning with applications to dynamic brain network analysis during development. Neuroimage 2024; 298:120771. [PMID: 39111376 DOI: 10.1016/j.neuroimage.2024.120771] [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: 04/11/2024] [Revised: 07/23/2024] [Accepted: 08/02/2024] [Indexed: 08/17/2024] Open
Abstract
Modeling dynamic interactions among network components is crucial to uncovering the evolution mechanisms of complex networks. Recently, spatio-temporal graph learning methods have achieved noteworthy results in characterizing the dynamic changes of inter-node relations (INRs). However, challenges remain: The spatial neighborhood of an INR is underexploited, and the spatio-temporal dependencies in INRs' dynamic changes are overlooked, ignoring the influence of historical states and local information. In addition, the model's explainability has been understudied. To address these issues, we propose an explainable spatio-temporal graph evolution learning (ESTGEL) model to model the dynamic evolution of INRs. Specifically, an edge attention module is proposed to utilize the spatial neighborhood of an INR at multi-level, i.e., a hierarchy of nested subgraphs derived from decomposing the initial node-relation graph. Subsequently, a dynamic relation learning module is proposed to capture the spatio-temporal dependencies of INRs. The INRs are then used as adjacent information to improve the node representation, resulting in comprehensive delineation of dynamic evolution of the network. Finally, the approach is validated with real data on brain development study. Experimental results on dynamic brain networks analysis reveal that brain functional networks transition from dispersed to more convergent and modular structures throughout development. Significant changes are observed in the dynamic functional connectivity (dFC) associated with functions including emotional control, decision-making, and language processing.
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Affiliation(s)
- Longyun Chen
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, 710049, China.
| | - Chen Qiao
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, 710049, China.
| | - Kai Ren
- Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China.
| | - Gang Qu
- Department of Biomedical Engineering, Tulane University, New Orleans, LA 70118, USA.
| | - Vince D Calhoun
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA 30303, USA.
| | | | - Tony W Wilson
- Institute for Human Neuroscience, Boys Town National Research Hospital, Boys Town, NE 68010, USA.
| | - Yu-Ping Wang
- Department of Biomedical Engineering, Tulane University, New Orleans, LA 70118, USA.
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3
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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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Liu R, Huang ZA, Hu Y, Zhu Z, Wong KC, Tan KC. Spatial-Temporal Co-Attention Learning for Diagnosis of Mental Disorders From Resting-State fMRI Data. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2024; 35:10591-10605. [PMID: 37027556 DOI: 10.1109/tnnls.2023.3243000] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Neuroimaging techniques have been widely adopted to detect the neurological brain structures and functions of the nervous system. As an effective noninvasive neuroimaging technique, functional magnetic resonance imaging (fMRI) has been extensively used in computer-aided diagnosis (CAD) of mental disorders, e.g., autism spectrum disorder (ASD) and attention deficit/hyperactivity disorder (ADHD). In this study, we propose a spatial-temporal co-attention learning (STCAL) model for diagnosing ASD and ADHD from fMRI data. In particular, a guided co-attention (GCA) module is developed to model the intermodal interactions of spatial and temporal signal patterns. A novel sliding cluster attention module is designed to address global feature dependency of self-attention mechanism in fMRI time series. Comprehensive experimental results demonstrate that our STCAL model can achieve competitive accuracies of 73.0 ± 4.5%, 72.0 ± 3.8%, and 72.5 ± 4.2% on the ABIDE I, ABIDE II, and ADHD-200 datasets, respectively. Moreover, the potential for feature pruning based on the co-attention scores is validated by the simulation experiment. The clinical interpretation analysis of STCAL can allow medical professionals to concentrate on the discriminative regions of interest and key time frames from fMRI data.
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Zhu QQ, Tian S, Zhang L, Ding HY, Gao YX, Tang Y, Yang X, Zhu Y, Qi M. Altered dynamic amplitude of low-frequency fluctuation in individuals at high risk for Alzheimer's disease. Eur J Neurosci 2024; 59:2391-2402. [PMID: 38314647 DOI: 10.1111/ejn.16267] [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: 03/31/2023] [Revised: 01/12/2024] [Accepted: 01/14/2024] [Indexed: 02/06/2024]
Abstract
The brain's dynamic spontaneous neural activity is significant in supporting cognition; however, how brain dynamics go awry in subjective cognitive decline (SCD) and mild cognitive impairment (MCI) remains unclear. Thus, the current study aimed to investigate the dynamic amplitude of low-frequency fluctuation (dALFF) alterations in patients at high risk for Alzheimer's disease and to explore its correlation with clinical cognitive assessment scales, to identify an early imaging sign for these special populations. A total of 152 participants, including 72 SCD patients, 44 MCI patients and 36 healthy controls (HCs), underwent a resting-state functional magnetic resonance imaging and were assessed with various neuropsychological tests. The dALFF was measured using sliding-window analysis. We employed canonical correlation analysis (CCA) to examine the bi-multivariate correlations between neuropsychological scales and altered dALFF among multiple regions in SCD and MCI patients. Compared to those in the HC group, both the MCI and SCD groups showed higher dALFF values in the right opercular inferior frontal gyrus (voxel P < .001, cluster P < .05, correction). Moreover, the CCA models revealed that behavioural tests relevant to inattention correlated with the dALFF of the right middle frontal gyrus and right opercular inferior frontal gyrus, which are involved in frontoparietal networks (R = .43, P = .024). In conclusion, the brain dynamics of neural activity in frontal areas provide insights into the shared neural basis underlying SCD and MCI.
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Affiliation(s)
- Qin-Qin Zhu
- Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shui Tian
- Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ling Zhang
- Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hong-Yuan Ding
- Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ya-Xin Gao
- Rehabilitation Center, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China
| | - Yin Tang
- Department of Medical imaging, Jingjiang People's Hospital, Jingjiang, China
| | - Xi Yang
- School of Rehabilitation Medicine, Nanjing Medical University, Nanjing, China
| | - Yi Zhu
- Rehabilitation Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ming Qi
- Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Zhao F, Lv K, Ye S, Chen X, Chen H, Fan S, Mao N, Ren Y. Integration of temporal & spatial properties of dynamic functional connectivity based on two-directional two-dimensional principal component analysis for disease analysis. PeerJ 2024; 12:e17078. [PMID: 38618569 PMCID: PMC11011592 DOI: 10.7717/peerj.17078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/19/2024] [Indexed: 04/16/2024] Open
Abstract
Dynamic functional connectivity, derived from resting-state functional magnetic resonance imaging (rs-fMRI), has emerged as a crucial instrument for investigating and supporting the diagnosis of neurological disorders. However, prevalent features of dynamic functional connectivity predominantly capture either temporal or spatial properties, such as mean and global efficiency, neglecting the significant information embedded in the fusion of spatial and temporal attributes. In addition, dynamic functional connectivity suffers from the problem of temporal mismatch, i.e., the functional connectivity of different subjects at the same time point cannot be matched. To address these problems, this article introduces a novel feature extraction framework grounded in two-directional two-dimensional principal component analysis. This framework is designed to extract features that integrate both spatial and temporal properties of dynamic functional connectivity. Additionally, we propose to use Fourier transform to extract temporal-invariance properties contained in dynamic functional connectivity. Experimental findings underscore the superior performance of features extracted by this framework in classification experiments compared to features capturing individual properties.
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Affiliation(s)
- Feng Zhao
- School of Computer Science and Technology, Shandong Technology and Business University, Yantai, China
| | - Ke Lv
- School of Computer Science and Technology, Shandong Technology and Business University, Yantai, China
| | - Shixin Ye
- School of Computer Science and Technology, Shandong Technology and Business University, Yantai, China
| | - Xiaobo Chen
- School of Computer Science and Technology, Shandong Technology and Business University, Yantai, China
| | - Hongyu Chen
- School Hospital, Shandong Technology and Business University, Yantai, China
| | - Sizhe Fan
- Canada Qingdao Secondary School (CQSS), Qingdao, China
| | - Ning Mao
- Department of Radiology, Yantai Yuhuangding Hospital, Yantai, China
| | - Yande Ren
- Department of Radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
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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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Kuang LD, Li HQ, Zhang J, Gui Y, Zhang J. Dynamic functional network connectivity analysis in schizophrenia based on a spatiotemporal CPD framework. J Neural Eng 2024; 21:016032. [PMID: 38335544 DOI: 10.1088/1741-2552/ad27ee] [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: 09/12/2023] [Accepted: 02/09/2024] [Indexed: 02/12/2024]
Abstract
Objective.Dynamic functional network connectivity (dFNC), based on data-driven group independent component (IC) analysis, is an important avenue for investigating underlying patterns of certain brain diseases such as schizophrenia. Canonical polyadic decomposition (CPD) of a higher-way dynamic functional connectivity tensor, can offer an innovative spatiotemporal framework to accurately characterize potential dynamic spatial and temporal fluctuations. Since multi-subject dFNC data from sliding-window analysis are also naturally a higher-order tensor, we propose an innovative sparse and low-rank CPD (SLRCPD) for the three-way dFNC tensor to excavate significant dynamic spatiotemporal aberrant changes in schizophrenia.Approach.The proposed SLRCPD approach imposes two constraints. First, the L1regularization on spatial modules is applied to extract sparse but significant dynamic connectivity and avoid overfitting the model. Second, low-rank constraint is added on time-varying weights to enhance the temporal state clustering quality. Shared dynamic spatial modules, group-specific dynamic spatial modules and time-varying weights can be extracted by SLRCPD. The strength of connections within- and between-IC networks and connection contribution are proposed to inspect the spatial modules. K-means clustering and classification are further conducted to explore temporal group difference.Main results.82 subject resting-state functional magnetic resonance imaging (fMRI) dataset and opening Center for Biomedical Research Excellence (COBRE) schizophrenia dataset both containing schizophrenia patients (SZs) and healthy controls (HCs) were utilized in our work. Three typical dFNC patterns between different brain functional regions were obtained. Compared to the spatial modules of HCs, the aberrant connections among auditory network, somatomotor, visual, cognitive control and cerebellar networks in 82 subject dataset and COBRE dataset were detected. Four temporal states reveal significant differences between SZs and HCs for these two datasets. Additionally, the accuracy values for SZs and HCs classification based on time-varying weights are larger than 0.96.Significance.This study significantly excavates spatio-temporal patterns for schizophrenia disease.
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Affiliation(s)
- Li-Dan Kuang
- School of Computer and Communication Engineering, Changsha University of Science and Technology, Changsha, People's Republic of China
| | - He-Qiang Li
- School of Computer and Communication Engineering, Changsha University of Science and Technology, Changsha, People's Republic of China
| | - Jianming Zhang
- School of Computer and Communication Engineering, Changsha University of Science and Technology, Changsha, People's Republic of China
| | - Yan Gui
- School of Computer and Communication Engineering, Changsha University of Science and Technology, Changsha, People's Republic of China
| | - Jin Zhang
- School of Computer and Communication Engineering, Changsha University of Science and Technology, Changsha, People's Republic of China
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10
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Wang M, Zhu L, Li X, Pan Y, Li L. Dynamic functional connectivity analysis with temporal convolutional network for attention deficit/hyperactivity disorder identification. Front Neurosci 2023; 17:1322967. [PMID: 38148943 PMCID: PMC10750397 DOI: 10.3389/fnins.2023.1322967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/24/2023] [Indexed: 12/28/2023] Open
Abstract
Introduction Dynamic functional connectivity (dFC), which can capture the abnormality of brain activity over time in resting-state functional magnetic resonance imaging (rs-fMRI) data, has a natural advantage in revealing the abnormal mechanism of brain activity in patients with Attention Deficit/Hyperactivity Disorder (ADHD). Several deep learning methods have been proposed to learn dynamic changes from rs-fMRI for FC analysis, and achieved superior performance than those using static FC. However, most existing methods only consider dependencies of two adjacent timestamps, which is limited when the change is related to the course of many timestamps. Methods In this paper, we propose a novel Temporal Dependence neural Network (TDNet) for FC representation learning and temporal-dependence relationship tracking from rs-fMRI time series for automated ADHD identification. Specifically, we first partition rs-fMRI time series into a sequence of consecutive and non-overlapping segments. For each segment, we design an FC generation module to learn more discriminative representations to construct dynamic FCs. Then, we employ the Temporal Convolutional Network (TCN) to efficiently capture long-range temporal patterns with dilated convolutions, followed by three fully connected layers for disease prediction. Results As the results, we found that considering the dynamic characteristics of rs-fMRI time series data is beneficial to obtain better diagnostic performance. In addition, dynamic FC networks generated in a data-driven manner are more informative than those constructed by Pearson correlation coefficients. Discussion We validate the effectiveness of the proposed approach through extensive experiments on the public ADHD-200 database, and the results demonstrate the superiority of the proposed model over state-of-the-art methods in ADHD identification.
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Affiliation(s)
- Mingliang Wang
- School of Computer and Software, Nanjing University of Information Science and Technology, Nanjing, China
- Nanjing Xinda Institute of Safety and Emergency Management, Nanjing, China
- MIIT Key Laboratory of Pattern Analysis and Machine Intelligence, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Lingyao Zhu
- School of Computer and Software, Nanjing University of Information Science and Technology, Nanjing, China
| | - Xizhi Li
- School of Computer and Software, Nanjing University of Information Science and Technology, Nanjing, China
| | - Yong Pan
- School of Accounting, Nanjing University of Finance and Economics, Nanjing, China
| | - Long Li
- Taian Tumor Prevention and Treatment Hospital, Taian, China
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Sui J, Zhi D, Calhoun VD. Data-driven multimodal fusion: approaches and applications in psychiatric research. PSYCHORADIOLOGY 2023; 3:kkad026. [PMID: 38143530 PMCID: PMC10734907 DOI: 10.1093/psyrad/kkad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/08/2023] [Accepted: 11/21/2023] [Indexed: 12/26/2023]
Abstract
In the era of big data, where vast amounts of information are being generated and collected at an unprecedented rate, there is a pressing demand for innovative data-driven multi-modal fusion methods. These methods aim to integrate diverse neuroimaging perspectives to extract meaningful insights and attain a more comprehensive understanding of complex psychiatric disorders. However, analyzing each modality separately may only reveal partial insights or miss out on important correlations between different types of data. This is where data-driven multi-modal fusion techniques come into play. By combining information from multiple modalities in a synergistic manner, these methods enable us to uncover hidden patterns and relationships that would otherwise remain unnoticed. In this paper, we present an extensive overview of data-driven multimodal fusion approaches with or without prior information, with specific emphasis on canonical correlation analysis and independent component analysis. The applications of such fusion methods are wide-ranging and allow us to incorporate multiple factors such as genetics, environment, cognition, and treatment outcomes across various brain disorders. After summarizing the diverse neuropsychiatric magnetic resonance imaging fusion applications, we further discuss the emerging neuroimaging analyzing trends in big data, such as N-way multimodal fusion, deep learning approaches, and clinical translation. Overall, multimodal fusion emerges as an imperative approach providing valuable insights into the underlying neural basis of mental disorders, which can uncover subtle abnormalities or potential biomarkers that may benefit targeted treatments and personalized medical interventions.
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Affiliation(s)
- Jing Sui
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China
| | - Dongmei Zhi
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing 100875, China
| | - Vince D Calhoun
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia Institute of Technology, Emory University and Georgia State University, Atlanta, GA 30303, United States
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12
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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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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: 6] [Impact Index Per Article: 6.0] [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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14
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Zhang C, Ma Y, Qiao L, Zhang L, Liu M. Learning to Fuse Multiple Brain Functional Networks for Automated Autism Identification. BIOLOGY 2023; 12:971. [PMID: 37508401 PMCID: PMC10376072 DOI: 10.3390/biology12070971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/03/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023]
Abstract
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.
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Affiliation(s)
- Chaojun Zhang
- The School of Computer Science and Technology, Shandong Jianzhu University, Jinan 250101, China
- The School of Mathematics Science, Liaocheng University, Liaocheng 252000, China
| | - Yunling Ma
- The School of Mathematics Science, Liaocheng University, Liaocheng 252000, China
| | - Lishan Qiao
- The School of Mathematics Science, Liaocheng University, Liaocheng 252000, China
| | - Limei Zhang
- The School of Computer Science and Technology, Shandong Jianzhu University, Jinan 250101, China
| | - Mingxia Liu
- Department of Radiology and BRIC, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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15
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Bedel HA, Sivgin I, Dalmaz O, Dar SUH, Çukur T. BolT: Fused window transformers for fMRI time series analysis. Med Image Anal 2023; 88:102841. [PMID: 37224718 DOI: 10.1016/j.media.2023.102841] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/07/2023] [Accepted: 05/10/2023] [Indexed: 05/26/2023]
Abstract
Deep-learning models have enabled performance leaps in analysis of high-dimensional functional MRI (fMRI) data. Yet, many previous methods are suboptimally sensitive for contextual representations across diverse time scales. Here, we present BolT, a blood-oxygen-level-dependent transformer model, for analyzing multi-variate fMRI time series. BolT leverages a cascade of transformer encoders equipped with a novel fused window attention mechanism. Encoding is performed on temporally-overlapped windows within the time series to capture local representations. To integrate information temporally, cross-window attention is computed between base tokens in each window and fringe tokens from neighboring windows. To gradually transition from local to global representations, the extent of window overlap and thereby number of fringe tokens are progressively increased across the cascade. Finally, a novel cross-window regularization is employed to align high-level classification features across the time series. Comprehensive experiments on large-scale public datasets demonstrate the superior performance of BolT against state-of-the-art methods. Furthermore, explanatory analyses to identify landmark time points and regions that contribute most significantly to model decisions corroborate prominent neuroscientific findings in the literature.
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Affiliation(s)
- Hasan A Bedel
- Department of Electrical and Electronics Engineering, Bilkent University, Ankara 06800, Turkey; National Magnetic Resonance Research Center (UMRAM), Bilkent University, Ankara 06800, Turkey
| | - Irmak Sivgin
- Department of Electrical and Electronics Engineering, Bilkent University, Ankara 06800, Turkey; National Magnetic Resonance Research Center (UMRAM), Bilkent University, Ankara 06800, Turkey
| | - Onat Dalmaz
- Department of Electrical and Electronics Engineering, Bilkent University, Ankara 06800, Turkey; National Magnetic Resonance Research Center (UMRAM), Bilkent University, Ankara 06800, Turkey
| | - Salman U H Dar
- Department of Electrical and Electronics Engineering, Bilkent University, Ankara 06800, Turkey; National Magnetic Resonance Research Center (UMRAM), Bilkent University, Ankara 06800, Turkey
| | - Tolga Çukur
- Department of Electrical and Electronics Engineering, Bilkent University, Ankara 06800, Turkey; National Magnetic Resonance Research Center (UMRAM), Bilkent University, Ankara 06800, Turkey; Neuroscience Program, Bilkent University, Ankara 06800, Turkey.
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16
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Li R, Li Z, Fan H, Teng S, Cao X. MCFSA-Net: A multi-scale channel fusion and spatial activation network for retinal vessel segmentation. JOURNAL OF BIOPHOTONICS 2023; 16:e202200295. [PMID: 36413066 DOI: 10.1002/jbio.202200295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 11/10/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
As the only vascular tissue that can be directly viewed in vivo, retinal vessels are medically important in assisting the diagnosis of ocular and cardiovascular diseases. They generally appear as different morphologies and uneven thickness in fundus images. Therefore, the single-scale segmentation method may fail to capture abundant morphological features, suffering from the deterioration in vessel segmentation, especially for tiny vessels. To alleviate this issue, we propose a multi-scale channel fusion and spatial activation network (MCFSA-Net) for retinal vessel segmentation with emphasis on tiny ones. Specifically, the Hybrid Convolution-DropBlock (HC-Drop) is first used to extract deep features of vessels and construct multi-scale feature maps by progressive down-sampling. Then, the Channel Cooperative Attention Fusion (CCAF) module is designed to handle different morphological vessels in a multi-scale manner. Finally, the Global Spatial Activation (GSA) module is introduced to aggregate global feature information for improving the attention on tiny vessels in the spatial domain and realizing effective segmentation for them. Experiments are carried out on three datasets including DRIVE, CHASE_DB1, and STARE. Our retinal vessel segmentation method achieves Accuracy of 96.95%, 97.57%, and 97.83%, and F1 score of 82.67%, 81.82%, and 82.95% in the above datasets, respectively. Qualitative and quantitative analysis show that the proposed method outperforms current advanced vessel segmentation methods, especially for tiny vessels.
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Affiliation(s)
- Rui Li
- College of Electronic and Information Engineering, Shandong University of Science and Technology, Qingdao, China
| | - Zuoyong Li
- Fujian Provincial Key Laboratory of Information Processing and Intelligent Control, College of Computer and Control Engineering, Minjiang University, Fuzhou, China
| | - Haoyi Fan
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou, China
| | - Shenghua Teng
- College of Electronic and Information Engineering, Shandong University of Science and Technology, Qingdao, China
| | - Xinrong Cao
- Fujian Provincial Key Laboratory of Information Processing and Intelligent Control, College of Computer and Control Engineering, Minjiang University, Fuzhou, China
- Fuzhou Digital Healthcare Industry Technology Innovation Center, Minjiang University, Fuzhou, China
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17
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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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18
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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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19
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Huang P, He P, Tian S, Ma M, Feng P, Xiao H, Mercaldo F, Santone A, Qin J. A ViT-AMC Network With Adaptive Model Fusion and Multiobjective Optimization for Interpretable Laryngeal Tumor Grading From Histopathological Images. IEEE TRANSACTIONS ON MEDICAL IMAGING 2023; 42:15-28. [PMID: 36018875 DOI: 10.1109/tmi.2022.3202248] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The tumor grading of laryngeal cancer pathological images needs to be accurate and interpretable. The deep learning model based on the attention mechanism-integrated convolution (AMC) block has good inductive bias capability but poor interpretability, whereas the deep learning model based on the vision transformer (ViT) block has good interpretability but weak inductive bias ability. Therefore, we propose an end-to-end ViT-AMC network (ViT-AMCNet) with adaptive model fusion and multiobjective optimization that integrates and fuses the ViT and AMC blocks. However, existing model fusion methods often have negative fusion: 1). There is no guarantee that the ViT and AMC blocks will simultaneously have good feature representation capability. 2). The difference in feature representations learning between the ViT and AMC blocks is not obvious, so there is much redundant information in the two feature representations. Accordingly, we first prove the feasibility of fusing the ViT and AMC blocks based on Hoeffding's inequality. Then, we propose a multiobjective optimization method to solve the problem that ViT and AMC blocks cannot simultaneously have good feature representation. Finally, an adaptive model fusion method integrating the metrics block and the fusion block is proposed to increase the differences between feature representations and improve the deredundancy capability. Our methods improve the fusion ability of ViT-AMCNet, and experimental results demonstrate that ViT-AMCNet significantly outperforms state-of-the-art methods. Importantly, the visualized interpretive maps are closer to the region of interest of concern by pathologists, and the generalization ability is also excellent. Our code is publicly available at https://github.com/Baron-Huang/ViT-AMCNet.
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20
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Xiao J, Uddin LQ, Meng Y, Li L, Gao L, Shan X, Huang X, Liao W, Chen H, Duan X. A spatio-temporal decomposition framework for dynamic functional connectivity in the human brain. Neuroimage 2022; 263:119618. [PMID: 36087902 DOI: 10.1016/j.neuroimage.2022.119618] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 08/15/2022] [Accepted: 09/06/2022] [Indexed: 11/29/2022] Open
Abstract
Much recent attention has been directed toward investigating the spatial and temporal organization of brain dynamics, but the rules which constrain the variation of spatio-temporal organization in functional connectivity under different brain states remain unclear. Here, we developed a novel computational approach based on tensor decomposition and regularization to represent dynamic functional connectivity as a linear combination of dynamic modules and time-varying weights. In this approach, dynamic modules represent co-activating functional connectivity patterns, and time-varying weights represent the temporal expression of dynamic modules. We applied this dynamic decomposition model (DDM) on a resting-state fMRI dataset and found that whole-brain dynamic functional connectivity can be decomposed as a linear combination of eight dynamic modules which we summarize as 'high order modules' and 'primary-high order modules', according to their spatial attributes and correspondence with existing intrinsic functional brain networks. By clustering the time-varying weights, we identified five brain states including three major states and two minor states. We found that state transitions mainly occurred between the three major states, and that temporal variation of dynamic modules may contribute to brain state transitions. We then conceptualized the variability of weights as the flexibility of the corresponding dynamic modules and found that different dynamic modules exhibit different amounts of flexibility and contribute to different cognitive measures. Finally, we applied DDM to a schizophrenia resting-state fMRI dataset and found that atypical flexibility of dynamic modules correlates with impaired cognitive flexibility in schizophrenia. Overall, this work provides a quantitative framework that characterizes temporal variation in the topology of dynamic functional connectivity.
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Affiliation(s)
- Jinming Xiao
- The Clinical Hospital of Chengdu Brain Science Institute, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China; High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, MOE Key Lab for Neuro Information, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Lucina Q Uddin
- Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA, United States
| | - Yao Meng
- The Clinical Hospital of Chengdu Brain Science Institute, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China; High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, MOE Key Lab for Neuro Information, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Lei Li
- The Clinical Hospital of Chengdu Brain Science Institute, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China; High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, MOE Key Lab for Neuro Information, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Leying Gao
- The Clinical Hospital of Chengdu Brain Science Institute, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China; High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, MOE Key Lab for Neuro Information, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Xiaolong Shan
- The Clinical Hospital of Chengdu Brain Science Institute, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China; High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, MOE Key Lab for Neuro Information, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Xinyue Huang
- The Clinical Hospital of Chengdu Brain Science Institute, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China; High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, MOE Key Lab for Neuro Information, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Wei Liao
- The Clinical Hospital of Chengdu Brain Science Institute, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China; High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, MOE Key Lab for Neuro Information, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Huafu Chen
- The Clinical Hospital of Chengdu Brain Science Institute, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China; High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, MOE Key Lab for Neuro Information, University of Electronic Science and Technology of China, Chengdu 611731, China.
| | - Xujun Duan
- The Clinical Hospital of Chengdu Brain Science Institute, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China; High-Field Magnetic Resonance Brain Imaging Key Laboratory of Sichuan Province, MOE Key Lab for Neuro Information, University of Electronic Science and Technology of China, Chengdu 611731, China.
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21
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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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22
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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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23
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Huang Z, Lei H, Chen G, Frangi AF, Xu Y, Elazab A, Qin J, Lei B. Parkinson's Disease Classification and Clinical Score Regression via United Embedding and Sparse Learning From Longitudinal Data. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2022; 33:3357-3371. [PMID: 33534713 DOI: 10.1109/tnnls.2021.3052652] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Parkinson's disease (PD) is known as an irreversible neurodegenerative disease that mainly affects the patient's motor system. Early classification and regression of PD are essential to slow down this degenerative process from its onset. In this article, a novel adaptive unsupervised feature selection approach is proposed by exploiting manifold learning from longitudinal multimodal data. Classification and clinical score prediction are performed jointly to facilitate early PD diagnosis. Specifically, the proposed approach performs united embedding and sparse regression, which can determine the similarity matrices and discriminative features adaptively. Meanwhile, we constrain the similarity matrix among subjects and exploit the l2,p norm to conduct sparse adaptive control for obtaining the intrinsic information of the multimodal data structure. An effective iterative optimization algorithm is proposed to solve this problem. We perform abundant experiments on the Parkinson's Progression Markers Initiative (PPMI) data set to verify the validity of the proposed approach. The results show that our approach boosts the performance on the classification and clinical score regression of longitudinal data and surpasses the state-of-the-art approaches.
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24
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Long Z, Li J, Liao H, Deng L, Du Y, Fan J, Li X, Miao J, Qiu S, Long C, Jing B. A Multi-Modal and Multi-Atlas Integrated Framework for Identification of Mild Cognitive Impairment. Brain Sci 2022; 12:751. [PMID: 35741636 PMCID: PMC9221217 DOI: 10.3390/brainsci12060751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/29/2022] [Accepted: 06/03/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Multi-modal neuroimaging with appropriate atlas is vital for effectively differentiating mild cognitive impairment (MCI) from healthy controls (HC). METHODS The resting-state functional magnetic resonance imaging (rs-fMRI) and structural MRI (sMRI) of 69 MCI patients and 61 HC subjects were collected. Then, the gray matter volumes obtained from the sMRI and Hurst exponent (HE) values calculated from rs-fMRI data in the Automated Anatomical Labeling (AAL-90), Brainnetome (BN-246), Harvard-Oxford (HOA-112) and AAL3-170 atlases were extracted, respectively. Next, these characteristics were selected with a minimal redundancy maximal relevance algorithm and a sequential feature collection method in single or multi-modalities, and only the optimal features were retained after this procedure. Lastly, the retained characteristics were served as the input features for the support vector machine (SVM)-based method to classify MCI patients, and the performance was estimated with a leave-one-out cross-validation (LOOCV). RESULTS Our proposed method obtained the best 92.00% accuracy, 94.92% specificity and 89.39% sensitivity with the sMRI in AAL-90 and the fMRI in HOA-112 atlas, which was much better than using the single-modal or single-atlas features. CONCLUSION The results demonstrated that the multi-modal and multi-atlas integrated method could effectively recognize MCI patients, which could be extended into various neurological and neuropsychiatric diseases.
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Affiliation(s)
- Zhuqing Long
- Medical Apparatus and Equipment Deployment, Hunan Children’s Hospital, Changsha 410007, China; (Z.L.); (J.L.); (H.L.); (Y.D.); (S.Q.)
- School of Biomedical Engineering, Capital Medical University, Beijing 100069, China
| | - Jie Li
- Medical Apparatus and Equipment Deployment, Hunan Children’s Hospital, Changsha 410007, China; (Z.L.); (J.L.); (H.L.); (Y.D.); (S.Q.)
| | - Haitao Liao
- Medical Apparatus and Equipment Deployment, Hunan Children’s Hospital, Changsha 410007, China; (Z.L.); (J.L.); (H.L.); (Y.D.); (S.Q.)
| | - Li Deng
- Department of Data Assessment and Examination, Hunan Children’s Hospital, Changsha 410007, China;
| | - Yukeng Du
- Medical Apparatus and Equipment Deployment, Hunan Children’s Hospital, Changsha 410007, China; (Z.L.); (J.L.); (H.L.); (Y.D.); (S.Q.)
| | - Jianghua Fan
- Department of Pediatric Emergency Center, Emergency Generally Department I, Hunan Children’s Hospital, Changsha 410007, China;
| | - Xiaofeng Li
- Hunan Guangxiu Hospital, Hunan Normal University, Changsha 410006, China;
| | - Jichang Miao
- Department of Medical Devices, Nanfang Hospital, Guangzhou 510515, China;
| | - Shuang Qiu
- Medical Apparatus and Equipment Deployment, Hunan Children’s Hospital, Changsha 410007, China; (Z.L.); (J.L.); (H.L.); (Y.D.); (S.Q.)
| | - Chaojie Long
- Medical Apparatus and Equipment Deployment, Hunan Children’s Hospital, Changsha 410007, China; (Z.L.); (J.L.); (H.L.); (Y.D.); (S.Q.)
| | - Bin Jing
- School of Biomedical Engineering, Capital Medical University, Beijing 100069, China
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25
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Cai C, Cao J, Yang C, Chen E. Diagnosis of Amnesic Mild Cognitive Impairment Using MGS-WBC and VGBN-LM Algorithms. Front Aging Neurosci 2022; 14:893250. [PMID: 35707699 PMCID: PMC9189381 DOI: 10.3389/fnagi.2022.893250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
Computer-aided diagnosis (CAD) has undergone rapid development with the advent of advanced neuroimaging and machine learning methods. Nevertheless, how to extract discriminative features from the limited and high-dimensional data is not ideal, especially for amnesic mild cognitive impairment (aMCI) data based on resting-state functional magnetic resonance imaging (rs-fMRI). Furthermore, a robust and reliable system for aMCI detection is conducive to timely detecting and screening subjects at a high risk of Alzheimer's disease (AD). In this scenario, we first develop the mask generation strategy based on within-class and between-class criterion (MGS-WBC), which primarily aims at reducing data redundancy and excavating multiscale features of the brain. Concurrently, vector generation for brain networks based on Laplacian matrix (VGBN-LM) is presented to obtain the global features of the functional network. Finally, all multiscale features are fused to further improve the diagnostic performance of aMCI. Typical classifiers for small data learning, such as naive Bayesian (NB), linear discriminant analysis (LDA), logistic regression (LR), and support vector machines (SVMs), are adopted to evaluate the diagnostic performance of aMCI. This study helps to reveal discriminative neuroimaging features, and outperforms the state-of-the-art methods, providing new insights for the intelligent construction of CAD system of aMCI.
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Affiliation(s)
- Chunting Cai
- School of Informatics, Xiamen University, Xiamen, China
| | | | - Chenhui Yang
- School of Informatics, Xiamen University, Xiamen, China
| | - E. Chen
- Department of Neurology, Zhongshan Hospital Affiliated to Xiamen University, Xiamen, China
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26
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Bi XA, Zhou W, Luo S, Mao Y, Hu X, Zeng B, Xu L. Feature aggregation graph convolutional network based on imaging genetic data for diagnosis and pathogeny identification of Alzheimer's disease. Brief Bioinform 2022; 23:6572662. [PMID: 35453149 DOI: 10.1093/bib/bbac137] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/15/2022] [Accepted: 03/23/2022] [Indexed: 12/30/2022] Open
Abstract
The roles of brain regions activities and gene expressions in the development of Alzheimer's disease (AD) remain unclear. Existing imaging genetic studies usually has the problem of inefficiency and inadequate fusion of data. This study proposes a novel deep learning method to efficiently capture the development pattern of AD. First, we model the interaction between brain regions and genes as node-to-node feature aggregation in a brain region-gene network. Second, we propose a feature aggregation graph convolutional network (FAGCN) to transmit and update the node feature. Compared with the trivial graph convolutional procedure, we replace the input from the adjacency matrix with a weight matrix based on correlation analysis and consider common neighbor similarity to discover broader associations of nodes. Finally, we use a full-gradient saliency graph mechanism to score and extract the pathogenetic brain regions and risk genes. According to the results, FAGCN achieved the best performance among both traditional and cutting-edge methods and extracted AD-related brain regions and genes, providing theoretical and methodological support for the research of related diseases.
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Affiliation(s)
- Xia-An Bi
- Hunan Provincial Key Laboratory of Intelligent Computing and Language Information Processing, and the College of Information Science and Engineering in Hunan Normal University, P.R. China
| | - Wenyan Zhou
- College of Information Science and Engineering, Hunan Normal University, Changsha, China
| | - Sheng Luo
- College of Information Science and Engineering, Hunan Normal University, Changsha, China
| | - Yuhua Mao
- College of Information Science and Engineering, Hunan Normal University, Changsha, China
| | - Xi Hu
- College of Information Science and Engineering, Hunan Normal University, Changsha, China
| | - Bin Zeng
- Hunan Youdao Information Technology Co., Ltd, P.R. China
| | - Luyun Xu
- College of Business in Hunan Normal University, P.R. China
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27
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Improved Multiple Vector Representations of Images and Robust Dictionary Learning. ELECTRONICS 2022. [DOI: 10.3390/electronics11060847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Each sparse representation classifier has different classification accuracy for different samples. It is difficult to achieve good performance with a single feature classification model. In order to balance the large-scale information and global features of images, a robust dictionary learning method based on image multi-vector representation is proposed in this paper. First, this proposed method generates a reasonable virtual image for the original image and obtains the multi-vector representation of all images. Second, the same dictionary learning algorithm is used for each vector representation to obtain multiple sets of image features. The proposed multi-vector representation can provide a good global understanding of the whole image contour and increase the content of dictionary learning. Last, the weighted fusion algorithm is used to classify the test samples. The introduction of influencing factors and the automatic adjustment of the weights of each classifier in the final decision results have a significant indigenous effect on better extracting image features. The study conducted experiments on the proposed algorithm on a number of widely used image databases. A large number of experimental results show that it effectively improves the accuracy of image classification. At the same time, to fully dig and exploit possible representation diversity might be a better way to lead to potential various appearances and high classification accuracy concerning the image.
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28
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Zhao K, Duka B, Xie H, Oathes DJ, Calhoun V, Zhang Y. A dynamic graph convolutional neural network framework reveals new insights into connectome dysfunctions in ADHD. Neuroimage 2022; 246:118774. [PMID: 34861391 PMCID: PMC10569447 DOI: 10.1016/j.neuroimage.2021.118774] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/26/2021] [Accepted: 11/29/2021] [Indexed: 12/23/2022] Open
Abstract
The pathological mechanism of attention deficit hyperactivity disorder (ADHD) is incompletely specified, which leads to difficulty in precise diagnosis. Functional magnetic resonance imaging (fMRI) has emerged as a common neuroimaging technique for studying the brain functional connectome. Most existing methods that have either ignored or simply utilized graph structure, do not fully leverage the potentially important topological information which may be useful in characterizing brain disorders. There is a crucial need for designing novel and efficient approaches which can capture such information. To this end, we propose a new dynamic graph convolutional network (dGCN), which is trained with sparse brain regional connections from dynamically calculated graph features. We also develop a novel convolutional readout layer to improve graph representation. Our extensive experimental analysis demonstrates significantly improved performance of dGCN for ADHD diagnosis compared with existing machine learning and deep learning methods. Visualizations of the salient regions of interest (ROIs) and connectivity based on informative features learned by our model show that the identified functional abnormalities mainly involve brain regions in temporal pole, gyrus rectus, and cerebellar gyri from temporal lobe, frontal lobe, and cerebellum, respectively. A positive correlation was further observed between the identified connectomic abnormalities and ADHD symptom severity. The proposed dGCN model shows great promise in providing a functional network-based precision diagnosis of ADHD and is also broadly applicable to brain connectome-based study of mental disorders.
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Affiliation(s)
- Kanhao Zhao
- Department of Bioengineering, Lehigh University, Bethlehem, PA, USA
| | - Boris Duka
- Department of Bioengineering, Lehigh University, Bethlehem, PA, USA
| | - Hua Xie
- Department of Psychology, University of Maryland, College Park, MD, USA
| | - Desmond J Oathes
- Center for Neuromodulation in Depression and Stress, Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, PA, USA
| | - Vince Calhoun
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, USA
| | - Yu Zhang
- Department of Bioengineering, Lehigh University, Bethlehem, PA, USA.
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29
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Chu Y, Wang G, Cao L, Qiao L, Liu M. Multi-Scale Graph Representation Learning for Autism Identification With Functional MRI. Front Neuroinform 2022; 15:802305. [PMID: 35095453 PMCID: PMC8792610 DOI: 10.3389/fninf.2021.802305] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 11/16/2022] Open
Abstract
Resting-state functional MRI (rs-fMRI) has been widely used for the early diagnosis of autism spectrum disorder (ASD). With rs-fMRI, the functional connectivity networks (FCNs) are usually constructed for representing each subject, with each element representing the pairwise relationship between brain region-of-interests (ROIs). Previous studies often first extract handcrafted network features (such as node degree and clustering coefficient) from FCNs and then construct a prediction model for ASD diagnosis, which largely requires expert knowledge. Graph convolutional networks (GCNs) have recently been employed to jointly perform FCNs feature extraction and ASD identification in a data-driven manner. However, existing studies tend to focus on the single-scale topology of FCNs by using one single atlas for ROI partition, thus ignoring potential complementary topology information of FCNs at different spatial scales. In this paper, we develop a multi-scale graph representation learning (MGRL) framework for rs-fMRI based ASD diagnosis. The MGRL consists of three major components: (1) multi-scale FCNs construction using multiple brain atlases for ROI partition, (2) FCNs representation learning via multi-scale GCNs, and (3) multi-scale feature fusion and classification for ASD diagnosis. The proposed MGRL is evaluated on 184 subjects from the public Autism Brain Imaging Data Exchange (ABIDE) database with rs-fMRI scans. Experimental results suggest the efficacy of our MGRL in FCN feature extraction and ASD identification, compared with several state-of-the-art methods.
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Affiliation(s)
- Ying Chu
- School of Mathematics Science, Liaocheng University, Liaocheng, China
- Department of Information Science and Technology, Taishan University, Taian, China
| | - Guangyu Wang
- School of Mathematics Science, Liaocheng University, Liaocheng, China
| | - Liang Cao
- Taian Tumor Prevention and Treatment Hospital, Taian, China
| | - Lishan Qiao
- School of Mathematics Science, Liaocheng University, Liaocheng, China
- *Correspondence: Lishan Qiao
| | - Mingxia Liu
- Department of Information Science and Technology, Taishan University, Taian, China
- Mingxia Liu
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30
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Li Y, Liu J, Jiang Y, Liu Y, Lei B. Virtual Adversarial Training-Based Deep Feature Aggregation Network From Dynamic Effective Connectivity for MCI Identification. IEEE TRANSACTIONS ON MEDICAL IMAGING 2022; 41:237-251. [PMID: 34491896 DOI: 10.1109/tmi.2021.3110829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Dynamic functional connectivity (dFC) network inferred from resting-state fMRI reveals macroscopic dynamic neural activity patterns for brain disease identification. However, dFC methods ignore the causal influence between the brain regions. Furthermore, due to the complex non-Euclidean structure of brain networks, advanced deep neural networks are difficult to be applied for learning high-dimensional representations from brain networks. In this paper, a group constrained Kalman filter (gKF) algorithm is proposed to construct dynamic effective connectivity (dEC), where the gKF provides a more comprehensive understanding of the directional interaction within the dynamic brain networks than the dFC methods. Then, a novel virtual adversarial training convolutional neural network (VAT-CNN) is employed to extract the local features of dEC. The VAT strategy improves the robustness of the model to adversarial perturbations, and therefore avoids the overfitting problem effectively. Finally, we propose the high-order connectivity weight-guided graph attention networks (cwGAT) to aggregate features of dEC. By injecting the weight information of high-order connectivity into the attention mechanism, the cwGAT provides more effective high-level feature representations than the conventional GAT. The high-level features generated from the cwGAT are applied for binary classification and multiclass classification tasks of mild cognitive impairment (MCI). Experimental results indicate that the proposed framework achieves the classification accuracy of 90.9%, 89.8%, and 82.7% for normal control (NC) vs. early MCI (EMCI), EMCI vs. late MCI (LMCI), and NC vs. EMCI vs. LMCI classification respectively, outperforming the state-of-the-art methods significantly.
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31
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Abstract
The probability of the basic HHO algorithm in choosing different search methods is symmetric: about 0.5 in the interval from 0 to 1. The optimal solution from the previous iteration of the algorithm affects the current solution, the search for prey in a linear way led to a single search result, and the overall number of updates of the optimal position was low. These factors limit Harris Hawks optimization algorithm. For example, an ease of falling into a local optimum and the efficiency of convergence is low. Inspired by the prey hunting behavior of Harris’s hawk, a multi-strategy search Harris Hawks optimization algorithm is proposed, and the least squares support vector machine (LSSVM) optimized by the proposed algorithm was used to model the reactive power output of the synchronous condenser. Firstly, we select the best Gauss chaotic mapping method from seven commonly used chaotic mapping population initialization methods to improve the accuracy. Secondly, the optimal neighborhood perturbation mechanism is introduced to avoid premature maturity of the algorithm. Simultaneously, the adaptive weight and variable spiral search strategy are designed to simulate the prey hunting behavior of Harris hawk to improve the convergence speed of the improved algorithm and enhance the global search ability of the improved algorithm. A numerical experiment is tested with the classical 23 test functions and the CEC2017 test function set. The results show that the proposed algorithm outperforms the Harris Hawks optimization algorithm and other intelligent optimization algorithms in terms of convergence speed, solution accuracy and robustness, and the model of synchronous condenser reactive power output established by the improved algorithm optimized LSSVM has good accuracy and generalization ability.
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32
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Ji J, Liu J, Han L, Wang F. Estimating Effective Connectivity by Recurrent Generative Adversarial Networks. IEEE TRANSACTIONS ON MEDICAL IMAGING 2021; 40:3326-3336. [PMID: 34038358 DOI: 10.1109/tmi.2021.3083984] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Estimating effective connectivity from functional magnetic resonance imaging (fMRI) time series data has become a very hot topic in neuroinformatics and brain informatics. However, it is hard for the current methods to accurately estimate the effective connectivity due to the high noise and small sample size of fMRI data. In this paper, we propose a novel framework for estimating effective connectivity based on recurrent generative adversarial networks, called EC-RGAN. The proposed framework employs the generator that consists of a set of effective connectivity generators based on recurrent neural networks to generate the fMRI time series of each brain region, and uses the discriminator to distinguish between the joint distributions of the real and generated fMRI time series. When the model is well-trained and generated fMRI data is similar to real fMRI data, EC-RGAN outputs the effective connectivity by means of the causal parameters of the effective connectivity generators. Experimental results on both simulated and real-world fMRI time series data demonstrate the efficacy of our proposed framework.
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33
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Li Y, Guo L, Liu Y, Liu J, Meng F. A Temporal-Spectral-Based Squeeze-and- Excitation Feature Fusion Network for Motor Imagery EEG Decoding. IEEE Trans Neural Syst Rehabil Eng 2021; 29:1534-1545. [PMID: 34310314 DOI: 10.1109/tnsre.2021.3099908] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Motor imagery (MI) electroencephalography (EEG) decoding plays an important role in brain-computer interface (BCI), which enables motor-disabled patients to communicate with the outside world via external devices. Recent deep learning methods, which fail to fully explore both deep-temporal characterizations in EEGs itself and multi-spectral information in different rhythms, generally ignore the temporal or spectral dependencies in MI-EEG. Also, the lack of effective feature fusion probably leads to redundant or irrelative information and thus fails to achieve the most discriminative features, resulting in the limited MI-EEG decoding performance. To address these issues, in this paper, a MI-EEG decoding framework is proposed, which uses a novel temporal-spectral-based squeeze-and-excitation feature fusion network (TS-SEFFNet). First, the deep-temporal convolution block (DT-Conv block) implements convolutions in a cascade architecture, which extracts high-dimension temporal representations from raw EEG signals. Second, the multi-spectral convolution block (MS-Conv block) is then conducted in parallel using multi-level wavelet convolutions to capture discriminative spectral features from corresponding clinical subbands. Finally, the proposed squeeze-and-excitation feature fusion block (SE-Feature-Fusion block) maps the deep-temporal and multi-spectral features into comprehensive fused feature maps, which highlights channel-wise feature responses by constructing interdependencies among different domain features. Competitive experimental results on two public datasets demonstrate that our method is able to achieve promising decoding performance compared with the state-of-the-art methods.
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34
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Calhoun VD, Pearlson GD, Sui J. Data-driven approaches to neuroimaging biomarkers for neurological and psychiatric disorders: emerging approaches and examples. Curr Opin Neurol 2021; 34:469-479. [PMID: 34054110 PMCID: PMC8263510 DOI: 10.1097/wco.0000000000000967] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
PURPOSE OF REVIEW The 'holy grail' of clinical applications of neuroimaging to neurological and psychiatric disorders via personalized biomarkers has remained mostly elusive, despite considerable effort. However, there are many reasons to continue to be hopeful, as the field has made remarkable advances over the past few years, fueled by a variety of converging technical and data developments. RECENT FINDINGS We discuss a number of advances that are accelerating the push for neuroimaging biomarkers including the advent of the 'neuroscience big data' era, biomarker data competitions, the development of more sophisticated algorithms including 'guided' data-driven approaches that facilitate automation of network-based analyses, dynamic connectivity, and deep learning. Another key advance includes multimodal data fusion approaches which can provide convergent and complementary evidence pointing to possible mechanisms as well as increase predictive accuracy. SUMMARY The search for clinically relevant neuroimaging biomarkers for neurological and psychiatric disorders is rapidly accelerating. Here, we highlight some of these aspects, provide recent examples from studies in our group, and link to other ongoing work in the field. It is critical that access and use of these advanced approaches becomes mainstream, this will help propel the community forward and facilitate the production of robust and replicable neuroimaging biomarkers.
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Affiliation(s)
- Vince D Calhoun
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, Georgia
| | - Godfrey D Pearlson
- Department of Psychiatry and Neuroscience, Yale School of Medicine, New Haven, Connecticut, USA
| | - Jing Sui
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, Georgia
- Institute of Automation, Chinese Academy of Sciences, and the University of Chinese Academy of Sciences, Beijing, China
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35
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Zhu Z, Xingming Z, Tao G, Dan T, Li J, Chen X, Li Y, Zhou Z, Zhang X, Zhou J, Chen D, Wen H, Cai H. Classification of COVID-19 by Compressed Chest CT Image through Deep Learning on a Large Patients Cohort. Interdiscip Sci 2021; 13:73-82. [PMID: 33565027 PMCID: PMC7872116 DOI: 10.1007/s12539-020-00408-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/27/2020] [Accepted: 12/03/2020] [Indexed: 01/08/2023]
Abstract
Abstract Corona Virus Disease (COVID-19) has spread globally quickly, and has resulted in a large number of causalities and medical resources insufficiency in many countries. Reverse-transcriptase polymerase chain reaction (RT-PCR) testing is adopted as biopsy tool for confirmation of virus infection. However, its accuracy is as low as 60-70%, which is inefficient to uncover the infected. In comparison, the chest CT has been considered as the prior choice in diagnosis and monitoring progress of COVID-19 infection. Although the COVID-19 diagnostic systems based on artificial intelligence have been developed for assisting doctors in diagnosis, the small sample size and the excessive time consumption limit their applications. To this end, this paper proposed a diagnosis prototype system for COVID-19 infection testing. The proposed deep learning model is trained and is tested on 2267 CT sequences from 1357 patients clinically confirmed with COVID-19 and 1235 CT sequences from non-infected people. The main highlights of the prototype system are: (1) no data augmentation is needed to accurately discriminate the COVID-19 from normal controls with the specificity of 0.92 and sensitivity of 0.93; (2) the raw DICOM image is not necessary in testing. Highly compressed image like Jpeg can be used to allow a quick diagnosis; and (3) it discriminates the virus infection within 6 seconds and thus allows an online test with light cost. We also applied our model on 48 asymptomatic patients diagnosed with COVID-19. We found that: (1) the positive rate of RT-PCR assay is 63.5% (687/1082). (2) 45.8% (22/48) of the RT-PCR assay is negative for asymptomatic patients, yet the accuracy of CT scans is 95.8%. The online detection system is available: http://212.64.70.65/covid. Graphic Abstract ![]()
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Affiliation(s)
- Ziwei Zhu
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, 510600, China
| | - Zhang Xingming
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, 510600, China.
| | - Guihua Tao
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, 510600, China
| | - Tingting Dan
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, 510600, China
| | - Jiao Li
- Department of Medical Imaging, Collaborative Innovation Center for Cancer Medicine, State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510006, China
| | - Xijie Chen
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, 510600, China
| | - Yang Li
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, 510600, China
| | - Zhichao Zhou
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, 510600, China
| | - Xiang Zhang
- Wuhan Huangpi District Hospital of Traditional Chinese Medicine, 430300, Wuhan, China
| | - Jinzhao Zhou
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, 510600, China
| | - Dongpei Chen
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, 510600, China
| | - Hanchun Wen
- Department of Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Guangxi, 530021, China
| | - Hongmin Cai
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, 510600, China.
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36
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Hu J, Chen H, Heidari AA, Wang M, Zhang X, Chen Y, Pan Z. Orthogonal learning covariance matrix for defects of grey wolf optimizer: Insights, balance, diversity, and feature selection. Knowl Based Syst 2021. [DOI: 10.1016/j.knosys.2020.106684] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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37
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Fan Y, Wang P, Mafarja M, Wang M, Zhao X, Chen H. A bioinformatic variant fruit fly optimizer for tackling optimization problems. Knowl Based Syst 2021. [DOI: 10.1016/j.knosys.2020.106704] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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38
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Ye H, Wu P, Zhu T, Xiao Z, Zhang X, Zheng L, Zheng R, Sun Y, Zhou W, Fu Q, Ye X, Chen A, Zheng S, Heidari AA, Wang M, Zhu J, Chen H, Li J. Diagnosing Coronavirus Disease 2019 (COVID-19): Efficient Harris Hawks-Inspired Fuzzy K-Nearest Neighbor Prediction Methods. IEEE ACCESS : PRACTICAL INNOVATIONS, OPEN SOLUTIONS 2021; 9:17787-17802. [PMID: 34786302 PMCID: PMC8545238 DOI: 10.1109/access.2021.3052835] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 01/15/2021] [Indexed: 05/26/2023]
Abstract
This study is devoted to proposing a useful intelligent prediction model to distinguish the severity of COVID-19, to provide a more fair and reasonable reference for assisting clinical diagnostic decision-making. Based on patients' necessary information, pre-existing diseases, symptoms, immune indexes, and complications, this article proposes a prediction model using the Harris hawks optimization (HHO) to optimize the Fuzzy K-nearest neighbor (FKNN), which is called HHO-FKNN. This model is utilized to distinguish the severity of COVID-19. In HHO-FKNN, the purpose of introducing HHO is to optimize the FKNN's optimal parameters and feature subsets simultaneously. Also, based on actual COVID-19 data, we conducted a comparative experiment between HHO-FKNN and several well-known machine learning algorithms, which result shows that not only the proposed HHO-FKNN can obtain better classification performance and higher stability on the four indexes but also screen out the key features that distinguish severe COVID-19 from mild COVID-19. Therefore, we can conclude that the proposed HHO-FKNN model is expected to become a useful tool for COVID-19 prediction.
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Affiliation(s)
- Hua Ye
- Department of Pulmonary and Critical Care MedicineAffiliated Yueqing Hospital, Wenzhou Medical UniversityYueqing325600China
| | - Peiliang Wu
- Department of Pulmonary and Critical Care MedicineThe 1st Affiliated Hospital, Wenzhou Medical UniversityWenzhou325000China
| | - Tianru Zhu
- The Second Clinical CollegeWenzhou Medical UniversityWenzhou325000China
| | - Zhongxiang Xiao
- Department of PharmacyAffiliated Yueqing Hospital, Wenzhou Medical UniversityYueqing325600China
| | - Xie Zhang
- Department of Pulmonary and Critical Care MedicineAffiliated Yueqing Hospital, Wenzhou Medical UniversityYueqing325600China
| | - Long Zheng
- Department of Pulmonary and Critical Care MedicineAffiliated Yueqing Hospital, Wenzhou Medical UniversityYueqing325600China
| | - Rongwei Zheng
- Department of UrologyAffiliated Yueqing Hospital, Wenzhou Medical UniversityYueqing325600China
| | - Yangjie Sun
- Department of Pulmonary and Critical Care MedicineAffiliated Yueqing Hospital, Wenzhou Medical UniversityYueqing325600China
| | - Weilong Zhou
- Department of Pulmonary and Critical Care MedicineAffiliated Yueqing Hospital, Wenzhou Medical UniversityYueqing325600China
| | - Qinlei Fu
- Department of Pulmonary and Critical Care MedicineAffiliated Yueqing Hospital, Wenzhou Medical UniversityYueqing325600China
| | - Xinxin Ye
- Department of Pulmonary and Critical Care MedicineAffiliated Yueqing Hospital, Wenzhou Medical UniversityYueqing325600China
| | - Ali Chen
- Department of Pulmonary and Critical Care MedicineAffiliated Yueqing Hospital, Wenzhou Medical UniversityYueqing325600China
| | - Shuang Zheng
- Department of Pulmonary and Critical Care MedicineAffiliated Yueqing Hospital, Wenzhou Medical UniversityYueqing325600China
| | - Ali Asghar Heidari
- School of Surveying and Geospatial Engineering, College of EngineeringUniversity of TehranTehran1417466191Iran
- Department of Computer ScienceSchool of ComputingNational University of SingaporeSingapore117417
| | - Mingjing Wang
- Institute of Research and Development, Duy Tan UniversityDa Nang550000Vietnam
| | - Jiandong Zhu
- Department of Surgical OncologyAffiliated Yueqing Hospital, Wenzhou Medical UniversityYueqing325600China
| | - Huiling Chen
- College of Computer Science and Artificial IntelligenceWenzhou UniversityWenzhou325035China
| | - Jifa Li
- Department of Pulmonary and Critical Care MedicineAffiliated Yueqing Hospital, Wenzhou Medical UniversityYueqing325600China
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Song X, Zhou F, Frangi AF, Cao J, Xiao X, Lei Y, Wang T, Lei B. Graph convolution network with similarity awareness and adaptive calibration for disease-induced deterioration prediction. Med Image Anal 2020; 69:101947. [PMID: 33388456 DOI: 10.1016/j.media.2020.101947] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 11/23/2020] [Accepted: 12/12/2020] [Indexed: 01/04/2023]
Abstract
Graph convolution networks (GCN) have been successfully applied in disease prediction tasks as they capture interactions (i.e., edges and edge weights on the graph) between individual elements. The interactions in existing works are constructed by fusing similarity between imaging information and distance between non-imaging information, whereas disregarding the disease status of those individuals in the training set. Besides, the similarity is being evaluated by computing the correlation distance between feature vectors, which limits prediction performance, especially for predicting significant memory concern (SMC) and mild cognitive impairment (MCI). In this paper, we propose three mechanisms to improve GCN, namely similarity-aware adaptive calibrated GCN (SAC-GCN), for predicting SMC and MCI. First, we design a similarity-aware graph using different receptive fields to consider disease status. The labelled subjects on the graph are only connected with those labelled subjects with the same status. Second, we propose an adaptive mechanism to evaluate similarity. Specifically, we construct initial GCN with evaluating similarity by using traditional correlation distance, then pre-train the initial GCN by using training samples and use it to score all subjects. Then, the difference between these scores replaces correlation distance to update similarity. Last, we devise a calibration mechanism to fuse functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI) information into edges. The proposed method is tested on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset. Experimental results demonstrate that our proposed method is useful to predict disease-induced deterioration and superior to other related algorithms, with a mean classification accuracy of 86.83% in our prediction tasks.
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Affiliation(s)
- Xuegang Song
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Centre, Shenzhen University, Shenzhen, 518060, China
| | - Feng Zhou
- Department of Industrial and Manufacturing, Systems Engineering, The University of Michigan, Dearborn, MI 42185, USA
| | - Alejandro F Frangi
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Centre, Shenzhen University, Shenzhen, 518060, China; CISTIB Centre for Computational Imaging & Simulation Technologies in Biomedicine, School of Computing, University of Leeds, Leeds LS2 9LU, United Kingdom; LICAMM Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, Leeds LS2 9LU, United Kingdom; Medical Imaging Research Center (MIRC) - University Hospital Gasthuisberg, KU Leuven, Herestraat 49, 3000 Leuven. Belgium
| | - Jiuwen Cao
- Artificial Intelligence Institute, Hangzhou Dianzi University, Zhejiang, 310010, China
| | - Xiaohua Xiao
- First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen, 518050, China
| | - Yi Lei
- First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen University, Shenzhen, 518050, China
| | - Tianfu Wang
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Centre, Shenzhen University, Shenzhen, 518060, China
| | - Baiying Lei
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Centre, Shenzhen University, Shenzhen, 518060, China.
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40
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Predicting Coronary Atherosclerotic Heart Disease: An Extreme Learning Machine with Improved Salp Swarm Algorithm. Symmetry (Basel) 2020. [DOI: 10.3390/sym12101651] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
To provide an available diagnostic model for diagnosing coronary atherosclerotic heart disease to provide an auxiliary function for doctors, we proposed a new evolutionary classification model in this paper. The core of the prediction model is a kernel extreme learning machine (KELM) optimized by an improved salp swarm algorithm (SSA). To get a better subset of parameters and features, the space transformation mechanism is introduced in the optimization core to improve SSA for obtaining an optimal KELM model. The KELM model for the diagnosis of coronary atherosclerotic heart disease (STSSA-KELM) is developed based on the optimal parameters and a subset of features. In the experiment, STSSA-KELM is compared with some widely adopted machine learning methods (MLM) in coronary atherosclerotic heart disease prediction. The experimental results show that STSSA-KELM can realize excellent classification performance and more robust stability under four indications. We also compare the convergence of STSSA-KELM with other MLM; the STSSA-KELM model has demonstrated a higher classification performance. Therefore, the STSSA-KELM model can effectively help doctors to diagnose coronary heart disease.
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41
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Chen Q, Wang Y, Qiu Y, Wu X, Zhou Y, Zhai G. A Deep Learning-Based Model for Classification of Different Subtypes of Subcortical Vascular Cognitive Impairment With FLAIR. Front Neurosci 2020; 14:557. [PMID: 32625048 PMCID: PMC7315844 DOI: 10.3389/fnins.2020.00557] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/06/2020] [Indexed: 11/17/2022] Open
Abstract
Deep learning methods have shown their great capability of extracting high-level features from image and have been used for effective medical imaging classification recently. However, training samples of medical images are restricted by the amount of patients as well as medical ethics issues, making it hard to train the neural networks. In this paper, we propose a novel end-to-end three-dimensional (3D) attention-based residual neural network (ResNet) architecture to classify different subtypes of subcortical vascular cognitive impairment (SVCI) with single-shot T2-weighted fluid-attenuated inversion recovery (FLAIR) sequence. Our aim is to develop a convolutional neural network to provide a convenient and effective way to assist doctors in the diagnosis and early treatment of the different subtypes of SVCI. The experiment data in this paper are collected from 242 patients from the Neurology Department of Renji Hospital, including 78 amnestic mild cognitive impairment (a-MCI), 70 nonamnestic MCI (na-MCI), and 94 no cognitive impairment (NCI). The accuracy of our proposed model has reached 98.6% on a training set and 97.3% on a validation set. The test accuracy on an untrained testing set reaches 93.8% with robustness. Our proposed method can provide a convenient and effective way to assist doctors in the diagnosis and early treatment.
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Affiliation(s)
- Qi Chen
- Institute of Image Communication and Network Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yao Wang
- Department of Radiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yage Qiu
- Department of Radiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaowei Wu
- Department of Radiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Zhou
- Department of Radiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Guangtao Zhai
- Institute of Image Communication and Network Engineering, Shanghai Jiao Tong University, Shanghai, China
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