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Multi-sequence cardiac magnetic resonance (CMR) provides essential pathology information (scar and edema) to diagnose myocardial infarction. However, automatic pathology segmentation can be challenging due to the difficulty of effectively exploring the underlying information from the multi-sequence CMR data. This paper aims to tackle the scar and edema segmentation from multi-sequence CMR with a novel auto-weighted supervision framework, where the interactions among different supervised layers are explored under a task-specific objective using reinforcement learning. Furthermore, we design a coarse-to-fine framework to boost the small myocardial pathology region segmentation with shape prior knowledge. The coarse segmentation model identifies the left ventricle myocardial structure as a shape prior, while the fine segmentation model integrates a pixel-wise attention strategy with an auto-weighted supervision model to learn and extract salient pathological structures from the multi-sequence CMR data. Extensive experimental results on a publicly available dataset from Myocardial pathology segmentation combining multi-sequence CMR (MyoPS 2020) demonstrate our method can achieve promising performance compared with other state-of-the-art methods. Our method is promising in advancing the myocardial pathology assessment on multi-sequence CMR data. To motivate the community, we have made our code publicly available via //github.com/soleilssss/AWSnet/tree/master.

We present MultiBodySync, a novel, end-to-end trainable multi-body motion segmentation and rigid registration framework for multiple input 3D point clouds. The two non-trivial challenges posed by this multi-scan multibody setting that we investigate are: (i) guaranteeing correspondence and segmentation consistency across multiple input point clouds capturing different spatial arrangements of bodies or body parts; and (ii) obtaining robust motion-based rigid body segmentation applicable to novel object categories. We propose an approach to address these issues that incorporates spectral synchronization into an iterative deep declarative network, so as to simultaneously recover consistent correspondences as well as motion segmentation. At the same time, by explicitly disentangling the correspondence and motion segmentation estimation modules, we achieve strong generalizability across different object categories. Our extensive evaluations demonstrate that our method is effective on various datasets ranging from rigid parts in articulated objects to individually moving objects in a 3D scene, be it single-view or full point clouds.

A key requirement for the success of supervised deep learning is a large labeled dataset - a condition that is difficult to meet in medical image analysis. Self-supervised learning (SSL) can help in this regard by providing a strategy to pre-train a neural network with unlabeled data, followed by fine-tuning for a downstream task with limited annotations. Contrastive learning, a particular variant of SSL, is a powerful technique for learning image-level representations. In this work, we propose strategies for extending the contrastive learning framework for segmentation of volumetric medical images in the semi-supervised setting with limited annotations, by leveraging domain-specific and problem-specific cues. Specifically, we propose (1) novel contrasting strategies that leverage structural similarity across volumetric medical images (domain-specific cue) and (2) a local version of the contrastive loss to learn distinctive representations of local regions that are useful for per-pixel segmentation (problem-specific cue). We carry out an extensive evaluation on three Magnetic Resonance Imaging (MRI) datasets. In the limited annotation setting, the proposed method yields substantial improvements compared to other self-supervision and semi-supervised learning techniques. When combined with a simple data augmentation technique, the proposed method reaches within 8% of benchmark performance using only two labeled MRI volumes for training, corresponding to only 4% (for ACDC) of the training data used to train the benchmark.

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{//github.com/juntang-zhuang/LadderNet}

Network embedding is the process of learning low-dimensional representations for nodes in a network, while preserving node features. Existing studies only leverage network structure information and focus on preserving structural features. However, nodes in real-world networks often have a rich set of attributes providing extra semantic information. It has been demonstrated that both structural and attribute features are important for network analysis tasks. To preserve both features, we investigate the problem of integrating structure and attribute information to perform network embedding and propose a Multimodal Deep Network Embedding (MDNE) method. MDNE captures the non-linear network structures and the complex interactions among structures and attributes, using a deep model consisting of multiple layers of non-linear functions. Since structures and attributes are two different types of information, a multimodal learning method is adopted to pre-process them and help the model to better capture the correlations between node structure and attribute information. We employ both structural proximity and attribute proximity in the loss function to preserve the respective features and the representations are obtained by minimizing the loss function. Results of extensive experiments on four real-world datasets show that the proposed method performs significantly better than baselines on a variety of tasks, which demonstrate the effectiveness and generality of our method.

Deep neural network models used for medical image segmentation are large because they are trained with high-resolution three-dimensional (3D) images. Graphics processing units (GPUs) are widely used to accelerate the trainings. However, the memory on a GPU is not large enough to train the models. A popular approach to tackling this problem is patch-based method, which divides a large image into small patches and trains the models with these small patches. However, this method would degrade the segmentation quality if a target object spans multiple patches. In this paper, we propose a novel approach for 3D medical image segmentation that utilizes the data-swapping, which swaps out intermediate data from GPU memory to CPU memory to enlarge the effective GPU memory size, for training high-resolution 3D medical images without patching. We carefully tuned parameters in the data-swapping method to obtain the best training performance for 3D U-Net, a widely used deep neural network model for medical image segmentation. We applied our tuning to train 3D U-Net with full-size images of 192 x 192 x 192 voxels in brain tumor dataset. As a result, communication overhead, which is the most important issue, was reduced by 17.1%. Compared with the patch-based method for patches of 128 x 128 x 128 voxels, our training for full-size images achieved improvement on the mean Dice score by 4.48% and 5.32 % for detecting whole tumor sub-region and tumor core sub-region, respectively. The total training time was reduced from 164 hours to 47 hours, resulting in 3.53 times of acceleration.

3D image segmentation plays an important role in biomedical image analysis. Many 2D and 3D deep learning models have achieved state-of-the-art segmentation performance on 3D biomedical image datasets. Yet, 2D and 3D models have their own strengths and weaknesses, and by unifying them together, one may be able to achieve more accurate results. In this paper, we propose a new ensemble learning framework for 3D biomedical image segmentation that combines the merits of 2D and 3D models. First, we develop a fully convolutional network based meta-learner to learn how to improve the results from 2D and 3D models (base-learners). Then, to minimize over-fitting for our sophisticated meta-learner, we devise a new training method that uses the results of the base-learners as multiple versions of "ground truths". Furthermore, since our new meta-learner training scheme does not depend on manual annotation, it can utilize abundant unlabeled 3D image data to further improve the model. Extensive experiments on two public datasets (the HVSMR 2016 Challenge dataset and the mouse piriform cortex dataset) show that our approach is effective under fully-supervised, semi-supervised, and transductive settings, and attains superior performance over state-of-the-art image segmentation methods.

Radiologist is "doctor's doctor", biomedical image segmentation plays a central role in quantitative analysis, clinical diagnosis, and medical intervention. In the light of the fully convolutional networks (FCN) and U-Net, deep convolutional networks (DNNs) have made significant contributions in biomedical image segmentation applications. In this paper, based on U-Net, we propose MDUnet, a multi-scale densely connected U-net for biomedical image segmentation. we propose three different multi-scale dense connections for U shaped architectures encoder, decoder and across them. The highlights of our architecture is directly fuses the neighboring different scale feature maps from both higher layers and lower layers to strengthen feature propagation in current layer. Which can largely improves the information flow encoder, decoder and across them. Multi-scale dense connections, which means containing shorter connections between layers close to the input and output, also makes much deeper U-net possible. We adopt the optimal model based on the experiment and propose a novel Multi-scale Dense U-Net (MDU-Net) architecture with quantization. Which reduce overfitting in MDU-Net for better accuracy. We evaluate our purpose model on the MICCAI 2015 Gland Segmentation dataset (GlaS). The three multi-scale dense connections improve U-net performance by up to 1.8% on test A and 3.5% on test B in the MICCAI Gland dataset. Meanwhile the MDU-net with quantization achieves the superiority over U-Net performance by up to 3% on test A and 4.1% on test B.

Real-time semantic segmentation plays an important role in practical applications such as self-driving and robots. Most research working on semantic segmentation focuses on accuracy with little consideration for efficiency. Several existing studies that emphasize high-speed inference often cannot produce high-accuracy segmentation results. In this paper, we propose a novel convolutional network named Efficient Dense modules with Asymmetric convolution (EDANet), which employs an asymmetric convolution structure incorporating the dilated convolution and the dense connectivity to attain high efficiency at low computational cost, inference time, and model size. Compared to FCN, EDANet is 11 times faster and has 196 times fewer parameters, while it achieves a higher the mean of intersection-over-union (mIoU) score without any additional decoder structure, context module, post-processing scheme, and pretrained model. We evaluate EDANet on Cityscapes and CamVid datasets to evaluate its performance and compare it with the other state-of-art systems. Our network can run on resolution 512x1024 inputs at the speed of 108 and 81 frames per second on a single GTX 1080Ti and Titan X, respectively.

In this paper, we adopt 3D Convolutional Neural Networks to segment volumetric medical images. Although deep neural networks have been proven to be very effective on many 2D vision tasks, it is still challenging to apply them to 3D tasks due to the limited amount of annotated 3D data and limited computational resources. We propose a novel 3D-based coarse-to-fine framework to effectively and efficiently tackle these challenges. The proposed 3D-based framework outperforms the 2D counterpart to a large margin since it can leverage the rich spatial infor- mation along all three axes. We conduct experiments on two datasets which include healthy and pathological pancreases respectively, and achieve the current state-of-the-art in terms of Dice-S{\o}rensen Coefficient (DSC). On the NIH pancreas segmentation dataset, we outperform the previous best by an average of over 2%, and the worst case is improved by 7% to reach almost 70%, which indicates the reliability of our framework in clinical applications.