Unsupervised deep learning for individualized brain functional network identification
University of Pennsylvania（宾夕法尼亚大学）；Perelman School of Medicine（佩雷尔曼医学院）；Department of Radiology（放射科）；Center for Biomedical Image Computing and Analytics (CBICA)（生物医学图像计算与分析中心（CBICA））
A novel unsupervised deep learning method is developed to identify individual-specific large scale brain functional networks (FNs) from resting-state fMRI (rsfMRI) in an end-to-end learning fashion. Our method leverages deep Encoder-Decoder networks and conventional brain decomposition models to identify individual-specific FNs in an unsupervised learning framework and facilitate fast inference for new individuals with one forward pass of the deep network. Particularly, convolutional neural networks (CNNs) with an Encoder-Decoder architecture are adopted to identify individual-specific FNs from rsfMRI data by optimizing their data fitting and sparsity regularization terms that are commonly used in brain decomposition models. Moreover, a time-invariant representation learning module is designed to learn features invariant to temporal orders of time points of rsfMRI data. The proposed method has been validated based on a large rsfMRI dataset and experimental results have demonstrated that our method could obtain individual-specific FNs which are consistent with well-established FNs and are informative for predicting brain age, indicating that the individual-specific FNs identified truly captured the underlying variability of individualized functional neuroanatomy.
Progressive Self-Supervised Learning with Individualized Community Assignment for Brain Network Analysis
Harbin Institute of Technology at Shenzhen（哈尔滨工业大学（深圳））；Peng Cheng Laboratory（鹏城实验室）；University of Tübingen（图宾根大学）；Max Planck Institute for Intelligent Systems（智能系统马克斯·普朗克研究所）
Synthesizing Individualized Aging Brains in Health and Disease with Generative Models and Parallel Transport
Division of Biomedical Imaging, KTH Royal Institute of Technology, Stockholm, Sweden（生物医学成像系，皇家理工学院，斯德哥尔摩，瑞典）；Division of Clinical Geriatrics, Center for Alzheimer Research, Karolinska Institute, Stockholm, Sweden（临床老年医学系，阿尔茨海默病研究中心，卡罗林斯卡研究所，斯德哥尔摩，瑞典）；Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden（基因技术系，皇家理工学院，斯德哥尔摩，瑞典）；Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, MA, USA（计算机科学与人工智能实验室，麻省理工学院，马萨诸塞州，美国）；MedTechLabs, BioClinicum, Karolinska University Hospital, Solna, Sweden（MedTechLabs，BioClinicum，卡罗林斯卡大学医院，索纳，瑞典）
Community-Level Modeling of Gyral Folding Patterns for Robust and Anatomically Informed Individualized Brain Mapping
Department of Computer Science and Engineering, University of Texas at Arlington（计算机科学与工程系，德克萨斯大学阿灵顿分校）；School of Computing, University of Georgia（计算学院，佐治亚大学）；Department of Computer Science, Indiana University Indianapolis（计算机科学系，印第安纳大学印第安纳波利斯分校）
We propose split-brain autoencoders, a straightforward modification of the traditional autoencoder architecture, for unsupervised representation learning. The method adds a split to the network, resulting in two disjoint sub-networks. Each sub-network is trained to perform a difficult task -- predicting one subset of the data channels from another. Together, the sub-networks extract features from the entire input signal. By forcing the network to solve cross-channel prediction tasks, we induce a representation within the network which transfers well to other, unseen tasks. This method achieves…
Brain image registration transforms a pair of images into one system with the matched imaging contents, which is of essential importance for brain image analysis. This paper presents a novel framework for unsupervised 3D brain image registration by capturing the feature-level transformation relationships between the unaligned image and reference image. To achieve this, we develop a feature-level probabilistic model to provide the direct regularization to the hidden layers of two deep convolutional neural networks, which are constructed from two input images. This model design is developed into…
University of Pennsylvania（宾夕法尼亚大学）；Columbia University（哥伦比亚大学）；Ludwig-Maximilian University（路德维希-马克西米利安大学）；University of Birmingham（伯明翰大学）
The imaging community has increasingly adopted machine learning (ML) methods to provide individualized imaging signatures related to disease diagnosis, prognosis, and response to treatment. Clinical neuroscience and cancer imaging have been two areas in which ML has offered particular promise. However, many neurologic and neuropsychiatric diseases, as well as cancer, are often heterogeneous in terms of their clinical manifestations, neuroanatomical patterns or genetic underpinnings. Therefore, in such cases, seeking a single disease signature might be ineffectual in delivering individualized p…
Lesion detection in brain Magnetic Resonance Images (MRI) remains a challenging task. State-of-the-art approaches are mostly based on supervised learning making use of large annotated datasets. Human beings, on the other hand, even non-experts, can detect most abnormal lesions after seeing a handful of healthy brain images. Replicating this capability of using prior information on the appearance of healthy brain structure to detect lesions can help computers achieve human level abnormality detection, specifically reducing the need for numerous labeled examples and bettering generalization of p…
TU Munich（慕尼黑工业大学）；Klinikum Rechts der Isar（Rechts der Isar 医院）；Johns Hopkins University（约翰斯·霍普金斯大学）
Reliably modeling normality and differentiating abnormal appearances from normal cases is a very appealing approach for detecting pathologies in medical images. A plethora of such unsupervised anomaly detection approaches has been made in the medical domain, based on statistical methods, content-based retrieval, clustering and recently also deep learning. Previous approaches towards deep unsupervised anomaly detection model patches of normal anatomy with variants of Autoencoders or GANs, and detect anomalies either as outliers in the learned feature space or from large reconstruction errors. I…
Imperial College London（帝国理工学院）；Microsoft Research Cambridge（微软剑桥研究院）；Cambridge University（剑桥大学）
Significant advances have been made towards building accurate automatic segmentation systems for a variety of biomedical applications using machine learning. However, the performance of these systems often degrades when they are applied on new data that differ from the training data, for example, due to variations in imaging protocols. Manually annotating new data for each test domain is not a feasible solution. In this work we investigate unsupervised domain adaptation using adversarial neural networks to train a segmentation method which is more invariant to differences in the input data, an…
Large Scale Unsupervised Brain MRI Image Registration Solution for Learn2Reg 2024
College of Electrical and Information Engineering, Hunan University（湖南大学电气与信息工程学院）；National Engineering Research Center of Robot Visual Perception and Control Technology, Hunan University（湖南大学机器人视觉感知与控制技术国家工程研究中心）
Medical School of Nanjing University（南京大学医学院）；National Institute of Healthcare Data Science at Nanjing University（南京大学国家健康医疗大数据研究院）；State Key Laboratory for Novel Software Technology, Nanjing University（南京大学计算机软件新技术国家重点实验室）；School of Computer Science and Technology, Nanjing University of Science and Technology（南京理工大学计算机科学与技术学院）；Department of Radiology, Nanjing Drum Tower Hospital, Nanjing University Medical School（南京大学医学院附属鼓楼医院放射科）；School of Biomedical Engineering, ShanghaiTech University（上海科技大学生物医学工程学院）；Department of Research and Development, Shanghai United Imaging Intelligence Co., Ltd.（上海联影智能医疗科技有限公司研发部）；Department of Artificial Intelligence, Korea University（高丽大学人工智能系）
Accurate segmentation of brain tumors from multi-modal Magnetic Resonance (MR) images is essential in brain tumor diagnosis and treatment. However, due to the existence of domain shifts among different modalities, the performance of networks decreases dramatically when training on one modality and performing on another, e.g., train on T1 image while performing on T2 image, which is often required in clinical applications. This also prohibits a network from being trained on labeled data and then transferred to unlabeled data from a different domain. To overcome this, unsupervised domain adaptat…
Mild traumatic brain injury is a growing public health problem with an estimated incidence of over 1.7 million people annually in US. Diagnosis is based on clinical history and symptoms, and accurate, concrete measures of injury are lacking. This work aims to directly use diffusion MR images obtained within one month of trauma to detect injury, by incorporating deep learning techniques. To overcome the challenge due to limited training data, we describe each brain region using the bag of word representation, which specifies the distribution of representative patch patterns. We apply a convolut…
Hamburg University of Technology（汉堡工业大学）；Jung Diagnostics GmbH（荣格诊断有限公司）
The use of supervised deep learning techniques to detect pathologies in brain MRI scans can be challenging due to the diversity of brain anatomy and the need for annotated data sets. An alternative approach is to use unsupervised anomaly detection, which only requires sample-level labels of healthy brains to create a reference representation. This reference representation can then be compared to unhealthy brain anatomy in a pixel-wise manner to identify abnormalities. To accomplish this, generative models are needed to create anatomically consistent MRI scans of healthy brains. While recent di…
Addressing Annotation Scarcity in Hyperspectral Brain Image Segmentation with Unsupervised Domain Adaptation
Technical University of Munich, Munich, Germany（慕尼黑技术大学）；Department of Computing, Imperial College London, London, UK（伦敦帝国学院计算机系）；Munich Center for Machine Learning (MCML), Munich, Germany（慕尼黑机器学习中心（MCML））
Institute of Medical Technology and Intelligent Systems, Hamburg University of Technology（汉堡工业大学医疗技术与智能系统研究所）；jung diagnostics GmbH（jung diagnostics GmbH公司）；Hamburg University of Technology（汉堡工业大学）
Lesion detection in brain Magnetic Resonance Images (MRIs) remains a challenging task. MRIs are typically read and interpreted by domain experts, which is a tedious and time-consuming process. Recently, unsupervised anomaly detection (UAD) in brain MRI with deep learning has shown promising results to provide a quick, initial assessment. So far, these methods only rely on the visual appearance of healthy brain anatomy for anomaly detection. Another biomarker for abnormal brain development is the deviation between the brain age and the chronological age, which is unexplored in combination with …
Unsupervised Detection of Post-Stroke Brain Abnormalities
Univ Rennes（里昂大学）；Inria（法国国家信息与自动化技术研究院）；CNRS（法国国家科学研究中心）；Inserm（法国国家医学研究院）；IRISA UMR 6074（里昂信息科学与自动化研究院）；CHU Rennes（里昂大学医院）；Siemens Healthineers（西门子医疗）；Centre de Kerpape（凯帕普中心）
Indian Institute of Technology, Madras（马德拉斯印度理工学院）；Healthcare Technology Innovation Centre, IIT Madras（印度理工学院马德拉斯分校医疗技术创新中心）
Anomaly detection in MRI is of high clinical value in imaging and diagnosis. Unsupervised methods for anomaly detection provide interesting formulations based on reconstruction or latent embedding, offering a way to observe properties related to factorization. We study four existing modeling methods, and report our empirical observations using simple data science tools, to seek outcomes from the perspective of factorization as it would be most relevant to the task of unsupervised anomaly detection, considering the case of brain structural MRI. Our study indicates that anomaly detection algorit…
Unsupervised Segmentation of Fetal Brain MRI using Deep Learning Cascaded Registration
Universitat Pompeu Fabra（庞培法布拉大学）；BCNatal；Institución Catalana de Investigación y Estudios Avanzados (ICREA)（加泰罗尼亚高级研究与发展研究院）；Centre for Biomedical Research on Rare Diseases (CIBERER)（罕见疾病生物医学研究中心）；European Commission, Joint Research Centre (JRC)（欧盟委员会联合研究中心）
CLISC: Bridging clip and sam by enhanced cam for unsupervised brain tumor segmentation
School of Computer Science and Engineering（计算机科学与工程学院）；School of Mechanical and Electrical Engineering（机械与电气工程学院）；University of Electronic Science and Technology of China（电子科技大学）；School of Medicine, University of Electronic Science and Technology of China（电子科技大学医学院）；Shanghai Artificial Intelligence Laboratory（上海人工智能实验室）
Durham University（杜伦大学）；University of Exeter（埃克塞特大学）；County Durham and Darlington NHS Foundation Trust（达勒姆郡和达灵顿国民保健服务基金会信托）
Medical segmentation is performed to determine the bounds of regions of interest (ROI) prior to surgery. By allowing the study of growth, structure, and behaviour of the ROI in the planning phase, critical information can be obtained, increasing the likelihood of a successful operation. Usually, segmentations are performed manually or via machine learning methods trained on manual annotations. In contrast, this paper proposes a fully automatic, unsupervised inpainting-based brain tumour segmentation system for T1-weighted MRI. First, a deep convolutional neural network (DCNN) is trained to rec…
The Hong Kong University of Science and Technology（香港科技大学）
Registration of pre-operative and post-recurrence brain images is often needed to evaluate the effectiveness of brain gliomas treatment. While recent deep learning-based deformable registration methods have achieved remarkable success with healthy brain images, most of them would be unable to accurately align images with pathologies due to the absent correspondences in the reference image. In this paper, we propose a deep learning-based deformable registration method that jointly estimates regions with absent correspondence and bidirectional deformation fields. A forward-backward consistency c…
We propose a registration algorithm for 2D CT/MRI medical images with a new unsupervised end-to-end strategy using convolutional neural networks. The contributions of our algorithm are threefold: (1) We transplant traditional image registration algorithms to an end-to-end convolutional neural network framework, while maintaining the unsupervised nature of image registration problems. The image-to-image integrated framework can simultaneously learn both image features and transformation matrix for registration. (2) Training with additional data without any label can further improve the registra…
Brain extraction and registration are important preprocessing steps in neuroimaging data analysis, where the goal is to extract the brain regions from MRI scans (i.e., extraction step) and align them with a target brain image (i.e., registration step). Conventional research mainly focuses on developing methods for the extraction and registration tasks separately under supervised settings. The performance of these methods highly depends on the amount of training samples and visual inspections performed by experts for error correction. However, in many medical studies, collecting voxel-level lab…
Institute of Medical Technology and Intelligent Systems, Hamburg University of Technology（汉堡工业大学医学技术与智能系统研究所）；jung diagnostics GmbH（jung diagnostics 有限公司）
Purpose. Brain Magnetic Resonance Images (MRIs) are essential for the diagnosis of neurological diseases. Recently, deep learning methods for unsupervised anomaly detection (UAD) have been proposed for the analysis of brain MRI. These methods rely on healthy brain MRIs and eliminate the requirement of pixel-wise annotated data compared to supervised deep learning. While a wide range of methods for UAD have been proposed, these methods are mostly 2D and only learn from MRI slices, disregarding that brain lesions are inherently 3D and the spatial context of MRI volumes remains unexploited. Metho…
Memorial Sloan Kettering Cancer Center（纪念斯隆-凯特琳癌症中心）；Indian Institute of Technology, Madras（印度理工学院马德拉斯分校）
Purpose: Lesion segmentation in medical imaging is key to evaluating treatment response. We have recently shown that reinforcement learning can be applied to radiological images for lesion localization. Furthermore, we demonstrated that reinforcement learning addresses important limitations of supervised deep learning; namely, it can eliminate the requirement for large amounts of annotated training data and can provide valuable intuition lacking in supervised approaches. However, we did not address the fundamental task of lesion/structure-of-interest segmentation. Here we introduce a method co…
PatchMorph: A Stochastic Deep Learning Approach for Unsupervised 3D Brain Image Registration with Small Patches
RIKEN Center for Brain Science（理化学研究所脑科学中心）；Institute of Fundamental Technological Research, Polish Academy of Sciences（波兰科学院基础技术研究所）；Central Institute for Experimental Animals（中央实验动物研究所）；Medical Center Freiburg, Faculty of Medicine, University of Freiburg（弗莱堡大学医学院弗莱堡医学中心）
LPIXEL Inc.（LPIXEL公司）；University of Cambridge（剑桥大学）；National Institute of Informatics（国立信息学研究所）；National Center for Global Health and Medicine（国立国际医疗研究中心）；Juntendo University（顺天堂大学）；ELTE Eötvös Loránd University（厄特沃什·罗兰大学）；The University of Tokyo（东京大学）
Unsupervised learning can discover various unseen abnormalities, relying on large-scale unannotated medical images of healthy subjects. Towards this, unsupervised methods reconstruct a 2D/3D single medical image to detect outliers either in the learned feature space or from high reconstruction loss. However, without considering continuity between multiple adjacent slices, they cannot directly discriminate diseases composed of the accumulation of subtle anatomical anomalies, such as Alzheimer's Disease (AD). Moreover, no study has shown how unsupervised anomaly detection is associated with eith…
Unsupervised Tumor-Aware Distillation for Multi-Modal Brain Image Translation
School of Computer Science and Engineering, South China University of Technology（华南理工大学计算机科学与工程学院）；Golisano College of Computing and Information Sciences, Rochester Institute of Technology（罗切斯特理工大学戈利萨诺计算与信息科学学院）
Platonic Representations in the Human Brain: Unsupervised Recovery of Universal Geometry
Department of Cognition, Development and Education Psychology, University of Barcelona（巴塞罗那大学认知、发展与教育心理学系）；Institute of Neurosciences, University of Barcelona（巴塞罗那大学神经科学研究所）；Department of Computer Science, Cornell University（康奈尔大学计算机科学系）；Bellvitge Institute for Biomedical Research, Spain（西班牙贝尔维德生物医学研究 institute）
TU Munich（慕尼黑工业大学）；Klinikum rechts der Isar（伊萨尔河右岸医院）；ETH Zurich（苏黎世联邦理工学院）；Johns Hopkins University（约翰斯·霍普金斯大学）
Brain pathologies can vary greatly in size and shape, ranging from few pixels (i.e. MS lesions) to large, space-occupying tumors. Recently proposed Autoencoder-based methods for unsupervised anomaly segmentation in brain MRI have shown promising performance, but face difficulties in modeling distributions with high fidelity, which is crucial for accurate delineation of particularly small lesions. Here, similar to these previous works, we model the distribution of healthy brain MRI to localize pathologies from erroneous reconstructions. However, to achieve improved reconstruction fidelity at hi…
Towards Label-Free Brain Tumor Segmentation: Unsupervised Learning with Multimodal MRI
Universitat Politècnica de Catalunya (UPC)（西班牙巴塞罗那理工大学）；University College Dublin (UCD)（都柏林大学）；Dublin City University (DCU)（都柏林城市大学）；Insight Research Ireland Center For Data Analytics（爱尔兰数据分析研究中心）
Automatic segmentation of brain abnormalities is challenging, as they vary considerably from one pathology to another. Current methods are supervised and require numerous annotated images for each pathology, a strenuous task. To tackle anatomical variability, Unsupervised Anomaly Detection (UAD) methods are proposed, detecting anomalies as outliers of a healthy model learned using a Variational Autoencoder (VAE). Previous work on UAD adopted a 2D approach, meaning that MRIs are processed as a collection of independent slices. Yet, it does not fully exploit the spatial information contained in …
University of Iceland（冰岛大学）；Landspitali - University Hospital（兰斯皮塔利大学医院）；The Icelandic Heart Association（冰岛心脏协会）；The Johns Hopkins University（约翰斯·霍普金斯大学）
Lesions that appear hyperintense in both Fluid Attenuated Inversion Recovery (FLAIR) and T2-weighted magnetic resonance images (MRIs) of the human brain are common in the brains of the elderly population and may be caused by ischemia or demyelination. Lesions are biomarkers for various neurodegenerative diseases, making accurate quantification of them important for both disease diagnosis and progression. Automatic lesion detection using supervised learning requires manually annotated images, which can often be impractical to acquire. Unsupervised lesion detection, on the other hand, does not r…
Hamburg University of Technology（汉堡工业大学）；Jung Diagnostics GmbH（荣格诊断有限公司）
The detection of lesions in magnetic resonance imaging (MRI)-scans of human brains remains challenging, time-consuming and error-prone. Recently, unsupervised anomaly detection (UAD) methods have shown promising results for this task. These methods rely on training data sets that solely contain healthy samples. Compared to supervised approaches, this significantly reduces the need for an extensive amount of labeled training data. However, data labelling remains error-prone. We study how unhealthy samples within the training data affect anomaly detection performance for brain MRI-scans. For our…
Segmenting the fine structure of the mouse brain on magnetic resonance (MR) images is critical for delineating morphological regions, analyzing brain function, and understanding their relationships. Compared to a single MRI modality, multimodal MRI data provide complementary tissue features that can be exploited by deep learning models, resulting in better segmentation results. However, multimodal mouse brain MRI data is often lacking, making automatic segmentation of mouse brain fine structure a very challenging task. To address this issue, it is necessary to fuse multimodal MRI data to produ…
Pathological brain appearances may be so heterogeneous as to be intelligible only as anomalies, defined by their deviation from normality rather than any specific pathological characteristic. Amongst the hardest tasks in medical imaging, detecting such anomalies requires models of the normal brain that combine compactness with the expressivity of the complex, long-range interactions that characterise its structural organisation. These are requirements transformers have arguably greater potential to satisfy than other current candidate architectures, but their application has been inhibited by …
International University of Business Agriculture and Technology（国际商业、农业与技术大学）
Tissue classification is one of the significant tasks in the field of biomedical image analysis. Magnetic Resonance Imaging (MRI) is of great importance in tissue classification especially in the areas of brain tissue classification which is able to recognize anatomical areas of interest such as surgical planning, monitoring therapy, clinical drug trials, image registration, stereotactic neurosurgery, radiotherapy etc. The task of this paper is to implement different unsupervised classification algorithms in ITK and perform tissue classification (white matter, gray matter, cerebrospinal fluid …
College of Computer Science and Technology, Zhejiang University（浙江大学计算机科学与技术学院）；University of North Carolina at Chapel Hill（北卡罗来纳大学教堂山分校）；Automotive Engineering Research Institute, Jiangsu University（江苏大学汽车工程研究院）；Stanford University（斯坦福大学）；School of Mathematics Science, Liaocheng University（聊城大学数学科学学院）；School of Electric Engineering, Zhengzhou University（郑州大学电气工程学院）；Korea University（高丽大学）
Brain functional network has become an increasingly used approach in understanding brain functions and diseases. Many network construction methods have been developed, whereas the majority of the studies still used static pairwise Pearson's correlation-based functional connectivity. The goal of this work is to introduce a toolbox namely "Brain Network Construction and Classification" (BrainNetClass) to the field to promote more advanced brain network construction methods. It comprises various brain network construction methods, including some state-of-the-art methods that were recently develop…
University of Girona（赫罗纳大学）；Technical University of Munich（慕尼黑工业大学）；Antwerp University Hospital（安特卫普大学医院）；University of Antwerp（安特卫普大学）；KU Leuven（鲁汶大学）
Anomaly detection (AD) is the identification of data samples that do not fit a learned data distribution. As such, AD systems can help physicians to determine the presence, severity, and extension of a pathology. Deep generative models, such as Generative Adversarial Networks (GANs), can be exploited to capture anatomical variability. Consequently, any outlier (i.e., sample falling outside of the learned distribution) can be detected as an abnormality in an unsupervised fashion. By using this method, we can not only detect expected or known lesions, but we can even unveil previously unrecogniz…
Research Center for Medical Big Data, National Institute of Informatics（日本情报学研究所医疗大数据研究中心）；LPixel Inc.（LPixel公司）；Graduate School of Information Science and Technology, The University of Tokyo（东京大学信息科学与技术研究生院）；Department of Radiology, University of Cambridge（剑桥大学放射科）；Cancer Research UK Cambridge Centre（英国癌症研究中心剑桥中心）；Department of Artificial Intelligence, ELTE Eötvös Loránd University（厄特沃什罗兰大学人工智能系）；Department of Rehabilitation Medicine, Juntendo University School of Medicine（顺天堂大学医学部康复医学科）；International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo（东京大学国际神经智能研究中心（WPI-IRCN））
Unsupervised learning can discover various unseen diseases, relying on large-scale unannotated medical images of healthy subjects. Towards this, unsupervised methods reconstruct a single medical image to detect outliers either in the learned feature space or from high reconstruction loss. However, without considering continuity between multiple adjacent slices, they cannot directly discriminate diseases composed of the accumulation of subtle anatomical anomalies, such as Alzheimer's Disease (AD). Moreover, no study has shown how unsupervised anomaly detection is associated with disease stages.…
Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School（哈佛医学院麻省总医院Martinos生物医学影像中心）；Massachusetts Institute of Technology（麻省理工学院）；Cornell University（康奈尔大学）；University College London（伦敦大学学院）
Probabilistic atlas priors have been commonly used to derive adaptive and robust brain MRI segmentation algorithms. Widely-used neuroimage analysis pipelines rely heavily on these techniques, which are often computationally expensive. In contrast, there has been a recent surge of approaches that leverage deep learning to implement segmentation tools that are computationally efficient at test time. However, most of these strategies rely on learning from manually annotated images. These supervised deep learning methods are therefore sensitive to the intensity profiles in the training dataset. To…
