Development of Skip Connection in Deep Neural Networks for Computer Vision and Medical Image Analysis: A Survey
School of Computer Science and Engineering, Hubei Key Laboratory of Intelligent Robot, Wuhan Institute of Technology（计算机科学与工程学院、智能机器人湖北省重点实验室、武汉理工大学）；School of Computer Science, Wuhan University（计算机科学学院、武汉大学）
Deep learning has made significant progress in computer vision, specifically in image classification, object detection, and semantic segmentation. The skip connection has played an essential role in the architecture of deep neural networks,enabling easier optimization through residual learning during the training stage and improving accuracy during testing. Many neural networks have inherited the idea of residual learning with skip connections for various tasks, and it has been the standard choice for designing neural networks. This survey provides a comprehensive summary and outlook on the development of skip connections in deep neural networks. The short history of skip connections is outlined, and the development of residual learning in deep neural networks is surveyed. The effectiveness of skip connections in the training and testing stages is summarized, and future directions for using skip connections in residual learning are discussed. Finally, we summarize seminal papers, source code, models, and datasets that utilize skip connections in computer vision, including image classification, object detection, semantic segmentation, and image reconstruction. We hope this survey could inspire peer researchers in the community to develop further skip connections in various forms and tasks and the theory of residual learning in deep neural networks. The project page can be found at https://github.com/apple1986/Residual_Learning_For_Images
COMSATS University Islamabad（伊斯兰堡COMSATS大学）；Umeå University（于默奥大学）
U-Net is a widely adopted neural network in the domain of medical image segmentation. Despite its quick embracement by the medical imaging community, its performance suffers on complicated datasets. The problem can be ascribed to its simple feature extracting blocks: encoder/decoder, and the semantic gap between encoder and decoder. Variants of U-Net (such as R2U-Net) have been proposed to address the problem of simple feature extracting blocks by making the network deeper, but it does not deal with the semantic gap problem. On the other hand, another variant UNET++ deals with the semantic gap…
Skip and Skip: Segmenting Medical Images with Prompts
Academy for Engineering and Technology, Fudan University（复旦大学工程与技术学院）；Engineering Research Center of AI and Robotics, Ministry of Education, China（教育部人工智能与机器人工程研究中心）；Jilin Provincial Key Laboratory of Intelligence Science（吉林省智能科学重点实验室）
In this paper, we present UNet++, a new, more powerful architecture for medical image segmentation. Our architecture is essentially a deeply-supervised encoder-decoder network where the encoder and decoder sub-networks are connected through a series of nested, dense skip pathways. The re-designed skip pathways aim at reducing the semantic gap between the feature maps of the encoder and decoder sub-networks. We argue that the optimizer would deal with an easier learning task when the feature maps from the decoder and encoder networks are semantically similar. We have evaluated UNet++ in compari…
National University of Sciences and Technology (NUST)（国立科技大学（NUST））
Recent escalation in the field of computer vision underpins a huddle of algorithms with the magnificent potential to unravel the information contained within images. These computer vision algorithms are being practised in medical image analysis and are transfiguring the perception and interpretation of Imaging data. Among these algorithms, Vision Transformers are evolved as one of the most contemporary and dominant architectures that are being used in the field of computer vision. These are immensely utilized by a plenty of researchers to perform new as well as former experiments. Here, in thi…
In medical imaging, there are clinically relevant segmentation tasks where the output mask is a projection to a subset of input image dimensions. In this work, we propose a novel convolutional neural network architecture that can effectively learn to produce a lower-dimensional segmentation mask than the input image. The network restores encoded representation only in a subset of input spatial dimensions and keeps the representation unchanged in the others. The newly proposed projective skip-connections allow linking the encoder and decoder in a UNet-like structure. We evaluated the proposed m…
We provide a high fidelity deep learning algorithm (HyperSeg) for interactive video segmentation tasks using a convolutional network with context-aware skip connections, and compressed, hypercolumn image features combined with a convolutional tessellation procedure. In order to maintain high output fidelity, our model crucially processes and renders all image features in high resolution, without utilizing downsampling or pooling procedures. We maintain this consistent, high grade fidelity efficiently in our model chiefly through two means: (1) We use a statistically-principled tensor decomposi…
Large language models (LLMs) have recently demonstrated their potential in clinical applications, providing valuable medical knowledge and advice. For example, a large dialog LLM like ChatGPT has successfully passed part of the US medical licensing exam. However, LLMs currently have difficulty processing images, making it challenging to interpret information from medical images, which are rich in information that supports clinical decisions. On the other hand, computer-aided diagnosis (CAD) networks for medical images have seen significant success in the medical field by using advanced deep-le…
Beijing Institute of Technology（北京理工大学）；Xuanwu Hospital, Capital Medical University（首都医科大学宣武医院）；National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College（中国医学科学院北京协和医学院肿瘤医院（国家癌症中心/国家肿瘤临床医学研究中心））
Current Computer-Aided Diagnosis (CAD) methods mainly depend on medical images. The clinical information, which usually needs to be considered in practical clinical diagnosis, has not been fully employed in CAD. In this paper, we propose a novel deep learning-based method for fusing Magnetic Resonance Imaging (MRI)/Computed Tomography (CT) images and clinical information for diagnostic tasks. Two paths of neural layers are performed to extract image features and clinical features, respectively, and at the same time clinical features are employed as the attention to guide the extraction of imag…
University of Waterloo（滑铁卢大学）；National Research Council Canada（加拿大国家研究委员会）
Computer vision and machine learning are playing an increasingly important role in computer-assisted diagnosis; however, the application of deep learning to medical imaging has challenges in data availability and data imbalance, and it is especially important that models for medical imaging are built to be trustworthy. Therefore, we propose TRUDLMIA, a trustworthy deep learning framework for medical image analysis, which adopts a modular design, leverages self-supervised pre-training, and utilizes a novel surrogate loss function. Experimental evaluations indicate that models generated from the…
Medical imaging AI systems such as disease classification and segmentation are increasingly inspired and transformed from computer vision based AI systems. Although an array of adversarial training and/or loss function based defense techniques have been developed and proved to be effective in computer vision, defending against adversarial attacks on medical images remains largely an uncharted territory due to the following unique challenges: 1) label scarcity in medical images significantly limits adversarial generalizability of the AI system; 2) vastly similar and dominant fore- and backgroun…
Huazhong University of Science and Technology（华中科技大学）；Guizhou Normal University（贵州师范大学）；Hubei University（湖北大学）
Mapping X-ray images, radiology reports, and other medical data as binary codes in the common space, which can assist clinicians to retrieve pathology-related data from heterogeneous modalities (i.e., hashing-based cross-modal medical data retrieval), provides a new view to promot computeraided diagnosis. Nevertheless, there remains a barrier to boost medical retrieval accuracy: how to reveal the ambiguous semantics of medical data without the distraction of superfluous information. To circumvent this drawback, we propose Deep Supervised Information Bottleneck Hashing (DSIBH), which effectivel…
Vanderbilt University（范德堡大学）；Vanderbilt University Medical Center（范德堡大学医学中心）；Siemens Healthineers（西门子医疗）
Although deep learning prediction models have been successful in the discrimination of different classes, they can often suffer from poor calibration across challenging domains including healthcare. Moreover, the long-tail distribution poses great challenges in deep learning classification problems including clinical disease prediction. There are approaches proposed recently to calibrate deep prediction in computer vision, but there are no studies found to demonstrate how the representative models work in different challenging contexts. In this paper, we bridge the confidence calibration from …
Narrowing the semantic gaps in U-Net with learnable skip connections: The case of medical image segmentation
Northeastern University（东北大学）；Key Laboratory of Intelligent Computing in Medical Image of Ministry of Education（教育部医学图像智能计算重点实验室）；DAMO Academy, Alibaba Group（阿里巴巴达摩院）；University of Alberta（阿尔伯塔大学）
Fueled by recent advances in machine learning, there has been tremendous progress in the field of semantic segmentation for the medical image computing community. However, developed algorithms are often optimized and validated by hand based on one task only. In combination with small datasets, interpreting the generalizability of the results is often difficult. The Medical Segmentation Decathlon challenge addresses this problem, and aims to facilitate development of generalizable 3D semantic segmentation algorithms that require no manual parametrization. Such an algorithm was developed and is …
Massachusetts General Hospital（麻省总医院）；Zhejiang University（浙江大学）；University of Michigan（密歇根大学）；Beijing Institute of Technology（北京理工大学）
Tissue characterization has long been an important component of Computer Aided Diagnosis (CAD) systems for automatic lesion detection and further clinical planning. Motivated by the superior performance of deep learning methods on various computer vision problems, there has been increasing work applying deep learning to medical image analysis. However, the development of a robust and reliable deep learning model for computer-aided diagnosis is still highly challenging due to the combination of the high heterogeneity in the medical images and the relative lack of training samples. Specifically,…
Residual network (ResNet) and densely connected network (DenseNet) have significantly improved the training efficiency and performance of deep convolutional neural networks (DCNNs) mainly for object classification tasks. In this paper, we propose an efficient network architecture by considering advantages of both networks. The proposed method is integrated into an encoder-decoder DCNN model for medical image segmentation. Our method adds additional skip connections compared to ResNet but uses significantly fewer model parameters than DenseNet. We evaluate the proposed method on a public datase…
The George Washington University Medical Center（乔治华盛顿大学医学中心）
Recently, deep learning has become much more popular in computer vision area. The Convolution Neural Network (CNN) has brought a breakthrough in images segmentation areas, especially, for medical images. In this regard, U-Net is the predominant approach to medical image segmentation task. The U-Net not only performs well in segmenting multimodal medical images generally, but also in some tough cases of them. However, we found that the classical U-Net architecture has limitation in several aspects. Therefore, we applied modifications: 1) designed efficient CNN architecture to replace encoder an…
With substantial public concerns on potential cancer risks and health hazards caused by the accumulated radiation exposure in medical imaging, reducing radiation dose in X-ray based medical imaging such as Computed Tomography Perfusion (CTP) has raised significant research interests. In this paper, we embrace the deep Convolutional Neural Networks (CNN) based approaches and introduce Smoothed Dense-Convolution Neural Network (SDCNet) to recover high-dose quality CTP images from low-dose ones. SDCNet is composed of sub-network blocks cascaded by skip-connections to infer the noise (differential…
COVID-19 Computer-aided Diagnosis through AI-assisted CT Imaging Analysis: Deploying a Medical AI System
University of Ioannina（约阿尼纳大学）；AIandMe SMPC（AIandMe SMPC公司）；National Technical University of Athens（雅典国立技术大学）；Queen Mary University of London（伦敦大学玛丽皇后学院）
As an essential prerequisite for developing a medical intelligent assistant system, medical image segmentation has received extensive research and concentration from the neural network community. A series of UNet-like networks with encoder-decoder architecture has achieved extraordinary success, in which UNet2+ and UNet3+ redesign skip connections, respectively proposing dense skip connection and full-scale skip connection and dramatically improving compared with UNet in medical image segmentation. However, UNet2+ lacks sufficient information explored from the full scale, which will affect the…
Federated Distillation for Medical Image Classification: Towards Trustworthy Computer-Aided Diagnosis
School of Information and Communication Engineering, Hainan University（海南大学信息与通信工程学院）；College of Mathematical Sciences, BoHai University（渤海大学数学科学学院）；Australian AI Institute, University of Technology Sydney（悉尼科技大学澳大利亚人工智能研究所）；School of Electronic Science and Technology, Hainan University（海南大学电子科学与技术学院）
Transformer, a model comprising attention-based encoder-decoder architecture, have gained prevalence in the field of natural language processing (NLP) and recently influenced the computer vision (CV) space. The similarities between computer vision and medical imaging, reviewed the question among researchers if the impact of transformers on computer vision be translated to medical imaging? In this paper, we attempt to provide a comprehensive and recent review on the application of transformers in medical imaging by; describing the transformer model comparing it with a diversity of convolutional…
In this paper we broadly consider techniques which utilize projections on rays for data collection, with particular emphasis on optical techniques. We formulate a variety of imaging techniques as either special cases or extensions of tomographic reconstruction. We then consider how the techniques must be extended to describe objects containing occlusion, as with a self-occluding opaque object. We formulate the reconstruction problem as a regularized nonlinear optimization problem to simultaneously solve for object brightness and attenuation, where the attenuation can become infinite. We demons…
Palo Alto High School（帕洛阿尔托高中）；Lunit Inc.（Lunit 公司）；KAIST（韩国科学技术院）；Adobe Research（Adobe 研究院）；Stanford University（斯坦福大学）
When the trained physician interprets medical images, they understand the clinical importance of visual features. By applying cognitive attention, they apply greater focus onto clinically relevant regions while disregarding unnecessary features. The use of computer vision to automate the classification of medical images is widely studied. However, the standard convolutional neural network (CNN) does not necessarily employ subconscious feature relevancy evaluation techniques similar to the trained medical specialist and evaluates features more generally. Self-attention mechanisms enable CNNs to…
Recent works on Multimodal 3D Computer-aided diagnosis have demonstrated that obtaining a competitive automatic diagnosis model when a 3D convolution neural network (CNN) brings more parameters and medical images are scarce remains nontrivial and challenging. Considering both consistencies of regions of interest in multimodal images and diagnostic accuracy, we propose a novel mutual attention-based hybrid dimensional network for MultiModal 3D medical image classification (MMNet). The hybrid dimensional network integrates 2D CNN with 3D convolution modules to generate deeper and more informativ…
The University of Hong Kong（香港大学）；ShanghaiTech University（上海科技大学）；Shanghai Engineering Research Center of Intelligent Vision and Imaging（上海智能视觉与成像工程技术研究中心）
Recent advances in self-supervised learning (SSL) in computer vision are primarily comparative, whose goal is to preserve invariant and discriminative semantics in latent representations by comparing siamese image views. However, the preserved high-level semantics do not contain enough local information, which is vital in medical image analysis (e.g., image-based diagnosis and tumor segmentation). To mitigate the locality problem of comparative SSL, we propose to incorporate the task of pixel restoration for explicitly encoding more pixel-level information into high-level semantics. We also ad…
Deep neural networks (DNN) have achieved unprecedented performance in computer-vision tasks almost ubiquitously in business, technology, and science. While substantial efforts are made to engineer highly accurate architectures and provide usable model explanations, most state-of-the-art approaches are first designed for natural vision and then translated to the medical domain. This dissertation seeks to address this gap by proposing novel architectures that integrate the domain-specific constraints of medical imaging into the DNN model and explanation design.
Indeed, these are exciting times. We are in the heart of a digital renaissance. Automation and computer technology allow engineers and scientists to fabricate processes that amalgamate quality of life. We anticipate much growth in medical image interpretation and understanding, due to the influx of computer technologies. This work should serve as a guide to introduce the reader to core themes in theoretical computer science, as well as imaging applications for understanding vocal-fold vibrations. In this work, we motivate the use of automation, review some mathematical models of computation. W…
Traditional breast cancer image classification methods require manual extraction of features from medical images, which not only require professional medical knowledge, but also have problems such as time-consuming and labor-intensive and difficulty in extracting high-quality features. Therefore, the paper proposes a computer-based feature fusion Convolutional neural network breast cancer image classification and detection method. The paper pre-trains two convolutional neural networks with different structures, and then uses the convolutional neural network to automatically extract the charact…
Shanghai Jiao Tong University（上海交通大学）；University of Georgia（佐治亚大学）；ShanghaiTech University（上海科技大学）；Shanghai United Imaging Intelligence Co., Ltd.（上海联影智能医疗科技有限公司）
When deep neural network (DNN) was first introduced to the medical image analysis community, researchers were impressed by its performance. However, it is evident now that a large number of manually labeled data is often a must to train a properly functioning DNN. This demand for supervision data and labels is a major bottleneck in current medical image analysis, since collecting a large number of annotations from experienced experts can be time-consuming and expensive. In this paper, we demonstrate that the eye movement of radiologists reading medical images can be a new form of supervision t…
Institute of Parallel and Distributed Systems, University of Stuttgart（斯图加特大学并行与分布式系统研究所）
Deformable image registration is a fundamental task in medical imaging. Due to the large computational complexity of deformable registration of volumetric images, conventional iterative methods usually face the tradeoff between the registration accuracy and the computation time in practice. In order to boost the registration performance in both accuracy and runtime, we propose a fast convolutional neural network. Specially, to efficiently utilize the memory resources and enlarge the model capacity, we adopt additive forwarding instead of channel concatenation and deepen the network in each enc…
Mining Gaze for Contrastive Learning toward Computer-Assisted Diagnosis
School of Biomedical Engineering, Shanghai Jiao Tong University（上海交通大学生物医学工程学院）；Shanghai United Imaging Intelligence Co., Ltd.（上海联影智能医疗科技有限公司）；Shanghai Clinical Research and Trial Center（上海临床研究与试验中心）
Ghent University Global Campus（根特大学全球校区）；Ghent University（根特大学）
Glaucoma is a major eye disease, leading to vision loss in the absence of proper medical treatment. Current diagnosis of glaucoma is performed by ophthalmologists who are often analyzing several types of medical images generated by different types of medical equipment. Capturing and analyzing these medical images is labor-intensive and expensive. In this paper, we present a novel computational approach towards glaucoma diagnosis and localization, only making use of eye fundus images that are analyzed by state-of-the-art deep learning techniques. Specifically, our approach leverages Convolution…
Medical Image Analysis is currently experiencing a paradigm shift due to Deep Learning. This technology has recently attracted so much interest of the Medical Imaging community that it led to a specialized conference in `Medical Imaging with Deep Learning' in the year 2018. This article surveys the recent developments in this direction, and provides a critical review of the related major aspects. We organize the reviewed literature according to the underlying Pattern Recognition tasks, and further sub-categorize it following a taxonomy based on human anatomy. This article does not assume prior…
CENet: Context Enhancement Network for Medical Image Segmentation
Faculty of Informatics and Data Science, University of Regensburg（信息学院与数据科学学院，雷根施塔特大学）；Department of Industrial and Systems Engineering, Tarbiat Modares University（工业与系统工程系，塔里克特莫达res大学）；Department of Radiology & Department of Medicine, University of British Columbia（放射科与医学系，不列颠哥伦比亚大学）；Fraunhofer Institute for Digital Medicine MEVIS（数字医学研究所MEVIS）
Interactive Medical-SAM2 GUI: A Napari-based semi-automatic annotation tool for medical images
Department of Biomechatronic Engineering, Sungkyunkwan University（生物机电工程系，全州大学）；Department of Neurosurgery, Seoul National University Hospital, Seoul National University College of Medicine（神经外科，首尔国立大学医院，首尔国立大学医学院）
Chinese Academy of Sciences（中国科学院）；Johns Hopkins Medical Institutes（约翰斯·霍普金斯医学院）；Vanderbilt University（范德堡大学）；University of Science and Technology of China（中国科学技术大学）
Transformer, the latest technological advance of deep learning, has gained prevalence in natural language processing or computer vision. Since medical imaging bear some resemblance to computer vision, it is natural to inquire about the status quo of Transformers in medical imaging and ask the question: can the Transformer models transform medical imaging? In this paper, we attempt to make a response to the inquiry. After a brief introduction of the fundamentals of Transformers, especially in comparison with convolutional neural networks (CNNs), and highlighting key defining properties that cha…
HySparK: Hybrid Sparse Masking for Large Scale Medical Image Pre-Training
Suzhou Institute for Advanced Research, University of Science and Technology of China（中国科学技术大学苏州高等研究院）；Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS（中国科学院计算技术研究所智能信息处理重点实验室）
Cloud computing offers the potential to help scientists to process massive number of computing resources often required in machine learning application such as computer vision problems. This proposal would like to show that which benefits can be obtained from cloud in order to help medical image analysis users (including scientists, clinicians, and research institutes). As security and privacy of algorithms are important for most of algorithms inventors, these algorithms can be hidden in a cloud to allow the users to use the algorithms as a package without any access to see/change their inside…
University of Central Florida（中佛罗里达大学）；National Institutes of Health（美国国立卫生研究院）；Soochow University（苏州大学）
This study introduced a novel system, called Gaze2Segment, integrating biological and computer vision techniques to support radiologists' reading experience with an automatic image segmentation task. During diagnostic assessment of lung CT scans, the radiologists' gaze information were used to create a visual attention map. This map was then combined with a computer-derived saliency map, extracted from the gray-scale CT images. The visual attention map was used as an input for indicating roughly the location of a object of interest. With computer-derived saliency information, on the other hand…
Deep learning has made a breakthrough in medical image segmentation in recent years due to its ability to extract high-level features without the need for prior knowledge. In this context, U-Net is one of the most advanced medical image segmentation models, with promising results in mammography. Despite its excellent overall performance in segmenting multimodal medical images, the traditional U-Net structure appears to be inadequate in various ways. There are certain U-Net design modifications, such as MultiResUNet, Connected-UNets, and AU-Net, that have improved overall performance in areas w…
College of Computer Science and Technology, Zhejiang University（浙江大学计算机科学与技术学院）；Sir Run Run Shaw Hospital（邵逸夫医院）；College of Information Science and Engineering, Ritsumeikan University（立命馆大学信息科学与工程学院）；Research Center for Healthcare Data Science, Zhejiang Lab（之江实验室医疗数据科学研究中心）
Recently, a growing interest has been seen in deep learning-based semantic segmentation. UNet, which is one of deep learning networks with an encoder-decoder architecture, is widely used in medical image segmentation. Combining multi-scale features is one of important factors for accurate segmentation. UNet++ was developed as a modified Unet by designing an architecture with nested and dense skip connections. However, it does not explore sufficient information from full scales and there is still a large room for improvement. In this paper, we propose a novel UNet 3+, which takes advantage of f…
Although convolutional neural networks (CNNs) are promoting the development of medical image semantic segmentation, the standard model still has some shortcomings. First, the feature mapping from the encoder and decoder sub-networks in the skip connection operation has a large semantic difference. Second, the remote feature dependence is not effectively modeled. Third, the global context information of different scales is ignored. In this paper, we try to eliminate semantic ambiguity in skip connection operations by adding attention gates (AGs), and use attention mechanisms to combine local fe…
University of Sydney（悉尼大学）；University of New South Wales（新南威尔士大学）；University of Pittsburg（匹兹堡大学）
U-Net, as an encoder-decoder architecture with forward skip connections, has achieved promising results in various medical image analysis tasks. Many recent approaches have also extended U-Net with more complex building blocks, which typically increase the number of network parameters considerably. Such complexity makes the inference stage highly inefficient for clinical applications. Towards an effective yet economic segmentation network design, in this work, we propose backward skip connections that bring decoded features back to the encoder. Our design can be jointly adopted with forward sk…
The state-of-the-art models for medical image segmentation are variants of U-Net and fully convolutional networks (FCN). Despite their success, these models have two limitations: (1) their optimal depth is apriori unknown, requiring extensive architecture search or inefficient ensemble of models of varying depths; and (2) their skip connections impose an unnecessarily restrictive fusion scheme, forcing aggregation only at the same-scale feature maps of the encoder and decoder sub-networks. To overcome these two limitations, we propose UNet++, a new neural architecture for semantic and instance…
U-Net has been providing state-of-the-art performance in many medical image segmentation problems. Many modifications have been proposed for U-Net, such as attention U-Net, recurrent residual convolutional U-Net (R2-UNet), and U-Net with residual blocks or blocks with dense connections. However, all these modifications have an encoder-decoder structure with skip connections, and the number of paths for information flow is limited. We propose LadderNet in this paper, which can be viewed as a chain of multiple U-Nets. Instead of only one pair of encoder branch and decoder branch in U-Net, a Ladd…
In this paper, we present Crossing Aggregation Network (CAggNet), a novel densely connected semantic segmentation approach for medical image analysis. The crossing aggregation network improves the idea from deep layer aggregation and makes significant innovations in semantic and spatial information fusion. In CAggNet, the simple skip connection structure of general U-Net is replaced by aggregations of multi-level down-sampling and up-sampling layers, which is a new form of nested skip connection. This aggregation architecture enables the network to fuse both coarse and fine features interactiv…
