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A semi-parametric, state-space compartmental model with time-dependent parameters for forecasting COVID-19 cases, hospitalizations and deaths

Short-term forecasts of the dynamics of coronavirus disease 2019 (COVID-19) in the period up to its decline following mass vaccination was a task that received much attention but proved difficult to do with high accuracy. However, the availability of standardized forecasts and versioned datasets fro...

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Detalles Bibliográficos
Autores principales: O’Dea, Eamon B., Drake, John M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Royal Society 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8847000/
https://www.ncbi.nlm.nih.gov/pubmed/35167769
http://dx.doi.org/10.1098/rsif.2021.0702
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author O’Dea, Eamon B.
Drake, John M.
author_facet O’Dea, Eamon B.
Drake, John M.
author_sort O’Dea, Eamon B.
collection PubMed
description Short-term forecasts of the dynamics of coronavirus disease 2019 (COVID-19) in the period up to its decline following mass vaccination was a task that received much attention but proved difficult to do with high accuracy. However, the availability of standardized forecasts and versioned datasets from this period allows for continued work in this area. Here, we introduce the Gaussian infection state space with time dependence (GISST) forecasting model. We evaluate its performance in one to four weeks ahead forecasts of COVID-19 cases, hospital admissions and deaths in the state of California made with official reports of COVID-19, Google’s mobility reports and vaccination data available each week. Evaluation of these forecasts with a weighted interval score shows them to consistently outperform a naive baseline forecast and often score closer to or better than a high-performing ensemble forecaster. The GISST model also provides parameter estimates for a compartmental model of COVID-19 dynamics, includes a regression submodel for the transmission rate and allows for parameters to vary over time according to a random walk. GISST provides a novel, balanced combination of computational efficiency, model interpretability and applicability to large multivariate datasets that may prove useful in improving the accuracy of infectious disease forecasts.
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spelling pubmed-88470002022-02-18 A semi-parametric, state-space compartmental model with time-dependent parameters for forecasting COVID-19 cases, hospitalizations and deaths O’Dea, Eamon B. Drake, John M. J R Soc Interface Life Sciences–Mathematics interface Short-term forecasts of the dynamics of coronavirus disease 2019 (COVID-19) in the period up to its decline following mass vaccination was a task that received much attention but proved difficult to do with high accuracy. However, the availability of standardized forecasts and versioned datasets from this period allows for continued work in this area. Here, we introduce the Gaussian infection state space with time dependence (GISST) forecasting model. We evaluate its performance in one to four weeks ahead forecasts of COVID-19 cases, hospital admissions and deaths in the state of California made with official reports of COVID-19, Google’s mobility reports and vaccination data available each week. Evaluation of these forecasts with a weighted interval score shows them to consistently outperform a naive baseline forecast and often score closer to or better than a high-performing ensemble forecaster. The GISST model also provides parameter estimates for a compartmental model of COVID-19 dynamics, includes a regression submodel for the transmission rate and allows for parameters to vary over time according to a random walk. GISST provides a novel, balanced combination of computational efficiency, model interpretability and applicability to large multivariate datasets that may prove useful in improving the accuracy of infectious disease forecasts. The Royal Society 2022-02-16 /pmc/articles/PMC8847000/ /pubmed/35167769 http://dx.doi.org/10.1098/rsif.2021.0702 Text en © 2022 The Authors. https://creativecommons.org/licenses/by/4.0/Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, provided the original author and source are credited.
spellingShingle Life Sciences–Mathematics interface
O’Dea, Eamon B.
Drake, John M.
A semi-parametric, state-space compartmental model with time-dependent parameters for forecasting COVID-19 cases, hospitalizations and deaths
title A semi-parametric, state-space compartmental model with time-dependent parameters for forecasting COVID-19 cases, hospitalizations and deaths
title_full A semi-parametric, state-space compartmental model with time-dependent parameters for forecasting COVID-19 cases, hospitalizations and deaths
title_fullStr A semi-parametric, state-space compartmental model with time-dependent parameters for forecasting COVID-19 cases, hospitalizations and deaths
title_full_unstemmed A semi-parametric, state-space compartmental model with time-dependent parameters for forecasting COVID-19 cases, hospitalizations and deaths
title_short A semi-parametric, state-space compartmental model with time-dependent parameters for forecasting COVID-19 cases, hospitalizations and deaths
title_sort semi-parametric, state-space compartmental model with time-dependent parameters for forecasting covid-19 cases, hospitalizations and deaths
topic Life Sciences–Mathematics interface
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8847000/
https://www.ncbi.nlm.nih.gov/pubmed/35167769
http://dx.doi.org/10.1098/rsif.2021.0702
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