tetano
Editor, Senior Moderator
Infect Dis Model
. 2022 Mar;7(1):30-44.
doi: 10.1016/j.idm.2021.11.004. Epub 2021 Nov 27.
Agent-based modeling of COVID-19 outbreaks for New York state and UK: Parameter identification algorithm
Olga Krivorotko[SUP] 1 2 [/SUP], Mariia Sosnovskaia[SUP] 2 [/SUP], Ivan Vashchenko[SUP] 2 [/SUP], Cliff Kerr[SUP] 3 [/SUP], Daniel Lesnic[SUP] 4 [/SUP]
Affiliations
Abstract
This paper uses Covasim, an agent-based model (ABM) of COVID-19, to evaluate and scenarios of epidemic spread in New York State (USA) and the UK. Epidemiological parameters such as contagiousness (virus transmission rate), initial number of infected people, and probability of being tested depend on the region's demographic and geographical features, the containment measures introduced; they are calibrated to data about COVID-19 spread in the region of interest. At the first stage of our study, epidemiological data (numbers of people tested, diagnoses, critical cases, hospitalizations, and deaths) for each of the mentioned regions were analyzed. The data were characterized in terms of seasonality, stationarity, and dependency spaces, and were extrapolated using machine learning techniques to specify unknown epidemiological parameters of the model. At the second stage, the Optuna optimizer based on the tree Parzen estimation method for objective function minimization was applied to determine the model's unknown parameters. The model was validated with the historical data of 2020. The modeled results of COVID-19 spread in New York State and the UK have demonstrated that if the level of testing and containment measures is preserved, the number of positive cases in New York State remain the same during March of 2021, while in the UK it will reduce.
Keywords: Agent-based modeling; COVID-19; Coronavirus data analysis; Epidemiology; Forecasting scenarios; Interventions analysis; Optimization; Parameter identification; Reproduction number.
. 2022 Mar;7(1):30-44.
doi: 10.1016/j.idm.2021.11.004. Epub 2021 Nov 27.
Agent-based modeling of COVID-19 outbreaks for New York state and UK: Parameter identification algorithm
Olga Krivorotko[SUP] 1 2 [/SUP], Mariia Sosnovskaia[SUP] 2 [/SUP], Ivan Vashchenko[SUP] 2 [/SUP], Cliff Kerr[SUP] 3 [/SUP], Daniel Lesnic[SUP] 4 [/SUP]
Affiliations
- PMID: 34869960
- PMCID: PMC8627046
- DOI: 10.1016/j.idm.2021.11.004
Abstract
This paper uses Covasim, an agent-based model (ABM) of COVID-19, to evaluate and scenarios of epidemic spread in New York State (USA) and the UK. Epidemiological parameters such as contagiousness (virus transmission rate), initial number of infected people, and probability of being tested depend on the region's demographic and geographical features, the containment measures introduced; they are calibrated to data about COVID-19 spread in the region of interest. At the first stage of our study, epidemiological data (numbers of people tested, diagnoses, critical cases, hospitalizations, and deaths) for each of the mentioned regions were analyzed. The data were characterized in terms of seasonality, stationarity, and dependency spaces, and were extrapolated using machine learning techniques to specify unknown epidemiological parameters of the model. At the second stage, the Optuna optimizer based on the tree Parzen estimation method for objective function minimization was applied to determine the model's unknown parameters. The model was validated with the historical data of 2020. The modeled results of COVID-19 spread in New York State and the UK have demonstrated that if the level of testing and containment measures is preserved, the number of positive cases in New York State remain the same during March of 2021, while in the UK it will reduce.
Keywords: Agent-based modeling; COVID-19; Coronavirus data analysis; Epidemiology; Forecasting scenarios; Interventions analysis; Optimization; Parameter identification; Reproduction number.