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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.

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.

In this project, we present ShelfNet, a lightweight convolutional neural network for accurate real-time semantic segmentation. Different from the standard encoder-decoder structure, ShelfNet has multiple encoder-decoder branch pairs with skip connections at each spatial level, which looks like a shelf with multiple columns. The shelf-shaped structure provides multiple paths for information flow and improves segmentation accuracy. Inspired by the success of recurrent convolutional neural networks, we use modified residual blocks where two convolutional layers share weights. The shared-weight block enables efficient feature extraction and model size reduction. We tested ShelfNet with ResNet50 and ResNet101 as the backbone respectively: they achieved 59 FPS and 42 FPS respectively on a GTX 1080Ti GPU with a 512x512 input image. ShelfNet achieved high accuracy: on PASCAL VOC 2012 test set, it achieved 84.2% mIoU with ResNet101 backbone and 82.8% mIoU with ResNet50 backbone; it achieved 75.8% mIoU with ResNet50 backbone on Cityscapes dataset. ShelfNet achieved both higher mIoU and faster inference speed compared with state-of-the-art real-time semantic segmentation models. We provide the implementation //github.com/juntang-zhuang/ShelfNet.

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.

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: //github.com/MarvinTeichmann/ConvCRF

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: //github.com/holgerroth/3Dunet_abdomen_cascade.

Spatial pyramid pooling module or encode-decoder structure are used in deep neural networks for semantic segmentation task. The former networks are able to encode multi-scale contextual information by probing the incoming features with filters or pooling operations at multiple rates and multiple effective fields-of-view, while the latter networks can capture sharper object boundaries by gradually recovering the spatial information. In this work, we propose to combine the advantages from both methods. Specifically, our proposed model, DeepLabv3+, extends DeepLabv3 by adding a simple yet effective decoder module to refine the segmentation results especially along object boundaries. We further explore the Xception model and apply the depthwise separable convolution to both Atrous Spatial Pyramid Pooling and decoder modules, resulting in a faster and stronger encoder-decoder network. We demonstrate the effectiveness of the proposed model on the PASCAL VOC 2012 semantic image segmentation dataset and achieve a performance of 89% on the test set without any post-processing. Our paper is accompanied with a publicly available reference implementation of the proposed models in Tensorflow.

Semantic image segmentation is one of the most challenged tasks in computer vision. In this paper, we propose a highly fused convolutional network, which consists of three parts: feature downsampling, combined feature upsampling and multiple predictions. We adopt a strategy of multiple steps of upsampling and combined feature maps in pooling layers with its corresponding unpooling layers. Then we bring out multiple pre-outputs, each pre-output is generated from an unpooling layer by one-step upsampling. Finally, we concatenate these pre-outputs to get the final output. As a result, our proposed network makes highly use of the feature information by fusing and reusing feature maps. In addition, when training our model, we add multiple soft cost functions on pre-outputs and final outputs. In this way, we can reduce the loss reduction when the loss is back propagated. We evaluate our model on three major segmentation datasets: CamVid, PASCAL VOC and ADE20K. We achieve a state-of-the-art performance on CamVid dataset, as well as considerable improvements on PASCAL VOC dataset and ADE20K dataset

Image segmentation is considered to be one of the critical tasks in hyperspectral remote sensing image processing. Recently, convolutional neural network (CNN) has established itself as a powerful model in segmentation and classification by demonstrating excellent performances. The use of a graphical model such as a conditional random field (CRF) contributes further in capturing contextual information and thus improving the segmentation performance. In this paper, we propose a method to segment hyperspectral images by considering both spectral and spatial information via a combined framework consisting of CNN and CRF. We use multiple spectral cubes to learn deep features using CNN, and then formulate deep CRF with CNN-based unary and pairwise potential functions to effectively extract the semantic correlations between patches consisting of three-dimensional data cubes. Effective piecewise training is applied in order to avoid the computationally expensive iterative CRF inference. Furthermore, we introduce a deep deconvolution network that improves the segmentation masks. We also introduce a new dataset and experimented our proposed method on it along with several widely adopted benchmark datasets to evaluate the effectiveness of our method. By comparing our results with those from several state-of-the-art models, we show the promising potential of our method.

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.