Semi-supervised Medical Image Classification with Relation-driven Self-ensembling Model
The Chinese University of Hong Kong（香港中文大学）；Stanford University（斯坦福大学）；Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences（中国科学院深圳先进技术研究院）
Training deep neural networks usually requires a large amount of labeled data to obtain good performance. However, in medical image analysis, obtaining high-quality labels for the data is laborious and expensive, as accurately annotating medical images demands expertise knowledge of the clinicians. In this paper, we present a novel relation-driven semi-supervised framework for medical image classification. It is a consistency-based method which exploits the unlabeled data by encouraging the prediction consistency of given input under perturbations, and leverages a self-ensembling model to produce high-quality consistency targets for the unlabeled data. Considering that human diagnosis often refers to previous analogous cases to make reliable decisions, we introduce a novel sample relation consistency (SRC) paradigm to effectively exploit unlabeled data by modeling the relationship information among different samples. Superior to existing consistency-based methods which simply enforce consistency of individual predictions, our framework explicitly enforces the consistency of semantic relation among different samples under perturbations, encouraging the model to explore extra semantic information from unlabeled data. We have conducted extensive experiments to evaluate our method on two public benchmark medical image classification datasets, i.e.,skin lesion diagnosis with ISIC 2018 challenge and thorax disease classification with ChestX-ray14. Our method outperforms many state-of-the-art semi-supervised learning methods on both single-label and multi-label image classification scenarios.
Polytechnique Montreal（蒙特利尔综合理工大学）；Pontifícia Universidade Católica do Rio Grande do Sul（南里奥格兰德天主教大学）；Universite de Montreal（蒙特利尔大学）
Recent advances in deep learning methods have come to define the state-of-the-art for many medical imaging applications, surpassing even human judgment in several tasks. Those models, however, when trained to reduce the empirical risk on a single domain, fail to generalize when applied to other domains, a very common scenario in medical imaging due to the variability of images and anatomical structures, even across the same imaging modality. In this work, we extend the method of unsupervised domain adaptation using self-ensembling for the semantic segmentation task and explore multiple facets …
Deep learning has demonstrated significant improvements in medical image segmentation using a sufficiently large amount of training data with manual labels. Acquiring well-representative labels requires expert knowledge and exhaustive labors. In this paper, we aim to boost the performance of semi-supervised learning for medical image segmentation with limited labels using a self-ensembling contrastive learning technique. To this end, we propose to train an encoder-decoder network at image-level with small amounts of labeled images, and more importantly, we learn latent representations directly…
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…
Mohamed Bin Zayed University of Artificial Intelligence（穆罕默德·本·扎耶德人工智能大学）
Vision Transformers (ViT) are competing to replace Convolutional Neural Networks (CNN) for various computer vision tasks in medical imaging such as classification and segmentation. While the vulnerability of CNNs to adversarial attacks is a well-known problem, recent works have shown that ViTs are also susceptible to such attacks and suffer significant performance degradation under attack. The vulnerability of ViTs to carefully engineered adversarial samples raises serious concerns about their safety in clinical settings. In this paper, we propose a novel self-ensembling method to enhance the …
Indian Institute of Information Technology Allahabad（阿拉哈巴德印度信息技术学院）
The use of Deep Learning (DL) based methods in medical histopathology images have been one of the most sought after solutions to classify, segment, and detect diseased biopsy samples. However, given the complex nature of medical datasets due to the presence of intra-class variability and heterogeneity, the use of complex DL models might not give the optimal performance up to the level which is suitable for assisting pathologists. Therefore, ensemble DL methods with the scope of including domain agnostic handcrafted Features (HC-F) inspired this work. We have, through experiments, tried to high…
VLSM-Ensemble: Ensembling CLIP-based Vision-Language Models for Enhanced Medical Image Segmentation
Insight Research Ireland Centre for Data Analytics, DCU, Dublin, Ireland（爱尔兰洞察研究爱尔兰数据分析中心，都柏林大学，都柏林）；Research Ireland Centre for Research Training in Machine Learning, DCU, Dublin, Ireland（爱尔兰研究爱尔兰机器学习研究培训中心，都柏林大学，都柏林）；School of Computing, Dublin City University, Dublin, Ireland（计算学院，都柏林城市大学，都柏林）
Chest X-ray (CXR) is perhaps the most frequently-performed radiological investigation globally. In this work, we present and study several machine learning approaches to develop automated CXR diagnostic models. In particular, we trained several Convolutional Neural Networks (CNN) on the CheXpert dataset, a large collection of more than 200k CXR labeled images. Then, we used the trained CNNs to compute embeddings of the CXR images, in order to train two sets of tree-based classifiers from them. Finally, we described and compared three ensembling strategies to combine together the classifiers tr…
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.
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…
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 …
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 …
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…
West China Hospital, Sichuan University（四川大学华西医院）；The University of Hong Kong（香港大学）；Shenzhen Research Institute of Big Data, The Chinese University of Hong Kong（香港中文大学深圳大数据研究院）；Deepwise Healthcare（深睿医疗）
Semi-Supervised classification and segmentation methods have been widely investigated in medical image analysis. Both approaches can improve the performance of fully-supervised methods with additional unlabeled data. However, as a fundamental task, semi-supervised object detection has not gained enough attention in the field of medical image analysis. In this paper, we propose a novel Semi-Supervised Medical image Detector (SSMD). The motivation behind SSMD is to provide free yet effective supervision for unlabeled data, by regularizing the predictions at each position to be consistent. To ach…
The University of Hong Kong（香港大学）；ShanghaiTech University（上海科技大学）；Deepwise AI Lab（深睿人工智能实验室）；Shenzhen Research Institute of Big Data, The Chinese University of Hong Kong (Shenzhen)（香港中文大学（深圳）深圳大数据研究院）
Preserving maximal information is one of principles of designing self-supervised learning methodologies. To reach this goal, contrastive learning adopts an implicit way which is contrasting image pairs. However, we believe it is not fully optimal to simply use the contrastive estimation for preservation. Moreover, it is necessary and complemental to introduce an explicit solution to preserve more information. From this perspective, we introduce Preservational Learning to reconstruct diverse image contexts in order to preserve more information in learned representations. Together with the contr…
Nabla Technologies（Nabla技术公司）；University of Cambridge（剑桥大学）
We consider the problem of classifying a medical image dataset when we have a limited amounts of labels. This is very common yet challenging setting as labelled data is expensive, time consuming to collect and may require expert knowledge. The current classification go-to of deep supervised learning is unable to cope with such a problem setup. However, using semi-supervised learning, one can produce accurate classifications using a significantly reduced amount of labelled data. Therefore, semi-supervised learning is perfectly suited for medical image classification. However, there has almost b…
Jadavpur University（贾达沃普尔大学）；University of Toronto（多伦多大学）
Privacy and annotation bottlenecks are two major issues that profoundly affect the practicality of machine learning-based medical image analysis. Although significant progress has been made in these areas, these issues are not yet fully resolved. In this paper, we seek to tackle these concerns head-on and systematically explore the applicability of non-contrastive self-supervised learning (SSL) algorithms under federated learning (FL) simulations for medical image analysis. We conduct thorough experimentation of recently proposed state-of-the-art non-contrastive frameworks under standard FL se…
Labeling medical images depends on professional knowledge, making it difficult to acquire large amount of annotated medical images with high quality in a short time. Thus, making good use of limited labeled samples in a small dataset to build a high-performance model is the key to medical image classification problem. In this paper, we propose a deeply supervised Layer Selective Attention Network (LSANet), which comprehensively uses label information in feature-level and prediction-level supervision. For feature-level supervision, in order to better fuse the low-level features and high-level f…
Towards Data-Efficient Medical Imaging: A Generative and Semi-Supervised Framework
Dept. of Electrical and Electronic Engineering Imperial College London（电气与电子工程系帝国理工学院伦敦）；Centre for Vision, Speech and Signal Processing University of Surrey（视觉、语音和信号处理中心萨里大学）
Self-supervised Visualisation of Medical Image Datasets
Hertie Institute for AI in Brain Health（赫蒂脑健康人工智能研究院）；University of Tübingen（蒂宾根大学）；Tübingen AI Center（蒂宾根人工智能中心）；Heidelberg University（海德堡大学）；IWR, Heidelberg University（海德堡大学IWR研究所）
Transfer learning is a standard technique to improve performance on tasks with limited data. However, for medical imaging, the value of transfer learning is less clear. This is likely due to the large domain mismatch between the usual natural-image pre-training (e.g. ImageNet) and medical images. However, recent advances in transfer learning have shown substantial improvements from scale. We investigate whether modern methods can change the fortune of transfer learning for medical imaging. For this, we study the class of large-scale pre-trained networks presented by Kolesnikov et al. on three …
Contrastive Learning (CL) is a recent representation learning approach, which encourages inter-class separability and intra-class compactness in learned image representations. Since medical images often contain multiple semantic classes in an image, using CL to learn representations of local features (as opposed to global) is important. In this work, we present a novel semi-supervised 2D medical segmentation solution that applies CL on image patches, instead of full images. These patches are meaningfully constructed using the semantic information of different classes obtained via pseudo labeli…
Pre-training a recognition model with contrastive learning on a large dataset of unlabeled data has shown great potential to boost the performance of a downstream task, e.g., image classification. However, in domains such as medical imaging, collecting unlabeled data can be challenging and expensive. In this work, we propose to adapt contrastive learning to work with meta-label annotations, for improving the model's performance in medical image segmentation even when no additional unlabeled data is available. Meta-labels such as the location of a 2D slice in a 3D MRI scan or the type of device…
In medical imaging, Class-Activation Map (CAM) serves as the main explainability tool by pointing to the region of interest. Since the localization accuracy from CAM is constrained by the resolution of the model's feature map, one may expect that segmentation models, which generally have large feature maps, would produce more accurate CAMs. However, we have found that this is not the case due to task mismatch. While segmentation models are developed for datasets with pixel-level annotation, only image-level annotation is available in most medical imaging datasets. Our experiments suggest that …
SimTxtSeg: Weakly-Supervised Medical Image Segmentation with Simple Text Cues
School of Computer Science and Engineering, Southeast University（东南大学计算机科学与工程学院）；Key Laboratory of New Generation Artificial Intelligence Technology and Its Interdisciplinary Applications, Ministry of Education, China（教育部新一代人工智能技术及交叉应用重点实验室）；Nanjing University of Science and Technology（南京理工大学）；Northwestern Polytechnical University（西北工业大学）
The University of Adelaide（阿德莱德大学）；Northwestern Polytechnical University（西北工业大学）
Self-supervised learning (SSL) opens up huge opportunities for medical image analysis that is well known for its lack of annotations. However, aggregating massive (unlabeled) 3D medical images like computerized tomography (CT) remains challenging due to its high imaging cost and privacy restrictions. In this paper, we advocate bringing a wealth of 2D images like chest X-rays as compensation for the lack of 3D data, aiming to build a universal medical self-supervised representation learning framework, called UniMiSS. The following problem is how to break the dimensionality barrier, \ie, making …
University of Haifa（海法大学）；IBM Research（IBM研究院）；Bar-Ilan University（巴伊兰大学）
This study presents a novel deep learning architecture for multi-class classification and localization of abnormalities in medical imaging illustrated through experiments on mammograms. The proposed network combines two learning branches. One branch is for region classification with a newly added normal-region class. Second branch is region detection branch for ranking regions relative to one another. Our method enables detection of abnormalities at full mammogram resolution for both weakly and semi-supervised settings. A novel objective function allows for the incorporation of local annotatio…
Hangzhou Dianzi University（杭州电子科技大学）；Zhejiang University of Science and Technology（浙江科技学院）
Weakly-supervised learning has become a popular technology in recent years. In this paper, we propose a novel medical image classification algorithm, called Weakly-Supervised Generative Adversarial Networks (WSGAN), which only uses a small number of real images without labels to generate fake images or mask images to enlarge the sample size of the training set. First, we combine with MixMatch to generate pseudo labels for the fake images and unlabeled images to do the classification. Second, contrastive learning and self-attention mechanism are introduced into the proposed problem to enhance t…
Siemens Healthineers（西门子医疗）；University of Michigan（密歇根大学）
Building accurate and robust artificial intelligence systems for medical image assessment requires not only the research and design of advanced deep learning models but also the creation of large and curated sets of annotated training examples. Constructing such datasets, however, is often very costly -- due to the complex nature of annotation tasks and the high level of expertise required for the interpretation of medical images (e.g., expert radiologists). To counter this limitation, we propose a method for self-supervised learning of rich image features based on contrastive learning and onl…
Moore Threads（摩尔线程）；University of Science and Technology of China（中国科学技术大学）
Although deep learning (DL) shows powerful potential in cell segmentation tasks, it suffers from poor generalization as DL-based methods originally simplified cell segmentation in detecting cell membrane boundary, lacking prominent cellular structures to position overall differentiating. Moreover, the scarcity of annotated cell images limits the performance of DL models. Segmentation limitations of a single category of cell make massive practice difficult, much less, with varied modalities. In this paper, we introduce a novel semi-supervised cell segmentation method called Multi-Microscopic-vi…
The performance of existing point cloud-based 3D object detection methods heavily relies on large-scale high-quality 3D annotations. However, such annotations are often tedious and expensive to collect. Semi-supervised learning is a good alternative to mitigate the data annotation issue, but has remained largely unexplored in 3D object detection. Inspired by the recent success of self-ensembling technique in semi-supervised image classification task, we propose SESS, a self-ensembling semi-supervised 3D object detection framework. Specifically, we design a thorough perturbation scheme to enhan…
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…
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…
Nanyang Technological University（南洋理工大学）；Agency for Science, Technology and Research（新加坡科技研究局）；National University of Singapore（新加坡国立大学）；Shanghai University（上海大学）；University of Science and Technology of China（中国科学技术大学）；Chinese Academy of Sciences（中国科学院）
While deep learning methods hitherto have achieved considerable success in medical image segmentation, they are still hampered by two limitations: (i) reliance on large-scale well-labeled datasets, which are difficult to curate due to the expert-driven and time-consuming nature of pixel-level annotations in clinical practices, and (ii) failure to generalize from one domain to another, especially when the target domain is a different modality with severe domain shifts. Recent unsupervised domain adaptation~(UDA) techniques leverage abundant labeled source data together with unlabeled target dat…
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-…
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）
