Deep learning has seen rapid growth in recent years and achieved state-of-the-art performance in a wide range of applications. However, training models typically requires expensive and time-consuming collection of large quantities of labeled data. This is particularly true within the scope of medical imaging analysis (MIA), where data are limited and labels are expensive to be acquired. Thus, label-efficient deep learning methods are developed to make comprehensive use of the labeled data as well as the abundance of unlabeled and weak-labeled data. In this survey, we extensively investigated over 300 recent papers to provide a comprehensive overview of recent progress on label-efficient learning strategies in MIA. We first present the background of label-efficient learning and categorize the approaches into different schemes. Next, we examine the current state-of-the-art methods in detail through each scheme. Specifically, we provide an in-depth investigation, covering not only canonical semi-supervised, self-supervised, and multi-instance learning schemes, but also recently emerged active and annotation-efficient learning strategies. Moreover, as a comprehensive contribution to the field, this survey not only elucidates the commonalities and unique features of the surveyed methods but also presents a detailed analysis of the current challenges in the field and suggests potential avenues for future research.
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Graph clustering, which aims to divide the nodes in the graph into several distinct clusters, is a fundamental and challenging task. In recent years, deep graph clustering methods have been increasingly proposed and achieved promising performance. However, the corresponding survey paper is scarce and it is imminent to make a summary in this field. From this motivation, this paper makes the first comprehensive survey of deep graph clustering. Firstly, the detailed definition of deep graph clustering and the important baseline methods are introduced. Besides, the taxonomy of deep graph clustering methods is proposed based on four different criteria including graph type, network architecture, learning paradigm, and clustering method. In addition, through the careful analysis of the existing works, the challenges and opportunities from five perspectives are summarized. At last, the applications of deep graph clustering in four domains are presented. It is worth mentioning that a collection of state-of-the-art deep graph clustering methods including papers, codes, and datasets is available on GitHub. We hope this work will serve as a quick guide and help researchers to overcome challenges in this vibrant field.
Over the past few years, the rapid development of deep learning technologies for computer vision has greatly promoted the performance of medical image segmentation (MedISeg). However, the recent MedISeg publications usually focus on presentations of the major contributions (e.g., network architectures, training strategies, and loss functions) while unwittingly ignoring some marginal implementation details (also known as "tricks"), leading to a potential problem of the unfair experimental result comparisons. In this paper, we collect a series of MedISeg tricks for different model implementation phases (i.e., pre-training model, data pre-processing, data augmentation, model implementation, model inference, and result post-processing), and experimentally explore the effectiveness of these tricks on the consistent baseline models. Compared to paper-driven surveys that only blandly focus on the advantages and limitation analyses of segmentation models, our work provides a large number of solid experiments and is more technically operable. With the extensive experimental results on both the representative 2D and 3D medical image datasets, we explicitly clarify the effect of these tricks. Moreover, based on the surveyed tricks, we also open-sourced a strong MedISeg repository, where each of its components has the advantage of plug-and-play. We believe that this milestone work not only completes a comprehensive and complementary survey of the state-of-the-art MedISeg approaches, but also offers a practical guide for addressing the future medical image processing challenges including but not limited to small dataset learning, class imbalance learning, multi-modality learning, and domain adaptation. The code has been released at: //github.com/hust-linyi/MedISeg
Clustering is a fundamental machine learning task which has been widely studied in the literature. Classic clustering methods follow the assumption that data are represented as features in a vectorized form through various representation learning techniques. As the data become increasingly complicated and complex, the shallow (traditional) clustering methods can no longer handle the high-dimensional data type. With the huge success of deep learning, especially the deep unsupervised learning, many representation learning techniques with deep architectures have been proposed in the past decade. Recently, the concept of Deep Clustering, i.e., jointly optimizing the representation learning and clustering, has been proposed and hence attracted growing attention in the community. Motivated by the tremendous success of deep learning in clustering, one of the most fundamental machine learning tasks, and the large number of recent advances in this direction, in this paper we conduct a comprehensive survey on deep clustering by proposing a new taxonomy of different state-of-the-art approaches. We summarize the essential components of deep clustering and categorize existing methods by the ways they design interactions between deep representation learning and clustering. Moreover, this survey also provides the popular benchmark datasets, evaluation metrics and open-source implementations to clearly illustrate various experimental settings. Last but not least, we discuss the practical applications of deep clustering and suggest challenging topics deserving further investigations as future directions.
Few-shot learning (FSL) has emerged as an effective learning method and shows great potential. Despite the recent creative works in tackling FSL tasks, learning valid information rapidly from just a few or even zero samples still remains a serious challenge. In this context, we extensively investigated 200+ latest papers on FSL published in the past three years, aiming to present a timely and comprehensive overview of the most recent advances in FSL along with impartial comparisons of the strengths and weaknesses of the existing works. For the sake of avoiding conceptual confusion, we first elaborate and compare a set of similar concepts including few-shot learning, transfer learning, and meta-learning. Furthermore, we propose a novel taxonomy to classify the existing work according to the level of abstraction of knowledge in accordance with the challenges of FSL. To enrich this survey, in each subsection we provide in-depth analysis and insightful discussion about recent advances on these topics. Moreover, taking computer vision as an example, we highlight the important application of FSL, covering various research hotspots. Finally, we conclude the survey with unique insights into the technology evolution trends together with potential future research opportunities in the hope of providing guidance to follow-up research.
Image registration is a critical component in the applications of various medical image analyses. In recent years, there has been a tremendous surge in the development of deep learning (DL)-based medical image registration models. This paper provides a comprehensive review of medical image registration. Firstly, a discussion is provided for supervised registration categories, for example, fully supervised, dual supervised, and weakly supervised registration. Next, similarity-based as well as generative adversarial network (GAN)-based registration are presented as part of unsupervised registration. Deep iterative registration is then described with emphasis on deep similarity-based and reinforcement learning-based registration. Moreover, the application areas of medical image registration are reviewed. This review focuses on monomodal and multimodal registration and associated imaging, for instance, X-ray, CT scan, ultrasound, and MRI. The existing challenges are highlighted in this review, where it is shown that a major challenge is the absence of a training dataset with known transformations. Finally, a discussion is provided on the promising future research areas in the field of DL-based medical image registration.
Following unprecedented success on the natural language tasks, Transformers have been successfully applied to several computer vision problems, achieving state-of-the-art results and prompting researchers to reconsider the supremacy of convolutional neural networks (CNNs) as {de facto} operators. Capitalizing on these advances in computer vision, the medical imaging field has also witnessed growing interest for Transformers that can capture global context compared to CNNs with local receptive fields. Inspired from this transition, in this survey, we attempt to provide a comprehensive review of the applications of Transformers in medical imaging covering various aspects, ranging from recently proposed architectural designs to unsolved issues. Specifically, we survey the use of Transformers in medical image segmentation, detection, classification, reconstruction, synthesis, registration, clinical report generation, and other tasks. In particular, for each of these applications, we develop taxonomy, identify application-specific challenges as well as provide insights to solve them, and highlight recent trends. Further, we provide a critical discussion of the field's current state as a whole, including the identification of key challenges, open problems, and outlining promising future directions. We hope this survey will ignite further interest in the community and provide researchers with an up-to-date reference regarding applications of Transformer models in medical imaging. Finally, to cope with the rapid development in this field, we intend to regularly update the relevant latest papers and their open-source implementations at \url{//github.com/fahadshamshad/awesome-transformers-in-medical-imaging}.
Deep Learning has revolutionized the fields of computer vision, natural language understanding, speech recognition, information retrieval and more. However, with the progressive improvements in deep learning models, their number of parameters, latency, resources required to train, etc. have all have increased significantly. Consequently, it has become important to pay attention to these footprint metrics of a model as well, not just its quality. We present and motivate the problem of efficiency in deep learning, followed by a thorough survey of the five core areas of model efficiency (spanning modeling techniques, infrastructure, and hardware) and the seminal work there. We also present an experiment-based guide along with code, for practitioners to optimize their model training and deployment. We believe this is the first comprehensive survey in the efficient deep learning space that covers the landscape of model efficiency from modeling techniques to hardware support. Our hope is that this survey would provide the reader with the mental model and the necessary understanding of the field to apply generic efficiency techniques to immediately get significant improvements, and also equip them with ideas for further research and experimentation to achieve additional gains.
With the advances of data-driven machine learning research, a wide variety of prediction problems have been tackled. It has become critical to explore how machine learning and specifically deep learning methods can be exploited to analyse healthcare data. A major limitation of existing methods has been the focus on grid-like data; however, the structure of physiological recordings are often irregular and unordered which makes it difficult to conceptualise them as a matrix. As such, graph neural networks have attracted significant attention by exploiting implicit information that resides in a biological system, with interactive nodes connected by edges whose weights can be either temporal associations or anatomical junctions. In this survey, we thoroughly review the different types of graph architectures and their applications in healthcare. We provide an overview of these methods in a systematic manner, organized by their domain of application including functional connectivity, anatomical structure and electrical-based analysis. We also outline the limitations of existing techniques and discuss potential directions for future research.
In recent years a vast amount of visual content has been generated and shared from various fields, such as social media platforms, medical images, and robotics. This abundance of content creation and sharing has introduced new challenges. In particular, searching databases for similar content, i.e. content based image retrieval (CBIR), is a long-established research area, and more efficient and accurate methods are needed for real time retrieval. Artificial intelligence has made progress in CBIR and has significantly facilitated the process of intelligent search. In this survey we organize and review recent CBIR works that are developed based on deep learning algorithms and techniques, including insights and techniques from recent papers. We identify and present the commonly-used databases, benchmarks, and evaluation methods used in the field. We collect common challenges and propose promising future directions. More specifically, we focus on image retrieval with deep learning and organize the state of the art methods according to the types of deep network structure, deep features, feature enhancement methods, and network fine-tuning strategies. Our survey considers a wide variety of recent methods, aiming to promote a global view of the field of category-based CBIR.
Small data challenges have emerged in many learning problems, since the success of deep neural networks often relies on the availability of a huge amount of labeled data that is expensive to collect. To address it, many efforts have been made on training complex models with small data in an unsupervised and semi-supervised fashion. In this paper, we will review the recent progresses on these two major categories of methods. A wide spectrum of small data models will be categorized in a big picture, where we will show how they interplay with each other to motivate explorations of new ideas. We will review the criteria of learning the transformation equivariant, disentangled, self-supervised and semi-supervised representations, which underpin the foundations of recent developments. Many instantiations of unsupervised and semi-supervised generative models have been developed on the basis of these criteria, greatly expanding the territory of existing autoencoders, generative adversarial nets (GANs) and other deep networks by exploring the distribution of unlabeled data for more powerful representations. While we focus on the unsupervised and semi-supervised methods, we will also provide a broader review of other emerging topics, from unsupervised and semi-supervised domain adaptation to the fundamental roles of transformation equivariance and invariance in training a wide spectrum of deep networks. It is impossible for us to write an exclusive encyclopedia to include all related works. Instead, we aim at exploring the main ideas, principles and methods in this area to reveal where we are heading on the journey towards addressing the small data challenges in this big data era.
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