An integrated framework for building trustworthy data-driven epidemiological models: Application to the COVID-19 outbreak in New York City

• Main Authors: Karniadakis, G. (Author), Lin, G. (Author), Ponce, J. (Author), Zhang, S. (Author), Zhang, Z. (Author)
• Format: Article
• Language: English
• Published: Public Library of Science 2021
• Subjects: Article; biology; calibration; communicable disease control; Communicable Disease Control; Computational Biology; coronavirus disease 2019; COVID-19; Disease Outbreaks; disease transmission; epidemic; epidemiology; government; health care system; hospitalization; human; Humans; mathematical analysis; Models, Statistical; mortality rate; New York; New York City; population size; prevention and control; SARS-CoV-2; sensitivity analysis; statistical model; time series analysis; uncertainty; vaccination; virus transmission; workflow
• Online Access: View Fulltext in Publisher

 Epidemiological models can provide the dynamic evolution of a pandemic but they are based on many assumptions and parameters that have to be adjusted over the time when the pandemic lasts. However, often the available data are not sufficient to identify the model parameters and hence infer the unobserved dynamics. Here, we develop a general framework for building a trustworthy data-driven epidemiological model, consisting of a workflow that integrates data acquisition and event timeline, model development, identifiability analysis, sensitivity analysis, model calibration, model robustness analysis, and projection with uncertainties in different scenarios. In particular, we apply this framework to propose a modified susceptible–exposed–infectious–recovered (SEIR) model, including new compartments and model vaccination in order to project the transmission dynamics of COVID-19 in New York City (NYC). We find that we can uniquely estimate the model parameters and accurately project the daily new infection cases, hospitalizations, and deaths, in agreement with the available data from NYC’s government’s website. In addition, we employ the calibrated data-driven model to study the effects of vaccination and timing of reopening indoor dining in NYC. Copyright: © 2021 Zhang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.