Weakly-Supervised Cross-Domain Adaptation for Endoscopic Lesions Segmentation
Shenyang Institute of Automation, Chinese Academy of Sciences（中国科学院沈阳自动化研究所）；Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences（中国科学院机器人与智能制造创新研究院）；University of Chinese Academy of Sciences（中国科学院大学）；Chinese PLA General Hospital（中国人民解放军总医院）；University of Arkansas at Little Rock（阿肯色大学小石城分校）；Indiana University-Purdue University Indianapolis（印第安纳大学-普渡大学印第安纳波利斯分校）
Jiahua Dong, Yang Cong, Gan Sun, Yunsheng Yang, Xiaowei Xu, Zhengming Ding
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Accepted to IEEE Transactions on Circuits and Systems for Video Technology (TCSVT 2020)
Weakly-supervised learning has attracted growing research attention on medical lesions segmentation due to significant saving in pixel-level annotation cost. However, 1) most existing methods require effective prior and constraints to explore the intrinsic lesions characterization, which only generates incorrect and rough prediction; 2) they neglect the underlying semantic dependencies among weakly-labeled target enteroscopy diseases and fully-annotated source gastroscope lesions, while forcefully utilizing untransferable dependencies leads to the negative performance. To tackle above issues, we propose a new weakly-supervised lesions transfer framework, which can not only explore transferable domain-invariant knowledge across different datasets, but also prevent the negative transfer of untransferable representations. Specifically, a Wasserstein quantified transferability framework is developed to highlight widerange transferable contextual dependencies, while neglecting the irrelevant semantic characterizations. Moreover, a novel selfsupervised pseudo label generator is designed to equally provide confident pseudo pixel labels for both hard-to-transfer and easyto-transfer target samples. It inhibits the enormous deviation of false pseudo pixel labels under the self-supervision manner. Afterwards, dynamically-searched feature centroids are aligned to narrow category-wise distribution shift. Comprehensive theoretical analysis and experiments show the superiority of our model on the endoscopic dataset and several public datasets.
Registration-Grounded Spectral Fusion for Unregistered WLI/NBI Endoscopic Lesion Segmentation
The First Affiliated Hospital of Sun Yat-sen University（中山大学附属第一医院）；School of Computer Science and Technology, Hainan University（海南大学计算机科学与技术学院）；School of Mathematics and Statistics, Xi’an Jiaotong University（西安交通大学数学与统计学院）；Chongqing University of Posts and Telecommunications（重庆邮电大学）
University of Chinese Academy of Sciences（中国科学院大学）；Huaqiao University（华侨大学）；University of Arkansas at Little Rock（阿肯色大学小石城分校）
Unsupervised domain adaptation has attracted growing research attention on semantic segmentation. However, 1) most existing models cannot be directly applied into lesions transfer of medical images, due to the diverse appearances of same lesion among different datasets; 2) equal attention has been paid into all semantic representations instead of neglecting irrelevant knowledge, which leads to negative transfer of untransferable knowledge. To address these challenges, we develop a new unsupervised semantic transfer model including two complementary modules (i.e., T_D and T_F ) for endoscopic l…
Tecnologico de Monterrey（蒙特雷理工学院）；University of Leeds（利兹大学）
Prevalence of gastrointestinal (GI) cancer is growing alarmingly every year leading to a substantial increase in the mortality rate. Endoscopic detection is providing crucial diagnostic support, however, subtle lesions in upper and lower GI are quite hard to detect and cause considerable missed detection. In this work, we leverage deep learning to develop a framework to improve the localization of difficult to detect lesions and minimize the missed detection rate. We propose an end to end student-teacher learning setup where class probabilities of a trained teacher model on one class with larg…
Zuse Institute Berlin (ZIB)（柏林祖斯研究所）；TU Darmstadt（达姆施塔特工业大学）
Purpose: Segmentation of surgical instruments in endoscopic videos is essential for automated surgical scene understanding and process modeling. However, relying on fully supervised deep learning for this task is challenging because manual annotation occupies valuable time of the clinical experts. Methods: We introduce a teacher-student learning approach that learns jointly from annotated simulation data and unlabeled real data to tackle the erroneous learning problem of the current consistency-based unsupervised domain adaptation framework. Results: Empirical results on three datasets highlig…
Tecnológico de Monterrey（蒙特雷理工学院）；CHU Nancy（南锡大学中心医院）；CHU Pellegrin（佩勒格兰大学中心医院）；Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional（国立理工学院高级研究中心）；Université de Lorraine（洛林大学）
Deep learning has shown great promise in diverse areas of computer vision, such as image classification, object detection and semantic segmentation, among many others. However, as it has been repeatedly demonstrated, deep learning methods trained on a dataset do not generalize well to datasets from other domains or even to similar datasets, due to data distribution shifts. In this work, we propose the use of a meta-learning based few-shot learning approach to alleviate these problems. In order to demonstrate its efficacy, we use two datasets of kidney stones samples acquired with different end…
While data-driven approaches excel at many image analysis tasks, the performance of these approaches is often limited by a shortage of annotated data available for training. Recent work in semi-supervised learning has shown that meaningful representations of images can be obtained from training with large quantities of unlabeled data, and that these representations can improve the performance of supervised tasks. Here, we demonstrate that an unsupervised jigsaw learning task, in combination with supervised training, results in up to a 9.8% improvement in correctly classifying lesions in colono…
University of Girona（赫罗纳大学）；Assiut University（艾斯尤特大学）；Vall d’Hebron University Hospital（瓦尔德希伯伦大学医院）；Girona Magnetic Resonance Center（赫罗纳磁共振中心）；Dr. Josep Trueta University Hospital（何塞普·特鲁埃塔大学医院）
In recent years, several convolutional neural network (CNN) methods have been proposed for the automated white matter lesion segmentation of multiple sclerosis (MS) patient images, due to their superior performance compared with those of other state-of-the-art methods. However, the accuracies of CNN methods tend to decrease significantly when evaluated on different image domains compared with those used for training, which demonstrates the lack of adaptability of CNNs to unseen imaging data. In this study, we analyzed the effect of intensity domain adaptation on our recently proposed CNN-based…
German Cancer Research Center (DKFZ)（德国癌症研究中心）；University Hospital Erlangen（埃尔兰根大学医院）；Radiological Practice at the ATOS Clinic（ATOS诊所放射科诊所）；Radiology Center Mannheim (RZM)（曼海姆放射中心）
End-to-end deep learning improves breast cancer classification on diffusion-weighted MR images (DWI) using a convolutional neural network (CNN) architecture. A limitation of CNN as opposed to previous model-based approaches is the dependence on specific DWI input channels used during training. However, in the context of large-scale application, methods agnostic towards heterogeneous inputs are desirable, due to the high deviation of scanning protocols between clinical sites. We propose model-based domain adaptation to overcome input dependencies and avoid re-training of networks at clinical si…
University of Chinese Academy of Sciences（中国科学院大学）
Weakly-supervised learning under image-level labels supervision has been widely applied to semantic segmentation of medical lesions regions. However, 1) most existing models rely on effective constraints to explore the internal representation of lesions, which only produces inaccurate and coarse lesions regions; 2) they ignore the strong probabilistic dependencies between target lesions dataset (e.g., enteroscopy images) and well-to-annotated source diseases dataset (e.g., gastroscope images). To better utilize these dependencies, we present a new semantic lesions representation transfer model…
Mitigating the Influence of Domain Shift in Skin Lesion Classification: A Benchmark Study of Unsupervised Domain Adaptation Methods on Dermoscopic Images
German Aerospace Center (DLR)（德国航空航天中心）；German Cancer Research Center (DKFZ)（德国癌症研究中心）
GIM-ENDO: A Multimodal Endoscopic Image and Video Dataset for Gastric Intestinal Metaplasia Morphology and Pathology
Gastroenterology and Liver Disease Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences（沙希德·贝赫什提医科大学胃肠病与肝病研究中心，胃肠病与肝病研究所）；Iran University of Medical Sciences（伊朗医科大学）；Shiraz University of Medical Sciences（设拉子医科大学）；Gastroenterology Department, Amiralam Hospital, Tehran University of Medical Sciences（德黑兰医科大学阿米拉拉姆医院胃肠病科）；Department of Computer Engineering, Science and Research Branch, Islamic Azad University（伊斯兰阿扎德大学科学与研究分校计算机工程系）
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…
Deep learning-based Computer-Aided Diagnosis (CAD) has attracted appealing attention in academic researches and clinical applications. Nevertheless, the Convolutional Neural Networks (CNNs) diagnosis system heavily relies on the well-labeled lesion dataset, and the sensitivity to the variation of data distribution also restricts the potential application of CNNs in CAD. Unsupervised Domain Adaptation (UDA) methods are developed to solve the expensive annotation and domain gaps problem and have achieved remarkable success in medical image analysis. Yet existing UDA approaches only adapt knowled…
Radboud University Medical Center（拉德堡德大学医学中心）；Radboud University（拉德堡德大学）；Screenpoint Medical；Delft University of Technology（代尔夫特理工大学）
Computer-aided detection aims to improve breast cancer screening programs by helping radiologists to evaluate digital mammography (DM) exams. DM exams are generated by devices from different vendors, with diverse characteristics between and even within vendors. Physical properties of these devices and postprocessing of the images can greatly influence the resulting mammogram. This results in the fact that a deep learning model trained on data from one vendor cannot readily be applied to data from another vendor. This paper investigates the use of tailored transfer learning methods based on adv…
This paper proposes a method for domain adaptation that extends the maximum margin domain transfer (MMDT) proposed by Hoffman et al., by introducing L2 distance constraints between samples of different domains; thus, our method is denoted as MMDTL2. Motivated by the differences between the images taken by narrow band imaging (NBI) endoscopic devices, we utilize different NBI devices as different domains and estimate the transformations between samples of different domains, i.e., image samples taken by different NBI endoscope systems. We first formulate the problem in the primal form, and then …
Radboud University Medical Center（拉德堡德大学医学中心）；Radboud University（拉德堡德大学）；University of British Columbia（不列颠哥伦比亚大学）
Magnetic Resonance Imaging (MRI) is widely used in routine clinical diagnosis and treatment. However, variations in MRI acquisition protocols result in different appearances of normal and diseased tissue in the images. Convolutional neural networks (CNNs), which have shown to be successful in many medical image analysis tasks, are typically sensitive to the variations in imaging protocols. Therefore, in many cases, networks trained on data acquired with one MRI protocol, do not perform satisfactorily on data acquired with different protocols. This limits the use of models trained with large an…
Zuse Institute Berlin (ZIB)（柏林祖斯研究所）；TU Darmstadt（达姆施塔特工业大学）
Surgical tool segmentation in endoscopic videos is an important component of computer assisted interventions systems. Recent success of image-based solutions using fully-supervised deep learning approaches can be attributed to the collection of big labeled datasets. However, the annotation of a big dataset of real videos can be prohibitively expensive and time consuming. Computer simulations could alleviate the manual labeling problem, however, models trained on simulated data do not generalize to real data. This work proposes a consistency-based framework for joint learning of simulated and r…
Ischemic Stroke Segmentation and Net Water Uptake Quantification on Multicenter Non-Contrast CT Using Supervised Target-Domain Adaptation
University Medical Center Hamburg-Eppendorf（汉堡-埃彭多夫大学医学中心）；University Hospital Marburg（马尔堡大学医院）；Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）；HELIOS Medical Center Schwerin（HELIOS什未林医疗中心）；MSH Medical School Hamburg（汉堡MSH医学院）；MSH Research, Development and Innovation GmbH（MSH研究开发与创新有限公司）；MSH Medical University of Applied Sciences and Medical University（MSH应用科学医科大学与医科大学）
McGill University（麦吉尔大学）；MILA (Quebec Artificial Intelligence Institute)（魁北克人工智能研究所（MILA））；University of Edinburgh（爱丁堡大学）；The Alan Turing Institute（阿兰·图灵研究所）；NeuroRx Research（NeuroRx研究公司）
Many automatic machine learning models developed for focal pathology (e.g. lesions, tumours) detection and segmentation perform well, but do not generalize as well to new patient cohorts, impeding their widespread adoption into real clinical contexts. One strategy to create a more diverse, generalizable training set is to naively pool datasets from different cohorts. Surprisingly, training on this \it{big data} does not necessarily increase, and may even reduce, overall performance and model generalizability, due to the existence of cohort biases that affect label distributions. In this paper,…
UCL（伦敦大学学院）；UCLH NHS Foundation Trust（伦敦大学学院医院NHS基金会信托）
The need for training data can impede the adoption of novel imaging modalities for learning-based medical image analysis. Domain adaptation methods partially mitigate this problem by translating training data from a related source domain to a novel target domain, but typically assume that a one-to-one translation is possible. Our work addresses the challenge of adapting to a more informative target domain where multiple target samples can emerge from a single source sample. In particular we consider translating from mp-MRI to VERDICT, a richer MRI modality involving an optimized acquisition pr…
UCL（伦敦大学学院）；UCLH NHS Foundation Trust（伦敦大学学院医院国民保健服务基金会信托）
Any novel medical imaging modality that differs from previous protocols e.g. in the number of imaging channels, introduces a new domain that is heterogeneous from previous ones. This common medical imaging scenario is rarely considered in the domain adaptation literature, which handles shifts across domains of the same dimensionality. In our work we rely on stochastic generative modeling to translate across two heterogeneous domains at pixel space and introduce two new loss functions that promote semantic consistency. Firstly, we introduce a semantic cycle-consistency loss in the source domain…
Politecnico di Milano（米兰理工大学）；CNRS-Université de Strasbourg（法国国家科学研究中心-斯特拉斯堡大学）；University of Calabria（卡拉布里亚大学）；Istituto Europeo di Oncologia (IRCCS)（欧洲肿瘤研究所（IRCCS））
Ureteroscopy and cystoscopy are the gold standard methods to identify and treat tumors along the urinary tract. It has been reported that during a normal procedure a rate of 10-20 % of the lesions could be missed. In this work we study the implementation of 3 different Convolutional Neural Networks (CNNs), using a 2-steps training strategy, to classify images from the urinary tract with and without lesions. A total of 6,101 images from ureteroscopy and cystoscopy procedures were collected. The CNNs were trained and tested using transfer learning in a two-steps fashion on 3 datasets. The datase…
Endoscopic videos from multicentres often have different imaging conditions, e.g., color and illumination, which make the models trained on one domain usually fail to generalize well to another. Domain adaptation is one of the potential solutions to address the problem. However, few of existing works focused on the translation of video-based data. In this work, we propose a novel generative adversarial network (GAN), namely VideoGAN, to transfer the video-based data across different domains. As the frames of a video may have similar content and imaging conditions, the proposed VideoGAN has an …
Intuitive, Inc.（直观医疗公司）；Konica Minolta, Inc.（柯尼卡美能达公司）；University College London（伦敦大学学院）；University of Genoa（热那亚大学）；University of Burgundy（勃艮第大学）；German Cancer Research Center (DKFZ)（德国癌症研究中心）；National Center for Tumor Diseases (NCT)（国家肿瘤疾病中心）
Surgical data science is revolutionizing minimally invasive surgery by enabling context-aware applications. However, many challenges exist around surgical data (and health data, more generally) needed to develop context-aware models. This work - presented as part of the Endoscopic Vision (EndoVis) challenge at the Medical Image Computing and Computer Assisted Intervention (MICCAI) 2020 conference - seeks to explore the potential for visual domain adaptation in surgery to overcome data privacy concerns. In particular, we propose to use video from virtual reality (VR) simulations of surgical exe…
Deep Learning-based Unsupervised Domain Adaptation via a Unified Model for Prostate Lesion Detection Using Multisite Bi-parametric MRI Datasets
Siemens Healthineers（西门子医疗）；Vanderbilt University（范德堡大学）；Radboud University Medical Center（拉德堡德大学医学中心）；New York University（纽约大学）；Universitätsspital Basel（巴塞尔大学医院）；Charité, Universitätsmedizin Berlin（柏林夏里特医学院）；Patero Clinic（帕特罗诊所）；Eunpyeong St. Mary's Hospital, Catholic University of Korea（韩国天主教大学恩平圣玛丽医院）；Changhai Hospital of Shanghai（上海长海医院）；Diagnostikum Graz Süd-West（格拉茨西南诊断中心）；Loyola University Medical Center（洛约拉大学医学中心）；Oregon Health and Science University（俄勒冈健康与科学大学）；Massachusetts General Hospital（麻省总医院）
MedFMC: A Real-world Dataset and Benchmark For Foundation Model Adaptation in Medical Image Classification
Shanghai AI Laboratory（上海人工智能实验室）；Shanghai Jiaotong University（上海交通大学）；Shanghai Ruijing Hospital, School of Medicine, Shanghai Jiao Tong University（上海交通大学医学院附属瑞金医院）；Shanghai Tenth People’s Hospital of Tongji University（同济大学附属上海市第十人民医院）；Xuzhou Central Hospital（徐州市中心医院）；Renji Hospital, School of Medicine, Shanghai Jiao Tong University（上海交通大学医学院附属仁济医院）；Sensetime Research（商汤科技研究院）；The First Affiliated Hospital of Zhengzhou University（郑州大学第一附属医院）；West China Hospital, Sichuan University（四川大学华西医院）
University of Sydney（悉尼大学）；University of New South Wales（新南威尔士大学）；Sydney Neuroimaging Analysis Centre（悉尼神经影像分析中心）
Multiple sclerosis (MS) is a chronic inflammatory and degenerative disease of the central nervous system, characterized by the appearance of focal lesions in the white and gray matter that topographically correlate with an individual patient's neurological symptoms and signs. Magnetic resonance imaging (MRI) provides detailed in-vivo structural information, permitting the quantification and categorization of MS lesions that critically inform disease management. Traditionally, MS lesions have been manually annotated on 2D MRI slices, a process that is inefficient and prone to inter-/intra-obser…
Universidad de Buenos Aires（布宜诺斯艾利斯大学）；Universidad Nacional del Litoral（国立滨海大学）
Automatic segmentation of white matter hyperintensities in magnetic resonance images is of paramount clinical and research importance. Quantification of these lesions serve as a predictor for risk of stroke, dementia and mortality. During the last years, convolutional neural networks (CNN) specifically tailored for biomedical image segmentation have outperformed all previous techniques in this task. However, they are extremely data-dependent, and maintain a good performance only when data distribution between training and test datasets remains unchanged. When such distribution changes but we s…
SPRMamba: Surgical Phase Recognition for Endoscopic Submucosal Dissection with Mamba
School of Biomedical Engineering（生物医学工程学院）；Division of Gastroenterology and Hepatology, Shanghai Institute of Digestive Disease, NHC Key Laboratory of Digestive Diseases, Renji Hospital（消化内科与肝病科、上海消化疾病研究所、国家消化疾病临床医学研究中心、仁济医院）；Aier Institute of Digital Ophthalmology and Visual Science（爱尔数字眼科与视觉科学研究院）；College of Media Engineering（媒体工程学院）
Domain Adaptive Skin Lesion Classification via Conformal Ensemble of Vision Transformers
Faculty of Mechanical Engineering（机械工程学院）；University of Victoria（维多利亚大学）；Faculty of Electrical and Computer Engineering（电气与计算机工程学院）；Faculty of Mechanical, Electrical, and Computer Engineering（机械、电气和计算机工程学院）
SLP-Net:An efficient lightweight network for segmentation of skin lesions
School of Computer and Software Engineering, Xihua University（西华大学计算机与软件工程学院）；School of Electrical Engineering and Electronic Information, Xihua University（西华大学电气工程与电子信息学院）；School of Computer Science, Nanjing University of Posts and Telecommunications（南京邮电大学计算机学院）
Small intestinal capsule endoscopy is the mainstream method for inspecting small intestinal lesions,but a single small intestinal capsule endoscopy will produce 60,000 - 120,000 images, the majority of which are similar and have no diagnostic value. It takes 2 - 3 hours for doctors to identify lesions from these images. This is time-consuming and increase the probability of misdiagnosis and missed diagnosis since doctors are likely to experience visual fatigue while focusing on a large number of similar images for an extended period of time.In order to solve these problems, we proposed a simil…
Deep learning based neural networks have gained popularity for a variety of biomedical imaging applications. In the last few years several works have shown the use of these methods for colon cancer detection and the early results have been promising. These methods can potentially be utilized to assist doctor's and may help in identifying the number of lesions or abnormalities in a diagnosis session. From our literature survey we found out that there is a lack of publicly available labeled data. Thus, as part of this work, we have aimed at open sourcing a dataset which contains annotations of p…
Airdoc LLC（爱丁堡医疗科技有限公司）；Monash University（莫纳什大学）；Nanjing University of Posts and Telecommunications（南京邮电大学）
For decades, advances in retinal imaging technology have enabled effective diagnosis and management of retinal disease using fundus cameras. Recently, ultra-wide-field (UWF) fundus imaging by Optos camera is gradually put into use because of its broader insights on fundus for some lesions that are not typically seen in traditional fundus images. Research on traditional fundus images is an active topic but studies on UWF fundus images are few. One of the most important reasons is that UWF fundus images are hard to obtain. In this paper, for the first time, we explore domain adaptation from the …
King’s College London（伦敦国王学院）；Biomediq A/S（Biomediq公司）；University College London（伦敦大学学院）；Chelsea and Westminster Hospital NHS Foundation Trust（切尔西和威斯敏斯特医院NHS基金会信托）；Cereriu A/S（Cereriu公司）
Supervised learning algorithms trained on medical images will often fail to generalize across changes in acquisition parameters. Recent work in domain adaptation addresses this challenge and successfully leverages labeled data in a source domain to perform well on an unlabeled target domain. Inspired by recent work in semi-supervised learning we introduce a novel method to adapt from one source domain to $n$ target domains (as long as there is paired data covering all domains). Our multi-domain adaptation method utilises a consistency loss combined with adversarial learning. We provide results…
Polyp-Gen: Realistic and Diverse Polyp Image Generation for Endoscopic Dataset Expansion
Department of Electronic Engineering, Chinese University of Hong Kong（香港中文大学电子工程系）；Centre for Artificial Intelligence and Robotics (CAIR), Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences（香港科学院人工智能与机器人中心）；Department of Electrical Engineering, The City University of Hong Kong（香港城市大学电子工程系）；Institute of Automation, Chinese Academy of Sciences（中国科学院自动化研究所）；The Sixth Affiliated Hospital, Sun Yat-sen University（中山大学第六附属医院）
