Over the last decade, supervised deep learning on manually annotated big data has been progressing significantly on computer vision tasks. But the application of deep learning in medical image analysis was limited by the scarcity of high-quality annotated medical imaging data. An emerging solution is self-supervised learning (SSL), among which contrastive SSL is the most successful approach to rivalling or outperforming supervised learning. This review investigates several state-of-the-art contrastive SSL algorithms originally on natural images as well as their adaptations for medical images, and concludes by discussing recent advances, current limitations, and future directions in applying contrastive SSL in the medical domain.
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Recently, Self-Supervised Representation Learning (SSRL) has attracted much attention in the field of computer vision, speech, natural language processing (NLP), and recently, with other types of modalities, including time series from sensors. The popularity of self-supervised learning is driven by the fact that traditional models typically require a huge amount of well-annotated data for training. Acquiring annotated data can be a difficult and costly process. Self-supervised methods have been introduced to improve the efficiency of training data through discriminative pre-training of models using supervisory signals that have been freely obtained from the raw data. Unlike existing reviews of SSRL that have pre-dominately focused upon methods in the fields of CV or NLP for a single modality, we aim to provide the first comprehensive review of multimodal self-supervised learning methods for temporal data. To this end, we 1) provide a comprehensive categorization of existing SSRL methods, 2) introduce a generic pipeline by defining the key components of a SSRL framework, 3) compare existing models in terms of their objective function, network architecture and potential applications, and 4) review existing multimodal techniques in each category and various modalities. Finally, we present existing weaknesses and future opportunities. We believe our work develops a perspective on the requirements of SSRL in domains that utilise multimodal and/or temporal data
Neural architecture-based recommender systems have achieved tremendous success in recent years. However, when dealing with highly sparse data, they still fall short of expectation. Self-supervised learning (SSL), as an emerging technique to learn with unlabeled data, recently has drawn considerable attention in many fields. There is also a growing body of research proceeding towards applying SSL to recommendation for mitigating the data sparsity issue. In this survey, a timely and systematical review of the research efforts on self-supervised recommendation (SSR) is presented. Specifically, we propose an exclusive definition of SSR, on top of which we build a comprehensive taxonomy to divide existing SSR methods into four categories: contrastive, generative, predictive, and hybrid. For each category, the narrative unfolds along its concept and formulation, the involved methods, and its pros and cons. Meanwhile, to facilitate the development and evaluation of SSR models, we release an open-source library SELFRec, which incorporates multiple benchmark datasets and evaluation metrics, and has implemented a number of state-of-the-art SSR models for empirical comparison. Finally, we shed light on the limitations in the current research and outline the future research directions.
Transformers have dominated the field of natural language processing, and recently impacted the computer vision area. In the field of medical image analysis, Transformers have also been successfully applied to full-stack clinical applications, including image synthesis/reconstruction, registration, segmentation, detection, and diagnosis. Our paper presents both a position paper and a primer, promoting awareness and application of Transformers in the field of medical image analysis. Specifically, we first overview the core concepts of the attention mechanism built into Transformers and other basic components. Second, we give a new taxonomy of various Transformer architectures tailored for medical image applications and discuss their limitations. Within this review, we investigate key challenges revolving around the use of Transformers in different learning paradigms, improving the model efficiency, and their coupling with other techniques. We hope this review can give a comprehensive picture of Transformers to the readers in the field of medical image analysis.
Deep learning on graphs has attracted significant interests recently. However, most of the works have focused on (semi-) supervised learning, resulting in shortcomings including heavy label reliance, poor generalization, and weak robustness. To address these issues, self-supervised learning (SSL), which extracts informative knowledge through well-designed pretext tasks without relying on manual labels, has become a promising and trending learning paradigm for graph data. Different from SSL on other domains like computer vision and natural language processing, SSL on graphs has an exclusive background, design ideas, and taxonomies. Under the umbrella of graph self-supervised learning, we present a timely and comprehensive review of the existing approaches which employ SSL techniques for graph data. We construct a unified framework that mathematically formalizes the paradigm of graph SSL. According to the objectives of pretext tasks, we divide these approaches into four categories: generation-based, auxiliary property-based, contrast-based, and hybrid approaches. We further conclude the applications of graph SSL across various research fields and summarize the commonly used datasets, evaluation benchmark, performance comparison and open-source codes of graph SSL. Finally, we discuss the remaining challenges and potential future directions in this research field.
Deep supervised learning has achieved great success in the last decade. However, its deficiencies of dependence on manual labels and vulnerability to attacks have driven people to explore a better solution. As an alternative, self-supervised learning attracts many researchers for its soaring performance on representation learning in the last several years. Self-supervised representation learning leverages input data itself as supervision and benefits almost all types of downstream tasks. In this survey, we take a look into new self-supervised learning methods for representation in computer vision, natural language processing, and graph learning. We comprehensively review the existing empirical methods and summarize them into three main categories according to their objectives: generative, contrastive, and generative-contrastive (adversarial). We further investigate related theoretical analysis work to provide deeper thoughts on how self-supervised learning works. Finally, we briefly discuss open problems and future directions for self-supervised learning. An outline slide for the survey is provided.
Deep models trained in supervised mode have achieved remarkable success on a variety of tasks. When labeled samples are limited, self-supervised learning (SSL) is emerging as a new paradigm for making use of large amounts of unlabeled samples. SSL has achieved promising performance on natural language and image learning tasks. Recently, there is a trend to extend such success to graph data using graph neural networks (GNNs). In this survey, we provide a unified review of different ways of training GNNs using SSL. Specifically, we categorize SSL methods into contrastive and predictive models. In either category, we provide a unified framework for methods as well as how these methods differ in each component under the framework. Our unified treatment of SSL methods for GNNs sheds light on the similarities and differences of various methods, setting the stage for developing new methods and algorithms. We also summarize different SSL settings and the corresponding datasets used in each setting. To facilitate methodological development and empirical comparison, we develop a standardized testbed for SSL in GNNs, including implementations of common baseline methods, datasets, and evaluation metrics.
Image segmentation is a key topic in image processing and computer vision with applications such as scene understanding, medical image analysis, robotic perception, video surveillance, augmented reality, and image compression, among many others. Various algorithms for image segmentation have been developed in the literature. Recently, due to the success of deep learning models in a wide range of vision applications, there has been a substantial amount of works aimed at developing image segmentation approaches using deep learning models. In this survey, we provide a comprehensive review of the literature at the time of this writing, covering a broad spectrum of pioneering works for semantic and instance-level segmentation, including fully convolutional pixel-labeling networks, encoder-decoder architectures, multi-scale and pyramid based approaches, recurrent networks, visual attention models, and generative models in adversarial settings. We investigate the similarity, strengths and challenges of these deep learning models, examine the most widely used datasets, report performances, and discuss promising future research directions in this area.
A key requirement for the success of supervised deep learning is a large labeled dataset - a condition that is difficult to meet in medical image analysis. Self-supervised learning (SSL) can help in this regard by providing a strategy to pre-train a neural network with unlabeled data, followed by fine-tuning for a downstream task with limited annotations. Contrastive learning, a particular variant of SSL, is a powerful technique for learning image-level representations. In this work, we propose strategies for extending the contrastive learning framework for segmentation of volumetric medical images in the semi-supervised setting with limited annotations, by leveraging domain-specific and problem-specific cues. Specifically, we propose (1) novel contrasting strategies that leverage structural similarity across volumetric medical images (domain-specific cue) and (2) a local version of the contrastive loss to learn distinctive representations of local regions that are useful for per-pixel segmentation (problem-specific cue). We carry out an extensive evaluation on three Magnetic Resonance Imaging (MRI) datasets. In the limited annotation setting, the proposed method yields substantial improvements compared to other self-supervision and semi-supervised learning techniques. When combined with a simple data augmentation technique, the proposed method reaches within 8% of benchmark performance using only two labeled MRI volumes for training, corresponding to only 4% (for ACDC) of the training data used to train the benchmark.
The rapid advancements in machine learning, graphics processing technologies and availability of medical imaging data has led to a rapid increase in use of machine learning models in the medical domain. This was exacerbated by the rapid advancements in convolutional neural network (CNN) based architectures, which were adopted by the medical imaging community to assist clinicians in disease diagnosis. Since the grand success of AlexNet in 2012, CNNs have been increasingly used in medical image analysis to improve the efficiency of human clinicians. In recent years, three-dimensional (3D) CNNs have been employed for analysis of medical images. In this paper, we trace the history of how the 3D CNN was developed from its machine learning roots, brief mathematical description of 3D CNN and the preprocessing steps required for medical images before feeding them to 3D CNNs. We review the significant research in the field of 3D medical imaging analysis using 3D CNNs (and its variants) in different medical areas such as classification, segmentation, detection, and localization. We conclude by discussing the challenges associated with the use of 3D CNNs in the medical imaging domain (and the use of deep learning models, in general) and possible future trends in the field.
Deep learning has become the most widely used approach for cardiac image segmentation in recent years. In this paper, we provide a review of over 100 cardiac image segmentation papers using deep learning, which covers common imaging modalities including magnetic resonance imaging (MRI), computed tomography (CT), and ultrasound (US) and major anatomical structures of interest (ventricles, atria and vessels). In addition, a summary of publicly available cardiac image datasets and code repositories are included to provide a base for encouraging reproducible research. Finally, we discuss the challenges and limitations with current deep learning-based approaches (scarcity of labels, model generalizability across different domains, interpretability) and suggest potential directions for future research.
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