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Register a new userMulti-level colonoscopy malignant tissue detection with adversarial CAC-UNet
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The automatic and objective medical diagnostic model can be valuable to achieve early cancer detection, and thus reducing the mortality rate. In this paper, we propose a highly efficient multi-level malignant tissue detection through the designed adversarial CAC-UNet. A patch-level model with a pre-prediction strategy and a malignancy area guided label smoothing is adopted to remove the negative WSIs, with which to lower the risk of false positive detection. For the selected key patches by multi-model ensemble, an adversarial context-aware and appearance consistency UNet (CAC-UNet) is designed to achieve robust segmentation. In CAC-UNet, mirror designed discriminators are able to seamlessly fuse the whole feature maps of the skillfully designed powerful backbone network without any information loss. Besides, a mask prior is further added to guide the accurate segmentation mask prediction through an extra mask-domain discriminator. The proposed scheme achieves the best results in MICCAI DigestPath2019 challenge on colonoscopy tissue segmentation and classification task. The full implementation details and the trained models are available at https://github.com/Raykoooo/CAC-UNet.
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The automatic detection of frames containing polyps from a colonoscopy video sequence is an important first step for a fully automated colonoscopy analysis tool. Typically, such detection system is built using a large annotated data set of frames with and without polyps, which is expensive to be obtained. In this paper, we introduce a new system that detects frames containing polyps as anomalies from a distribution of frames from exams that do not contain any polyps. The system is trained using a one-class training set consisting of colonoscopy frames without polyps -- such training set is considerably less expensive to obtain, compared to the 2-class data set mentioned above. During inference, the system is only able to reconstruct frames without polyps, and when it tries to reconstruct a frame with polyp, it automatically removes (i.e., photoshop) it from the frame -- the difference between the input and reconstructed frames is used to detect frames with polyps. We name our proposed model as anomaly detection generative adversarial network (ADGAN), comprising a dual GAN with two generators and two discriminators. We show that our proposed approach achieves the state-of-the-art result on this data set, compared with recently proposed anomaly detection systems.
Mitotic count is the most important morphological feature of breast cancer grading. Many deep learning-based methods have been proposed but suffer from domain shift. In this work, we construct a Fourier-based segmentation model for mitosis detection to address the problem. Swapping the low-frequency spectrum of source and target images is shown effective to alleviate the discrepancy between different scanners. Our Fourier-based segmentation method can achieve F1 with 0.7456 on the preliminary test set.
Deep learning based analysis of histopathology images shows promise in advancing the understanding of tumor progression, tumor micro-environment, and their underpinning biological processes. So far, these approaches have focused on extracting information associated with annotations. In this work, we ask how much information can be learned from the tissue architecture itself. We present an adversarial learning model to extract feature representations of cancer tissue, without the need for manual annotations. We show that these representations are able to identify a variety of morphological characteristics across three cancer types: Breast, colon, and lung. This is supported by 1) the separation of morphologic characteristics in the latent space; 2) the ability to classify tissue type with logistic regression using latent representations, with an AUC of 0.97 and 85% accuracy, comparable to supervised deep models; 3) the ability to predict the presence of tumor in Whole Slide Images (WSIs) using multiple instance learning (MIL), achieving an AUC of 0.98 and 94% accuracy. Our results show that our model captures distinct phenotypic characteristics of real tissue samples, paving the way for further understanding of tumor progression and tumor micro-environment, and ultimately refining histopathological classification for diagnosis and treatment. The code and pretrained models are available at: https://github.com/AdalbertoCq/Adversarial-learning-of-cancer-tissue-representations
Colorectal cancer (CRC) is a common and lethal disease. Globally, CRC is the third most commonly diagnosed cancer in males and the second in females. For colorectal cancer, the best screening test available is the colonoscopy. During a colonoscopic procedure, a tiny camera at the tip of the endoscope generates a video of the internal mucosa of the colon. The video data are displayed on a monitor for the physician to examine the lining of the entire colon and check for colorectal polyps. Detection and removal of colorectal polyps are associated with a reduction in mortality from colorectal cancer. However, the miss rate of polyp detection during colonoscopy procedure is often high even for very experienced physicians. The reason lies in the high variation of polyp in terms of shape, size, textural, color and illumination. Though challenging, with the great advances in object detection techniques, automated polyp detection still demonstrates a great potential in reducing the false negative rate while maintaining a high precision. In this paper, we propose a novel anchor free polyp detector that can localize polyps without using predefined anchor boxes. To further strengthen the model, we leverage a Context Enhancement Module and Cosine Ground truth Projection. Our approach can respond in real time while achieving state-of-the-art performance with 99.36% precision and 96.44% recall.
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 https://github.com/HuCaoFighting/Swin-Unet.
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