Deep learning based image segmentation has achieved the state-of-the-art performance in many medical applications such as lesion quantification, organ detection, etc. However, most of the methods rely on supervised learning, which require a large set of high-quality labeled data. Data annotation is generally an extremely time-consuming process. To address this problem, we propose a generic semi-supervised learning framework for image segmentation based on a deep convolutional neural network (DCNN). An encoder-decoder based DCNN is initially trained using a few annotated training samples. This initially trained model is then copied into sub-models and improved iteratively using random subsets of unlabeled data with pseudo labels generated from models trained in the previous iteration. The number of sub-models is gradually decreased to one in the final iteration. We evaluate the proposed method on a public grand-challenge dataset for skin lesion segmentation. Our method is able to significantly improve beyond fully supervised model learning by incorporating unlabeled data.
In this paper, we propose a novel medical image segmentation using iterative deep learning framework. We have combined an iterative learning approach and an encoder-decoder network to improve segmentation results, which enables to precisely localize the regions of interest (ROIs) including complex shapes or detailed textures of medical images in an iterative manner. The proposed iterative deep convolutional encoder-decoder network consists of two main paths: convolutional encoder path and convolutional decoder path with iterative learning. Experimental results show that the proposed iterative …
We propose a novel technique to incorporate attention within convolutional neural networks using feature maps generated by a separate convolutional autoencoder. Our attention architecture is well suited for incorporation with deep convolutional networks. We evaluate our model on benchmark segmentation datasets in skin cancer segmentation and lung lesion segmentation. Results show highly competitive performance when compared with U-Net and it's residual variant.
In recent years, deep learning has rapidly become a method of choice for the segmentation of medical images. Deep Neural Network (DNN) architectures such as UNet have achieved state-of-the-art results on many medical datasets. To further improve the performance in the segmentation task, we develop an ensemble system which combines various deep learning architectures. We propose a two-layer ensemble of deep learning models for the segmentation of medical images. The prediction for each training image pixel made by each model in the first layer is used as the augmented data of the training image…
Convolutional Neural Networks (CNNs) have achieved promising results in medical image segmentation. However, CNNs require lots of training data and are incapable of handling pose and deformation of objects. Furthermore, their pooling layers tend to discard important information such as positions as well as CNNs are sensitive to rotation and affine transformation. Capsule network is a recent new architecture that has achieved better robustness in part-whole representation learning by replacing pooling layers with dynamic routing and convolutional strides, which has shown potential results on po…
Deep learning (DL) based semantic segmentation methods have been providing state-of-the-art performance in the last few years. More specifically, these techniques have been successfully applied to medical image classification, segmentation, and detection tasks. One deep learning technique, U-Net, has become one of the most popular for these applications. In this paper, we propose a Recurrent Convolutional Neural Network (RCNN) based on U-Net as well as a Recurrent Residual Convolutional Neural Network (RRCNN) based on U-Net models, which are named RU-Net and R2U-Net respectively. The proposed …
University of Michigan（密歇根大学）；Indian Institute of Technology - Bombay（印度理工学院孟买分校）
For medical image segmentation, most fully convolutional networks (FCNs) need strong supervision through a large sample of high-quality dense segmentations, which is taxing in terms of costs, time and logistics involved. This burden of annotation can be alleviated by exploiting weak inexpensive annotations such as bounding boxes and anatomical landmarks. However, it is very difficult to \textit{a priori} estimate the optimal balance between the number of annotations needed for each supervision type that leads to maximum performance with the least annotation cost. To optimize this cost-performa…
A variety of deep neural networks have been applied in medical image segmentation and achieve good performance. Unlike natural images, medical images of the same imaging modality are characterized by the same pattern, which indicates that same normal organs or tissues locate at similar positions in the images. Thus, in this paper we try to incorporate the prior knowledge of medical images into the structure of neural networks such that the prior knowledge can be utilized for accurate segmentation. Based on this idea, we propose a novel deep network called knowledge-based fully convolutional ne…
National Institute of Technology Karnataka（卡纳塔克邦国家技术研究所）
Computer-aided medical image analysis plays a significant role in assisting medical practitioners for expert clinical diagnosis and deciding the optimal treatment plan. At present, convolutional neural networks (CNN) are the preferred choice for medical image analysis. In addition, with the rapid advancements in three-dimensional (3D) imaging systems and the availability of excellent hardware and software support to process large volumes of data, 3D deep learning methods are gaining popularity in medical image analysis. Here, we present an extensive review of the recently evolved 3D deep learn…
Johns Hopkins University（约翰斯·霍普金斯大学）；Rutgers, The State University of New Jersey（罗格斯新泽西州立大学）
Over the past decade, Deep Convolutional Neural Networks have been widely adopted for medical image segmentation and shown to achieve adequate performance. However, due to the inherent inductive biases present in the convolutional architectures, they lack understanding of long-range dependencies in the image. Recently proposed Transformer-based architectures that leverage self-attention mechanism encode long-range dependencies and learn representations that are highly expressive. This motivates us to explore Transformer-based solutions and study the feasibility of using Transformer-based netwo…
Dual-Teacher Ensemble Models with Double-Copy-Paste for 3D Semi-Supervised Medical Image Segmentation
State Key Laboratory for Novel Software Technology, Nanjing University（南京大学计算机软件新技术国家重点实验室）；National Institute of Healthcare Data Science, Nanjing University（南京大学国家医疗数据科学研究院）；Key Laboratory of New Generation Artificial Intelligence Technology and Its Interdisciplinary Applications(Ministry of Education), Southeast University（东南大学新一代人工智能技术及交叉应用教育部重点实验室）；School of Data and Computer Science, Shandong Women’s University（山东女子学院数据与计算机科学学院）
In this article, we look into some essential aspects of convolutional neural networks (CNNs) with the focus on medical image segmentation. First, we discuss the CNN architecture, thereby highlighting the spatial origin of the data, voxel-wise classification and the receptive field. Second, we discuss the sampling of input-output pairs, thereby highlighting the interaction between voxel-wise classification, patch size and the receptive field. Finally, we give a historical overview of crucial changes to CNN architectures for classification and segmentation, giving insights in the relation betwee…
Department of Statistics and Applied Probability National University of Singapore（新加坡国立大学统计与应用概率系）
In recent years, convolutional neural networks (CNNs) have revolutionized medical image analysis. One of the most well-known CNN architectures in semantic segmentation is the U-net, which has achieved much success in several medical image segmentation applications. Also more recently, with the rise of autoML ad advancements in neural architecture search (NAS), methods like NAS-Unet have been proposed for NAS in medical image segmentation. In this paper, with inspiration from LadderNet, U-Net, autoML and NAS, we propose an ensemble deep neural network with an underlying U-Net framework consisti…
Institute of Computer Engineering, Technische Universität Wien (TU Wien)（维也纳工业大学（TU Wien）计算机工程研究所）；Division of Engineering, New York University Abu Dhabi（纽约大学阿布扎比分校工程系）
Reliable classification and detection of certain medical conditions, in images, with state-of-the-art semantic segmentation networks, require vast amounts of pixel-wise annotation. However, the public availability of such datasets is minimal. Therefore, semantic segmentation with image-level labels presents a promising alternative to this problem. Nevertheless, very few works have focused on evaluating this technique and its applicability to the medical sector. Due to their complexity and the small number of training examples in medical datasets, classifier-based weakly supervised networks lik…
Segmentation is a critical step in medical image analysis. Fully Convolutional Networks (FCNs) have emerged as powerful segmentation models achieving state-of-the-art results in various medical image datasets. Network architectures are usually designed manually for a specific segmentation task so applying them to other medical datasets requires extensive experience and time. Moreover, the segmentation requires handling large volumetric data that results in big and complex architectures. Recently, methods that automatically design neural networks for medical image segmentation have been present…
Nagoya University（名古屋大学）；Aichi Cancer Center Hospital（爱知县癌症中心医院）
One of the most common tasks in medical imaging is semantic segmentation. Achieving this segmentation automatically has been an active area of research, but the task has been proven very challenging due to the large variation of anatomy across different patients. However, recent advances in deep learning have made it possible to significantly improve the performance of image recognition and semantic segmentation methods in the field of computer vision. Due to the data driven approaches of hierarchical feature learning in deep learning frameworks, these advances can be translated to medical ima…
University of Bucharest（布加勒斯特大学）；“Carol Davila” University of Medicine and Pharmacy（卡罗尔·达维拉医药大学）
Medical image segmentation is an actively studied task in medical imaging, where the precision of the annotations is of utter importance towards accurate diagnosis and treatment. In recent years, the task has been approached with various deep learning systems, among the most popular models being U-Net. In this work, we propose a novel strategy to generate ensembles of different architectures for medical image segmentation, by leveraging the diversity (decorrelation) of the models forming the ensemble. More specifically, we utilize the Dice score among model pairs to estimate the correlation be…
Accurate and fast segmentation of medical images is clinically essential, yet current research methods include convolutional neural networks with fast inference speed but difficulty in learning image contextual features, and transformer with good performance but high hardware requirements. In this paper, we present a Patch Network (PNet) that incorporates the Swin Transformer notion into a convolutional neural network, allowing it to gather richer contextual information while achieving the balance of speed and accuracy. We test our PNet on Polyp(CVC-ClinicDB and ETIS- LaribPolypDB), Skin(ISIC-…
We propose a novel transformer model, capable of segmenting medical images of varying modalities. Challenges posed by the fine grained nature of medical image analysis mean that the adaptation of the transformer for their analysis is still at nascent stages. The overwhelming success of the UNet lay in its ability to appreciate the fine-grained nature of the segmentation task, an ability which existing transformer based models do not currently posses. To address this shortcoming, we propose The Fully Convolutional Transformer (FCT), which builds on the proven ability of Convolutional Neural Net…
The shapes and morphology of the organs and tissues are important prior knowledge in medical imaging recognition and segmentation. The morphological operation is a well-known method for morphological feature extraction. As the morphological operation is performed well in hand-crafted image segmentation techniques, it is also promising to design an approach to approximate morphological operation in the convolutional networks. However, using the traditional convolutional neural network as a black-box is usually hard to specify the morphological operation action. Here, we introduced a 3D morpholo…
CiT-Net: Convolutional Neural Networks Hand in Hand with Vision Transformers for Medical Image Segmentation
Shaanxi University of Science and Technology（陕西科技大学）；Xi’an Jiaotong University（西安交通大学）；Northwestern Polytechnical University（西北工业大学）；Brunel University London（伦敦布鲁内尔大学）
Boston Children’s Hospital（波士顿儿童医院）；Harvard Medical School（哈佛医学院）
Transfer learning is widely used for training machine learning models. Here, we study the role of transfer learning for training fully convolutional networks (FCNs) for medical image segmentation. Our experiments show that although transfer learning reduces the training time on the target task, the improvement in segmentation accuracy is highly task/data-dependent. Larger improvements in accuracy are observed when the segmentation task is more challenging and the target training data is smaller. We observe that convolutional filters of an FCN change little during training for medical image seg…
X-Ray image enhancement, along with many other medical image processing applications, requires the segmentation of images into bone, soft tissue, and open beam regions. We apply a machine learning approach to this problem, presenting an end-to-end solution which results in robust and efficient inference. Since medical institutions frequently do not have the resources to process and label the large quantity of X-Ray images usually needed for neural network training, we design an end-to-end solution for small datasets, while achieving state-of-the-art results. Our implementation produces an over…
TEC-Net: Vision Transformer Embrace Convolutional Neural Networks for Medical Image Segmentation
Shaanxi University of Science and Technology（陕西科技大学）；Xi’an Jiaotong University（西安交通大学）；Griffith University（格里菲斯大学）；Northwestern Polytechnical University（西北工业大学）；Brunel University London（伦敦布鲁内尔大学）
SimulaMet；UiT The Arctic University of Norway（挪威北极大学）；Oslo Metropolitan University（奥斯陆城市大学）
Semantic image segmentation is the process of labeling each pixel of an image with its corresponding class. An encoder-decoder based approach, like U-Net and its variants, is a popular strategy for solving medical image segmentation tasks. To improve the performance of U-Net on various segmentation tasks, we propose a novel architecture called DoubleU-Net, which is a combination of two U-Net architectures stacked on top of each other. The first U-Net uses a pre-trained VGG-19 as the encoder, which has already learned features from ImageNet and can be transferred to another task easily. To capt…
Detection of colon polyps has become a trending topic in the intersecting fields of machine learning and gastrointestinal endoscopy. The focus has mainly been on per-frame classification. More recently, polyp segmentation has gained attention in the medical community. Segmentation has the advantage of being more accurate than per-frame classification or object detection as it can show the affected area in greater detail. For our contribution to the EndoCV 2021 segmentation challenge, we propose two separate approaches. First, a segmentation model named TriUNet composed of three separate UNet m…
The increased availability and usage of modern medical imaging induced a strong need for automatic medical image segmentation. Still, current image segmentation platforms do not provide the required functionalities for plain setup of medical image segmentation pipelines. Already implemented pipelines are commonly standalone software, optimized on a specific public data set. Therefore, this paper introduces the open-source Python library MIScnn. The aim of MIScnn is to provide an intuitive API allowing fast building of medical image segmentation pipelines including data I/O, preprocessing, data…
University of Sydney（悉尼大学）；Royal Prince Alfred Hospital（皇家阿尔弗雷德王子医院）；Shanghai Jiao Tong University（上海交通大学）
Medical image analysis using supervised deep learning methods remains problematic because of the reliance of deep learning methods on large amounts of labelled training data. Although medical imaging data repositories continue to expand there has not been a commensurate increase in the amount of annotated data. Hence, we propose a new unsupervised feature learning method that learns feature representations to then differentiate dissimilar medical images using an ensemble of different convolutional neural networks (CNNs) and K-means clustering. It jointly learns feature representations and clus…
University of Engineering and Technology Taxila（塔克西拉工程技术大学）；University of Surrey（萨里大学）；King Abdul Aziz University（阿卜杜勒·阿齐兹国王大学）；King Saud University（沙特国王大学）
The science of solving clinical problems by analyzing images generated in clinical practice is known as medical image analysis. The aim is to extract information in an effective and efficient manner for improved clinical diagnosis. The recent advances in the field of biomedical engineering has made medical image analysis one of the top research and development area. One of the reason for this advancement is the application of machine learning techniques for the analysis of medical images. Deep learning is successfully used as a tool for machine learning, where a neural network is capable of au…
Activation functions play a vital role in the training of Convolutional Neural Networks. For this reason, to develop efficient and performing functions is a crucial problem in the deep learning community. Key to these approaches is to permit a reliable parameter learning, avoiding vanishing gradient problems. The goal of this work is to propose an ensemble of Convolutional Neural Networks trained using several different activation functions. Moreover, a novel activation function is here proposed for the first time. Our aim is to improve the performance of Convolutional Neural Networks in small…
University of Hamburg（汉堡大学）；Knowledge Technology（知识技术学院）
Social robots able to continually learn facial expressions could progressively improve their emotion recognition capability towards people interacting with them. Semi-supervised learning through ensemble predictions is an efficient strategy to leverage the high exposure of unlabelled facial expressions during human-robot interactions. Traditional ensemble-based systems, however, are composed of several independent classifiers leading to a high degree of redundancy, and unnecessary allocation of computational resources. In this paper, we proposed an ensemble based on convolutional networks wher…
An ensemble method that fuses the output decision vectors of multiple feedforward-designed convolutional neural networks (FF-CNNs) to solve the image classification problem is proposed in this work. To enhance the performance of the ensemble system, it is critical to increasing the diversity of FF-CNN models. To achieve this objective, we introduce diversities by adopting three strategies: 1) different parameter settings in convolutional layers, 2) flexible feature subsets fed into the Fully-connected (FC) layers, and 3) multiple image embeddings of the same input source. Furthermore, we parti…
Content-based image retrieval (CBIR) in large medical image archives is a challenging and necessary task. Generally, different feature extraction methods are used to assign expressive and invariant features to each image such that the search for similar images comes down to feature classification and/or matching. The present work introduces a new image retrieval method for medical applications that employs a convolutional neural network (CNN) with recently introduced Radon barcodes. We combine neural codes for global classification with Radon barcodes for the final retrieval. We also examine i…
University of Engineering and Technology Taxila（塔克西拉工程技术大学）；University of Surrey（萨里大学）；Cerebrai Artificial Intelligence（Cerebrai人工智能公司）
With a widespread use of digital imaging data in hospitals, the size of medical image repositories is increasing rapidly. This causes difficulty in managing and querying these large databases leading to the need of content based medical image retrieval (CBMIR) systems. A major challenge in CBMIR systems is the semantic gap that exists between the low level visual information captured by imaging devices and high level semantic information perceived by human. The efficacy of such systems is more crucial in terms of feature representations that can characterize the high-level information complete…
Technische Universität München（慕尼黑工业大学）；Johns Hopkins University（约翰斯·霍普金斯大学）；Klinikum Grosshadern（大哈登医院）；Ludwig-Maximilians-Universität München（慕尼黑大学）
Convolutional Neural Networks (CNNs) have been recently employed to solve problems from both the computer vision and medical image analysis fields. Despite their popularity, most approaches are only able to process 2D images while most medical data used in clinical practice consists of 3D volumes. In this work we propose an approach to 3D image segmentation based on a volumetric, fully convolutional, neural network. Our CNN is trained end-to-end on MRI volumes depicting prostate, and learns to predict segmentation for the whole volume at once. We introduce a novel objective function, that we o…
In this manuscript, we automate the procedure of grading of diabetic retinopathy and macular edema from fundus images using an ensemble of convolutional neural networks. The availability of limited amount of labeled data to perform supervised learning was circumvented by using transfer learning approach. The models in the ensemble were pre-trained on a large dataset comprising natural images and were later fine-tuned with the limited data for the task of choice. For an image, the ensemble of classifiers generate multiple predictions, and a max-voting based approach was utilized to attain the f…
Hand pose estimation from monocular depth images is an important and challenging problem for human-computer interaction. Recently deep convolutional networks (ConvNet) with sophisticated design have been employed to address it, but the improvement over traditional methods is not so apparent. To promote the performance of directly 3D coordinate regression, we propose a tree-structured Region Ensemble Network (REN), which partitions the convolution outputs into regions and integrates the results from multiple regressors on each regions. Compared with multi-model ensemble, our model is completely…
Faculty of Informatics, University of Debrecen（德布勒森大学信息学院）
Skin cancer is a major public health problem, with over 5 million newly diagnosed cases in the United States each year. Melanoma is the deadliest form of skin cancer, responsible for over 9,000 deaths each year. In this paper, we propose an ensemble of deep convolutional neural networks to classify dermoscopy images into three classes. To achieve the highest classification accuracy, we fuse the outputs of the softmax layers of four different neural architectures. For aggregation, we consider the individual accuracies of the networks weighted by the confidence values provided by their final sof…
School of Electronics Engineering and Computer Science Peking University（北京大学电子工程与计算机科学学院）；Institute of Sports Medicine Peking University Third Hospital（北京大学第三医院运动医学研究所）
The process of determining which disease or condition explains a person's symptoms and signs can be very complicated and may be inaccurate in some cases. The general belief is that diagnosing diseases relies on doctors' keen intuition, rich experience and professional equipment. In this work, we employ ideas from recent advances in plantar pressure research and from the powerful capacity of the convolutional neural network for learning representations. Here, we propose a model using convolutional neural network based on plantar pressure for medical diagnosis. Our model learns a network that ma…
School of Computer Science, University of Sydney（悉尼大学计算机科学学院）；Royal Prince Alfred Hospital（皇家阿尔弗雷德王子医院）；Sydney Medical School, University of Sydney（悉尼大学悉尼医学院）；Med-X Research Institute, Shanghai Jiao Tong University（上海交通大学Med-X研究院）
The availability of large-scale annotated image datasets and recent advances in supervised deep learning methods enable the end-to-end derivation of representative image features that can impact a variety of image analysis problems. Such supervised approaches, however, are difficult to implement in the medical domain where large volumes of labelled data are difficult to obtain due to the complexity of manual annotation and inter- and intra-observer variability in label assignment. We propose a new convolutional sparse kernel network (CSKN), which is a hierarchical unsupervised feature learning…
Isfahan University of Technology（伊斯法罕理工大学）；University of Michigan（密歇根大学）
Automating classification and segmentation process of abnormal regions in different body organs has a crucial role in most of medical imaging applications such as funduscopy, endoscopy, and dermoscopy. Detecting multiple abnormalities in each type of images is necessary for better and more accurate diagnosis procedure and medical decisions. In recent years portable medical imaging devices such as capsule endoscopy and digital dermatoscope have been introduced and made the diagnosis procedure easier and more efficient. However, these portable devices have constrained power resources and limited…
International Islamic University Malaysia（马来西亚国际伊斯兰大学）；University of Oklahoma（俄克拉荷马大学）；University of Memphis（孟菲斯大学）
Driver drowsiness detection using videos/images is one of the most essential areas in today's time for driver safety. The development of deep learning techniques, notably Convolutional Neural Networks (CNN), applied in computer vision applications such as drowsiness detection, has shown promising results due to the tremendous increase in technology in the recent few decades. Eyes that are closed or blinking excessively, yawning, nodding, and occlusion are all key aspects of drowsiness. In this work, we have applied four different Convolutional Neural Network (CNN) techniques on the YawDD datas…
Universidade Tecnológica Federal do Paraná (UTFPR)（巴拉那联邦科技大学）；Universidade Federal da Bahia (UFBA)（巴伊亚联邦大学）；University of South Florida (USF)（南佛罗里达大学）
We describe in this paper Hydra, an ensemble of convolutional neural networks (CNN) for geospatial land classification. The idea behind Hydra is to create an initial CNN that is coarsely optimized but provides a good starting pointing for further optimization, which will serve as the Hydra's body. Then, the obtained weights are fine-tuned multiple times with different augmentation techniques, crop styles, and classes weights to form an ensemble of CNNs that represent the Hydra's heads. By doing so, we prompt convergence to different endpoints, which is a desirable aspect for ensembles. With th…
Pneumothorax is a relatively common disease, but in some cases, it may be difficult to find with chest radiography. In this paper, we propose a novel method of detecting pneumothorax in chest radiography. We propose an ensemble model of identical convolutional neural networks (CNN) with three different sizes of radiography images. Conventional methods may not properly characterize lost features while resizing large size images into 256 x 256 or 224 x 224 sizes. Our model is evaluated with ChestX-ray dataset which contains over 100,000 chest radiography images. As a result of the experiment, th…
Uncertainty-Aware Retinal Vessel Segmentation via Ensemble Distillation
University of Ibadan（伊巴迪安大学）；African Institute for Mathematical Sciences（非洲数学科学研究所）；University College London（伦敦大学学院）；Hertie Institute for Brain Health（海德研究所）
Cross modal image syntheses is gaining significant interests for its ability to estimate target images of a different modality from a given set of source images,like estimating MR to MR, MR to CT, CT to PET etc, without the need for an actual acquisition.Though they show potential for applications in radiation therapy planning,image super resolution, atlas construction, image segmentation etc.The synthesis results are not as accurate as the actual acquisition.In this paper,we address the problem of multi modal image synthesis by proposing a fully convolutional deep learning architecture called…
Spanish National Centre for Biotechnology (CNB–CSIC)（西班牙国家生物技术中心（CNB–CSIC））；University of Novi Sad（诺威萨大学）；NTNU（挪威科技大学）；Uppsala University（乌普萨拉大学）；Mathematical Institute of the Serbian Academy of Sciences and Arts（塞尔维亚科学与艺术学院数学研究所）
In this report, we are presenting our automated prediction system for disease classification within dermoscopic images. The proposed solution is based on deep learning, where we employed transfer learning strategy on VGG16 and GoogLeNet architectures. The key feature of our solution is preprocessing based primarily on image augmentation and colour normalization. The solution was evaluated on Task 3: Lesion Diagnosis of the ISIC 2018: Skin Lesion Analysis Towards Melanoma Detection.
The fast growing deep learning technologies have become the main solution of many machine learning problems for medical image analysis. Deep convolution neural networks (CNNs), as one of the most important branch of the deep learning family, have been widely investigated for various computer-aided diagnosis tasks including long-term problems and continuously emerging new problems. Image contour detection is a fundamental but challenging task that has been studied for more than four decades. Recently, we have witnessed the significantly improved performance of contour detection thanks to the de…
Image denoising is an important pre-processing step in medical image analysis. Different algorithms have been proposed in past three decades with varying denoising performances. More recently, having outperformed all conventional methods, deep learning based models have shown a great promise. These methods are however limited for requirement of large training sample size and high computational costs. In this paper we show that using small sample size, denoising autoencoders constructed using convolutional layers can be used for efficient denoising of medical images. Heterogeneous images can be…
