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Register a new userDomain adaptation based self-correction model for COVID-19 infection segmentation in CT images
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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.
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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.
Early and accurate severity assessment of Coronavirus disease 2019 (COVID-19) based on computed tomography (CT) images offers a great help to the estimation of intensive care unit event and the clinical decision of treatment planning. To augment the labeled data and improve the generalization ability of the classification model, it is necessary to aggregate data from multiple sites. This task faces several challenges including class imbalance between mild and severe infections, domain distribution discrepancy between sites, and presence of heterogeneous features. In this paper, we propose a novel domain adaptation (DA) method with two components to address these problems. The first component is a stochastic class-balanced boosting sampling strategy that overcomes the imbalanced learning problem and improves the classification performance on poorly-predicted classes. The second component is a representation learning that guarantees three properties: 1) domain-transferability by prototype triplet loss, 2) discriminant by conditional maximum mean discrepancy loss, and 3) completeness by multi-view reconstruction loss. Particularly, we propose a domain translator and align the heterogeneous data to the estimated class prototypes (i.e., class centers) in a hyper-sphere manifold. Experiments on cross-site severity assessment of COVID-19 from CT images show that the proposed method can effectively tackle the imbalanced learning problem and outperform recent DA approaches.
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}.
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.
One of the key challenges in the battle against the Coronavirus (COVID-19) pandemic is to detect and quantify the severity of the disease in a timely manner. Computed tomographies (CT) of the lungs are effective for assessing the state of the infection. Unfortunately, labeling CT scans can take a lot of time and effort, with up to 150 minutes per scan. We address this challenge introducing a scalable, fast, and accurate active learning system that accelerates the labeling of CT scan images. Conventionally, active learning methods require the labelers to annotate whole images with full supervision, but that can lead to wasted efforts as many of the annotations could be redundant. Thus, our system presents the annotator with unlabeled regions that promise high information content and low annotation cost. Further, the system allows annotators to label regions using point-level supervision, which is much cheaper to acquire than per-pixel annotations. Our experiments on open-source COVID-19 datasets show that using an entropy-based method to rank unlabeled regions yields to significantly better results than random labeling of these regions. Also, we show that labeling small regions of images is more efficient than labeling whole images. Finally, we show that with only 7% of the labeling effort required to label the whole training set gives us around 90% of the performance obtained by training the model on the fully annotated training set. Code is available at: url{https://github.com/IssamLaradji/covid19_active_learning}.
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