An open challenge to advance probabilistic forecasting for dengue epidemics.


Journal

Proceedings of the National Academy of Sciences of the United States of America
ISSN: 1091-6490
Titre abrégé: Proc Natl Acad Sci U S A
Pays: United States
ID NLM: 7505876

Informations de publication

Date de publication:
26 11 2019
Historique:
pubmed: 13 11 2019
medline: 28 4 2020
entrez: 13 11 2019
Statut: ppublish

Résumé

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.

Identifiants

pubmed: 31712420
pii: 1909865116
doi: 10.1073/pnas.1909865116
pmc: PMC6883829
doi:

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

IM

Pagination

24268-24274

Subventions

Organisme : NIBIB NIH HHS
ID : T32 EB009403
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM119582
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM100467
Pays : United States
Organisme : Howard Hughes Medical Institute
Pays : United States
Organisme : NIGMS NIH HHS
ID : U01 GM087728
Pays : United States
Organisme : NIGMS NIH HHS
ID : U01 GM110748
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI102939
Pays : United States
Organisme : NIAID NIH HHS
ID : R21 AI115173
Pays : United States
Organisme : NIGMS NIH HHS
ID : U54 GM088491
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI122284
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM133439
Pays : United States

Commentaires et corrections

Type : ErratumIn
Type : ErratumIn

Informations de copyright

Copyright © 2019 the Author(s). Published by PNAS.

Déclaration de conflit d'intérêts

The authors declare no competing interest.

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Auteurs

Michael A Johansson (MA)

Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan 00920, Puerto Rico; mjohansson@cdc.gov.
Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115.

Karyn M Apfeldorf (KM)

Data Analytics, Areté Associates, Northridge, CA 91324.

Scott Dobson (S)

Data Analytics, Areté Associates, Northridge, CA 91324.

Jason Devita (J)

Data Analytics, Areté Associates, Northridge, CA 91324.

Anna L Buczak (AL)

Systems Integration Branch, Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723.

Benjamin Baugher (B)

Systems Integration Branch, Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723.

Linda J Moniz (LJ)

Systems Integration Branch, Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723.

Thomas Bagley (T)

Systems Integration Branch, Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723.

Steven M Babin (SM)

Systems Integration Branch, Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723.

Erhan Guven (E)

Systems Integration Branch, Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723.

Teresa K Yamana (TK)

Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032.

Jeffrey Shaman (J)

Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032.

Terry Moschou (T)

Data to Decisions Cooperative Research Center, Kent Town, SA 5067, Australia.

Nick Lothian (N)

Data to Decisions Cooperative Research Center, Kent Town, SA 5067, Australia.

Aaron Lane (A)

Data to Decisions Cooperative Research Center, Kent Town, SA 5067, Australia.

Grant Osborne (G)

Data to Decisions Cooperative Research Center, Kent Town, SA 5067, Australia.

Gao Jiang (G)

Heinz College Information System Management, Carnegie Mellon University, Adelaide, SA 5000, Australia.

Logan C Brooks (LC)

School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213.

David C Farrow (DC)

School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213.

Sangwon Hyun (S)

Department of Statistics, Carnegie Mellon University, Pittsburgh, PA 15213.

Ryan J Tibshirani (RJ)

School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213.
Department of Statistics, Carnegie Mellon University, Pittsburgh, PA 15213.

Roni Rosenfeld (R)

School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213.

Justin Lessler (J)

Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205.

Nicholas G Reich (NG)

Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA 01003.

Derek A T Cummings (DAT)

Department of Biology, University of Florida, Gainesville, FL 32611.
Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611.

Stephen A Lauer (SA)

Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA 01003.

Sean M Moore (SM)

Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556.
Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556.

Hannah E Clapham (HE)

Hospital for Tropical Diseases, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.

Rachel Lowe (R)

Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, United Kingdom.
Climate and Health Program, Barcelona Institute for Global Health, 08003 Barcelona, Spain.

Trevor C Bailey (TC)

College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter EX4 4QF, United Kingdom.

Markel García-Díez (M)

Predictia Intelligent Data Solutions, 39005 Santander, Spain.

Marilia Sá Carvalho (MS)

Scientific Computation Program, Oswaldo Cruz Foundation, Rio de Janeiro 21040-900, Brazil.

Xavier Rodó (X)

Climate and Health Program, Barcelona Institute for Global Health, 08003 Barcelona, Spain.
Catalan Institution for Research and Advanced Studies, 08010 Barcelona, Spain.

Tridip Sardar (T)

Catalan Institution for Research and Advanced Studies, 08010 Barcelona, Spain.

Richard Paul (R)

Department of Mathematical Biology, Indian Statistical Institute, Kolkata, India 700108.
Pasteur Kyoto International Joint Research Unit for Integrative Vaccinomics, 606-8501 Kyoto, Japan.

Evan L Ray (EL)

Department of Global Health, Centre National de la Recherche Scientifique, 75016 Paris, France.

Krzysztof Sakrejda (K)

Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA 01003.

Alexandria C Brown (AC)

Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA 01003.

Xi Meng (X)

Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA 01003.

Osonde Osoba (O)

Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA 01075.

Raffaele Vardavas (R)

Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA 01075.

David Manheim (D)

RAND Corporation, Santa MonicaCA 90401.

Melinda Moore (M)

Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA 01075.

Dhananjai M Rao (DM)

Open Philanthropy, San Francisco, CA 94105.

Travis C Porco (TC)

Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056.

Sarah Ackley (S)

Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056.

Fengchen Liu (F)

Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056.

Lee Worden (L)

Department of Computer Science and Software Engineering, Miami University, Oxford, OH 45056.

Matteo Convertino (M)

F. I. Proctor Foundation for Research in Ophthalmology, University of California, San Francisco, CA 94122.

Yang Liu (Y)

Information Science and Technology, Hokkaido University, Sapporo 060-0808, Japan.

Abraham Reddy (A)

Information Science and Technology, Hokkaido University, Sapporo 060-0808, Japan.

Eloy Ortiz (E)

Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Twin Cities, MN 55455.

Jorge Rivero (J)

Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Twin Cities, MN 55455.

Humberto Brito (H)

Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Twin Cities, MN 55455.
VectorAnalytica, Washington, DC 20007.

Alicia Juarrero (A)

Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Twin Cities, MN 55455.
Department of Aeronautical Engineering, Universidade de Sao Paolo, Sao Paolo 13566-590, Brazil.

Leah R Johnson (LR)

Department of Philosophy, University of Miami, Coral Gables, FL 33146.

Robert B Gramacy (RB)

Department of Statistics, Virginia Tech, Blacksburg, VA 24060.

Jeremy M Cohen (JM)

Department of Statistics, Virginia Tech, Blacksburg, VA 24060.

Erin A Mordecai (EA)

Integrative Biology, University of South Florida, Tampa, FL 33620.

Courtney C Murdock (CC)

Department of Biology, Stanford University, Stanford, CA 94305.
Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602.

Jason R Rohr (JR)

Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556.
Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556.

Sadie J Ryan (SJ)

Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611.
Odum School of Ecology, University of Georgia, Athens, GA 30602.
Department of Geography, University of Florida, Gainesville, FL 32608.

Anna M Stewart-Ibarra (AM)

School of Life Sciences, University of KwaZulu, Natal 3629, South Africa.

Daniel P Weikel (DP)

Department of Medicine, State University of New York Upstate Medical University, Syracuse, NY 13421.

Antarpreet Jutla (A)

Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109.

Rakibul Khan (R)

Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109.

Marissa Poultney (M)

Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109.

Rita R Colwell (RR)

Department of Civil and Environmental Engineering, West Virginia University, Morgantown, WV 26505.

Brenda Rivera-García (B)

Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742.

Christopher M Barker (CM)

Puerto Rico Department of Health, San Juan 00927, Puerto Rico.

Jesse E Bell (JE)

Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, CA 95616.

Matthew Biggerstaff (M)

Department of Environmental, Agricultural, and Occupational Health, College of Public Health, University of Nebraska Medical Center, Omaha, NE 68198.

David Swerdlow (D)

Department of Environmental, Agricultural, and Occupational Health, College of Public Health, University of Nebraska Medical Center, Omaha, NE 68198.

Luis Mier-Y-Teran-Romero (L)

Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan 00920, Puerto Rico.
Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205.

Brett M Forshey (BM)

Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329.

Juli Trtanj (J)

Armed Forces Health Surveillance Branch, Department of Defense, Silver Spring, MD 20904.

Jason Asher (J)

Climate Program Office, National Oceanic and Atmospheric Administration, Silver Spring, MD 20910.

Matt Clay (M)

Climate Program Office, National Oceanic and Atmospheric Administration, Silver Spring, MD 20910.

Harold S Margolis (HS)

Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan 00920, Puerto Rico.

Andrew M Hebbeler (AM)

Leidos supporting the Biomedical Advanced Research and Development Authority, Department of Health and Human Services, Washington, DC 20201.
Bureau of Oceans, International Environmental and Scientific Affairs, US Department of State, Washington, DC 20520.

Dylan George (D)

Bureau of Oceans, International Environmental and Scientific Affairs, US Department of State, Washington, DC 20520.
Office of Science and Technology Policy, The White House, Washington, DC 20502.

Jean-Paul Chretien (JP)

Bureau of Oceans, International Environmental and Scientific Affairs, US Department of State, Washington, DC 20520.
BNext, In-Q-Tel, Arlington, VA 22201.

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