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An open challenge to advance probabilistic forecasting for dengue epidemics
A wide range of research has promised new tools for forecasting infectious disease dynamics, but little of that research is currently being applied in practice, because tools do not address key public health needs, do not produce probabilistic forecasts, have not been evaluated on external data, or...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
National Academy of Sciences
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6883829/ https://www.ncbi.nlm.nih.gov/pubmed/31712420 http://dx.doi.org/10.1073/pnas.1909865116 |
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author | Johansson, Michael A. Apfeldorf, Karyn M. Dobson, Scott Devita, Jason Buczak, Anna L. Baugher, Benjamin Moniz, Linda J. Bagley, Thomas Babin, Steven M. Guven, Erhan Yamana, Teresa K. Shaman, Jeffrey Moschou, Terry Lothian, Nick Lane, Aaron Osborne, Grant Jiang, Gao Brooks, Logan C. Farrow, David C. Hyun, Sangwon Tibshirani, Ryan J. Rosenfeld, Roni Lessler, Justin Reich, Nicholas G. Cummings, Derek A. T. Lauer, Stephen A. Moore, Sean M. Clapham, Hannah E. Lowe, Rachel Bailey, Trevor C. García-Díez, Markel Carvalho, Marilia Sá Rodó, Xavier Sardar, Tridip Paul, Richard Ray, Evan L. Sakrejda, Krzysztof Brown, Alexandria C. Meng, Xi Osoba, Osonde Vardavas, Raffaele Manheim, David Moore, Melinda Rao, Dhananjai M. Porco, Travis C. Ackley, Sarah Liu, Fengchen Worden, Lee Convertino, Matteo Liu, Yang Reddy, Abraham Ortiz, Eloy Rivero, Jorge Brito, Humberto Juarrero, Alicia Johnson, Leah R. Gramacy, Robert B. Cohen, Jeremy M. Mordecai, Erin A. Murdock, Courtney C. Rohr, Jason R. Ryan, Sadie J. Stewart-Ibarra, Anna M. Weikel, Daniel P. Jutla, Antarpreet Khan, Rakibul Poultney, Marissa Colwell, Rita R. Rivera-García, Brenda Barker, Christopher M. Bell, Jesse E. Biggerstaff, Matthew Swerdlow, David Mier-y-Teran-Romero, Luis Forshey, Brett M. Trtanj, Juli Asher, Jason Clay, Matt Margolis, Harold S. Hebbeler, Andrew M. George, Dylan Chretien, Jean-Paul |
author_facet | Johansson, Michael A. Apfeldorf, Karyn M. Dobson, Scott Devita, Jason Buczak, Anna L. Baugher, Benjamin Moniz, Linda J. Bagley, Thomas Babin, Steven M. Guven, Erhan Yamana, Teresa K. Shaman, Jeffrey Moschou, Terry Lothian, Nick Lane, Aaron Osborne, Grant Jiang, Gao Brooks, Logan C. Farrow, David C. Hyun, Sangwon Tibshirani, Ryan J. Rosenfeld, Roni Lessler, Justin Reich, Nicholas G. Cummings, Derek A. T. Lauer, Stephen A. Moore, Sean M. Clapham, Hannah E. Lowe, Rachel Bailey, Trevor C. García-Díez, Markel Carvalho, Marilia Sá Rodó, Xavier Sardar, Tridip Paul, Richard Ray, Evan L. Sakrejda, Krzysztof Brown, Alexandria C. Meng, Xi Osoba, Osonde Vardavas, Raffaele Manheim, David Moore, Melinda Rao, Dhananjai M. Porco, Travis C. Ackley, Sarah Liu, Fengchen Worden, Lee Convertino, Matteo Liu, Yang Reddy, Abraham Ortiz, Eloy Rivero, Jorge Brito, Humberto Juarrero, Alicia Johnson, Leah R. Gramacy, Robert B. Cohen, Jeremy M. Mordecai, Erin A. Murdock, Courtney C. Rohr, Jason R. Ryan, Sadie J. Stewart-Ibarra, Anna M. Weikel, Daniel P. Jutla, Antarpreet Khan, Rakibul Poultney, Marissa Colwell, Rita R. Rivera-García, Brenda Barker, Christopher M. Bell, Jesse E. Biggerstaff, Matthew Swerdlow, David Mier-y-Teran-Romero, Luis Forshey, Brett M. Trtanj, Juli Asher, Jason Clay, Matt Margolis, Harold S. Hebbeler, Andrew M. George, Dylan Chretien, Jean-Paul |
author_sort | Johansson, Michael A. |
collection | PubMed |
description | A wide range of research has promised new tools for forecasting infectious disease dynamics, but little of that research is currently being applied in practice, because tools do not address key public health needs, do not produce probabilistic forecasts, have not been evaluated on external data, or do not provide sufficient forecast skill to be useful. We developed an open collaborative forecasting challenge to assess probabilistic forecasts for seasonal epidemics of dengue, a major global public health problem. Sixteen teams used a variety of methods and data to generate forecasts for 3 epidemiological targets (peak incidence, the week of the peak, and total incidence) over 8 dengue seasons in Iquitos, Peru and San Juan, Puerto Rico. Forecast skill was highly variable across teams and targets. While numerous forecasts showed high skill for midseason situational awareness, early season skill was low, and skill was generally lowest for high incidence seasons, those for which forecasts would be most valuable. A comparison of modeling approaches revealed that average forecast skill was lower for models including biologically meaningful data and mechanisms and that both multimodel and multiteam ensemble forecasts consistently outperformed individual model forecasts. Leveraging these insights, data, and the forecasting framework will be critical to improve forecast skill and the application of forecasts in real time for epidemic preparedness and response. Moreover, key components of this project—integration with public health needs, a common forecasting framework, shared and standardized data, and open participation—can help advance infectious disease forecasting beyond dengue. |
format | Online Article Text |
id | pubmed-6883829 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | National Academy of Sciences |
record_format | MEDLINE/PubMed |
spelling | pubmed-68838292019-12-04 An open challenge to advance probabilistic forecasting for dengue epidemics Johansson, Michael A. Apfeldorf, Karyn M. Dobson, Scott Devita, Jason Buczak, Anna L. Baugher, Benjamin Moniz, Linda J. Bagley, Thomas Babin, Steven M. Guven, Erhan Yamana, Teresa K. Shaman, Jeffrey Moschou, Terry Lothian, Nick Lane, Aaron Osborne, Grant Jiang, Gao Brooks, Logan C. Farrow, David C. Hyun, Sangwon Tibshirani, Ryan J. Rosenfeld, Roni Lessler, Justin Reich, Nicholas G. Cummings, Derek A. T. Lauer, Stephen A. Moore, Sean M. Clapham, Hannah E. Lowe, Rachel Bailey, Trevor C. García-Díez, Markel Carvalho, Marilia Sá Rodó, Xavier Sardar, Tridip Paul, Richard Ray, Evan L. Sakrejda, Krzysztof Brown, Alexandria C. Meng, Xi Osoba, Osonde Vardavas, Raffaele Manheim, David Moore, Melinda Rao, Dhananjai M. Porco, Travis C. Ackley, Sarah Liu, Fengchen Worden, Lee Convertino, Matteo Liu, Yang Reddy, Abraham Ortiz, Eloy Rivero, Jorge Brito, Humberto Juarrero, Alicia Johnson, Leah R. Gramacy, Robert B. Cohen, Jeremy M. Mordecai, Erin A. Murdock, Courtney C. Rohr, Jason R. Ryan, Sadie J. Stewart-Ibarra, Anna M. Weikel, Daniel P. Jutla, Antarpreet Khan, Rakibul Poultney, Marissa Colwell, Rita R. Rivera-García, Brenda Barker, Christopher M. Bell, Jesse E. Biggerstaff, Matthew Swerdlow, David Mier-y-Teran-Romero, Luis Forshey, Brett M. Trtanj, Juli Asher, Jason Clay, Matt Margolis, Harold S. Hebbeler, Andrew M. George, Dylan Chretien, Jean-Paul Proc Natl Acad Sci U S A Biological Sciences A wide range of research has promised new tools for forecasting infectious disease dynamics, but little of that research is currently being applied in practice, because tools do not address key public health needs, do not produce probabilistic forecasts, have not been evaluated on external data, or do not provide sufficient forecast skill to be useful. We developed an open collaborative forecasting challenge to assess probabilistic forecasts for seasonal epidemics of dengue, a major global public health problem. Sixteen teams used a variety of methods and data to generate forecasts for 3 epidemiological targets (peak incidence, the week of the peak, and total incidence) over 8 dengue seasons in Iquitos, Peru and San Juan, Puerto Rico. Forecast skill was highly variable across teams and targets. While numerous forecasts showed high skill for midseason situational awareness, early season skill was low, and skill was generally lowest for high incidence seasons, those for which forecasts would be most valuable. A comparison of modeling approaches revealed that average forecast skill was lower for models including biologically meaningful data and mechanisms and that both multimodel and multiteam ensemble forecasts consistently outperformed individual model forecasts. Leveraging these insights, data, and the forecasting framework will be critical to improve forecast skill and the application of forecasts in real time for epidemic preparedness and response. Moreover, key components of this project—integration with public health needs, a common forecasting framework, shared and standardized data, and open participation—can help advance infectious disease forecasting beyond dengue. National Academy of Sciences 2019-11-26 2019-11-11 /pmc/articles/PMC6883829/ /pubmed/31712420 http://dx.doi.org/10.1073/pnas.1909865116 Text en Copyright © 2019 the Author(s). Published by PNAS. http://creativecommons.org/licenses/by/4.0/ https://creativecommons.org/licenses/by/4.0/This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY) (http://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Biological Sciences Johansson, Michael A. Apfeldorf, Karyn M. Dobson, Scott Devita, Jason Buczak, Anna L. Baugher, Benjamin Moniz, Linda J. Bagley, Thomas Babin, Steven M. Guven, Erhan Yamana, Teresa K. Shaman, Jeffrey Moschou, Terry Lothian, Nick Lane, Aaron Osborne, Grant Jiang, Gao Brooks, Logan C. Farrow, David C. Hyun, Sangwon Tibshirani, Ryan J. Rosenfeld, Roni Lessler, Justin Reich, Nicholas G. Cummings, Derek A. T. Lauer, Stephen A. Moore, Sean M. Clapham, Hannah E. Lowe, Rachel Bailey, Trevor C. García-Díez, Markel Carvalho, Marilia Sá Rodó, Xavier Sardar, Tridip Paul, Richard Ray, Evan L. Sakrejda, Krzysztof Brown, Alexandria C. Meng, Xi Osoba, Osonde Vardavas, Raffaele Manheim, David Moore, Melinda Rao, Dhananjai M. Porco, Travis C. Ackley, Sarah Liu, Fengchen Worden, Lee Convertino, Matteo Liu, Yang Reddy, Abraham Ortiz, Eloy Rivero, Jorge Brito, Humberto Juarrero, Alicia Johnson, Leah R. Gramacy, Robert B. Cohen, Jeremy M. Mordecai, Erin A. Murdock, Courtney C. Rohr, Jason R. Ryan, Sadie J. Stewart-Ibarra, Anna M. Weikel, Daniel P. Jutla, Antarpreet Khan, Rakibul Poultney, Marissa Colwell, Rita R. Rivera-García, Brenda Barker, Christopher M. Bell, Jesse E. Biggerstaff, Matthew Swerdlow, David Mier-y-Teran-Romero, Luis Forshey, Brett M. Trtanj, Juli Asher, Jason Clay, Matt Margolis, Harold S. Hebbeler, Andrew M. George, Dylan Chretien, Jean-Paul An open challenge to advance probabilistic forecasting for dengue epidemics |
title | An open challenge to advance probabilistic forecasting for dengue epidemics |
title_full | An open challenge to advance probabilistic forecasting for dengue epidemics |
title_fullStr | An open challenge to advance probabilistic forecasting for dengue epidemics |
title_full_unstemmed | An open challenge to advance probabilistic forecasting for dengue epidemics |
title_short | An open challenge to advance probabilistic forecasting for dengue epidemics |
title_sort | open challenge to advance probabilistic forecasting for dengue epidemics |
topic | Biological Sciences |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6883829/ https://www.ncbi.nlm.nih.gov/pubmed/31712420 http://dx.doi.org/10.1073/pnas.1909865116 |
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