The encoder-decoder network is widely used to learn deep feature representations from pixel-wise annotations in biomedical image analysis. Under this structure, the performance profoundly relies on the effectiveness of feature extraction achieved by the encoding network. However, few models have considered adapting the attention of the feature extractor even in different kinds of tasks. In this paper, we propose a novel training strategy by adapting the attention of the feature extractor according to different tasks for effective representation learning. Specifically, the framework, named T-Net, consists of an encoding network supervised by task-specific attention maps and a posterior network that takes in the learned features to predict the corresponding results. The attention map is obtained by the transformation from pixel-wise annotations according to the specific task, which is used as the supervision to regularize the feature extractor to focus on different locations of the recognition object. To show the effectiveness of our method, we evaluate T-Net on two different tasks, i.e. , segmentation and localization. Extensive results on three public datasets (BraTS-17, MoNuSeg and IDRiD) have indicated the effectiveness and efficiency of our proposed supervision method, especially over the conventional encoding-decoding network.
This thesis studies how the segmentation results, produced by convolutional neural networks (CNN), is different from each other when applied to small biomedical datasets. We use different architectures, parameters and hyper-parameters, trying to find out the better configurations for our task, and trying to find out underlying regularities. Two working datasets are from biomedical area of research. We conducted a lot of experiments with the two types of networks and the received results have shown the preference of some conditions of experiments and parameters of the networks over the others. …
Department of Brain and Cognitive Engineering, Korea University（高丽大学脑与认知工程系）
Semantic segmentation is essentially important to biomedical image analysis. Many recent works mainly focus on integrating the Fully Convolutional Network (FCN) architecture with sophisticated convolution implementation and deep supervision. In this paper, we propose to decompose the single segmentation task into three subsequent sub-tasks, including (1) pixel-wise image segmentation, (2) prediction of the class labels of the objects within the image, and (3) classification of the scene the image belonging to. While these three sub-tasks are trained to optimize their individual loss functions …
With the advent of advancements in deep learning approaches, such as deep convolution neural network, residual neural network, adversarial network; U-Net architectures are most widely utilized in biomedical image segmentation to address the automation in identification and detection of the target regions or sub-regions. In recent studies, U-Net based approaches have illustrated state-of-the-art performance in different applications for the development of computer-aided diagnosis systems for early diagnosis and treatment of diseases such as brain tumor, lung cancer, alzheimer, breast cancer, et…
Compression is a standard procedure for making convolutional neural networks (CNNs) adhere to some specific computing resource constraints. However, searching for a compressed architecture typically involves a series of time-consuming training/validation experiments to determine a good compromise between network size and performance accuracy. To address this, we propose an image complexity-guided network compression technique for biomedical image segmentation. Given any resource constraints, our framework utilizes data complexity and network architecture to quickly estimate a compressed model …
Concordia Institute for Information Systems Engineering（康考迪亚信息系统工程研究院）；Concordia University（康考迪亚大学）
The U-Net architecture, built upon the fully convolutional network, has proven to be effective in biomedical image segmentation. However, U-Net applies skip connections to merge semantically different low- and high-level convolutional features, resulting in not only blurred feature maps, but also over- and under-segmented target regions. To address these limitations, we propose a simple, yet effective end-to-end depthwise encoder-decoder fully convolutional network architecture, called Sharp U-Net, for binary and multi-class biomedical image segmentation. The key rationale of Sharp U-Net is th…
Cancers are the leading cause of death in many countries. Early diagnosis plays a crucial role in having proper treatment for this debilitating disease. The automated classification of the type of cancer is a challenging task since pathologists must examine a huge number of histopathological images to detect infinitesimal abnormalities. In this study, we propose a novel convolutional neural network (CNN) architecture composed of a Concatenation of multiple Networks, called C-Net, to classify biomedical images. The model incorporates multiple CNNs including Outer, Middle, and Inner. The first t…
Computer Vision and Pattern Recognition Unit, Indian Statistical Institute（印度统计研究所计算机视觉与模式识别部）；Østfold University College（东福尔大学学院）；Oslo Metropolitan University（奥斯陆城市大学）
Methods based on convolutional neural networks have improved the performance of biomedical image segmentation. However, most of these methods cannot efficiently segment objects of variable sizes and train on small and biased datasets, which are common for biomedical use cases. While methods exist that incorporate multi-scale fusion approaches to address the challenges arising with variable sizes, they usually use complex models that are more suitable for general semantic segmentation problems. In this paper, we propose a novel architecture called Multi-Scale Residual Fusion Network (MSRF-Net),…
Indian Institute of Information Technology Allahabad（阿拉哈巴德印度信息技术学院）
Deep learning has brought the most profound contribution towards biomedical image segmentation to automate the process of delineation in medical imaging. To accomplish such task, the models are required to be trained using huge amount of annotated or labelled data that highlights the region of interest with a binary mask. However, efficient generation of the annotations for such huge data requires expert biomedical analysts and extensive manual effort. It is a tedious and expensive task, while also being vulnerable to human error. To address this problem, a self-supervised learning framework, …
Johns Hopkins University（约翰斯·霍普金斯大学）；Rutgers, The State University of New Jersey（罗格斯大学，新泽西州立大学）
Due to its excellent performance, U-Net is the most widely used backbone architecture for biomedical image segmentation in the recent years. However, in our studies, we observe that there is a considerable performance drop in the case of detecting smaller anatomical landmarks with blurred noisy boundaries. We analyze this issue in detail, and address it by proposing an over-complete architecture (Ki-Net) which involves projecting the data onto higher dimensions (in the spatial sense). This network, when augmented with U-Net, results in significant improvements in the case of segmenting small a…
Cornell University（康奈尔大学）；Cornell Tech（康奈尔理工学院）；Massachusetts Institute of Technology（麻省理工学院）；Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）
The convolution operation is a central building block of neural network architectures widely used in computer vision. The size of the convolution kernels determines both the expressiveness of convolutional neural networks (CNN), as well as the number of learnable parameters. Increasing the network capacity to capture rich pixel relationships requires increasing the number of learnable parameters, often leading to overfitting and/or lack of robustness. In this paper, we propose a powerful novel building block, the hyper-convolution, which implicitly represents the convolution kernel as a functi…
Sun Yat-sen University（中山大学）；The University of Hong Kong（香港大学）；Deepwise AI Lab（深智云人工智能实验室）
Recent progress in biomedical image segmentation based on deep convolutional neural networks (CNNs) has drawn much attention. However, its vulnerability towards adversarial samples cannot be overlooked. This paper is the first one that discovers that all the CNN-based state-of-the-art biomedical image segmentation models are sensitive to adversarial perturbations. This limits the deployment of these methods in safety-critical biomedical fields. In this paper, we discover that global spatial dependencies and global contextual information in a biomedical image can be exploited to defend against …
SimulaMet（SimulaMet研究所）；UiT The Arctic University of Norway（挪威北极大学）；University of Oxford（牛津大学）；Oslo Metropolitan University（奥斯陆城市大学）；Oxford NIHR Biomedical Research Centre（牛津NIHR生物医学研究中心）
The increase of available large clinical and experimental datasets has contributed to a substantial amount of important contributions in the area of biomedical image analysis. Image segmentation, which is crucial for any quantitative analysis, has especially attracted attention. Recent hardware advancement has led to the success of deep learning approaches. However, although deep learning models are being trained on large datasets, existing methods do not use the information from different learning epochs effectively. In this work, we leverage the information of each training epoch to prune th…
University of Ottawa（渥太华大学）；the Korea University Anam Hospital（高丽大学安岩医院）
Image interpolation in medical area is of high importance as most 3D biomedical volume images are sampled where the distance between consecutive slices significantly greater than the in-plane pixel size due to radiation dose or scanning time. Image interpolation creates a number of new slices between known slices in order to obtain an isotropic volume image. The results can be used for the higher quality of 3D reconstruction and visualization of human body structures. Semantic interpolation on the manifold has been proved to be very useful for smoothing image interpolation. Nevertheless, all p…
Image segmentation is one of the most essential biomedical image processing problems for different imaging modalities, including microscopy and X-ray in the Internet-of-Medical-Things (IoMT) domain. However, annotating biomedical images is knowledge-driven, time-consuming, and labor-intensive, making it difficult to obtain abundant labels with limited costs. Active learning strategies come into ease the burden of human annotation, which queries only a subset of training data for annotation. Despite receiving attention, most of active learning methods generally still require huge computational …
Research institute for signals, systems and computational intelligence, sinc(i), FICH-UNL / CONICET（信号、系统与计算智能研究所sinc(i)，国立滨海大学工程与水文系/国家科学技术研究委员会）；École de Technologie Supérieure（高等技术学院）
Despite the astonishing performance of deep-learning based approaches for visual tasks such as semantic segmentation, they are known to produce miscalibrated predictions, which could be harmful for critical decision-making processes. Ensemble learning has shown to not only boost the performance of individual models but also reduce their miscalibration by averaging independent predictions. In this scenario, model diversity has become a key factor, which facilitates individual models converging to different functional solutions. In this work, we introduce Orthogonal Ensemble Networks (OEN), a no…
University of Cambridge（剑桥大学）；Imperial College London（帝国理工学院）
In recent years, there has been increasing interest to incorporate attention into deep learning architectures for biomedical image segmentation. The modular design of attention mechanisms enables flexible integration into convolutional neural network architectures, such as the U-Net. Whether attention is appropriate to use, what type of attention to use, and where in the network to incorporate attention modules, are all important considerations that are currently overlooked. In this paper, we investigate the role of the Focal parameter in modulating attention, revealing a link between attentio…
University of Cambridge（剑桥大学）；Imperial College London（帝国理工学院）；University of Salerno（萨勒诺大学）
The Dice similarity coefficient (DSC) is both a widely used metric and loss function for biomedical image segmentation due to its robustness to class imbalance. However, it is well known that the DSC loss is poorly calibrated, resulting in overconfident predictions that cannot be usefully interpreted in biomedical and clinical practice. Performance is often the only metric used to evaluate segmentations produced by deep neural networks, and calibration is often neglected. However, calibration is important for translation into biomedical and clinical practice, providing crucial contextual infor…
TTT-Unet: Enhancing U-Net with Test-Time Training Layers for Biomedical Image Segmentation
Lehigh University（里海大学）；Northeastern University（东北大学）；University of Notre Dame（圣母大学）；University of Georgia（佐治亚大学）；Massachusetts General Hospital（麻省总医院）；Harvard Medical School（哈佛医学院）
PP-Net: A Hybrid Physical-Prior Neural Network for Scattered Light Removal in Biomedical Images on Embedded Devices
Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences（中国科学院长春光学精密机械与物理研究所）；University of Chinese Academy of Sciences（中国科学院大学）；University of Melbourne（墨尔本大学）；Chinese Academy of Sciences（中国科学院）
Boston University School of Medicine（波士顿大学医学院）；Academic Medical Center（学术医学中心）；Leiden University Medical Center（莱顿大学医学中心）；University of Amsterdam（阿姆斯特丹大学）；Arkana laboratories（Arkana实验室）；Amsterdam Cardiovascular Sciences（阿姆斯特丹心血管科学）；Veterans Affairs Boston Healthcare System（退伍军人事务部波士顿医疗系统）；Boston University（波士顿大学）
Development of deep learning systems for biomedical segmentation often requires access to expert-driven, manually annotated datasets. If more than a single expert is involved in the annotation of the same images, then the inter-expert agreement is not necessarily perfect, and no single expert annotation can precisely capture the so-called ground truth of the regions of interest on all images. Also, it is not trivial to generate a reference estimate using annotations from multiple experts. Here we present a deep neural network, defined as U-Net-and-a-half, which can simultaneously learn from an…
In this paper, we propose a novel network named Vision Transformer for Biomedical Image Segmentation (ViTBIS). Our network splits the input feature maps into three parts with $1\times 1$, $3\times 3$ and $5\times 5$ convolutions in both encoder and decoder. Concat operator is used to merge the features before being fed to three consecutive transformer blocks with attention mechanism embedded inside it. Skip connections are used to connect encoder and decoder transformer blocks. Similarly, transformer blocks and multi scale architecture is used in decoder before being linearly projected to prod…
We describe a point-set registration algorithm based on a novel free point transformer (FPT) network, designed for points extracted from multimodal biomedical images for registration tasks, such as those frequently encountered in ultrasound-guided interventional procedures. FPT is constructed with a global feature extractor which accepts unordered source and target point-sets of variable size. The extracted features are conditioned by a shared multilayer perceptron point transformer module to predict a displacement vector for each source point, transforming it into the target space. The point …
U-Mamba: Enhancing Long-range Dependency for Biomedical Image Segmentation
Peter Munk Cardiac Centre, University Health Network（彼得·蒙克心脏中心，大学健康网络）；University of Toronto（多伦多大学）；Vector Institute for Artificial Intelligence（向量人工智能研究所）
In this paper we present a methodology that uses convolutional neural networks (CNNs) for segmentation by iteratively growing predicted mask regions in each coordinate direction. The CNN is used to predict class probability scores in a small neighborhood of the center pixel in a tile of an image. We use a threshold on the CNN probability scores to determine whether pixels are added to the region and the iteration continues until no new pixels are added to the region. Our method is able to achieve high segmentation accuracy and preserve biologically realistic morphological features while levera…
In practice, data augmentation is assigned a predefined budget in terms of newly created samples per epoch. When using several types of data augmentation, the budget is usually uniformly distributed over the set of augmentations but one can wonder if this budget should not be allocated to each type in a more efficient way. This paper leverages online learning to allocate on the fly this budget as part of neural network training. This meta-algorithm can be run at almost no extra cost as it exploits gradient based signals to determine which type of data augmentation should be preferred. Experime…
