@article {Bogu2021.01.08.21249474, author = {Bogu, Gireesh K. and Snyder, Michael P.}, title = {Deep learning-based detection of COVID-19 using wearables data}, elocation-id = {2021.01.08.21249474}, year = {2021}, doi = {10.1101/2021.01.08.21249474}, publisher = {Cold Spring Harbor Laboratory Press}, abstract = {Background COVID-19 is an infectious disease caused by SARS-CoV-2 that is primarily diagnosed using laboratory tests, which are frequently not administered until after symptom onset. However, SARS-CoV-2 is contagious multiple days before symptom onset and diagnosis, thus enhancing its transmission through the population.Methods In this retrospective study, we collected 15 seconds to one-minute heart rate and steps interval data from Fitbit devices during the COVID-19 period (February 2020 until June 2020). Resting heart rate was computed by selecting the heart rate intervals where steps were zero for 12 minutes ahead of an interrogated time point. Data for each participant was divided into train or baseline by taking the days before the non-infectious period and test data by taking the days during the COVID-19 infectious period. Data augmentation was used to increase the size of the training days. Here, we developed a deep learning approach based on a Long Short-Term Memory Networks-based autoencoder, called LAAD, to predict COVID-19 infection by detecting abnormal resting heart rate in test data relative to the user{\textquoteright}s baseline.Findings We detected an abnormal resting heart rate during the period of viral infection (7 days before the symptom onset and 21 days after) in 92\% (23 out of 25 cases) of patients with laboratory-confirmed COVID-19. In 56\% (14) of cases, LAAD detection identified cases in their pre-symptomatic phase whereas 36\% (9 cases) were detected after the onset of symptoms with an average precision score of 0{\textperiodcentered}91 (SD 0{\textperiodcentered}13, 95\% CI 0{\textperiodcentered}854{\textendash}0{\textperiodcentered}967), a recall score of 0{\textperiodcentered}36 (0{\textperiodcentered}295, 0{\textperiodcentered}232{\textendash}0{\textperiodcentered}487), and a F-beta score of 0{\textperiodcentered}79 (0{\textperiodcentered}226, 0{\textperiodcentered}693{\textendash}0{\textperiodcentered}888). In COVID-19 positive patients, abnormal RHR patterns start 5 days before symptom onset (6{\textperiodcentered}9 days in pre-symptomatic cases and 1{\textperiodcentered}9 days later in post-symptomatic cases). COVID-19+ patients have longer abnormal resting heart rate periods (89 hours or 3{\textperiodcentered}7 days) as compared to healthy individuals (25 hours or 1{\textperiodcentered}1 days).Interpretation These findings show that deep learning neural networks and wearables data are an effective method for the early detection of COVID-19 infection. Additional validation data will help guide the use of this and similar techniques in real-world infection surveillance and isolation policies to reduce transmission and end the pandemic.Funding This work was supported by NIH grants and gifts from the Flu Lab, as well as departmental funding from the Stanford Genetics department. The Google Cloud Platform costs were covered by Google for Education academic research and COVID-19 grant awards.Evidence before the study COVID-19 resulted in up to 1{\textperiodcentered}7 million deaths worldwide in 2020. COVID-19 detection using laboratory tests is usually performed after symptom onset. This delay can allow the spread of viral infection and can cause outbreaks. We searched PubMed, Google, and Google Scholar for research articles published in English up to Dec 1, 2020, using common search terms including {\textquotedblleft}COVID-19 and wearables{\textquotedblright}, {\textquotedblleft}Resting heart rate and viral infection{\textquotedblright}, {\textquotedblleft}Resting heart rate and COVID-19{\textquotedblright}, {\textquotedblleft}machine learning and COVID-19{\textquotedblright} and {\textquotedblleft}deep-learning and COVID-19{\textquotedblright}. Previous studies have attempted to use an elevated resting heart rate as an indicator of viral infection. Although these studies have investigated the early prediction of COVID-19 using resting heart rate and other wearables data, studies to investigate a deep learning-based prediction model with performance evaluation metrics at the user level has not been reported.Added value of this study In this study, we created a deep-learning system that used wearables data such as abnormal resting heart rate to predict COVID-19 before the symptom onset. The deep-learning system was created using retrospective time-series datasets collected from 25 COVID-19+ patients, 11 non-COVID-19, and 70 healthy individuals. To our knowledge, this is the first deep-learning model to identify an early viral infection using wearables data at the user level. This study also greatly extends our previous phase-1 study and factors unpredictable behavior and time-series nature of the data, limited data size, and lack of data labels to evaluate performance metrics. The use of a real-time version of this model using more data along with user feedback may help to scale early detection as the number of patients with COVID-19 continues to grow.Implications of all the available evidence In the future, wearable devices may provide high-resolution sleep, temperature, saturated oxygen, respiration rate, and electrocardiogram, which could be used to further characterize an individual{\textquoteright}s baseline and improve the deep-learning model performance for infectious disease detection. Using multi-sensor data with a real-time deep-learning model has the potential to alert individuals of illness prior to symptom onset and may greatly reduce the viral spread.Competing Interest StatementM.P.S. is cofounder and a member of the scientific advisory board of Personalis, Qbio, January, SensOmics, Protos, Mirvie and Oralome. He is on the scientific advisory board of Danaher, GenapSys and Jupiter.Funding StatementThis work was supported by NIH grants and gifts from the Flu Lab, as well as departmental funding from the Stanford Genetics department. The Google Cloud Platform costs were covered by Google for Education academic research and COVID-19 grant awards.Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:Stanford University Institutional Review Board (IRB 55577, IRB 23602).All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesDe-identified data is available at https://storage.googleapis.com/gbsc-gcp-project-ipop_public/COVID-19/COVID-19-Wearables.zip and code is open-sourced for non-commercial purposes, and available at https://github.com/gireeshkbogu/LAAD.}, URL = {https://www.medrxiv.org/content/early/2021/01/09/2021.01.08.21249474}, eprint = {https://www.medrxiv.org/content/early/2021/01/09/2021.01.08.21249474.full.pdf}, journal = {medRxiv} }