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Register a new userPSGR: Pixel-wise Sparse Graph Reasoning for COVID-19 Pneumonia Segmentation in CT Images
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Added by
Yong Xia
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Automated and accurate segmentation of the infected regions in computed tomography (CT) images is critical for the prediction of the pathological stage and treatment response of COVID-19. Several deep convolutional neural networks (DCNNs) have been designed for this task, whose performance, however, tends to be suppressed by their limited local receptive fields and insufficient global reasoning ability. In this paper, we propose a pixel-wise sparse graph reasoning (PSGR) module and insert it into a segmentation network to enhance the modeling of long-range dependencies for COVID-19 infected region segmentation in CT images. In the PSGR module, a graph is first constructed by projecting each pixel on a node based on the features produced by the segmentation backbone, and then converted into a sparsely-connected graph by keeping only K strongest connections to each uncertain pixel. The long-range information reasoning is performed on the sparsely-connected graph to generate enhanced features. The advantages of this module are two-fold: (1) the pixel-wise mapping strategy not only avoids imprecise pixel-to-node projections but also preserves the inherent information of each pixel for global reasoning; and (2) the sparsely-connected graph construction results in effective information retrieval and reduction of the noise propagation. The proposed solution has been evaluated against four widely-used segmentation models on three public datasets. The results show that the segmentation model equipped with our PSGR module can effectively segment COVID-19 infected regions in CT images, outperforming all other competing models.
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The new coronavirus infection has shocked the world since early 2020 with its aggressive outbreak. Rapid detection of the disease saves lives, and relying on medical imaging (Computed Tomography and X-ray) to detect infected lungs has shown to be effective. Deep learning and convolutional neural networks have been used for image analysis in this context. However, accurate identification of infected regions has proven challenging for two main reasons. Firstly, the characteristics of infected areas differ in different images. Secondly, insufficient training data makes it challenging to train various machine learning algorithms, including deep-learning models. This paper proposes an approach to segment lung regions infected by COVID-19 to help cardiologists diagnose the disease more accurately, faster, and more manageable. We propose a bifurcated 2-D model for two types of segmentation. This model uses a shared encoder and a bifurcated connection to two separate decoders. One decoder is for segmentation of the healthy region of the lungs, while the other is for the segmentation of the infected regions. Experiments on publically available images show that the bifurcated structure segments infected regions of the lungs better than state of the art.
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 capability of generalization to unseen domains is crucial for deep learning models when considering real-world scenarios. However, current available medical image datasets, such as those for COVID-19 CT images, have large variations of infections and domain shift problems. To address this issue, we propose a prior knowledge driven domain adaptation and a dual-domain enhanced self-correction learning scheme. Based on the novel learning schemes, a domain adaptation based self-correction model (DASC-Net) is proposed for COVID-19 infection segmentation on CT images. DASC-Net consists of a novel attention and feature domain enhanced domain adaptation model (AFD-DA) to solve the domain shifts and a self-correction learning process to refine segmentation results. The innovations in AFD-DA include an image-level activation feature extractor with attention to lung abnormalities and a multi-level discrimination module for hierarchical feature domain alignment. The proposed self-correction learning process adaptively aggregates the learned model and corresponding pseudo labels for the propagation of aligned source and target domain information to alleviate the overfitting to noises caused by pseudo labels. Extensive experiments over three publicly available COVID-19 CT datasets demonstrate that DASC-Net consistently outperforms state-of-the-art segmentation, domain shift, and coronavirus infection segmentation methods. Ablation analysis further shows the effectiveness of the major components in our model. The DASC-Net enriches the theory of domain adaptation and self-correction learning in medical imaging and can be generalized to multi-site COVID-19 infection segmentation on CT images for clinical deployment.
Coronavirus Disease 2019 (COVID-19) has spread aggressively across the world causing an existential health crisis. Thus, having a system that automatically detects COVID-19 in tomography (CT) images can assist in quantifying the severity of the illness. Unfortunately, labelling chest CT scans requires significant domain expertise, time, and effort. We address these labelling challenges by only requiring point annotations, a single pixel for each infected region on a CT image. This labeling scheme allows annotators to label a pixel in a likely infected region, only taking 1-3 seconds, as opposed to 10-15 seconds to segment a region. Conventionally, segmentation models train on point-level annotations using the cross-entropy loss function on these labels. However, these models often suffer from low precision. Thus, we propose a consistency-based (CB) loss function that encourages the output predictions to be consistent with spatial transformations of the input images. The experiments on 3 open-source COVID-19 datasets show that this loss function yields significant improvement over conventional point-level loss functions and almost matches the performance of models trained with full supervision with much less human effort. Code is available at: url{https://github.com/IssamLaradji/covid19_weak_supervision}.
CT imaging is crucial for diagnosis, assessment and staging COVID-19 infection. Follow-up scans every 3-5 days are often recommended for disease progression. It has been reported that bilateral and peripheral ground glass opacification (GGO) with or without consolidation are predominant CT findings in COVID-19 patients. However, due to lack of computerized quantification tools, only qualitative impression and rough description of infected areas are currently used in radiological reports. In this paper, a deep learning (DL)-based segmentation system is developed to automatically quantify infection regions of interest (ROIs) and their volumetric ratios w.r.t. the lung. The performance of the system was evaluated by comparing the automatically segmented infection regions with the manually-delineated ones on 300 chest CT scans of 300 COVID-19 patients. For fast manual delineation of training samples and possible manual intervention of automatic results, a human-in-the-loop (HITL) strategy has been adopted to assist radiologists for infection region segmentation, which dramatically reduced the total segmentation time to 4 minutes after 3 iterations of model updating. The average Dice simiarility coefficient showed 91.6% agreement between automatic and manual infaction segmentations, and the mean estimation error of percentage of infection (POI) was 0.3% for the whole lung. Finally, possible applications, including but not limited to analysis of follow-up CT scans and infection distributions in the lobes and segments correlated with clinical findings, were discussed.
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