Medical image segmentation is an essential prerequisite for developing healthcare systems, especially for disease diagnosis and treatment planning. On various medical image segmentation tasks, the ushaped architecture, also known as U-Net, has become the de-facto standard and achieved tremendous success. However, due to the intrinsic locality of convolution operations, U-Net generally demonstrates limitations in explicitly modeling long-range dependency. Transformers, designed for sequence-to-sequence prediction, have emerged as alternative architectures with innate global self-attention mechanisms, but can result in limited localization abilities due to insufficient low-level details. In this paper, we propose TransUNet, which merits both Transformers and U-Net, as a strong alternative for medical image segmentation. On one hand, the Transformer encodes tokenized image patches from a convolution neural network (CNN) feature map as the input sequence for extracting global contexts. On the other hand, the decoder upsamples the encoded features which are then combined with the high-resolution CNN feature maps to enable precise localization. We argue that Transformers can serve as strong encoders for medical image segmentation tasks, with the combination of U-Net to enhance finer details by recovering localized spatial information. TransUNet achieves superior performances to various competing methods on different medical applications including multi-organ segmentation and cardiac segmentation. Code and models are available at https://github.com/Beckschen/ TransUNet.

Though CNNs have achieved the state-of-the-art performance on various vision tasks, they are vulnerable to adversarial examples -crafted by adding human-imperceptible perturbations to clean images. However, most of the existing adversarial attacks only achieve relatively low success rates under the challenging black-box setting, where the attackers have no knowledge of the model structure and parameters. To this end, we propose to improve the transferability of adversarial examples by creating diverse input patterns. Instead of only using the original images to generate adversarial examples, our method applies random transformations to the input images at each iteration. Extensive experiments on ImageNet show that the proposed attack method can generate adversarial examples that transfer much better to different networks than existing baselines. By evaluating our method against top defense solutions and official baselines from NIPS 2017 adversarial competition, the enhanced attack reaches an average success rate of 73.0%, which outperforms the top-1 attack submission in the NIPS competition by a large margin of 6.6%. We hope that our proposed attack strategy can serve as a strong benchmark baseline for evaluating the robustness of networks to adversaries and the effectiveness of different defense methods in the future. Code is available at https: //github.com/cihangxie/DI-2-FGSM .

It has been well demonstrated that adversarial examples, i.e., natural images with visually imperceptible perturbations added, cause deep networks to fail on image classification. In this paper, we extend adversarial examples to semantic segmentation and object detection which are much more difficult. Our observation is that both segmentation and detection are based on classifying multiple targets on an image (e.g., the target is a pixel or a receptive field in segmentation, and an object proposal in detection). This inspires us to optimize a loss function over a set of pixels/proposals for generating adversarial perturbations. Based on this idea, we propose a novel algorithm named Dense Adversary Generation (DAG), which generates a large family of adversarial examples, and applies to a wide range of state-of-the-art deep networks for segmentation and detection. We also find that the adversarial perturbations can be transferred across networks with different training data, based on different architectures, and even for different recognition tasks. In particular, the transferability across networks with the same architecture is more significant than in other cases. Besides, summing up heterogeneous perturbations often leads to better transfer performance, which provides an effective method of blackbox adversarial attack.

Abstract. Deep neural networks have been widely adopted for automatic organ segmentation from abdominal CT scans. However, the segmentation accuracy of some small organs (e.g., the pancreas) is sometimes below satisfaction, arguably because deep networks are easily disrupted by the complex and variable background regions which occupies a large fraction of the input volume. In this paper, we formulate this problem into a fixed-point model which uses a predicted segmentation mask to shrink the input region. This is motivated by the fact that a smaller input region often leads to more accurate segmentation. In the training process, we use the ground-truth annotation to generate accurate input regions and optimize network weights. On the testing stage, we fix the network parameters and update the segmentation results in an iterative manner. We evaluate our approach on the NIH pancreas segmentation dataset, and outperform the state-of-the-art by more than 4%, measured by the average Dice-Sørensen Coefficient (DSC). In addition, we report 62.43% DSC in the worst case, which guarantees the reliability of our approach in clinical applications.

We aim at segmenting small organs (e.g., the pancreas) from abdominal CT scans. As the target often occupies a relatively small region in the input image, deep neural networks can be easily confused by the complex and variable background. To alleviate this, researchers proposed a coarse-to-fine approach [46], which used prediction from the first (coarse) stage to indicate a smaller input region for the second (fine) stage. Despite its effectiveness, this algorithm dealt with two stages individually, which lacked optimizing a global energy function, and limited its ability to incorporate multi-stage visual cues. Missing contextual information led to unsatisfying convergence in iterations, and that the fine stage sometimes produced even lower segmentation accuracy than the coarse stage.This paper presents a Recurrent Saliency Transformation Network. The key innovation is a saliency transformation module, which repeatedly converts the segmentation probability map from the previous iteration as spatial weights and applies these weights to the current iteration. This brings us two-fold benefits. In training, it allows joint optimization over the deep networks dealing with different input scales. In testing, it propagates multi-stage visual information throughout iterations to improve segmentation accuracy. Experiments in the NIH pancreas segmentation dataset demonstrate the state-of-the-art accuracy, which outperforms the previous best by an average of over 2%. Much higher accuracies are also reported on several small organs in a larger dataset collected by ourselves. In addition, our approach enjoys better convergence properties, making it more efficient and reliable in practice.

Accurate and robust segmentation of abdominal organs on CT is essential for many clinical applications such as computer-aided diagnosis and computer-aided surgery. But this task is challenging due to the weak boundaries of organs, the complexity of the background, and the variable sizes of different organs. To address these challenges, we introduce a novel framework for multi-organ segmentation of abdominal regions by using organ-attention networks with reverse connections (OAN-RCs) which are applied to 2D views, of the 3D CT volume, and output estimates which are combined by statistical fusion exploiting structural similarity. More specifically, OAN is a two-stage deep convolutional network, where deep network features from the first stage are combined with the original image, in a second stage, to reduce the complex background and enhance the discriminative information for the target organs. Intuitively, OAN reduces the effect of the complex background by focusing attention so that each organ only needs to be discriminated from its local background. RCs are added to the first stage to give the lower layers more semantic information thereby enabling them to adapt to the sizes of different organs. Our networks are trained on 2D views (slices) enabling us to use holistic information and allowing efficient computation (compared to using 3D patches). To compensate for the limited cross-sectional information of the original 3D volumetric CT, e.g., the connectivity between neighbor slices, multi-sectional images are reconstructed from the three different 2D view directions. Then we combine the segmentation results from the different views using statistical fusion, with a novel term relating the structural similarity of the 2D views to the original 3D structure. To train the network and evaluate results, 13 structures were manually annotated by four human raters and confirmed by a senior expert on 236 normal cases. We tested our algorithm by 4-fold cross-validation and computed Dice-Sørensen similarity coefficients (DSC) and surface distances for evaluating our estimates of the 13 structures. Our experiments show that the proposed approach gives strong results and outperforms 2D-and 3D-patch based state-of-the-art methods in terms of DSC and mean surface distances.

In multi-organ segmentation of abdominal CT scans, most existing fully supervised deep learning algorithms require lots of voxel-wise annotations, which are usually difficult, expensive, and slow to obtain. In comparison, massive unlabeled 3D CT volumes are usually easily accessible. Current mainstream works to address semi-supervised biomedical image segmentation problem are mostly graphbased. By contrast, deep network based semi-supervised learning methods have not drawn much attention in this field. In this work, we propose Deep Multi-Planar Co-Training (DMPCT), whose contributions can be divided into two folds: 1) The deep model is learned in a co-training style which can mine consensus information from multiple planes like the sagittal, coronal, and axial planes; 2) Multiplanar fusion is applied to generate more reliable pseudolabels, which alleviates the errors occurring in the pseudolabels and thus can help to train better segmentation networks. Experiments are done on our newly collected large dataset with 100 unlabeled cases as well as 210 labeled cases where 16 anatomical structures are manually annotated by four radiologists and confirmed by a senior expert. The results suggest that DMPCT significantly outperforms the fully supervised method by more than 4% especially when only a small set of annotations is used.

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