A review of deep learning in medical imaging: Imaging traits, technology trends, case studies with progress highlights, and future promises
School of Biomedical Engineering, University of Science and Technology of China（中国科学技术大学生物医学工程学院）；Institute of Computing Technology, Chinese Academy of Sciences（中国科学院计算技术研究所）；Tel-Aviv University（特拉维夫大学）；University of Pennsylvania（宾夕法尼亚大学）；Yale University（耶鲁大学）；Radboud University Medical Center（拉德堡德大学医学中心）；Case Western Reserve University（凯斯西储大学）；Louis Stokes Cleveland Veterans Administration Medical Center（路易斯·斯托克斯克利夫兰退伍军人事务医疗中心）；Johns Hopkins University（约翰霍普金斯大学）；Klinikum rechts der Isar, TU Munich（慕尼黑工业大学右岸医院）；Imperial College（帝国理工学院）；National Institute of Health Clinical Center（美国国立卫生研究院临床中心）
S. Kevin Zhou, Hayit Greenspan, Christos Davatzikos, James S. Duncan, Bram van Ginneken, Anant Madabhushi, Jerry L. Prince, Daniel Rueckert, Ronald M. Summers
Since its renaissance, deep learning has been widely used in various medical imaging tasks and has achieved remarkable success in many medical imaging applications, thereby propelling us into the so-called artificial intelligence (AI) era. It is known that the success of AI is mostly attributed to the availability of big data with annotations for a single task and the advances in high performance computing. However, medical imaging presents unique challenges that confront deep learning approaches. In this survey paper, we first present traits of medical imaging, highlight both clinical needs and technical challenges in medical imaging, and describe how emerging trends in deep learning are addressing these issues. We cover the topics of network architecture, sparse and noisy labels, federating learning, interpretability, uncertainty quantification, etc. Then, we present several case studies that are commonly found in clinical practice, including digital pathology and chest, brain, cardiovascular, and abdominal imaging. Rather than presenting an exhaustive literature survey, we instead describe some prominent research highlights related to these case study applications. We conclude with a discussion and presentation of promising future directions.
Amirkabir University of Technology（阿米尔卡比尔理工大学）；The University of Texas at Dallas（德克萨斯大学达拉斯分校）
Purpose: Manual medical image segmentation is an exhausting and time-consuming task along with high inter-observer variability. In this study, our objective is to improve the multi-resolution image segmentation performance of U-Net architecture. Approach: We have proposed a fully convolutional neural network for image segmentation in a multi-resolution framework. We used U-Net as the base architecture and modified that to improve its image segmentation performance. In the proposed architecture (mrU-Net), the input image and its down-sampled versions were used as the network inputs. We added mo…
Purdue University Northwest（普渡大学西北校区）；Michigan Technological University（密歇根理工大学）
U-net is an image segmentation technique developed primarily for medical image analysis that can precisely segment images using a scarce amount of training data. These traits provide U-net with a very high utility within the medical imaging community and have resulted in extensive adoption of U-net as the primary tool for segmentation tasks in medical imaging. The success of U-net is evident in its widespread use in all major image modalities from CT scans and MRI to X-rays and microscopy. Furthermore, while U-net is largely a segmentation tool, there have been instances of the use of U-net in…
False Promises in Medical Imaging AI? Assessing Validity of Outperformance Claims
German Cancer Research Center (DKFZ) Heidelberg（德国癌症研究中心（DKFZ）海德堡）；National Center for Tumor Diseases (NCT)（肿瘤疾病国家中心（NCT））；Heidelberg University Hospital（海德堡大学医院）；DKFZ Heidelberg（德国癌症研究中心（DKFZ）海德堡）；Sorbonne Université（索邦大学）；HIDSS4Health - Helmholtz Information and Data Science School for Health（HIDSS4Health - 健康信息与数据科学学校）；MRC Unit for Lifelong Health and Ageing at UCL（UCL的长寿健康与衰老研究中心）；Centre for Medical Image Computing（医学图像计算中心）；University College London（伦敦大学学院）；School of Biomedical Engineering and Imaging Science（生物医学工程与成像科学学院）；CentraleSupelec；Paris-Saclay University（巴黎-萨克雷大学）；IT University of Copenhagen（哥本哈根技术大学）；Masaryk University（马萨里克大学）；NVIDIA；Queen’s University（皇后大学）；DKFZ（德国癌症研究中心（DKFZ））；INRIA Saclay-Île de France；Heidelberg University（海德堡大学）
A Review of Uncertainty Estimation and its Application in Medical Imaging
Sichuan University（四川大学）；Tianjin University（天津大学）；Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR)（新加坡科技研究局高性能计算研究所（IHPC））
Public Health Ontario（安大略省公共卫生局）；University of Toronto（多伦多大学）；Vector Institute（向量研究所）
Deep learning and knowledge transfer techniques have permeated the field of medical imaging and are considered as key approaches for revolutionizing diagnostic imaging practices. However, there are still challenges for the successful integration of deep learning into medical imaging tasks due to a lack of large annotated imaging data. To address this issue, we propose a teacher-student learning framework to transfer knowledge from a carefully pre-trained convolutional neural network (CNN) teacher to a student CNN. In this study, we explore the performance of knowledge transfer in the medical i…
When Eye-Tracking Meets Machine Learning: A Systematic Review on Applications in Medical Image Analysis
Macquarie University（麦考瑞大学）；Macquarie Medical School（麦考瑞医学院）；Faculty of Medicine, Health and Human Sciences（医学与健康科学学院）；School of Computing（计算机学院）；Faculty of Science and Engineering（科学与工程学院）；Centre for Health Informatics（健康信息学中心）；Australian Institute of Health Innovation（澳大利亚健康创新研究院）
Technion Institute of Technology（以色列理工学院）；Rambam Health Care Campus（兰巴姆医疗中心）
A key concern in integrating machine learning models in medicine is the ability to interpret their reasoning. Popular explainability methods have demonstrated satisfactory results in natural image recognition, yet in medical image analysis, many of these approaches provide partial and noisy explanations. Recently, attention mechanisms have shown compelling results both in their predictive performance and in their interpretable qualities. A fundamental trait of attention is that it leverages salient parts of the input which contribute to the model's prediction. To this end, our work focuses on …
Image denoising is an important pre-processing step in medical image analysis. Different algorithms have been proposed in past three decades with varying denoising performances. More recently, having outperformed all conventional methods, deep learning based models have shown a great promise. These methods are however limited for requirement of large training sample size and high computational costs. In this paper we show that using small sample size, denoising autoencoders constructed using convolutional layers can be used for efficient denoising of medical images. Heterogeneous images can be…
Arizona State University（亚利桑那州立大学）；Mayo Clinic（梅奥诊所）；Emory University（埃默里大学）
The use of artificial intelligence (AI) in healthcare has become a very active research area in the last few years. While significant progress has been made in image classification tasks, only a few AI methods are actually being deployed in hospitals. A major hurdle in actively using clinical AI models currently is the trustworthiness of these models. More often than not, these complex models are black boxes in which promising results are generated. However, when scrutinized, these models begin to reveal implicit biases during the decision making, such as detecting race and having bias towards…
Leiden University Medical Center（莱顿大学医学中心）；Centrum Wiskunde & Informatica（荷兰数学与计算机科学研究院）
Finding a realistic deformation that transforms one image into another, in case large deformations are required, is considered a key challenge in medical image analysis. Having a proper image registration approach to achieve this could unleash a number of applications requiring information to be transferred between images. Clinical adoption is currently hampered by many existing methods requiring extensive configuration effort before each use, or not being able to (realistically) capture large deformations. A recent multi-objective approach that uses the Multi-Objective Real-Valued Gene-pool O…
Physics-Inspired Generative Models in Medical Imaging: A Review
KTH Royal Institute of Technology（瑞典皇家理工学院）；Karolinska University Hospital（卡罗林斯卡大学医院）；University of Regensburg（雷根斯堡大学）；Fraunhofer Institute for Digital Medicine MEVIS（弗劳恩霍夫数字医学MEVIS研究所）；Rensselaer Polytechnic Institute（伦斯勒理工学院）
Image-based characterization and disease understanding involve integrative analysis of morphological, spatial, and topological information across biological scales. The development of graph convolutional networks (GCNs) has created the opportunity to address this information complexity via graph-driven architectures, since GCNs can perform feature aggregation, interaction, and reasoning with remarkable flexibility and efficiency. These GCNs capabilities have spawned a new wave of research in medical imaging analysis with the overarching goal of improving quantitative disease understanding, mon…
We present a fast learning-based algorithm for deformable, pairwise 3D medical image registration. Current registration methods optimize an objective function independently for each pair of images, which can be time-consuming for large data. We define registration as a parametric function, and optimize its parameters given a set of images from a collection of interest. Given a new pair of scans, we can quickly compute a registration field by directly evaluating the function using the learned parameters. We model this function using a convolutional neural network (CNN), and use a spatial transf…
Modality-Projection Universal Model for Comprehensive Full-Body Medical Imaging Segmentation
the Institute of Medical Technology and National Biomedical Imaging Center, Peking University（北京大学医学技术研究所暨国家生物医学成像中心）；The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital（山东第一医科大学第一附属医院暨山东省千佛山医院）；Peking University Third Hospital（北京大学第三医院）；Guangdong Provincial People’s Hospital（广东省人民医院）；Peking University Cancer Hospital & Institute（北京大学肿瘤医院暨肿瘤研究所）
Virginia Tech（弗吉尼亚理工大学）；University of Virginia（弗吉尼亚大学）
Advances in deep neural networks (DNNs) have shown tremendous promise in the medical domain. However, the deep learning tools that are helping the domain, can also be used against it. Given the prevalence of fraud in the healthcare domain, it is important to consider the adversarial use of DNNs in manipulating sensitive data that is crucial to patient healthcare. In this work, we present the design and implementation of a DNN-based image translation attack on biomedical imagery. More specifically, we propose Jekyll, a neural style transfer framework that takes as input a biomedical image of a …
SUNY Buffalo（纽约州立大学布法罗分校）；Medical College of Wisconsin（威斯康星医学院）；Washington University School of Medicine（华盛顿大学医学院）；University of California, Davis Medical Center（加州大学戴维斯医学中心）
Neural networks promise to bring robust, quantitative analysis to medical fields, but adoption is limited by the technicalities of training these networks. To address this translation gap between medical researchers and neural networks in the field of pathology, we have created an intuitive interface which utilizes the commonly used whole slide image (WSI) viewer, Aperio ImageScope (Leica Biosystems Imaging, Inc.), for the annotation and display of neural network predictions on WSIs. Leveraging this, we propose the use of a human-in-the-loop strategy to reduce the burden of WSI annotation. We …
Read Like a Radiologist: Efficient Vision-Language Model for 3D Medical Imaging Interpretation
Kim Jaechul Graduate School of AI, Korea Advanced Institute of Science and Technology (KAIST)（金在哲人工智能研究生院，韩国科学技术院（KAIST））；Yonsei University College of Medicine（延世大学医学院）；Seoul National University College of Medicine（首尔大学医学院）；Seoul National University Hospital（首尔大学医院）；Chung-Ang University College of Medicine（中央大学医学院）；Chungnam National University College of Medicine（忠南大学医学院）
Transparency in Machine Learning (ML), attempts to reveal the working mechanisms of complex models. Transparent ML promises to advance human factors engineering goals of human-centered AI in the target users. From a human-centered design perspective, transparency is not a property of the ML model but an affordance, i.e. a relationship between algorithm and user; as a result, iterative prototyping and evaluation with users is critical to attaining adequate solutions that afford transparency. However, following human-centered design principles in healthcare and medical image analysis is challeng…
The combination of tomographic imaging and deep learning, or machine learning in general, promises to empower not only image analysis but also image reconstruction. The latter aspect is considered in this perspective article with an emphasis on medical imaging to develop a new generation of image reconstruction theories and techniques. This direction might lead to intelligent utilization of domain knowledge from big data, innovative approaches for image reconstruction, and superior performance in clinical and preclinical applications. To realize the full impact of machine learning on medical i…
Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）
The use of Convolutional Neural Networks (CNN) in natural image classification systems has produced very impressive results. Combined with the inherent nature of medical images that make them ideal for deep-learning, further application of such systems to medical image classification holds much promise. However, the usefulness and potential impact of such a system can be completely negated if it does not reach a target accuracy. In this paper, we present a study on determining the optimum size of the training data set necessary to achieve high classification accuracy with low variance in medic…
Google Research（谷歌研究院）；Georgia Institute of Technology（佐治亚理工学院）；Northwestern University（西北大学）
Recent progress in Medical Artificial Intelligence (AI) has delivered systems that can reach clinical expert level performance. However, such systems tend to demonstrate sub-optimal "out-of-distribution" performance when evaluated in clinical settings different from the training environment. A common mitigation strategy is to develop separate systems for each clinical setting using site-specific data [1]. However, this quickly becomes impractical as medical data is time-consuming to acquire and expensive to annotate [2]. Thus, the problem of "data-efficient generalization" presents an ongoing …
Stony Brook University（石溪大学）；Rensselaer Polytechnic Institute（伦斯勒理工学院）；UT Southwestern Medical Center（德克萨斯大学西南医学中心）
Deep learning has shown great promise for CT image reconstruction, in particular to enable low dose imaging and integrated diagnostics. These merits, however, stand at great odds with the low availability of diverse image data which are needed to train these neural networks. We propose to overcome this bottleneck via a deep reinforcement learning (DRL) approach that is integrated with a style-transfer (ST) methodology, where the DRL generates the anatomical shapes and the ST synthesizes the texture detail. We show that our method bears high promise for generating novel and anatomically accurat…
The histological assessment of human tissue has emerged as the key challenge for detection and treatment of cancer. A plethora of different data sources ranging from tissue microarray data to gene expression, proteomics or metabolomics data provide a detailed overview of the health status of a patient. Medical doctors need to assess these information sources and they rely on data driven automatic analysis tools. Methods for classification, grouping and segmentation of heterogeneous data sources as well as regression of noisy dependencies and estimation of survival probabilities enter the proce…
Investigating Data Memorization in 3D Latent Diffusion Models for Medical Image Synthesis
Heidelberg University Hospital（海德堡大学医院）；German Centre for Cardiovascular Research（德国心血管研究中心）；Heidelberg University（海德堡大学）；University Medical Center Mannheim（曼海姆大学医学中心）
Institute for AI in Medicine (IKIM), University Medicine Essen（埃森大学医学人工智能研究所（IKIM））；Computer Vision and Learning Lab (CVL), Heidelberg University（海德堡大学计算机视觉与学习实验室（CVL））
Deep neural networks are commonly used for medical purposes such as image generation, segmentation, or classification. Besides this, they are often criticized as black boxes as their decision process is often not human interpretable. Encouraging the latent representation of a generative model to be disentangled offers new perspectives of control and interpretability. Understanding the data generation process could help to create artificial medical data sets without violating patient privacy, synthesizing different data modalities, or discovering data generating characteristics. These character…
Automated medical image segmentation is an important step in many medical procedures. Recently, deep learning networks have been widely used for various medical image segmentation tasks, with U-Net and generative adversarial nets (GANs) being some of the commonly used ones. Foreground-background class imbalance is a common occurrence in medical images, and U-Net has difficulty in handling class imbalance because of its cross entropy (CE) objective function. Similarly, GAN also suffers from class imbalance because the discriminator looks at the entire image to classify it as real or fake. Since…
University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）；Food and Drug Administration（美国食品药品监督管理局）
Modern generative models, such as generative adversarial networks (GANs), hold tremendous promise for several areas of medical imaging, such as unconditional medical image synthesis, image restoration, reconstruction and translation, and optimization of imaging systems. However, procedures for establishing stochastic image models (SIMs) using GANs remain generic and do not address specific issues relevant to medical imaging. In this work, canonical SIMs that simulate realistic vessels in angiography images are employed to evaluate procedures for establishing SIMs using GANs. The GAN-based SIM …
University of Utah（犹他大学）；University of Arizona（亚利桑那大学）；Michigan State University（密歇根州立大学）；Carnegie Mellon University（卡内基梅隆大学）
YouTube presents an unprecedented opportunity to explore how machine learning methods can improve healthcare information dissemination. We propose an interdisciplinary lens that synthesizes machine learning methods with healthcare informatics themes to address the critical issue of developing a scalable algorithmic solution to evaluate videos from a health literacy and patient education perspective. We develop a deep learning method to understand the level of medical knowledge encoded in YouTube videos. Preliminary results suggest that we can extract medical knowledge from YouTube videos and c…
