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Zhu Q, Li S, Meng X, Xu Q, Zhang Z, Shao W, Zhang D. Spatio-Temporal Graph Hubness Propagation Model for Dynamic Brain Network Classification. IEEE TRANSACTIONS ON MEDICAL IMAGING 2024; 43:2381-2394. [PMID: 38319754 DOI: 10.1109/tmi.2024.3363014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Dynamic brain network has the advantage over static brain network in characterizing the variation pattern of functional brain connectivity, and it has attracted increasing attention in brain disease diagnosis. However, most of the existing dynamic brain networks analysis methods rely on extracting features from independent brain networks divided by sliding windows, making them hard to reveal the high-order dynamic evolution laws of functional brain networks. Additionally, they cannot effectively extract the spatio-temporal topology features in dynamic brain networks. In this paper, we propose to use optimal transport (OT) theory to capture the topology evolution of the dynamic brain networks, and develop a multi-channel spatio-temporal graph convolutional network that collaboratively extracts the temporal and spatial features from the evolution networks. Specifically, we first adaptively evaluate the graph hubness of brain regions in the brain network of each time window, which comprehensively models information transmission among multiple brain regions. Second, the hubness propagation information across adjacent time windows is captured by optimal transport, describing high-order topology evolution of dynamic brain networks. Moreover, we develop a spatio-temporal graph convolutional network with attention mechanism to collaboratively extract the intrinsic temporal and spatial topology information from the above networks. Finally, the multi-layer perceptron is adopted for classifying the dynamic brain network. The extensive experiment on the collected epilepsy dataset and the public ADNI dataset show that our proposed method not only outperforms several state-of-the-art methods in brain disease diagnosis, but also reveals the key dynamic alterations of brain connectivities between patients and healthy controls.
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2
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Pentari A, Kafentzis G, Tsiknakis M. Speech emotion recognition via graph-based representations. Sci Rep 2024; 14:4484. [PMID: 38396002 PMCID: PMC10891082 DOI: 10.1038/s41598-024-52989-2] [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: 06/23/2023] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Speech emotion recognition (SER) has gained an increased interest during the last decades as part of enriched affective computing. As a consequence, a variety of engineering approaches have been developed addressing the challenge of the SER problem, exploiting different features, learning algorithms, and datasets. In this paper, we propose the application of the graph theory for classifying emotionally-colored speech signals. Graph theory provides tools for extracting statistical as well as structural information from any time series. We propose to use the mentioned information as a novel feature set. Furthermore, we suggest setting a unique feature-based identity for each emotion belonging to each speaker. The emotion classification is performed by a Random Forest classifier in a Leave-One-Speaker-Out Cross Validation (LOSO-CV) scheme. The proposed method is compared with two state-of-the-art approaches involving well known hand-crafted features as well as deep learning architectures operating on mel-spectrograms. Experimental results on three datasets, EMODB (German, acted) and AESDD (Greek, acted), and DEMoS (Italian, in-the-wild), reveal that our proposed method outperforms the comparative methods in these datasets. Specifically, we observe an average UAR increase of almost [Formula: see text], [Formula: see text] and [Formula: see text], respectively.
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Affiliation(s)
- Anastasia Pentari
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Heraklion, GR-700 13, Greece.
| | - George Kafentzis
- Computer Science Department, University of Crete, Heraklion, GR-700 13, Greece
| | - Manolis Tsiknakis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Heraklion, GR-700 13, Greece
- Department of Electrical and Computer Engineering, Hellenic Mediterranean University, Heraklion, Greece
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3
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Marzi SJ, Schilder BM, Nott A, Frigerio CS, Willaime-Morawek S, Bucholc M, Hanger DP, James C, Lewis PA, Lourida I, Noble W, Rodriguez-Algarra F, Sharif JA, Tsalenchuk M, Winchester LM, Yaman Ü, Yao Z, Ranson JM, Llewellyn DJ. Artificial intelligence for neurodegenerative experimental models. Alzheimers Dement 2023; 19:5970-5987. [PMID: 37768001 DOI: 10.1002/alz.13479] [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: 04/17/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 09/29/2023]
Abstract
INTRODUCTION Experimental models are essential tools in neurodegenerative disease research. However, the translation of insights and drugs discovered in model systems has proven immensely challenging, marred by high failure rates in human clinical trials. METHODS Here we review the application of artificial intelligence (AI) and machine learning (ML) in experimental medicine for dementia research. RESULTS Considering the specific challenges of reproducibility and translation between other species or model systems and human biology in preclinical dementia research, we highlight best practices and resources that can be leveraged to quantify and evaluate translatability. We then evaluate how AI and ML approaches could be applied to enhance both cross-model reproducibility and translation to human biology, while sustaining biological interpretability. DISCUSSION AI and ML approaches in experimental medicine remain in their infancy. However, they have great potential to strengthen preclinical research and translation if based upon adequate, robust, and reproducible experimental data. HIGHLIGHTS There are increasing applications of AI in experimental medicine. We identified issues in reproducibility, cross-species translation, and data curation in the field. Our review highlights data resources and AI approaches as solutions. Multi-omics analysis with AI offers exciting future possibilities in drug discovery.
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Affiliation(s)
- Sarah J Marzi
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | - Brian M Schilder
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | - Alexi Nott
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | | | | | - Magda Bucholc
- School of Computing, Engineering & Intelligent Systems, Ulster University, Derry, UK
| | - Diane P Hanger
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | | | - Patrick A Lewis
- Royal Veterinary College, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | | | - Wendy Noble
- Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | | | - Jalil-Ahmad Sharif
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | - Maria Tsalenchuk
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | | | - Ümran Yaman
- UK Dementia Research Institute at UCL, London, UK
| | | | | | - David J Llewellyn
- University of Exeter Medical School, Exeter, UK
- Alan Turing Institute, London, UK
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Li F, Dong Z, Zhao Q, Payne P, Province M, Cruchaga C, Zhang M, Zhao T, Chen Y. Highly accurate disease diagnosis and highly reproducible biomarker identification with PathFormer. RESEARCH SQUARE 2023:rs.3.rs-3576068. [PMID: 38014034 PMCID: PMC10680938 DOI: 10.21203/rs.3.rs-3576068/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Biomarker identification is critical for precise disease diagnosis and understanding disease pathogenesis in omics data analysis, like using fold change and regression analysis. Graph neural networks (GNNs) have been the dominant deep learning model for analyzing graph-structured data. However, we found two major limitations of existing GNNs in omics data analysis, i.e., limited-prediction/diagnosis accuracy and limited-reproducible biomarker identification capacity across multiple datasets. The root of the challenges is the unique graph structure of biological signaling pathways, which consists of a large number of targets and intensive and complex signaling interactions among these targets. To resolve these two challenges, in this study, we presented a novel GNN model architecture, named PathFormer , which systematically integrate signaling network, priori knowledge and omics data to rank biomarkers and predict disease diagnosis. In the comparison results, PathFormer outperformed existing GNN models significantly in terms of highly accurate prediction capability (~ 30% accuracy improvement in disease diagnosis compared with existing GNN models) and high reproducibility of biomarker ranking across different datasets. The improvement was confirmed using two independent Alzheimer's Disease (AD) and cancer transcriptomic datasets. The PathFormer model can be directly applied to other omics data analysis studies.
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Zhang S, Yang J, Zhang Y, Zhong J, Hu W, Li C, Jiang J. The Combination of a Graph Neural Network Technique and Brain Imaging to Diagnose Neurological Disorders: A Review and Outlook. Brain Sci 2023; 13:1462. [PMID: 37891830 PMCID: PMC10605282 DOI: 10.3390/brainsci13101462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/06/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Neurological disorders (NDs), such as Alzheimer's disease, have been a threat to human health all over the world. It is of great importance to diagnose ND through combining artificial intelligence technology and brain imaging. A graph neural network (GNN) can model and analyze the brain, imaging from morphology, anatomical structure, function features, and other aspects, thus becoming one of the best deep learning models in the diagnosis of ND. Some researchers have investigated the application of GNN in the medical field, but the scope is broad, and its application to NDs is less frequent and not detailed enough. This review focuses on the research progress of GNNs in the diagnosis of ND. Firstly, we systematically investigated the GNN framework of ND, including graph construction, graph convolution, graph pooling, and graph prediction. Secondly, we investigated common NDs using the GNN diagnostic model in terms of data modality, number of subjects, and diagnostic accuracy. Thirdly, we discussed some research challenges and future research directions. The results of this review may be a valuable contribution to the ongoing intersection of artificial intelligence technology and brain imaging.
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Affiliation(s)
- Shuoyan Zhang
- School of Communication and Information Engineering, Shanghai University, Shanghai 200444, China
| | - Jiacheng Yang
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Ying Zhang
- School of Communication and Information Engineering, Shanghai University, Shanghai 200444, China
| | - Jiayi Zhong
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Wenjing Hu
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Chenyang Li
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Jiehui Jiang
- Shanghai Institute of Biomedical Engineering, Shanghai University, Shanghai 200444, China
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Kim SY. Personalized Explanations for Early Diagnosis of Alzheimer's Disease Using Explainable Graph Neural Networks with Population Graphs. Bioengineering (Basel) 2023; 10:701. [PMID: 37370632 DOI: 10.3390/bioengineering10060701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Leveraging recent advances in graph neural networks, our study introduces an application of graph convolutional networks (GCNs) within a correlation-based population graph, aiming to enhance Alzheimer's disease (AD) prognosis and illuminate the intricacies of AD progression. This methodological approach leverages the inherent structure and correlations in demographic and neuroimaging data to predict amyloid-beta (Aβ) positivity. To validate our approach, we conducted extensive performance comparisons with conventional machine learning models and a GCN model with randomly assigned edges. The results consistently highlighted the superior performance of the correlation-based GCN model across different sample groups in the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset, suggesting the importance of accurately reflecting the correlation structure in population graphs for effective pattern recognition and accurate prediction. Furthermore, our exploration of the model's decision-making process using GNNExplainer identified unique sets of biomarkers indicative of Aβ positivity in different groups, shedding light on the heterogeneity of AD progression. This study underscores the potential of our proposed approach for more nuanced AD prognoses, potentially informing more personalized and precise therapeutic strategies. Future research can extend these findings by integrating diverse data sources, employing longitudinal data, and refining the interpretability of the model, which potentially has broad applicability to other complex diseases.
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Affiliation(s)
- So Yeon Kim
- Department of Artificial Intelligence, Ajou University, Suwon 16499, Republic of Korea
- Department of Software and Computer Engineering, Ajou University, Suwon 16499, Republic of Korea
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7
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Zhu Q, Xu B, Huang J, Wang H, Xu R, Shao W, Zhang D. Deep Multi-Modal Discriminative and Interpretability Network for Alzheimer's Disease Diagnosis. IEEE TRANSACTIONS ON MEDICAL IMAGING 2023; 42:1472-1483. [PMID: 37015464 DOI: 10.1109/tmi.2022.3230750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Multi-modal fusion has become an important data analysis technology in Alzheimer's disease (AD) diagnosis, which is committed to effectively extract and utilize complementary information among different modalities. However, most of the existing fusion methods focus on pursuing common feature representation by transformation, and ignore discriminative structural information among samples. In addition, most fusion methods use high-order feature extraction, such as deep neural network, by which it is difficult to identify biomarkers. In this paper, we propose a novel method named deep multi-modal discriminative and interpretability network (DMDIN), which aligns samples in a discriminative common space and provides a new approach to identify significant brain regions (ROIs) in AD diagnosis. Specifically, we reconstruct each modality with a hierarchical representation through multilayer perceptron (MLP), and take advantage of the shared self-expression coefficients constrained by diagonal blocks to embed the structural information of inter-class and the intra-class. Further, the generalized canonical correlation analysis (GCCA) is adopted as a correlation constraint to generate a discriminative common space, in which samples of the same category gather while samples of different categories stay away. Finally, in order to enhance the interpretability of the deep learning model, we utilize knowledge distillation to reproduce coordinated representations and capture influence of brain regions in AD classification. Experiments show that the proposed method performs better than several state-of-the-art methods in AD diagnosis.
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8
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Lin L, Xiong M, Zhang G, Kang W, Sun S, Wu S. A Convolutional Neural Network and Graph Convolutional Network Based Framework for AD Classification. SENSORS (BASEL, SWITZERLAND) 2023; 23:1914. [PMID: 36850510 PMCID: PMC9961367 DOI: 10.3390/s23041914] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/29/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
The neuroscience community has developed many convolutional neural networks (CNNs) for the early detection of Alzheimer's disease (AD). Population graphs are thought of as non-linear structures that capture the relationships between individual subjects represented as nodes, which allows for the simultaneous integration of imaging and non-imaging information as well as individual subjects' features. Graph convolutional networks (GCNs) generalize convolution operations to accommodate non-Euclidean data and aid in the mining of topological information from the population graph for a disease classification task. However, few studies have examined how GCNs' input properties affect AD-staging performance. Therefore, we conducted three experiments in this work. Experiment 1 examined how the inclusion of demographic information in the edge-assigning function affects the classification of AD versus cognitive normal (CN). Experiment 2 was designed to examine the effects of adding various neuropsychological tests to the edge-assigning function on the mild cognitive impairment (MCI) classification. Experiment 3 studied the impact of the edge assignment function. The best result was obtained in Experiment 2 on multi-class classification (AD, MCI, and CN). We applied a novel framework for the diagnosis of AD that integrated CNNs and GCNs into a unified network, taking advantage of the excellent feature extraction capabilities of CNNs and population-graph processing capabilities of GCNs. To learn high-level anatomical features, DenseNet was used; a set of population graphs was represented with nodes defined by imaging features and edge weights determined by different combinations of imaging or/and non-imaging information, and the generated graphs were then fed to the GCNs for classification. Both binary classification and multi-class classification showed improved performance, with an accuracy of 91.6% for AD versus CN, 91.2% for AD versus MCI, 96.8% for MCI versus CN, and 89.4% for multi-class classification. The population graph's imaging features and edge-assigning functions can both significantly affect classification accuracy.
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Affiliation(s)
- Lan Lin
- Department of Biomedical Engineering, Faculty of Environment and Life, Beijing University of Technology, Beijing 100124, China
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9
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OViTAD: Optimized Vision Transformer to Predict Various Stages of Alzheimer's Disease Using Resting-State fMRI and Structural MRI Data. Brain Sci 2023; 13:brainsci13020260. [PMID: 36831803 PMCID: PMC9954686 DOI: 10.3390/brainsci13020260] [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: 11/12/2022] [Revised: 01/19/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Advances in applied machine learning techniques for neuroimaging have encouraged scientists to implement models to diagnose brain disorders such as Alzheimer's disease at early stages. Predicting the exact stage of Alzheimer's disease is challenging; however, complex deep learning techniques can precisely manage this. While successful, these complex architectures are difficult to interrogate and computationally expensive. Therefore, using novel, simpler architectures with more efficient pattern extraction capabilities, such as transformers, is of interest to neuroscientists. This study introduced an optimized vision transformer architecture to predict the group membership by separating healthy adults, mild cognitive impairment, and Alzheimer's brains within the same age group (>75 years) using resting-state functional (rs-fMRI) and structural magnetic resonance imaging (sMRI) data aggressively preprocessed by our pipeline. Our optimized architecture, known as OViTAD is currently the sole vision transformer-based end-to-end pipeline and outperformed the existing transformer models and most state-of-the-art solutions. Our model achieved F1-scores of 97%±0.0 and 99.55%±0.39 from the testing sets for the rs-fMRI and sMRI modalities in the triple-class prediction experiments. Furthermore, our model reached these performances using 30% fewer parameters than a vanilla transformer. Furthermore, the model was robust and repeatable, producing similar estimates across three runs with random data splits (we reported the averaged evaluation metrics). Finally, to challenge the model, we observed how it handled increasing noise levels by inserting varying numbers of healthy brains into the two dementia groups. Our findings suggest that optimized vision transformers are a promising and exciting new approach for neuroimaging applications, especially for Alzheimer's disease prediction.
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10
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Li MM, Huang K, Zitnik M. Graph representation learning in biomedicine and healthcare. Nat Biomed Eng 2022; 6:1353-1369. [PMID: 36316368 PMCID: PMC10699434 DOI: 10.1038/s41551-022-00942-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 08/09/2022] [Indexed: 11/11/2022]
Abstract
Networks-or graphs-are universal descriptors of systems of interacting elements. In biomedicine and healthcare, they can represent, for example, molecular interactions, signalling pathways, disease co-morbidities or healthcare systems. In this Perspective, we posit that representation learning can realize principles of network medicine, discuss successes and current limitations of the use of representation learning on graphs in biomedicine and healthcare, and outline algorithmic strategies that leverage the topology of graphs to embed them into compact vectorial spaces. We argue that graph representation learning will keep pushing forward machine learning for biomedicine and healthcare applications, including the identification of genetic variants underlying complex traits, the disentanglement of single-cell behaviours and their effects on health, the assistance of patients in diagnosis and treatment, and the development of safe and effective medicines.
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Affiliation(s)
- Michelle M Li
- Bioinformatics and Integrative Genomics Program, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Kexin Huang
- Health Data Science Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Marinka Zitnik
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Data Science Initiative, Cambridge, MA, USA.
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11
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Wang X, Xin J, Wang Z, Chen Q, Wang Z. An evolving graph convolutional network for dynamic functional brain network. APPL INTELL 2022. [DOI: 10.1007/s10489-022-04203-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Huang C, Wang J, Wang SH, Zhang YD. Applicable artificial intelligence for brain disease: A survey. Neurocomputing 2022. [DOI: 10.1016/j.neucom.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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13
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Li Y, Wei Q, Adeli E, Pohl KM, Zhao Q. Joint Graph Convolution for Analyzing Brain Structural and Functional Connectome. MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION : MICCAI ... INTERNATIONAL CONFERENCE ON MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION 2022; 13431:231-240. [PMID: 36321855 PMCID: PMC9620868 DOI: 10.1007/978-3-031-16431-6_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The white-matter (micro-)structural architecture of the brain promotes synchrony among neuronal populations, giving rise to richly patterned functional connections. A fundamental problem for systems neuroscience is determining the best way to relate structural and functional networks quantified by diffusion tensor imaging and resting-state functional MRI. As one of the state-of-the-art approaches for network analysis, graph convolutional networks (GCN) have been separately used to analyze functional and structural networks, but have not been applied to explore inter-network relationships. In this work, we propose to couple the two networks of an individual by adding inter-network edges between corresponding brain regions, so that the joint structure-function graph can be directly analyzed by a single GCN. The weights of inter-network edges are learnable, reflecting non-uniform structure-function coupling strength across the brain. We apply our Joint-GCN to predict age and sex of 662 participants from the public dataset of the National Consortium on Alcohol and Neurodevelopment in Adolescence (NCANDA) based on their functional and micro-structural white-matter networks. Our results support that the proposed Joint-GCN outperforms existing multi-modal graph learning approaches for analyzing structural and functional networks.
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Affiliation(s)
- Yueting Li
- Stanford University, Stanford, CA 94305, USA
| | - Qingyue Wei
- Stanford University, Stanford, CA 94305, USA
| | - Ehsan Adeli
- Stanford University, Stanford, CA 94305, USA
| | - Kilian M Pohl
- Stanford University, Stanford, CA 94305, USA
- SRI International, Menlo Park, CA 94025, USA
| | - Qingyu Zhao
- Stanford University, Stanford, CA 94305, USA
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14
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A CAD System for Alzheimer's Disease Classification Using Neuroimaging MRI 2D Slices. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:8680737. [PMID: 35983528 PMCID: PMC9381208 DOI: 10.1155/2022/8680737] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/21/2022] [Accepted: 05/27/2022] [Indexed: 11/22/2022]
Abstract
Developments in medical care have inspired wide interest in the current decade, especially to their services to individuals living prolonged and healthier lives. Alzheimer's disease (AD) is the most chronic neurodegeneration and dementia-causing disorder. Economic expense of treating AD patients is expected to grow. The requirement of developing a computer-aided technique for early AD categorization becomes even more essential. Deep learning (DL) models offer numerous benefits against machine learning tools. Several latest experiments that exploited brain magnetic resonance imaging (MRI) scans and convolutional neural networks (CNN) for AD classification showed promising conclusions. CNN's receptive field aids in the extraction of main recognizable features from these MRI scans. In order to increase classification accuracy, a new adaptive model based on CNN and support vector machines (SVM) is presented in the research, combining both the CNN's capabilities in feature extraction and SVM in classification. The objective of this research is to build a hybrid CNN-SVM model for classifying AD using the MRI ADNI dataset. Experimental results reveal that the hybrid CNN-SVM model outperforms the CNN model alone, with relative improvements of 3.4%, 1.09%, 0.85%, and 2.82% on the testing dataset for AD vs. cognitive normal (CN), CN vs. mild cognitive impairment (MCI), AD vs. MCI, and CN vs. MCI vs. AD, respectively. Finally, the proposed approach has been further experimented on OASIS dataset leading to accuracy of 86.2%.
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15
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Li Z, Huang K, Liu L, Zhang Z. Early detection of COPD based on graph convolutional network and small and weakly labeled data. Med Biol Eng Comput 2022; 60:2321-2333. [PMID: 35750976 PMCID: PMC9244127 DOI: 10.1007/s11517-022-02589-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 05/08/2022] [Indexed: 11/25/2022]
Affiliation(s)
- Zongli Li
- Department of Pulmonary and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, People's Republic of China
- Beijing Institute of Respiratory Medicine, Beijing, 100020, People's Republic of China
- Department of Respiratory, Shijingshan Teaching Hospital of Capital Medical University, Beijing Shijingshan Hospital, Beijing, 100043, People's Republic of China
| | - Kewu Huang
- Department of Pulmonary and Critical Care Medicine, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, People's Republic of China.
- Beijing Institute of Respiratory Medicine, Beijing, 100020, People's Republic of China.
| | - Ligong Liu
- Department of Enterprise Management, China Energy Engineering Corporation Limited, Beijing, 100022, People's Republic of China
| | - Zuoqing Zhang
- Department of Respiratory, Shijingshan Teaching Hospital of Capital Medical University, Beijing Shijingshan Hospital, Beijing, 100043, People's Republic of China
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16
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Krishnagopal S, Lohse K, Braun R. Stroke recovery phenotyping through network trajectory approaches and graph neural networks. Brain Inform 2022; 9:13. [PMID: 35717640 PMCID: PMC9206968 DOI: 10.1186/s40708-022-00160-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 04/23/2022] [Indexed: 11/23/2022] Open
Abstract
Stroke is a leading cause of neurological injury characterized by impairments in multiple neurological domains including cognition, language, sensory and motor functions. Clinical recovery in these domains is tracked using a wide range of measures that may be continuous, ordinal, interval or categorical in nature, which can present challenges for multivariate regression approaches. This has hindered stroke researchers’ ability to achieve an integrated picture of the complex time-evolving interactions among symptoms. Here, we use tools from network science and machine learning that are particularly well-suited to extracting underlying patterns in such data, and may assist in prediction of recovery patterns. To demonstrate the utility of this approach, we analyzed data from the NINDS tPA trial using the Trajectory Profile Clustering (TPC) method to identify distinct stroke recovery patterns for 11 different neurological domains at 5 discrete time points. Our analysis identified 3 distinct stroke trajectory profiles that align with clinically relevant stroke syndromes, characterized both by distinct clusters of symptoms, as well as differing degrees of symptom severity. We then validated our approach using graph neural networks to determine how well our model performed predictively for stratifying patients into these trajectory profiles at early vs. later time points post-stroke. We demonstrate that trajectory profile clustering is an effective method for identifying clinically relevant recovery subtypes in multidimensional longitudinal datasets, and for early prediction of symptom progression subtypes in individual patients. This paper is the first work introducing network trajectory approaches for stroke recovery phenotyping, and is aimed at enhancing the translation of such novel computational approaches for practical clinical application.
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Affiliation(s)
- Sanjukta Krishnagopal
- Gatsby Computational Neuroscience Unit, University College London, London, W1T 4JG, UK.
| | - Keith Lohse
- Physical Therapy and Neurology, Washington University School of Medicine, 4444 Forest Park Ave., Suite 1101, St. Louis, MO, 63108-2212, USA
| | - Robynne Braun
- Department of Neurology, University of Maryland School of Medicine, 655 W. Baltimore Street, Bressler Research Building, 12th Floor, Baltimore, MD, 21201, USA, on behalf of the GPAS Collaboration, Phenotyping Core
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Li W, Zhao J, Shen C, Zhang J, Hu J, Xiao M, Zhang J, Chen M. Regional Brain Fusion: Graph Convolutional Network for Alzheimer's Disease Prediction and Analysis. Front Neuroinform 2022; 16:886365. [PMID: 35571869 PMCID: PMC9100702 DOI: 10.3389/fninf.2022.886365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/30/2022] [Indexed: 11/24/2022] Open
Abstract
Alzheimer's disease (AD) has raised extensive concern in healthcare and academia as one of the most prevalent health threats to the elderly. Due to the irreversible nature of AD, early and accurate diagnoses are significant for effective prevention and treatment. However, diverse clinical symptoms and limited neuroimaging accuracy make diagnoses challenging. In this article, we built a brain network for each subject, which assembles several commonly used neuroimaging data simply and reasonably, including structural magnetic resonance imaging (MRI), diffusion-weighted imaging (DWI), and amyloid positron emission tomography (PET). Based on some existing research results, we applied statistical methods to analyze (i) the distinct affinity of AD burden on each brain region, (ii) the topological lateralization between left and right hemispheric sub-networks, and (iii) the asymmetry of the AD attacks on the left and right hemispheres. In the light of advances in graph convolutional networks for graph classifications and summarized characteristics of brain networks and AD pathologies, we proposed a regional brain fusion-graph convolutional network (RBF-GCN), which is constructed with an RBF framework mainly, including three sub-modules, namely, hemispheric network generation module, multichannel GCN module, and feature fusion module. In the multichannel GCN module, the improved GCN by our proposed adaptive native node attribute (ANNA) unit embeds within each channel independently. We not only fully verified the effectiveness of the RBF framework and ANNA unit but also achieved competitive results in multiple sets of AD stages' classification tasks using hundreds of experiments over the ADNI clinical dataset.
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Affiliation(s)
- Wenchao Li
- Intelligent Information Processing Laboratory, Hangzhou Dianzi University, Hangzhou, China
| | - Jiaqi Zhao
- Research Center for Healthcare Data Science, Zhejiang Lab, Hangzhou, China
| | - Chenyu Shen
- Intelligent Information Processing Laboratory, Hangzhou Dianzi University, Hangzhou, China
| | - Jingwen Zhang
- Department of Computer Science, Wake Forest University, Winston-Salem, NC, United States
| | - Ji Hu
- Intelligent Information Processing Laboratory, Hangzhou Dianzi University, Hangzhou, China
| | - Mang Xiao
- Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jiyong Zhang
- Intelligent Information Processing Laboratory, Hangzhou Dianzi University, Hangzhou, China
- *Correspondence: Jiyong Zhang
| | - Minghan Chen
- Department of Computer Science, Wake Forest University, Winston-Salem, NC, United States
- Minghan Chen
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18
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Helaly HA, Badawy M, Haikal AY. Deep Learning Approach for Early Detection of Alzheimer's Disease. Cognit Comput 2021; 14:1711-1727. [PMID: 34745371 PMCID: PMC8563360 DOI: 10.1007/s12559-021-09946-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 09/29/2021] [Indexed: 01/13/2023]
Abstract
Alzheimer's disease (AD) is a chronic, irreversible brain disorder, no effective cure for it till now. However, available medicines can delay its progress. Therefore, the early detection of AD plays a crucial role in preventing and controlling its progression. The main objective is to design an end-to-end framework for early detection of Alzheimer's disease and medical image classification for various AD stages. A deep learning approach, specifically convolutional neural networks (CNN), is used in this work. Four stages of the AD spectrum are multi-classified. Furthermore, separate binary medical image classifications are implemented between each two-pair class of AD stages. Two methods are used to classify the medical images and detect AD. The first method uses simple CNN architectures that deal with 2D and 3D structural brain scans from the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset based on 2D and 3D convolution. The second method applies the transfer learning principle to take advantage of the pre-trained models for medical image classifications, such as the VGG19 model. Due to the COVID-19 pandemic, it is difficult for people to go to hospitals periodically to avoid gatherings and infections. As a result, Alzheimer's checking web application is proposed using the final qualified proposed architectures. It helps doctors and patients to check AD remotely. It also determines the AD stage of the patient based on the AD spectrum and advises the patient according to its AD stage. Nine performance metrics are used in the evaluation and the comparison between the two methods. The experimental results prove that the CNN architectures for the first method have the following characteristics: suitable simple structures that reduce computational complexity, memory requirements, overfitting, and provide manageable time. Besides, they achieve very promising accuracies, 93.61% and 95.17% for 2D and 3D multi-class AD stage classifications. The VGG19 pre-trained model is fine-tuned and achieved an accuracy of 97% for multi-class AD stage classifications.
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Affiliation(s)
- Hadeer A. Helaly
- Electrical Engineering Department, Faculty of Engineering, Damietta University, Damietta, Egypt
- Computers and Control Systems Engineering Department, Faculty of Engineering, Mansoura University, Mansoura, Egypt
| | - Mahmoud Badawy
- Computers and Control Systems Engineering Department, Faculty of Engineering, Mansoura University, Mansoura, Egypt
- Department of Computer Science and Informatics, Taibah University, Medina, Saudi Arabia
| | - Amira Y. Haikal
- Computers and Control Systems Engineering Department, Faculty of Engineering, Mansoura University, Mansoura, Egypt
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Yi HC, You ZH, Huang DS, Kwoh CK. Graph representation learning in bioinformatics: trends, methods and applications. Brief Bioinform 2021; 23:6361044. [PMID: 34471921 DOI: 10.1093/bib/bbab340] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/18/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022] Open
Abstract
Graph is a natural data structure for describing complex systems, which contains a set of objects and relationships. Ubiquitous real-life biomedical problems can be modeled as graph analytics tasks. Machine learning, especially deep learning, succeeds in vast bioinformatics scenarios with data represented in Euclidean domain. However, rich relational information between biological elements is retained in the non-Euclidean biomedical graphs, which is not learning friendly to classic machine learning methods. Graph representation learning aims to embed graph into a low-dimensional space while preserving graph topology and node properties. It bridges biomedical graphs and modern machine learning methods and has recently raised widespread interest in both machine learning and bioinformatics communities. In this work, we summarize the advances of graph representation learning and its representative applications in bioinformatics. To provide a comprehensive and structured analysis and perspective, we first categorize and analyze both graph embedding methods (homogeneous graph embedding, heterogeneous graph embedding, attribute graph embedding) and graph neural networks. Furthermore, we summarize their representative applications from molecular level to genomics, pharmaceutical and healthcare systems level. Moreover, we provide open resource platforms and libraries for implementing these graph representation learning methods and discuss the challenges and opportunities of graph representation learning in bioinformatics. This work provides a comprehensive survey of emerging graph representation learning algorithms and their applications in bioinformatics. It is anticipated that it could bring valuable insights for researchers to contribute their knowledge to graph representation learning and future-oriented bioinformatics studies.
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Affiliation(s)
- Hai-Cheng Yi
- Chinese Academy of Sciences, Xinjiang Technical Institute of Physics and Chemistry, Urumqi 830011, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhu-Hong You
- School of Computer Science, Northwestern Polytechnical University, Xi'an 710129, China
| | - De-Shuang Huang
- Institute of Machine Learning and Systems Biology, School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China
| | - Chee Keong Kwoh
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore
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20
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Ahmedt-Aristizabal D, Armin MA, Denman S, Fookes C, Petersson L. Graph-Based Deep Learning for Medical Diagnosis and Analysis: Past, Present and Future. SENSORS (BASEL, SWITZERLAND) 2021; 21:4758. [PMID: 34300498 PMCID: PMC8309939 DOI: 10.3390/s21144758] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 01/17/2023]
Abstract
With the advances of data-driven machine learning research, a wide variety of prediction problems have been tackled. It has become critical to explore how machine learning and specifically deep learning methods can be exploited to analyse healthcare data. A major limitation of existing methods has been the focus on grid-like data; however, the structure of physiological recordings are often irregular and unordered, which makes it difficult to conceptualise them as a matrix. As such, graph neural networks have attracted significant attention by exploiting implicit information that resides in a biological system, with interacting nodes connected by edges whose weights can be determined by either temporal associations or anatomical junctions. In this survey, we thoroughly review the different types of graph architectures and their applications in healthcare. We provide an overview of these methods in a systematic manner, organized by their domain of application including functional connectivity, anatomical structure, and electrical-based analysis. We also outline the limitations of existing techniques and discuss potential directions for future research.
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Affiliation(s)
- David Ahmedt-Aristizabal
- Imaging and Computer Vision Group, CSIRO Data61, Canberra 2601, Australia; (M.A.A.); (L.P.)
- Signal Processing, Artificial Intelligence and Vision Technologies (SAIVT) Research Program, Queensland University of Technology, Brisbane 4000, Australia; (S.D.); (C.F.)
| | - Mohammad Ali Armin
- Imaging and Computer Vision Group, CSIRO Data61, Canberra 2601, Australia; (M.A.A.); (L.P.)
| | - Simon Denman
- Signal Processing, Artificial Intelligence and Vision Technologies (SAIVT) Research Program, Queensland University of Technology, Brisbane 4000, Australia; (S.D.); (C.F.)
| | - Clinton Fookes
- Signal Processing, Artificial Intelligence and Vision Technologies (SAIVT) Research Program, Queensland University of Technology, Brisbane 4000, Australia; (S.D.); (C.F.)
| | - Lars Petersson
- Imaging and Computer Vision Group, CSIRO Data61, Canberra 2601, Australia; (M.A.A.); (L.P.)
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22
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Abstract
Electroencephalogram signals are used to assess neurodegenerative diseases and develop sophisticated brain machine interfaces for rehabilitation and gaming. Most of the applications use only motor imagery or evoked potentials. Here, a deep learning network based on a sensory motor paradigm (auditory, olfactory, movement, and motor-imagery) that employs a subject-agnostic Bidirectional Long Short-Term Memory (BLSTM) Network is developed to assess cognitive functions and identify its relationship with brain signal features, which is hypothesized to consistently indicate cognitive decline. Testing occurred with healthy subjects of age 20–40, 40–60, and >60, and mildly cognitive impaired subjects. Auditory and olfactory stimuli were presented to the subjects and the subjects imagined and conducted movement of each arm during which Electroencephalogram (EEG)/Electromyogram (EMG) signals were recorded. A deep BLSTM Neural Network is trained with Principal Component features from evoked signals and assesses their corresponding pathways. Wavelet analysis is used to decompose evoked signals and calculate the band power of component frequency bands. This deep learning system performs better than conventional deep neural networks in detecting MCI. Most features studied peaked at the age range 40–60 and were lower for the MCI group than for any other group tested. Detection accuracy of left-hand motor imagery signals best indicated cognitive aging (p = 0.0012); here, the mean classification accuracy per age group declined from 91.93% to 81.64%, and is 69.53% for MCI subjects. Motor-imagery-evoked band power, particularly in gamma bands, best indicated (p = 0.007) cognitive aging. Although the classification accuracy of the potentials effectively distinguished cognitive aging from MCI (p < 0.05), followed by gamma-band power.
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Zhang L, Wang M, Liu M, Zhang D. A Survey on Deep Learning for Neuroimaging-Based Brain Disorder Analysis. Front Neurosci 2020; 14:779. [PMID: 33117114 PMCID: PMC7578242 DOI: 10.3389/fnins.2020.00779] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 06/02/2020] [Indexed: 12/12/2022] Open
Abstract
Deep learning has recently been used for the analysis of neuroimages, such as structural magnetic resonance imaging (MRI), functional MRI, and positron emission tomography (PET), and it has achieved significant performance improvements over traditional machine learning in computer-aided diagnosis of brain disorders. This paper reviews the applications of deep learning methods for neuroimaging-based brain disorder analysis. We first provide a comprehensive overview of deep learning techniques and popular network architectures by introducing various types of deep neural networks and recent developments. We then review deep learning methods for computer-aided analysis of four typical brain disorders, including Alzheimer's disease, Parkinson's disease, Autism spectrum disorder, and Schizophrenia, where the first two diseases are neurodegenerative disorders and the last two are neurodevelopmental and psychiatric disorders, respectively. More importantly, we discuss the limitations of existing studies and present possible future directions.
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Affiliation(s)
- Li Zhang
- College of Computer Science and Technology, Nanjing Forestry University, Nanjing, China
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Mingliang Wang
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Mingxia Liu
- Department of Radiology and Biomedical Research Imaging Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Daoqiang Zhang
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, China
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