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-level segmentation'. In this paper, we propose a simple semantic-aware contrastive learning approach leveraging attention masks to advance multi-object semantic segmentation. Briefly, we embed different semantic objects to different clusters rather than the traditional image-level embeddings. We evaluate our proposed method on a multi-organ medical image segmentation task with both in-house data and MICCAI Challenge 2015 BTCV datasets. Compared with current state-of-the-art training strategies, our proposed pipeline yields a substantial improvement of 5.53% and 6.09% on Dice score for both medical image segmentation cohorts respectively (p-value<0.01). The performance of the proposed method is further assessed on natural images via the PASCAL VOC 2012 dataset, and achieves a substantial improvement of 2.75% on mIoU (p-value<0.01).
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…
Many recent approaches in contrastive learning have worked to close the gap between pretraining on iconic images like ImageNet and pretraining on complex scenes like COCO. This gap exists largely because commonly used random crop augmentations obtain semantically inconsistent content in crowded scene images of diverse objects. Previous works use preprocessing pipelines to localize salient objects for improved cropping, but an end-to-end solution is still elusive. In this work, we propose a framework which accomplishes this goal via joint learning of representations and segmentation. We leverag…
North University of China（中北大学）；Dalian University of Technology（大连理工大学）
Predicting medications is a crucial task in many intelligent healthcare systems. It can assist doctors in making informed medication decisions for patients according to electronic medical records (EMRs). However, medication prediction is a challenging data mining task due to the complex relations between medical codes. Most existing studies focus on utilizing inherent relations between homogeneous codes of medical ontology graph to enhance their representations using supervised methods, and few studies pay attention to the valuable relations between heterogeneous or homogeneous medical codes f…
Technical University of Munich（慕尼黑工业大学）；Helmholtz Zentrum Munich（慕尼黑亥姆霍兹中心）；Imperial College London（伦敦帝国理工学院）
Image-text contrastive learning has proven effective for pretraining medical image models. When targeting localized downstream tasks like semantic segmentation or object detection, additional local contrastive losses that align image regions with sentences have shown promising results. We study how local contrastive losses are related to global (per-sample) contrastive losses and which effects they have on localized medical downstream tasks. Based on a theoretical comparison, we propose to remove some components of local losses and replace others by a novel distribution prior which enforces un…
Collecting labeled data for the task of semantic segmentation is expensive and time-consuming, as it requires dense pixel-level annotations. While recent Convolutional Neural Network (CNN) based semantic segmentation approaches have achieved impressive results by using large amounts of labeled training data, their performance drops significantly as the amount of labeled data decreases. This happens because deep CNNs trained with the de facto cross-entropy loss can easily overfit to small amounts of labeled data. To address this issue, we propose a simple and effective contrastive learning-base…
Hasso Plattner Institute for Digital Engineering, University of Potsdam（波茨坦大学哈索·普拉特纳数字工程研究所）；TU Kaiserslautern（凯泽斯劳滕工业大学）；Hasso Plattner Institute for Digital Health at the Icahn School of Medicine at Mount Sinai（西奈山伊坎医学院哈索·普拉特纳数字健康研究所）
High annotation costs are a substantial bottleneck in applying modern deep learning architectures to clinically relevant medical use cases, substantiating the need for novel algorithms to learn from unlabeled data. In this work, we propose ContIG, a self-supervised method that can learn from large datasets of unlabeled medical images and genetic data. Our approach aligns images and several genetic modalities in the feature space using a contrastive loss. We design our method to integrate multiple modalities of each individual person in the same model end-to-end, even when the available modalit…
SupReMix: Supervised Contrastive Learning for Medical Imaging Regression with Mixup
Yong Loo Lin School of Medicine, National University of Singapore（杨潞龄医学院，新加坡国立大学）；National University of Singapore（新加坡国立大学）；Duke University（杜克大学）；ETH Zurich（苏黎世联邦理工学院）
Queen Mary University of London（伦敦玛丽女王大学）；Communication University of Zhejiang（浙江传媒学院）；University of Leicester（莱斯特大学）；Hangzhou Dianzi University（杭州电子科技大学）
In this paper, we introduce an unsupervised cancer segmentation framework for histology images. The framework involves an effective contrastive learning scheme for extracting distinctive visual representations for segmentation. The encoder is a Deep U-Net (DU-Net) structure that contains an extra fully convolution layer compared to the normal U-Net. A contrastive learning scheme is developed to solve the problem of lacking training sets with high-quality annotations on tumour boundaries. A specific set of data augmentation techniques are employed to improve the discriminability of the learned …
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-…
Parotid gland tumor is a common type of head and neck tumor. Segmentation of the parotid glands and tumors by MR images is important for the treatment of parotid gland tumors. However, segmentation of the parotid glands is particularly challenging due to their variable shape and low contrast with surrounding structures. Recently deep learning has developed rapidly, which can handle complex problems. However, most of the current deep learning methods for processing medical images are still based on supervised learning. Compared with natural images, medical images are difficult to acquire and co…
Recent advances in self-supervised contrastive learning yield good image-level representation, which favors classification tasks but usually neglects pixel-level detailed information, leading to unsatisfactory transfer performance to dense prediction tasks such as semantic segmentation. In this work, we propose a pixel-wise contrastive learning method called CP2 (Copy-Paste Contrastive Pretraining), which facilitates both image- and pixel-level representation learning and therefore is more suitable for downstream dense prediction tasks. In detail, we copy-paste a random crop from an image (the…
We present a self-supervised learning (SSL) method suitable for semi-global tasks such as object detection and semantic segmentation. We enforce local consistency between self-learned features, representing corresponding image locations of transformed versions of the same image, by minimizing a pixel-level local contrastive (LC) loss during training. LC-loss can be added to existing self-supervised learning methods with minimal overhead. We evaluate our SSL approach on two downstream tasks -- object detection and semantic segmentation, using COCO, PASCAL VOC, and CityScapes datasets. Our metho…
University of Rome Tor Vergata（罗马第二大学）；University of Cambridge（剑桥大学）；Athinoula A. Martinos Center for Biomedical Imaging（阿西诺拉·A·马蒂诺斯生物医学成像中心）
The lack of large labeled medical imaging datasets, along with significant inter-individual variability compared to clinically established disease classes, poses significant challenges in exploiting medical imaging information in a precision medicine paradigm, where in principle dense patient-specific data can be employed to formulate individual predictions and/or stratify patients into finer-grained groups which may follow more homogeneous trajectories and therefore empower clinical trials. In order to efficiently explore the effective degrees of freedom underlying variability in medical imag…
Medical report generation is a challenging task since it is time-consuming and requires expertise from experienced radiologists. The goal of medical report generation is to accurately capture and describe the image findings. Previous works pretrain their visual encoding neural networks with large datasets in different domains, which cannot learn general visual representation in the specific medical domain. In this work, we propose a medical report generation framework that uses a contrastive learning approach to pretrain the visual encoder and requires no additional meta information. In additi…
A large amount of manual segmentation is typically required to train a robust segmentation network so that it can segment objects of interest in a new imaging modality. The manual efforts can be alleviated if the manual segmentation in one imaging modality (e.g., CT) can be utilized to train a segmentation network in another imaging modality (e.g., CBCT/MRI/PET). In this work, we developed an anatomy-constrained contrastive synthetic segmentation network (AccSeg-Net) to train a segmentation network for a target imaging modality without using its ground truth. Specifically, we proposed to use a…
Yale University（耶鲁大学）；Rice University（莱斯大学）；University of Texas Health Science Center（德克萨斯大学健康科学中心）
The proliferation of Deep Learning (DL)-based methods for radiographic image analysis has created a great demand for expert-labeled radiology data. Recent self-supervised frameworks have alleviated the need for expert labeling by obtaining supervision from associated radiology reports. These frameworks, however, struggle to distinguish the subtle differences between different pathologies in medical images. Additionally, many of them do not provide interpretation between image regions and text, making it difficult for radiologists to assess model predictions. In this work, we propose Local Regi…
Samsung SDS Research America（三星SDS美国研究院）；UC Berkeley（加州大学伯克利分校）
3D deep learning is a growing field of interest due to the vast amount of information stored in 3D formats. Triangular meshes are an efficient representation for irregular, non-uniform 3D objects. However, meshes are often challenging to annotate due to their high geometrical complexity. Specifically, creating segmentation masks for meshes is tedious and time-consuming. Therefore, it is desirable to train segmentation networks with limited-labeled data. Self-supervised learning (SSL), a form of unsupervised representation learning, is a growing alternative to fully-supervised learning which ca…
Tsinghua University（清华大学）；Tencent Youtu Lab（腾讯优图实验室）；University College London（伦敦大学学院）
Few-shot semantic segmentation aims to segment novel-class objects in a query image with only a few annotated examples in support images. Most of advanced solutions exploit a metric learning framework that performs segmentation through matching each pixel to a learned foreground prototype. However, this framework suffers from biased classification due to incomplete construction of sample pairs with the foreground prototype only. To address this issue, in this paper, we introduce a complementary self-contrastive task into few-shot semantic segmentation. Our new model is able to associate the pi…
Nanyang Technological University（南洋理工大学）；National University of Singapore（新加坡国立大学）
With large-scale well-labeled datasets, deep learning has shown significant success in medical image segmentation. However, it is challenging to acquire abundant annotations in clinical practice due to extensive expertise requirements and costly labeling efforts. Recently, contrastive learning has shown a strong capacity for visual representation learning on unlabeled data, achieving impressive performance rivaling supervised learning in many domains. In this work, we propose a novel multi-scale multi-view global-local contrastive learning (MMGL) framework to thoroughly explore global and loca…
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…
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 …
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）
We develop and approach to unsupervised semantic medical image segmentation that extends previous work with generative adversarial networks. We use existing edge detection methods to construct simple edge diagrams, train a generative model to convert them into synthetic medical images, and construct a dataset of synthetic images with known segmentations using variations on extracted edge diagrams. This synthetic dataset is then used to train a supervised image segmentation model. We test our approach on a clinical dataset of kidney ultrasound images and the benchmark ISIC 2018 skin lesion data…
A Learnable Multi-views Contrastive Framework with Reconstruction Discrepancy for Medical Time-Series
School of Medicine, The Chinese University of Hong Kong, Shenzhen（香港中文大学（深圳）医学院）；Digital Department, China Unicom Global Co., Ltd（中国联通全球有限公司数字部）；University of the Chinese Academy of Sciences（中国科学院大学）；Shenzhen International Graduate School, Tsinghua University（清华大学深圳国际研究生院）
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 …
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）
Mohamed bin Zayed University of Artificial Intelligence（穆罕默德·本·扎耶德人工智能大学）
Contrastive learning has proven useful in many applications where access to labelled data is limited. The lack of annotated data is particularly problematic in medical image segmentation as it is difficult to have clinical experts manually annotate large volumes of data such as cardiac structures in ultrasound images of the heart. In this paper, We propose a self supervised contrastive learning method to segment the left ventricle from echocardiography when limited annotated images exist. Furthermore, we study the effect of contrastive pretraining on two well-known segmentation networks, UNet …
FUJIFILM Corporation（富士胶片公司）；AWS AI Labs（AWS人工智能实验室）；Massachusetts Institute of Technology（麻省理工学院）；Stanford University（斯坦福大学）
Learning visual representations of medical images (e.g., X-rays) is core to medical image understanding but its progress has been held back by the scarcity of human annotations. Existing work commonly relies on fine-tuning weights transferred from ImageNet pretraining, which is suboptimal due to drastically different image characteristics, or rule-based label extraction from the textual report data paired with medical images, which is inaccurate and hard to generalize. Meanwhile, several recent studies show exciting results from unsupervised contrastive learning from natural images, but we fin…
TreeGaussian: Tree-Guided Cascaded Contrastive Learning for Hierarchical Consistent 3D Gaussian Scene Segmentation and Understanding
Institute of Computing Technology, Chinese Academy of Sciences（中国科学院计算技术研究所）；University of Chinese Academy of Sciences（中国科学院大学）；Beihang University（北京航空航天大学）
To overcome the data-hungry challenge, we have proposed a semi-supervised contrastive learning framework for the task of class-imbalanced semantic segmentation. First and foremost, to make the model operate in a semi-supervised manner, we proposed the confidence-level-based contrastive learning to achieve instance discrimination in an explicit manner, and make the low-confidence low-quality features align with the high-confidence counterparts. Moreover, to tackle the problem of class imbalance in crack segmentation and road components extraction, we proposed the data imbalance loss to replace …
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…
University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）；X The Moonshot Factory（X 登月工厂）
We present a novel semi-supervised semantic segmentation method which jointly achieves two desiderata of segmentation model regularities: the label-space consistency property between image augmentations and the feature-space contrastive property among different pixels. We leverage the pixel-level L2 loss and the pixel contrastive loss for the two purposes respectively. To address the computational efficiency issue and the false negative noise issue involved in the pixel contrastive loss, we further introduce and investigate several negative sampling techniques. Extensive experiments demonstrat…
GS-EMA: Integrating Gradient Surgery Exponential Moving Average with Boundary-Aware Contrastive Learning for Enhanced Domain Generalization in Aneurysm Segmentation
University of Leeds（利兹大学）；University of Manchester（曼彻斯特大学）
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,…
Knowledge Boosting: Rethinking Medical Contrastive Vision-Language Pre-Training
Southeast University（东南大学）；Nanjing University of Aeronautics and Astronautics（南京航空航天大学）；Case Western Reserve University（凯斯西储大学）；Centre de Recherche en Information Biomédicale Sino-Français（中法生物医学信息研究中心）
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）
The paper is a short review of medical image segmentation using U-Net and its variants. As we understand going through a medical images is not an easy job for any clinician either radiologist or pathologist. Analysing medical images is the only way to perform non-invasive diagnosis. Segmenting out the regions of interest has significant importance in medical images and is key for diagnosis. This paper also gives a bird eye view of how medical image segmentation has evolved. Also discusses challenge's and success of the deep neural architectures. Following how different hybrid architectures hav…
Sun Yat-Sen University（中山大学）；Xidian University（西安电子科技大学）；The Sixth Affiliated Hospital, Sun Yat-sen University（中山大学附属第六医院）
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 …
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 …
