Semi-supervised learning (SSL), which aims at leveraging a few labeled images and a large number of unlabeled images for network training, is beneficial for relieving the burden of data annotation in medical image segmentation. According to the experience of medical imaging experts, local attributes such as texture, luster and smoothness are very important factors for identifying target objects like lesions and polyps in medical images. Motivated by this, we propose a cross-level contrastive learning scheme to enhance representation capacity for local features in semi-supervised medical image segmentation. Compared to existing image-wise, patch-wise and point-wise contrastive learning algorithms, our devised method is capable of exploring more complex similarity cues, namely the relational characteristics between global and local patch-wise representations. Additionally, for fully making use of cross-level semantic relations, we devise a novel consistency constraint that compares the predictions of patches against those of the full image. With the help of the cross-level contrastive learning and consistency constraint, the unlabelled data can be effectively explored to improve segmentation performance on two medical image datasets for polyp and skin lesion segmentation respectively. Code of our approach is available.
University of Science and Technology of China（中国科学技术大学）
Contrastive learning and self-supervised techniques have gained prevalence in computer vision for the past few years. It is essential for medical image analysis, which is often notorious for its lack of annotations. Most existing self-supervised methods applied in natural imaging tasks focus on designing proxy tasks for unlabeled data. For example, contrastive learning is often based on the fact that an image and its transformed version share the same identity. However, pixel annotations contain much valuable information for medical image segmentation, which is largely ignored in contrastive l…
Jilin University（吉林大学）；Baidu Research（百度研究院）；National Engineering Laboratory for Deep Learning Technology and Application（深度学习技术及应用国家工程实验室）
Current semi-supervised semantic segmentation methods mainly focus on designing pixel-level consistency and contrastive regularization. However, pixel-level regularization is sensitive to noise from pixels with incorrect predictions, and pixel-level contrastive regularization has memory and computational cost with O(pixel_num^2). To address the issues, we propose a novel region-level contrastive and consistency learning framework (RC^2L) for semi-supervised semantic segmentation. Specifically, we first propose a Region Mask Contrastive (RMC) loss and a Region Feature Contrastive (RFC) loss to …
Medical image segmentation is a relevant task as it serves as the first step for several diagnosis processes, thus it is indispensable in clinical usage. Whilst major success has been reported using supervised techniques, they assume a large and well-representative labelled set. This is a strong assumption in the medical domain where annotations are expensive, time-consuming, and inherent to human bias. To address this problem, unsupervised techniques have been proposed in the literature yet it is still an open problem due to the difficulty of learning any transformation pattern. In this work,…
Prototype Contrastive Consistency Learning for Semi-Supervised Medical Image Segmentation
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences（中国科学院深圳先进技术研究院）；Computer Vision Institute, College of Computer Science and Software Engineering, Shenzhen University（深圳大学计算机与软件学院计算机视觉研究所）；Baoan Central Hospital of Shenzhen（深圳市宝安中心医院）
Medical image segmentation has been widely recognized as a pivot procedure for clinical diagnosis, analysis, and treatment planning. However, the laborious and expensive annotation process lags down the speed of further advances. Contrastive learning-based weight pre-training provides an alternative by leveraging unlabeled data to learn a good representation. In this paper, we investigate how contrastive learning benefits the general supervised medical segmentation tasks. To this end, patch-dragsaw contrastive regularization (PDCR) is proposed to perform patch-level tugging and repulsing with …
Language-guided Medical Image Segmentation with Target-informed Multi-level Contrastive Alignments
School of Computer Science, The University of Sydney（悉尼大学计算机科学学院）；Institute of Translational Medicine, Shanghai Jiao Tong University（上海交通大学转化医学研究院）；Zhongguancun Academy & Zhongguancun Institute of Artificial Intelligence, Beijing, China（北京中关村学院及中关村人工智能研究院）；Department of Molecular Imaging, Royal Prince Alfred Hospital（皇家珀斯阿尔弗雷德医院分子成像部）
Contrastive learning has shown great promise over annotation scarcity problems in the context of medical image segmentation. Existing approaches typically assume a balanced class distribution for both labeled and unlabeled medical images. However, medical image data in reality is commonly imbalanced (i.e., multi-class label imbalance), which naturally yields blurry contours and usually incorrectly labels rare objects. Moreover, it remains unclear whether all negative samples are equally negative. In this work, we present ACTION, an Anatomical-aware ConTrastive dIstillatiON framework, for semi-…
Carleton University（卡尔顿大学）；Canada CIFAR AI Chair（加拿大CIFAR人工智能讲席）
Medical image segmentation methods typically rely on numerous dense annotated images for model training, which are notoriously expensive and time-consuming to collect. To alleviate this burden, weakly supervised techniques have been exploited to train segmentation models with less expensive annotations. In this paper, we propose a novel point-supervised contrastive variance method (PSCV) for medical image semantic segmentation, which only requires one pixel-point from each organ category to be annotated. The proposed method trains the base segmentation network by using a novel contrastive vari…
Self-supervised instance discrimination is an effective contrastive pretext task to learn feature representations and address limited medical image annotations. The idea is to make features of transformed versions of the same images similar while forcing all other augmented images' representations to contrast. However, this instance-based contrastive learning leaves performance on the table by failing to maximize feature affinity between images with similar content while counter-productively pushing their representations apart. Recent improvements on this paradigm (e.g., leveraging multi-modal…
Yale University（耶鲁大学）；The University of Texas at Austin（德克萨斯大学奥斯汀分校）
Contrastive learning (CL) aims to learn useful representation without relying on expert annotations in the context of medical image segmentation. Existing approaches mainly contrast a single positive vector (i.e., an augmentation of the same image) against a set of negatives within the entire remainder of the batch by simply mapping all input features into the same constant vector. Despite the impressive empirical performance, those methods have the following shortcomings: (1) it remains a formidable challenge to prevent the collapsing problems to trivial solutions; and (2) we argue that not a…
Unsupervised pre-training has been proven as an effective approach to boost various downstream tasks given limited labeled data. Among various methods, contrastive learning learns a discriminative representation by constructing positive and negative pairs. However, it is not trivial to build reasonable pairs for a segmentation task in an unsupervised way. In this work, we propose a novel unsupervised pre-training framework that avoids the drawback of contrastive learning. Our framework consists of two principles: unsupervised over-segmentation as a pre-train task using mutual information maxim…
Institute of Information Science, Beijing Jiaotong University（北京交通大学信息科学研究所）；Beijing Key Laboratory of Advanced Information Science and Network Technology, Beijing Jiaotong University（北京交通大学先进信息科学与网络技术北京市重点实验室）；Department of Computer Science and Engineering, Michigan State University（密歇根州立大学计算机科学与工程系）
To bridge the gap between the source and target domains in unsupervised domain adaptation (UDA), the most common strategy puts focus on matching the marginal distributions in the feature space through adversarial learning. However, such category-agnostic global alignment lacks of exploiting the class-level joint distributions, causing the aligned distribution less discriminative. To address this issue, we propose in this paper a novel margin preserving self-paced contrastive Learning (MPSCL) model for cross-modal medical image segmentation. Unlike the conventional construction of contrastive p…
Unets have become the standard method for semantic segmentation of medical images, along with fully convolutional networks (FCN). Unet++ was introduced as a variant of Unet, in order to solve some of the problems facing Unet and FCNs. Unet++ provided networks with an ensemble of variable depth Unets, hence eliminating the need for professionals estimating the best suitable depth for a task. While Unet and all its variants, including Unet++ aimed at providing networks that were able to train well without requiring large quantities of annotated data, none of them attempted to eliminate the need …
University of Notre Dame（圣母大学）；Guangdong Provincial People’s Hospital（广东省人民医院）
The success of deep learning methods in medical image segmentation tasks heavily depends on a large amount of labeled data to supervise the training. On the other hand, the annotation of biomedical images requires domain knowledge and can be laborious. Recently, contrastive learning has demonstrated great potential in learning latent representation of images even without any label. Existing works have explored its application to biomedical image segmentation where only a small portion of data is labeled, through a pre-training phase based on self-supervised contrastive learning without using a…
Contrastive Graph Modeling for Cross-Domain Few-Shot Medical Image Segmentation
School of Computer Science and Engineering, Nanjing University of Science and Technology（计算机科学与工程学院，南京理工大学）；University of Chinese Academy of Sciences（中国科学院大学）
Medical image segmentation, or computing voxelwise semantic masks, is a fundamental yet challenging task to compute a voxel-level semantic mask. To increase the ability of encoder-decoder neural networks to perform this task across large clinical cohorts, contrastive learning provides an opportunity to stabilize model initialization and enhance encoders without labels. However, multiple target objects (with different semantic meanings) may exist in a single image, which poses a problem for adapting traditional contrastive learning methods from prevalent 'image-level classification' to 'pixel-l…
SuperCL: Superpixel Guided Contrastive Learning for Medical Image Segmentation Pre-training
Institute of Medical Technology, Peking University Health Science Center, Peking University（北京大学医学部医学技术研究所）；Department of Biomedical Engineering, Peking University（北京大学生物医学工程系）；National Biomedical Imaging Center, Peking University（北京大学国家生物医学成像中心）；Institute of Biomedical Engineering, Shenzhen Bay Laboratory（深圳湾实验室生物医学工程研究所）；Institute of Biomedical Engineering, Peking University Shenzhen Graduate School（北京大学深圳研究生院生物医学工程研究所）
Multi-level Asymmetric Contrastive Learning for Volumetric Medical Image Segmentation Pre-training
Peking University（北京大学）；Peking University Health Science Center（北京大学医学部）；National Biomedical Imaging Center（国家生物医学成像中心）；Peking University Shenzhen Graduate School（北京大学深圳研究生院）；Georgia Institute of Technology（佐治亚理工学院）；UT Southwestern Medical Center（西南大学达拉斯医学中心）
Devil is in Channels: Contrastive Single Domain Generalization for Medical Image Segmentation
Northwestern Polytechnical University（西北工业大学）；Ningbo Institute of Northwestern Polytechnical University（西北工业大学宁波研究院）；Research and Development Institute of Northwestern Polytechnical University in Shenzhen（西北工业大学深圳研究院）
Medical image annotation typically requires expert knowledge and hence incurs time-consuming and expensive data annotation costs. To alleviate this burden, we propose a novel learning scenario, Exemplar Learning (EL), to explore automated learning processes for medical image segmentation with a single annotated image example. This innovative learning task is particularly suitable for medical image segmentation, where all categories of organs can be presented in one single image and annotated all at once. To address this challenging EL task, we propose an Exemplar Learning-based Synthesis Net (…
Unsupervised domain adaptation (UDA) for semantic segmentation has been well-studied in recent years. However, most existing works largely neglect the local regional consistency across different domains and are less robust to changes in outdoor environments. In this paper, we propose a novel and fully end-to-end trainable approach, called regional contrastive consistency regularization (RCCR) for domain adaptive semantic segmentation. Our core idea is to pull the similar regional features extracted from the same location of different images, i.e., the original image and augmented image, to be …
Yale University（耶鲁大学）；The University of Texas at Austin（德克萨斯大学奥斯汀分校）
Automated segmentation in medical image analysis is a challenging task that requires a large amount of manually labeled data. However, most existing learning-based approaches usually suffer from limited manually annotated medical data, which poses a major practical problem for accurate and robust medical image segmentation. In addition, most existing semi-supervised approaches are usually not robust compared with the supervised counterparts, and also lack explicit modeling of geometric structure and semantic information, both of which limit the segmentation accuracy. In this work, we present S…
Computer Vision Laboratory, ETH Zurich（苏黎世联邦理工学院计算机视觉实验室）
Supervised deep learning-based methods yield accurate results for medical image segmentation. However, they require large labeled datasets for this, and obtaining them is a laborious task that requires clinical expertise. Semi/self-supervised learning-based approaches address this limitation by exploiting unlabeled data along with limited annotated data. Recent self-supervised learning methods use contrastive loss to learn good global level representations from unlabeled images and achieve high performance in classification tasks on popular natural image datasets like ImageNet. In pixel-level …
Generalizability is seen as one of the major challenges in deep learning, in particular in the domain of medical imaging, where a change of hospital or in imaging routines can lead to a complete failure of a model. To tackle this, we introduce Consistency Training, a training procedure and alternative to data augmentation based on maximizing models' prediction consistency across augmented and unaugmented data in order to facilitate better out-of-distribution generalization. To this end, we develop a novel region-based segmentation loss function called Segmentation Inconsistency Loss (SIL), whi…
Enhancing Multimodal Medical Image Classification using Cross-Graph Modal Contrastive Learning
Department of Systems Engineering, Stevens Institute of Technology, Hoboken, New Jersey, USA（系统工程系，史蒂文斯理工学院）；Department of Nuclear Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan（高雄长庚纪念医院核医学部）；Institute of Statistics, National University of Kaohsiung, Kaohsiung, Taiwan（国立高雄大学统计研究所）；Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China（深圳先进技术研究院，中国科学院）
Department of Computer Science, University of Oxford（牛津大学计算机科学系）；University of Oxford（牛津大学）；Oxford, UK（英国牛津（这里仅保留城市和国家，实际机构为牛津大学））
A label-efficient paradigm in computer vision is based on self-supervised contrastive pre-training on unlabeled data followed by fine-tuning with a small number of labels. Making practical use of a federated computing environment in the clinical domain and learning on medical images poses specific challenges. In this work, we propose FedMoCo, a robust federated contrastive learning (FCL) framework, which makes efficient use of decentralized unlabeled medical data. FedMoCo has two novel modules: metadata transfer, an inter-node statistical data augmentation module, and self-adaptive aggregation…
Contrastive learning has been proved to be a promising technique for image-level representation learning from unlabeled data. Many existing works have demonstrated improved results by applying contrastive learning in classification and object detection tasks for either natural images or medical images. However, its application to medical image segmentation tasks has been limited. In this work, we use lung segmentation in chest X-rays as a case study and propose a contrastive learning framework with temporal correlated medical images, named CL-TCI, to learn superior encoders for initializing th…
Multimodal Medical Endoscopic Image Analysis via Progressive Disentangle-aware Contrastive Learning
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences（深圳先进技术研究院，中国科学院）；First Affiliated Hospital, Sun Yat-sen University（中山大学第一附属医院）；College of Big Data and Internet, Shenzhen Technology University（深圳技术大学大数据与互联网学院）
Sun Yat-sen University（中山大学）；Southern University of Science and Technology（南方科技大学）
Manually annotating medical images is extremely expensive, especially for large-scale datasets. Self-supervised contrastive learning has been explored to learn feature representations from unlabeled images. However, unlike natural images, the application of contrastive learning to medical images is relatively limited. In this work, we propose a self-supervised framework, namely lesion-based contrastive learning for automated diabetic retinopathy (DR) grading. Instead of taking entire images as the input in the common contrastive learning scheme, lesion patches are employed to encourage the fea…
University of Oxford（牛津大学）；Tel-Aviv University（特拉维夫大学）
Self-supervised contrastive representation learning offers the advantage of learning meaningful visual representations from unlabeled medical datasets for transfer learning. However, applying current contrastive learning approaches to medical data without considering its domain-specific anatomical characteristics may lead to visual representations that are inconsistent in appearance and semantics. In this paper, we propose to improve visual representations of medical images via anatomy-aware contrastive learning (AWCL), which incorporates anatomy information to augment the positive/negative pa…
University of Pittsburgh（匹兹堡大学）；University of Notre Dame（圣母大学）
Supervised deep learning needs a large amount of labeled data to achieve high performance. However, in medical imaging analysis, each site may only have a limited amount of data and labels, which makes learning ineffective. Federated learning (FL) can help in this regard by learning a shared model while keeping training data local for privacy. Traditional FL requires fully-labeled data for training, which is inconvenient or sometimes infeasible to obtain due to high labeling cost and the requirement of expertise. Contrastive learning (CL), as a self-supervised learning approach, can effectivel…
Cockrell School of Engineering, The University of Texas at Austin（德克萨斯大学奥斯汀分校科克雷尔工程学院）；School of Information, The University of Texas at Austin（德克萨斯大学奥斯汀分校信息学院）；Weill Cornell Medicine（威尔康奈尔医学院）
Chest X-ray becomes one of the most common medical diagnoses due to its noninvasiveness. The number of chest X-ray images has skyrocketed, but reading chest X-rays still have been manually performed by radiologists, which creates huge burnouts and delays. Traditionally, radiomics, as a subfield of radiology that can extract a large number of quantitative features from medical images, demonstrates its potential to facilitate medical imaging diagnosis before the deep learning era. With the rise of deep learning, the explainability of deep neural networks on chest X-ray diagnosis remains opaque. …
Technical University of Munich（慕尼黑工业大学）；University of Zurich（苏黎世大学）；Southern University of Science and Technology（南方科技大学）；Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）
Quantifying the perceptual similarity of two images is a long-standing problem in low-level computer vision. The natural image domain commonly relies on supervised learning, e.g., a pre-trained VGG, to obtain a latent representation. However, due to domain shift, pre-trained models from the natural image domain might not apply to other image domains, such as medical imaging. Notably, in medical imaging, evaluating the perceptual similarity is exclusively performed by specialists trained extensively in diverse medical fields. Thus, medical imaging remains devoid of task-specific, objective perc…
