Automated detection of genetic relatedness from fundus photographs using Siamese Neural Networks.

Heritability of common eye diseases and ocular traits are relatively high. Here, we develop an automated algorithm to detect genetic relatedness from color fundus photographs (FPs). We estimated the degree of shared ancestry amongst individuals in the UK Biobank using KING software. A convolutional Siamese neural network-based algorithm was trained to output a measure of genetic relatedness using 7224 pairs (3612 related and 3612 unrelated) of FPs. The model achieved high performance for prediction of genetic relatedness; when computed Euclidean distances were used to determine probability of relatedness, the area under the receiver operating characteristic curve (AUROC) for identifying related FPs reached 0.926. We performed external validation of our model using FPs from the LIFE-Adult study and achieved an AUROC of 0.69. An occlusion map indicates that the optic nerve and its surrounding area may be the most predictive of genetic relatedness. We demonstrate that genetic relatedness can be captured from FP features. This approach may be used to uncover novel biomarkers for common ocular diseases.

Multi-population generalizability of a deep learning-based chest radiograph severity score for COVID-19.

To tune and test the generalizability of a deep learning-based model for assessment of COVID-19 lung disease severity on chest radiographs (CXRs) from different patient populations. A published convolutional Siamese neural network-based model previously trained on hospitalized patients with COVID-19 was tuned using 250 outpatient CXRs. This model produces a quantitative measure of COVID-19 lung disease severity (pulmonary x-ray severity (PXS) score). The model was evaluated on CXRs from 4 test sets, including 3 from the United States (patients hospitalized at an academic medical center (N = 154), patients hospitalized at a community hospital (N = 113), and outpatients (N = 108)) and 1 from Brazil (patients at an academic medical center emergency department (N = 303)). Radiologists from both countries independently assigned reference standard CXR severity scores, which were correlated with the PXS scores as a measure of model performance (Pearson R). The Uniform Manifold Approximation and Projection (UMAP) technique was used to visualize the neural network results. Tuning the deep learning model with outpatient data showed high model performance in 2 United States hospitalized patient datasets (R = 0.88 and R = 0.90, compared to baseline R = 0.86). Model performance was similar, though slightly lower, when tested on the United States outpatient and Brazil emergency department datasets (R = 0.86 and R = 0.85, respectively). UMAP showed that the model learned disease severity information that generalized across test sets. A deep learning model that extracts a COVID-19 severity score on CXRs showed generalizable performance across multiple populations from 2 continents, including outpatients and hospitalized patients.

QU-BraTS: MICCAI BraTS 2020 Challenge on Quantifying Uncertainty in Brain Tumor Segmentation - Analysis of Ranking Scores and Benchmarking Results.

Deep learning (DL) models have provided state-of-the-art performance in various medical imaging benchmarking challenges, including the Brain Tumor Segmentation (BraTS) challenges. However, the task of focal pathology multi-compartment segmentation (e.g., tumor and lesion sub-regions) is particularly challenging, and potential errors hinder translating DL models into clinical workflows. Quantifying the reliability of DL model predictions in the form of uncertainties could enable clinical review of the most uncertain regions, thereby building trust and paving the way toward clinical translation. Several uncertainty estimation methods have recently been introduced for DL medical image segmentation tasks. Developing scores to evaluate and compare the performance of uncertainty measures will assist the end-user in making more informed decisions. In this study, we explore and evaluate a score developed during the BraTS 2019 and BraTS 2020 task on uncertainty quantification (QU-BraTS) and designed to assess and rank uncertainty estimates for brain tumor multi-compartment segmentation. This score (1) rewards uncertainty estimates that produce high confidence in correct assertions and those that assign low confidence levels at incorrect assertions, and (2) penalizes uncertainty measures that lead to a higher percentage of under-confident correct assertions. We further benchmark the segmentation uncertainties generated by 14 independent participating teams of QU-BraTS 2020, all of which also participated in the main BraTS segmentation task. Overall, our findings confirm the importance and complementary value that uncertainty estimates provide to segmentation algorithms, highlighting the need for uncertainty quantification in medical image analyses. Finally, in favor of transparency and reproducibility, our evaluation code is made publicly available at https://github.com/RagMeh11/QU-BraTS.

Assessing the Trustworthiness of Saliency Maps for Localizing Abnormalities in Medical Imaging.

PURPOSE: To evaluate the trustworthiness of saliency maps for abnormality localization in medical imaging. MATERIALS AND METHODS: Using two large publicly available radiology datasets (Society for Imaging Informatics in Medicine-American College of Radiology Pneumothorax Segmentation dataset and Radiological Society of North America Pneumonia Detection Challenge dataset), the performance of eight commonly used saliency map techniques were quantified in regard to (a) localization utility (segmentation and detection), (b) sensitivity to model weight randomization, (c) repeatability, and (d) reproducibility. Their performances versus baseline methods and localization network architectures were compared, using area under the precision-recall curve (AUPRC) and structural similarity index measure (SSIM) as metrics. RESULTS: All eight saliency map techniques failed at least one of the criteria and were inferior in performance compared with localization networks. For pneumothorax segmentation, the AUPRC ranged from 0.024 to 0.224, while a U-Net achieved a significantly superior AUPRC of 0.404 (P < .005). For pneumonia detection, the AUPRC ranged from 0.160 to 0.519, while a RetinaNet achieved a significantly superior AUPRC of 0.596 (P <.005). Five and two saliency methods (of eight) failed the model randomization test on the segmentation and detection datasets, respectively, suggesting that these methods are not sensitive to changes in model parameters. The repeatability and reproducibility of the majority of the saliency methods were worse than localization networks for both the segmentation and detection datasets. CONCLUSION: The use of saliency maps in the high-risk domain of medical imaging warrants additional scrutiny and recommend that detection or segmentation models be used if localization is the desired output of the network.Keywords: Technology Assessment, Technical Aspects, Feature Detection, Convolutional Neural Network (CNN) Supplemental material is available for this article. © RSNA, 2021.

Improvement and Multi-Population Generalizability of a Deep Learning-Based Chest Radiograph Severity Score for COVID-19.

PURPOSE: To improve and test the generalizability of a deep learning-based model for assessment of COVID-19 lung disease severity on chest radiographs (CXRs) from different patient populations. MATERIALS AND METHODS: A published convolutional Siamese neural network-based model previously trained on hospitalized patients with COVID-19 was tuned using 250 outpatient CXRs. This model produces a quantitative measure of COVID-19 lung disease severity (pulmonary x-ray severity (PXS) score). The model was evaluated on CXRs from four test sets, including 3 from the United States (patients hospitalized at an academic medical center (N=154), patients hospitalized at a community hospital (N=113), and outpatients (N=108)) and 1 from Brazil (patients at an academic medical center emergency department (N=303)). Radiologists from both countries independently assigned reference standard CXR severity scores, which were correlated with the PXS scores as a measure of model performance (Pearson r). The Uniform Manifold Approximation and Projection (UMAP) technique was used to visualize the neural network results. RESULTS: Tuning the deep learning model with outpatient data improved model performance in two United States hospitalized patient datasets (r=0.88 and r=0.90, compared to baseline r=0.86). Model performance was similar, though slightly lower, when tested on the United States outpatient and Brazil emergency department datasets (r=0.86 and r=0.85, respectively). UMAP showed that the model learned disease severity information that generalized across test sets. CONCLUSIONS: Performance of a deep learning-based model that extracts a COVID-19 severity score on CXRs improved using training data from a different patient cohort (outpatient versus hospitalized) and generalized across multiple populations.

Automated assessment of COVID-19 pulmonary disease severity on chest radiographs using convolutional Siamese neural networks.

Purpose To develop an automated measure of COVID-19 pulmonary disease severity on chest radiographs (CXRs), for longitudinal disease evaluation and clinical risk stratification. Materials and Methods A convolutional Siamese neural network-based algorithm was trained to output a measure of pulmonary disease severity on anterior-posterior CXRs (pulmonary x-ray severity (PXS) score), using weakly-supervised pretraining on ~160,000 images from CheXpert and transfer learning on 314 CXRs from patients with COVID-19. The algorithm was evaluated on internal and external test sets from different hospitals, containing 154 and 113 CXRs respectively. The PXS score was correlated with a radiographic severity score independently assigned by two thoracic radiologists and one in-training radiologist. For 92 internal test set patients with follow-up CXRs, the change in PXS score was compared to radiologist assessments of change. The association between PXS score and subsequent intubation or death was assessed. Results The PXS score correlated with the radiographic pulmonary disease severity score assigned to CXRs in the COVID-19 internal and external test sets (ρ=0.84 and ρ=0.78 respectively). The direction of change in PXS score in follow-up CXRs agreed with radiologist assessment (ρ=0.74). In patients not intubated on the admission CXR, the PXS score predicted subsequent intubation or death within three days of hospital admission (area under the receiver operator characteristic curve=0.80 (95%CI 0.75-0.85)). Conclusion A Siamese neural network-based severity score automatically measures COVID-19 pulmonary disease severity in chest radiographs, which can be scaled and rapidly deployed for clinical triage and workflow optimization.

Multi-Institutional Assessment and Crowdsourcing Evaluation of Deep Learning for Automated Classification of Breast Density.

OBJECTIVE: We developed deep learning algorithms to automatically assess BI-RADS breast density. METHODS: Using a large multi-institution patient cohort of 108,230 digital screening mammograms from the Digital Mammographic Imaging Screening Trial, we investigated the effect of data, model, and training parameters on overall model performance and provided crowdsourcing evaluation from the attendees of the ACR 2019 Annual Meeting. RESULTS: Our best-performing algorithm achieved good agreement with radiologists who were qualified interpreters of mammograms, with a four-class κ of 0.667. When training was performed with randomly sampled images from the data set versus sampling equal number of images from each density category, the model predictions were biased away from the low-prevalence categories such as extremely dense breasts. The net result was an increase in sensitivity and a decrease in specificity for predicting dense breasts for equal class compared with random sampling. We also found that the performance of the model degrades when we evaluate on digital mammography data formats that differ from the one that we trained on, emphasizing the importance of multi-institutional training sets. Lastly, we showed that crowdsourced annotations, including those from attendees who routinely read mammograms, had higher agreement with our algorithm than with the original interpreting radiologists. CONCLUSION: We demonstrated the possible parameters that can influence the performance of the model and how crowdsourcing can be used for evaluation. This study was performed in tandem with the development of the ACR AI-LAB, a platform for democratizing artificial intelligence.

Automated Assessment and Tracking of COVID-19 Pulmonary Disease Severity on Chest Radiographs using Convolutional Siamese Neural Networks.

PURPOSE: To develop an automated measure of COVID-19 pulmonary disease severity on chest radiographs (CXRs), for longitudinal disease tracking and outcome prediction. MATERIALS AND METHODS: A convolutional Siamese neural network-based algorithm was trained to output a measure of pulmonary disease severity on CXRs (pulmonary x-ray severity (PXS) score), using weakly-supervised pretraining on ∼160,000 anterior-posterior images from CheXpert and transfer learning on 314 frontal CXRs from COVID-19 patients. The algorithm was evaluated on internal and external test sets from different hospitals (154 and 113 CXRs respectively). PXS scores were correlated with radiographic severity scores independently assigned by two thoracic radiologists and one in-training radiologist (Pearson r). For 92 internal test set patients with follow-up CXRs, PXS score change was compared to radiologist assessments of change (Spearman ρ). The association between PXS score and subsequent intubation or death was assessed. Bootstrap 95% confidence intervals (CI) were calculated. RESULTS: PXS scores correlated with radiographic pulmonary disease severity scores assigned to CXRs in the internal and external test sets (r=0.86 (95%CI 0.80-0.90) and r=0.86 (95%CI 0.79-0.90) respectively). The direction of change in PXS score in follow-up CXRs agreed with radiologist assessment (ρ=0.74 (95%CI 0.63-0.81)). In patients not intubated on the admission CXR, the PXS score predicted subsequent intubation or death within three days of hospital admission (area under the receiver operating characteristic curve=0.80 (95%CI 0.75-0.85)). CONCLUSION: A Siamese neural network-based severity score automatically measures radiographic COVID-19 pulmonary disease severity, which can be used to track disease change and predict subsequent intubation or death.