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

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.Author summary: The transmission dynamics of pandemics are often modeled by ordinary differential equations, which normally involve many undetermined parameters needed to be estimated from data. In this study, we provide a general framework, which includes identifiability analysis, sensitivity analysis, model robustness analysis, and uncertainty quantification, to examine the relationship between the model dynamics, data, and parameters. We apply our framework to the modeling of the COVID-19 outbreak in New York City and project the evolution of the pandemic.