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Register a new userCOVID CT-Net: Predicting Covid-19 From Chest CT Images Using Attentional Convolutional Network
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The novel corona-virus disease (COVID-19) pandemic has caused a major outbreak in more than 200 countries around the world, leading to a severe impact on the health and life of many people globally. As of Aug 25th of 2020, more than 20 million people are infected, and more than 800,000 death are reported. Computed Tomography (CT) images can be used as a as an alternative to the time-consuming reverse transcription polymerase chain reaction (RT-PCR) test, to detect COVID-19. In this work we developed a deep learning framework to predict COVID-19 from CT images. We propose to use an attentional convolution network, which can focus on the infected areas of chest, enabling it to perform a more accurate prediction. We trained our model on a dataset of more than 2000 CT images, and report its performance in terms of various popular metrics, such as sensitivity, specificity, area under the curve, and also precision-recall curve, and achieve very promising results. We also provide a visualization of the attention maps of the model for several test images, and show that our model is attending to the infected regions as intended. In addition to developing a machine learning modeling framework, we also provide the manual annotation of the potentionally infected regions of chest, with the help of a board-certified radiologist, and make that publicly available for other researchers.
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The health and socioeconomic difficulties caused by the COVID-19 pandemic continues to cause enormous tensions around the world. In particular, this extraordinary surge in the number of cases has put considerable strain on health care systems around the world. A critical step in the treatment and management of COVID-19 positive patients is severity assessment, which is challenging even for expert radiologists given the subtleties at different stages of lung disease severity. Motivated by this challenge, we introduce COVID-Net CT-S, a suite of deep convolutional neural networks for predicting lung disease severity due to COVID-19 infection. More specifically, a 3D residual architecture design is leveraged to learn volumetric visual indicators characterizing the degree of COVID-19 lung disease severity. Experimental results using the patient cohort collected by the China National Center for Bioinformation (CNCB) showed that the proposed COVID-Net CT-S networks, by leveraging volumetric features, can achieve significantly improved severity assessment performance when compared to traditional severity assessment networks that learn and leverage 2D visual features to characterize COVID-19 severity.
The novel corona-virus disease (COVID-19) pandemic has caused a major outbreak in more than 200 countries around the world, leading to a severe impact on the health and life of many people globally. As of mid-July 2020, more than 12 million people were infected, and more than 570,000 death were reported. Computed Tomography (CT) images can be used as an alternative to the time-consuming RT-PCR test, to detect COVID-19. In this work we propose a segmentation framework to detect chest regions in CT images, which are infected by COVID-19. We use an architecture similar to U-Net model, and train it to detect ground glass regions, on pixel level. As the infected regions tend to form a connected component (rather than randomly distributed pixels), we add a suitable regularization term to the loss function, to promote connectivity of the segmentation map for COVID-19 pixels. 2D-anisotropic total-variation is used for this purpose, and therefore the proposed model is called TV-UNet. Through experimental results on a relatively large-scale CT segmentation dataset of around 900 images, we show that adding this new regularization term leads to 2% gain on overall segmentation performance compared to the U-Net model. Our experimental analysis, ranging from visual evaluation of the predicted segmentation results to quantitative assessment of segmentation performance (precision, recall, Dice score, and mIoU) demonstrated great ability to identify COVID-19 associated regions of the lungs, achieving a mIoU rate of over 99%, and a Dice score of around 86%.
A novel coronavirus disease 2019 (COVID-19) was detected and has spread rapidly across various countries around the world since the end of the year 2019, Computed Tomography (CT) images have been used as a crucial alternative to the time-consuming RT-PCR test. However, pure manual segmentation of CT images faces a serious challenge with the increase of suspected cases, resulting in urgent requirements for accurate and automatic segmentation of COVID-19 infections. Unfortunately, since the imaging characteristics of the COVID-19 infection are diverse and similar to the backgrounds, existing medical image segmentation methods cannot achieve satisfactory performance. In this work, we try to establish a new deep convolutional neural network tailored for segmenting the chest CT images with COVID-19 infections. We firstly maintain a large and new chest CT image dataset consisting of 165,667 annotated chest CT images from 861 patients with confirmed COVID-19. Inspired by the observation that the boundary of the infected lung can be enhanced by adjusting the global intensity, in the proposed deep CNN, we introduce a feature variation block which adaptively adjusts the global properties of the features for segmenting COVID-19 infection. The proposed FV block can enhance the capability of feature representation effectively and adaptively for diverse cases. We fuse features at different scales by proposing Progressive Atrous Spatial Pyramid Pooling to handle the sophisticated infection areas with diverse appearance and shapes. We conducted experiments on the data collected in China and Germany and show that the proposed deep CNN can produce impressive performance effectively.
Coronavirus Disease 2019 (COVID-19) spread globally in early 2020, causing the world to face an existential health crisis. Automated detection of lung infections from computed tomography (CT) images offers a great potential to augment the traditional healthcare strategy for tackling COVID-19. However, segmenting infected regions from CT slices faces several challenges, including high variation in infection characteristics, and low intensity contrast between infections and normal tissues. Further, collecting a large amount of data is impractical within a short time period, inhibiting the training of a deep model. To address these challenges, a novel COVID-19 Lung Infection Segmentation Deep Network (Inf-Net) is proposed to automatically identify infected regions from chest CT slices. In our Inf-Net, a parallel partial decoder is used to aggregate the high-level features and generate a global map. Then, the implicit reverse attention and explicit edge-attention are utilized to model the boundaries and enhance the representations. Moreover, to alleviate the shortage of labeled data, we present a semi-supervised segmentation framework based on a randomly selected propagation strategy, which only requires a few labeled images and leverages primarily unlabeled data. Our semi-supervised framework can improve the learning ability and achieve a higher performance. Extensive experiments on our COVID-SemiSeg and real CT volumes demonstrate that the proposed Inf-Net outperforms most cutting-edge segmentation models and advances the state-of-the-art performance.
The novel coronavirus disease 2019 (COVID-19) has been spreading rapidly around the world and caused significant impact on the public health and economy. However, there is still lack of studies on effectively quantifying the lung infection caused by COVID-19. As a basic but challenging task of the diagnostic framework, segmentation plays a crucial role in accurate quantification of COVID-19 infection measured by computed tomography (CT) images. To this end, we proposed a novel deep learning algorithm for automated segmentation of multiple COVID-19 infection regions. Specifically, we use the Aggregated Residual Transformations to learn a robust and expressive feature representation and apply the soft attention mechanism to improve the capability of the model to distinguish a variety of symptoms of the COVID-19. With a public CT image dataset, we validate the efficacy of the proposed algorithm in comparison with other competing methods. Experimental results demonstrate the outstanding performance of our algorithm for automated segmentation of COVID-19 Chest CT images. Our study provides a promising deep leaning-based segmentation tool to lay a foundation to quantitative diagnosis of COVID-19 lung infection in CT images.
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