An open challenge to advance probabilistic forecasting for dengue epidemics

被引:131
作者
Johansson, Michael A. [1 ,2 ]
Apfeldorf, Karyn M. [3 ]
Dobson, Scott [3 ]
Devita, Jason [3 ]
Buczak, Anna L. [4 ]
Baugher, Benjamin [4 ]
Moniz, Linda J. [4 ]
Bagley, Thomas [4 ]
Babin, Steven M. [4 ]
Guven, Erhan [4 ]
Yamana, Teresa K. [5 ]
Shaman, Jeffrey [5 ]
Moschou, Terry [6 ]
Lothian, Nick [6 ]
Lane, Aaron [6 ]
Osborne, Grant [6 ]
Jiang, Gao [7 ]
Brooks, Logan C. [8 ]
Farrow, David C. [8 ]
Hyun, Sangwon [9 ]
Tibshirani, Ryan J. [8 ,9 ]
Rosenfeld, Roni [8 ]
Lessler, Justin [10 ]
Reich, Nicholas G. [11 ]
Cummings, Derek A. T. [12 ,13 ]
Lauer, Stephen A. [11 ]
Moore, Sean M. [14 ,15 ]
Clapham, Hannah E. [16 ]
Lowe, Rachel [17 ,18 ]
Bailey, Trevor C. [19 ]
Garcia-Diez, Markel [20 ]
Carvalho, Marilia Sa [21 ]
Rodo, Xavier [18 ]
Sardar, Tridip [22 ]
Paul, Richard [23 ,24 ]
Ray, Evan L. [25 ]
Sakrejda, Krzysztof [11 ]
Brown, Alexandria C. [11 ]
Meng, Xi [11 ]
Osoba, Osonde [26 ]
Vardavas, Raffaele [26 ]
Manheim, David [27 ]
Moore, Melinda [26 ]
Rao, Dhananjai M. [28 ]
Porco, Travis C. [29 ]
Ackley, Sarah [29 ]
Liu, Fengchen [29 ]
Worden, Lee [29 ]
Convertino, Matteo [30 ]
Liu, Yang [31 ]
机构
[1] Ctr Dis Control & Prevent, Div Vector Borne Dis, San Juan, PR 00920 USA
[2] Harvard TH Chan Sch Publ Hlth, Dept Epidemiol, Boston, MA 02115 USA
[3] Arete Associates, Data Analyt, Northridge, CA 91324 USA
[4] Johns Hopkins Univ, Appl Phys Lab, Syst Integrat Branch, Laurel, MD 20723 USA
[5] Columbia Univ, Mailman Sch Publ Hlth, Dept Environm Hlth Sci, New York, NY 10032 USA
[6] Data Decis Cooperat Res Ctr, Kent Town, SA 5067, Australia
[7] Carnegie Mellon Univ, Heinz Coll Informat Syst Management, Adelaide, SA 5000, Australia
[8] Carnegie Mellon Univ, Sch Comp Sci, Pittsburgh, PA 15213 USA
[9] Carnegie Mellon Univ, Dept Stat, Pittsburgh, PA 15213 USA
[10] Johns Hopkins Bloomberg Sch Publ Hlth, Dept Epidemiol, Baltimore, MD 21205 USA
[11] Univ Massachusetts, Sch Publ Hlth & Hlth Sci, Dept Biostat & Epidemiol, Amherst, MA 01003 USA
[12] Univ Florida, Dept Biol, Gainesville, FL 32611 USA
[13] Univ Florida, Emerging Pathogens Inst, Gainesville, FL 32611 USA
[14] Univ Notre Dame, Dept Biol Sci, Notre Dame, IN 46556 USA
[15] Univ Notre Dame, Eck Inst Global Hlth, Notre Dame, IN 46556 USA
[16] Univ Oxford, Clin Res Unit, Hosp Trop Dis, Ho Chi Minh City, Vietnam
[17] London Sch Hyg & Trop Med, Dept Infect Dis Epidemiol, London WC1E 7HT, England
[18] Barcelona Inst Global Hlth, Climate & Hlth Program, Barcelona 08003, Spain
[19] Univ Exeter, Coll Engn Math & Phys Sci, Exeter EX4 4QF, Devon, England
[20] Predictia Intelligent Data Solut, Santander 39005, Spain
[21] Fundacao Oswaldo Cruz, Sci Computat Program, BR-21040900 Rio De Janeiro, Brazil
[22] Indian Stat Inst, Dept Math Biol, Kolkata 700108, India
[23] Pasteur Kyoto Int Joint Res Unit Integrat Vaccin, Kyoto 6068501, Japan
[24] CNRS, Dept Global Hlth, F-75016 Paris, France
[25] Mt Holyoke Coll, Dept Math & Stat, S Hadley, MA 01075 USA
[26] RAND Corp, Santa Monica, CA 90401 USA
[27] Open Philanthropy, San Francisco, CA 94105 USA
[28] Miami Univ, Dept Comp Sci & Software Engn, Oxford, OH 45056 USA
[29] Univ Calif San Francisco, FI Proctor Fdn Res Ophthalmol, San Francisco, CA 94122 USA
[30] Hokkaido Univ, Informat Sci & Technol, Sapporo, Hokkaido 0600808, Japan
[31] Univ Minnesota, Sch Publ Hlth, Div Environm Hlth Sci, Minneapolis, MN 55455 USA
[32] VectorAnalytica, Washington, DC 20007 USA
[33] Univ Sao Paolo, Dept Aeronaut Engn, BR-13566590 Sao Paulo, Brazil
[34] Univ Miami, Dept Philosophy, Coral Gables, FL 33146 USA
[35] Virginia Tech, Dept Stat, Blacksburg, VA 24060 USA
[36] Univ S Florida, Integrat Biol, Tampa, FL 33620 USA
[37] Stanford Univ, Dept Biol, Stanford, CA 94305 USA
[38] Univ Georgia, Coll Vet Med, Infect Dis, Athens, GA 30602 USA
[39] Univ Georgia, Odum Sch Ecol, Athens, GA 30602 USA
[40] Univ Florida, Dept Geog, Gainesville, FL 32608 USA
[41] Univ KwaZulu, Sch Life Sci, ZA-3629 Natal, South Africa
[42] SUNY Upstate Med Univ, Dept Med, Syracuse, NY 13421 USA
[43] Univ Michigan, Dept Biostat, Ann Arbor, MI 48109 USA
[44] West Virginia Univ, Dept Civil & Environm Engn, Morgantown, WV 26505 USA
[45] Univ Maryland, Dept Cell Biol & Mol Genet, College Pk, MD 20742 USA
[46] Puerto Rico Dept Hlth, San Juan, PR 00927 USA
[47] Univ Calif Davis, Sch Vet Med, Dept Pathol Microbiol & Immunol, Davis, CA 95616 USA
[48] Univ Nebraska Med Ctr, Coll Publ Hlth, Dept Environm Agr & Occupat Hlth, Omaha, NE 68198 USA
[49] Ctr Dis Control & Prevent, Influenza Div, Atlanta, GA 30329 USA
[50] Armed Forces Hlth Surveillance Branch, Dept Def, Silver Spring, MD 20904 USA
关键词
forecast; dengue; epidemic; Peru; Puerto Rico; DEPENDENT ENHANCEMENT; BURDEN;
D O I
10.1073/pnas.1909865116
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
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.
引用
收藏
页码:24268 / 24274
页数:7
相关论文
共 42 条
[1]   Cross-protective immunity can account for the alternating epidemic pattern of dengue virus serotypes circulating in Bangkok [J].
Adams, B. ;
Holmes, E. C. ;
Zhang, C. ;
Mammen, M. P., Jr. ;
Nimmannitya, S. ;
Kalayanarooj, S. ;
Boots, M. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (38) :14234-14239
[2]  
[Anonymous], 2009, DENG GUID DIAGN TREA
[3]   The global distribution and burden of dengue [J].
Bhatt, Samir ;
Gething, Peter W. ;
Brady, Oliver J. ;
Messina, Jane P. ;
Farlow, Andrew W. ;
Moyes, Catherine L. ;
Drake, John M. ;
Brownstein, John S. ;
Hoen, Anne G. ;
Sankoh, Osman ;
Myers, Monica F. ;
George, Dylan B. ;
Jaenisch, Thomas ;
Wint, G. R. William ;
Simmons, Cameron P. ;
Scott, Thomas W. ;
Farrar, Jeremy J. ;
Hay, Simon I. .
NATURE, 2013, 496 (7446) :504-507
[4]   Results from the second year of a collaborative effort to forecast influenza seasons in the United States [J].
Biggerstaff, Matthew ;
Johansson, Michael ;
Alper, David ;
Brooks, Logan C. ;
Chakraborty, Prithwish ;
Farrow, David C. ;
Hyun, Sangwon ;
Kandula, Sasikiran ;
McGowan, Craig ;
Ramakrishnan, Naren ;
Rosenfeld, Roni ;
Shaman, Jeffrey ;
Tibshirani, Rob ;
Tibshirani, Ryan J. ;
Vespignani, Alessandro ;
Yang, Wan ;
Zhang, Qian ;
Reed, Carrie .
EPIDEMICS, 2018, 24 :26-33
[5]   Dengue disease outbreak definitions are implicitly variable [J].
Brady, Oliver J. ;
Smith, David L. ;
Scott, Thomas W. ;
Hay, Simon I. .
EPIDEMICS, 2015, 11 :92-102
[6]  
Brier G. W., 1950, Mon Weather Rev, V78, P1, DOI [DOI 10.1175/1520-0493(1950)0782.0.CO
[7]  
2, DOI 10.1175/1520-0493(1950)078ANDLT
[8]  
0001:VOFEITANDGT
[9]  
2.0.CO
[10]  
2]