This study presents an innovative method for Alzheimer's disease diagnosis using 3D MRI designed to enhance the explainability of model decisions. Our approach adopts a soft attention mechanism, enabling 2D CNNs to extract volumetric representations. At the same time, the importance of each slice in decision-making is learned, allowing the generation of a voxel-level attention map to produce an explainable MRI. To test our method and ensure the reproducibility of our results, we chose a standardized collection of MRI data from the Alzheimer's Disease Neuroimaging Initiative (ADNI). On this dataset, our method significantly outperforms state-of-the-art methods in (i) distinguishing AD from cognitive normal (CN) with an accuracy of 0.856 and Matthew's correlation coefficient (MCC) of 0.712, representing improvements of 2.4% and 5.3% respectively over the second-best, and (ii) in the prognostic task of discerning stable from progressive mild cognitive impairment (MCI) with an accuracy of 0.725 and MCC of 0.443, showing improvements of 10.2% and 20.5% respectively over the second-best. We achieved this prognostic result by adopting a double transfer learning strategy, which enhanced sensitivity to morphological changes and facilitated early-stage AD detection. With voxel-level precision, our method identified which specific areas are being paid attention to, identifying these predominant brain regions: the hippocampus, the amygdala, the parahippocampal, and the inferior lateral ventricles. All these areas are clinically associated with AD development. Furthermore, our approach consistently found the same AD-related areas across different cross-validation folds, proving its robustness and precision in highlighting areas that align closely with known pathological markers of the disease.
Deep Convolutional Neural Networks (CNNs) are becoming prominent models for semi-automated diagnosis of Alzheimer's Disease (AD) using brain Magnetic Resonance Imaging (MRI). Although being highly accurate, deep CNN models lack transparency and interpretability, precluding adequate clinical reasoning and not complying with most current regulatory demands. One popular choice for explaining deep image models is occluding regions of the image to isolate their influence on the prediction. However, existing methods for occluding patches of brain scans generate images outside the distribution to whi…
Generative artificial intelligence in ophthalmology: multimodal retinal images for the diagnosis of Alzheimer's disease with convolutional neural networks
Enhancing Early Alzheimer Disease Detection through Big Data and Ensemble Few-Shot Learning
Robotics and Internet of Things Laboratory, Prince Sultan University（王子苏大学机器人与物联网实验室）；RIADI Laboratory, National School of Computer Science, University of Manouba（RIADI实验室，国家计算机科学学院，曼努巴大学）
Charité – Universitätsmedizin Berlin（柏林夏里特医学院）；Freie Universität Berlin（柏林自由大学）；Humboldt-Universität zu Berlin（柏林洪堡大学）；Berlin Institute of Health（柏林健康研究所）；Bernstein Center for Computational Neuroscience（伯恩斯坦计算神经科学中心）；Berlin Center for Advanced Neuroimaging（柏林高级神经影像中心）；Technical University Berlin（柏林工业大学）
Visualizing and interpreting convolutional neural networks (CNNs) is an important task to increase trust in automatic medical decision making systems. In this study, we train a 3D CNN to detect Alzheimer's disease based on structural MRI scans of the brain. Then, we apply four different gradient-based and occlusion-based visualization methods that explain the network's classification decisions by highlighting relevant areas in the input image. We compare the methods qualitatively and quantitatively. We find that all four methods focus on brain regions known to be involved in Alzheimer's diseas…
Humboldt Universität Berlin（柏林洪堡大学）；Freie Universität Berlin（柏林自由大学）；Charité - Universitätsmedizin Berlin（柏林夏里特医学院）
Neuroimaging studies based on magnetic resonance imaging (MRI) typically employ rigorous forms of preprocessing. Images are spatially normalized to a standard template using linear and non-linear transformations. Thus, one can assume that a patch at location (x, y, height, width) contains the same brain region across the entire data set. Most analyses applied on brain MRI using convolutional neural networks (CNNs) ignore this distinction from natural images. Here, we suggest a new layer type called patch individual filter (PIF) layer, which trains higher-level filters locally as we assume that…
Leveraging Deep Learning and Xception Architecture for High-Accuracy MRI Classification in Alzheimer Diagnosis
Huacong Qingjiao Information Technology (Beijing) Co., Ltd.（华聪青教信息技术（北京）有限公司）；Chongqing Technology and Business University（重庆工商大学）；University of Maine at Presque Isle（缅因大学普雷斯克艾尔分校）；San Francisco Bay University（旧金山湾大学）；Universitario Tecnológico Universitam；Northern Arizona University（北亚利桑那大学）
VisTA: Vision-Text Alignment Model with Contrastive Learning using Multimodal Data for Evidence-Driven, Reliable, and Explainable Alzheimer's Disease Diagnosis
Centre hospitalier universitaire vaudois (CHUV)（洛桑大学医院中心（CHUV））；Université de Lausanne (UNIL)（洛桑大学（UNIL））；VNU University of Engineering and Technology, Vietnam National University（越南国家大学下属越南工程技术大学）；University of Science, Vietnam National University Ho Chi Minh City（胡志明市越南国家大学下属科学大学）；Military Hospital 175（175军事医院）；School of Biomedical Engineering, International University, Vietnam National University（越南国家大学下属国际大学生物医学工程学院）
Symmetry Interactive Transformer with CNN Framework for Diagnosis of Alzheimer's Disease Using Structural MRI
College of Electronics and Information Engineering, Sichuan University, China（四川大学电子信息工程学院）；Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (GSU, Georgia Tech, Emory), Atlanta, USA（跨机构神经影像与数据科学转化研究中心）；College of Information and Electrical Engineering, China Agricultural University, China（中国农业大学信息与电气工程学院）；School of Biomedical Engineering and Imaging Sciences, King's College London, UK（伦敦国王学院生物医学工程与影像科学学院）
Tumor Location-weighted MRI-Report Contrastive Learning: A Framework for Improving the Explainability of Pediatric Brain Tumor Diagnosis
The Hospital for Sick Children（病童医院）；University of Toronto（多伦多大学）；Vector Institute for Artificial Intelligence（矢量人工智能研究所）；University Hospital Augsburg（奥格斯堡大学医院）
Lab for Artificial Intelligence in Medical Imaging (AI-Med), KJP, LMU Klinikum（慕尼黑大学附属医院儿童与青少年精神病学系医学影像人工智能实验室）；Technical University of Munich, School of Medicine（慕尼黑工业大学医学院）
Alzheimer's Disease (AD) is the most common form of dementia and often difficult to diagnose due to the multifactorial etiology of dementia. Recent works on neuroimaging-based computer-aided diagnosis with deep neural networks (DNNs) showed that fusing structural magnetic resonance images (sMRI) and fluorodeoxyglucose positron emission tomography (FDG-PET) leads to improved accuracy in a study population of healthy controls and subjects with AD. However, this result conflicts with the established clinical knowledge that FDG-PET better captures AD-specific pathologies than sMRI. Therefore, we p…
Early Alzheimer's Disease Detection from Retinal OCT Images: A UK Biobank Study
Department of Computer Engineering Isik University Istanbul, Turkey（计算机工程系伊斯肯大学）；Department of Artificial Intelligence and Data Engineering（人工智能与数据工程系）；Data Engineering Istanbul Technical University Istanbul, Turkey（数据工程系伊斯坦布尔技术大学）
University of Electronic Science and Technology of China（电子科技大学）；SenseTime Research（商汤科技研究院）；University Hospitals Leuven（鲁汶大学医院）；King’s College London（伦敦国王学院）；University College London（伦敦大学学院）
Accurate medical image segmentation is essential for diagnosis and treatment planning of diseases. Convolutional Neural Networks (CNNs) have achieved state-of-the-art performance for automatic medical image segmentation. However, they are still challenged by complicated conditions where the segmentation target has large variations of position, shape and scale, and existing CNNs have a poor explainability that limits their application to clinical decisions. In this work, we make extensive use of multiple attentions in a CNN architecture and propose a comprehensive attention-based CNN (CA-Net) f…
Attention-based Saliency Maps Improve Interpretability of Pneumothorax Classification
Munich Institute of Biomedical Engineering, Technical University of Munich（慕尼黑工业大学慕尼黑生物医学工程研究所）；Technical University of Munich（慕尼黑工业大学）；University Hospital LMU（慕尼黑大学附属医院）；Munich School of Technology in Society, Technical University of Munich（慕尼黑工业大学慕尼黑技术与社会学院）
Graph Theory and GNNs to Unravel the Topographical Organization of Brain Lesions in Variants of Alzheimer's Disease Progression
Sorbonne Université（索邦大学）；Paris Brain Institute - ICM（巴黎脑研究所 - ICM）；CNRS（法国国家科学研究中心）；Inria（法国国家信息与自动化研究所）；Inserm（法国国家健康与医学研究院）；AP-HP（巴黎公共医疗集团）；Hôpital de la Pitié Salpêtrière（皮蒂-萨尔皮特里耶医院）
Caption-Driven Explainability: Probing CNNs for Bias via CLIP
Northwestern University, Evanston, IL, USA（西北大学）；University of California, Berkeley, CA, USA（加州大学伯克利分校）；Eastern Switzerland University of Applied Sciences, Rapperswil, SG, CH（东瑞士应用科学大学）
Universidade da Coruña（拉科鲁尼亚大学）；Instituto de Investigación Biomédica de A Coruña (INIBIC)（拉科鲁尼亚生物医学研究所）；Hospital Clínico San Carlos（圣卡洛斯临床医院）；Instituto de Investigación Sanitaria (IdISSC)（圣卡洛斯健康研究所）；Centro Internacional de Oftalmología Avanzada（国际高级眼科中心）
Age-related macular degeneration (AMD) is a degenerative disorder affecting the macula, a key area of the retina for visual acuity. Nowadays, it is the most frequent cause of blindness in developed countries. Although some promising treatments have been developed, their effectiveness is low in advanced stages. This emphasizes the importance of large-scale screening programs. Nevertheless, implementing such programs for AMD is usually unfeasible, since the population at risk is large and the diagnosis is challenging. All this motivates the development of automatic methods. In this sense, severa…
A BERT-Style Self-Supervised Learning CNN for Disease Identification from Retinal Images
School of Computing and Augmented Intelligence, Arizona State University（计算与增强智能学院，亚利桑那州立大学）；McKeley School of Engineering, Washington University in St. Louis（工程学院，华盛顿大学圣路易斯分校）；Department of Neurology, Mayo Clinic（神经病学部，梅奥诊所）
Neuroimaging of large populations is valuable to identify factors that promote or resist brain disease, and to assist diagnosis, subtyping, and prognosis. Data-driven models such as convolutional neural networks (CNNs) have increasingly been applied to brain images to perform diagnostic and prognostic tasks by learning robust features. Vision transformers (ViT) - a new class of deep learning architectures - have emerged in recent years as an alternative to CNNs for several computer vision applications. Here we tested variants of the ViT architecture for a range of desired neuroimaging downstre…
Resting state functional magnetic resonance images (fMRI) are commonly used for classification of patients as having Alzheimer's disease (AD), mild cognitive impairment (MCI), or being cognitive normal (CN). Most methods use time-series correlation of voxels signals during the observation period as a basis for the classification. In this paper we show that Convolutional Neural Network (CNN) classification based on spatial correlation of time-averaged signals yield a classification accuracy of up to 82% (sensitivity 86%, specificity 80%)for a data set with 429 subjects (246 cognitive normal and…
Explainable Artificial Intelligence (AI) in the form of an interpretable and semiautomatic approach to stage grading ocular pathologies such as Diabetic retinopathy, Hypertensive retinopathy, and other retinopathies on the backdrop of major systemic diseases. The experimental study aims to evaluate an explainable staged grading process without using deep Convolutional Neural Networks (CNNs) directly. Many current CNN-based deep neural networks used for diagnosing retinal disorders might have appreciable performance but fail to pinpoint the basis driving their decisions. To improve these decisi…
Texas Tech Neuroimaging Institute, Texas Tech University（德克萨斯理工大学神经影像研究所，德克萨斯理工大学）
Accurate diagnosis of Alzheimer's disease (AD) is both challenging and time consuming. With a systematic approach for early detection and diagnosis of AD, steps can be taken towards the treatment and prevention of the disease. This study explores the practical application of deep learning models for diagnosis of AD. Due to computational complexity, large training times and limited availability of labelled dataset, a 3D full brain CNN (convolutional neural network) is not commonly used, and researchers often prefer 2D CNN variants. In this study, full brain 3D version of well-known 2D CNNs were…
New York University（纽约大学）；New York University Langone Medical Center（纽约大学朗格尼医学中心）
Early detection is a crucial goal in the study of Alzheimer's Disease (AD). In this work, we describe several techniques to boost the performance of 3D deep convolutional neural networks (CNNs) trained to detect AD using structural brain MRI scans. Specifically, we provide evidence that (1) instance normalization outperforms batch normalization, (2) early spatial downsampling negatively affects performance, (3) widening the model brings consistent gains while increasing the depth does not, and (4) incorporating age information yields moderate improvement. Together, these insights yield an incr…
ETH Zurich（苏黎世联邦理工学院）；SIB Swiss Institute of Bioinformatics（瑞士生物信息学研究所）
Alzheimer's disease (AD) is associated with local (e.g. brain tissue atrophy) and global brain changes (loss of cerebral connectivity), which can be detected by high-resolution structural magnetic resonance imaging. Conventionally, these changes and their relation to AD are investigated independently. Here, we introduce a novel, highly-scalable approach that simultaneously captures $\textit{local}$ and $\textit{global}$ changes in the diseased brain. It is based on a neural network architecture that combines patch-based, high-resolution 3D-CNNs with global topological features, evaluating mult…
Diagnosing Alzheimer's disease (AD) involves a deliberate diagnostic process owing to its innate traits of irreversibility with subtle and gradual progression. These characteristics make AD biomarker identification from structural brain imaging (e.g., structural MRI) scans quite challenging. Furthermore, there is a high possibility of getting entangled with normal aging. We propose a novel deep-learning approach through eXplainable AD Likelihood Map Estimation (XADLiME) for AD progression modeling over 3D sMRIs using clinically-guided prototype learning. Specifically, we establish a set of top…
Charité – Universitätsmedizin Berlin（柏林夏里特医学院）；Freie Universität Berlin（柏林自由大学）；Humboldt-Universität zu Berlin（柏林洪堡大学）；Berlin Institute of Health（柏林健康研究所）
Machine learning-based imaging diagnostics has recently reached or even superseded the level of clinical experts in several clinical domains. However, classification decisions of a trained machine learning system are typically non-transparent, a major hindrance for clinical integration, error tracking or knowledge discovery. In this study, we present a transparent deep learning framework relying on convolutional neural networks (CNNs) and layer-wise relevance propagation (LRP) for diagnosing multiple sclerosis (MS). MS is commonly diagnosed utilizing a combination of clinical presentation and …
Université Clermont Auvergne（克莱蒙奥弗涅大学）；CNRS（法国国家科学研究中心）；ENSMSE（圣艾蒂安国立矿业工程师学校）；INRAE（法国国家农业食品与环境研究院）；VetAgro Sup（法国兽医与农学高等学院）；Université de Lyon（里昂大学）；CHU Clermont-Ferrand（克莱蒙费朗大学医院）；Inserm（法国国家健康与医学研究院）；Tous Chercheurs Laboratory（全民研究者实验室）；CPIE Champenoux（尚佩努环境倡议中心）；University Hospital of Nancy（南锡大学医院）；University Hospital of Saint Etienne（圣艾蒂安大学医院）；IHU-Méditerranée Infection（地中海感染大学医院研究所）；Aix Marseille Univ（艾克斯-马赛大学）；IRD（法国发展研究院）；AP-HM（马赛公立医院援助机构）；SSA（法国军队卫生勤务局）；Hôpitaux Universitaires（斯特拉斯堡大学医院）；Pontchaillou University Hospital（蓬查卢大学医院）；CHR Orléans（奥尔良地区中心医院）；Hospital of Villeneuve-Saint-Georges（维勒讷夫圣乔治医院）；Centre Hospitalier Universitaire de Rennes（雷恩大学医院）
Lyme disease which is one of the most common infectious vector-borne diseases manifests itself in most cases with erythema migrans (EM) skin lesions. Recent studies show that convolutional neural networks (CNNs) perform well to identify skin lesions from images. Lightweight CNN based pre-scanner applications for resource-constrained mobile devices can help users with early diagnosis of Lyme disease and prevent the transition to a severe late form thanks to appropriate antibiotic therapy. Also, resource-intensive CNN based robust computer applications can assist non-expert practitioners with an…
A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland（东芬兰大学A.I.维尔塔宁分子科学研究所）
Transfer learning refers to machine learning techniques that focus on acquiring knowledge from related tasks to improve generalization in the tasks of interest. In MRI, transfer learning is important for developing strategies that address the variation in MR images. Additionally, transfer learning is beneficial to re-utilize machine learning models that were trained to solve related tasks to the task of interest. Our goal is to identify research directions, gaps of knowledge, applications, and widely used strategies among the transfer learning approaches applied in MR brain imaging. We perform…
