Correcting Data Imbalance for Semi-Supervised Covid-19 Detection Using X-ray Chest Images
Centre for Computational Intelligence (CCI), De Montfort University（德蒙福特大学计算智能中心）；Instituto Tecnologico de Costa Rica（哥斯达黎加理工学院）；School of Computer Science, University of Nottingham（诺丁汉大学计算机科学学院）；Imágenes Médicas Dr Chavarría Estrada（查瓦里亚·埃斯特拉达医学影像中心）；Biomedic Research Institute of Málaga (IBIMA)（马拉加生物医学研究所）
Saul Calderon-Ramirez, Shengxiang-Yang, Armaghan Moemeni, David Elizondo, Simon Colreavy-Donnelly, Luis Fernando Chavarria-Estrada, Miguel A. Molina-Cabello
The Corona Virus (COVID-19) is an internationalpandemic that has quickly propagated throughout the world. The application of deep learning for image classification of chest X-ray images of Covid-19 patients, could become a novel pre-diagnostic detection methodology. However, deep learning architectures require large labelled datasets. This is often a limitation when the subject of research is relatively new as in the case of the virus outbreak, where dealing with small labelled datasets is a challenge. Moreover, in the context of a new highly infectious disease, the datasets are also highly imbalanced,with few observations from positive cases of the new disease. In this work we evaluate the performance of the semi-supervised deep learning architecture known as MixMatch using a very limited number of labelled observations and highly imbalanced labelled dataset. We propose a simple approach for correcting data imbalance, re-weight each observationin the loss function, giving a higher weight to the observationscorresponding to the under-represented class. For unlabelled observations, we propose the usage of the pseudo and augmentedlabels calculated by MixMatch to choose the appropriate weight. The MixMatch method combined with the proposed pseudo-label based balance correction improved classification accuracy by up to 10%, with respect to the non balanced MixMatch algorithm, with statistical significance. We tested our proposed approach with several available datasets using 10, 15 and 20 labelledobservations. Additionally, a new dataset is included among thetested datasets, composed of chest X-ray images of Costa Rican adult patients
UiT The Arctic University of Norway（挪威北极大学）；Technical University of Berlin（柏林工业大学）
The recent trend of integrating multi-source Chest X-Ray datasets to improve automated diagnostics raises concerns that models learn to exploit source-specific correlations to improve performance by recognizing the source domain of an image rather than the medical pathology. We hypothesize that this effect is enforced by and leverages label-imbalance across the source domains, i.e, prevalence of a disease corresponding to a source. Therefore, in this work, we perform a thorough study of the effect of label-imbalance in multi-source training for the task of pneumonia detection on the widely use…
People all over the globe are affected by pneumonia but deaths due to it are highest in Sub-Saharan Asia and South Asia. In recent years, the overall incidence and mortality rate of pneumonia regardless of the utilization of effective vaccines and compelling antibiotics has escalated. Thus, pneumonia remains a disease that needs spry prevention and treatment. The widespread prevalence of pneumonia has caused the research community to come up with a framework that helps detect, diagnose and analyze diseases accurately and promptly. One of the major hurdles faced by the Artificial Intelligence (…
Universidad Politécnica de Madrid（马德里理工大学）；Universidad Autónoma de Madrid（马德里自治大学）；TECNALIA（特克纳利亚研究中心）；Basque Research & Technology Alliance（巴斯克研究与技术联盟）
Over the last few years, convolutional neural networks (CNNs) have dominated the field of computer vision thanks to their ability to extract features and their outstanding performance in classification problems, for example in the automatic analysis of X-rays. Unfortunately, these neural networks are considered black-box algorithms, i.e. it is impossible to understand how the algorithm has achieved the final result. To apply these algorithms in different fields and test how the methodology works, we need to use eXplainable AI techniques. Most of the work in the medical field focuses on binary …
School of Professional Studies（专业研究学院）；Northwestern University（西北大学）
Artificial intelligence (AI) is disrupting the medical field as advances in modern technology allow common household computers to learn anatomical and pathological features that distinguish between healthy and disease with the accuracy of highly specialized, trained physicians. Computer vision AI applications use medical imaging, such as lung chest X-Rays (LCXRs), to facilitate diagnoses by providing second-opinions in addition to a physician's or radiologist's interpretation. Considering the advent of the current Coronavirus disease (COVID-19) pandemic, LCXRs may provide rapid insights to ind…
We introduce a new dataset called Synthetic COVID-19 Chest X-ray Dataset for training machine learning models. The dataset consists of 21,295 synthetic COVID-19 chest X-ray images to be used for computer-aided diagnosis. These images, generated via an unsupervised domain adaptation approach, are of high quality. We find that the synthetic images not only improve performance of various deep learning architectures when used as additional training data under heavy imbalance conditions, but also detect the target class with high confidence. We also find that comparable performance can also be achi…
A common problem in computer vision -- particularly in medical applications -- is a lack of sufficiently diverse, large sets of training data. These datasets often suffer from severe class imbalance. As a result, networks often overfit and are unable to generalize to novel examples. Generative Adversarial Networks (GANs) offer a novel method of synthetic data augmentation. In this work, we evaluate the use of GAN- based data augmentation to artificially expand the CheXpert dataset of chest radiographs. We compare performance to traditional augmentation and find that GAN-based augmentation lead…
We propose a highly data-efficient active learning framework for image classification. Our novel framework combines: (1) unsupervised representation learning of a Convolutional Neural Network and (2) the Gaussian Process (GP) method, in sequence to achieve highly data and label efficient classifications. Moreover, both elements are less sensitive to the prevalent and challenging class imbalance issue, thanks to the (1) feature learned without labels and (2) the Bayesian nature of GP. The GP-provided uncertainty estimates enable active learning by ranking samples based on the uncertainty and se…
University College London（伦敦大学学院）；King’s College London（伦敦国王学院）；Royal Free London NHS Foundation Trust（伦敦皇家自由NHS基金会信托）
During the COVID-19 pandemic, the sheer volume of imaging performed in an emergency setting for COVID-19 diagnosis has resulted in a wide variability of clinical CXR acquisitions. This variation is seen in the CXR projections used, image annotations added and in the inspiratory effort and degree of rotation of clinical images. The image analysis community has attempted to ease the burden on overstretched radiology departments during the pandemic by developing automated COVID-19 diagnostic algorithms, the input for which has been CXR imaging. Large publicly available CXR datasets have been leve…
Neural Architecture Search (NAS) provides state-of-the-art results when trained on well-curated datasets with annotated labels. However, annotating data or even having balanced number of samples can be a luxury for practitioners from different scientific fields, e.g., in the medical domain. To that end, we propose a NAS-based framework that bears the threefold contributions: (a) we focus on the self-supervised scenario, i.e., where no labels are required to determine the architecture, and (b) we assume the datasets are imbalanced, (c) we design each component to be able to run on a resource co…
Medical Imaging Center, Vingroup Big Data Institute（Vingroup大数据研究院医学影像中心）；College of Engineering & Computer Science, VinUniversity（VinUniversity工程与计算机科学学院）
Chest radiograph (CXR) interpretation in pediatric patients is error-prone and requires a high level of understanding of radiologic expertise. Recently, deep convolutional neural networks (D-CNNs) have shown remarkable performance in interpreting CXR in adults. However, there is a lack of evidence indicating that D-CNNs can recognize accurately multiple lung pathologies from pediatric CXR scans. In particular, the development of diagnostic models for the detection of pediatric chest diseases faces significant challenges such as (i) lack of physician-annotated datasets and (ii) class imbalance …
University of Waterloo（滑铁卢大学）；Waterloo AI Institute（滑铁卢人工智能研究所）；DarwinAI Corp.（达尔文人工智能公司）
Computed tomography (CT) has been widely explored as a COVID-19 screening and assessment tool to complement RT-PCR testing. To assist radiologists with CT-based COVID-19 screening, a number of computer-aided systems have been proposed. However, many proposed systems are built using CT data which is limited in both quantity and diversity. Motivated to support efforts in the development of machine learning-driven screening systems, we introduce COVIDx CT-3, a large-scale multinational benchmark dataset for detection of COVID-19 cases from chest CT images. COVIDx CT-3 includes 431,205 CT slices f…
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）
Deep learning models were frequently reported to learn from shortcuts like dataset biases. As deep learning is playing an increasingly important role in the modern healthcare system, it is of great need to combat shortcut learning in medical data as well as develop unbiased and trustworthy models. In this paper, we study the problem of developing debiased chest X-ray diagnosis models from the biased training data without knowing exactly the bias labels. We start with the observations that the imbalance of bias distribution is one of the key reasons causing shortcut learning, and the dataset bi…
University of Pittsburgh（匹兹堡大学）；National University of Defense Technology（国防科技大学）；University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh（匹兹堡大学医学中心匹兹堡儿童医院）
Medical image data are usually imbalanced across different classes. One-class classification has attracted increasing attention to address the data imbalance problem by distinguishing the samples of the minority class from the majority class. Previous methods generally aim to either learn a new feature space to map training samples together or to fit training samples by autoencoder-like models. These methods mainly focus on capturing either compact or descriptive features, where the information of the samples of a given one class is not sufficiently utilized. In this paper, we propose a novel …
Johns Hopkins University（约翰斯·霍普金斯大学）；Technical University of Munich（慕尼黑工业大学）；Kyung Hee University（庆熙大学）
Convolutional neural networks are showing promise in the automatic diagnosis of thoracic pathologies on chest x-rays. Their black-box nature has sparked many recent works to explain the prediction via input feature attribution methods (aka saliency methods). However, input feature attribution methods merely identify the importance of input regions for the prediction and lack semantic interpretation of model behavior. In this work, we first identify the semantics associated with internal units (feature maps) of the network. We proceed to investigate the following questions; Does a regression mo…
National Library of Medicine, National Institutes of Health（美国国立卫生研究院国家医学图书馆）；Stanford University（斯坦福大学）
In medical image classification tasks, it is common to find that the number of normal samples far exceeds the number of abnormal samples. In such class-imbalanced situations, reliable training of deep neural networks continues to be a major challenge. Under these circumstances, the predicted class probabilities may be biased toward the majority class. Calibration has been suggested to alleviate some of these effects. However, there is insufficient analysis explaining when and whether calibrating a model would be beneficial in improving performance. In this study, we perform a systematic analys…
Chest X-Ray (CXR) images are commonly used for clinical screening and diagnosis. Automatically writing reports for these images can considerably lighten the workload of radiologists for summarizing descriptive findings and conclusive impressions. The complex structures between and within sections of the reports pose a great challenge to the automatic report generation. Specifically, the section Impression is a diagnostic summarization over the section Findings; and the appearance of normality dominates each section over that of abnormality. Existing studies rarely explore and consider this fun…
University of Electronic Science and Technology of China（电子科技大学）；Sichuan University West China Hospital（四川大学华西医院）；Shanghai United Imaging Intelligence Co., Ltd.（上海联影智能医疗科技有限公司）
With the rapidly worldwide spread of Coronavirus disease (COVID-19), it is of great importance to conduct early diagnosis of COVID-19 and predict the time that patients might convert to the severe stage, for designing effective treatment plan and reducing the clinicians' workloads. In this study, we propose a joint classification and regression method to determine whether the patient would develop severe symptoms in the later time, and if yes, predict the possible conversion time that the patient would spend to convert to the severe stage. To do this, the proposed method takes into account 1) …
IQVIA（艾昆纬）；University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
To test the possibility of differentiating chest x-ray images of COVID-19 against other pneumonia and healthy patients using deep neural networks. We construct the X-ray imaging data from two publicly available sources, which include 5508 chest x-ray images across 2874 patients with four classes: normal, bacterial pneumonia, non-COVID-19 viral pneumonia, and COVID-19. To identify COVID-19, we propose a Focal Loss Based Neural Ensemble Network (FLANNEL), a flexible module to ensemble several convolutional neural network (CNN) models and fuse with a focal loss for accurate COVID-19 detection on …
We propose a data collecting and annotation pipeline that extracts information from Vietnamese radiology reports to provide accurate labels for chest X-ray (CXR) images. This can benefit Vietnamese radiologists and clinicians by annotating data that closely match their endemic diagnosis categories which may vary from country to country. To assess the efficacy of the proposed labeling technique, we built a CXR dataset containing 9,752 studies and evaluated our pipeline using a subset of this dataset. With an F1-score of at least 0.9923, the evaluation demonstrates that our labeling tool perform…
Loss Design and Architecture Selection for Long-Tailed Multi-Label Chest X-Ray Classification
Department of Computer Science and Engineering（计算机科学与工程系）；Rajiv Gandhi University of Knowledge Technologies（拉贾戈丁德知识技术大学）；Gandhi University of Knowledge Technologies（戈丁德知识技术大学）
AI Models Close to your Chest: Robust Federated Learning Strategies for Multi-site CT
School of Medicine, Stanford University（斯坦福大学医学院）；Insight Centre for Data Analytics, University College Dublin（都柏林大学学院洞察数据分析中心）；Icahn School of Medicine at Mount Sinai（西奈山伊坎医学院）；Koç University School of Medicine（科克大学医学院）；Amiralam Hospital, Tehran University of Medical Sciences（德黑兰医科大学阿米拉拉姆医院）；Unity Health Toronto, St. Michael’s Hospital and University of Toronto（多伦多联合健康中心、圣迈克尔医院与多伦多大学）；Amazon Web Services（亚马逊网络服务）；Universidade Federal de São Paulo（圣保罗联邦大学）；Fleni（弗莱尼）；Radiology Department Centre International Carthage Médicale（迦太基国际医疗中心放射科）；Hospital Israelita Albert Einstein（以色列裔爱因斯坦医院）；Kyungpook National University Hospital（庆北国立大学医院）；St. Joseph’s Hospital and Medical Center（圣约瑟夫医院与医疗中心）；Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences（伊朗医科大学拉贾伊心血管医疗与研究中心）；Henry Ford Health System（亨利福特医疗系统）；Guilan University of Medical Sciences（吉兰医科大学）；Ann & Robert H. Lurie Children's Hospital of Chicago（芝加哥安与罗伯特·H·卢里儿童医院）
University of Assiut（艾斯尤特大学）；Birmingham City University（伯明翰城市大学）
Due to the high availability of large-scale annotated image datasets, knowledge transfer from pre-trained models showed outstanding performance in medical image classification. However, building a robust image classification model for datasets with data irregularity or imbalanced classes can be a very challenging task, especially in the medical imaging domain. In this paper, we propose a novel deep convolutional neural network, we called Self Supervised Super Sample Decomposition for Transfer learning (4S-DT) model. 4S-DT encourages a coarse-to-fine transfer learning from large-scale image rec…
University of Cambridge（剑桥大学）；Indian Institute of Technology Madras（马德拉斯印度理工学院）；Indian Institute of Technology Patna（巴特那印度理工学院）；Kalinga Institute of Industrial Technology Bhubaneswar（布巴内斯瓦尔卡林加工业技术学院）
This paper introduces a paradigm of smartphone application based disease diagnostics that may completely revolutionise the way healthcare services are being provided. Although primarily aimed to assist the problems in rendering the healthcare services during the coronavirus pandemic, the model can also be extended to identify the exact disease that the patient is caught with from a broad spectrum of pulmonary diseases. The app inputs Chest X-Ray images captured from the mobile camera which is then relayed to the AI architecture in a cloud platform, and diagnoses the disease with state of the a…
Fudan University（复旦大学）；Children’s Hospital of Fudan University（复旦大学附属儿科医院）；National Children’s Medical Center（国家儿童医学中心）
This paper presents our solution for the 2nd COVID-19 Severity Detection Competition. This task aims to distinguish the Mild, Moderate, Severe, and Critical grades in COVID-19 chest CT images. In our approach, we devise a novel infection-aware 3D Contrastive Mixup Classification network for severity grading. Specifcally, we train two segmentation networks to first extract the lung region and then the inner lesion region. The lesion segmentation mask serves as complementary information for the original CT slices. To relieve the issue of imbalanced data distribution, we further improve the advan…
University of Oxford（牛津大学）；UiT The Arctic University of Norway（挪威北极大学）；Sun Yat-sen University（中山大学）；Carnegie Mellon University（卡内基梅隆大学）；Mohamed bin Zayed University of Artificial Intelligence（穆罕默德·本·扎耶德人工智能大学）
The data-driven nature of deep learning (DL) models for semantic segmentation requires a large number of pixel-level annotations. However, large-scale and fully labeled medical datasets are often unavailable for practical tasks. Recently, partially supervised methods have been proposed to utilize images with incomplete labels in the medical domain. To bridge the methodological gaps in partially supervised learning (PSL) under data scarcity, we propose Vicinal Labels Under Uncertainty (VLUU), a simple yet efficient framework utilizing the human structure similarity for partially supervised medi…
Luxembourg Centre for Systems Biomedicine（卢森堡系统生物医学中心）；University of Luxembourg（卢森堡大学）；National Dept. of Neurosurgery（国家神经外科部）；Centre Hospitalier de Luxembourg（卢森堡医院中心）
Machine learning based methods for diagnosis and progression prediction of COVID-19 from imaging data have gained significant attention in the last months, in particular by the use of deep learning models. In this context hundreds of models where proposed with the majority of them trained on public datasets. Data scarcity, mismatch between training and target population, group imbalance, and lack of documentation are important sources of bias, hindering the applicability of these models to real-world clinical practice. Considering that datasets are an essential part of model building and evalu…
University Hospital Erlangen（埃尔朗根大学医院）；Friedrich-Alexander-Universität Erlangen-Nürnberg（弗里德里希-亚历山大 埃尔朗根-纽伦堡大学）；Comprehensive Cancer Center Erlangen-EMN（埃尔朗根-EMN综合癌症中心）；Siemens Healthcare GmbH（西门子医疗有限公司）；Shanghai Jiao Tong University（上海交通大学）
In cone-beam X-ray transmission imaging, perspective deformation causes difficulty in direct, accurate geometric assessments of anatomical structures. In this work, the perspective deformation correction problem is formulated and addressed in a framework using two complementary (180°) views. The complementary view setting provides a practical way to identify perspectively deformed structures by assessing the deviation between the two views. It also provides bounding information and reduces uncertainty for learning perspective deformation. Two representative networks Pix2pixGAN and TransU-Net f…
In the research, we developed a computer vision solution to support diagnostic radiology in differentiating between COVID-19 pneumonia, influenza virus pneumonia, and normal biomarkers. The chest radiograph appearance of COVID-19 pneumonia is thought to be nonspecific, having presented a challenge to identify an optimal architecture of a convolutional neural network (CNN) that would classify with a high sensitivity among the pulmonary inflammation features of COVID-19 and non-COVID-19 types of pneumonia. Rahman (2021) states that COVID-19 radiography images observe unavailability and quality i…
Vision-Language Model Based Multi-Expert Fusion for CT Image Classification
College of Computer Science and Artificial Intelligence, Shanghai Key Laboratory of Intelligent Information Processing, Fudan University（复旦大学计算机科学与人工智能学院，上海智能信息处理重点实验室）；University of Oxford（牛津大学）；The Hong Kong University of Science and Technology（香港科技大学）
