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Register a new userRapid quantification of COVID-19 pneumonia burden from computed tomography with convolutional LSTM networks
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Quantitative lung measures derived from computed tomography (CT) have been demonstrated to improve prognostication in coronavirus disease (COVID-19) patients, but are not part of the clinical routine since required manual segmentation of lung lesions is prohibitively time-consuming. We propose a new fully automated deep learning framework for rapid quantification and differentiation between lung lesions in COVID-19 pneumonia from both contrast and non-contrast CT images using convolutional Long Short-Term Memory (ConvLSTM) networks. Utilizing the expert annotations, model training was performed 5 times with separate hold-out sets using 5-fold cross-validation to segment ground-glass opacity and high opacity (including consolidation and pleural effusion). The performance of the method was evaluated on CT data sets from 197 patients with positive reverse transcription polymerase chain reaction test result for SARS-CoV-2. Strong agreement between expert manual and automatic segmentation was obtained for lung lesions with a Dice score coefficient of 0.876 $pm$ 0.005; excellent correlations of 0.978 and 0.981 for ground-glass opacity and high opacity volumes. In the external validation set of 67 patients, there was dice score coefficient of 0.767 $pm$ 0.009 as well as excellent correlations of 0.989 and 0.996 for ground-glass opacity and high opacity volumes. Computations for a CT scan comprising 120 slices were performed under 2 seconds on a personal computer equipped with NVIDIA Titan RTX graphics processing unit. Therefore, our deep learning-based method allows rapid fully-automated quantitative measurement of pneumonia burden from CT and may generate results with an accuracy similar to the expert readers.
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Detecting COVID-19 in computed tomography (CT) or radiography images has been proposed as a supplement to the definitive RT-PCR test. We present a deep learning ensemble for detecting COVID-19 infection, combining slice-based (2D) and volume-based (3D) approaches. The 2D system detects the infection on each CT slice independently, combining them to obtain the patient-level decision via different methods (averaging and long-short term memory networks). The 3D system takes the whole CT volume to arrive to the patient-level decision in one step. A new high resolution chest CT scan dataset, called the IST-C dataset, is also collected in this work. The proposed ensemble, called IST-CovNet, obtains 90.80% accuracy and 0.95 AUC score overall on the IST-C dataset in detecting COVID-19 among normal controls and other types of lung pathologies; and 93.69% accuracy and 0.99 AUC score on the publicly available MosMed dataset that consists of COVID-19 scans and normal controls only. The system is deployed at Istanbul University Cerrahpasa School of Medicine.
Recently, accurate mandible segmentation in CT scans based on deep learning methods has attracted much attention. However, there still exist two major challenges, namely, metal artifacts among mandibles and large variations in shape or size among individuals. To address these two challenges, we propose a recurrent segmentation convolutional neural network (RSegCNN) that embeds segmentation convolutional neural network (SegCNN) into the recurrent neural network (RNN) for robust and accurate segmentation of the mandible. Such a design of the system takes into account the similarity and continuity of the mandible shapes captured in adjacent image slices in CT scans. The RSegCNN infers the mandible information based on the recurrent structure with the embedded encoder-decoder segmentation (SegCNN) components. The recurrent structure guides the system to exploit relevant and important information from adjacent slices, while the SegCNN component focuses on the mandible shapes from a single CT slice. We conducted extensive experiments to evaluate the proposed RSegCNN on two head and neck CT datasets. The experimental results show that the RSegCNN is significantly better than the state-of-the-art models for accurate mandible segmentation.
COVID-19 is a virus with high transmission rate that demands rapid identification of the infected patients to reduce the spread of the disease. The current gold-standard test, Reverse-Transcription Polymerase Chain Reaction (RT-PCR), has a high rate of false negatives. Diagnosing from CT-scan images as a more accurate alternative has the challenge of distinguishing COVID-19 from other pneumonia diseases. Artificial intelligence can help radiologists and physicians to accelerate the process of diagnosis, increase its accuracy, and measure the severity of the disease. We designed a new interpretable deep neural network to distinguish healthy people, patients with COVID-19, and patients with other pneumonia diseases from axial lung CT-scan images. Our model also detects the infected areas and calculates the percentage of the infected lung volume. We first preprocessed the images to eliminate the batch effects of different devices, and then adopted a weakly supervised method to train the model without having any tags for the infected parts. We trained and evaluated the model on a large dataset of 3359 samples from 6 different medical centers. The model reached sensitivities of 97.75% and 98.15%, and specificities of 87% and 81.03% in separating healthy people from the diseased and COVID-19 from other diseases, respectively. It also demonstrated similar performance for 1435 samples from 6 different medical centers which proves its generalizability. The performance of the model on a large diverse dataset, its generalizability, and interpretability makes it suitable to be used as a reliable diagnostic system.
Existing deep learning technologies generally learn the features of chest X-ray data generated by Generative Adversarial Networks (GAN) to diagnose COVID-19 pneumonia. However, the above methods have a critical challenge: data privacy. GAN will leak the semantic information of the training data which can be used to reconstruct the training samples by attackers, thereby this method will leak the privacy of the patient. Furthermore, for this reason that is the limitation of the training data sample, different hospitals jointly train the model through data sharing, which will also cause the privacy leakage. To solve this problem, we adopt the Federated Learning (FL) frame-work which is a new technique being used to protect the data privacy. Under the FL framework and Differentially Private thinking, we propose a FederatedDifferentially Private Generative Adversarial Network (FedDPGAN) to detectCOVID-19 pneumonia for sustainable smart cities. Specifically, we use DP-GAN to privately generate diverse patient data in which differential privacy technology is introduced to make sure the privacy protection of the semantic information of training dataset. Furthermore, we leverage FL to allow hospitals to collaboratively train COVID-19 models without sharing the original data. Under Independent and Identically Distributed (IID) and non-IID settings, The evaluation of the proposed model is on three types of chest X-ray (CXR) images dataset (COVID-19, normal, and normal pneumonia). A large number of the truthful reports make the verification of our model can effectively diagnose COVID-19 without compromising privacy.
The worldwide spread of coronavirus disease (COVID-19) has become a threatening risk for global public health. It is of great importance to rapidly and accurately screen patients with COVID-19 from community acquired pneumonia (CAP). In this study, a total of 1658 patients with COVID-19 and 1027 patients of CAP underwent thin-section CT. All images were preprocessed to obtain the segmentations of both infections and lung fields, which were used to extract location-specific features. An infection Size Aware Random Forest method (iSARF) was proposed, in which subjects were automated categorized into groups with different ranges of infected lesion sizes, followed by random forests in each group for classification. Experimental results show that the proposed method yielded sensitivity of 0.907, specificity of 0.833, and accuracy of 0.879 under five-fold cross-validation. Large performance margins against comparison methods were achieved especially for the cases with infection size in the medium range, from 0.01% to 10%. The further inclusion of Radiomics features show slightly improvement. It is anticipated that our proposed framework could assist clinical decision making.
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