Coronavirus Disease 2019 (COVID-19) has spread aggressively across the world causing an existential health crisis. Thus, having a system that automatically detects COVID-19 in tomography (CT) images can assist in quantifying the severity of the illness. Unfortunately, labelling chest CT scans requires significant domain expertise, time, and effort. We address these labelling challenges by only requiring point annotations, a single pixel for each infected region on a CT image. This labeling scheme allows annotators to label a pixel in a likely infected region, only taking 1-3 seconds, as opposed to 10-15 seconds to segment a region. Conventionally, segmentation models train on point-level annotations using the cross-entropy loss function on these labels. However, these models often suffer from low precision. Thus, we propose a consistency-based (CB) loss function that encourages the output predictions to be consistent with spatial transformations of the input images. The experiments on 3 open-source COVID-19 datasets show that this loss function yields significant improvement over conventional point-level loss functions and almost matches the performance of models trained with full supervision with much less human effort. Code is available at: \url{https://github.com/IssamLaradji/covid19_weak_supervision}.
Peng Cheng Laboratory（鹏城实验室）；Sun Yat-sen University（中山大学）；Harbin Institute of Technology, Shenzhen（哈尔滨工业大学（深圳））；Shenzhen People's Hospital（深圳市人民医院）；Shenzhen Institute of Respiratory Diseases（深圳呼吸疾病研究所）；Peking University Shenzhen Graduate School（北京大学深圳研究生院）
Despite tremendous efforts, it is very challenging to generate a robust model to assist in the accurate quantification assessment of COVID-19 on chest CT images. Due to the nature of blurred boundaries, the supervised segmentation methods usually suffer from annotation biases. To support unbiased lesion localisation and to minimise the labeling costs, we propose a data-driven framework supervised by only image-level labels. The framework can explicitly separate potential lesions from original images, with the help of a generative adversarial network and a lesion-specific decoder. Experiments o…
National Center for Biotechnology Information (NCBI)（美国国家生物技术信息中心）；National Library of Medicine (NLM)（美国国家医学图书馆）；National Institutes of Health (NIH)（美国国立卫生研究院）；Weill Cornell Medicine（威尔康奈尔医学院）；University of Texas at Arlington（德克萨斯大学阿灵顿分校）
The latest threat to global health is the COVID-19 outbreak. Although there exist large datasets of chest X-rays (CXR) and computed tomography (CT) scans, few COVID-19 image collections are currently available due to patient privacy. At the same time, there is a rapid growth of COVID-19-relevant articles in the biomedical literature. Here, we present COVID-19-CT-CXR, a public database of COVID-19 CXR and CT images, which are automatically extracted from COVID-19-relevant articles from the PubMed Central Open Access (PMC-OA) Subset. We extracted figures, associated captions, and relevant figure…
Imsight AI Research Lab（Imsight人工智能研究实验室）；The Chinese University of Hong Kong（香港中文大学）；The Hong Kong University of Science and Technology（香港科技大学）；Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences（中国科学院深圳先进技术研究院）
The novel coronavirus disease 2019 (COVID-19) characterized by atypical pneumonia has caused millions of deaths worldwide. Automatically segmenting lesions from chest Computed Tomography (CT) is a promising way to assist doctors in COVID-19 screening, treatment planning, and follow-up monitoring. However, voxel-wise annotations are extremely expert-demanding and scarce, especially when it comes to novel diseases, while an abundance of unlabeled data could be available. To tackle the challenge of limited annotations, in this paper, we propose an uncertainty-guided dual-consistency learning netw…
Inception Institute of Artificial Intelligence（起源人工智能研究院）；Indian Institute of Technology, Kanpur（印度理工学院坎普尔分校）
While medical image segmentation is an important task for computer aided diagnosis, the high expertise requirement for pixelwise manual annotations makes it a challenging and time consuming task. Since conventional data augmentations do not fully represent the underlying distribution of the training set, the trained models have varying performance when tested on images captured from different sources. Most prior work on image synthesis for data augmentation ignore the interleaved geometric relationship between different anatomical labels. We propose improvements over previous GAN-based medical…
Tsinghua University（清华大学）；Huazhong University of Science and Technology（华中科技大学）
Segmentation of infected areas in chest CT volumes is of great significance for further diagnosis and treatment of COVID-19 patients. Due to the complex shapes and varied appearances of lesions, a large number of voxel-level labeled samples are generally required to train a lesion segmentation network, which is a main bottleneck for developing deep learning based medical image segmentation algorithms. In this paper, we propose a weakly-supervised lesion segmentation framework by embedding the Generative Adversarial training process into the Segmentation Network, which is called GASNet. GASNet …
Element AI；Xtract AI；University of British Columbia（不列颠哥伦比亚大学）；SapienML；McGill University（麦吉尔大学）
One of the key challenges in the battle against the Coronavirus (COVID-19) pandemic is to detect and quantify the severity of the disease in a timely manner. Computed tomographies (CT) of the lungs are effective for assessing the state of the infection. Unfortunately, labeling CT scans can take a lot of time and effort, with up to 150 minutes per scan. We address this challenge introducing a scalable, fast, and accurate active learning system that accelerates the labeling of CT scan images. Conventionally, active learning methods require the labelers to annotate whole images with full supervis…
Hospital of Wuhan Red Cross Society（武汉红十字会医院）；Institute of Biomedical Engineering, University of Oxford（牛津大学生物医学工程研究所）；Aladdin Healthcare Technologies Ltd（阿拉丁医疗科技有限公司）；Hangzhou Ocean's Smart Boya Co., Ltd（杭州奥盛博雅智能科技有限公司）；Mind Rank Ltd（Mind Rank有限公司）；IIAT；University of Oslo（奥斯陆大学）；Shenzhen Second People’s Hospital（深圳市第二人民医院）；Hunan Cancer Hospital（湖南省肿瘤医院）；NHLI, Imperial College London（伦敦帝国理工学院国家心肺研究所）；Royal Brompton Hospital（皇家布朗普顿医院）
An outbreak of a novel coronavirus disease (i.e., COVID-19) has been recorded in Wuhan, China since late December 2019, which subsequently became pandemic around the world. Although COVID-19 is an acutely treated disease, it can also be fatal with a risk of fatality of 4.03% in China and the highest of 13.04% in Algeria and 12.67% Italy (as of 8th April 2020). The onset of serious illness may result in death as a consequence of substantial alveolar damage and progressive respiratory failure. Although laboratory testing, e.g., using reverse transcription polymerase chain reaction (RT-PCR), is t…
University of California, San Diego（加州大学圣迭戈分校）；University of Oxford（牛津大学）；Aladdin Healthcare Technologies Ltd（阿拉丁医疗科技有限公司）；Nantong University（南通大学）；University of Edinburgh（爱丁堡大学）；Mind Rank Ltd（Mind Rank有限公司）；University of Oslo（奥斯陆大学）；Royal Brompton Hospital（皇家布朗普顿医院）；Imperial College London（伦敦帝国理工学院）
The world is currently experiencing an ongoing pandemic of an infectious disease named coronavirus disease 2019 (i.e., COVID-19), which is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Computed Tomography (CT) plays an important role in assessing the severity of the infection and can also be used to identify those symptomatic and asymptomatic COVID-19 carriers. With a surge of the cumulative number of COVID-19 patients, radiologists are increasingly stressed to examine the CT scans manually. Therefore, an automated 3D CT scan recognition tool is highly in demand s…
Autodesk Research（Autodesk 研究院）；University of Illinois, Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
The ability to determine what parts of objects and surfaces people touch as they go about their daily lives would be useful in understanding how the COVID-19 virus spreads. To determine whether a person has touched an object or surface using visual data, images, or videos, is a hard problem. Computer vision 3D reconstruction approaches project objects and the human body from the 2D image domain to 3D and perform 3D space intersection directly. However, this solution would not meet the accuracy requirement in applications due to projection error. Another standard approach is to train a neural n…
Automatic lesion segmentation on thoracic CT enables rapid quantitative analysis of lung involvement in COVID-19 infections. However, obtaining a large amount of voxel-level annotations for training segmentation networks is prohibitively expensive. Therefore, we propose a weakly-supervised segmentation method based on dense regression activation maps (dRAMs). Most weakly-supervised segmentation approaches exploit class activation maps (CAMs) to localize objects. However, because CAMs were trained for classification, they do not align precisely with the object segmentations. Instead, we produce…
Moscow Institute of Physics and Technology（莫斯科物理技术学院）；Skolkovo Institute of Science and Technology（斯科尔科沃科学技术研究院）；Artificial Intelligence Research Institute (AIRI)（人工智能研究院（AIRI））
Deep learning methods provide significant assistance in analyzing coronavirus disease (COVID-19) in chest computed tomography (CT) images, including identification, severity assessment, and segmentation. Although the earlier developed methods address the lack of data and specific annotations, the current goal is to build a robust algorithm for clinical use, having a larger pool of available data. With the larger datasets, the domain shift problem arises, affecting the performance of methods on the unseen data. One of the critical sources of domain shift in CT images is the difference in recons…
Beihang University（北京航空航天大学）；Taiyuan University of Technology（太原理工大学）；Hefei Innovation Research Institute, Beihang University（北京航空航天大学合肥创新研究院）；Beijing Advanced Innovation Centre for Biomedical Engineering（北京生物医学工程高精尖创新中心）；Beijing Advanced Innovation Centre for Big Data-Based Precision Medicine（北京大数据精准医疗高精尖创新中心）
The novel Coronavirus disease (COVID-19) is a highly contagious virus and has spread all over the world, posing an extremely serious threat to all countries. Automatic lung infection segmentation from computed tomography (CT) plays an important role in the quantitative analysis of COVID-19. However, the major challenge lies in the inadequacy of annotated COVID-19 datasets. Currently, there are several public non-COVID lung lesion segmentation datasets, providing the potential for generalizing useful information to the related COVID-19 segmentation task. In this paper, we propose a novel relati…
University of Waterloo（滑铁卢大学）；DarwinAI Corp.（DarwinAI公司）；Niagara Health（尼亚加拉医疗）；McMaster University（麦克马斯特大学）；Thunder Bay Regional Health Sciences Centre（桑德贝地区健康科学中心）；Northern Ontario School of Medicine（北部安大略医学院）
The world is still struggling in controlling and containing the spread of the COVID-19 pandemic caused by the SARS-CoV-2 virus. The medical conditions associated with SARS-CoV-2 infections have resulted in a surge in the number of patients at clinics and hospitals, leading to a significantly increased strain on healthcare resources. As such, an important part of managing and handling patients with SARS-CoV-2 infections within the clinical workflow is severity assessment, which is often conducted with the use of chest x-ray (CXR) images. In this work, we introduce COVID-Net CXR-S, a convolution…
Shahid Sadoughi University of Medical Sciences（沙希德·萨杜吉医科大学）；Mashhad University of Medical Sciences（马什哈德医科大学）；Geneva University Hospital（日内瓦大学医院）
This study aimed to evaluate the performance of a novel unsupervised deep learning-based framework for automated infections lesion segmentation from CT images of Covid patients. In the first step, two residual networks were independently trained to identify the lung tissue for normal and Covid patients in a supervised manner. These two models, referred to as DL-Covid and DL-Norm for Covid-19 and normal patients, respectively, generate the voxel-wise probability maps for lung tissue identification. To detect Covid lesions, the CT image of the Covid patient is processed by the DL-Covid and DL-No…
National Heart and Lung Institute, Imperial College London（帝国理工学院国家心肺研究所）；Royal Brompton Hospital（皇家布朗普顿医院）；Shenzhen Second People’s Hospital（深圳市第二人民医院）；TECNALIA（泰克纳利亚研究中心）；University of the Basque Country（巴斯克大学）
The upheaval brought by the arrival of the COVID-19 pandemic has continued to bring fresh challenges over the past two years. During this COVID-19 pandemic, there has been a need for rapid identification of infected patients and specific delineation of infection areas in computed tomography (CT) images. Although deep supervised learning methods have been established quickly, the scarcity of both image-level and pixel-level labels as well as the lack of explainable transparency still hinder the applicability of AI. Can we identify infected patients and delineate the infections with extreme mini…
University College London（伦敦大学学院）；Frimley Health NHS Foundation Trust（弗林姆利健康国民医疗服务基金会信托）；Royal Berkshire NHS Foundation Trust（皇家伯克郡国民医疗服务基金会信托）；Hospital de La Santa Creu I Sant Pau（圣克鲁和圣保罗医院）；West Suffolk NHS Foundation Trust（西萨福克国民医疗服务基金会信托）；Cambridge University Hospital（剑桥大学医院）；University of Cambridge（剑桥大学）；Great Ormond Street Children's Hospital NHS Foundation Trust（大奥蒙德街儿童医院国民医疗服务基金会信托）；Institute of Child Health, University College London（伦敦大学学院儿童健康研究所）；UCL Queen Square Institute of Neurology（伦敦大学学院皇后广场神经病学研究所）；University of Pavia（帕维亚大学）
Lung ultrasound imaging has been shown effective in detecting typical patterns for interstitial pneumonia, as a point-of-care tool for both patients with COVID-19 and other community-acquired pneumonia (CAP). In this work, we focus on the hyperechoic B-line segmentation task. Using deep neural networks, we automatically outline the regions that are indicative of pathology-sensitive artifacts and their associated sonographic patterns. With a real-world data-scarce scenario, we investigate approaches to utilize both COVID-19 and CAP lung ultrasound data to train the networks; comparing fine-tuni…
Xiamen University（厦门大学）；The Hong Kong University of Science and Technology (Guangzhou)（香港科技大学（广州））；The Hong Kong University of Science and Technology（香港科技大学）；The Chinese University of Hong Kong（香港中文大学）；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）；The Hong Kong Polytechnic University（香港理工大学）；The Education University of Hong Kong（香港教育大学）；Zhongshan Hospital, Xiamen University（厦门大学附属中山医院）；Western University（韦仕敦大学）
Automated detecting lung infections from computed tomography (CT) data plays an important role for combating COVID-19. However, there are still some challenges for developing AI system. 1) Most current COVID-19 infection segmentation methods mainly relied on 2D CT images, which lack 3D sequential constraint. 2) Existing 3D CT segmentation methods focus on single-scale representations, which do not achieve the multiple level receptive field sizes on 3D volume. 3) The emergent breaking out of COVID-19 makes it hard to annotate sufficient CT volumes for training deep model. To address these issue…
Christian Brothers University（基督教兄弟大学）；University of Dayton（代顿大学）
With a Coronavirus disease (COVID-19) case count exceeding 10 million worldwide, there is an increased need for a diagnostic capability. The main variables in increasing diagnostic capability are reduced cost, turnaround or diagnosis time, and upfront equipment cost and accessibility. Two candidates for machine learning COVID-19 diagnosis are Computed Tomography (CT) scans and plain chest X-rays. While CT scans score higher in sensitivity, they have a higher cost, maintenance requirement, and turnaround time as compared to plain chest X-rays. The use of portable chest X-radiograph (CXR) is rec…
Shenzhen Research Institute of Big Data, The Chinese University of Hong Kong, Shenzhen（香港中文大学（深圳）深圳大数据研究院）
Ultrasound (US) is a non-invasive yet effective medical diagnostic imaging technique for the COVID-19 global pandemic. However, due to complex feature behaviors and expensive annotations of US images, it is difficult to apply Artificial Intelligence (AI) assisting approaches for lung's multi-symptom (multi-label) classification. To overcome these difficulties, we propose a novel semi-supervised Two-Stream Active Learning (TSAL) method to model complicated features and reduce labeling costs in an iterative procedure. The core component of TSAL is the multi-label learning mechanism, in which lab…
MambaEviScrib: Mamba and Evidence-Guided Consistency Enhance CNN Robustness for Scribble-Based Weakly Supervised Ultrasound Image Segmentation
School of Communication and Information Engineering, Shanghai University（上海大学通信与信息工程学院）；The SMART (Smart Medicine and AI-based Radiology Technology) Lab, Shanghai Institute for Advanced Communication and Data Science, Shanghai University（上海大学先进通信与数据科学研究院智能医学与AI放射技术实验室）；School of Health Science and Engineering, University of Shanghai for Science and Technology（上海科技大学健康科学与工程学院）；Department of Pediatric Cardiology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine（上海交通大学医学院儿童心脏科部）；School of Medical Instruments, Shanghai University of Medicine and Health Sciences（医学仪器学院，上海医学院与健康科学大学）
Sharif University of Technology（谢里夫理工大学）；Tehran University of Medical Sciences（德黑兰医科大学）；Iran University of Medical Sciences（伊朗医科大学）
COVID-19 is a virus with high transmission rate that demands rapid identification of the infected patients to reduce the spread of the disease. The current gold-standard test, Reverse-Transcription Polymerase Chain Reaction (RT-PCR), has a high rate of false negatives. Diagnosing from CT-scan images as a more accurate alternative has the challenge of distinguishing COVID-19 from other pneumonia diseases. Artificial intelligence can help radiologists and physicians to accelerate the process of diagnosis, increase its accuracy, and measure the severity of the disease. We designed a new interpret…
Southeast University（东南大学）；Centre de Recherche en Information Biomédicale Sino-Français (CRIBs)（中法生物医学信息研究中心）；The First Affiliated Hospital of Nanjing Medical University（南京医科大学第一附属医院）；Univ Rennes, Inserm, LTSI - UMR1099（雷恩大学，法国国家健康与医学研究院，信号与图像处理实验室）；University of Western Ontario（西安大略大学）
Renal compartment segmentation on CT images targets on extracting the 3D structure of renal compartments from abdominal CTA images and is of great significance to the diagnosis and treatment for kidney diseases. However, due to the unclear compartment boundary, thin compartment structure and large anatomy variation of 3D kidney CT images, deep-learning based renal compartment segmentation is a challenging task. We propose a novel weakly supervised learning framework, Cycle Prototype Network, for 3D renal compartment segmentation. It has three innovations: 1) A Cycle Prototype Learning (CPL) is…
In this work we design an end-to-end deep learning architecture for predicting, on Chest X-rays images (CXR), a multi-regional score conveying the degree of lung compromise in COVID-19 patients. Such semi-quantitative scoring system, namely Brixia~score, is applied in serial monitoring of such patients, showing significant prognostic value, in one of the hospitals that experienced one of the highest pandemic peaks in Italy. To solve such a challenging visual task, we adopt a weakly supervised learning strategy structured to handle different tasks (segmentation, spatial alignment, and score est…
Daegu Gyeongbuk Institute of Science and Technology (DGIST)（大邱庆北科学技术院）；Yeungnam University（岭南大学）；Yeungnam University Medical Center（岭南大学医疗中心）
Following the pandemic outbreak, several works have proposed to diagnose COVID-19 with deep learning in computed tomography (CT); reporting performance on-par with experts. However, models trained/tested on the same in-distribution data may rely on the inherent data biases for successful prediction, failing to generalize on out-of-distribution samples or CT with different scanning protocols. Early attempts have partly addressed bias-mitigation and generalization through augmentation or re-sampling, but are still limited by collection costs and the difficulty of quantifying bias in medical imag…
Carnegie Mellon University（卡内基梅隆大学）；Louisiana State University（路易斯安那州立大学）；Cosmeticsurg.net, LLC（Cosmeticsurg.net有限责任公司）
With the onset of the COVID-19 pandemic, ultrasound has emerged as an effective tool for bedside monitoring of patients. Due to this, a large amount of lung ultrasound scans have been made available which can be used for AI based diagnosis and analysis. Several AI-based patient severity scoring models have been proposed that rely on scoring the appearance of the ultrasound scans. AI models are trained using ultrasound-appearance severity scores that are manually labeled based on standardized visual features. We address the challenge of labeling every ultrasound frame in the video clips. Our co…
We present a novel approach to train pixel resolution segmentation models on whole slide images in a weakly supervised setup. The model is trained to classify patches extracted from slides. This leads the training to be made under noisy labeled data. We solve the problem with two complementary strategies. First, the patches are sampled online using the model's knowledge by focusing on regions where the model's confidence is higher. Second, we propose an extension of the KL divergence that is robust to noisy labels. Our preliminary experiment on CAMELYON 16 data set show promising results. The …
