Dense regression activation maps for lesion segmentation in CT scans of COVID-19 patients.

Automatic lesion segmentation on thoracic CT enables rapid quantitative analysis of lung involvement in COVID-19 infections. However, obtaining a large amount of voxel-level annotations for training segmentation networks is prohibitively expensive. Therefore, we propose a weakly-supervised segmentation method based on dense regression activation maps (dRAMs). Most weakly-supervised segmentation approaches exploit class activation maps (CAMs) to localize objects. However, because CAMs were trained for classification, they do not align precisely with the object segmentations. Instead, we produce high-resolution activation maps using dense features from a segmentation network that was trained to estimate a per-lobe lesion percentage. In this way, the network can exploit knowledge regarding the required lesion volume. In addition, we propose an attention neural network module to refine dRAMs, optimized together with the main regression task. We evaluated our algorithm on 90 subjects. Results show our method achieved 70.2% Dice coefficient, substantially outperforming the CAM-based baseline at 48.6%. We published our source code at https://github.com/DIAGNijmegen/bodyct-dram.

Automated COVID-19 Grading With Convolutional Neural Networks in Computed Tomography Scans: A Systematic Comparison.

Amidst the ongoing pandemic, the assessment of computed tomography (CT) images for COVID-19 presence can exceed the workload capacity of radiologists. Several studies addressed this issue by automating COVID-19 classification and grading from CT images with convolutional neural networks (CNNs). Many of these studies reported initial results of algorithms that were assembled from commonly used components. However, the choice of the components of these algorithms was often pragmatic rather than systematic and systems were not compared to each other across papers in a fair manner. We systematically investigated the effectiveness of using 3-D CNNs instead of 2-D CNNs for seven commonly used architectures, including DenseNet, Inception, and ResNet variants. For the architecture that performed best, we furthermore investigated the effect of initializing the network with pretrained weights, providing automatically computed lesion maps as additional network input, and predicting a continuous instead of a categorical output. A 3-D DenseNet-201 with these components achieved an area under the receiver operating characteristic curve of 0.930 on our test set of 105 CT scans and an AUC of 0.919 on a publicly available set of 742 CT scans, a substantial improvement in comparison with a previously published 2-D CNN. This article provides insights into the performance benefits of various components for COVID-19 classification and grading systems. We have created a challenge on grand-challenge.org to allow for a fair comparison between the results of this and future research.

Deep learning with robustness to missing data: A novel approach to the detection of COVID-19.

In the context of the current global pandemic and the limitations of the RT-PCR test, we propose a novel deep learning architecture, DFCN (Denoising Fully Connected Network). Since medical facilities around the world differ enormously in what laboratory tests or chest imaging may be available, DFCN is designed to be robust to missing input data. An ablation study extensively evaluates the performance benefits of the DFCN as well as its robustness to missing inputs. Data from 1088 patients with confirmed RT-PCR results are obtained from two independent medical facilities. The data includes results from 27 laboratory tests and a chest x-ray scored by a deep learning model. Training and test datasets are taken from different medical facilities. Data is made publicly available. The performance of DFCN in predicting the RT-PCR result is compared with 3 related architectures as well as a Random Forest baseline. All models are trained with varying levels of masked input data to encourage robustness to missing inputs. Missing data is simulated at test time by masking inputs randomly. DFCN outperforms all other models with statistical significance using random subsets of input data with 2-27 available inputs. When all 28 inputs are available DFCN obtains an AUC of 0.924, higher than any other model. Furthermore, with clinically meaningful subsets of parameters consisting of just 6 and 7 inputs respectively, DFCN achieves higher AUCs than any other model, with values of 0.909 and 0.919.

Automated Assessment of COVID-19 Reporting and Data System and Chest CT Severity Scores in Patients Suspected of Having COVID-19 Using Artificial Intelligence.

Background The coronavirus disease 2019 (COVID-19) pandemic has spread across the globe with alarming speed, morbidity, and mortality. Immediate triage of patients with chest infections suspected to be caused by COVID-19 using chest CT may be of assistance when results from definitive viral testing are delayed. Purpose To develop and validate an artificial intelligence (AI) system to score the likelihood and extent of pulmonary COVID-19 on chest CT scans using the COVID-19 Reporting and Data System (CO-RADS) and CT severity scoring systems. Materials and Methods The CO-RADS AI system consists of three deep-learning algorithms that automatically segment the five pulmonary lobes, assign a CO-RADS score for the suspicion of COVID-19, and assign a CT severity score for the degree of parenchymal involvement per lobe. This study retrospectively included patients who underwent a nonenhanced chest CT examination because of clinical suspicion of COVID-19 at two medical centers. The system was trained, validated, and tested with data from one of the centers. Data from the second center served as an external test set. Diagnostic performance and agreement with scores assigned by eight independent observers were measured using receiver operating characteristic analysis, linearly weighted κ values, and classification accuracy. Results A total of 105 patients (mean age, 62 years ± 16 [standard deviation]; 61 men) and 262 patients (mean age, 64 years ± 16; 154 men) were evaluated in the internal and external test sets, respectively. The system discriminated between patients with COVID-19 and those without COVID-19, with areas under the receiver operating characteristic curve of 0.95 (95% CI: 0.91, 0.98) and 0.88 (95% CI: 0.84, 0.93), for the internal and external test sets, respectively. Agreement with the eight human observers was moderate to substantial, with mean linearly weighted κ values of 0.60 ± 0.01 for CO-RADS scores and 0.54 ± 0.01 for CT severity scores. Conclusion With high diagnostic performance, the CO-RADS AI system correctly identified patients with COVID-19 using chest CT scans and assigned standardized CO-RADS and CT severity scores that demonstrated good agreement with findings from eight independent observers and generalized well to external data. © RSNA, 2020 Supplemental material is available for this article.

COVID-19 on Chest Radiographs: A Multireader Evaluation of an Artificial Intelligence System.

Background Chest radiography may play an important role in triage for coronavirus disease 2019 (COVID-19), particularly in low-resource settings. Purpose To evaluate the performance of an artificial intelligence (AI) system for detection of COVID-19 pneumonia on chest radiographs. Materials and Methods An AI system (CAD4COVID-XRay) was trained on 24 678 chest radiographs, including 1540 used only for validation while training. The test set consisted of a set of continuously acquired chest radiographs (n = 454) obtained in patients suspected of having COVID-19 pneumonia between March 4 and April 6, 2020, at one center (223 patients with positive reverse transcription polymerase chain reaction [RT-PCR] results, 231 with negative RT-PCR results). Radiographs were independently analyzed by six readers and by the AI system. Diagnostic performance was analyzed with the receiver operating characteristic curve. Results For the test set, the mean age of patients was 67 years ± 14.4 (standard deviation) (56% male). With RT-PCR test results as the reference standard, the AI system correctly classified chest radiographs as COVID-19 pneumonia with an area under the receiver operating characteristic curve of 0.81. The system significantly outperformed each reader (P < .001 using the McNemar test) at their highest possible sensitivities. At their lowest sensitivities, only one reader significantly outperformed the AI system (P = .04). Conclusion The performance of an artificial intelligence system in the detection of coronavirus disease 2019 on chest radiographs was comparable with that of six independent readers. © RSNA, 2020.

Relational Modeling for Robust and Efficient Pulmonary Lobe Segmentation in CT Scans.

Pulmonary lobe segmentation in computed tomography scans is essential for regional assessment of pulmonary diseases. Recent works based on convolution neural networks have achieved good performance for this task. However, they are still limited in capturing structured relationships due to the nature of convolution. The shape of the pulmonary lobes affect each other and their borders relate to the appearance of other structures, such as vessels, airways, and the pleural wall. We argue that such structural relationships play a critical role in the accurate delineation of pulmonary lobes when the lungs are affected by diseases such as COVID-19 or COPD. In this paper, we propose a relational approach (RTSU-Net) that leverages structured relationships by introducing a novel non-local neural network module. The proposed module learns both visual and geometric relationships among all convolution features to produce self-attention weights. With a limited amount of training data available from COVID-19 subjects, we initially train and validate RTSU-Net on a cohort of 5000 subjects from the COPDGene study (4000 for training and 1000 for evaluation). Using models pre-trained on COPDGene, we apply transfer learning to retrain and evaluate RTSU-Net on 470 COVID-19 suspects (370 for retraining and 100 for evaluation). Experimental results show that RTSU-Net outperforms three baselines and performs robustly on cases with severe lung infection due to COVID-19.

CO-RADS: A Categorical CT Assessment Scheme for Patients Suspected of Having COVID-19-Definition and Evaluation.

Background A categorical CT assessment scheme for suspicion of pulmonary involvement of coronavirus disease 2019 (COVID-19 provides a basis for gathering scientific evidence and improved communication with referring physicians. Purpose To introduce the COVID-19 Reporting and Data System (CO-RADS) for use in the standardized assessment of pulmonary involvement of COVID-19 on unenhanced chest CT images and to report its initial interobserver agreement and performance. Materials and Methods The Dutch Radiological Society developed CO-RADS based on other efforts for standardization, such as the Lung Imaging Reporting and Data System or Breast Imaging Reporting and Data System. CO-RADS assesses the suspicion for pulmonary involvement of COVID-19 on a scale from 1 (very low) to 5 (very high). The system is meant to be used in patients with moderate to severe symptoms of COVID-19. The system was evaluated by using 105 chest CT scans of patients admitted to the hospital with clinical suspicion of COVID-19 and in whom reverse transcription-polymerase chain reaction (RT-PCR) was performed (mean, 62 years ± 16 [standard deviation]; 61 men, 53 with positive RT-PCR results). Eight observers used CO-RADS to assess the scans. Fleiss κ value was calculated, and scores of individual observers were compared with the median of the remaining seven observers. The resulting area under the receiver operating characteristics curve (AUC) was compared with results from RT-PCR and clinical diagnosis of COVID-19. Results There was absolute agreement among observers in 573 (68.2%) of 840 observations. Fleiss κ value was 0.47 (95% confidence interval [CI]: 0.45, 0.47), with the highest κ value for CO-RADS categories 1 (0.58, 95% CI: 0.54, 0.62) and 5 (0.68, 95% CI: 0.65, 0.72). The average AUC was 0.91 (95% CI: 0.85, 0.97) for predicting RT-PCR outcome and 0.95 (95% CI: 0.91, 0.99) for clinical diagnosis. The false-negative rate for CO-RADS 1 was nine of 161 cases (5.6%; 95% CI: 1.0%, 10%), and the false-positive rate for CO-RADS category 5 was one of 286 (0.3%; 95% CI: 0%, 1.0%). Conclusion The coronavirus disease 2019 (COVID-19) Reporting and Data System (CO-RADS) is a categorical assessment scheme for pulmonary involvement of COVID-19 at unenhanced chest CT that performs very well in predicting COVID-19 in patients with moderate to severe symptoms and has substantial interobserver agreement, especially for categories 1 and 5. © RSNA, 2020 Online supplemental material is available for this article.