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Ou Z, Wang H, Zhang B, Liang H, Hu B, Ren L, Liu Y, Zhang Y, Dai C, Wu H, Li W, Li X. Early identification of stroke through deep learning with multi-modal human speech and movement data. Neural Regen Res 2025; 20:234-241. [PMID: 38767488 DOI: 10.4103/1673-5374.393103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/21/2023] [Indexed: 05/22/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202501000-00031/figure1/v/2024-05-14T021156Z/r/image-tiff Early identification and treatment of stroke can greatly improve patient outcomes and quality of life. Although clinical tests such as the Cincinnati Pre-hospital Stroke Scale (CPSS) and the Face Arm Speech Test (FAST) are commonly used for stroke screening, accurate administration is dependent on specialized training. In this study, we proposed a novel multimodal deep learning approach, based on the FAST, for assessing suspected stroke patients exhibiting symptoms such as limb weakness, facial paresis, and speech disorders in acute settings. We collected a dataset comprising videos and audio recordings of emergency room patients performing designated limb movements, facial expressions, and speech tests based on the FAST. We compared the constructed deep learning model, which was designed to process multi-modal datasets, with six prior models that achieved good action classification performance, including the I3D, SlowFast, X3D, TPN, TimeSformer, and MViT. We found that the findings of our deep learning model had a higher clinical value compared with the other approaches. Moreover, the multi-modal model outperformed its single-module variants, highlighting the benefit of utilizing multiple types of patient data, such as action videos and speech audio. These results indicate that a multi-modal deep learning model combined with the FAST could greatly improve the accuracy and sensitivity of early stroke identification of stroke, thus providing a practical and powerful tool for assessing stroke patients in an emergency clinical setting.
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Affiliation(s)
- Zijun Ou
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Haitao Wang
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Bin Zhang
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, China
| | - Haobang Liang
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Bei Hu
- Department of Emergency Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, China
| | - Longlong Ren
- Department of Emergency Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, China
| | - Yanjuan Liu
- Department of Emergency Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, China
| | - Yuhu Zhang
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, China
| | - Chengbo Dai
- Department of Neurology, Guangdong Neuroscience Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, China
| | - Hejun Wu
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Weifeng Li
- Department of Emergency Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, China
| | - Xin Li
- Department of Emergency Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, China
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2
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Shimakawa H, Kumada A, Sato M. Prevention of Leakage in Machine Learning Prediction for Polymer Composite Properties. J Chem Inf Model 2024; 64:3621-3629. [PMID: 38642039 DOI: 10.1021/acs.jcim.3c01894] [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: 04/22/2024]
Abstract
Machine learning (ML) has facilitated property prediction for intricate materials by integrating materials and experimental features such as processing and measurement conditions. However, ML models designed for material properties have often disregarded a common issue of "leakage," resulting in an overestimation of model performance and a decrease in model transferability. This issue can arise from biases inherent in multiple data points obtained from the same experimental group. We provide a critical examination and prevention method of leakage in property prediction for polymer composites. Our proposed method utilizes data partitioning based on the experimental group to ensure that data from the same group are not mixed in both the training and test sets. Evaluation results highlight that the conventional random partitioning unintentionally inflates ML performance through the misuse of experimental features for leaking data bias within the same experimental group rather than explaining the physical causality. In contrast, the proposed method enables the leakage-free utilization of experimental features to improve prediction accuracy while ensuring model transferability. Specifically, when integrating experimental features with polymer and filler features, the conventional method overestimates the prediction performance of electrical conductivity in reducing RMSE by 26% depending on leakage, whereas the proposed method achieves a reduction in RMSE by 5% without leakage. These findings offer valuable guidance for the effective utilization of experimental features in data-driven materials science.
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Affiliation(s)
- Hajime Shimakawa
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akiko Kumada
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Masahiro Sato
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-8656, Japan
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3
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Mehmood A, Shahid F, Khan R, Ibrahim MM, Zheng Z. Utilizing Siamese 4D-AlzNet and Transfer Learning to Identify Stages of Alzheimer's Disease. Neuroscience 2024; 545:69-85. [PMID: 38492797 DOI: 10.1016/j.neuroscience.2024.03.007] [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: 10/18/2023] [Revised: 03/05/2024] [Accepted: 03/10/2024] [Indexed: 03/18/2024]
Abstract
Alzheimer's disease (AD) is the general form of dementia, leading to a progressive neurological disorder characterized by memory loss due to brain cell damage. Artificial Intelligence (AI) assists in the early identification and prediction of AD patients, determining future risks and benefits for radiologists and doctors to save time and cost. Since deep learning (DL) approaches work well with massive datasets and have recently become helpful for AD detection, there remains an area for improvement in automating detection performance. Present approaches somehow addressed the challenges of limited annotated data samples for binary classification. This contrasts with prior state-of-the-art techniques, which were constrained by their incapacity to capture abstract-level information. In this paper, we proposed a Siamese 4D-AlzNet model comprised of four parallel convolutional neural network (CNN) streams (Five CNN layer blocks) and customized transfer learning models (Frozen VGG-19, Frozen VGG-16, and customized AlexNet). Siamese 4D-AlzNet was vertically and horizontally stored, and the spatial features were passed to the final layer for classification. For experiments, T1-weighted MRI images comprised of four distinct subject classes, normal control (NC), mild cognitive impairment (MCI), late mild cognitive impairment (LMCI), and AD, have been employed. Our proposed models achieved outstanding accuracy, with a remarkable 95.05% accuracy distinguishing between normal and AD subjects. The performance across remaining binary class pairs consistently exceeded 90%. We thoroughly compared our model with the latest methods using the same dataset as our reference. Our proposed model improved NC-AD and MCI-AD classification accuracy by 2% 7%.
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Affiliation(s)
- Atif Mehmood
- School of Computer Science and Technology, Zhejiang Normal University, Jinhua 321004, China; Zhejiang Institute of Photoelectronics & Zhejiang Institute for Advanced Light Source, Zhejiang Normal University, Jinhua, Zhejiang 321004, China
| | - Farah Shahid
- School of Computer Science and Technology, Zhejiang Normal University, Jinhua 321004, China; Zhejiang Institute of Photoelectronics & Zhejiang Institute for Advanced Light Source, Zhejiang Normal University, Jinhua, Zhejiang 321004, China.
| | - Rizwan Khan
- School of Computer Science and Technology, Zhejiang Normal University, Jinhua 321004, China
| | - Mostafa M Ibrahim
- Department of Electrical Engineering, Faculty of Engineering, Minia University, Minia 61519, Egypt
| | - Zhonglong Zheng
- School of Computer Science and Technology, Zhejiang Normal University, Jinhua 321004, China.
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4
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Brookshire G, Kasper J, Blauch NM, Wu YC, Glatt R, Merrill DA, Gerrol S, Yoder KJ, Quirk C, Lucero C. Data leakage in deep learning studies of translational EEG. Front Neurosci 2024; 18:1373515. [PMID: 38765672 PMCID: PMC11099244 DOI: 10.3389/fnins.2024.1373515] [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: 01/19/2024] [Accepted: 04/04/2024] [Indexed: 05/22/2024] Open
Abstract
A growing number of studies apply deep neural networks (DNNs) to recordings of human electroencephalography (EEG) to identify a range of disorders. In many studies, EEG recordings are split into segments, and each segment is randomly assigned to the training or test set. As a consequence, data from individual subjects appears in both the training and the test set. Could high test-set accuracy reflect data leakage from subject-specific patterns in the data, rather than patterns that identify a disease? We address this question by testing the performance of DNN classifiers using segment-based holdout (in which segments from one subject can appear in both the training and test set), and comparing this to their performance using subject-based holdout (where all segments from one subject appear exclusively in either the training set or the test set). In two datasets (one classifying Alzheimer's disease, and the other classifying epileptic seizures), we find that performance on previously-unseen subjects is strongly overestimated when models are trained using segment-based holdout. Finally, we survey the literature and find that the majority of translational DNN-EEG studies use segment-based holdout. Most published DNN-EEG studies may dramatically overestimate their classification performance on new subjects.
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Affiliation(s)
| | - Jake Kasper
- SPARK Neuro Inc., New York, NY, United States
| | - Nicholas M. Blauch
- SPARK Neuro Inc., New York, NY, United States
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, United States
| | | | - Ryan Glatt
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, United States
| | - David A. Merrill
- Pacific Brain Health Center, Pacific Neuroscience Institute and Foundation, Santa Monica, CA, United States
- Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, United States
- Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, United States
| | | | | | - Colin Quirk
- SPARK Neuro Inc., New York, NY, United States
| | - Ché Lucero
- SPARK Neuro Inc., New York, NY, United States
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Li L, Liang Z, Li G, Xu H, Yang X, Liu X, Zhang X, Wang J, Zhang Z, Zhou Y. Unveiling convergent and divergent intrinsic brain network alternations in depressed adolescents engaged in non-suicidal self-injurious behaviors with and without suicide attempts. CNS Neurosci Ther 2024; 30:e14684. [PMID: 38739217 PMCID: PMC11090151 DOI: 10.1111/cns.14684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/28/2024] [Accepted: 02/19/2024] [Indexed: 05/14/2024] Open
Abstract
AIMS Limited understanding exists regarding the neurobiological mechanisms underlying non-suicidal self-injury (NSSI) and suicide attempts (SA) in depressed adolescents. The maturation of brain network is crucial during adolescence, yet the abnormal alternations in depressed adolescents with NSSI or NSSI+SA remain poorly understood. METHODS Resting-state functional magnetic resonance imaging data were collected from 114 depressed adolescents, classified into three groups: clinical control (non-self-harm), NSSI only, and NSSI+SA based on self-harm history. The alternations of resting-state functional connectivity (RSFC) were identified through support vector machine-based classification. RESULTS Convergent alterations in NSSI and NSSI+SA predominantly centered on the inter-network RSFC between the Limbic network and the three core neurocognitive networks (SalVAttn, Control, and Default networks). Divergent alterations in the NSSI+SA group primarily focused on the Visual, Limbic, and Subcortical networks. Additionally, the severity of depressive symptoms only showed a significant correlation with altered RSFCs between Limbic and DorsAttn or Visual networks, strengthening the fact that increased depression severity alone does not fully explain observed FC alternations in the NSSI+SA group. CONCLUSION Convergent alterations suggest a shared neurobiological mechanism along the self-destructiveness continuum. Divergent alterations may indicate biomarkers differentiating risk for SA, informing neurobiologically guided interventions.
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Affiliation(s)
- Linling Li
- Guangdong Provincial Key Laboratory of Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, International Health Science Innovation Center, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Zhen Liang
- Guangdong Provincial Key Laboratory of Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, International Health Science Innovation Center, Shenzhen University Medical School, Shenzhen University, Shenzhen, China
| | - Guohua Li
- Department of Psychiatric Rehabilitation, Shenzhen Mental Health Center/Shenzhen Kangning Hospital, Shenzhen, China
| | - Hong Xu
- Department of Psychiatric Rehabilitation, Shenzhen Mental Health Center/Shenzhen Kangning Hospital, Shenzhen, China
| | - Xing Yang
- Department of Psychiatric Rehabilitation, Shenzhen Mental Health Center/Shenzhen Kangning Hospital, Shenzhen, China
| | - Xia Liu
- Department of Psychiatric Rehabilitation, Shenzhen Mental Health Center/Shenzhen Kangning Hospital, Shenzhen, China
| | - Xin Zhang
- Department of Psychiatric Rehabilitation, Shenzhen Mental Health Center/Shenzhen Kangning Hospital, Shenzhen, China
| | - Jianhong Wang
- Department of Psychiatric Rehabilitation, Shenzhen Mental Health Center/Shenzhen Kangning Hospital, Shenzhen, China
| | - Zhiguo Zhang
- Department of Computer Science and Technology, Harbin Institute of Technology, Peng Cheng Laboratory, Shenzhen, China
| | - Yongjie Zhou
- Department of Psychiatric Rehabilitation, Shenzhen Mental Health Center/Shenzhen Kangning Hospital, Shenzhen, China
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6
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Han K, Li G, Fang Z, Yang F. Multi-Template Meta-Information Regularized Network for Alzheimer's Disease Diagnosis Using Structural MRI. IEEE TRANSACTIONS ON MEDICAL IMAGING 2024; 43:1664-1676. [PMID: 38109240 DOI: 10.1109/tmi.2023.3344384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Structural magnetic resonance imaging (sMRI) has been widely applied in computer-aided Alzheimer's disease (AD) diagnosis, owing to its capabilities in providing detailed brain morphometric patterns and anatomical features in vivo. Although previous works have validated the effectiveness of incorporating metadata (e.g., age, gender, and educational years) for sMRI-based AD diagnosis, existing methods solely paid attention to metadata-associated correlation to AD (e.g., gender bias in AD prevalence) or confounding effects (e.g., the issue of normal aging and metadata-related heterogeneity). Hence, it is difficult to fully excavate the influence of metadata on AD diagnosis. To address these issues, we constructed a novel Multi-template Meta-information Regularized Network (MMRN) for AD diagnosis. Specifically, considering diagnostic variation resulting from different spatial transformations onto different brain templates, we first regarded different transformations as data augmentation for self-supervised learning after template selection. Since the confounding effects may arise from excessive attention to meta-information owing to its correlation with AD, we then designed the modules of weakly supervised meta-information learning and mutual information minimization to learn and disentangle meta-information from learned class-related representations, which accounts for meta-information regularization for disease diagnosis. We have evaluated our proposed MMRN on two public multi-center cohorts, including the Alzheimer's Disease Neuroimaging Initiative (ADNI) with 1,950 subjects and the National Alzheimer's Coordinating Center (NACC) with 1,163 subjects. The experimental results have shown that our proposed method outperformed the state-of-the-art approaches in both tasks of AD diagnosis, mild cognitive impairment (MCI) conversion prediction, and normal control (NC) vs. MCI vs. AD classification.
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Xia Z, Zhou T, Mamoon S, Lu J. Inferring brain causal and temporal-lag networks for recognizing abnormal patterns of dementia. Med Image Anal 2024; 94:103133. [PMID: 38458094 DOI: 10.1016/j.media.2024.103133] [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: 04/17/2022] [Revised: 11/21/2022] [Accepted: 03/01/2024] [Indexed: 03/10/2024]
Abstract
Brain functional network analysis has become a popular method to explore the laws of brain organization and identify biomarkers of neurological diseases. However, it is still a challenging task to construct an ideal brain network due to the limited understanding of the human brain. Existing methods often ignore the impact of temporal-lag on the results of brain network modeling, which may lead to some unreliable conclusions. To overcome this issue, we propose a novel brain functional network estimation method, which can simultaneously infer the causal mechanisms and temporal-lag values among brain regions. Specifically, our method converts the lag learning into an instantaneous effect estimation problem, and further embeds the search objectives into a deep neural network model as parameters to be learned. To verify the effectiveness of the proposed estimation method, we perform experiments on the Alzheimer's Disease Neuroimaging Initiative (ADNI) database by comparing the proposed model with several existing methods, including correlation-based and causality-based methods. The experimental results show that our brain networks constructed by the proposed estimation method can not only achieve promising classification performance, but also exhibit some characteristics of physiological mechanisms. Our approach provides a new perspective for understanding the pathogenesis of brain diseases. The source code is released at https://github.com/NJUSTxiazw/CTLN.
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Affiliation(s)
- Zhengwang Xia
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Tao Zhou
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Saqib Mamoon
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Jianfeng Lu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, China.
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8
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Yaqoob N, Khan MA, Masood S, Albarakati HM, Hamza A, Alhayan F, Jamel L, Masood A. Prediction of Alzheimer's disease stages based on ResNet-Self-attention architecture with Bayesian optimization and best features selection. Front Comput Neurosci 2024; 18:1393849. [PMID: 38725868 PMCID: PMC11081001 DOI: 10.3389/fncom.2024.1393849] [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: 02/29/2024] [Accepted: 03/28/2024] [Indexed: 05/12/2024] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative illness that impairs cognition, function, and behavior by causing irreversible damage to multiple brain areas, including the hippocampus. The suffering of the patients and their family members will be lessened with an early diagnosis of AD. The automatic diagnosis technique is widely required due to the shortage of medical experts and eases the burden of medical staff. The automatic artificial intelligence (AI)-based computerized method can help experts achieve better diagnosis accuracy and precision rates. This study proposes a new automated framework for AD stage prediction based on the ResNet-Self architecture and Fuzzy Entropy-controlled Path-Finding Algorithm (FEcPFA). A data augmentation technique has been utilized to resolve the dataset imbalance issue. In the next step, we proposed a new deep-learning model based on the self-attention module. A ResNet-50 architecture is modified and connected with a self-attention block for important information extraction. The hyperparameters were optimized using Bayesian optimization (BO) and then utilized to train the model, which was subsequently employed for feature extraction. The self-attention extracted features were optimized using the proposed FEcPFA. The best features were selected using FEcPFA and passed to the machine learning classifiers for the final classification. The experimental process utilized a publicly available MRI dataset and achieved an improved accuracy of 99.9%. The results were compared with state-of-the-art (SOTA) techniques, demonstrating the improvement of the proposed framework in terms of accuracy and time efficiency.
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Affiliation(s)
- Nabeela Yaqoob
- Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon
| | - Muhammad Attique Khan
- Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon
| | - Saleha Masood
- IRC for Finance and Digital Economy, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
| | - Hussain Mobarak Albarakati
- Department of Computer and Network Engineering, College of Computer and Information Systems, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ameer Hamza
- Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon
| | - Fatimah Alhayan
- Department of Information Systems, College of Computer and Information Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Leila Jamel
- Department of Information Systems, College of Computer and Information Sciences, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Anum Masood
- Department of Physics, Norwegian University of Science and Technology, Trondheim, Norway
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9
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Jomeiri A, Navin AH, Shamsi M. Longitudinal MRI analysis using a hybrid DenseNet-BiLSTM method for Alzheimer's disease prediction. Behav Brain Res 2024; 463:114900. [PMID: 38341100 DOI: 10.1016/j.bbr.2024.114900] [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: 07/30/2023] [Revised: 12/16/2023] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Alzheimer's disease is a progressive neurological disorder characterized by brain atrophy and cell death, leading to cognitive decline and impaired functioning. Previous research has primarily focused on using cross-sectional data for Alzheimer's disease identification, but analyzing longitudinal sequential MR images is crucial for improved diagnostic accuracy and understanding disease progression. However, existing deep learning models face challenges in learning spatial and temporal features from such data. To address these challenges, this study presents a novel hybrid DenseNet-BiLSTM method for Alzheimer's disease prediction using longitudinal MRI analysis. The proposed framework combines Convolutional DenseNet for spatial information extraction and joined BiLSTM layers for capturing temporal characteristics and relationships between longitudinal images at different time points. This approach overcomes issues like overfitting, vanishing gradients, and incomplete patient data. We evaluated the model on 684 longitudinal MRI images from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database, including normal controls, individuals with mild cognitive impairment, and Alzheimer's disease patients. The results demonstrate high classification accuracy, with 95.28% for AD/CN, 88.19% for NC/MCI, 83.51% for sMCI/pMCI, and 92.14% for MCI/AD. These findings highlight the substantial improvement in Alzheimer's disease diagnosis achieved through the utilization of longitudinal MRI images. The contributions of this study lie in both the deep learning and medical domains. In the deep learning domain, our hybrid framework effectively learns spatial and temporal features from longitudinal data, addressing the challenges associated with multi-dimensional and sequential time series data. In the medical domain, our study emphasizes the importance of analyzing baseline and longitudinal MR images for accurate diagnosis and understanding disease progression.
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Affiliation(s)
- Alireza Jomeiri
- Department of Computer Engineering, Qom Branch, Islamic Azad University, Qom, Iran
| | - Ahmad Habibizad Navin
- Department of Computer Engineering, Tabriz Branch, Islamic Azad University, Tabriz, Iran.
| | - Mahboubeh Shamsi
- Department of Engineering, Qom University of Technology, Qom, Iran
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Loizillon S, Bottani S, Maire A, Ströer S, Dormont D, Colliot O, Burgos N. Automatic motion artefact detection in brain T1-weighted magnetic resonance images from a clinical data warehouse using synthetic data. Med Image Anal 2024; 93:103073. [PMID: 38176355 DOI: 10.1016/j.media.2023.103073] [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: 03/29/2023] [Revised: 12/12/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024]
Abstract
Containing the medical data of millions of patients, clinical data warehouses (CDWs) represent a great opportunity to develop computational tools. Magnetic resonance images (MRIs) are particularly sensitive to patient movements during image acquisition, which will result in artefacts (blurring, ghosting and ringing) in the reconstructed image. As a result, a significant number of MRIs in CDWs are corrupted by these artefacts and may be unusable. Since their manual detection is impossible due to the large number of scans, it is necessary to develop tools to automatically exclude (or at least identify) images with motion in order to fully exploit CDWs. In this paper, we propose a novel transfer learning method from research to clinical data for the automatic detection of motion in 3D T1-weighted brain MRI. The method consists of two steps: a pre-training on research data using synthetic motion, followed by a fine-tuning step to generalise our pre-trained model to clinical data, relying on the labelling of 4045 images. The objectives were both (1) to be able to exclude images with severe motion, (2) to detect mild motion artefacts. Our approach achieved excellent accuracy for the first objective with a balanced accuracy nearly similar to that of the annotators (balanced accuracy>80 %). However, for the second objective, the performance was weaker and substantially lower than that of human raters. Overall, our framework will be useful to take advantage of CDWs in medical imaging and highlight the importance of a clinical validation of models trained on research data.
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Affiliation(s)
- Sophie Loizillon
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Inria, Inserm, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris 75013, France
| | - Simona Bottani
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Inria, Inserm, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris 75013, France
| | - Aurélien Maire
- AP-HP, Innovation & Données - Département des Services Numériques, Paris 75012, France
| | - Sebastian Ströer
- AP-HP, Hôpital de la Pitié Salpêtrière, Department of Neuroradiology, Paris 75013, France
| | - Didier Dormont
- AP-HP, Hôpital de la Pitié Salpêtrière, Department of Neuroradiology, Paris 75013, France; Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Inria, Inserm, AP-HP, Hôpital de la Pitié-Salpêtrière, DMU DIAMENT, Paris 75013, France
| | - Olivier Colliot
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Inria, Inserm, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris 75013, France
| | - Ninon Burgos
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Inria, Inserm, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris 75013, France.
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11
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Li Q, Lv H, Chen Y, Shen J, Shi J, Zhou C, Yan F. Development and validation of a machine learning prediction model for perioperative red blood cell transfusions in cardiac surgery. Int J Med Inform 2024; 184:105343. [PMID: 38286086 DOI: 10.1016/j.ijmedinf.2024.105343] [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: 08/25/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 01/31/2024]
Abstract
OBJECTIVE Several machine learning (ML) models have been used in perioperative red blood cell (RBC) transfusion risk for cardiac surgery with limited generalizability and no external validation. Hence, we sought to develop and comprehensively externally validate a ML model in a large dataset to estimate RBC transfusion in cardiac surgery with cardiopulmonary bypass (CPB). DESIGN A retrospective analysis of a multicenter clinical trial (NCT03782350). PATIENTS The study patients who underwent cardiac surgery with CPB came from four cardiac centers in China and Medical Information Mart for Intensive Cared (MIMIC-IV) dataset. MEASUREMENTS Data from Fuwai Hospital were used to develop an individualized prediction model for RBC transfusion. The model was externally validated in the data from three other centers and MIMIC-IV dataset. Twelve models were constructed. MAIN RESULTS A total of 11,201 eligible patients were included in the model development (2420 in Fuwai Hospital) and external validation (563 in the other three centers and 8218 in the MIMIC-IV dataset). A significant difference was observed between the Logistic Regression and CatboostClassifier (0.72 Vs. 0.74, P = 0.031) or RandomForestClassifier (0.72 Vs. 0.75 p = 0.012) in the external validation and MIMIV-IV datasets (age ≤ 70:0.63 Vs. 0.71, p < 0.001; age > 70:0.63 Vs. 0.70, 0.63 Vs. 0.71, p < 0.001). The CatboostClassifier and RandomForestClassifier model was comparable in development (0.83 Vs. 0.82, p = 0.419), external (0.74 Vs. 0.75, p = 0.268), and MIMIC-IV datasets (age ≤ 70: 0.71 Vs. 0.71, p = 0.574; age > 70: 0.70 Vs. 0.71, p = 0.981). Of note, they outperformed other ML models with excellent discrimination and calibration. The CatboostClassifier and RandomForestClassifier models achieved higher area under precision-recall curve and lower brier loss score in validation and MIMIC-IV datasets. Additionally, we confirmed that low preoperative hemoglobin, low body mass index, old age, and female sex increased the risk of RBC transfusion. CONCLUSIONS In our study, enrolling a broad range of cardiovascular surgeries with CPB and utilizing a restrictive RBC transfusion strategy, robustly validates the generalizability of ML algorithms for predicting RBC transfusion risk. Notably, the CatboostClassifier and RandomForestClassifier exhibit strong external clinical applicability, underscoring their potential for widespread adoption. This study provides compelling evidence supporting the efficacy and practical value of ML-based approaches in enhancing transfusion risk prediction in clinical practice.
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Affiliation(s)
- Qian Li
- Department of Anesthesiology, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College/National Center for Cardiovascular Diseases, Beijing 100037, China
| | - Hong Lv
- Department of Anesthesiology, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College/National Center for Cardiovascular Diseases, Beijing 100037, China
| | - Yuye Chen
- Department of Anesthesiology, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College/National Center for Cardiovascular Diseases, Beijing 100037, China
| | - Jingjia Shen
- Department of Anesthesiology, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College/National Center for Cardiovascular Diseases, Beijing 100037, China
| | - Jia Shi
- Department of Anesthesiology, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College/National Center for Cardiovascular Diseases, Beijing 100037, China
| | - Chenghui Zhou
- Department of Anesthesiology, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College/National Center for Cardiovascular Diseases, Beijing 100037, China; Center for Anesthesiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China.
| | - Fuxia Yan
- Department of Anesthesiology, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College/National Center for Cardiovascular Diseases, Beijing 100037, China.
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12
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Attyé A, Renard F, Anglade V, Krainik A, Kahane P, Mansencal B, Coupé P, Calamante F. Data-driven normative values based on generative manifold learning for quantitative MRI. Sci Rep 2024; 14:7563. [PMID: 38555415 PMCID: PMC10981723 DOI: 10.1038/s41598-024-58141-4] [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: 04/20/2023] [Accepted: 03/26/2024] [Indexed: 04/02/2024] Open
Abstract
In medicine, abnormalities in quantitative metrics such as the volume reduction of one brain region of an individual versus a control group are often provided as deviations from so-called normal values. These normative reference values are traditionally calculated based on the quantitative values from a control group, which can be adjusted for relevant clinical co-variables, such as age or sex. However, these average normative values do not take into account the globality of the available quantitative information. For example, quantitative analysis of T1-weighted magnetic resonance images based on anatomical structure segmentation frequently includes over 100 cerebral structures in the quantitative reports, and these tend to be analyzed separately. In this study, we propose a global approach to personalized normative values for each brain structure using an unsupervised Artificial Intelligence technique known as generative manifold learning. We test the potential benefit of these personalized normative values in comparison with the more traditional average normative values on a population of patients with drug-resistant epilepsy operated for focal cortical dysplasia, as well as on a supplementary healthy group and on patients with Alzheimer's disease.
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Affiliation(s)
| | | | - Vanina Anglade
- Department of Neuroradiology and MRI, SFR RMN Neurosciences, University Grenoble Alpes Hospital, Grenoble, France
| | - Alexandre Krainik
- Department of Neuroradiology and MRI, SFR RMN Neurosciences, University Grenoble Alpes Hospital, Grenoble, France
| | - Philippe Kahane
- Department of Neurology, University Grenoble Alpes Hospital, Grenoble, France
| | - Boris Mansencal
- CNRS, Univ. Bordeaux, Bordeaux INP, LABRI, UMR5800, 33400, Talence, France
| | - Pierrick Coupé
- CNRS, Univ. Bordeaux, Bordeaux INP, LABRI, UMR5800, 33400, Talence, France
| | - Fernando Calamante
- School of Biomedical Engineering, The University of Sydney, Sydney, NSW, 2006, Australia
- Sydney Imaging-The University of Sydney, Sydney, Australia
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13
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Wen J, Zhao B, Yang Z, Erus G, Skampardoni I, Mamourian E, Cui Y, Hwang G, Bao J, Boquet-Pujadas A, Zhou Z, Veturi Y, Ritchie MD, Shou H, Thompson PM, Shen L, Toga AW, Davatzikos C. The genetic architecture of multimodal human brain age. Nat Commun 2024; 15:2604. [PMID: 38521789 PMCID: PMC10960798 DOI: 10.1038/s41467-024-46796-6] [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: 05/13/2023] [Accepted: 03/06/2024] [Indexed: 03/25/2024] Open
Abstract
The complex biological mechanisms underlying human brain aging remain incompletely understood. This study investigated the genetic architecture of three brain age gaps (BAG) derived from gray matter volume (GM-BAG), white matter microstructure (WM-BAG), and functional connectivity (FC-BAG). We identified sixteen genomic loci that reached genome-wide significance (P-value < 5×10-8). A gene-drug-disease network highlighted genes linked to GM-BAG for treating neurodegenerative and neuropsychiatric disorders and WM-BAG genes for cancer therapy. GM-BAG displayed the most pronounced heritability enrichment in genetic variants within conserved regions. Oligodendrocytes and astrocytes, but not neurons, exhibited notable heritability enrichment in WM and FC-BAG, respectively. Mendelian randomization identified potential causal effects of several chronic diseases on brain aging, such as type 2 diabetes on GM-BAG and AD on WM-BAG. Our results provide insights into the genetics of human brain aging, with clinical implications for potential lifestyle and therapeutic interventions. All results are publicly available at https://labs.loni.usc.edu/medicine .
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Affiliation(s)
- Junhao Wen
- Laboratory of AI and Biomedical Science (LABS), Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA.
| | - Bingxin Zhao
- Department of Statistics and Data Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhijian Yang
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Guray Erus
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ioanna Skampardoni
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth Mamourian
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yuhan Cui
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gyujoon Hwang
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jingxuan Bao
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Zhen Zhou
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yogasudha Veturi
- Department of Biobehavioral Health and Statistics, Penn State University, University Park, PA, USA
| | - Marylyn D Ritchie
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Haochang Shou
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Marina del Rey, CA, USA
| | - Li Shen
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Arthur W Toga
- Laboratory of Neuro Imaging (LONI), Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Christos Davatzikos
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AI2D), Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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14
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Bottani S, Thibeau-Sutre E, Maire A, Ströer S, Dormont D, Colliot O, Burgos N. Contrast-enhanced to non-contrast-enhanced image translation to exploit a clinical data warehouse of T1-weighted brain MRI. BMC Med Imaging 2024; 24:67. [PMID: 38504179 PMCID: PMC10953143 DOI: 10.1186/s12880-024-01242-3] [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: 05/22/2023] [Accepted: 03/07/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Clinical data warehouses provide access to massive amounts of medical images, but these images are often heterogeneous. They can for instance include images acquired both with or without the injection of a gadolinium-based contrast agent. Harmonizing such data sets is thus fundamental to guarantee unbiased results, for example when performing differential diagnosis. Furthermore, classical neuroimaging software tools for feature extraction are typically applied only to images without gadolinium. The objective of this work is to evaluate how image translation can be useful to exploit a highly heterogeneous data set containing both contrast-enhanced and non-contrast-enhanced images from a clinical data warehouse. METHODS We propose and compare different 3D U-Net and conditional GAN models to convert contrast-enhanced T1-weighted (T1ce) into non-contrast-enhanced (T1nce) brain MRI. These models were trained using 230 image pairs and tested on 77 image pairs from the clinical data warehouse of the Greater Paris area. RESULTS Validation using standard image similarity measures demonstrated that the similarity between real and synthetic T1nce images was higher than between real T1nce and T1ce images for all the models compared. The best performing models were further validated on a segmentation task. We showed that tissue volumes extracted from synthetic T1nce images were closer to those of real T1nce images than volumes extracted from T1ce images. CONCLUSION We showed that deep learning models initially developed with research quality data could synthesize T1nce from T1ce images of clinical quality and that reliable features could be extracted from the synthetic images, thus demonstrating the ability of such methods to help exploit a data set coming from a clinical data warehouse.
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Affiliation(s)
- Simona Bottani
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Inria, Inserm, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, 75013, France
| | - Elina Thibeau-Sutre
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Inria, Inserm, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, 75013, France
| | - Aurélien Maire
- Innovation & Données - Département des Services Numériques, AP-HP, Paris, 75013, France
| | - Sebastian Ströer
- Hôpital Pitié Salpêtrière, Department of Neuroradiology, AP-HP, Paris, 75012, France
| | - Didier Dormont
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Inria, Inserm, AP-HP, Hôpital de la Pitié-Salpêtrière, DMU DIAMENT, Paris, 75013, France
| | - Olivier Colliot
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Inria, Inserm, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, 75013, France
| | - Ninon Burgos
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Inria, Inserm, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, 75013, France.
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15
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Arvidsson I, Strandberg O, Palmqvist S, Stomrud E, Cullen N, Janelidze S, Tideman P, Heyden A, Åström K, Hansson O, Mattsson-Carlgren N. Comparing a pre-defined versus deep learning approach for extracting brain atrophy patterns to predict cognitive decline due to Alzheimer's disease in patients with mild cognitive symptoms. Alzheimers Res Ther 2024; 16:61. [PMID: 38504336 PMCID: PMC10949809 DOI: 10.1186/s13195-024-01428-5] [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: 11/06/2023] [Accepted: 03/10/2024] [Indexed: 03/21/2024]
Abstract
BACKGROUND Predicting future Alzheimer's disease (AD)-related cognitive decline among individuals with subjective cognitive decline (SCD) or mild cognitive impairment (MCI) is an important task for healthcare. Structural brain imaging as measured by magnetic resonance imaging (MRI) could potentially contribute when making such predictions. It is unclear if the predictive performance of MRI can be improved using entire brain images in deep learning (DL) models compared to using pre-defined brain regions. METHODS A cohort of 332 individuals with SCD/MCI were included from the Swedish BioFINDER-1 study. The goal was to predict longitudinal SCD/MCI-to-AD dementia progression and change in Mini-Mental State Examination (MMSE) over four years. Four models were evaluated using different predictors: (1) clinical data only, including demographics, cognitive tests and APOE ε4 status, (2) clinical data plus hippocampal volume, (3) clinical data plus all regional MRI gray matter volumes (N = 68) extracted using FreeSurfer software, (4) a DL model trained using multi-task learning with MRI images, Jacobian determinant images and baseline cognition as input. A double cross-validation scheme, with five test folds and for each of those ten validation folds, was used. External evaluation was performed on part of the ADNI dataset, including 108 patients. Mann-Whitney U-test was used to determine statistically significant differences in performance, with p-values less than 0.05 considered significant. RESULTS In the BioFINDER cohort, 109 patients (33%) progressed to AD dementia. The performance of the clinical data model for prediction of progression to AD dementia was area under the curve (AUC) = 0.85 and four-year cognitive decline was R2 = 0.14. The performance was improved for both outcomes when adding hippocampal volume (AUC = 0.86, R2 = 0.16). Adding FreeSurfer brain regions improved prediction of four-year cognitive decline but not progression to AD (AUC = 0.83, R2 = 0.17), while the DL model worsened the performance for both outcomes (AUC = 0.84, R2 = 0.08). A sensitivity analysis showed that the Jacobian determinant image was more informative than the MRI image, but that performance was maximized when both were included. In the external evaluation cohort from ADNI, 23 patients (21%) progressed to AD dementia. The results for predicted progression to AD dementia were similar to the results for the BioFINDER test data, while the performance for the cognitive decline was deteriorated. CONCLUSIONS The DL model did not significantly improve the prediction of clinical disease progression in AD, compared to regression models with a single pre-defined brain region.
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Affiliation(s)
- Ida Arvidsson
- Centre for Mathematical Sciences, Lund University, Lund, Sweden.
| | - Olof Strandberg
- Clinical Memory Research Unit, Department of Clinical Sciences, Malmö, Lund University, Lund, Sweden
| | - Sebastian Palmqvist
- Clinical Memory Research Unit, Department of Clinical Sciences, Malmö, Lund University, Lund, Sweden
- Memory Clinic, Skåne University Hospital, Malmö, Sweden
| | - Erik Stomrud
- Clinical Memory Research Unit, Department of Clinical Sciences, Malmö, Lund University, Lund, Sweden
- Memory Clinic, Skåne University Hospital, Malmö, Sweden
| | - Nicholas Cullen
- Clinical Memory Research Unit, Department of Clinical Sciences, Malmö, Lund University, Lund, Sweden
| | - Shorena Janelidze
- Clinical Memory Research Unit, Department of Clinical Sciences, Malmö, Lund University, Lund, Sweden
| | - Pontus Tideman
- Clinical Memory Research Unit, Department of Clinical Sciences, Malmö, Lund University, Lund, Sweden
- Memory Clinic, Skåne University Hospital, Malmö, Sweden
| | - Anders Heyden
- Centre for Mathematical Sciences, Lund University, Lund, Sweden
| | - Karl Åström
- Centre for Mathematical Sciences, Lund University, Lund, Sweden
| | - Oskar Hansson
- Clinical Memory Research Unit, Department of Clinical Sciences, Malmö, Lund University, Lund, Sweden
- Memory Clinic, Skåne University Hospital, Malmö, Sweden
| | - Niklas Mattsson-Carlgren
- Clinical Memory Research Unit, Department of Clinical Sciences, Malmö, Lund University, Lund, Sweden.
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden.
- Department of Neurology, Skåne University Hospital, Lund, Sweden.
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16
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Mitrovska A, Safari P, Ritter K, Shariati B, Fischer JK. Secure federated learning for Alzheimer's disease detection. Front Aging Neurosci 2024; 16:1324032. [PMID: 38515517 PMCID: PMC10954782 DOI: 10.3389/fnagi.2024.1324032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/22/2024] [Indexed: 03/23/2024] Open
Abstract
Machine Learning (ML) is considered a promising tool to aid and accelerate diagnosis in various medical areas, including neuroimaging. However, its success is set back by the lack of large-scale public datasets. Indeed, medical institutions possess a large amount of data; however, open-sourcing is prevented by the legal requirements to protect the patient's privacy. Federated Learning (FL) is a viable alternative that can overcome this issue. This work proposes training an ML model for Alzheimer's Disease (AD) detection based on structural MRI (sMRI) data in a federated setting. We implement two aggregation algorithms, Federated Averaging (FedAvg) and Secure Aggregation (SecAgg), and compare their performance with the centralized ML model training. We simulate heterogeneous environments and explore the impact of demographical (sex, age, and diagnosis) and imbalanced data distributions. The simulated heterogeneous environments allow us to observe these statistical differences' effect on the ML models trained using FL and highlight the importance of studying such differences when training ML models for AD detection. Moreover, as part of the evaluation, we demonstrate the increased privacy guarantees of FL with SecAgg via simulated membership inference attacks.
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Affiliation(s)
- Angela Mitrovska
- Fraunhofer-Institut fur Nachrichtentechnik, Heinrich-Hertz-Institute (HHI), Berlin, Germany
- Bernstein Center for Computational Neuroscience, Berlin, Germany
| | - Pooyan Safari
- Fraunhofer-Institut fur Nachrichtentechnik, Heinrich-Hertz-Institute (HHI), Berlin, Germany
| | - Kerstin Ritter
- Bernstein Center for Computational Neuroscience, Berlin, Germany
- Department of Psychiatry and Psychotherapy, Charite – Universitatsmedizin Berlin (corporate member of Freie Universitat Berlin, Humboldt-Universitat zu Berlin, and Berlin Institute of Health), Berlin, Germany
| | - Behnam Shariati
- Fraunhofer-Institut fur Nachrichtentechnik, Heinrich-Hertz-Institute (HHI), Berlin, Germany
| | - Johannes Karl Fischer
- Fraunhofer-Institut fur Nachrichtentechnik, Heinrich-Hertz-Institute (HHI), Berlin, Germany
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17
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Bloch L, Friedrich CM. Systematic comparison of 3D Deep learning and classical machine learning explanations for Alzheimer's Disease detection. Comput Biol Med 2024; 170:108029. [PMID: 38308870 DOI: 10.1016/j.compbiomed.2024.108029] [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: 07/09/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/05/2024]
Abstract
Black-box deep learning (DL) models trained for the early detection of Alzheimer's Disease (AD) often lack systematic model interpretation. This work computes the activated brain regions during DL and compares those with classical Machine Learning (ML) explanations. The architectures used for DL were 3D DenseNets, EfficientNets, and Squeeze-and-Excitation (SE) networks. The classical models include Random Forests (RFs), Support Vector Machines (SVMs), eXtreme Gradient Boosting (XGBoost), Light Gradient Boosting (LightGBM), Decision Trees (DTs), and Logistic Regression (LR). For explanations, SHapley Additive exPlanations (SHAP) values, Local Interpretable Model-agnostic Explanations (LIME), Gradient-weighted Class Activation Mapping (GradCAM), GradCAM++ and permutation-based feature importance were implemented. During interpretation, correlated features were consolidated into aspects. All models were trained on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset. The validation includes internal and external validation on the Australian Imaging and Lifestyle flagship study of Ageing (AIBL) and the Open Access Series of Imaging Studies (OASIS). DL and ML models reached similar classification performances. Regarding the brain regions, both types focus on different regions. The ML models focus on the inferior and middle temporal gyri, and the hippocampus, and amygdala regions previously associated with AD. The DL models focus on a wider range of regions including the optical chiasm, the entorhinal cortices, the left and right vessels, and the 4th ventricle which were partially associated with AD. One explanation for the differences is the input features (textures vs. volumes). Both types show reasonable similarity to a ground truth Voxel-Based Morphometry (VBM) analysis. Slightly higher similarities were measured for ML models.
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Affiliation(s)
- Louise Bloch
- Department of Computer Science, University of Applied Sciences and Arts Dortmund (FH Dortmund), Emil-Figge-Straße 42, Dortmund, 44227, North Rhine-Westphalia, Germany; Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital Essen, Hufelandstraße 55, Essen, 45122, North Rhine-Westphalia, Germany; Institute for Artificial Intelligence in Medicine (IKIM), University Hospital Essen, Hufelandstraße 55, Essen, 45122, North Rhine-Westphalia, Germany.
| | - Christoph M Friedrich
- Department of Computer Science, University of Applied Sciences and Arts Dortmund (FH Dortmund), Emil-Figge-Straße 42, Dortmund, 44227, North Rhine-Westphalia, Germany; Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital Essen, Hufelandstraße 55, Essen, 45122, North Rhine-Westphalia, Germany.
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18
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Baghoolizadeh M, Jasim DJ, Sajadi SM, Renani RR, Renani MR, Hekmatifar M. Using of artificial neural networks and different evolutionary algorithms to predict the viscosity and thermal conductivity of silica-alumina-MWCN/water nanofluid. Heliyon 2024; 10:e26279. [PMID: 38379995 PMCID: PMC10877415 DOI: 10.1016/j.heliyon.2024.e26279] [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: 08/30/2023] [Revised: 02/01/2024] [Accepted: 02/09/2024] [Indexed: 02/22/2024] Open
Abstract
This study predicts the parameters such as viscosity and thermal conductivity in silica-alumina-MWCN/water nanofluid using the artificial intelligence method and using design variables such as solid volume fraction and temperature. In this study, 6 optimization algorithms were used to predict and numerically model the μnf and TC of silica-alumina-MWCNT/water-NF. In this study, six measurement criteria were used to evaluate the estimates obtained from the coupling process of GMDH ANN with each of these 6 optimization algorithms. The results reveal that the influence of the φ is notably higher on both μnf and TC with values of 0.83 for μnf and 0.92 for TC, while Temp has a relatively weaker impact with -0.5 for μnf and 0.38 for TC. Among various algorithms, the coupling of the evolutionary algorithm NSGA II with ANN and GMDH performs best in predicting μnf and TC for the NF, with a maximum margin of deviation of -0.108 and an R2 evaluation criterion of 0.99996 for μnf and 1 for TC, indicating exceptional model accuracy. In the subsequent phase, a meta-heuristic Genetic Algorithm minimizes μnf and TC values. Four points (A, B, C, and D) along the Pareto front are selected, with point A representing the optimal state characterized by low values of φ and Temp (0.0002 and 50.8772, respectively) and corresponding target function values of 0.9988 for μnf and 0.6344 for TC. In contrast, point D represents the highest values of φ and Temp (0.49986 and 59.9775, respectively) and yields target function values of 2.382 for μnf and 0.8517 for TC. This analysis aids in identifying the optimal operating conditions for maximizing NF performance.
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Affiliation(s)
| | - Dheyaa J. Jasim
- Department of Petroleum Engineering, Al-Amarah University College, Maysan, Iraq
| | | | | | | | - Maboud Hekmatifar
- Department of mechanical engineering, Khomeinishahr branch, Islamic Azad University, Khomeinishahr, Iran
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19
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Kim MJ, Hong E, Yum MS, Lee YJ, Kim J, Ko TS. Deep learning-based, fully automated, pediatric brain segmentation. Sci Rep 2024; 14:4344. [PMID: 38383725 PMCID: PMC10881508 DOI: 10.1038/s41598-024-54663-z] [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: 07/24/2023] [Accepted: 02/15/2024] [Indexed: 02/23/2024] Open
Abstract
The purpose of this study was to demonstrate the performance of a fully automated, deep learning-based brain segmentation (DLS) method in healthy controls and in patients with neurodevelopmental disorders, SCN1A mutation, under eleven. The whole, cortical, and subcortical volumes of previously enrolled 21 participants, under 11 years of age, with a SCN1A mutation, and 42 healthy controls, were obtained using a DLS method, and compared to volumes measured by Freesurfer with manual correction. Additionally, the volumes which were calculated with the DLS method between the patients and the control group. The volumes of total brain gray and white matter using DLS method were consistent with that volume which were measured by Freesurfer with manual correction in healthy controls. Among 68 cortical parcellated volume analysis, the volumes of only 7 areas measured by DLS methods were significantly different from that measured by Freesurfer with manual correction, and the differences decreased with increasing age in the subgroup analysis. The subcortical volume measured by the DLS method was relatively smaller than that of the Freesurfer volume analysis. Further, the DLS method could perfectly detect the reduced volume identified by the Freesurfer software and manual correction in patients with SCN1A mutations, compared with healthy controls. In a pediatric population, this new, fully automated DLS method is compatible with the classic, volumetric analysis with Freesurfer software and manual correction, and it can also well detect brain morphological changes in children with a neurodevelopmental disorder.
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Affiliation(s)
- Min-Jee Kim
- Department of Pediatrics, Asan Medical Center Children's Hospital, Ulsan University College of Medicine, 88, Olympic-ro 43-Gil, Songpa-Gu, Seoul, 05505, South Korea
| | | | - Mi-Sun Yum
- Department of Pediatrics, Asan Medical Center Children's Hospital, Ulsan University College of Medicine, 88, Olympic-ro 43-Gil, Songpa-Gu, Seoul, 05505, South Korea.
| | - Yun-Jeong Lee
- Department of Pediatrics, Kyungpook National University Hospital and School of Medicine, Kyungpook National University, Daegu, South Korea
| | | | - Tae-Sung Ko
- Department of Pediatrics, Asan Medical Center Children's Hospital, Ulsan University College of Medicine, 88, Olympic-ro 43-Gil, Songpa-Gu, Seoul, 05505, South Korea
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20
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Wang R, Gao L, Zhang X, Han J. SVFR: A novel slice-to-volume feature representation framework using deep neural networks and a clustering model for the diagnosis of Alzheimer's disease. Heliyon 2024; 10:e23008. [PMID: 38148809 PMCID: PMC10750062 DOI: 10.1016/j.heliyon.2023.e23008] [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: 12/09/2022] [Revised: 09/30/2023] [Accepted: 11/23/2023] [Indexed: 12/28/2023] Open
Abstract
Deep neural networks (DNNs) have been effective in classifying structural magnetic resonance imaging (sMRI) images for Alzheimer's disease (AD) diagnosis. In this study, we propose a novel two-phase slice-to-volume feature representation (SVFR) framework for AD diagnosis. Specifically, we design a slice-level feature extractor to automatically select informative slice images and extract their slice-level features, by combining DNN and clustering models. Furthermore, we propose a joint volume-level feature generator and classifier to hierarchically aggregate the slice-level features into volume-level features and to classify images, by devising a spatial pyramid set pooling module and a fusion module. Experimental results demonstrate the superior performance of the proposed SVFR, surpassing the majority of the state-of-the-art methods and achieving comparable results to the best-performing approach. Experimental results also showcase the efficacy of the slice-level feature extractor in the selection of informative slice images, as well as the effectiveness of the volume-level feature generator and classifier in the integration of slice-level features for image classification. The source code for this study is publicly available at https://github.com/gll89/SVFR.
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Affiliation(s)
- Rubing Wang
- Faculty of Electrical Engineering and Computer Science, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo, China
| | - Linlin Gao
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, China
- Faculty of Electrical Engineering and Computer Science, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo, China
| | | | - Jinming Han
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - the Alzheimer's Disease Neuroimaging Initiative
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, China
- Faculty of Electrical Engineering and Computer Science, Zhejiang Engineering Research Center of Advanced Mass Spectrometry and Clinical Application, Ningbo University, Ningbo, China
- Ningbo Medical Center Lihuili Hospital, Ningbo, China
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing, China
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21
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Belov V, Erwin-Grabner T, Aghajani M, Aleman A, Amod AR, Basgoze Z, Benedetti F, Besteher B, Bülow R, Ching CRK, Connolly CG, Cullen K, Davey CG, Dima D, Dols A, Evans JW, Fu CHY, Gonul AS, Gotlib IH, Grabe HJ, Groenewold N, Hamilton JP, Harrison BJ, Ho TC, Mwangi B, Jaworska N, Jahanshad N, Klimes-Dougan B, Koopowitz SM, Lancaster T, Li M, Linden DEJ, MacMaster FP, Mehler DMA, Melloni E, Mueller BA, Ojha A, Oudega ML, Penninx BWJH, Poletti S, Pomarol-Clotet E, Portella MJ, Pozzi E, Reneman L, Sacchet MD, Sämann PG, Schrantee A, Sim K, Soares JC, Stein DJ, Thomopoulos SI, Uyar-Demir A, van der Wee NJA, van der Werff SJA, Völzke H, Whittle S, Wittfeld K, Wright MJ, Wu MJ, Yang TT, Zarate C, Veltman DJ, Schmaal L, Thompson PM, Goya-Maldonado R. Multi-site benchmark classification of major depressive disorder using machine learning on cortical and subcortical measures. Sci Rep 2024; 14:1084. [PMID: 38212349 PMCID: PMC10784593 DOI: 10.1038/s41598-023-47934-8] [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: 01/23/2023] [Accepted: 11/19/2023] [Indexed: 01/13/2024] Open
Abstract
Machine learning (ML) techniques have gained popularity in the neuroimaging field due to their potential for classifying neuropsychiatric disorders. However, the diagnostic predictive power of the existing algorithms has been limited by small sample sizes, lack of representativeness, data leakage, and/or overfitting. Here, we overcome these limitations with the largest multi-site sample size to date (N = 5365) to provide a generalizable ML classification benchmark of major depressive disorder (MDD) using shallow linear and non-linear models. Leveraging brain measures from standardized ENIGMA analysis pipelines in FreeSurfer, we were able to classify MDD versus healthy controls (HC) with a balanced accuracy of around 62%. But after harmonizing the data, e.g., using ComBat, the balanced accuracy dropped to approximately 52%. Accuracy results close to random chance levels were also observed in stratified groups according to age of onset, antidepressant use, number of episodes and sex. Future studies incorporating higher dimensional brain imaging/phenotype features, and/or using more advanced machine and deep learning methods may yield more encouraging prospects.
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Affiliation(s)
- Vladimir Belov
- Laboratory of Systems Neuroscience and Imaging in Psychiatry (SNIP-Lab), Department of Psychiatry and Psychotherapy, University Medical Center Göttingen (UMG), Georg-August University, Von-Siebold-Str. 5, 37075, Göttingen, Germany
| | - Tracy Erwin-Grabner
- Laboratory of Systems Neuroscience and Imaging in Psychiatry (SNIP-Lab), Department of Psychiatry and Psychotherapy, University Medical Center Göttingen (UMG), Georg-August University, Von-Siebold-Str. 5, 37075, Göttingen, Germany
| | - Moji Aghajani
- Department of Psychiatry, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Institute of Education and Child Studies, Section Forensic Family and Youth Care, Leiden University, Leiden, The Netherlands
| | - Andre Aleman
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alyssa R Amod
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Zeynep Basgoze
- Department of Psychiatry and Behavioral Science, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Francesco Benedetti
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Bianca Besteher
- Department of Psychiatry and Psychotherapy, Jena University Hospital, Jena, Germany
| | - Robin Bülow
- Institute for Radiology and Neuroradiology, University Medicine Greifswald, Greifswald, Germany
| | - Christopher R K Ching
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
| | - Colm G Connolly
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL, USA
| | - Kathryn Cullen
- Department of Psychiatry and Behavioral Science, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Christopher G Davey
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne, Parkville, VIC, Australia
| | - Danai Dima
- Department of Psychology, School of Arts and Social Sciences, City, University of London, London, UK
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Annemiek Dols
- Department of Psychiatry, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jennifer W Evans
- Experimental Therapeutics and Pathophysiology Branch, National Institute for Mental Health, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia H Y Fu
- School of Psychology, University of East London, London, UK
- Centre for Affective Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Ali Saffet Gonul
- SoCAT Lab, Department of Psychiatry, School of Medicine, Ege University, Izmir, Turkey
| | - Ian H Gotlib
- Department of Psychology, Stanford University, Stanford, CA, USA
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Nynke Groenewold
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - J Paul Hamilton
- Center for Social and Affective Neuroscience, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Center for Medical Imaging and Visualization, Linköping University, Linköping, Sweden
| | - Ben J Harrison
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne, Parkville, VIC, Australia
| | - Tiffany C Ho
- Department of Psychiatry and Behavioral Sciences, Division of Child and Adolescent Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Psychology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Benson Mwangi
- Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center Of Excellence On Mood Disorders, Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences at McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Natalia Jaworska
- Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Neda Jahanshad
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
| | | | | | - Thomas Lancaster
- Cardiff University Brain Research Imaging Center, Cardiff University, Cardiff, UK
- MRC Center for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Meng Li
- Department of Psychiatry and Psychotherapy, Jena University Hospital, Jena, Germany
| | - David E J Linden
- Cardiff University Brain Research Imaging Center, Cardiff University, Cardiff, UK
- MRC Center for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
- School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Frank P MacMaster
- Departments of Psychiatry and Pediatrics, University of Calgary, Calgary, AB, Canada
| | - David M A Mehler
- Cardiff University Brain Research Imaging Center, Cardiff University, Cardiff, UK
- MRC Center for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
- Department of Psychiatry, Psychotherapy and Psychosomatics, Medical School, RWTH Aachen University, Aachen, Germany
| | - Elisa Melloni
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Bryon A Mueller
- Department of Psychiatry and Behavioral Science, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Amar Ojha
- Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Neural Basis of Cognition, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mardien L Oudega
- Department of Psychiatry, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sara Poletti
- Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Edith Pomarol-Clotet
- FIDMAG Germanes Hospitalàries Research Foundation, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Barcelona, Catalonia, Spain
| | - Maria J Portella
- Sant Pau Mental Health Research Group, Institut de Recerca de L'Hospital de La Santa Creu I Sant Pau, Barcelona, Catalonia, Spain
| | - Elena Pozzi
- Centre for Youth Mental Health, The University of Melbourne, Parkville, VIC, Australia
- Orygen, Parkville, VIC, Australia
| | - Liesbeth Reneman
- Department of Radiology and Nuclear Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Matthew D Sacchet
- Meditation Research Program, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Anouk Schrantee
- Department of Radiology and Nuclear Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Kang Sim
- West Region, Institute of Mental Health, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jair C Soares
- Center Of Excellence On Mood Disorders, Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences at McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Dan J Stein
- SA MRC Research Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Sophia I Thomopoulos
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
| | - Aslihan Uyar-Demir
- SoCAT Lab, Department of Psychiatry, School of Medicine, Ege University, Izmir, Turkey
| | - Nic J A van der Wee
- Leiden Institute for Brain and Cognition, Leiden University Medical Center, Leiden, The Netherlands
| | - Steven J A van der Werff
- Leiden Institute for Brain and Cognition, Leiden University Medical Center, Leiden, The Netherlands
- Department of Psychiatry, Leiden University Medical Center, Leiden, The Netherlands
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Sarah Whittle
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne and Melbourne Health, Melbourne, VIC, Australia
| | - Katharina Wittfeld
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
- German Center for Neurodegenerative Diseases (DZNE), Site Rostock/ Greifswald, Greifswald, Germany
| | - Margaret J Wright
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Mon-Ju Wu
- Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center Of Excellence On Mood Disorders, Louis A. Faillace, MD, Department of Psychiatry and Behavioral Sciences at McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Tony T Yang
- Department of Psychiatry and Behavioral Sciences, Division of Child and Adolescent Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Carlos Zarate
- Section on the Neurobiology and Treatment of Mood Disorders, National Institute of Mental Health, Bethesda, MD, USA
| | - Dick J Veltman
- Department of Psychiatry, Amsterdam UMC, Amsterdam Neuroscience, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Lianne Schmaal
- Centre for Youth Mental Health, The University of Melbourne, Parkville, VIC, Australia
- Orygen, Parkville, VIC, Australia
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
| | - Roberto Goya-Maldonado
- Laboratory of Systems Neuroscience and Imaging in Psychiatry (SNIP-Lab), Department of Psychiatry and Psychotherapy, University Medical Center Göttingen (UMG), Georg-August University, Von-Siebold-Str. 5, 37075, Göttingen, Germany.
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22
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Hao X, Li J, Ma M, Qin J, Zhang D, Liu F. Hypergraph convolutional network for longitudinal data analysis in Alzheimer's disease. Comput Biol Med 2024; 168:107765. [PMID: 38042101 DOI: 10.1016/j.compbiomed.2023.107765] [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: 07/20/2023] [Revised: 11/06/2023] [Accepted: 11/21/2023] [Indexed: 12/04/2023]
Abstract
Alzheimer's disease (AD) is an irreversible and progressive neurodegenerative disease. Longitudinal structural magnetic resonance imaging (sMRI) data have been widely used for tracking AD pathogenesis and diagnosis. However, existing methods tend to treat each time point equally without considering the temporal characteristics of longitudinal data. In this paper, we propose a weighted hypergraph convolution network (WHGCN) to use the internal correlations among different time points and leverage high-order relationships between subjects for AD detection. Specifically, we construct hypergraphs for sMRI data at each time point using the K-nearest neighbor (KNN) method to represent relationships between subjects, and then fuse the hypergraphs according to the importance of the data at each time point to obtain the final hypergraph. Subsequently, we use hypergraph convolution to learn high-order information between subjects while performing feature dimensionality reduction. Finally, we conduct experiments on 518 subjects selected from the Alzheimer's disease neuroimaging initiative (ADNI) database, and the results show that the WHGCN can get higher AD detection performance and has the potential to improve our understanding of the pathogenesis of AD.
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Affiliation(s)
- Xiaoke Hao
- School of Artificial Intelligence, Hebei University of Technology, Tianjin, 300401, China.
| | - Jiawang Li
- School of Artificial Intelligence, Hebei University of Technology, Tianjin, 300401, China
| | - Mingming Ma
- School of Artificial Intelligence, Hebei University of Technology, Tianjin, 300401, China
| | - Jing Qin
- Centre for Smart Health, School of Nursing, The Hong Kong Polytechnic University, Hong Kong, 999077, China
| | - Daoqiang Zhang
- College of Computer Science and Technology, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China.
| | - Feng Liu
- Department of Radiology, Tianjin Medical University General Hospital, Tianjin, 300052, China.
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23
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Yang Z, Li K, Gan H, Huang Z, Shi M, Zhou R. An Alzheimer's Disease classification network based on MRI utilizing diffusion maps for multi-scale feature fusion in graph convolution. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2024; 21:1554-1572. [PMID: 38303477 DOI: 10.3934/mbe.2024067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Graph convolutional networks (GCN) have been widely utilized in Alzheimer's disease (AD) classification research due to its ability to automatically learn robust and powerful feature representations. Inter-patient relationships are effectively captured by constructing patients magnetic resonance imaging (MRI) data as graph data, where nodes represent individuals and edges denote the relationships between them. However, the performance of GCNs might be constrained by the construction of the graph adjacency matrix, thereby leading to learned features potentially overlooking intrinsic correlations among patients, which ultimately causes inaccurate disease classifications. To address this issue, we propose an Alzheimer's disease Classification network based on MRI utilizing diffusion maps for multi-scale feature fusion in graph convolution. This method aims to tackle the problem of features neglecting intrinsic relationships among patients while integrating features from diffusion mapping with different neighbor counts to better represent patients and achieve an accurate AD classification. Initially, the diffusion maps method conducts diffusion information in the feature space, thus breaking free from the constraints of diffusion based on the adjacency matrix. Subsequently, the diffusion features with different neighbor counts are merged, and a self-attention mechanism is employed to adaptively adjust the weights of diffusion features at different scales, thereby comprehensively and accurately capturing patient characteristics. Finally, metric learning techniques enhance the similarity of node features within the same category in the graph structure and bring node features of different categories more distant from each other. This study aims to enhance the classification accuracy of AD, by providing an effective tool for early diagnosis and intervention. It offers valuable information for clinical decisions and personalized treatment. Experimentation on the publicly accessible Alzheimer's disease neuroimaging initiative (ADNI) dataset validated our method's competitive performance across various AD-related classification tasks. Compared to existing methodologies, our approach captures patient characteristics more effectively and demonstrates superior generalization capabilities.
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Affiliation(s)
- Zhi Yang
- School of Computer Science, Hubei University of Technology, Wuhan 430068, China
| | - Kang Li
- School of Computer Science, Hubei University of Technology, Wuhan 430068, China
| | - Haitao Gan
- School of Computer Science, Hubei University of Technology, Wuhan 430068, China
| | - Zhongwei Huang
- School of Computer Science, Hubei University of Technology, Wuhan 430068, China
| | - Ming Shi
- School of Computer Science, Hubei University of Technology, Wuhan 430068, China
| | - Ran Zhou
- School of Computer Science, Hubei University of Technology, Wuhan 430068, China
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24
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Bapat R, Ma D, Duong TQ. Predicting Four-Year's Alzheimer's Disease Onset Using Longitudinal Neurocognitive Tests and MRI Data Using Explainable Deep Convolutional Neural Networks. J Alzheimers Dis 2024; 97:459-469. [PMID: 38143361 DOI: 10.3233/jad-230893] [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] [Indexed: 12/26/2023]
Abstract
BACKGROUND Prognosis of future risk of dementia from neuroimaging and cognitive data is important for optimizing clinical management for patients at early stage of Alzheimer's disease (AD). However, existing studies lack an efficient way to integrate longitudinal information from both modalities to improve prognosis performance. OBJECTIVE In this study, we aim to develop and evaluate an explainable deep learning-based framework to predict mild cognitive impairment (MCI) to AD conversion within four years using longitudinal whole-brain 3D MRI and neurocognitive tests. METHODS We proposed a two-stage framework that first uses a 3D convolutional neural network to extract single-timepoint MRI-based AD-related latent features, followed by multi-modal longitudinal feature concatenation and a 1D convolutional neural network to predict the risk of future dementia onset in four years. RESULTS The proposed deep learning framework showed promising to predict MCI to AD conversion within 4 years using longitudinal whole-brain 3D MRI and cognitive data without extracting regional brain volumes or cortical thickness, reaching a balanced accuracy of 0.834, significantly improved from models trained from single timepoint or single modality. The post hoc model explainability revealed heatmap indicating regions that are important for predicting future risk of AD. CONCLUSIONS The proposed framework sets the stage for future studies for using multi-modal longitudinal data to achieve optimal prediction for prognosis of AD onset, leading to better management of the diseases, thereby improving the quality of life.
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Affiliation(s)
- Rohan Bapat
- Department of Radiology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
| | - Da Ma
- Department of Internal Medicine Section of Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston-Salam, NC, USA
| | - Tim Q Duong
- Department of Radiology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
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25
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Wen J, Nasrallah IM, Abdulkadir A, Satterthwaite TD, Yang Z, Erus G, Robert-Fitzgerald T, Singh A, Sotiras A, Boquet-Pujadas A, Mamourian E, Doshi J, Cui Y, Srinivasan D, Skampardoni I, Chen J, Hwang G, Bergman M, Bao J, Veturi Y, Zhou Z, Yang S, Dazzan P, Kahn RS, Schnack HG, Zanetti MV, Meisenzahl E, Busatto GF, Crespo-Facorro B, Pantelis C, Wood SJ, Zhuo C, Shinohara RT, Gur RC, Gur RE, Koutsouleris N, Wolf DH, Saykin AJ, Ritchie MD, Shen L, Thompson PM, Colliot O, Wittfeld K, Grabe HJ, Tosun D, Bilgel M, An Y, Marcus DS, LaMontagne P, Heckbert SR, Austin TR, Launer LJ, Espeland M, Masters CL, Maruff P, Fripp J, Johnson SC, Morris JC, Albert MS, Bryan RN, Resnick SM, Fan Y, Habes M, Wolk D, Shou H, Davatzikos C. Genomic loci influence patterns of structural covariance in the human brain. Proc Natl Acad Sci U S A 2023; 120:e2300842120. [PMID: 38127979 PMCID: PMC10756284 DOI: 10.1073/pnas.2300842120] [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: 01/16/2023] [Accepted: 10/31/2023] [Indexed: 12/23/2023] Open
Abstract
Normal and pathologic neurobiological processes influence brain morphology in coordinated ways that give rise to patterns of structural covariance (PSC) across brain regions and individuals during brain aging and diseases. The genetic underpinnings of these patterns remain largely unknown. We apply a stochastic multivariate factorization method to a diverse population of 50,699 individuals (12 studies and 130 sites) and derive data-driven, multi-scale PSCs of regional brain size. PSCs were significantly correlated with 915 genomic loci in the discovery set, 617 of which are newly identified, and 72% were independently replicated. Key pathways influencing PSCs involve reelin signaling, apoptosis, neurogenesis, and appendage development, while pathways of breast cancer indicate potential interplays between brain metastasis and PSCs associated with neurodegeneration and dementia. Using support vector machines, multi-scale PSCs effectively derive imaging signatures of several brain diseases. Our results elucidate genetic and biological underpinnings that influence structural covariance patterns in the human brain.
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Affiliation(s)
- Junhao Wen
- Laboratory of AI and Biomedical Science, Department of Neurology, Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA90033
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Ilya M. Nasrallah
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Radiology, University of Pennsylvania, Philadelphia, PA19104
| | - Ahmed Abdulkadir
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Theodore D. Satterthwaite
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Zhijian Yang
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Guray Erus
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Timothy Robert-Fitzgerald
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Ashish Singh
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Aristeidis Sotiras
- Department of Radiology, Washington University School of Medicine, St. Louis, MO63110
| | - Aleix Boquet-Pujadas
- Biomedical Imaging Group, Department of Biomedical Engineering, École Polytechnique Fédérale de Lausanne, Lausanne1015, Switzerland
| | - Elizabeth Mamourian
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Jimit Doshi
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Yuhan Cui
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Dhivya Srinivasan
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Ioanna Skampardoni
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Jiong Chen
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Gyujoon Hwang
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Mark Bergman
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Jingxuan Bao
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA19104
| | - Yogasudha Veturi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Zhen Zhou
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Shu Yang
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA19104
| | - Paola Dazzan
- Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, LondonWC2R 2LS, United Kingdom
| | - Rene S. Kahn
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Hugo G. Schnack
- Department of Psychiatry, University Medical Center Utrecht, Utrecht 3584 CX Ut, Netherlands
| | - Marcus V. Zanetti
- Institute of Psychiatry, Department of Psychiatry, Faculty of Medicine, University of São Paulo, São Paulo05508-070, Brazil
| | - Eva Meisenzahl
- Department of Psychiatry and Psychotherapy, Heinrich Heine University, Düsseldorf40204, Germany
| | - Geraldo F. Busatto
- Institute of Psychiatry, Department of Psychiatry, Faculty of Medicine, University of São Paulo, São Paulo05508-070, Brazil
| | - Benedicto Crespo-Facorro
- Hospital Universitario Virgen del Rocio, School of Medicine, University of Sevilla,Sevilla41004, Spain
| | - Christos Pantelis
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Stephen J. Wood
- Orygen and the Centre for Youth Mental Health, Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Chuanjun Zhuo
- Key Laboratory of Real Tine Tracing of Brain Circuits in Psychiatry and Neurology, Department of Psychiatry, Tianjin Medical University, Tianjin300070, China
| | - Russell T. Shinohara
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Ruben C. Gur
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Raquel E. Gur
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Nikolaos Koutsouleris
- Department of Psychiatry and Psychotherapy, Ludwig-Maximilian University, Munich 80539, Germany
| | - Daniel H. Wolf
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Andrew J. Saykin
- Indiana Alzheimer’s Disease Research Center, Department of Radiology, Indiana University School of Medicine, Indianapolis, IN46202-3082
| | - Marylyn D. Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Li Shen
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA19104
| | - Paul M. Thompson
- Imaging Genetics Center, Department of Neurology, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA90033
| | - Olivier Colliot
- Institut du Cerveau, Sorbonne Université, Paris75013, France
| | - Katharina Wittfeld
- Department of Psychiatry and Psychotherapy, German Center for Neurodegenerative Diseases, University Medicine Greifswald, Greifswald17475, Germany
| | - Hans J. Grabe
- Department of Psychiatry and Psychotherapy, German Center for Neurodegenerative Diseases, University Medicine Greifswald, Greifswald17475, Germany
| | - Duygu Tosun
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA 94143
| | - Murat Bilgel
- Laboratory of Behavioral Neuroscience, National Institute on Aging, NIH, Baltimore21224, MD
| | - Yang An
- Laboratory of Behavioral Neuroscience, National Institute on Aging, NIH, Baltimore21224, MD
| | - Daniel S. Marcus
- Department of Radiology, Washington University School of Medicine, St. Louis, MO63110
| | - Pamela LaMontagne
- Department of Radiology, Washington University School of Medicine, St. Louis, MO63110
| | - Susan R. Heckbert
- Department of Epidemiology, University of Washington, Seattle, WA98195
| | - Thomas R. Austin
- Department of Epidemiology, University of Washington, Seattle, WA98195
| | - Lenore J. Launer
- Neuroepidemiology Section, Intramural Research Program, National Institute on Aging, Washington, MD20817
| | - Mark Espeland
- Sticht Center for Healthy Aging and Alzheimer’s Prevention, Divisions of Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, NC27101
| | - Colin L. Masters
- Florey Institute of Neuroscience and Mental Health, Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC3010, Australia
| | - Paul Maruff
- Florey Institute of Neuroscience and Mental Health, Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC3010, Australia
| | - Jurgen Fripp
- Health and Biosecurity, Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation, Brisbane, QLD4029, Australia
| | - Sterling C. Johnson
- Wisconsin Alzheimer's Institute, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI53792
| | - John C. Morris
- Knight Alzheimer Disease Research Center, Department of Neurology, Washington University in St. Louis, St. Louis, MO63110
| | - Marilyn S. Albert
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD21205
| | - R. Nick Bryan
- Department of Radiology, University of Pennsylvania, Philadelphia, PA19104
| | - Susan M. Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, NIH, Baltimore21224, MD
| | - Yong Fan
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Mohamad Habes
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, Department of Radiology, University of Texas Health Science Center at San Antonio, San Antonio, TX78229
| | - David Wolk
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Department of Neurology, University of Pennsylvania, Philadelphia, PA19104
| | - Haochang Shou
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Christos Davatzikos
- AI in Biomedical Imaging Laboratory, Department of Radiology, Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
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Biswas R, Sripada S. Causal functional connectivity in Alzheimer's disease computed from time series fMRI data. Front Comput Neurosci 2023; 17:1251301. [PMID: 38169714 PMCID: PMC10758424 DOI: 10.3389/fncom.2023.1251301] [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: 07/01/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
Functional connectivity between brain regions is known to be altered in Alzheimer's disease and promises to be a biomarker for early diagnosis. Several approaches for functional connectivity obtain an un-directed network representing stochastic associations (correlations) between brain regions. However, association does not necessarily imply causation. In contrast, Causal Functional Connectivity (CFC) is more informative, providing a directed network representing causal relationships between brain regions. In this paper, we obtained the causal functional connectome for the whole brain from resting-state functional magnetic resonance imaging (rs-fMRI) recordings of subjects from three clinical groups: cognitively normal, mild cognitive impairment, and Alzheimer's disease. We applied the recently developed Time-aware PC (TPC) algorithm to infer the causal functional connectome for the whole brain. TPC supports model-free estimation of whole brain CFC based on directed graphical modeling in a time series setting. We compared the CFC outcome of TPC with that of other related approaches in the literature. Then, we used the CFC outcomes of TPC and performed an exploratory analysis of the difference in strengths of CFC edges between Alzheimer's and cognitively normal groups, based on edge-wise p-values obtained by Welch's t-test. The brain regions thus identified are found to be in agreement with literature on brain regions impacted by Alzheimer's disease, published by researchers from clinical/medical institutions.
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Affiliation(s)
- Rahul Biswas
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, United States
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27
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O'Connell S, Cannon DM, Broin PÓ. Predictive modelling of brain disorders with magnetic resonance imaging: A systematic review of modelling practices, transparency, and interpretability in the use of convolutional neural networks. Hum Brain Mapp 2023; 44:6561-6574. [PMID: 37909364 PMCID: PMC10681646 DOI: 10.1002/hbm.26521] [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: 03/17/2023] [Revised: 09/28/2023] [Accepted: 10/10/2023] [Indexed: 11/03/2023] Open
Abstract
Brain disorders comprise several psychiatric and neurological disorders which can be characterized by impaired cognition, mood alteration, psychosis, depressive episodes, and neurodegeneration. Clinical diagnoses primarily rely on a combination of life history information and questionnaires, with a distinct lack of discriminative biomarkers in use for psychiatric disorders. Symptoms across brain conditions are associated with functional alterations of cognitive and emotional processes, which can correlate with anatomical variation; structural magnetic resonance imaging (MRI) data of the brain are therefore an important focus of research, particularly for predictive modelling. With the advent of large MRI data consortia (such as the Alzheimer's Disease Neuroimaging Initiative) facilitating a greater number of MRI-based classification studies, convolutional neural networks (CNNs)-deep learning models well suited to image processing tasks-have become increasingly popular for research into brain conditions. This has resulted in a myriad of studies reporting impressive predictive performances, demonstrating the potential clinical value of deep learning systems. However, methodologies can vary widely across studies, making them difficult to compare and/or reproduce, potentially limiting their clinical application. Here, we conduct a qualitative systematic literature review of 55 studies carrying out CNN-based predictive modelling of brain disorders using MRI data and evaluate them based on three principles-modelling practices, transparency, and interpretability. We propose several recommendations to enhance the potential for the integration of CNNs into clinical care.
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Affiliation(s)
- Shane O'Connell
- School of Mathematical and Statistical Sciences, College of Science and EngineeringUniversity of GalwayGalwayIreland
| | - Dara M. Cannon
- Clinical Neuroimaging Laboratory, Galway Neuroscience Centre, College of MedicineNursing and Health SciencesUniversity of GalwayGalwayIreland
| | - Pilib Ó. Broin
- School of Mathematical and Statistical Sciences, College of Science and EngineeringUniversity of GalwayGalwayIreland
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28
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Bolla G, Berente DB, Andrássy A, Zsuffa JA, Hidasi Z, Csibri E, Csukly G, Kamondi A, Kiss M, Horvath AA. Comparison of the diagnostic accuracy of resting-state fMRI driven machine learning algorithms in the detection of mild cognitive impairment. Sci Rep 2023; 13:22285. [PMID: 38097674 PMCID: PMC10721802 DOI: 10.1038/s41598-023-49461-y] [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: 04/12/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023] Open
Abstract
Mild cognitive impairment (MCI) is a potential therapeutic window in the prevention of dementia; however, automated detection of early cognitive deterioration is an unresolved issue. The aim of our study was to compare various classification approaches to differentiate MCI patients from healthy controls, based on rs-fMRI data, using machine learning (ML) algorithms. Own dataset (from two centers) and ADNI database were used during the analysis. Three fMRI parameters were applied in five feature selection algorithms: local correlation, intrinsic connectivity, and fractional amplitude of low frequency fluctuations. Support vector machine (SVM) and random forest (RF) methods were applied for classification. We achieved a relatively wide range of 78-87% accuracy for the various feature selection methods with SVM combining the three rs-fMRI parameters. In the ADNI datasets case we can also see even 90% accuracy scores. RF provided a more harmonized result among the feature selection algorithms in both datasets with 80-84% accuracy for our local and 74-82% for the ADNI database. Despite some lower performance metrics of some algorithms, most of the results were positive and could be seen in two unrelated datasets which increase the validity of our methods. Our results highlight the potential of ML-based fMRI applications for automated diagnostic techniques to recognize MCI patients.
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Affiliation(s)
- Gergo Bolla
- Neurocognitive Research Center, National Institute of Mental Health, Neurology and Neurosurgery, Budapest, Hungary
- School of PhD Studies, Semmelweis University, Budapest, Hungary
| | - Dalida Borbala Berente
- Neurocognitive Research Center, National Institute of Mental Health, Neurology and Neurosurgery, Budapest, Hungary
- School of PhD Studies, Semmelweis University, Budapest, Hungary
| | - Anita Andrássy
- Neurocognitive Research Center, National Institute of Mental Health, Neurology and Neurosurgery, Budapest, Hungary
| | - Janos Andras Zsuffa
- Neurocognitive Research Center, National Institute of Mental Health, Neurology and Neurosurgery, Budapest, Hungary
- Department of Family Medicine, Semmelweis University, Budapest, Hungary
| | - Zoltan Hidasi
- Department of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary
| | - Eva Csibri
- Department of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary
| | - Gabor Csukly
- Neurocognitive Research Center, National Institute of Mental Health, Neurology and Neurosurgery, Budapest, Hungary
- Department of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary
| | - Anita Kamondi
- Neurocognitive Research Center, National Institute of Mental Health, Neurology and Neurosurgery, Budapest, Hungary
- Department of Neurology, Semmelweis University, Budapest, Hungary
| | - Mate Kiss
- Siemens Healthcare, Budapest, Hungary
| | - Andras Attila Horvath
- Department of Anatomy Histology and Embryology, Semmelweis University, Budapest, Hungary.
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Bucholc M, James C, Khleifat AA, Badhwar A, Clarke N, Dehsarvi A, Madan CR, Marzi SJ, Shand C, Schilder BM, Tamburin S, Tantiangco HM, Lourida I, Llewellyn DJ, Ranson JM. Artificial intelligence for dementia research methods optimization. Alzheimers Dement 2023; 19:5934-5951. [PMID: 37639369 DOI: 10.1002/alz.13441] [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: 04/03/2023] [Revised: 07/19/2023] [Accepted: 07/23/2023] [Indexed: 08/31/2023]
Abstract
Artificial intelligence (AI) and machine learning (ML) approaches are increasingly being used in dementia research. However, several methodological challenges exist that may limit the insights we can obtain from high-dimensional data and our ability to translate these findings into improved patient outcomes. To improve reproducibility and replicability, researchers should make their well-documented code and modeling pipelines openly available. Data should also be shared where appropriate. To enhance the acceptability of models and AI-enabled systems to users, researchers should prioritize interpretable methods that provide insights into how decisions are generated. Models should be developed using multiple, diverse datasets to improve robustness, generalizability, and reduce potentially harmful bias. To improve clarity and reproducibility, researchers should adhere to reporting guidelines that are co-produced with multiple stakeholders. If these methodological challenges are overcome, AI and ML hold enormous promise for changing the landscape of dementia research and care. HIGHLIGHTS: Machine learning (ML) can improve diagnosis, prevention, and management of dementia. Inadequate reporting of ML procedures affects reproduction/replication of results. ML models built on unrepresentative datasets do not generalize to new datasets. Obligatory metrics for certain model structures and use cases have not been defined. Interpretability and trust in ML predictions are barriers to clinical translation.
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Affiliation(s)
- Magda Bucholc
- Cognitive Analytics Research Lab, School of Computing, Engineering & Intelligent Systems, Ulster University, Derry, UK
| | - Charlotte James
- NIHR Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust and University of Bristol, Bristol, UK
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - AmanPreet Badhwar
- Multiomics Investigation of Neurodegenerative Diseases (MIND) Lab, Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, Montréal, Quebec, Canada
- Institut de génie biomédical, Université de Montréal, Montréal, Quebec, Canada
- Département de Pharmacologie et Physiologie, Université de Montréal, Montréal, Quebec, Canada
| | - Natasha Clarke
- Multiomics Investigation of Neurodegenerative Diseases (MIND) Lab, Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, Montréal, Quebec, Canada
| | - Amir Dehsarvi
- Aberdeen Biomedical Imaging Centre, School of Medicine, Medical Sciences, and Nutrition, University of Aberdeen, Aberdeen, UK
| | | | - Sarah J Marzi
- UK Dementia Research Institute, Imperial College London, London, UK
- Department of Brain Sciences, Imperial College London, London, UK
| | - Cameron Shand
- Centre for Medical Image Computing, Department of Computer Science, University 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
| | - Stefano Tamburin
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | | | | | - David J Llewellyn
- University of Exeter Medical School, Exeter, UK
- The Alan Turing Institute, London, UK
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Arvidsson I, Strandberg O, Palmqvist S, Stomrud E, Cullen N, Janelidze S, Tideman P, Heyden A, Åström K, Hansson O, Mattsson-Carlgren N. Comparing a pre-defined versus deep learning approach for extracting brain atrophy patterns to predict cognitive decline due to Alzheimer's disease in patients with mild cognitive symptoms. RESEARCH SQUARE 2023:rs.3.rs-3569391. [PMID: 37986841 PMCID: PMC10659533 DOI: 10.21203/rs.3.rs-3569391/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Background Predicting future Alzheimer's disease (AD)-related cognitive decline among individuals with subjective cognitive decline (SCD) or mild cognitive impairment (MCI) is an important task for healthcare. Structural brain imaging as measured by magnetic resonance imaging (MRI) could potentially contribute when making such predictions. It is unclear if the predictive performance of MRI can be improved using entire brain images in deep learning (DL) models compared to using pre-defined brain regions. Methods A cohort of 332 individuals with SCD/MCI were included from the Swedish BioFINDER-1 study. The goal was to predict longitudinal SCD/MCI-to-AD dementia progression and change in Mini-Mental State Examination (MMSE) over four years. Four models were evaluated using different predictors: 1) clinical data only, including demographics, cognitive tests and APOE e4 status, 2) clinical data plus hippocampal volume, 3) clinical data plus all regional MRI gray matter volumes (N=68) extracted using FreeSurfer software, 4) a DL model trained using multi-task learning with MRI images, Jacobian determinant images and baseline cognition as input. Models were developed on 80% of subjects (N=267) and tested on the remaining 20% (N=65). Mann-Whitney U-test was used to determine statistically significant differences in performance, with p-values less than 0.05 considered significant. Results In the test set, 21 patients (32.3%) progressed to AD dementia. The performance of the clinical data model for prediction of progression to AD dementia was area under the curve (AUC)=0.87 and four-year cognitive decline was R2=0.17. The performance was significantly improved for both outcomes when adding hippocampal volume (AUC=0.91, R2=0.26, p-values <0.05) or FreeSurfer brain regions (AUC=0.90, R2=0.27, p-values <0.05). Conversely, the DL model did not show any significant difference from the clinical data model (AUC=0.86, R2=0.13). A sensitivity analysis showed that the Jacobian determinant image was more informative than the MRI image, but that performance was maximized when both were included. Conclusions The DL model did not significantly improve the prediction of clinical disease progression in AD, compared to regression models with a single pre-defined brain region.
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Moshe YH, Buchsweiler Y, Teicher M, Artzi M. Handling Missing MRI Data in Brain Tumors Classification Tasks: Usage of Synthetic Images vs. Duplicate Images and Empty Images. J Magn Reson Imaging 2023. [PMID: 37864370 DOI: 10.1002/jmri.29072] [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: 04/25/2023] [Revised: 09/30/2023] [Accepted: 10/02/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND Deep-learning is widely used for lesion classification. However, in the clinic patient data often has missing images. PURPOSE To evaluate the use of generated, duplicate and empty(black) images for replacing missing MRI data in AI brain tumor classification tasks. STUDY TYPE Retrospective. POPULATION 224 patients (local-dataset; low-grade-glioma (LGG) = 37, high-grade-glioma (HGG) = 187) and 335 patients (public-dataset (BraTS); LGG = 76, HGG = 259). The local-dataset was divided into training (64), validation (16), and internal-test-data (20), while the public-dataset was an independent test-set. FIELD STRENGTH/SEQUENCE T1WI, T1WI+C, T2WI, and FLAIR images (1.5T/3.0T-MR), obtained from different suppliers. ASSESSMENT Three image-to-image translation generative-adversarial-network (Pix2Pix-GAN) models were trained on the local-dataset, to generate T1WI, T2WI, and FLAIR images. The rating-and-preference-judgment assessment was performed by three human-readers (radiologist (MD) and two MRI-technicians). Resnet152 was used for classification, and inference was performed on both datasets, with baseline input, and with missing data replaced by 1) generated images; 2) duplication of existing images; and 3) black images. STATISTICAL TESTS The similarity between the generated and the original images was evaluated using the peak-signal-to-noise-ratio (PSNR) and the structural-similarity-index-measure (SSIM). Classification results were evaluated using accuracy, F1-score and the Kolmogorov-Smirnov test and distance. RESULTS For baseline-state, the classification model reached to accuracy = 0.93,0.82 on the local and public-datasets. For the missing-data methods, high similarity was obtained between the generated and the original images with mean PSNR = 35.65,32.94 and SSIM = 0.87,0.91 on the local and public-datasets; 39% of the generated-images were labeled as real images by the human-readers. The classification model using generated-images to replace missing images produced the highest results with mean accuracy = 0.91,0.82 compared to 0.85,0.79 for duplicated and 0.77,0.68 for use of black images; DATA CONCLUSION: The feasibility for inference classification model on an MRI dataset with missing images using the Pix2pix-GAN generated images, was shown. The stability and generalization ability of the model was demonstrated by producing consistent results on two independent datasets. LEVEL OF EVIDENCE 3 TECHNICAL EFFICACY: Stage 5.
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Affiliation(s)
- Yael H Moshe
- Sagol Brain Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Department of Mathematics, Bar Ilan University, Ramat Gan, Israel
| | - Yuval Buchsweiler
- Sagol Brain Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Mina Teicher
- Department of Mathematics, Bar Ilan University, Ramat Gan, Israel
- Gonda Brain Research Center, Bar-Ilan University, Ramat Gan, Israel
| | - Moran Artzi
- Sagol Brain Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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Bottani S, Burgos N, Maire A, Saracino D, Ströer S, Dormont D, Colliot O. Evaluation of MRI-based machine learning approaches for computer-aided diagnosis of dementia in a clinical data warehouse. Med Image Anal 2023; 89:102903. [PMID: 37523918 DOI: 10.1016/j.media.2023.102903] [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: 03/30/2022] [Revised: 06/01/2023] [Accepted: 07/12/2023] [Indexed: 08/02/2023]
Abstract
A variety of algorithms have been proposed for computer-aided diagnosis of dementia from anatomical brain MRI. These approaches achieve high accuracy when applied to research data sets but their performance on real-life clinical routine data has not been evaluated yet. The aim of this work was to study the performance of such approaches on clinical routine data, based on a hospital data warehouse, and to compare the results to those obtained on a research data set. The clinical data set was extracted from the hospital data warehouse of the Greater Paris area, which includes 39 different hospitals. The research set was composed of data from the Alzheimer's Disease Neuroimaging Initiative data set. In the clinical set, the population of interest was identified by exploiting the diagnostic codes from the 10th revision of the International Classification of Diseases that are assigned to each patient. We studied how the imbalance of the training sets, in terms of contrast agent injection and image quality, may bias the results. We demonstrated that computer-aided diagnosis performance was strongly biased upwards (over 17 percent points of balanced accuracy) by the confounders of image quality and contrast agent injection, a phenomenon known as the Clever Hans effect or shortcut learning. When these biases were removed, the performance was very poor. In any case, the performance was considerably lower than on the research data set. Our study highlights that there are still considerable challenges for translating dementia computer-aided diagnosis systems to clinical routine.
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Affiliation(s)
- Simona Bottani
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Inria, Inserm, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, 75013, France
| | - Ninon Burgos
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Inria, Inserm, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, 75013, France
| | | | - Dario Saracino
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Inria, Inserm, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, 75013, France; IM2A, Reference Centre for Rare or Early-Onset Dementias, Département de Neurologie, AP-HP, Hôpital de la Pitié Salpêtrière, Paris, 75013, France
| | - Sebastian Ströer
- AP-HP, Hôpital de la Pitié Salpêtrière, Department of Neuroradiology, Paris, 75013, France
| | - Didier Dormont
- AP-HP, Hôpital de la Pitié Salpêtrière, Department of Neuroradiology, Paris, 75013, France; Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Inria, Inserm, AP-HP, Hôpital de la Pitié-Salpêtrière, DMU DIAMENT, Paris, 75013, France
| | - Olivier Colliot
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, CNRS, Inria, Inserm, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, 75013, France.
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Shin S, Kim K. Prediction of suicidal ideation in children and adolescents using machine learning and deep learning algorithm: A case study in South Korea where suicide is the leading cause of death. Asian J Psychiatr 2023; 88:103725. [PMID: 37595385 DOI: 10.1016/j.ajp.2023.103725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/20/2023]
Abstract
BACKGROUND Korea has the highest suicide rate among Organisation for Economic Co-operation and Development (OECD) countries. Consequently, central and local governments and private organizations in Korea cooperate in promoting various suicide prevention projects to actively respond to suicide problems. Machine learning has been used to predict suicidal ideation in the fields of health and medicine but not from a social science perspective. OBJECTIVE Since suicidal ideation is a major predictor of suicide attempts, being able to anticipate and mitigate it helps prevent suicide. Therefore, this study presents a data-based analysis method for predicting suicidal thoughts quickly and effectively and suggests countermeasures against the causes of suicidal thoughts. PARTICIPANTS AND METHODS To predict early signs of suicidal ideation in children and adolescents, big data collected for approximately 4 years (from 2017 to 2020) from the Korea Youth Policy Institute (NYPI) were used. To accurately predict suicidal ideation, supervised ma- chine learning classification algorithms such as logistic regression, random forest, XGBoost, multilayer perceptron (MLP), and convolutional neural network (CNN) were used. RESULTS Using CNN, suicidal ideation was predicted with an accuracy of approximately 90 %. The logistic regression results showed that sadness and depression increased suicidal thoughts by more than 25 times, and anxiety, loneliness, and experience of abusive language increased suicidal thoughts by more than three times. CONCLUSIONS Machine learning and deep learning approaches have the potential to predict and respond to suicidal thoughts in children, adolescents, and the general population, as well as help respond to the suicide crisis by preemptively identifying the cause.
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Affiliation(s)
- Soomin Shin
- Department of Health and Welfare, Yuhan University, Bucheon 14780, the Republic of Korea
| | - Kyungwon Kim
- School of International Trade and Business, Incheon National University, Incheon 22012, the Republic of Korea.
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Dai Y, Zou B, Zhu C, Li Y, Chen Z, Ji Z, Kui X, Zhang W. DE-JANet: A unified network based on dual encoder and joint attention for Alzheimer's disease classification using multi-modal data. Comput Biol Med 2023; 165:107396. [PMID: 37703717 DOI: 10.1016/j.compbiomed.2023.107396] [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: 04/27/2023] [Revised: 07/28/2023] [Accepted: 08/26/2023] [Indexed: 09/15/2023]
Abstract
Structural magnetic resonance imaging (sMRI), which can reflect cerebral atrophy, plays an important role in the early detection of Alzheimer's disease (AD). However, the information provided by analyzing only the morphological changes in sMRI is relatively limited, and the assessment of the atrophy degree is subjective. Therefore, it is meaningful to combine sMRI with other clinical information to acquire complementary diagnosis information and achieve a more accurate classification of AD. Nevertheless, how to fuse these multi-modal data effectively is still challenging. In this paper, we propose DE-JANet, a unified AD classification network that integrates image data sMRI with non-image clinical data, such as age and Mini-Mental State Examination (MMSE) score, for more effective multi-modal analysis. DE-JANet consists of three key components: (1) a dual encoder module for extracting low-level features from the image and non-image data according to specific encoding regularity, (2) a joint attention module for fusing multi-modal features, and (3) a token classification module for performing AD-related classification according to the fused multi-modal features. Our DE-JANet is evaluated on the ADNI dataset, with a mean accuracy of 0.9722 and 0.9538 for AD classification and mild cognition impairment (MCI) classification, respectively, which is superior to existing methods and indicates advanced performance on AD-related diagnosis tasks.
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Affiliation(s)
- Yulan Dai
- School of Computer Science and Engineering, Central South University, Changsha, China; Hunan Engineering Research Center of Machine Vision and Intelligent Medicine, Changsha, China
| | - Beiji Zou
- School of Computer Science and Engineering, Central South University, Changsha, China; Hunan Engineering Research Center of Machine Vision and Intelligent Medicine, Changsha, China
| | - Chengzhang Zhu
- School of Computer Science and Engineering, Central South University, Changsha, China; Hunan Engineering Research Center of Machine Vision and Intelligent Medicine, Changsha, China.
| | - Yang Li
- School of Computer Science and Engineering, Central South University, Changsha, China; Hunan Engineering Research Center of Machine Vision and Intelligent Medicine, Changsha, China
| | - Zhi Chen
- School of Computer Science and Engineering, Central South University, Changsha, China; Hunan Engineering Research Center of Machine Vision and Intelligent Medicine, Changsha, China
| | - Zexin Ji
- School of Computer Science and Engineering, Central South University, Changsha, China; Hunan Engineering Research Center of Machine Vision and Intelligent Medicine, Changsha, China
| | - Xiaoyan Kui
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Wensheng Zhang
- Institute of Automation, Chinese Academy of Sciences, Beijing, China
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35
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Wen J, Zhao B, Yang Z, Erus G, Skampardoni I, Mamourian E, Cui Y, Hwang G, Bao J, Boquet-Pujadas A, Zhou Z, Veturi Y, Ritchie MD, Shou H, Thompson PM, Shen L, Toga AW, Davatzikos C. The Genetic Architecture of Multimodal Human Brain Age. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.13.536818. [PMID: 37333190 PMCID: PMC10274645 DOI: 10.1101/2023.04.13.536818] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The complex biological mechanisms underlying human brain aging remain incompletely understood, involving multiple body organs and chronic diseases. In this study, we used multimodal magnetic resonance imaging and artificial intelligence to examine the genetic architecture of the brain age gap (BAG) derived from gray matter volume (GM-BAG, N=31,557 European ancestry), white matter microstructure (WM-BAG, N=31,674), and functional connectivity (FC-BAG, N=32,017). We identified sixteen genomic loci that reached genome-wide significance (P-value<5×10-8). A gene-drug-disease network highlighted genes linked to GM-BAG for treating neurodegenerative and neuropsychiatric disorders and WM-BAG genes for cancer therapy. GM-BAG showed the highest heritability enrichment for genetic variants in conserved regions, whereas WM-BAG exhibited the highest heritability enrichment in the 5' untranslated regions; oligodendrocytes and astrocytes, but not neurons, showed significant heritability enrichment in WM and FC-BAG, respectively. Mendelian randomization identified potential causal effects of several exposure variables on brain aging, such as type 2 diabetes on GM-BAG (odds ratio=1.05 [1.01, 1.09], P-value=1.96×10-2) and AD on WM-BAG (odds ratio=1.04 [1.02, 1.05], P-value=7.18×10-5). Overall, our results provide valuable insights into the genetics of human brain aging, with clinical implications for potential lifestyle and therapeutic interventions. All results are publicly available at the MEDICINE knowledge portal: https://labs.loni.usc.edu/medicine.
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Affiliation(s)
- Junhao Wen
- Laboratory of AI and Biomedical Science (LABS), Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, USA
| | - Bingxin Zhao
- Department of Statistics and Data Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhijian Yang
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Guray Erus
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Ioanna Skampardoni
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Elizabeth Mamourian
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Yuhan Cui
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Gyujoon Hwang
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Jingxuan Bao
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | | | - Zhen Zhou
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Yogasudha Veturi
- Department of Biobehavioral Health and Statistics, Penn State University, University Park, PA, USA
| | - Marylyn D Ritchie
- Department of Genetics and Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Haochang Shou
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Marina del Rey, California
| | - Li Shen
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Arthur W Toga
- Laboratory of Neuro Imaging (LONI), Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, USA
| | - Christos Davatzikos
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
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Shahzadi S, Butt NA, Sana MU, Pascual IE, Urbano MB, Díez IDLT, Ashraf I. Voxel Extraction and Multiclass Classification of Identified Brain Regions across Various Stages of Alzheimer's Disease Using Machine Learning Approaches. Diagnostics (Basel) 2023; 13:2871. [PMID: 37761238 PMCID: PMC10527683 DOI: 10.3390/diagnostics13182871] [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: 07/17/2023] [Revised: 08/25/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
This study sought to investigate how different brain regions are affected by Alzheimer's disease (AD) at various phases of the disease, using independent component analysis (ICA). The study examines six regions in the mild cognitive impairment (MCI) stage, four in the early stage of Alzheimer's disease (AD), six in the moderate stage, and six in the severe stage. The precuneus, cuneus, middle frontal gyri, calcarine cortex, superior medial frontal gyri, and superior frontal gyri were the areas impacted at all phases. A general linear model (GLM) is used to extract the voxels of the previously mentioned regions. The resting fMRI data for 18 AD patients who had advanced from MCI to stage 3 of the disease were obtained from the ADNI public source database. The subjects include eight women and ten men. The voxel dataset is used to train and test ten machine learning algorithms to categorize the MCI, mild, moderate, and severe stages of Alzheimer's disease. The accuracy, recall, precision, and F1 score were used as conventional scoring measures to evaluate the classification outcomes. AdaBoost fared better than the other algorithms and obtained a phenomenal accuracy of 98.61%, precision of 99.00%, and recall and F1 scores of 98.00% each.
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Affiliation(s)
- Samra Shahzadi
- Department of Computer Science, Faculty of Computing and Information Technology, University of Gujrat, Gujrat 50700, Pakistan; (S.S.); (N.A.B.)
| | - Naveed Anwer Butt
- Department of Computer Science, Faculty of Computing and Information Technology, University of Gujrat, Gujrat 50700, Pakistan; (S.S.); (N.A.B.)
| | - Muhammad Usman Sana
- Department of Information Technology, University of Gujrat, Gujrat 50700, Pakistan;
| | - Iñaki Elío Pascual
- Universidad Europea del Atlántico, Isabel Torres 21, 39011 Santander, Spain; (I.E.P.); (M.B.U.)
- Universidade Internacional do Cuanza, Cuito EN250, Bié, Angola
- Fundación Universitaria Internacional de Colombia, Bogotá 11001, Colombia
| | - Mercedes Briones Urbano
- Universidad Europea del Atlántico, Isabel Torres 21, 39011 Santander, Spain; (I.E.P.); (M.B.U.)
- Universidad Internacional Iberoamericana, Campeche 24560, Mexico
- Universidad Internacional Iberoamericana, Arecibo, PR 00613, USA
| | - Isabel de la Torre Díez
- Department of Signal Theory, Communications and Telematics Engineering, Unviersity of Valladolid, Paseo de Belén, 15, 47011 Valladolid, Spain
| | - Imran Ashraf
- Department of Information and Communication Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
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37
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Zhang X, Li Z, Zhang Q, Yin Z, Lu Z, Li Y. A new weakly supervised deep neural network for recognizing Alzheimer's disease. Comput Biol Med 2023; 163:107079. [PMID: 37321100 DOI: 10.1016/j.compbiomed.2023.107079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/15/2023] [Accepted: 05/27/2023] [Indexed: 06/17/2023]
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative disease that mainly affects older adults, causing memory loss and decline in thinking skills. In recent years, many traditional machine learning and deep learning methods have been used to assist in the diagnosis of AD, and most existing methods focus on early prediction of disease on a supervised basis. In reality, there is a massive amount of medical data available. However, some of those data have problems with the low-quality or lack of labels, and the cost of labeling them will be too high. To solve above problem, a new Weakly Supervised Deep Learning model (WSDL) is proposed, which adds attention mechanisms and consistency regularization to the EfficientNet framework and uses data augmentation techniques on the original data that can take full advantage of this unlabeled data. Validation of the proposed WSDL method on the brain MRI datasets of the Alzheimer's Disease Neuroimaging Program by setting five different unlabeled ratios to complete weakly supervised training showed better performance according to the compared experimental results with others baselines.
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Affiliation(s)
- Xiaobo Zhang
- School of Computing and Artificial Intelligence, SouthWest JiaoTong University, Chengdu 611756, China; Engineering Research Center of Sustainable Urban Intelligent Transportation, Ministry of Education, Chengdu 611756, China; National Engineering Laboratory of Integrated Transportation Big Data Application Technology, Southwest Jiaotong University, Chengdu 611756, China
| | - Zhimin Li
- School of Computing and Artificial Intelligence, SouthWest JiaoTong University, Chengdu 611756, China
| | - Qian Zhang
- School of Economics and Management, Chengdu Textile College, Chengdu 611731, China.
| | - Zegang Yin
- Department of Neurology, The General Hospital of Western Theater Command, Chengdu 610083, China
| | - Zhijie Lu
- Department of Neurology, The General Hospital of Western Theater Command, Chengdu 610083, China
| | - Yang Li
- School of Automation Science and Electrical Engineering, Beijing University of Aeronautics and Astronautics, Beijing 100191, China
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38
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Wen J, Li Y, Fang M, Zhu L, Feng DD, Li P. Fine-Grained and Multiple Classification for Alzheimer's Disease With Wavelet Convolution Unit Network. IEEE Trans Biomed Eng 2023; 70:2592-2603. [PMID: 37030751 DOI: 10.1109/tbme.2023.3256042] [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: 03/19/2023]
Abstract
In this article, we propose a novel wavelet convolution unit for the image-oriented neural network to integrate wavelet analysis with a vanilla convolution operator to extract deep abstract features more efficiently. On one hand, in order to acquire non-local receptive fields and avoid information loss, we define a new convolution operation by composing a traditional convolution function and approximate and detailed representations after single-scale wavelet decomposition of source images. On the other hand, multi-scale wavelet decomposition is introduced to obtain more comprehensive multi-scale feature information. Then, we fuse all these cross-scale features to improve the problem of inaccurate localization of singular points. Given the novel wavelet convolution unit, we further design a network based on it for fine-grained Alzheimer's disease classifications (i.e., Alzheimer's disease, Normal controls, early mild cognitive impairment, late mild cognitive impairment). Up to now, only a few methods have studied one or several fine-grained classifications, and even fewer methods can achieve both fine-grained and multi-class classifications. We adopt the novel network and diffuse tensor images to achieve fine-grained classifications, which achieved state-of-the-art accuracy for all eight kinds of fine-grained classifications, up to 97.30%, 95.78%, 95.00%, 94.00%, 97.89%, 95.71%, 95.07%, 93.79%. In order to build a reference standard for Alzheimer's disease classifications, we actually implemented all twelve coarse-grained and fine-grained classifications. The results show that the proposed method achieves solidly high accuracy for them. Its classification ability greatly exceeds any kind of existing Alzheimer's disease classification method.
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Wu Z, Tang X, Wu J, Huang J, Shen J, Hong H. Portable deep-learning decoder for motor imaginary EEG signals based on a novel compact convolutional neural network incorporating spatial-attention mechanism. Med Biol Eng Comput 2023; 61:2391-2404. [PMID: 37095297 DOI: 10.1007/s11517-023-02840-z] [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: 10/10/2022] [Accepted: 04/13/2023] [Indexed: 04/26/2023]
Abstract
Due to high computational requirements, deep-learning decoders for motor imaginary (MI) electroencephalography (EEG) signals are usually implemented on bulky and heavy computing devices that are inconvenient for physical actions. To date, the application of deep-learning techniques in independent portable brain-computer-interface (BCI) devices has not been extensively explored. In this study, we proposed a high-accuracy MI EEG decoder by incorporating spatial-attention mechanism into convolution neural network (CNN), and deployed it on fully integrated single-chip microcontroller unit (MCU). After the CNN model was trained on workstation computer using GigaDB MI datasets (52 subjects), its parameters were then extracted and converted to build deep-learning architecture interpreter on MCU. For comparison, EEG-Inception model was also trained using the same dataset, and was deployed on MCU. The results indicate that our deep-learning model can independently decode imaginary left-/right-hand motions. The mean accuracy of the proposed compact CNN reaches 96.75 ± 2.41% (8 channels: Frontocentral3 (FC3), FC4, Central1 (C1), C2, Central-Parietal1 (CP1), CP2, C3, and C4), versus 76.96 ± 19.08% of EEG-Inception (6 channels: FC3, FC4, C1, C2, CP1, and CP2). To the best of our knowledge, this is the first portable deep-learning decoder for MI EEG signals. The findings demonstrate high-accuracy deep-learning decoding of MI EEG in a portable mode, which has great implications for hand-disabled patients. Our portable system can be used for developing artificial-intelligent wearable BCI devices, as it is less computationally expensive and convenient for real-life application.
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Affiliation(s)
- Zhanxiong Wu
- School of Electronic Information, Hangzhou Dianzi University, Hangzhou, 310018, Zhejiang, China.
| | - Xudong Tang
- School of Electronic Information, Hangzhou Dianzi University, Hangzhou, 310018, Zhejiang, China
| | - Jinhui Wu
- School of Electronic Information, Hangzhou Dianzi University, Hangzhou, 310018, Zhejiang, China
| | - Jiye Huang
- School of Electronic Information, Hangzhou Dianzi University, Hangzhou, 310018, Zhejiang, China
| | - Jian Shen
- Neurosurgery Department, The First Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Hui Hong
- School of Electronic Information, Hangzhou Dianzi University, Hangzhou, 310018, Zhejiang, China
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Zhang Y, He X, Chan YH, Teng Q, Rajapakse JC. Multi-modal graph neural network for early diagnosis of Alzheimer's disease from sMRI and PET scans. Comput Biol Med 2023; 164:107328. [PMID: 37573721 DOI: 10.1016/j.compbiomed.2023.107328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/27/2023] [Accepted: 08/07/2023] [Indexed: 08/15/2023]
Abstract
In recent years, deep learning models have been applied to neuroimaging data for early diagnosis of Alzheimer's disease (AD). Structural magnetic resonance imaging (sMRI) and positron emission tomography (PET) images provide structural and functional information about the brain, respectively. Combining these features leads to improved performance than using a single modality alone in building predictive models for AD diagnosis. However, current multi-modal approaches in deep learning, based on sMRI and PET, are mostly limited to convolutional neural networks, which do not facilitate integration of both image and phenotypic information of subjects. We propose to use graph neural networks (GNN) that are designed to deal with problems in non-Euclidean domains. In this study, we demonstrate how brain networks are created from sMRI or PET images and can be used in a population graph framework that combines phenotypic information with imaging features of the brain networks. Then, we present a multi-modal GNN framework where each modality has its own branch of GNN and a technique that combines the multi-modal data at both the level of node vectors and adjacency matrices. Finally, we perform late fusion to combine the preliminary decisions made in each branch and produce a final prediction. As multi-modality data becomes available, multi-source and multi-modal is the trend of AD diagnosis. We conducted explorative experiments based on multi-modal imaging data combined with non-imaging phenotypic information for AD diagnosis and analyzed the impact of phenotypic information on diagnostic performance. Results from experiments demonstrated that our proposed multi-modal approach improves performance for AD diagnosis. Our study also provides technical reference and support the need for multivariate multi-modal diagnosis methods.
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Affiliation(s)
- Yanteng Zhang
- College of Electronics and Information Engineering, Sichuan University, Chengdu, 610065, China; School of Computer Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Xiaohai He
- College of Electronics and Information Engineering, Sichuan University, Chengdu, 610065, China
| | - Yi Hao Chan
- School of Computer Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore
| | - Qizhi Teng
- College of Electronics and Information Engineering, Sichuan University, Chengdu, 610065, China
| | - Jagath C Rajapakse
- School of Computer Science and Engineering, Nanyang Technological University, Singapore, 639798, Singapore.
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Mendis L, Palaniswami M, Brownfoot F, Keenan E. Computerised Cardiotocography Analysis for the Automated Detection of Fetal Compromise during Labour: A Review. Bioengineering (Basel) 2023; 10:1007. [PMID: 37760109 PMCID: PMC10525263 DOI: 10.3390/bioengineering10091007] [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: 07/12/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
The measurement and analysis of fetal heart rate (FHR) and uterine contraction (UC) patterns, known as cardiotocography (CTG), is a key technology for detecting fetal compromise during labour. This technology is commonly used by clinicians to make decisions on the mode of delivery to minimise adverse outcomes. A range of computerised CTG analysis techniques have been proposed to overcome the limitations of manual clinician interpretation. While these automated techniques can potentially improve patient outcomes, their adoption into clinical practice remains limited. This review provides an overview of current FHR and UC monitoring technologies, public and private CTG datasets, pre-processing steps, and classification algorithms used in automated approaches for fetal compromise detection. It aims to highlight challenges inhibiting the translation of automated CTG analysis methods from research to clinical application and provide recommendations to overcome them.
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Affiliation(s)
- Lochana Mendis
- Department of Electrical and Electronic Engineering, The University of Melbourne, Parkville, VIC 3010, Australia; (M.P.); (E.K.)
| | - Marimuthu Palaniswami
- Department of Electrical and Electronic Engineering, The University of Melbourne, Parkville, VIC 3010, Australia; (M.P.); (E.K.)
| | - Fiona Brownfoot
- Obstetric Diagnostics and Therapeutics Group, Department of Obstetrics and Gynaecology, The University of Melbourne, Heidelberg, VIC 3084, Australia;
| | - Emerson Keenan
- Department of Electrical and Electronic Engineering, The University of Melbourne, Parkville, VIC 3010, Australia; (M.P.); (E.K.)
- Obstetric Diagnostics and Therapeutics Group, Department of Obstetrics and Gynaecology, The University of Melbourne, Heidelberg, VIC 3084, Australia;
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Wen J, Skampardoni I, Tian YE, Yang Z, Cui Y, Erus G, Hwang G, Varol E, Boquet-Pujadas A, Chand GB, Nasrallah I, Satterthwaite T, Shou H, Shen L, Toga AW, Zaleskey A, Davatzikos C. Neuroimaging-AI Endophenotypes of Brain Diseases in the General Population: Towards a Dimensional System of Vulnerability. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.16.23294179. [PMID: 37662256 PMCID: PMC10473785 DOI: 10.1101/2023.08.16.23294179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Disease heterogeneity poses a significant challenge for precision diagnostics in both clinical and sub-clinical stages. Recent work leveraging artificial intelligence (AI) has offered promise to dissect this heterogeneity by identifying complex intermediate phenotypes - herein called dimensional neuroimaging endophenotypes (DNEs) - which subtype various neurologic and neuropsychiatric diseases. We investigate the presence of nine such DNEs derived from independent yet harmonized studies on Alzheimer's disease (AD1-2)1, autism spectrum disorder (ASD1-3)2, late-life depression (LLD1-2)3, and schizophrenia (SCZ1-2)4, in the general population of 39,178 participants in the UK Biobank study. Phenome-wide associations revealed prominent associations between the nine DNEs and phenotypes related to the brain and other human organ systems. This phenotypic landscape aligns with the SNP-phenotype genome-wide associations, revealing 31 genomic loci associated with the nine DNEs (Bonferroni corrected P-value < 5×10-8/9). The DNEs exhibited significant genetic correlations, colocalization, and causal relationships with multiple human organ systems and chronic diseases. A causal effect (odds ratio=1.25 [1.11, 1.40], P-value=8.72×1-4) was established from AD2, characterized by focal medial temporal lobe atrophy, to AD. The nine DNEs and their polygenic risk scores significantly improved the prediction accuracy for 14 systemic disease categories and mortality. These findings underscore the potential of the nine DNEs to identify individuals at a high risk of developing the four brain diseases during preclinical stages for precision diagnostics. All results are publicly available at: http://labs.loni.usc.edu/medicine/.
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Affiliation(s)
- Junhao Wen
- Laboratory of AI and Biomedical Science (LABS), Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, USA
| | - Ioanna Skampardoni
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Ye Ella Tian
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia
| | - Zhijian Yang
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Yuhan Cui
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Guray Erus
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Gyujoon Hwang
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Erdem Varol
- Department of Computer Science and Engineering, New York University, New York, USA
| | | | - Ganesh B. Chand
- Department of Radiology, School of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Ilya Nasrallah
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Theodore Satterthwaite
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Haochang Shou
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Li Shen
- Department of Biostatistics, Epidemiology and Informatics University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Arthur W. Toga
- Laboratory of Neuro Imaging (LONI), Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, USA
| | - Andrew Zaleskey
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia
| | - Christos Davatzikos
- Artificial Intelligence in Biomedical Imaging Laboratory (AIBIL), Center for AI and Data Science for Integrated Diagnostics (AID), Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
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Zhang ZC, Zhao X, Dong G, Zhao XM. Improving Alzheimer's Disease Diagnosis With Multi-Modal PET Embedding Features by a 3D Multi-Task MLP-Mixer Neural Network. IEEE J Biomed Health Inform 2023; 27:4040-4051. [PMID: 37247318 DOI: 10.1109/jbhi.2023.3280823] [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: 05/31/2023]
Abstract
Positron emission tomography (PET) with fluorodeoxyglucose (FDG) or florbetapir (AV45) has been proved effective in the diagnosis of Alzheimer's disease. However, the expensive and radioactive nature of PET has limited its application. Here, employing multi-layer perceptron mixer architecture, we present a deep learning model, namely 3-dimensional multi-task multi-layer perceptron mixer, for simultaneously predicting the standardized uptake value ratios (SUVRs) for FDG-PET and AV45-PET from the cheap and widely used structural magnetic resonance imaging data, and the model can be further used for Alzheimer's disease diagnosis based on embedding features derived from SUVR prediction. Experiment results demonstrate the high prediction accuracy of the proposed method for FDG/AV45-PET SUVRs, where we achieved Pearson's correlation coefficients of 0.66 and 0.61 respectively between the estimated and actual SUVR and the estimated SUVRs also show high sensitivity and distinct longitudinal patterns for different disease status. By taking into account PET embedding features, the proposed method outperforms other competing methods on five independent datasets in the diagnosis of Alzheimer's disease and discriminating between stable and progressive mild cognitive impairments, achieving the area under receiver operating characteristic curves of 0.968 and 0.776 respectively on ADNI dataset, and generalizes better to other external datasets. Moreover, the top-weighted patches extracted from the trained model involve important brain regions related to Alzheimer's disease, suggesting good biological interpretability of our proposed method."
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Zhang J, He X, Liu Y, Cai Q, Chen H, Qing L. Multi-modal cross-attention network for Alzheimer's disease diagnosis with multi-modality data. Comput Biol Med 2023; 162:107050. [PMID: 37269680 DOI: 10.1016/j.compbiomed.2023.107050] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 04/26/2023] [Accepted: 05/03/2023] [Indexed: 06/05/2023]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder, the most common cause of dementia, so the accurate diagnosis of AD and its prodromal stage mild cognitive impairment (MCI) is significant. Recent studies have demonstrated that multiple neuroimaging and biological measures contain complementary information for diagnosis. Many existing multi-modal models based on deep learning simply concatenate each modality's features despite substantial differences in representation spaces. In this paper, we propose a novel multi-modal cross-attention AD diagnosis (MCAD) framework to learn the interaction between modalities for better playing their complementary roles for AD diagnosis with multi-modal data including structural magnetic resonance imaging (sMRI), fluorodeoxyglucose-positron emission tomography (FDG-PET) and cerebrospinal fluid (CSF) biomarkers. Specifically, the imaging and non-imaging representations are learned by the image encoder based on cascaded dilated convolutions and CSF encoder, respectively. Then, a multi-modal interaction module is introduced, which takes advantage of cross-modal attention to integrate imaging and non-imaging information and reinforce relationships between these modalities. Moreover, an extensive objective function is designed to reduce the discrepancy between modalities for effectively fusing the features of multi-modal data, which could further improve the diagnosis performance. We evaluate the effectiveness of our proposed method on the ADNI dataset, and the extensive experiments demonstrate that our MCAD achieves superior performance for multiple AD-related classification tasks, compared to several competing methods. Also, we investigate the importance of cross-attention and the contribution of each modality to the diagnostics performance. The experimental results demonstrate that combining multi-modality data via cross-attention is helpful for accurate AD diagnosis.
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Affiliation(s)
- Jin Zhang
- College of Electronics and Information Engineering, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Xiaohai He
- College of Electronics and Information Engineering, Sichuan University, Chengdu, Sichuan, 610065, China.
| | - Yan Liu
- Department of Neurology, The Affiliated Hospital of Southwest Jiaotong University, The Third People's Hospital of Chengdu, Chengdu, Sichuan, 610031, China
| | - Qingyan Cai
- Department of Geriatric Medicine, The Fourth People's Hospital of Chengdu, Chengdu, Sichuan, 610036, China
| | - Honggang Chen
- College of Electronics and Information Engineering, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Linbo Qing
- College of Electronics and Information Engineering, Sichuan University, Chengdu, Sichuan, 610065, China
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Zhang Y, Li H, Zheng Q. A comprehensive characterization of hippocampal feature ensemble serves as individualized brain signature for Alzheimer's disease: deep learning analysis in 3238 participants worldwide. Eur Radiol 2023; 33:5385-5397. [PMID: 36892643 DOI: 10.1007/s00330-023-09519-x] [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: 08/10/2022] [Revised: 12/19/2022] [Accepted: 02/02/2023] [Indexed: 03/10/2023]
Abstract
OBJECTIVES Hippocampal characterization is one of the most significant hallmarks of Alzheimer's disease (AD); rather, the single-level feature is insufficient. A comprehensive hippocampal characterization is pivotal for developing a well-performing biomarker for AD. To verify whether a comprehensive characterization of hippocampal features of gray matter volume, segmentation probability, and radiomics features could better distinguish AD from normal control (NC), and to investigate whether the classification decision score could serve as a robust and individualized brain signature. METHODS A total of 3238 participants' structural MRI from four independent databases were employed to conduct a 3D residual attention network (3DRA-Net) to classify NC, mild cognitive impairment (MCI), and AD. The generalization was validated under inter-database cross-validation. The neurobiological basis of the classification decision score as a neuroimaging biomarker was systematically investigated by association with clinical profiles, as well as longitudinal trajectory analysis to reveal AD progression. All image analyses were performed only upon the single modality of T1-weighted MRI. RESULTS Our study exhibited an outstanding performance (ACC = 91.6%, AUC = 0.95) of the comprehensive characterization of hippocampal features in distinguishing AD (n = 282) from NC (n = 603) in Alzheimer's Disease Neuroimaging Initiative cohort, and ACC = 89.2% and AUC = 0.93 under external validation. More importantly, the constructed score was significantly correlated with clinical profiles (p < 0.05), and dynamically altered over the AD longitudinal progression, provided compelling evidence of a solid neurobiological basis. CONCLUSIONS This systemic study highlights the potential of the comprehensive characterization of hippocampal features to provide an individualized, generalizable, and biologically plausible neuroimaging biomarker for early detection of AD. KEY POINTS • The comprehensive characterization of hippocampal features exhibited ACC = 91.6% (AUC = 0.95) in classifying AD from NC under intra-database cross-validation, and ACC = 89.2% (AUC = 0.93) in external validation. • The constructed classification score was significantly associated with clinical profiles, and dynamically altered over the AD longitudinal progression, which highlighted its potential of being an individualized, generalizable, and biologically plausible neuroimaging biomarker for early detection of AD.
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Affiliation(s)
- Yiyu Zhang
- School of Computer and Control Engineering, Yantai University, No. 30, Qingquan Road, Laishan District, Yantai City, 264005, Shandong Province, China
| | - Hongming Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Qiang Zheng
- School of Computer and Control Engineering, Yantai University, No. 30, Qingquan Road, Laishan District, Yantai City, 264005, Shandong Province, China.
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Yi F, Yang H, Chen D, Qin Y, Han H, Cui J, Bai W, Ma Y, Zhang R, Yu H. XGBoost-SHAP-based interpretable diagnostic framework for alzheimer's disease. BMC Med Inform Decis Mak 2023; 23:137. [PMID: 37491248 PMCID: PMC10369804 DOI: 10.1186/s12911-023-02238-9] [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: 10/09/2022] [Accepted: 07/13/2023] [Indexed: 07/27/2023] Open
Abstract
BACKGROUND Due to the class imbalance issue faced when Alzheimer's disease (AD) develops from normal cognition (NC) to mild cognitive impairment (MCI), present clinical practice is met with challenges regarding the auxiliary diagnosis of AD using machine learning (ML). This leads to low diagnosis performance. We aimed to construct an interpretable framework, extreme gradient boosting-Shapley additive explanations (XGBoost-SHAP), to handle the imbalance among different AD progression statuses at the algorithmic level. We also sought to achieve multiclassification of NC, MCI, and AD. METHODS We obtained patient data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database, including clinical information, neuropsychological test results, neuroimaging-derived biomarkers, and APOE-ε4 gene statuses. First, three feature selection algorithms were applied, and they were then included in the XGBoost algorithm. Due to the imbalance among the three classes, we changed the sample weight distribution to achieve multiclassification of NC, MCI, and AD. Then, the SHAP method was linked to XGBoost to form an interpretable framework. This framework utilized attribution ideas that quantified the impacts of model predictions into numerical values and analysed them based on their directions and sizes. Subsequently, the top 10 features (optimal subset) were used to simplify the clinical decision-making process, and their performance was compared with that of a random forest (RF), Bagging, AdaBoost, and a naive Bayes (NB) classifier. Finally, the National Alzheimer's Coordinating Center (NACC) dataset was employed to assess the impact path consistency of the features within the optimal subset. RESULTS Compared to the RF, Bagging, AdaBoost, NB and XGBoost (unweighted), the interpretable framework had higher classification performance with accuracy improvements of 0.74%, 0.74%, 1.46%, 13.18%, and 0.83%, respectively. The framework achieved high sensitivity (81.21%/74.85%), specificity (92.18%/89.86%), accuracy (87.57%/80.52%), area under the receiver operating characteristic curve (AUC) (0.91/0.88), positive clinical utility index (0.71/0.56), and negative clinical utility index (0.75/0.68) on the ADNI and NACC datasets, respectively. In the ADNI dataset, the top 10 features were found to have varying associations with the risk of AD onset based on their SHAP values. Specifically, the higher SHAP values of CDRSB, ADAS13, ADAS11, ventricle volume, ADASQ4, and FAQ were associated with higher risks of AD onset. Conversely, the higher SHAP values of LDELTOTAL, mPACCdigit, RAVLT_immediate, and MMSE were associated with lower risks of AD onset. Similar results were found for the NACC dataset. CONCLUSIONS The proposed interpretable framework contributes to achieving excellent performance in imbalanced AD multiclassification tasks and provides scientific guidance (optimal subset) for clinical decision-making, thereby facilitating disease management and offering new research ideas for optimizing AD prevention and treatment programs.
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Affiliation(s)
- Fuliang Yi
- Department of Health Statistics, School of Public Health, Shanxi Medical University, 56 South XinJian Road, Taiyuan, 030001 P.R. China
| | - Hui Yang
- Department of Health Statistics, School of Public Health, Shanxi Medical University, 56 South XinJian Road, Taiyuan, 030001 P.R. China
| | - Durong Chen
- Department of Health Statistics, School of Public Health, Shanxi Medical University, 56 South XinJian Road, Taiyuan, 030001 P.R. China
| | - Yao Qin
- Department of Health Statistics, School of Public Health, Shanxi Medical University, 56 South XinJian Road, Taiyuan, 030001 P.R. China
| | - Hongjuan Han
- Department of Health Statistics, School of Public Health, Shanxi Medical University, 56 South XinJian Road, Taiyuan, 030001 P.R. China
| | - Jing Cui
- Department of Health Statistics, School of Public Health, Shanxi Medical University, 56 South XinJian Road, Taiyuan, 030001 P.R. China
| | - Wenlin Bai
- Department of Health Statistics, School of Public Health, Shanxi Medical University, 56 South XinJian Road, Taiyuan, 030001 P.R. China
| | - Yifei Ma
- Department of Health Statistics, School of Public Health, Shanxi Medical University, 56 South XinJian Road, Taiyuan, 030001 P.R. China
| | - Rong Zhang
- Department of Health Statistics, School of Public Health, Shanxi Medical University, 56 South XinJian Road, Taiyuan, 030001 P.R. China
| | - Hongmei Yu
- Department of Health Statistics, School of Public Health, Shanxi Medical University, 56 South XinJian Road, Taiyuan, 030001 P.R. China
- Shanxi Provincial Key Laboratory of Major Diseases Risk Assessment, Taiyuan, China
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Azeem M, Javaid S, Khalil RA, Fahim H, Althobaiti T, Alsharif N, Saeed N. Neural Networks for the Detection of COVID-19 and Other Diseases: Prospects and Challenges. Bioengineering (Basel) 2023; 10:850. [PMID: 37508877 PMCID: PMC10416184 DOI: 10.3390/bioengineering10070850] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/09/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Artificial neural networks (ANNs) ability to learn, correct errors, and transform a large amount of raw data into beneficial medical decisions for treatment and care has increased in popularity for enhanced patient safety and quality of care. Therefore, this paper reviews the critical role of ANNs in providing valuable insights for patients' healthcare decisions and efficient disease diagnosis. We study different types of ANNs in the existing literature that advance ANNs' adaptation for complex applications. Specifically, we investigate ANNs' advances for predicting viral, cancer, skin, and COVID-19 diseases. Furthermore, we propose a deep convolutional neural network (CNN) model called ConXNet, based on chest radiography images, to improve the detection accuracy of COVID-19 disease. ConXNet is trained and tested using a chest radiography image dataset obtained from Kaggle, achieving more than 97% accuracy and 98% precision, which is better than other existing state-of-the-art models, such as DeTraC, U-Net, COVID MTNet, and COVID-Net, having 93.1%, 94.10%, 84.76%, and 90% accuracy and 94%, 95%, 85%, and 92% precision, respectively. The results show that the ConXNet model performed significantly well for a relatively large dataset compared with the aforementioned models. Moreover, the ConXNet model reduces the time complexity by using dropout layers and batch normalization techniques. Finally, we highlight future research directions and challenges, such as the complexity of the algorithms, insufficient available data, privacy and security, and integration of biosensing with ANNs. These research directions require considerable attention for improving the scope of ANNs for medical diagnostic and treatment applications.
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Affiliation(s)
- Muhammad Azeem
- School of Science, Engineering & Environment, University of Salford, Manchester M5 4WT, UK;
| | - Shumaila Javaid
- Department of Control Science and Engineering, College of Electronics and Information Engineering, Tongji University, Shanghai 201804, China; (S.J.); (H.F.)
| | - Ruhul Amin Khalil
- Department of Electrical Engineering, University of Engineering and Technology, Peshawar 25120, Pakistan;
- Department of Electrical and Communication Engineering, United Arab Emirates University (UAEU), Al-Ain 15551, United Arab Emirates
| | - Hamza Fahim
- Department of Control Science and Engineering, College of Electronics and Information Engineering, Tongji University, Shanghai 201804, China; (S.J.); (H.F.)
| | - Turke Althobaiti
- Department of Computer Science, Faculty of Science, Northern Border University, Arar 73222, Saudi Arabia;
| | - Nasser Alsharif
- Department of Administrative and Financial Sciences, Ranyah University Collage, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Nasir Saeed
- Department of Electrical and Communication Engineering, United Arab Emirates University (UAEU), Al-Ain 15551, United Arab Emirates
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Leming MJ, Bron EE, Bruffaerts R, Ou Y, Iglesias JE, Gollub RL, Im H. Challenges of implementing computer-aided diagnostic models for neuroimages in a clinical setting. NPJ Digit Med 2023; 6:129. [PMID: 37443276 DOI: 10.1038/s41746-023-00868-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Advances in artificial intelligence have cultivated a strong interest in developing and validating the clinical utilities of computer-aided diagnostic models. Machine learning for diagnostic neuroimaging has often been applied to detect psychological and neurological disorders, typically on small-scale datasets or data collected in a research setting. With the collection and collation of an ever-growing number of public datasets that researchers can freely access, much work has been done in adapting machine learning models to classify these neuroimages by diseases such as Alzheimer's, ADHD, autism, bipolar disorder, and so on. These studies often come with the promise of being implemented clinically, but despite intense interest in this topic in the laboratory, limited progress has been made in clinical implementation. In this review, we analyze challenges specific to the clinical implementation of diagnostic AI models for neuroimaging data, looking at the differences between laboratory and clinical settings, the inherent limitations of diagnostic AI, and the different incentives and skill sets between research institutions, technology companies, and hospitals. These complexities need to be recognized in the translation of diagnostic AI for neuroimaging from the laboratory to the clinic.
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Affiliation(s)
- Matthew J Leming
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA.
- Massachusetts Alzheimer's Disease Research Center, Charlestown, MA, USA.
| | - Esther E Bron
- Department of Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Rose Bruffaerts
- Computational Neurology, Experimental Neurobiology Unit (ENU), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Yangming Ou
- Boston Children's Hospital, 300 Longwood Ave, Boston, MA, USA
| | - Juan Eugenio Iglesias
- Center for Medical Image Computing, University College London, London, UK
- Martinos Center for Biomedical Imaging, Harvard Medical School, Boston, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Randy L Gollub
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hyungsoon Im
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA.
- Massachusetts Alzheimer's Disease Research Center, Charlestown, MA, USA.
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA.
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Liu L, Liu S, Zhang L, To XV, Nasrallah F, Chandra SS. Cascaded Multi-Modal Mixing Transformers for Alzheimer's Disease Classification with Incomplete Data. Neuroimage 2023:120267. [PMID: 37422279 DOI: 10.1016/j.neuroimage.2023.120267] [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: 02/20/2023] [Revised: 06/27/2023] [Accepted: 07/05/2023] [Indexed: 07/10/2023] Open
Abstract
Accurate medical classification requires a large number of multi-modal data, and in many cases, different feature types. Previous studies have shown promising results when using multi-modal data, outperforming single-modality models when classifying diseases such as Alzheimer's Disease (AD). However, those models are usually not flexible enough to handle missing modalities. Currently, the most common workaround is discarding samples with missing modalities which leads to considerable data under-utilisation. Adding to the fact that labelled medical images are already scarce, the performance of data-driven methods like deep learning can be severely hampered. Therefore, a multi-modal method that can handle missing data in various clinical settings is highly desirable. In this paper, we present Multi-Modal Mixing Transformer (3MT), a disease classification transformer that not only leverages multi-modal data but also handles missing data scenarios. In this work, we test 3MT for AD and Cognitively normal (CN) classification and mild cognitive impairment (MCI) conversion prediction to progressive MCI (pMCI) or stable MCI (sMCI) using clinical and neuroimaging data. The model uses a novel Cascaded Modality Transformers architecture with cross-attention to incorporate multi-modal information for more informed predictions. We propose a novel modality dropout mechanism to ensure an unprecedented level of modality independence and robustness to handle missing data scenarios. The result is a versatile network that enables the mixing of arbitrary numbers of modalities with different feature types and also ensures full data utilization in missing data scenarios. The model is trained and evaluated on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset with the state-of-the-art performance and further evaluated with The Australian Imaging Biomarker & Lifestyle Flagship Study of Ageing (AIBL) dataset with missing data.
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Affiliation(s)
- Linfeng Liu
- Queensland Brain Institute, The University of Queensland, Australia.
| | - Siyu Liu
- School of Information Technology and Electrical Engineering, The University of Queensland, Australia
| | - Lu Zhang
- Queensland Brain Institute, The University of Queensland, Australia; School of Information Technology and Electrical Engineering, The University of Queensland, Australia
| | - Xuan Vinh To
- Queensland Brain Institute, The University of Queensland, Australia
| | - Fatima Nasrallah
- Queensland Brain Institute, The University of Queensland, Australia
| | - Shekhar S Chandra
- School of Information Technology and Electrical Engineering, The University of Queensland, Australia
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50
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Zhang Y, Teng Q, He X, Niu T, Zhang L, Liu Y, Ren C. Attention-based 3D CNN with Multi-layer Features for Alzheimer's Disease Diagnosis using Brain Images. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2023; 2023:1-4. [PMID: 38083225 DOI: 10.1109/embc40787.2023.10340536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Structural MRI and PET imaging play an important role in the diagnosis of Alzheimer's disease (AD), showing the morphological changes and glucose metabolism changes in the brain respectively. The manifestations in the brain image of some cognitive impairment patients are relatively inconspicuous, for example, it still has difficulties in achieving accurate diagnosis through sMRI in clinical practice. With the emergence of deep learning, convolutional neural network (CNN) has become a valuable method in AD-aided diagnosis, but some CNN methods cannot effectively learn the features of brain image, making the diagnosis of AD still presents some challenges. In this work, we propose an end-to-end 3D CNN framework for AD diagnosis based on ResNet, which integrates multi-layer features obtained under the effect of the attention mechanism to better capture subtle differences in brain images. The attention maps showed our model can focus on key brain regions related to the disease diagnosis. Our method was verified in ablation experiments with two modality images on 792 subjects from the ADNI database, where AD diagnostic accuracies of 89.71% and 91.18% were achieved based on sMRI and PET respectively, and also outperformed some state-of-the-art methods.
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