Literature DB >> 28958414

The RAPIDD ebola forecasting challenge: Synthesis and lessons learnt.

Cécile Viboud1, Kaiyuan Sun2, Robert Gaffey3, Marco Ajelli4, Laura Fumanelli4, Stefano Merler4, Qian Zhang2, Gerardo Chowell5, Lone Simonsen6, Alessandro Vespignani7.   

Abstract

Infectious disease forecasting is gaining traction in the public health community; however, limited systematic comparisons of model performance exist. Here we present the results of a synthetic forecasting challenge inspired by the West African Ebola crisis in 2014-2015 and involving 16 international academic teams and US government agencies, and compare the predictive performance of 8 independent modeling approaches. Challenge participants were invited to predict 140 epidemiological targets across 5 different time points of 4 synthetic Ebola outbreaks, each involving different levels of interventions and "fog of war" in outbreak data made available for predictions. Prediction targets included 1-4 week-ahead case incidences, outbreak size, peak timing, and several natural history parameters. With respect to weekly case incidence targets, ensemble predictions based on a Bayesian average of the 8 participating models outperformed any individual model and did substantially better than a null auto-regressive model. There was no relationship between model complexity and prediction accuracy; however, the top performing models for short-term weekly incidence were reactive models with few parameters, fitted to a short and recent part of the outbreak. Individual model outputs and ensemble predictions improved with data accuracy and availability; by the second time point, just before the peak of the epidemic, estimates of final size were within 20% of the target. The 4th challenge scenario - mirroring an uncontrolled Ebola outbreak with substantial data reporting noise - was poorly predicted by all modeling teams. Overall, this synthetic forecasting challenge provided a deep understanding of model performance under controlled data and epidemiological conditions. We recommend such "peace time" forecasting challenges as key elements to improve coordination and inspire collaboration between modeling groups ahead of the next pandemic threat, and to assess model forecasting accuracy for a variety of known and hypothetical pathogens. Published by Elsevier B.V.

Entities:  

Keywords:  Data accuracy; Ebola epidemic; Forecasting challenge; Mathematical modeling; Model comparison; Prediction horizon; Prediction performance; Synthetic data

Mesh:

Year:  2017        PMID: 28958414      PMCID: PMC5927600          DOI: 10.1016/j.epidem.2017.08.002

Source DB:  PubMed          Journal:  Epidemics        ISSN: 1878-0067            Impact factor:   4.396


  29 in total

1.  Improving the evidence base for decision making during a pandemic: the example of 2009 influenza A/H1N1.

Authors:  Marc Lipsitch; Lyn Finelli; Richard T Heffernan; Gabriel M Leung; Stephen C Redd
Journal:  Biosecur Bioterror       Date:  2011-06

2.  The RAPIDD Ebola forecasting challenge: Model description and synthetic data generation.

Authors:  Marco Ajelli; Qian Zhang; Kaiyuan Sun; Stefano Merler; Laura Fumanelli; Gerardo Chowell; Lone Simonsen; Cecile Viboud; Alessandro Vespignani
Journal:  Epidemics       Date:  2017-09-20       Impact factor: 4.396

3.  Two approaches to forecast Ebola synthetic epidemics.

Authors:  David Champredon; Michael Li; Benjamin M Bolker; Jonathan Dushoff
Journal:  Epidemics       Date:  2017-02-24       Impact factor: 4.396

4.  Using phenomenological models for forecasting the 2015 Ebola challenge.

Authors:  Bruce Pell; Yang Kuang; Cecile Viboud; Gerardo Chowell
Journal:  Epidemics       Date:  2016-11-19       Impact factor: 4.396

5.  Model-based projections of Zika virus infections in childbearing women in the Americas.

Authors:  T Alex Perkins; Amir S Siraj; Corrine W Ruktanonchai; Moritz U G Kraemer; Andrew J Tatem
Journal:  Nat Microbiol       Date:  2016-07-25       Impact factor: 17.745

6.  Spatiotemporal dynamics of the Ebola epidemic in Guinea and implications for vaccination and disease elimination: a computational modeling analysis.

Authors:  Marco Ajelli; Stefano Merler; Laura Fumanelli; Ana Pastore Y Piontti; Natalie E Dean; Ira M Longini; M Elizabeth Halloran; Alessandro Vespignani
Journal:  BMC Med       Date:  2016-09-07       Impact factor: 8.775

7.  Containing Ebola at the Source with Ring Vaccination.

Authors:  Stefano Merler; Marco Ajelli; Laura Fumanelli; Stefano Parlamento; Ana Pastore Y Piontti; Natalie E Dean; Giovanni Putoto; Dante Carraro; Ira M Longini; M Elizabeth Halloran; Alessandro Vespignani
Journal:  PLoS Negl Trop Dis       Date:  2016-11-02

8.  A simple approach to measure transmissibility and forecast incidence.

Authors:  Pierre Nouvellet; Anne Cori; Tini Garske; Isobel M Blake; Ilaria Dorigatti; Wes Hinsley; Thibaut Jombart; Harriet L Mills; Gemma Nedjati-Gilani; Maria D Van Kerkhove; Christophe Fraser; Christl A Donnelly; Neil M Ferguson; Steven Riley
Journal:  Epidemics       Date:  2017-02-24       Impact factor: 4.396

Review 9.  Modeling infectious disease dynamics in the complex landscape of global health.

Authors:  Hans Heesterbeek; Roy M Anderson; Viggo Andreasen; Shweta Bansal; Daniela De Angelis; Chris Dye; Ken T D Eames; W John Edmunds; Simon D W Frost; Sebastian Funk; T Deirdre Hollingsworth; Thomas House; Valerie Isham; Petra Klepac; Justin Lessler; James O Lloyd-Smith; C Jessica E Metcalf; Denis Mollison; Lorenzo Pellis; Juliet R C Pulliam; Mick G Roberts; Cecile Viboud
Journal:  Science       Date:  2015-03-13       Impact factor: 47.728

10.  Ebola virus disease in West Africa--the first 9 months of the epidemic and forward projections.

Authors:  Bruce Aylward; Philippe Barboza; Luke Bawo; Eric Bertherat; Pepe Bilivogui; Isobel Blake; Rick Brennan; Sylvie Briand; Jethro Magwati Chakauya; Kennedy Chitala; Roland M Conteh; Anne Cori; Alice Croisier; Jean-Marie Dangou; Boubacar Diallo; Christl A Donnelly; Christopher Dye; Tim Eckmanns; Neil M Ferguson; Pierre Formenty; Caroline Fuhrer; Keiji Fukuda; Tini Garske; Alex Gasasira; Stephen Gbanyan; Peter Graaff; Emmanuel Heleze; Amara Jambai; Thibaut Jombart; Francis Kasolo; Albert Mbule Kadiobo; Sakoba Keita; Daniel Kertesz; Moussa Koné; Chris Lane; Jered Markoff; Moses Massaquoi; Harriet Mills; John Mike Mulba; Emmanuel Musa; Joel Myhre; Abdusalam Nasidi; Eric Nilles; Pierre Nouvellet; Deo Nshimirimana; Isabelle Nuttall; Tolbert Nyenswah; Olushayo Olu; Scott Pendergast; William Perea; Jonathan Polonsky; Steven Riley; Olivier Ronveaux; Keita Sakoba; Ravi Santhana Gopala Krishnan; Mikiko Senga; Faisal Shuaib; Maria D Van Kerkhove; Rui Vaz; Niluka Wijekoon Kannangarage; Zabulon Yoti
Journal:  N Engl J Med       Date:  2014-09-22       Impact factor: 91.245

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  71 in total

1.  The RAPIDD Ebola forecasting challenge: Model description and synthetic data generation.

Authors:  Marco Ajelli; Qian Zhang; Kaiyuan Sun; Stefano Merler; Laura Fumanelli; Gerardo Chowell; Lone Simonsen; Cecile Viboud; Alessandro Vespignani
Journal:  Epidemics       Date:  2017-09-20       Impact factor: 4.396

2.  Real-time Epidemic Forecasting: Challenges and Opportunities.

Authors:  Angel N Desai; Moritz U G Kraemer; Sangeeta Bhatia; Anne Cori; Pierre Nouvellet; Mark Herringer; Emily L Cohn; Malwina Carrion; John S Brownstein; Lawrence C Madoff; Britta Lassmann
Journal:  Health Secur       Date:  2019 Jul/Aug

3.  The future of influenza forecasts.

Authors:  Cécile Viboud; Alessandro Vespignani
Journal:  Proc Natl Acad Sci U S A       Date:  2019-02-08       Impact factor: 11.205

4.  Evaluating short-term forecasting of COVID-19 cases among different epidemiological models under a Bayesian framework.

Authors:  Qiwei Li; Tejasv Bedi; Christoph U Lehmann; Guanghua Xiao; Yang Xie
Journal:  Gigascience       Date:  2021-02-19       Impact factor: 6.524

5.  Detection, forecasting and control of infectious disease epidemics: modelling outbreaks in humans, animals and plants.

Authors:  Robin N Thompson; Ellen Brooks-Pollock
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2019-06-24       Impact factor: 6.237

6.  Thinking clearly about social aspects of infectious disease transmission.

Authors:  Caroline Buckee; Abdisalan Noor; Lisa Sattenspiel
Journal:  Nature       Date:  2021-06-30       Impact factor: 49.962

Review 7.  Social Media- and Internet-Based Disease Surveillance for Public Health.

Authors:  Allison E Aiello; Audrey Renson; Paul N Zivich
Journal:  Annu Rev Public Health       Date:  2020-01-06       Impact factor: 21.981

8.  Initial growth rates of malware epidemics fail to predict their reach.

Authors:  Lev Muchnik; Elad Yom-Tov; Nir Levy; Amir Rubin; Yoram Louzoun
Journal:  Sci Rep       Date:  2021-06-03       Impact factor: 4.379

9.  How New Mexico Leveraged a COVID-19 Case Forecasting Model to Preemptively Address the Health Care Needs of the State: Quantitative Analysis.

Authors:  Lauren A Castro; Courtney D Shelley; Dave Osthus; Isaac Michaud; Jason Mitchell; Carrie A Manore; Sara Y Del Valle
Journal:  JMIR Public Health Surveill       Date:  2021-06-09

10.  Incubation periods impact the spatial predictability of cholera and Ebola outbreaks in Sierra Leone.

Authors:  Rebecca Kahn; Corey M Peak; Juan Fernández-Gracia; Alexandra Hill; Amara Jambai; Louisa Ganda; Marcia C Castro; Caroline O Buckee
Journal:  Proc Natl Acad Sci U S A       Date:  2020-02-13       Impact factor: 11.205

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