Supervised learning method requires a large volume of annotated datasets. Collecting such datasets is time-consuming and expensive. Until now, very few annotated COVID-19 imaging datasets are available. Although self-supervised learning enables us to bootstrap the training by exploiting unlabeled data, the generic self-supervised methods for natural images do not sufficiently incorporate the context. For medical images, a desirable method should be sensitive enough to detect deviation from normal-appearing tissue of each anatomical region; here, anatomy is the context. We introduce a novel approach with two levels of self-supervised representation learning objectives: one on the regional anatomical level and another on the patient-level. We use graph neural networks to incorporate the relationship between different anatomical regions. The structure of the graph is informed by anatomical correspondences between each patient and an anatomical atlas. In addition, the graph representation has the advantage of handling any arbitrarily sized image in full resolution. Experiments on large-scale Computer Tomography (CT) datasets of lung images show that our approach compares favorably to baseline methods that do not account for the context. We use the learnt embedding to quantify the clinical progression of COVID-19 and show that our method generalizes well to COVID-19 patients from different hospitals. Qualitative results suggest that our model can identify clinically relevant regions in the images.
Self-supervised pretraining followed by supervised fine-tuning has seen success in image recognition, especially when labeled examples are scarce, but has received limited attention in medical image analysis. This paper studies the effectiveness of self-supervised learning as a pretraining strategy for medical image classification. We conduct experiments on two distinct tasks: dermatology skin condition classification from digital camera images and multi-label chest X-ray classification, and demonstrate that self-supervised learning on ImageNet, followed by additional self-supervised learning …
Jordan University of Science and Technology（约旦科技大学）
The scarcity of high-quality annotated medical imaging datasets is a major problem that collides with machine learning applications in the field of medical imaging analysis and impedes its advancement. Self-supervised learning is a recent training paradigm that enables learning robust representations without the need for human annotation which can be considered an effective solution for the scarcity of annotated medical data. This article reviews the state-of-the-art research directions in self-supervised learning approaches for image data with a concentration on their applications in the fiel…
Witnessed the development of deep learning, increasing number of studies try to build computer aided diagnosis systems for 3D volumetric medical data. However, as the annotations of 3D medical data are difficult to acquire, the number of annotated 3D medical images is often not enough to well train the deep learning networks. The self-supervised learning deeply exploiting the information of raw data is one of the potential solutions to loose the requirement of training data. In this paper, we propose a self-supervised learning framework for the volumetric medical images. A novel proxy task, i.…
How does self-supervised pretraining improve robustness against noisy labels across various medical image classification datasets?
Center for Imaging Science, RIT（罗切斯特理工学院成像科学中心）；University of Aberdeen（阿伯丁大学）；NepAl Applied Mathematics and Informatics Institute for Research (NAAMII)（尼泊尔应用数学与信息学研究所）；Biomedical Engineering, RIT（罗切斯特理工学院生物医学工程系）
Inception Institute of Artificial Intelligence（英赛普申人工智能研究院）
In many real world medical image classification settings we do not have access to samples of all possible disease classes, while a robust system is expected to give high performance in recognizing novel test data. We propose a generalized zero shot learning (GZSL) method that uses self supervised learning (SSL) for: 1) selecting anchor vectors of different disease classes; and 2) training a feature generator. Our approach does not require class attribute vectors which are available for natural images but not for medical images. SSL ensures that the anchor vectors are representative of each cla…
Deep learning highly relies on the quantity of annotated data. However, the annotations for 3D volumetric medical data require experienced physicians to spend hours or even days for investigation. Self-supervised learning is a potential solution to get rid of the strong requirement of training data by deeply exploiting raw data information. In this paper, we propose a novel self-supervised learning framework for volumetric medical images. Specifically, we propose a context restoration task, i.e., Rubik's cube++, to pre-train 3D neural networks. Different from the existing context-restoration-b…
Technical University of Berlin, Germany（柏林工业大学（德国））；Hasso Plattner Institute for Digital Engineering, University of Potsdam, Germany（波茨坦大学哈索普拉特纳数字工程研究所（德国））；Hasso Plattner Institute for Digital Health at the Icahn School of Medicine at Mount Sinai, NYC, USA（西奈山伊坎医学院哈索普拉特纳数字健康研究所（美国纽约市））
Self-supervised learning methods can be used to learn meaningful representations from unlabeled data that can be transferred to supervised downstream tasks to reduce the need for labeled data. In this paper, we propose a 3D self-supervised method that is based on the contrastive (SimCLR) method. Additionally, we show that employing Bayesian neural networks (with Monte-Carlo Dropout) during the inference phase can further enhance the results on the downstream tasks. We showcase our models on two medical imaging segmentation tasks: i) Brain Tumor Segmentation from 3D MRI, ii) Pancreas Tumor Segm…
Although self-supervised learning enables us to bootstrap the training by exploiting unlabeled data, the generic self-supervised methods for natural images do not sufficiently incorporate the context. For medical images, a desirable method should be sensitive enough to detect deviation from normal-appearing tissue of each anatomical region; here, anatomy is the context. We introduce a novel approach with two levels of self-supervised representation learning objectives: one on the regional anatomical level and another on the patient-level. We use graph neural networks to incorporate the relatio…
Interpretation of medical images for diagnosis and treatment of complex disease from high-dimensional and heterogeneous data remains a key challenge in transforming healthcare. In the last few years, both supervised and unsupervised deep learning achieved promising results in the area of medical imaging and image analysis. Unlike supervised learning which is biased towards how it is being supervised and manual efforts to create class label for the algorithm, unsupervised learning derive insights directly from the data itself, group the data and help to make data driven decisions without any ex…
Eindhoven University of Technology（埃因霍温理工大学）；Erasmus Medical Center（伊拉斯谟医学中心）；University of Copenhagen（哥本哈根大学）；University Medical Center Utrecht（乌得勒支大学医学中心）
Machine learning (ML) algorithms have made a tremendous impact in the field of medical imaging. While medical imaging datasets have been growing in size, a challenge for supervised ML algorithms that is frequently mentioned is the lack of annotated data. As a result, various methods which can learn with less/other types of supervision, have been proposed. We review semi-supervised, multiple instance, and transfer learning in medical imaging, both in diagnosis/detection or segmentation tasks. We also discuss connections between these learning scenarios, and opportunities for future research.
Arizona State University（亚利桑那州立大学）；Stanford University（斯坦福大学）；Mayo Clinic（梅奥诊所）
Transfer learning from supervised ImageNet models has been frequently used in medical image analysis. Yet, no large-scale evaluation has been conducted to benchmark the efficacy of newly-developed pre-training techniques for medical image analysis, leaving several important questions unanswered. As the first step in this direction, we conduct a systematic study on the transferability of models pre-trained on iNat2021, the most recent large-scale fine-grained dataset, and 14 top self-supervised ImageNet models on 7 diverse medical tasks in comparison with the supervised ImageNet model. Furtherm…
Budapest University of Technology and Economics（布达佩斯技术与经济大学）
Supervised machine learning provides state-of-the-art solutions to a wide range of computer vision problems. However, the need for copious labelled training data limits the capabilities of these algorithms in scenarios where such input is scarce or expensive. Self-supervised learning offers a way to lower the need for manually annotated data by pretraining models for a specific domain on unlabelled data. In this approach, labelled data are solely required to fine-tune models for downstream tasks. Medical image segmentation is a field where labelling data requires expert knowledge and collectin…
Medical image classification is often challenging for two reasons: a lack of labelled examples due to expensive and time-consuming annotation protocols, and imbalanced class labels due to the relative scarcity of disease-positive individuals in the wider population. Semi-supervised learning (SSL) methods exist for dealing with a lack of labels, but they generally do not address the problem of class imbalance. In this study we propose Adaptive Blended Consistency Loss (ABCL), a drop-in replacement for consistency loss in perturbation-based SSL methods. ABCL counteracts data skew by adaptively m…
Arizona State University（亚利桑那州立大学）；Mayo Clinic（梅奥诊所）
Discriminative learning, restorative learning, and adversarial learning have proven beneficial for self-supervised learning schemes in computer vision and medical imaging. Existing efforts, however, omit their synergistic effects on each other in a ternary setup, which, we envision, can significantly benefit deep semantic representation learning. To realize this vision, we have developed DiRA, the first framework that unites discriminative, restorative, and adversarial learning in a unified manner to collaboratively glean complementary visual information from unlabeled medical images for fine-…
Computer-aided diagnosis via deep learning relies on large-scale annotated data sets, which can be costly when involving expert knowledge. Semi-supervised learning (SSL) mitigates this challenge by leveraging unlabeled data. One effective SSL approach is to regularize the local smoothness of neural functions via perturbations around single data points. In this work, we argue that regularizing the global smoothness of neural functions by filling the void in between data points can further improve SSL. We present a novel SSL approach that trains the neural network on linear mixing of labeled and…
Semise: Semi-supervised learning for severity representation in medical image
Hanoi University of Science and Technology（河内理工大学）；University of Southern California（南加州大学）；VinUni-Illinois Smart Health Center, VinUniversity（VinUniversity-VinUniversity伊利诺伊智能健康中心）
Tongji University（同济大学）；University of Shanghai for Science and Technology（上海理工大学）；National University of Singapore（新加坡国立大学）
The application of deep learning to medical image segmentation has been hampered due to the lack of abundant pixel-level annotated data. Few-shot Semantic Segmentation (FSS) is a promising strategy for breaking the deadlock. However, a high-performing FSS model still requires sufficient pixel-level annotated classes for training to avoid overfitting, which leads to its performance bottleneck in medical image segmentation due to the unmet need for annotations. Thus, semi-supervised FSS for medical images is accordingly proposed to utilize unlabeled data for further performance improvement. Neve…
University of Calgary（卡尔加里大学）；University of Alberta（阿尔伯塔大学）；Alberta Machine Intelligence Institute (AMII)（阿尔伯塔机器智能研究所（AMII））
Many successful methods developed for medical image analysis that are based on machine learning use supervised learning approaches, which often require large datasets annotated by experts to achieve high accuracy. However, medical data annotation is time-consuming and expensive, especially for segmentation tasks. To solve the problem of learning with limited labeled medical image data, an alternative deep learning training strategy based on self-supervised pretraining on unlabeled MRI scans is proposed in this work. Our pretraining approach first, randomly applies different distortions to rand…
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-…
Arizona State University（亚利桑那州立大学）；Mayo Clinic（梅奥诊所）
Recently, self-supervised instance discrimination methods have achieved significant success in learning visual representations from unlabeled photographic images. However, given the marked differences between photographic and medical images, the efficacy of instance-based objectives, focusing on learning the most discriminative global features in the image (i.e., wheels in bicycle), remains unknown in medical imaging. Our preliminary analysis showed that high global similarity of medical images in terms of anatomy hampers instance discrimination methods for capturing a set of distinct features…
Science Foundation Ireland Centre for Research Training in Machine Learning（爱尔兰科学基金会机器学习研究中心）；School of Computer Science, University College Dublin（都柏林大学计算机科学学院）；Insight Centre for Data Analytics, University College Dublin（都柏林大学洞察数据分析中心）
Noisy data present in medical imaging datasets can often aid the development of robust models that are equipped to handle real-world data. However, if the bad data contains insufficient anatomical information, it can have a severe negative effect on the model's performance. We propose a novel methodology using a semi-supervised Siamese network to identify bad data. This method requires only a small pool of 'reference' medical images to be reviewed by a non-expert human to ensure the major anatomical structures are present in the Field of View. The model trains on this reference set and identif…
Semi-Supervised Disease Classification based on Limited Medical Image Data
School of Science, Minzu University of China（中央民族大学理学院）；Joint Research Center on Computational Mathematics and Control, Shenzhen MSU-BIT University（深圳北理莫斯科大学计算数学与控制联合研究中心）；Institute of Data Science, National University of Singapore（新加坡国立大学数据科学研究院）
The scarcity of pixel-level annotation is a prevalent problem in medical image segmentation tasks. In this paper, we introduce a novel regularization strategy involving interpolation-based mixing for semi-supervised medical image segmentation. The proposed method is a new consistency regularization strategy that encourages segmentation of interpolation of two unlabelled data to be consistent with the interpolation of segmentation maps of those data. This method represents a specific type of data-adaptive regularization paradigm which aids to minimize the overfitting of labelled data under high…
Saratoga High School（萨拉托加高中）；Stanford University（斯坦福大学）；University of California, Los Angeles（加州大学洛杉矶分校）；VoxelCloud, Inc.（体云公司）
Semi-supervised learning via learning from limited quantities of labeled data has been investigated as an alternative to supervised counterparts. Maximizing knowledge gains from copious unlabeled data benefit semi-supervised learning settings. Moreover, learning multiple tasks within the same model further improves model generalizability. We propose a novel multitask learning model, namely MultiMix, which jointly learns disease classification and anatomical segmentation in a sparingly supervised manner, while preserving explainability through bridge saliency between the two tasks. Our extensiv…
Peking University（北京大学）；Yizhun Medical AI Co., Ltd（医准医疗人工智能有限公司）
Applying artificial intelligence techniques in medical imaging is one of the most promising areas in medicine. However, most of the recent success in this area highly relies on large amounts of carefully annotated data, whereas annotating medical images is a costly process. In this paper, we propose a novel method, called FocalMix, which, to the best of our knowledge, is the first to leverage recent advances in semi-supervised learning (SSL) for 3D medical image detection. We conducted extensive experiments on two widely used datasets for lung nodule detection, LUNA16 and NLST. Results show th…
Erasmus MC（伊拉斯谟医学中心）；COSMONiO；University of Copenhagen（哥本哈根大学）
The scarcity of labeled data often limits the application of supervised deep learning techniques for medical image segmentation. This has motivated the development of semi-supervised techniques that learn from a mixture of labeled and unlabeled images. In this paper, we propose a novel semi-supervised method that, in addition to supervised learning on labeled training images, learns to predict segmentations consistent under a given class of transformations on both labeled and unlabeled images. More specifically, in this work we explore learning equivariance to elastic deformations. We implemen…
University of Electronic Science and Technology of China（电子科技大学）；Shanghai Artificial Intelligence Laboratory（上海人工智能实验室）；Johns Hopkins University（约翰斯·霍普金斯大学）；West China Hospital, Sichuan University（四川大学华西医院）
Background and Objective: Open-source deep learning toolkits are one of the driving forces for developing medical image segmentation models. Existing toolkits mainly focus on fully supervised segmentation and require full and accurate pixel-level annotations that are time-consuming and difficult to acquire for segmentation tasks, which makes learning from imperfect labels highly desired for reducing the annotation cost. We aim to develop a new deep learning toolkit to support annotation-efficient learning for medical image segmentation. Methods: Our proposed toolkit named PyMIC is a modular de…
Deepwise Artificial Intelligence Laboratory（深睿人工智能实验室）；The University of Hong Kong（香港大学）
The difficulties in both data acquisition and annotation substantially restrict the sample sizes of training datasets for 3D medical imaging applications. As a result, constructing high-performance 3D convolutional neural networks from scratch remains a difficult task in the absence of a sufficient pre-training parameter. Previous efforts on 3D pre-training have frequently relied on self-supervised approaches, which use either predictive or contrastive learning on unlabeled data to build invariant 3D representations. However, because of the unavailability of large-scale supervision information…
The Chinese University of Hong Kong（香港中文大学）；Stanford University（斯坦福大学）
Deep convolutional neural networks have achieved remarkable progress on a variety of medical image computing tasks. A common problem when applying supervised deep learning methods to medical images is the lack of labeled data, which is very expensive and time-consuming to be collected. In this paper, we present a novel semi-supervised method for medical image segmentation, where the network is optimized by the weighted combination of a common supervised loss for labeled inputs only and a regularization loss for both labeled and unlabeled data. To utilize the unlabeled data, our method encourag…
Vision Transformers (ViT)s have shown great performance in self-supervised learning of global and local representations that can be transferred to downstream applications. Inspired by these results, we introduce a novel self-supervised learning framework with tailored proxy tasks for medical image analysis. Specifically, we propose: (i) a new 3D transformer-based model, dubbed Swin UNEt TRansformers (Swin UNETR), with a hierarchical encoder for self-supervised pre-training; (ii) tailored proxy tasks for learning the underlying pattern of human anatomy. We demonstrate successful pre-training of…
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…
A generalizable 3D framework and model for self-supervised learning in medical imaging
Department of Medical Biophysics, University of Toronto（多伦多大学医学生物物理学系）；Department of Computer Science, University of Toronto（多伦多大学计算机科学系）；Institute for Aerospace Studies, University of Toronto（多伦多大学航空航天研究所）；Physical Sciences Platform, Sunnybrook Research Institute（圣母医院研究学院物理科学平台）；Vector Institute, Toronto（多伦多向量研究所）；Department of Laboratory Medicine and Pathobiology, University of Toronto（多伦多大学实验室医学与病理学系）；Hurvitz Brain Sciences, Sunnybrook Health Sciences Centre（圣母医院健康科学中心Hurvitz脑科学）；Harquail Centre for Neuromodulation, Sunnybrook Health Sciences Centre（圣母医院健康科学中心Harquail神经调制中心）
Stanford University（斯坦福大学）；The University of Hong Kong（香港大学）；University of California, Santa Cruz（加州大学圣克鲁兹分校）
The collection and curation of large-scale medical datasets from multiple institutions is essential for training accurate deep learning models, but privacy concerns often hinder data sharing. Federated learning (FL) is a promising solution that enables privacy-preserving collaborative learning among different institutions, but it generally suffers from performance deterioration due to heterogeneous data distributions and a lack of quality labeled data. In this paper, we present a robust and label-efficient self-supervised FL framework for medical image analysis. Our method introduces a novel T…
In the past few years, deep learning-based methods have demonstrated enormous success for solving inverse problems in medical imaging. In this work, we address the following question:\textit{Given a set of measurements obtained from real imaging experiments, what is the best way to use a learnable model and the physics of the modality to solve the inverse problem and reconstruct the latent image?} Standard supervised learning based methods approach this problem by collecting data sets of known latent images and their corresponding measurements. However, these methods are often impractical due …
Kyushu University（九州大学）；Kyoto University（京都大学）；The University of Tokyo（东京大学）
Semi-supervised domain adaptation is a technique to build a classifier for a target domain by modifying a classifier in another (source) domain using many unlabeled samples and a small number of labeled samples from the target domain. In this paper, we develop a semi-supervised domain adaptation method, which has robustness to class-imbalanced situations, which are common in medical image classification tasks. For robustness, we propose a weakly-supervised clustering pipeline to obtain high-purity clusters and utilize the clusters in representation learning for domain adaptation. The proposed …
Shanghai Jiaotong University（上海交通大学）；Shanghai AI Lab（上海人工智能实验室）；University of Electronic Science and Technology of China（电子科技大学）；Sensetime Research（商汤科技研究院）
Deep neural networks usually require accurate and a large number of annotations to achieve outstanding performance in medical image segmentation. One-shot segmentation and weakly-supervised learning are promising research directions that lower labeling effort by learning a new class from only one annotated image and utilizing coarse labels instead, respectively. Previous works usually fail to leverage the anatomical structure and suffer from class imbalance and low contrast problems. Hence, we present an innovative framework for 3D medical image segmentation with one-shot and weakly-supervised…
J. J. Strossmayer University of Osijek（约西普·尤拉伊·斯特罗斯马耶奥西耶克大学）；Ghent University（根特大学）
One of the largest problems in medical image processing is the lack of annotated data. Labeling medical images often requires highly trained experts and can be a time-consuming process. In this paper, we evaluate a method of reducing the need for labeled data in medical image object detection by using self-supervised neural network pretraining. We use a dataset of chest X-ray images with bounding box labels for 13 different classes of anomalies. The networks are pretrained on a percentage of the dataset without labels and then fine-tuned on the rest of the dataset. We show that it is possible …
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…
Limited availability of annotated medical imaging data poses a challenge for deep learning algorithms. Although transfer learning minimizes this hurdle in general, knowledge transfer across disparate domains is shown to be less effective. On the other hand, smaller architectures were found to be more compelling in learning better features. Consequently, we propose a lightweight architecture that uses mixed asymmetric kernels (MAKNet) to reduce the number of parameters significantly. Additionally, we train the proposed architecture using semi-supervised learning to provide pseudo-labels for a l…
Applications on Medical Image Analysis suffer from acute shortage of large volume of data properly annotated by medical experts. Supervised Learning algorithms require a large volumes of balanced data to learn robust representations. Often supervised learning algorithms require various techniques to deal with imbalanced data. Self-supervised learning algorithms on the other hand are robust to imbalance in the data and are capable of learning robust representations. In this work, we train a 3D BYOL self-supervised model using gradient accumulation technique to deal with the large number of samp…
Technische Universität München（慕尼黑工业大学）；Klinikum rechts der Isar（伊萨尔河右岸医院）；TranslaTUM - Central Institute for Translational Cancer Research（慕尼黑转化癌症研究中心）；University of Zurich（苏黎世大学）；Helmholtz Zentrum München（慕尼黑亥姆霍兹中心）
Self-supervision has demonstrated to be an effective learning strategy when training target tasks on small annotated data-sets. While current research focuses on creating novel pretext tasks to learn meaningful and reusable representations for the target task, these efforts obtain marginal performance gains compared to fully-supervised learning. Meanwhile, little attention has been given to study the robustness of networks trained in a self-supervised manner. In this work, we demonstrate that networks trained via self-supervised learning have superior robustness and generalizability compared t…
