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Retrospective evaluation of short-term forecast performance of ensemble sub-epidemic frameworks and other time-series models: The 2022-2023 mpox outbreak across multiple geographical scales, July 14(th), 2022, through February 26th, 2023

In May 2022, public health officials noted an unprecedented surge in mpox cases in non-endemic countries worldwide. As the epidemic accelerated, multi-model forecasts of the epidemic’s trajectory were critical in guiding the implementation of public health interventions and determining policy. As th...

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Autores principales: Bleichrodt, Amanda, Luo, Ruiyan, Kirpich, Alexander, Chowell, Gerardo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10615009/
https://www.ncbi.nlm.nih.gov/pubmed/37905035
http://dx.doi.org/10.1101/2023.05.15.23289989
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author Bleichrodt, Amanda
Luo, Ruiyan
Kirpich, Alexander
Chowell, Gerardo
author_facet Bleichrodt, Amanda
Luo, Ruiyan
Kirpich, Alexander
Chowell, Gerardo
author_sort Bleichrodt, Amanda
collection PubMed
description In May 2022, public health officials noted an unprecedented surge in mpox cases in non-endemic countries worldwide. As the epidemic accelerated, multi-model forecasts of the epidemic’s trajectory were critical in guiding the implementation of public health interventions and determining policy. As the case levels have significantly decreased as of early September 2022, evaluating model performance is essential to advance the growing field of epidemic forecasting. Using laboratory-confirmed mpox case data from the Centers for Disease Control and Prevention (CDC) and Our World in Data (OWID) teams through the week of January 26th, 2023, we generated retrospective sequential weekly forecasts (e.g., 1–4-weeks) for Brazil, Canada, France, Germany, Spain, the United Kingdom, the USA, and at the global scale using models that require minimal input data including the auto-regressive integrated moving average (ARIMA), general additive model (GAM), simple linear regression (SLR), Facebook’s Prophet model, as well as the sub-epidemic wave (spatial-wave) and [Formula: see text]-sub-epidemic modeling frameworks. We assess forecast performance using average mean squared error (MSE), mean absolute error (MAE), weighted interval score (WIS), 95% prediction interval coverage (95% PI coverage), and skill scores. Average Winkler scores were used to calculate skill scores for 95% PI coverage. Overall, the [Formula: see text]-sub-epidemic modeling framework outcompeted other models across most locations and forecasting horizons, with the unweighted ensemble model performing best across all forecasting horizons for most locations regarding average MSE, MAE, WIS, and 95% PI coverage. However, many locations had multiple models performing equally well for the average 95% PI coverage. The [Formula: see text]-sub-epidemic and spatial-wave frameworks improved considerably in average MSE, MAE, and WIS, and Winkler scores (95% PI coverage) relative to the ARIMA model. Findings lend further support to sub-epidemic frameworks for short-term forecasting epidemics of emerging and re-emerging infectious diseases.
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spelling pubmed-106150092023-10-31 Retrospective evaluation of short-term forecast performance of ensemble sub-epidemic frameworks and other time-series models: The 2022-2023 mpox outbreak across multiple geographical scales, July 14(th), 2022, through February 26th, 2023 Bleichrodt, Amanda Luo, Ruiyan Kirpich, Alexander Chowell, Gerardo medRxiv Article In May 2022, public health officials noted an unprecedented surge in mpox cases in non-endemic countries worldwide. As the epidemic accelerated, multi-model forecasts of the epidemic’s trajectory were critical in guiding the implementation of public health interventions and determining policy. As the case levels have significantly decreased as of early September 2022, evaluating model performance is essential to advance the growing field of epidemic forecasting. Using laboratory-confirmed mpox case data from the Centers for Disease Control and Prevention (CDC) and Our World in Data (OWID) teams through the week of January 26th, 2023, we generated retrospective sequential weekly forecasts (e.g., 1–4-weeks) for Brazil, Canada, France, Germany, Spain, the United Kingdom, the USA, and at the global scale using models that require minimal input data including the auto-regressive integrated moving average (ARIMA), general additive model (GAM), simple linear regression (SLR), Facebook’s Prophet model, as well as the sub-epidemic wave (spatial-wave) and [Formula: see text]-sub-epidemic modeling frameworks. We assess forecast performance using average mean squared error (MSE), mean absolute error (MAE), weighted interval score (WIS), 95% prediction interval coverage (95% PI coverage), and skill scores. Average Winkler scores were used to calculate skill scores for 95% PI coverage. Overall, the [Formula: see text]-sub-epidemic modeling framework outcompeted other models across most locations and forecasting horizons, with the unweighted ensemble model performing best across all forecasting horizons for most locations regarding average MSE, MAE, WIS, and 95% PI coverage. However, many locations had multiple models performing equally well for the average 95% PI coverage. The [Formula: see text]-sub-epidemic and spatial-wave frameworks improved considerably in average MSE, MAE, and WIS, and Winkler scores (95% PI coverage) relative to the ARIMA model. Findings lend further support to sub-epidemic frameworks for short-term forecasting epidemics of emerging and re-emerging infectious diseases. Cold Spring Harbor Laboratory 2023-10-17 /pmc/articles/PMC10615009/ /pubmed/37905035 http://dx.doi.org/10.1101/2023.05.15.23289989 Text en https://creativecommons.org/licenses/by-nd/4.0/This work is licensed under a Creative Commons Attribution-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, and only so long as attribution is given to the creator. The license allows for commercial use.
spellingShingle Article
Bleichrodt, Amanda
Luo, Ruiyan
Kirpich, Alexander
Chowell, Gerardo
Retrospective evaluation of short-term forecast performance of ensemble sub-epidemic frameworks and other time-series models: The 2022-2023 mpox outbreak across multiple geographical scales, July 14(th), 2022, through February 26th, 2023
title Retrospective evaluation of short-term forecast performance of ensemble sub-epidemic frameworks and other time-series models: The 2022-2023 mpox outbreak across multiple geographical scales, July 14(th), 2022, through February 26th, 2023
title_full Retrospective evaluation of short-term forecast performance of ensemble sub-epidemic frameworks and other time-series models: The 2022-2023 mpox outbreak across multiple geographical scales, July 14(th), 2022, through February 26th, 2023
title_fullStr Retrospective evaluation of short-term forecast performance of ensemble sub-epidemic frameworks and other time-series models: The 2022-2023 mpox outbreak across multiple geographical scales, July 14(th), 2022, through February 26th, 2023
title_full_unstemmed Retrospective evaluation of short-term forecast performance of ensemble sub-epidemic frameworks and other time-series models: The 2022-2023 mpox outbreak across multiple geographical scales, July 14(th), 2022, through February 26th, 2023
title_short Retrospective evaluation of short-term forecast performance of ensemble sub-epidemic frameworks and other time-series models: The 2022-2023 mpox outbreak across multiple geographical scales, July 14(th), 2022, through February 26th, 2023
title_sort retrospective evaluation of short-term forecast performance of ensemble sub-epidemic frameworks and other time-series models: the 2022-2023 mpox outbreak across multiple geographical scales, july 14(th), 2022, through february 26th, 2023
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10615009/
https://www.ncbi.nlm.nih.gov/pubmed/37905035
http://dx.doi.org/10.1101/2023.05.15.23289989
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