TY - JOUR
T1 - An open challenge to advance probabilistic forecasting for dengue epidemics
AU - Johansson, Michael A.
AU - Apfeldorf, Karyn M.
AU - Dobson, Scott
AU - Devita, Jason
AU - Buczak, Anna L.
AU - Baugher, Benjamin
AU - Moniz, Linda J.
AU - Bagley, Thomas
AU - Babin, Steven M.
AU - Guven, Erhan
AU - Yamana, Teresa K.
AU - Shaman, Jeffrey
AU - Moschou, Terry
AU - Lothian, Nick
AU - Lane, Aaron
AU - Osborne, Grant
AU - Jiang, Gao
AU - Brooks, Logan C.
AU - Farrow, David C.
AU - Hyun, Sangwon
AU - Tibshirani, Ryan J.
AU - Rosenfeld, Roni
AU - Lessler, Justin
AU - Reich, Nicholas G.
AU - Cummings, Derek A.T.
AU - Lauer, Stephen A.
AU - Moore, Sean M.
AU - Clapham, Hannah E.
AU - Lowe, Rachel
AU - Bailey, Trevor C.
AU - García-Díez, Markel
AU - Carvalho, Marilia Sá
AU - Rodó, Xavier
AU - Sardar, Tridip
AU - Paul, Richard
AU - Ray, Evan L.
AU - Sakrejda, Krzysztof
AU - Brown, Alexandria C.
AU - Meng, Xi
AU - Osoba, Osonde
AU - Vardavas, Raffaele
AU - Manheim, David
AU - Moore, Melinda
AU - Rao, Dhananjai M.
AU - Porco, Travis C.
AU - Ackley, Sarah
AU - Liu, Fengchen
AU - Worden, Lee
AU - Convertino, Matteo
AU - Liu, Yang
AU - Reddy, Abraham
AU - Ortiz, Eloy
AU - Rivero, Jorge
AU - Brito, Humberto
AU - Juarrero, Alicia
AU - Johnson, Leah R.
AU - Gramacy, Robert B.
AU - Cohen, Jeremy M.
AU - Mordecai, Erin A.
AU - Murdock, Courtney C.
AU - Rohr, Jason R.
AU - Ryan, Sadie J.
AU - Stewart-Ibarra, Anna M.
AU - Weikel, Daniel P.
AU - Jutla, Antarpreet
AU - Khan, Rakibul
AU - Poultney, Marissa
AU - Colwell, Rita R.
AU - Rivera-García, Brenda
AU - Barker, Christopher M.
AU - Bell, Jesse E.
AU - Biggerstaff, Matthew
AU - Swerdlow, David
AU - Mier-Y-Teran-Romero, Luis
AU - Forshey, Brett M.
AU - Trtanj, Juli
AU - Asher, Jason
AU - Clay, Matt
AU - Margolis, Harold S.
AU - Hebbeler, Andrew M.
AU - George, Dylan
AU - Chretien, Jean Paul
N1 - Funding Information:
ACKNOWLEDGMENTS. T.K.Y. and J.S. were supported by National Institute of General Medical Sciences (NIGMS) Grant GM110748 and Defense Threat Reduction Agency Contract HDTRA1-15-C-0018. L.C.B., D.C.F., S.H., R.J.T., and R.R. were supported by NIGMS Award U54 GM088491 and NSF Graduate Research Fellowship Program Grant DGE-1252522. D.C.F. was a predoctoral trainee supported by NIH T32 Training Grant T32 EB009403 and the HHMI– National Institute of Biomedical Imaging and Bioengineering Interfaces Initiative. R.J.T. was supported by NSF Grant DMS-1309174. J.L., N.G.R., D.A.T.C., S.A.L., S.M.M., and H.E.C. were supported by National Institute of Allergy and Infectious Diseases (NIAID) Grant AI102939. N.G.R., E.L.R., K.S., A.C.B., and X.M. were supported by NIAID and NIGMS Grants R21AI115173, R01AI102939, and R35GM119582. R.L. was supported by a Royal Society Dorothy Hodgkin Fellowship. O.O., R.V., D.M., and M.M. were supported by the Forces and Resources Policy Center of the RAND National Defense Research Institute with discretionary US Department of Defense funds. T.C.P. and L.W. were supported by NIGMS Grant U01-GM087728. M.C., Y.L., and A.R. were supported by Global Institute for Collaborative Research and Education Big-Data and Cybersecurity Station and a Faculty in Industry Award at the University of Minnesota Informatics Institute. L.R.J., R.B.G., J.M.C., E.A.M., C.C.M., J.R.R., S.J.R., A.M.S.-I., and D.P.W. were supported by NIH– NSF–US Department of Agriculture Ecology of Infectious Diseases Grant 1R01AI122284. J.A. and M.C. were funded with federal funds from Office of the Assistant Secretary for Preparedness and Response, Biomedical Advanced Research and Development Authority Contract HHSO100201600017I.
Funding Information:
T.K.Y. and J.S. were supported by National Institute of General Medical Sciences (NIGMS) Grant GM110748 and Defense Threat Reduction Agency Contract HDTRA1-15-C-0018. L.C.B., D.C.F., S.H., R.J.T., and R.R. were supported by NIGMS Award U54 GM088491 and NSF Graduate Research Fellowship Program Grant DGE-1252522. D.C.F. was a predoctoral trainee supported by NIH T32 Training Grant T32 EB009403 and the HHMI-National Institute of Biomedical Imaging and Bioengineering Interfaces Initiative. R.J.T. was supported by NSF Grant DMS-1309174. J.L., N.G.R., D.A.T.C., S.A.L., S.M.M., and H.E.C. were supported by National Institute of Allergy and Infectious Diseases (NIAID) Grant AI102939. N.G.R., E.L.R., K.S., A.C.B., and X.M. were supported by NIAID and NIGMS Grants R21AI115173, R01AI102939, and R35GM119582. R.L. was supported by a Royal Society Dorothy Hodgkin Fellowship. O.O., R.V., D.M., and M.M. were supported by the Forces and Resources Policy Center of the RAND National Defense Research Institute with discretionary US Department of Defense funds. T.C.P. and L.W. were supported by NIGMS Grant U01-GM087728. M.C., Y.L., and A.R. were supported by Global Institute for Collaborative Research and Education Big-Data and Cybersecurity Station and a Faculty in Industry Award at the University of Minnesota Informatics Institute. L.R.J., R.B.G., J.M.C., E.A.M., C.C.M., J.R.R., S.J.R., A.M.S.-I., and D.P.W. were supported by NIH-NSF-US Department of Agriculture Ecology of Infectious Diseases Grant 1R01AI122284. J.A. and M.C. were funded with federal funds from Office of the Assistant Secretary for Preparedness and Response, Biomedical Advanced Research and Development Authority Contract HHSO100201600017I.
Publisher Copyright:
© 2019 National Academy of Sciences. All rights reserved.
PY - 2019/11/26
Y1 - 2019/11/26
N2 - 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.
AB - 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.
KW - Dengue
KW - Epidemic
KW - Forecast
KW - Peru
KW - Puerto Rico
UR - http://www.scopus.com/inward/record.url?scp=85075648042&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85075648042&partnerID=8YFLogxK
U2 - 10.1073/pnas.1909865116
DO - 10.1073/pnas.1909865116
M3 - Article
C2 - 31712420
AN - SCOPUS:85075648042
SN - 0027-8424
VL - 116
SP - 24268
EP - 24274
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 48
ER -