Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States

  • Estee Y. Cramer
  • , Evan L. Ray
  • , Velma K. Lopez
  • , Johannes Bracher
  • , Andrea Brennen
  • , Alvaro J. Castro Rivadeneira
  • , Aaron Gerding
  • , Tilmann Gneiting
  • , Katie H. House
  • , Yuxin Huang
  • , Dasuni Jayawardena
  • , Abdul H. Kanji
  • , Ayush Khandelwal
  • , Khoa Le
  • , Anja Mühlemann
  • , Jarad Niemi
  • , Apurv Shah
  • , Ariane Stark
  • , Yijin Wang
  • , Nutcha Wattanachit
  • Martha W. Zorn, Youyang Gu, Sansiddh Jain, Nayana Bannur, Ayush Deva, Mihir Kulkarni, Srujana Merugu, Alpan Raval, Siddhant Shingi, Avtansh Tiwari, Jerome White, Neil F. Abernethy, Spencer Woody, Maytal Dahan, Spencer Fox, Kelly Gaither, Michael Lachmann, Lauren Ancel Meyers, James G. Scott, Mauricio Tec, Ajitesh Srivastava, Glover E. George, Jeffrey C. Cegan, Ian D. Dettwiller, William P. England, Matthew W. Farthing, Robert H. Hunter, Brandon Lafferty, Igor Linkov, Michael L. Mayo, Matthew D. Parno, Michael A. Rowland, Benjamin D. Trump, Yanli Zhang-James, Samuel Chen, Stephen V. Faraone, Jonathan Hess, Christopher P. Morley, Asif Salekin, Dongliang Wang, Sabrina M. Corsetti, Thomas M. Baer, Marisa C. Eisenberg, Karl Falb, Yitao Huang, Emily T. Martin, Ella McCauley, Robert L. Myers, Tom Schwarz, Daniel Sheldon, Graham Casey Gibson, Rose Yu, Liyao Gao, Yian Ma, Dongxia Wu, Xifeng Yan, Xiaoyong Jin, Yu Xiang Wang, Yang Quan Chen, Lihong Guo, Yanting Zhao, Quanquan Gu, Jinghui Chen, Lingxiao Wang, Pan Xu, Weitong Zhang, Difan Zou, Hannah Biegel, Joceline Lega, Steve McConnell, V. P. Nagraj, Stephanie L. Guertin, Christopher Hulme-Lowe, Stephen D. Turner, Yunfeng Shi, Xuegang Ban, Robert Walraven, Qi Jun Hong, Stanley Kong, Axel van de Walle, James A. Turtle, Michal Ben-Nun, Steven Riley, Pete Riley, Ugur Koyluoglu, David DesRoches, Pedro Forli, Bruce Hamory, Christina Kyriakides, Helen Leis, John Milliken, Michael Moloney, James Morgan, Ninad Nirgudkar, Gokce Ozcan, Noah Piwonka, Matt Ravi, Chris Schrader, Elizabeth Shakhnovich, Daniel Siegel, Ryan Spatz, Chris Stiefeling, Barrie Wilkinson, Alexander Wong, Sean Cavany, Guido España, Sean Moore, Rachel Oidtman, Alex Perkins, David Kraus, Andrea Kraus, Zhifeng Gao, Jiang Bian, Wei Cao, Juan Lavista Ferres, Chaozhuo Li, Tie Yan Liu, Xing Xie, Shun Zhang, Shun Zheng, Alessandro Vespignani, Matteo Chinazzi, Jessica T. Davis, Kunpeng Mu, Ana Pastore y Piontti, Xinyue Xiong, Andrew Zheng, Jackie Baek, Vivek Farias, Andreea Georgescu, Retsef Levi, Deeksha Sinha, Joshua Wilde, Georgia Perakis, Mohammed Amine Bennouna, David Nze-Ndong, Divya Singhvi, Ioannis Spantidakis, Leann Thayaparan, Asterios Tsiourvas, Arnab Sarker, Ali Jadbabaie, Devavrat Shah, Nicolas Della Penna, Leo A. Celi, Saketh Sundar, Russ Wolfinger, Dave Osthus, Lauren Castro, Geoffrey Fairchild, Isaac Michaud, Dean Karlen, Matt Kinsey, Luke C. Mullany, Kaitlin Rainwater-Lovett, Lauren Shin, Katharine Tallaksen, Shelby Wilson, Elizabeth C. Lee, Juan Dent, Kyra H. Grantz, Alison L. Hill, Joshua Kaminsky, Kathryn Kaminsky, Lindsay T. Keegan, Stephen A. Lauer, Joseph C. Lemaitre, Justin Lessler, Hannah R. Meredith, Javier Perez-Saez, Sam Shah, Claire P. Smith, Shaun A. Truelove, Josh Wills, Maximilian Marshall, Lauren Gardner, Kristen Nixon, John C. Burant, Lily Wang, Lei Gao, Zhiling Gu, Myungjin Kim, Xinyi Li, Guannan Wang, Yueying Wang, Shan Yu, Robert C. Reiner, Ryan Barber, Emmanuela Gakidou, Simon I. Hay, Steve Lim, Chris Murray, David Pigott, Heidi L. Gurung, Prasith Baccam, Steven A. Stage, Bradley T. Suchoski, B. Aditya Prakash, Bijaya Adhikari, Jiaming Cui, Alexander Rodríguez, Anika Tabassum, Jiajia Xie, Pinar Keskinocak, John Asplund, Arden Baxter, Buse Eylul Oruc, Nicoleta Serban, Sercan O. Arik, Mike Dusenberry, Arkady Epshteyn, Elli Kanal, Long T. Le, Chun Liang Li, Tomas Pfister, Dario Sava, Rajarishi Sinha, Thomas Tsai, Nate Yoder, Jinsung Yoon, Leyou Zhang, Sam Abbott, Nikos I. Bosse, Sebastian Funk, Joel Hellewell, Sophie R. Meakin, Katharine Sherratt, Mingyuan Zhou, Rahi Kalantari, Teresa K. Yamana, Sen Pei, Jeffrey Shaman, Michael L. Li, Dimitris Bertsimas, Omar Skali Lami, Saksham Soni, Hamza Tazi Bouardi, Turgay Ayer, Madeline Adee, Jagpreet Chhatwal, Ozden O. Dalgic, Mary A. Ladd, Benjamin P. Linas, Peter Mueller, Jade Xiao, Yuanjia Wang, Qinxia Wang, Shanghong Xie, Donglin Zeng, Alden Green, Jacob Bien, Logan Brooks, Addison J. Hu, Maria Jahja, Daniel McDonald, Balasubramanian Narasimhan, Collin Politsch, Samyak Rajanala, Aaron Rumack, Noah Simon, Ryan J. Tibshirani, Rob Tibshirani, Valerie Ventura, Larry Wasserman, Eamon B. O’Dea, John M. Drake, Robert Pagano, Quoc T. Tran, Lam Si Tung Ho, Huong Huynh, Jo W. Walker, Rachel B. Slayton, Michael A. Johansson, Matthew Biggerstaff, Nicholas G. Reich

Research output: Contribution to journalArticlepeer-review

211 Scopus citations

Abstract

Short-term probabilistic forecasts of the trajectory of the COVID-19 pandemic in the United States have served as a visible and important communication channel between the scientific modeling community and both the general public and decision-makers. Forecasting models provide specific, quantitative, and evaluable predictions that inform short-term decisions such as healthcare staffing needs, school closures, and allocation of medical supplies. Starting in April 2020, the US COVID-19 Forecast Hub (https://covid19forecasthub.org/) collected, disseminated, and synthesized tens of millions of specific predictions from more than 90 different academic, industry, and independent research groups. A multimodel ensemble forecast that combined predictions from dozens of groups every week provided the most consistently accurate probabilistic forecasts of incident deaths due to COVID-19 at the state and national level from April 2020 through October 2021. The performance of 27 individual models that submitted complete forecasts of COVID-19 deaths consistently throughout this year showed high variability in forecast skill across time, geospatial units, and forecast horizons. Two-thirds of the models evaluated showed better accuracy than a naïve baseline model. Forecast accuracy degraded as models made predictions further into the future, with probabilistic error at a 20-wk horizon three to five times larger than when predicting at a 1-wk horizon. This project underscores the role that collaboration and active coordination between governmental public-health agencies, academic modeling teams, and industry partners can play in developing modern modeling capabilities to support local, state, and federal response to outbreaks.

Original languageEnglish
Article numbere2113561119
JournalProceedings of the National Academy of Sciences of the United States of America
Volume119
Issue number15
DOIs
StatePublished - Apr 12 2022
Externally publishedYes

Funding

ACKNOWLEDGMENTS. We report the funding and disclosures below for all teams. The content is solely the responsibility of the authors and does not necessarily represent the official views of any of the funding agencies. CMU-TimeSeries: CDC Center of Excellence, gifts from Google and Facebook; CU-select: NSF DMS-2027369 and a gift from the Morris-Singer Foundation; COVIDhub: US CDC (1U01IP001122); National Institute of General Medical Sciences (NIGMS) (R35GM119582); Helmholtz Foundation (SIMCARD Information & Data Science Pilot Project); Klaus Tschira Foundation. Columbia_UNC-Surv-Con: GM124104. DDS-NBDS: NSF III-1812699. EPIFORECASTS-ENSEMBLE1: Wellcome Trust (210758/Z/18/Z); GT_CHHS-COVID19: William W. George Endowment, Virginia C. and Joseph C. Mello Endowments, NSF DGE-1650044, NSF MRI 1828187, CDC and Council of state and Territorial Epidemiologists (CSTE) NU38OT000297, The Partnership for Advanced Computing Environment (PACE) at Georgia Tech. Andrea Laliberte, Joseph C. Mello, Richard “Rick” E. and Charlene Zalesky, and Claudia and Paul Raines; GT-DeepCOVID: CDC Modeling Infectious Diseases in Healthcare (MinD-Healthcare) U01CK000531-Supplement; NSF (Expeditions CCF-1918770, CAREER IIS-2028586, Rapid Response Research (RAPID) IIS-2027862, Medium IIS-1955883, and NSF Research Traineeship (NRT) DGE-1545362), CDC MInD program, Oak Ridge National Laboratory (ORNL) and funds/computing resources from Georgia Tech and Georgia Tech Research Institute (GTRI); Institute for Health Metrics and Evaluation (IHME): The Bill & Melinda Gates Foundation; the state of Washington and NSF (FAIN: 2031096); IowaStateLW-STEM: Iowa State University Plant Sciences Institute Scholars Program, NSF DMS-1916204, NSF CCF-1934884, Laurence H. Baker Center for Bioinformatics and Biological Statistics; Johns Hopkins University (JHU) CSSE: NSF RAPID (2108526 and 2028604); JHU_IDD-CovidSP: State of California, US Health and Human Services (HHS), US Department of Health Services (DHS), US Office of Foreign Disaster Assistance, Johns Hopkins Health System, Office of the Dean Johns Hopkins Bloom-berg School of Public Health (JHBSPH), Johns Hopkins University Modeling and Policy Hub, CDC (5U01CK000538-03), University of Utah Immunology, Inflammation, & Infectious Disease Initiative (26798 Seed Grant); LANL-GrowthRate: Los Alamos National Lab (LANL) Laboratory Directed Research and Development (LDRD) 20200700ER; MOBS-GLEAM_COVID: COVID Supplement CDC-HHS-6U01IP001137-01; CSTE Cooperative Agreement No. NU38OT000297; NotreDame-mobility and NotreDame-FRED: NSF RAPID Division of Environmental Biology (DEB) 2027718; PSI-DRAFT: NSF RAPID Grant No. 2031536; UA-EpiCovDA: NSF RAPID DMS 2028401; UCSB-ACTS: NSF RAPID Division of Information and Intelligent Systems (IIS) 2029626; UCSD-NEU: Google Faculty Award, Defense Advanced Research Projects Agency (DARPA) W31P4Q-21-C-0014, COVID Supplement CDC-HHS-6U01IP001137-01; UMass-MechBayes: NIGMS R35GM119582, NSF 1749854; UMich-RidgeTfReg: University of Michigan Physics Department and Office of Research; Covid19Sim-Simulator: NSF awards 2035360 and 2035361; and Gordon and Betty Moore Foundation and Rockefeller Foundation to support the work of the Society for Medical Decision Making COVID-19 Decision Modeling Initiative. We report the funding and disclosures below for all teams. The content is solely the responsibility of the authors and does not necessarily represent the official views of any of the funding agencies. CMU-TimeSeries: CDC Center of Excellence, gifts from Google and Facebook; CU-select: NSF DMS-2027369 and a gift from the Morris-Singer Foundation; COVIDhub: US CDC (1U01IP001122); National Institute of General Medical Sciences (NIGMS) (R35GM119582); Helmholtz Foundation (SIMCARD Information & Data Science Pilot Project); Klaus Tschira Foundation. Columbia_UNC-SurvCon: GM124104. DDS-NBDS: NSF III-1812699. EPIFORECASTS-ENSEMBLE1: Wellcome Trust (210758/Z/18/Z);_GT_CHHS-COVID19: William W. George Endowment, Virginia C. and Joseph C. Mello Endowments, NSF DGE-1650044, NSF MRI 1828187, CDC and Council of state and Territorial Epidemiologists (CSTE) NU38OT000297, The Partnership for Advanced Computing Environment (PACE) at Georgia Tech. Andrea Laliberte, Joseph C. Mello, Richard “Rick” E. and Charlene Zalesky, and Claudia and Paul Raines; GT-DeepCOVID: CDC Modeling Infectious Diseases in Healthcare (MinD-Healthcare) U01CK000531-Supplement; NSF (Expeditions CCF-1918770, CAREER IIS-2028586, Rapid Response Research (RAPID) IIS-2027862, Medium IIS-1955883, and NSF Research Traineeship (NRT) DGE-1545362), CDC MInD program, Oak Ridge National Laboratory (ORNL) and funds/computing resources from Georgia Tech and Georgia Tech Research Institute (GTRI); Institute for Health Metrics and Evaluation (IHME): The Bill & Melinda Gates Foundation; the state of Washington and NSF (FAIN: 2031096); IowaStateLW-STEM: Iowa State University Plant Sciences Institute Scholars Program, NSF DMS-1916204, NSF CCF-1934884, Laurence H. Baker Center for Bioinformatics and Biological Statistics; Johns Hopkins University (JHU) CSSE: NSF RAPID (2108526 and 2028604); JHU_IDD-CovidSP: State of California, US Health and Human Services (HHS), US Department of Health Services (DHS), US Office of Foreign Disaster Assistance, Johns Hopkins Health System, Office of the Dean Johns Hopkins Bloomberg School of Public Health (JHBSPH), Johns Hopkins University Modeling and Policy Hub, CDC (5U01CK000538-03), University of Utah Immunology, Inflammation, & Infectious Disease Initiative (26798 Seed Grant); LANL-GrowthRate: Los Alamos National Lab (LANL) Laboratory Directed Research and Development (LDRD) 20200700ER; MOBS-GLEAM_COVID: COVID Supplement CDC-HHS-6U01IP001137-01; CSTE Cooperative Agreement No. NU38OT000297; NotreDame-mobility and NotreDame-FRED: NSF RAPID Division of Environmental Biology (DEB) 2027718; PSI-DRAFT: NSF RAPID Grant No. 2031536; UA-EpiCovDA: NSF RAPID DMS 2028401; UCSB-ACTS: NSF RAPID Division of Information and Intelligent Systems (IIS) 2029626; UCSD-NEU: Google Faculty Award, Defense Advanced Research Projects Agency (DARPA) W31P4Q-21-C-0014, COVID Supplement CDC-HHS-6U01IP001137-01; UMass-MechBayes: NIGMS R35GM119582, NSF 1749854; UMich-RidgeTfReg: University of Michigan Physics Department and Office of Research; Covid19Sim-Simulator: NSF awards 2035360 and 2035361; and Gordon and Betty Moore Foundation and Rockefeller Foundation to support the work of the Society for Medical Decision Making COVID-19 Decision Modeling Initiative.

Keywords

  • COVID-19
  • ensemble forecast
  • forecasting
  • model evaluation

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