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Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation.
TL;DR: Wang et al. as mentioned in this paper proposed a pure transformer-based U-shaped Encoder-Decoder architecture with skip-connections for local-global semantic feature learning for medical image segmentation.
Abstract: In the past few years, convolutional neural networks (CNNs) have achieved milestones in medical image analysis. Especially, the deep neural networks based on U-shaped architecture and skip-connections have been widely applied in a variety of medical image tasks. However, although CNN has achieved excellent performance, it cannot learn global and long-range semantic information interaction well due to the locality of the convolution operation. In this paper, we propose Swin-Unet, which is an Unet-like pure Transformer for medical image segmentation. The tokenized image patches are fed into the Transformer-based U-shaped Encoder-Decoder architecture with skip-connections for local-global semantic feature learning. Specifically, we use hierarchical Swin Transformer with shifted windows as the encoder to extract context features. And a symmetric Swin Transformer-based decoder with patch expanding layer is designed to perform the up-sampling operation to restore the spatial resolution of the feature maps. Under the direct down-sampling and up-sampling of the inputs and outputs by 4x, experiments on multi-organ and cardiac segmentation tasks demonstrate that the pure Transformer-based U-shaped Encoder-Decoder network outperforms those methods with full-convolution or the combination of transformer and convolution. The codes and trained models will be publicly available at this https URL.
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TL;DR: A comprehensive overview of applying deep learning methods in various medical image analysis tasks can be found in this article, where the authors highlight the latest progress and contributions of state-of-the-art unsupervised and semi-supervised deep learning in medical images, which are summarized based on different application scenarios.
Abstract: Deep learning has become the mainstream technology in computer vision, and it has received extensive research interest in developing new medical image processing algorithms to support disease detection and diagnosis. As compared to conventional machine learning technologies, the major advantage of deep learning is that models can automatically identify and recognize representative features through the hierarchal model architecture, while avoiding the laborious development of hand-crafted features. In this paper, we reviewed and summarized more than 200 recently published papers to provide a comprehensive overview of applying deep learning methods in various medical image analysis tasks. Especially, we emphasize the latest progress and contributions of state-of-the-art unsupervised and semi-supervised deep learning in medical images, which are summarized based on different application scenarios, including lesion classification, segmentation, detection, and image registration. Additionally, we also discussed the major technical challenges and suggested the possible solutions in future research efforts.
78 citations
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TL;DR: UCTransNet as discussed by the authors proposes a channel-wise cross-attention module in U-Net to solve the semantic gaps for an accurate automatic medical image segmentation and achieves consistent improvements over the state-of-the-art for semantic segmentation across different datasets and conventional architectures involving transformer or U-shaped framework.
Abstract: Most recent semantic segmentation methods adopt a U-Net framework with an encoder-decoder architecture. It is still challenging for U-Net with a simple skip connection scheme to model the global multi-scale context: 1) Not each skip connection setting is effective due to the issue of incompatible feature sets of encoder and decoder stage, even some skip connection negatively influence the segmentation performance; 2) The original U-Net is worse than the one without any skip connection on some datasets. Based on our findings, we propose a new segmentation framework, named UCTransNet (with a proposed CTrans module in U-Net), from the channel perspective with attention mechanism. Specifically, the CTrans module is an alternate of the U-Net skip connections, which consists of a sub-module to conduct the multi-scale Channel Cross fusion with Transformer (named CCT) and a sub-module Channel-wise Cross-Attention (named CCA) to guide the fused multi-scale channel-wise information to effectively connect to the decoder features for eliminating the ambiguity. Hence, the proposed connection consisting of the CCT and CCA is able to replace the original skip connection to solve the semantic gaps for an accurate automatic medical image segmentation. The experimental results suggest that our UCTransNet produces more precise segmentation performance and achieves consistent improvements over the state-of-the-art for semantic segmentation across different datasets and conventional architectures involving transformer or U-shaped framework. Code: this https URL.
62 citations
28 Jun 2022
TL;DR: UCTransNet as discussed by the authors proposes a channel-wise cross-attention mechanism to solve the problem of incompatible feature sets of encoder and decoder stage, which negatively affects the segmentation performance.
Abstract: Most recent semantic segmentation methods adopt a U-Net framework with an encoder-decoder architecture. It is still challenging for U-Net with a simple skip connection scheme to model the global multi-scale context: 1) Not each skip connection setting is effective due to the issue of incompatible feature sets of encoder and decoder stage, even some skip connection negatively influence the segmentation performance; 2) The original U-Net is worse than the one without any skip connection on some datasets. Based on our findings, we propose a new segmentation framework, named UCTransNet (with a proposed CTrans module in U-Net), from the channel perspective with attention mechanism. Specifically, the CTrans (Channel Transformer) module is an alternate of the U-Net skip connections, which consists of a sub-module to conduct the multi-scale Channel Cross fusion with Transformer (named CCT) and a sub-module Channel-wise Cross-Attention (named CCA) to guide the fused multi-scale channel-wise information to effectively connect to the decoder features for eliminating the ambiguity. Hence, the proposed connection consisting of the CCT and CCA is able to replace the original skip connection to solve the semantic gaps for an accurate automatic medical image segmentation. The experimental results suggest that our UCTransNet produces more precise segmentation performance and achieves consistent improvements over the state-of-the-art for semantic segmentation across different datasets and conventional architectures involving transformer or U-shaped framework. Code: https://github.com/McGregorWwww/UCTransNet.
61 citations
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TL;DR: Transformer as mentioned in this paper is a type of deep neural network mainly based on the self-attention mechanism, which has been applied to the field of natural language processing, and has received more and more attention from the computer vision community.
Abstract: Transformer, first applied to the field of natural language processing, is a type of deep neural network mainly based on the self-attention mechanism. Thanks to its strong representation capabilities, researchers are looking at ways to apply transformer to computer vision tasks. In a variety of visual benchmarks, transformer-based models perform similar to or better than other types of networks such as convolutional and recurrent networks. Given its high performance and less need for vision-specific inductive bias, transformer is receiving more and more attention from the computer vision community. In this paper, we review these vision transformer models by categorizing them in different tasks and analyzing their advantages and disadvantages. The main categories we explore include the backbone network, high/mid-level vision, low-level vision, and video processing. We also include efficient transformer methods for pushing transformer into real device-based applications. Furthermore, we also take a brief look at the self-attention mechanism in computer vision, as it is the base component in transformer. Toward the end of this paper, we discuss the challenges and provide several further research directions for vision transformers.
36 citations
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TL;DR: In this article, Axial Fusion Transformer UNet (AFTer-UNet) is proposed, which takes both advantages of convolutional layers' capability of extracting detailed features and transformers' strength on long sequence modeling.
Abstract: Recent advances in transformer-based models have drawn attention to exploring these techniques in medical image segmentation, especially in conjunction with the U-Net model (or its variants), which has shown great success in medical image segmentation, under both 2D and 3D settings. Current 2D based methods either directly replace convolutional layers with pure transformers or consider a transformer as an additional intermediate encoder between the encoder and decoder of U-Net. However, these approaches only consider the attention encoding within one single slice and do not utilize the axial-axis information naturally provided by a 3D volume. In the 3D setting, convolution on volumetric data and transformers both consume large GPU memory. One has to either downsample the image or use cropped local patches to reduce GPU memory usage, which limits its performance. In this paper, we propose Axial Fusion Transformer UNet (AFTer-UNet), which takes both advantages of convolutional layers' capability of extracting detailed features and transformers' strength on long sequence modeling. It considers both intra-slice and inter-slice long-range cues to guide the segmentation. Meanwhile, it has fewer parameters and takes less GPU memory to train than the previous transformer-based models. Extensive experiments on three multi-organ segmentation datasets demonstrate that our method outperforms current state-of-the-art methods.
30 citations
References
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05 Oct 2015
TL;DR: Neber et al. as discussed by the authors proposed a network and training strategy that relies on the strong use of data augmentation to use the available annotated samples more efficiently, which can be trained end-to-end from very few images and outperforms the prior best method (a sliding-window convolutional network) on the ISBI challenge for segmentation of neuronal structures in electron microscopic stacks.
Abstract: There is large consent that successful training of deep networks requires many thousand annotated training samples. In this paper, we present a network and training strategy that relies on the strong use of data augmentation to use the available annotated samples more efficiently. The architecture consists of a contracting path to capture context and a symmetric expanding path that enables precise localization. We show that such a network can be trained end-to-end from very few images and outperforms the prior best method (a sliding-window convolutional network) on the ISBI challenge for segmentation of neuronal structures in electron microscopic stacks. Using the same network trained on transmitted light microscopy images (phase contrast and DIC) we won the ISBI cell tracking challenge 2015 in these categories by a large margin. Moreover, the network is fast. Segmentation of a 512x512 image takes less than a second on a recent GPU. The full implementation (based on Caffe) and the trained networks are available at http://lmb.informatik.uni-freiburg.de/people/ronneber/u-net .
49,590 citations
11 Oct 2018
TL;DR: BERT as mentioned in this paper pre-trains deep bidirectional representations from unlabeled text by jointly conditioning on both left and right context in all layers, which can be fine-tuned with just one additional output layer to create state-of-the-art models for a wide range of tasks.
Abstract: We introduce a new language representation model called BERT, which stands for Bidirectional Encoder Representations from Transformers. Unlike recent language representation models (Peters et al., 2018a; Radford et al., 2018), BERT is designed to pre-train deep bidirectional representations from unlabeled text by jointly conditioning on both left and right context in all layers. As a result, the pre-trained BERT model can be fine-tuned with just one additional output layer to create state-of-the-art models for a wide range of tasks, such as question answering and language inference, without substantial task-specific architecture modifications. BERT is conceptually simple and empirically powerful. It obtains new state-of-the-art results on eleven natural language processing tasks, including pushing the GLUE score to 80.5 (7.7 point absolute improvement), MultiNLI accuracy to 86.7% (4.6% absolute improvement), SQuAD v1.1 question answering Test F1 to 93.2 (1.5 point absolute improvement) and SQuAD v2.0 Test F1 to 83.1 (5.1 point absolute improvement).
24,672 citations
TL;DR: This work addresses the task of semantic image segmentation with Deep Learning and proposes atrous spatial pyramid pooling (ASPP), which is proposed to robustly segment objects at multiple scales, and improves the localization of object boundaries by combining methods from DCNNs and probabilistic graphical models.
Abstract: In this work we address the task of semantic image segmentation with Deep Learning and make three main contributions that are experimentally shown to have substantial practical merit. First , we highlight convolution with upsampled filters, or ‘atrous convolution’, as a powerful tool in dense prediction tasks. Atrous convolution allows us to explicitly control the resolution at which feature responses are computed within Deep Convolutional Neural Networks. It also allows us to effectively enlarge the field of view of filters to incorporate larger context without increasing the number of parameters or the amount of computation. Second , we propose atrous spatial pyramid pooling (ASPP) to robustly segment objects at multiple scales. ASPP probes an incoming convolutional feature layer with filters at multiple sampling rates and effective fields-of-views, thus capturing objects as well as image context at multiple scales. Third , we improve the localization of object boundaries by combining methods from DCNNs and probabilistic graphical models. The commonly deployed combination of max-pooling and downsampling in DCNNs achieves invariance but has a toll on localization accuracy. We overcome this by combining the responses at the final DCNN layer with a fully connected Conditional Random Field (CRF), which is shown both qualitatively and quantitatively to improve localization performance. Our proposed “DeepLab” system sets the new state-of-art at the PASCAL VOC-2012 semantic image segmentation task, reaching 79.7 percent mIOU in the test set, and advances the results on three other datasets: PASCAL-Context, PASCAL-Person-Part, and Cityscapes. All of our code is made publicly available online.
11,856 citations
21 Jul 2017
TL;DR: This paper exploits the capability of global context information by different-region-based context aggregation through the pyramid pooling module together with the proposed pyramid scene parsing network (PSPNet) to produce good quality results on the scene parsing task.
Abstract: Scene parsing is challenging for unrestricted open vocabulary and diverse scenes. In this paper, we exploit the capability of global context information by different-region-based context aggregation through our pyramid pooling module together with the proposed pyramid scene parsing network (PSPNet). Our global prior representation is effective to produce good quality results on the scene parsing task, while PSPNet provides a superior framework for pixel-level prediction. The proposed approach achieves state-of-the-art performance on various datasets. It came first in ImageNet scene parsing challenge 2016, PASCAL VOC 2012 benchmark and Cityscapes benchmark. A single PSPNet yields the new record of mIoU accuracy 85.4% on PASCAL VOC 2012 and accuracy 80.2% on Cityscapes.
10,189 citations
18 Jun 2018
TL;DR: In this article, the non-local operation computes the response at a position as a weighted sum of the features at all positions, which can be used to capture long-range dependencies.
Abstract: Both convolutional and recurrent operations are building blocks that process one local neighborhood at a time. In this paper, we present non-local operations as a generic family of building blocks for capturing long-range dependencies. Inspired by the classical non-local means method [4] in computer vision, our non-local operation computes the response at a position as a weighted sum of the features at all positions. This building block can be plugged into many computer vision architectures. On the task of video classification, even without any bells and whistles, our nonlocal models can compete or outperform current competition winners on both Kinetics and Charades datasets. In static image recognition, our non-local models improve object detection/segmentation and pose estimation on the COCO suite of tasks. Code will be made available.
8,059 citations