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 network (KFCN) for medical image segmentation. The segmentation function and corresponding error is analyzed. We show the existence of an asymptotically stable region for KFCN which traditional FCN doesn't possess. Experiments validate our knowledge assumption about the incorporation of prior knowledge into the convolution kernels of KFCN and show that KFCN can achieve a reasonable segmentation and a satisfactory accuracy.

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Networking:IFIP International Conferences on Networking。 Explanation:国际网络会议。 Publisher:IFIP。 SIT: http://dblp.uni-trier.de/db/conf/networking/index.html

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 LadderNet has multiple pairs of encoder-decoder branches, and has skip connections between every pair of adjacent decoder and decoder branches in each level. Inspired by the success of ResNet and R2-UNet, we use modified residual blocks where two convolutional layers in one block share the same weights. A LadderNet has more paths for information flow because of skip connections and residual blocks, and can be viewed as an ensemble of Fully Convolutional Networks (FCN). The equivalence to an ensemble of FCNs improves segmentation accuracy, while the shared weights within each residual block reduce parameter number. Semantic segmentation is essential for retinal disease detection. We tested LadderNet on two benchmark datasets for blood vessel segmentation in retinal images, and achieved superior performance over methods in the literature. The implementation is provided \url{https://github.com/juntang-zhuang/LadderNet}

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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.

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Deep neural network architectures have traditionally been designed and explored with human expertise in a long-lasting trial-and-error process. This process requires huge amount of time, expertise, and resources. To address this tedious problem, we propose a novel algorithm to optimally find hyperparameters of a deep network architecture automatically. We specifically focus on designing neural architectures for medical image segmentation task. Our proposed method is based on a policy gradient reinforcement learning for which the reward function is assigned a segmentation evaluation utility (i.e., dice index). We show the efficacy of the proposed method with its low computational cost in comparison with the state-of-the-art medical image segmentation networks. We also present a new architecture design, a densely connected encoder-decoder CNN, as a strong baseline architecture to apply the proposed hyperparameter search algorithm. We apply the proposed algorithm to each layer of the baseline architectures. As an application, we train the proposed system on cine cardiac MR images from Automated Cardiac Diagnosis Challenge (ACDC) MICCAI 2017. Starting from a baseline segmentation architecture, the resulting network architecture obtains the state-of-the-art results in accuracy without performing any trial-and-error based architecture design approaches or close supervision of the hyperparameters changes.

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In this paper, we focus on three problems in deep learning based medical image segmentation. Firstly, U-net, as a popular model for medical image segmentation, is difficult to train when convolutional layers increase even though a deeper network usually has a better generalization ability because of more learnable parameters. Secondly, the exponential ReLU (ELU), as an alternative of ReLU, is not much different from ReLU when the network of interest gets deep. Thirdly, the Dice loss, as one of the pervasive loss functions for medical image segmentation, is not effective when the prediction is close to ground truth and will cause oscillation during training. To address the aforementioned three problems, we propose and validate a deeper network that can fit medical image datasets that are usually small in the sample size. Meanwhile, we propose a new loss function to accelerate the learning process and a combination of different activation functions to improve the network performance. Our experimental results suggest that our network is comparable or superior to state-of-the-art methods.

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In this paper, we propose a novel fully convolutional two-stream fusion network (FCTSFN) for interactive image segmentation. The proposed network includes two sub-networks: a two-stream late fusion network (TSLFN) that predicts the foreground at a reduced resolution, and a multi-scale refining network (MSRN) that refines the foreground at full resolution. The TSLFN includes two distinct deep streams followed by a fusion network. The intuition is that, since user interactions are more direction information on foreground/background than the image itself, the two-stream structure of the TSLFN reduces the number of layers between the pure user interaction features and the network output, allowing the user interactions to have a more direct impact on the segmentation result. The MSRN fuses the features from different layers of TSLFN with different scales, in order to seek the local to global information on the foreground to refine the segmentation result at full resolution. We conduct comprehensive experiments on four benchmark datasets. The results show that the proposed network achieves competitive performance compared to current state-of-the-art interactive image segmentation methods.

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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 models utilize the power of U-Net, Residual Network, as well as RCNN. There are several advantages of these proposed architectures for segmentation tasks. First, a residual unit helps when training deep architecture. Second, feature accumulation with recurrent residual convolutional layers ensures better feature representation for segmentation tasks. Third, it allows us to design better U-Net architecture with same number of network parameters with better performance for medical image segmentation. The proposed models are tested on three benchmark datasets such as blood vessel segmentation in retina images, skin cancer segmentation, and lung lesion segmentation. The experimental results show superior performance on segmentation tasks compared to equivalent models including U-Net and residual U-Net (ResU-Net).

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For the challenging semantic image segmentation task the most efficient models have traditionally combined the structured modelling capabilities of Conditional Random Fields (CRFs) with the feature extraction power of CNNs. In more recent works however, CRF post-processing has fallen out of favour. We argue that this is mainly due to the slow training and inference speeds of CRFs, as well as the difficulty of learning the internal CRF parameters. To overcome both issues we propose to add the assumption of conditional independence to the framework of fully-connected CRFs. This allows us to reformulate the inference in terms of convolutions, which can be implemented highly efficiently on GPUs. Doing so speeds up inference and training by a factor of more then 100. All parameters of the convolutional CRFs can easily be optimized using backpropagation. To facilitating further CRF research we make our implementation publicly available. Please visit: https://github.com/MarvinTeichmann/ConvCRF

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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 images without much difficulty. Several variations of deep convolutional neural networks have been successfully applied to medical images. Especially fully convolutional architectures have been proven efficient for segmentation of 3D medical images. In this article, we describe how to build a 3D fully convolutional network (FCN) that can process 3D images in order to produce automatic semantic segmentations. The model is trained and evaluated on a clinical computed tomography (CT) dataset and shows state-of-the-art performance in multi-organ segmentation.

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Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ~10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. Our code and trained models are available for download: https://github.com/holgerroth/3Dunet_abdomen_cascade.

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Convolutional networks are powerful visual models that yield hierarchies of features. We show that convolutional networks by themselves, trained end-to-end, pixels-to-pixels, exceed the state-of-the-art in semantic segmentation. Our key insight is to build "fully convolutional" networks that take input of arbitrary size and produce correspondingly-sized output with efficient inference and learning. We define and detail the space of fully convolutional networks, explain their application to spatially dense prediction tasks, and draw connections to prior models. We adapt contemporary classification networks (AlexNet, the VGG net, and GoogLeNet) into fully convolutional networks and transfer their learned representations by fine-tuning to the segmentation task. We then define a novel architecture that combines semantic information from a deep, coarse layer with appearance information from a shallow, fine layer to produce accurate and detailed segmentations. Our fully convolutional network achieves state-of-the-art segmentation of PASCAL VOC (20% relative improvement to 62.2% mean IU on 2012), NYUDv2, and SIFT Flow, while inference takes one third of a second for a typical image.

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