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Wang S, Tang H, Himeno R, Solé-Casals J, Caiafa CF, Han S, Aoki S, Sun Z. Optimizing graph neural network architectures for schizophrenia spectrum disorder prediction using evolutionary algorithms. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2024; 257:108419. [PMID: 39293231 DOI: 10.1016/j.cmpb.2024.108419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 09/01/2024] [Accepted: 09/08/2024] [Indexed: 09/20/2024]
Abstract
BACKGROUND AND OBJECTIVE The accurate diagnosis of schizophrenia spectrum disorder plays an important role in improving patient outcomes, enabling timely interventions, and optimizing treatment plans. Functional connectivity analysis, utilizing functional magnetic resonance imaging data, has been demonstrated to offer invaluable biomarkers conducive to clinical diagnosis. However, previous studies mainly focus on traditional machine learning methods or hand-crafted neural networks, which may not fully capture the spatial topological relationship between brain regions. METHODS This paper proposes an evolutionary algorithm (EA) based graph neural architecture search (GNAS) method. EA-GNAS has the ability to search for high-performance graph neural networks for schizophrenia spectrum disorder prediction. Moreover, we adopt GNNExplainer to investigate the explainability of the acquired architectures, ensuring that the model's predictions are both accurate and comprehensible. RESULTS The results suggest that the graph neural network model, derived using genetic algorithm search, outperforms under five-fold cross-validation, achieving a fitness of 0.1850. Relative to conventional machine learning and other deep learning approaches, the proposed method yields superior accuracy, F1 score, and AUC values of 0.8246, 0.8438, and 0.8258, respectively. CONCLUSION Based on a multi-site dataset from schizophrenia spectrum disorder patients, the findings reveal an enhancement over prior methods, advancing our comprehension of brain function and potentially offering a biomarker for diagnosing schizophrenia spectrum disorder.
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Affiliation(s)
- Shurun Wang
- School of Information Science and Technology, University of Science and Technology of China, Hefei, 230027, China; School of Electrical Engineering and Automation, Hefei University of Technology, Hefei, 230009, China; Graduate School of Medicine, Juntendo University, Tokyo, 1138421, Japan.
| | - Hao Tang
- School of Electrical Engineering and Automation, Hefei University of Technology, Hefei, 230009, China; Industrial Automation Engineering Technology Research Center of Anhui Province, Hefei, 230009, China
| | - Ryutaro Himeno
- Graduate School of Medicine, Juntendo University, Tokyo, 1138421, Japan
| | - Jordi Solé-Casals
- Data and Signal Processing Research Group, University of Vic-Central University of Catalonia, Vic, 08500, Spain; Department of Psychiatry, University of Cambridge, Cambridge, CB2 3EB, United Kingdom
| | - Cesar F Caiafa
- Instituto Argentino de Radioastronomía-CONICET CCT La Plata/CIC-PBA/UNLP, V. Elisa, 1894, Argentina
| | - Shuning Han
- Data and Signal Processing Research Group, University of Vic-Central University of Catalonia, Vic, 08500, Spain; Image Processing Research Group, RIKEN Center for Advanced Photonics, RIKEN, Wako-Shi, Saitama, 351-0198, Japan
| | - Shigeki Aoki
- Graduate School of Medicine, Juntendo University, Tokyo, 1138421, Japan
| | - Zhe Sun
- Graduate School of Medicine, Juntendo University, Tokyo, 1138421, Japan.
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Yang Y, Luo S, Wang W, Gao X, Yao X, Wu T. From bench to bedside: Overview of magnetoencephalography in basic principle, signal processing, source localization and clinical applications. Neuroimage Clin 2024; 42:103608. [PMID: 38653131 PMCID: PMC11059345 DOI: 10.1016/j.nicl.2024.103608] [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: 11/22/2023] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
Magnetoencephalography (MEG) is a non-invasive technique that can precisely capture the dynamic spatiotemporal patterns of the brain by measuring the magnetic fields arising from neuronal activity along the order of milliseconds. Observations of brain dynamics have been used in cognitive neuroscience, the diagnosis of neurological diseases, and the brain-computer interface (BCI). In this study, we outline the basic principle, signal processing, and source localization of MEG, and describe its clinical applications for cognitive assessment, the diagnoses of neurological diseases and mental disorders, preoperative evaluation, and the BCI. This review not only provides an overall perspective of MEG, ranging from practical techniques to clinical applications, but also enhances the prevalent understanding of neural mechanisms. The use of MEG is expected to lead to significant breakthroughs in neuroscience.
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Affiliation(s)
- Yanling Yang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China; College of Medical Imaging, Jiading District Central Hospital Affiliated Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Shichang Luo
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China; College of Medical Imaging, Jiading District Central Hospital Affiliated Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Wenjie Wang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China; College of Medical Imaging, Jiading District Central Hospital Affiliated Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Xiumin Gao
- School of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Xufeng Yao
- College of Medical Imaging, Jiading District Central Hospital Affiliated Shanghai University of Medicine and Health Sciences, Shanghai, China.
| | - Tao Wu
- College of Medical Imaging, Jiading District Central Hospital Affiliated Shanghai University of Medicine and Health Sciences, Shanghai, China
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Zheng K, Yu S, Chen L, Dang L, Chen B. BPI-GNN: Interpretable brain network-based psychiatric diagnosis and subtyping. Neuroimage 2024; 292:120594. [PMID: 38569980 DOI: 10.1016/j.neuroimage.2024.120594] [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: 11/03/2023] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 04/05/2024] Open
Abstract
Converging evidence increasingly suggests that psychiatric disorders, such as major depressive disorder (MDD) and autism spectrum disorder (ASD), are not unitary diseases, but rather heterogeneous syndromes that involve diverse, co-occurring symptoms and divergent responses to treatment. This clinical heterogeneity has hindered the progress of precision diagnosis and treatment effectiveness in psychiatric disorders. In this study, we propose BPI-GNN, a new interpretable graph neural network (GNN) framework for analyzing functional magnetic resonance images (fMRI), by leveraging the famed prototype learning. In addition, we introduce a novel generation process of prototype subgraph to discover essential edges of distinct prototypes and employ total correlation (TC) to ensure the independence of distinct prototype subgraph patterns. BPI-GNN can effectively discriminate psychiatric patients and healthy controls (HC), and identify biological meaningful subtypes of psychiatric disorders. We evaluate the performance of BPI-GNN against 11 popular brain network classification methods on three psychiatric datasets and observe that our BPI-GNN always achieves the highest diagnosis accuracy. More importantly, we examine differences in clinical symptom profiles and gene expression profiles among identified subtypes and observe that our identified brain-based subtypes have the clinical relevance. It also discovers the subtype biomarkers that align with current neuro-scientific knowledge.
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Affiliation(s)
- Kaizhong Zheng
- National Key Laboratory of Human-Machine Hybrid Augmented Intelligence, National Engineering Research Center for Visual Information and Applications, and Institute of Artificial Intelligence and Robotics, Xi'an Jiaotong University, Xi'an, China.
| | - Shujian Yu
- Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands; Machine Learning Group, UiT - Arctic University of Norway, Tromsø, Norway.
| | - Liangjun Chen
- National Key Laboratory of Human-Machine Hybrid Augmented Intelligence, National Engineering Research Center for Visual Information and Applications, and Institute of Artificial Intelligence and Robotics, Xi'an Jiaotong University, Xi'an, China.
| | - Lujuan Dang
- National Key Laboratory of Human-Machine Hybrid Augmented Intelligence, National Engineering Research Center for Visual Information and Applications, and Institute of Artificial Intelligence and Robotics, Xi'an Jiaotong University, Xi'an, China.
| | - Badong Chen
- National Key Laboratory of Human-Machine Hybrid Augmented Intelligence, National Engineering Research Center for Visual Information and Applications, and Institute of Artificial Intelligence and Robotics, Xi'an Jiaotong University, Xi'an, China.
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Alharthi AG, Alzahrani SM. Do it the transformer way: A comprehensive review of brain and vision transformers for autism spectrum disorder diagnosis and classification. Comput Biol Med 2023; 167:107667. [PMID: 37939407 DOI: 10.1016/j.compbiomed.2023.107667] [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: 06/17/2023] [Revised: 10/25/2023] [Accepted: 10/31/2023] [Indexed: 11/10/2023]
Abstract
Autism spectrum disorder (ASD) is a condition observed in children who display abnormal patterns of interaction, behavior, and communication with others. Despite extensive research efforts, the underlying causes of this neurodevelopmental disorder and its biomarkers remain unknown. However, advancements in artificial intelligence and machine learning have improved clinicians' ability to diagnose ASD. This review paper investigates various MRI modalities to identify distinct features that characterize individuals with ASD compared to typical control subjects. The review then moves on to explore deep learning models for ASD diagnosis, including convolutional neural networks (CNNs), autoencoders, graph convolutions, attention networks, and other models. CNNs and their variations are particularly effective due to their capacity to learn structured image representations and identify reliable biomarkers for brain disorders. Computer vision transformers often employ CNN architectures with transfer learning techniques like fine-tuning and layer freezing to enhance image classification performance, surpassing traditional machine learning models. This review paper contributes in three main ways. Firstly, it provides a comprehensive overview of a recommended architecture for using vision transformers in the systematic ASD diagnostic process. To this end, the paper investigates various pre-trained vision architectures such as VGG, ResNet, Inception, InceptionResNet, DenseNet, and Swin models that were fine-tuned for ASD diagnosis and classification. Secondly, it discusses the vision transformers of 2020th like BiT, ViT, MobileViT, and ConvNeXt, and applying transfer learning methods in relation to their prospective practicality in ASD classification. Thirdly, it explores brain transformers that are pre-trained on medically rich data and MRI neuroimaging datasets. The paper recommends a systematic architecture for ASD diagnosis using brain transformers. It also reviews recently developed brain transformer-based models, such as METAFormer, Com-BrainTF, Brain Network, ST-Transformer, STCAL, BolT, and BrainFormer, discussing their deep transfer learning architectures and results in ASD detection. Additionally, the paper summarizes and discusses brain-related transformers for various brain disorders, such as MSGTN, STAGIN, and MedTransformer, in relation to their potential usefulness in ASD. The study suggests that developing specialized transformer-based models, following the success of natural language processing (NLP), can offer new directions for image classification problems in ASD brain biomarkers learning and classification. By incorporating the attention mechanism, treating MRI modalities as sequence prediction tasks trained on brain disorder classification problems, and fine-tuned on ASD datasets, brain transformers can show a great promise in ASD diagnosis.
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Affiliation(s)
- Asrar G Alharthi
- Department of Computer Science, College of Computers and Information Technology, Taif University, Saudi Arabia.
| | - Salha M Alzahrani
- Department of Computer Science, College of Computers and Information Technology, Taif University, Saudi Arabia
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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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Pisarchik AN, Andreev AV, Kurkin SA, Stoyanov D, Badarin AA, Paunova R, Hramov AE. Topology switching during window thresholding fMRI-based functional networks of patients with major depressive disorder: Consensus network approach. CHAOS (WOODBURY, N.Y.) 2023; 33:093122. [PMID: 37712918 DOI: 10.1063/5.0166148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/29/2023] [Indexed: 09/16/2023]
Abstract
We present a novel method for analyzing brain functional networks using functional magnetic resonance imaging data, which involves utilizing consensus networks. In this study, we compare our approach to a standard group-based method for patients diagnosed with major depressive disorder (MDD) and a healthy control group, taking into account different levels of connectivity. Our findings demonstrate that the consensus network approach uncovers distinct characteristics in network measures and degree distributions when considering connection strengths. In the healthy control group, as connection strengths increase, we observe a transition in the network topology from a combination of scale-free and random topologies to a small-world topology. Conversely, the MDD group exhibits uncertainty in weak connections, while strong connections display small-world properties. In contrast, the group-based approach does not exhibit significant differences in behavior between the two groups. However, it does indicate a transition in topology from a scale-free-like structure to a combination of small-world and scale-free topologies. The use of the consensus network approach also holds immense potential for the classification of MDD patients, as it unveils substantial distinctions between the two groups.
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Affiliation(s)
- Alexander N Pisarchik
- Baltic Center for Neurotechnology and Artificial Intelligence, Immanuel Kant Baltic Federal University, 14, A. Nevskogo Str., Kaliningrad 236016, Russia
- Center for Biomedical Technology, Universidad Politécnica de Madrid, Campus Montegancedo, Pozuelo de Alarcón 28223, Spain
| | - Andrey V Andreev
- Baltic Center for Neurotechnology and Artificial Intelligence, Immanuel Kant Baltic Federal University, 14, A. Nevskogo Str., Kaliningrad 236016, Russia
| | - Semen A Kurkin
- Baltic Center for Neurotechnology and Artificial Intelligence, Immanuel Kant Baltic Federal University, 14, A. Nevskogo Str., Kaliningrad 236016, Russia
| | - Drozdstoy Stoyanov
- Department of Psychiatry and Medical Psychology, Research Institute, Medical University Plovdiv, 15A Vassil Aprilov Blvd., Plovdiv 4002, Bulgaria
| | - Artem A Badarin
- Baltic Center for Neurotechnology and Artificial Intelligence, Immanuel Kant Baltic Federal University, 14, A. Nevskogo Str., Kaliningrad 236016, Russia
| | - Rossitsa Paunova
- Department of Psychiatry and Medical Psychology, Research Institute, Medical University Plovdiv, 15A Vassil Aprilov Blvd., Plovdiv 4002, Bulgaria
| | - Alexander E Hramov
- Baltic Center for Neurotechnology and Artificial Intelligence, Immanuel Kant Baltic Federal University, 14, A. Nevskogo Str., Kaliningrad 236016, Russia
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7
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Karpov OE, Pitsik EN, Kurkin SA, Maksimenko VA, Gusev AV, Shusharina NN, Hramov AE. Analysis of Publication Activity and Research Trends in the Field of AI Medical Applications: Network Approach. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:5335. [PMID: 37047950 PMCID: PMC10094658 DOI: 10.3390/ijerph20075335] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/17/2023] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Artificial intelligence (AI) has revolutionized numerous industries, including medicine. In recent years, the integration of AI into medical practices has shown great promise in enhancing the accuracy and efficiency of diagnosing diseases, predicting patient outcomes, and personalizing treatment plans. This paper aims at the exploration of the AI-based medicine research using network approach and analysis of existing trends based on PubMed. Our findings are based on the results of PubMed search queries and analysis of the number of papers obtained by the different search queries. Our goal is to explore how are the AI-based methods used in healthcare research, which approaches and techniques are the most popular, and to discuss the potential reasoning behind the obtained results. Using analysis of the co-occurrence network constructed using VOSviewer software, we detected the main clusters of interest in AI-based healthcare research. Then, we proceeded with the thorough analysis of publication activity in various categories of medical AI research, including research on different AI-based methods applied to different types of medical data. We analyzed the results of query processing in the PubMed database over the past 5 years obtained via a specifically designed strategy for generating search queries based on the thorough selection of keywords from different categories of interest. We provide a comprehensive analysis of existing applications of AI-based methods to medical data of different modalities, including the context of various medical fields and specific diseases that carry the greatest danger to the human population.
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Affiliation(s)
- Oleg E. Karpov
- National Medical and Surgical Center Named after N. I. Pirogov, Ministry of Healthcare of the Russian Federation, 105203 Moscow, Russia
| | - Elena N. Pitsik
- Baltic Center for Neurotechnology and Artificial Intelligence, Immanuel Kant Baltic Federal University, 236041 Kaliningrad, Russia; (E.N.P.); (S.A.K.); (V.A.M.); (N.N.S.)
| | - Semen A. Kurkin
- Baltic Center for Neurotechnology and Artificial Intelligence, Immanuel Kant Baltic Federal University, 236041 Kaliningrad, Russia; (E.N.P.); (S.A.K.); (V.A.M.); (N.N.S.)
| | - Vladimir A. Maksimenko
- Baltic Center for Neurotechnology and Artificial Intelligence, Immanuel Kant Baltic Federal University, 236041 Kaliningrad, Russia; (E.N.P.); (S.A.K.); (V.A.M.); (N.N.S.)
| | - Alexander V. Gusev
- K-Skai LLC, 185031 Petrozavodsk, Russia
- Federal Research Institute for Health Organization and Informatics, 127254 Moscow, Russia
| | - Natali N. Shusharina
- Baltic Center for Neurotechnology and Artificial Intelligence, Immanuel Kant Baltic Federal University, 236041 Kaliningrad, Russia; (E.N.P.); (S.A.K.); (V.A.M.); (N.N.S.)
| | - Alexander E. Hramov
- Baltic Center for Neurotechnology and Artificial Intelligence, Immanuel Kant Baltic Federal University, 236041 Kaliningrad, Russia; (E.N.P.); (S.A.K.); (V.A.M.); (N.N.S.)
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