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Lei B, Li Y, Fu W, Yang P, Chen S, Wang T, Xiao X, Niu T, Fu Y, Wang S, Han H, Qin J. Alzheimer's disease diagnosis from multi-modal data via feature inductive learning and dual multilevel graph neural network. Med Image Anal 2024; 97:103213. [PMID: 38850625 DOI: 10.1016/j.media.2024.103213] [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: 09/12/2023] [Revised: 05/13/2024] [Accepted: 05/17/2024] [Indexed: 06/10/2024]
Abstract
Multi-modal data can provide complementary information of Alzheimer's disease (AD) and its development from different perspectives. Such information is closely related to the diagnosis, prevention, and treatment of AD, and hence it is necessary and critical to study AD through multi-modal data. Existing learning methods, however, usually ignore the influence of feature heterogeneity and directly fuse features in the last stages. Furthermore, most of these methods only focus on local fusion features or global fusion features, neglecting the complementariness of features at different levels and thus not sufficiently leveraging information embedded in multi-modal data. To overcome these shortcomings, we propose a novel framework for AD diagnosis that fuses gene, imaging, protein, and clinical data. Our framework learns feature representations under the same feature space for different modalities through a feature induction learning (FIL) module, thereby alleviating the impact of feature heterogeneity. Furthermore, in our framework, local and global salient multi-modal feature interaction information at different levels is extracted through a novel dual multilevel graph neural network (DMGNN). We extensively validate the proposed method on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset and experimental results demonstrate our method consistently outperforms other state-of-the-art multi-modal fusion methods. The code is publicly available on the GitHub website. (https://github.com/xiankantingqianxue/MIA-code.git).
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Affiliation(s)
- Baiying Lei
- National-Regional Key Technology Engineering Lab. for Medical Ultrasound, Guangdong Key Lab. for Biomedical Measurements and Ultrasound Imaging, Marshall Lab. of Biomedical Engineering, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Yafeng Li
- National-Regional Key Technology Engineering Lab. for Medical Ultrasound, Guangdong Key Lab. for Biomedical Measurements and Ultrasound Imaging, Marshall Lab. of Biomedical Engineering, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Wanyi Fu
- Department of Electronic Engineering, Tsinghua University, Beijing Key Laboratory of Magnetic Resonance Imaging Devices and Technology, China
| | - Peng Yang
- National-Regional Key Technology Engineering Lab. for Medical Ultrasound, Guangdong Key Lab. for Biomedical Measurements and Ultrasound Imaging, Marshall Lab. of Biomedical Engineering, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Shaobin Chen
- National-Regional Key Technology Engineering Lab. for Medical Ultrasound, Guangdong Key Lab. for Biomedical Measurements and Ultrasound Imaging, Marshall Lab. of Biomedical Engineering, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Tianfu Wang
- National-Regional Key Technology Engineering Lab. for Medical Ultrasound, Guangdong Key Lab. for Biomedical Measurements and Ultrasound Imaging, Marshall Lab. of Biomedical Engineering, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Xiaohua Xiao
- The First Affiliated Hospital of Shenzhen University, Shenzhen University Medical School, Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 530031, China
| | - Tianye Niu
- Shenzhen Bay Laboratory, Shenzhen, 518067, China
| | - Yu Fu
- Department of Neurology, Peking University Third Hospital, No. 49, North Garden Rd., Haidian District, Beijing, 100191, China.
| | - Shuqiang Wang
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Hongbin Han
- Institute of Medical Technology, Peking University Health Science Center, Department of Radiology, Peking University Third Hospital, Beijing Key Laboratory of Magnetic Resonance Imaging Devices and Technology, Beijing, 100191, China; The second hospital of Dalian Medical University,Research and developing center of medical technology, Dalian, 116027, China.
| | - Jing Qin
- Center for Smart Health, School of Nursing, The Hong Kong Polytechnic University, Hong Kong, China
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Jiao CN, Shang J, Li F, Cui X, Wang YL, Gao YL, Liu JX. Diagnosis-Guided Deep Subspace Clustering Association Study for Pathogenetic Markers Identification of Alzheimer's Disease Based on Comparative Atlases. IEEE J Biomed Health Inform 2024; 28:3029-3041. [PMID: 38427553 DOI: 10.1109/jbhi.2024.3372294] [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: 03/03/2024]
Abstract
The roles of brain region activities and genotypic functions in the pathogenesis of Alzheimer's disease (AD) remain unclear. Meanwhile, current imaging genetics methods are difficult to identify potential pathogenetic markers by correlation analysis between brain network and genetic variation. To discover disease-related brain connectome from the specific brain structure and the fine-grained level, based on the Automated Anatomical Labeling (AAL) and human Brainnetome atlases, the functional brain network is first constructed for each subject. Specifically, the upper triangle elements of the functional connectivity matrix are extracted as connectivity features. The clustering coefficient and the average weighted node degree are developed to assess the significance of every brain area. Since the constructed brain network and genetic data are characterized by non-linearity, high-dimensionality, and few subjects, the deep subspace clustering algorithm is proposed to reconstruct the original data. Our multilayer neural network helps capture the non-linear manifolds, and subspace clustering learns pairwise affinities between samples. Moreover, most approaches in neuroimaging genetics are unsupervised learning, neglecting the diagnostic information related to diseases. We presented a label constraint with diagnostic status to instruct the imaging genetics correlation analysis. To this end, a diagnosis-guided deep subspace clustering association (DDSCA) method is developed to discover brain connectome and risk genetic factors by integrating genotypes with functional network phenotypes. Extensive experiments prove that DDSCA achieves superior performance to most association methods and effectively selects disease-relevant genetic markers and brain connectome at the coarse-grained and fine-grained levels.
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Zhang P, Zhang W, Sun W, Xu J, Hu H, Wang L, Wong L. Identification of gene biomarkers for brain diseases via multi-network topological semantics extraction and graph convolutional network. BMC Genomics 2024; 25:175. [PMID: 38350848 PMCID: PMC10865627 DOI: 10.1186/s12864-024-09967-9] [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: 09/06/2023] [Accepted: 01/03/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Brain diseases pose a significant threat to human health, and various network-based methods have been proposed for identifying gene biomarkers associated with these diseases. However, the brain is a complex system, and extracting topological semantics from different brain networks is necessary yet challenging to identify pathogenic genes for brain diseases. RESULTS In this study, we present a multi-network representation learning framework called M-GBBD for the identification of gene biomarker in brain diseases. Specifically, we collected multi-omics data to construct eleven networks from different perspectives. M-GBBD extracts the spatial distributions of features from these networks and iteratively optimizes them using Kullback-Leibler divergence to fuse the networks into a common semantic space that represents the gene network for the brain. Subsequently, a graph consisting of both gene and large-scale disease proximity networks learns representations through graph convolution techniques and predicts whether a gene is associated which brain diseases while providing associated scores. Experimental results demonstrate that M-GBBD outperforms several baseline methods. Furthermore, our analysis supported by bioinformatics revealed CAMP as a significantly associated gene with Alzheimer's disease identified by M-GBBD. CONCLUSION Collectively, M-GBBD provides valuable insights into identifying gene biomarkers for brain diseases and serves as a promising framework for brain networks representation learning.
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Affiliation(s)
- Ping Zhang
- College of Information Science and Engineering, Zaozhuang University, Zaozhuang, 277100, Shandong, China
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Weihan Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Hubei Hongshan Laboratory, Wuhan, 430074, China
| | - Weicheng Sun
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinsheng Xu
- College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hua Hu
- College of Information Science and Engineering, Zaozhuang University, Zaozhuang, 277100, Shandong, China.
| | - Lei Wang
- College of Information Science and Engineering, Zaozhuang University, Zaozhuang, 277100, Shandong, China.
- Guangxi Key Lab of Human-Machine Interaction and Intelligent Decision, Guangxi Academy of Sciences, Nanning, 530007, China.
| | - Leon Wong
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen, 518118, China.
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Wen J, Gao Y, Li M, Hu S, Zhao M, Su C, Wang Q, Xi H, Zhan L, Lv Y, Antwi CO, Ren J, Jia X. Regional abnormalities of spontaneous brain activity in migraine: A coordinate‐based meta‐analysis. J Neurosci Res 2023. [DOI: 10.1002/jnr.25191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/17/2023] [Accepted: 03/13/2023] [Indexed: 04/03/2023]
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Ma H, Cao Y, Li M, Zhan L, Xie Z, Huang L, Gao Y, Jia X. Abnormal amygdala functional connectivity and deep learning classification in multifrequency bands in autism spectrum disorder: A multisite functional magnetic resonance imaging study. Hum Brain Mapp 2023; 44:1094-1104. [PMID: 36346215 PMCID: PMC9875923 DOI: 10.1002/hbm.26141] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 11/11/2022] Open
Abstract
Previous studies have explored resting-state functional connectivity (rs-FC) of the amygdala in patients with autism spectrum disorder (ASD). However, it remains unclear whether there are frequency-specific FC alterations of the amygdala in ASD and whether FC in specific frequency bands can be used to distinguish patients with ASD from typical controls (TCs). Data from 306 patients with ASD and 314 age-matched and sex-matched TCs were collected from 28 sites in the Autism Brain Imaging Data Exchange database. The bilateral amygdala, defined as the seed regions, was used to perform seed-based FC analyses in the conventional, slow-5, and slow-4 frequency bands at each site. Image-based meta-analyses were used to obtain consistent brain regions across 28 sites in the three frequency bands. By combining generative adversarial networks and deep neural networks, a deep learning approach was applied to distinguish patients with ASD from TCs. The meta-analysis results showed frequency band specificity of FC in ASD, which was reflected in the slow-5 frequency band instead of the conventional and slow-4 frequency bands. The deep learning results showed that, compared with the conventional and slow-4 frequency bands, the slow-5 frequency band exhibited a higher accuracy of 74.73%, precision of 74.58%, recall of 75.05%, and area under the curve of 0.811 to distinguish patients with ASD from TCs. These findings may help us to understand the pathological mechanisms of ASD and provide preliminary guidance for the clinical diagnosis of ASD.
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Affiliation(s)
- Huibin Ma
- School of Information and Electronics Technology, Jiamusi University, Jiamusi, China
| | - Yikang Cao
- School of Information and Electronics Technology, Jiamusi University, Jiamusi, China
| | - Mengting Li
- College of Teacher Education, Zhejiang Normal University, Jinhua, China.,Key Laboratory of Intelligent Education Technology and Application, Zhejiang Normal University, Jinhua, China
| | - Linlin Zhan
- Faculty of Western Languages, Heilongjiang University, Harbin, China
| | - Zhou Xie
- School of Information and Electronics Technology, Jiamusi University, Jiamusi, China
| | - Lina Huang
- Department of Radiology, Changshu No. 2 People's Hospital, The Affiliated Changshu Hospital of Xuzhou Medical University, Changshu, China
| | - Yanyan Gao
- College of Teacher Education, Zhejiang Normal University, Jinhua, China.,Key Laboratory of Intelligent Education Technology and Application, Zhejiang Normal University, Jinhua, China
| | - Xize Jia
- Department of Radiology, Changshu No. 2 People's Hospital, The Affiliated Changshu Hospital of Xuzhou Medical University, Changshu, China
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