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Open resource of clinical data from patients with pneumonia for the prediction of COVID-19 outcomes via deep learning.

ABSTRACT: Data from patients with coronavirus disease 2019 (COVID-19) are essential for guiding clinical decision making, for furthering the understanding of this viral disease, and for diagnostic modelling. Here, we describe an open resource containing data from 1,521 patients with pneumonia (including COVID-19 pneumonia) consisting of chest computed tomography (CT) images, 130 clinical features (from a range of biochemical and cellular analyses of blood and urine samples) and laboratory-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) clinical status. We show the utility of the database for prediction of COVID-19 morbidity and mortality outcomes using a deep learning algorithm trained with data from 1,170 patients and 19,685 manually labelled CT slices. In an independent validation cohort of 351 patients, the algorithm discriminated between negative, mild and severe cases with areas under the receiver operating characteristic curve of 0.944, 0.860 and 0.884, respectively. The open database may have further uses in the diagnosis and management of patients with COVID-19.

SUBMITTER: Ning W

PROVIDER: S-EPMC7723858 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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Open resource of clinical data from patients with pneumonia for the prediction of COVID-19 outcomes via deep learning.

Ning Wanshan W Lei Shijun S Yang Jingjing J Cao Yukun Y Jiang Peiran P Yang Qianqian Q Zhang Jiao J Wang Xiaobei X Chen Fenghua F Geng Zhi Z Xiong Liang L Zhou Hongmei H Guo Yaping Y Zeng Yulan Y Shi Heshui H Wang Lin L Xue Yu Y Wang Zheng Z

Nature biomedical engineering 20201118 12

Data from patients with coronavirus disease 2019 (COVID-19) are essential for guiding clinical decision making, for furthering the understanding of this viral disease, and for diagnostic modelling. Here, we describe an open resource containing data from 1,521 patients with pneumonia (including COVID-19 pneumonia) consisting of chest computed tomography (CT) images, 130 clinical features (from a range of biochemical and cellular analyses of blood and urine samples) and laboratory-confirmed severe ...[more]

PMID: 33208927

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Project description:The main objective of this work is to develop and evaluate an artificial intelligence system based on deep learning capable of automatically identifying, quantifying, and characterizing COVID-19 pneumonia patterns in order to assess disease severity and predict clinical outcomes, and to compare the prediction performance with respect to human reader severity assessment and whole lung radiomics. We propose a deep learning based scheme to automatically segment the different lesion subtypes in nonenhanced CT scans. The automatic lesion quantification was used to predict clinical outcomes. The proposed technique has been independently tested in a multicentric cohort of 103 patients, retrospectively collected between March and July of 2020. Segmentation of lesion subtypes was evaluated using both overlapping (Dice) and distance-based (Hausdorff and average surface) metrics, while the proposed system to predict clinically relevant outcomes was assessed using the area under the curve (AUC). Additionally, other metrics including sensitivity, specificity, positive predictive value and negative predictive value were estimated. 95% confidence intervals were properly calculated. The agreement between the automatic estimate of parenchymal damage (%) and the radiologists' severity scoring was strong, with a Spearman correlation coefficient (R) of 0.83. The automatic quantification of lesion subtypes was able to predict patient mortality, admission to the Intensive Care Units (ICU) and need for mechanical ventilation with an AUC of 0.87, 0.73 and 0.68 respectively. The proposed artificial intelligence system enabled a better prediction of those clinically relevant outcomes when compared to the radiologists' interpretation and to whole lung radiomics. In conclusion, deep learning lesion subtyping in COVID-19 pneumonia from noncontrast chest CT enables quantitative assessment of disease severity and better prediction of clinical outcomes with respect to whole lung radiomics or radiologists' severity score.

Project description:BackgroundRecent work has shown the potential of using audio data (eg, cough, breathing, and voice) in the screening for COVID-19. However, these approaches only focus on one-off detection and detect the infection, given the current audio sample, but do not monitor disease progression in COVID-19. Limited exploration has been put forward to continuously monitor COVID-19 progression, especially recovery, through longitudinal audio data. Tracking disease progression characteristics and patterns of recovery could bring insights and lead to more timely treatment or treatment adjustment, as well as better resource management in health care systems.ObjectiveThe primary objective of this study is to explore the potential of longitudinal audio samples over time for COVID-19 progression prediction and, especially, recovery trend prediction using sequential deep learning techniques.MethodsCrowdsourced respiratory audio data, including breathing, cough, and voice samples, from 212 individuals over 5-385 days were analyzed, alongside their self-reported COVID-19 test results. We developed and validated a deep learning-enabled tracking tool using gated recurrent units (GRUs) to detect COVID-19 progression by exploring the audio dynamics of the individuals' historical audio biomarkers. The investigation comprised 2 parts: (1) COVID-19 detection in terms of positive and negative (healthy) tests using sequential audio signals, which was primarily assessed in terms of the area under the receiver operating characteristic curve (AUROC), sensitivity, and specificity, with 95% CIs, and (2) longitudinal disease progression prediction over time in terms of probability of positive tests, which was evaluated using the correlation between the predicted probability trajectory and self-reported labels.ResultsWe first explored the benefits of capturing longitudinal dynamics of audio biomarkers for COVID-19 detection. The strong performance, yielding an AUROC of 0.79, a sensitivity of 0.75, and a specificity of 0.71 supported the effectiveness of the approach compared to methods that do not leverage longitudinal dynamics. We further examined the predicted disease progression trajectory, which displayed high consistency with longitudinal test results with a correlation of 0.75 in the test cohort and 0.86 in a subset of the test cohort with 12 (57.1%) of 21 COVID-19-positive participants who reported disease recovery. Our findings suggest that monitoring COVID-19 evolution via longitudinal audio data has potential in the tracking of individuals' disease progression and recovery.ConclusionsAn audio-based COVID-19 progression monitoring system was developed using deep learning techniques, with strong performance showing high consistency between the predicted trajectory and the test results over time, especially for recovery trend predictions. This has good potential in the postpeak and postpandemic era that can help guide medical treatment and optimize hospital resource allocations. The changes in longitudinal audio samples, referred to as audio dynamics, are associated with COVID-19 progression; thus, modeling the audio dynamics can potentially capture the underlying disease progression process and further aid COVID-19 progression prediction. This framework provides a flexible, affordable, and timely tool for COVID-19 tracking, and more importantly, it also provides a proof of concept of how telemonitoring could be applicable to respiratory diseases monitoring, in general.

Dataset Information

Open resource of clinical data from patients with pneumonia for the prediction of COVID-19 outcomes via deep learning.

Publications

Open resource of clinical data from patients with pneumonia for the prediction of COVID-19 outcomes via deep learning.

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