Autor: Ullrich, Alexander - Prolib Integro

Skocz do pozycji: 1.

Tytuł:: A pre-registered short-term forecasting study of COVID-19 in Germany and Poland during the second wave
Autorzy:: Ożański, Tomasz
Görgen, Konstantin
Bhatia, Sangeeta
Kirsten, Holger
Soni, Saksham
Bodych, Marcin
Hotz, Thomas
Krueger, Tyll
Castro, Lauren
Ullrich, Alexander
Meinke, Jan H.
Gogolewski, Krzysztof
Zielinski, Jakub
Rakowski, Franciszek
Gu, Quanquan
Scholz, Markus
Gneiting, Tilmann
Krymova, Ekaterina
Deuschel, Jannik
Bracher, Johannes
Bertsimas, Dimitris
Funk, Sebastian
Niedzielewski, Karol
Fuhrmann, Jan
Wolffram, Daniel
Burgard, Jan Pablo
Barbarossa, Maria Vittoria
Heyder, Stefan
Zou, Difan
Kheifetz, Yuri
Li, Michael Lingzhi
Fairchild, Geoffrey
Michaud, Isaac
Srivastava, Ajitesh
Ketterer, Jakob L.
Abbott, Sam
Bosse, Nikos I.
Schienle, Melanie
Wydawca:: Springer Nature
Cytata wydawnicza:: Bracher, J., Wolffram, D., Deuschel, J. et al. A pre-registered short-term forecasting study of COVID-19 in Germany and Poland during the second wave. Nat Commun 12, 5173 (2021). https://doi.org/10.1038/s41467-021-25207-0
Opis:: Open Access funding enabled and organized by Projekt DEAL
Disease modelling has had considerable policy impact during the ongoing COVID-19 pandemic, and it is increasingly acknowledged that combining multiple models can improve the reliability of outputs. Here we report insights from ten weeks of collaborative short-term forecasting of COVID-19 in Germany and Poland (12 October–19 December 2020). The study period covers the onset of the second wave in both countries, with tightening non-pharmaceutical interventions (NPIs) and subsequently a decay (Poland) or plateau and renewed increase (Germany) in reported cases. Thirteen independent teams provided probabilistic real-time forecasts of COVID-19 cases and deaths. These were reported for lead times of one to four weeks, with evaluation focused on one- and two-week horizons, which are less affected by changing NPIs. Heterogeneity between forecasts was considerable both in terms of point predictions and forecast spread. Ensemble forecasts showed good relative performance, in particular in terms of coverage, but did not clearly dominate single-model predictions. The study was preregistered and will be followed up in future phases of the pandemic.
The online version contains supplementary materialavailable athttps://doi.org/10.1038/s41467-021-25207-0.
Dostawca treści:: Repozytorium Centrum Otwartej Nauki

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Skocz do pozycji: 2.

Tytuł:: National and subnational short-term forecasting of COVID-19 in Germany and Poland during early 2021
Autorzy:: Wolffram, Danie
Görgen, Konstantin
Bhatia, Sangeeta
Kirsten, Holger
Mohring, Jan
Soni, Saksham
Bodych, Marcin
Hotz, Thomas
Nowosielski, Jędrzej M.
Krueger, Tyll
Castro, Lauren
Ullrich, Alexander
Leithäuser, Neele
Gogolewski, Krzysztof
Meinke, Jan H.
Radwan, Maciej
Rakowski, Franciszek
Scholz, Markus
Gneiting, Tilmann
Krymova, Ekaterina
Deuschel, Jannik
Barbarossa, Maria V.
Miasojedow, Błażej
Bracher, Johannes
Bertsimas, Dimitris
Funk, Sebastian
Fiedler, Jochen
Li, Michael L.
Fuhrmann, Jan
Michaud, Isaac J.
Ozanski, Tomasz
Nouvellet, Pierre
Burgard, Jan Pablo
Heyder, Stefan
Gambin, Anna
Kheifetz, Yuri
Fairchild, Geoffrey
Srivastava, Ajitesh
Ketterer, Jakob L.
Abbott, Sam
Bosse, Nikos I.
Schienle, Melanie
Wydawca:: Springer Nature
Cytata wydawnicza:: Bracher, J., Wolffram, D., Deuschel, J. et al. National and subnational short-term forecasting of COVID-19 in Germany and Poland during early 2021. Communications Medicine 2, 136 (2022). https://doi.org/10.1038/s43856-022-00191-8
Opis:: Background: During the COVID-19 pandemic there has been a strong interest in forecasts ofthe short-term development of epidemiological indicators to inform decision makers. In thisstudy we evaluate probabilistic real-time predictions of confirmed cases and deaths from COVID-19 in Germany and Poland for the period from January through April 2021.Methods: We evaluate probabilistic real-time predictions of confirmed cases and deaths from COVID-19 in Germany and Poland. These were issued by 15 different forecasting models, run by independent research teams. Moreover, we study the performance of combined ensemble forecasts. Evaluation of probabilistic forecasts is based on proper scoring rules, along with interval coverage proportions to assess calibration. The presented work is part of a pre-registered evaluation study. Results: We find that many, though not all, models outperform a simple baseline model up to four weeks ahead for the considered targets. Ensemble methods show very good relative performance. The addressed time period is characterized by rather stable non-pharmaceutical interventions in both countries, making short-term predictions morestraightforward than in previous periods. However, major trend changes in reported cases,like the rebound in cases due to the rise of the B.1.1.7 (Alpha) variant in March 2021, prove challenging to predict. Conclusions: Multi-model approaches can help to improve the performance of epidemiological forecasts. However, while death numbers can be predicted with some success based on current case and hospitalization data, predictability of case numbers remains low beyond quite short time horizons. Additional data sources including sequencing and mobility data, which were not extensively used in the present study, may help to improve performance.
Dostawca treści:: Repozytorium Centrum Otwartej Nauki

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Skocz do pozycji: 3.

Tytuł:: Predictive performance of multi-model ensemble forecasts of COVID-19 across European nations
Autorzy:: Reina, Borja
Krupa, Bartosz
Lasinio, Giovanna Jona
Ullrich, Alexander
Montero-Manso, Pablo
Priesemann, Viola
Bejar, Benjamin
Bracher, Johannes
Tucek, Vit
Smid, Martin
Perez Alvarez, Cesar
Fuhrmann, Jan
Kraus, David
Rodiah, Isti
Kraus, Andrea
Nowosielski, Jedrzej
Redlarski, Grzegorz
Filinski, Maciej
Kisielewski, Jan
Michaud, Isaac
Pennoni, Fulvia
Gurung, Heidi
Leithauser, Neele
Venkatramanan, Srinivasan
Lopez, Daniel
Hurt, Benjamin
Pribylova, Lenka
Zibert, Janez
Schneider, Johanna
Stage, Steven
Bartczuk, Rafal P
Szczurek, Ewa
Holger, Kirsten
Hotz, Thomas
Wattanachit, Nutcha
Farcomeni, Alessio
Lewis, Bryan
Wang, Lijing
Castro, Lauren
Bodych, Marcin
Dehning, Jonas
Villanueva, Inmaculada
Mohr, Sebastian
Alaimo Di Loro, Pierfrancesco
Parolini, Nicola
Deuschel, Jannik
Suchoski, Bradley
Grah, Rok
Giudici, Paolo
Catala, Marti
Budzinski, Jozef
Alonso, Sergio
Marathe, Madhav
Morina, David
Idzikowski, Radoslaw
Sun, Tao
Sherratt, Katharine
Meinke, Jan H
Kuhlmann, Alexander
Walraven, Robert
Abbott, Sam
Saksham, Soni
Porebski, Przemyslaw
Zimmermann, Tom
Bartolucci, Francesco
Obozinski, Guillaume
Gogolewski, Krzysztof
Zielinski, Jakub
Rakowski, Franciszek
Pottier, Loic
Tarantino, Barbara
Moszyński, Antoni
Gruson, Hugo
Wang, Yijin
Ardenghi, Giovanni
Biecek, Przemyslaw
Alvarez, Enric
Funk, Sebastian
Mingione, Marco
Bock, Wolfgang
Bosse, Nikos I
Guzman- Merino, Miguel
Dreger, Filip
Ray, Evan L
Wolffram, Daniel
Aznarte, Jose L
Burgard, Jan Pablo
Barbarossa, Maria Vittoria
Singh, David E
Gambin, Anna
Dimitris, Bertsimas
Pabjan, Barbara
Gruziel-Slomka, Magdalena
Kheifetz, Yuri
Divino, Fabio
Zajicek, Milan
Srivastava, Ajitesh
Niehus, Rene
Lovison, Gianfranco
Adiga, Aniruddha
Mohring, Jan
Prats, Clara
Johnson, Helen
Krueger, Tyll
Osthus, Dave
Baccam, Prasith
Prasse, Bastian
Radwan, Maciej
Semeniuk, Marcin
Maruotti, Antonello
Eclerova, Veronika
Scholz, Markus
Krymova, Ekaterina
Trnka, Jan
Thanou, Dorina
Niedzielewski, Karol
Reich, Nicholas G
Meakin, Sophie R
Wlazlo, Jaroslaw
Sheldon, Daniel
Ozanski, Tomasz
Ziarelli, Giovanni
Gibson, Graham
Heyder, Stefan
Rodloff, Arne
Li, Michael Lingzhi
Fairchild, Geoffrey
Sandmann, Frank
Lange, Berit
Wydawca:: eLife Sciences Publications Ltd.
Cytata wydawnicza:: Sherratt K, Gruson H, Grah R, Johnson H, Niehus R, Prasse B, Sandmann F, Deuschel J, Wolffram D, Abbott S, Ullrich A, Gibson G, Ray EL, Reich NG, Sheldon D, Wang Y, Wattanachit N, Wang L, Trnka J, Obozinski G, Sun T, Thanou D, Pottier L, Krymova E, Meinke JH, Barbarossa MV, Leithauser N, Mohring J, Schneider J, Wlazlo J, Fuhrmann J, Lange B, Rodiah I, Baccam P, Gurung H, Stage S, Suchoski B, Budzinski J, Walraven R, Villanueva I, Tucek V, Smid M, Zajicek M, Perez Alvarez C, Reina B, Bosse NI, Meakin SR, Castro L, Fairchild G, Michaud I, Osthus D, Alaimo Di Loro P, Maruotti A, Eclerova V, Kraus A, Kraus D, Pribylova L, Dimitris B, Li ML, Saksham S, Dehning J, Mohr S, Priesemann V, Redlarski G, Bejar B, Ardenghi G, Parolini N, Ziarelli G, Bock W, Heyder S, Hotz T, Singh DE, Guzman-Merino M, Aznarte JL, Morina D, Alonso S, Alvarez E, Lopez D, Prats C, Burgard JP, Rodloff A, Zimmermann T, Kuhlmann A, Zibert J, Pennoni F, Divino F, Catala M, Lovison G, Giudici P, Tarantino B, Bartolucci F, Jona Lasinio G, Mingione M, Farcomeni A, Srivastava A, Montero-Manso P, Adiga A, Hurt B, Lewis B, Marathe M, Porebski P, Venkatramanan S, Bartczuk RP, Dreger F, Gambin A, Gogolewski K, Gruziel-Slomka M, Krupa B, Moszyński A, Niedzielewski K, Nowosielski J, Radwan M, Rakowski F, Semeniuk M, Szczurek E, Zielinski J, Kisielewski J, Pabjan B, Holger K, Kheifetz Y, Scholz M, Przemyslaw B, Bodych M, Filinski M, Idzikowski R, Krueger T, Ozanski T, Bracher J, Funk S. Predictive performance of multi-model ensemble forecasts of COVID-19 across European nations. Elife. 2023 Apr 21;12:e81916. doi: 10.7554/eLife.81916.
Opis:: Wellcome Trust (Grant number 221003/Z/20/Z) in collaboration with the Foreign, Commonwealth, and Development Office, United Kingdom. AA, BH, BL, LWa, MMa, PP, SV funded by National Institutes of Health (NIH) Grant 1R01GM109718, NSF BIG DATA Grant IIS-1633028, NSF Grant No.: OAC-1916805, NSF Expeditions in Computing Grant CCF-1918656, CCF-1917819, NSF RAPID CNS-2028004, NSF RAPID OAC-2027541, US Centers for Disease Control and Prevention 75D30119C05935, a grant from Google, University of Virginia Strategic Investment Fund award number SIF160, Defense Threat Reduction Agency (DTRA) under Contract No. HDTRA1-19-D- 0007, and respectively Virginia Dept of Health Grant VDH- 21- 501- 0141, VDH- 21- 501- 0143, VDH- 21- 501- 0147, VDH- 21- 501- 0145, VDH- 21- 501- 0146, VDH- 21-501-0142, VDH-21-501-0148. AF, AMa, GL funded by SMIGE - Modelli statistici inferenziali per governare l'epidemia, FISR 2020-Covid-19 I Fase, FISR2020IP-00156, Codice Progetto: PRJ-0695. AM, BK, FD, FR, JK, JN, JZ, KN, MG, MR, MS, RB funded by Ministry of Science and Higher Education of Poland with grant 28/WFSN/2021 to the University of Warsaw. BRe, CPe, JLAz funded by Ministerio de Sanidad/ISCIII. BT, PG funded by PERISCOPE European H2020 project, contract number 101016233. CP, DL, EA, MC, SA funded by European Commission - Directorate-General for Communications Networks, Content and Technology through the contract LC-01485746, and Ministerio de Ciencia, Innovacion y Universidades and FEDER, with the project PGC2018- 095456-B- I00. DE., MGu funded by Spanish Ministry of Health / REACT-UE (FEDER). DO, GF, IMi, LC funded by Laboratory Directed Research and Development program of Los Alamos National Laboratory (LANL) under project number 20200700ER. DS, ELR, GG, NGR, NW, YW funded by National Institutes of General Medical Sciences (R35GM119582; the content is solely the responsibility of the authors and does not necessarily represent the official views of NIGMS or the National Institutes of Health). FB, FP funded by InPresa, Lombardy Region, Italy. HG, KS funded by European Centre for Disease Prevention and Control. IV funded by Agencia de Qualitat i Avaluacio Sanitaries de Catalunya (AQuAS) through contract 2021-021OE. JDe, SMo, VP funded by Netzwerk Universitatsmedizin (NUM) project egePan (01KX2021). JPB, SH, TH funded by Federal Ministry of Education and Research (BMBF; grant 05M18SIA). KH, MSc, YKh funded by Project SaxoCOV, funded by the German Free State of Saxony. Presentation of data, model results and simulations also funded by the NFDI4Health Task Force COVID-19 (https://www.nfdi4health.de/task-force-covid-19-2) within the framework of a DFG-project (LO-342/17-1). LP, VE funded by Mathematical and Statistical modelling project (MUNI/A/1615/2020), Online platform for real-time monitoring, analysis and management of epidemic situations (MUNI/11/02202001/2020); VE also supported by RECETOX research infrastructure (Ministry of Education, Youth and Sports of the Czech Republic: LM2018121), the CETOCOEN EXCELLENCE (CZ.02.1.01/0.0/0.0/17-043/0009632), RECETOX RI project (CZ.02.1.01/0.0/0.0/16-013/0001761). NIB funded by Health Protection Research Unit (grant code NIHR200908). SAb, SF funded by Wellcome Trust (210758/Z/18/Z).
Background: Short-term forecasts of infectious disease burden can contribute to situational awareness and aid capacity planning. Based on best practice in other fields and recent insights in infectious disease epidemiology, one can maximise the predictive performance of such forecasts if multiple models are combined into an ensemble. Here, we report on the performance of ensembles in predicting COVID-19 cases and deaths across Europe between 08 March 2021 and 07 March 2022. Methods: We used open-source tools to develop a public European COVID-19 Forecast Hub. We invited groups globally to contribute weekly forecasts for COVID-19 cases and deaths reported by a standardised source for 32 countries over the next 1–4 weeks. Teams submitted forecasts from March 2021 using standardised quantiles of the predictive distribution. Each week we created an ensemble forecast, where each predictive quantile was calculated as the equally-weighted average (initially the mean and then from 26th July the median) of all individual models’ predictive quantiles. We measured the performance of each model using the relative Weighted Interval Score (WIS), comparing models’ forecast accuracy relative to all other models. We retrospectively explored alternative methods for ensemble forecasts, including weighted averages based on models’ past predictive performance. Results: Over 52 weeks, we collected forecasts from 48 unique models. We evaluated 29 models’ forecast scores in comparison to the ensemble model. We found a weekly ensemble had a consistently strong performance across countries over time. Across all horizons and locations, the ensemble performed better on relative WIS than 83% of participating models’ forecasts of incident cases (with a total N=886 predictions from 23 unique models), and 91% of participating models’ forecasts of deaths (N=763 predictions from 20 models). Across a 1–4 week time horizon, ensemble performance declined with longer forecast periods when forecasting cases, but remained stable over 4 weeks for incident death forecasts. In every forecast across 32 countries, the ensemble outperformed most contributing models when forecasting either cases or deaths, frequently outperforming all of its individual component models. Among several choices of ensemble methods we found that the most influential and best choice was to use a median average of models instead of using the mean, regardless of methods of weighting component forecast models. Conclusions: Our results support the use of combining forecasts from individual models into an ensemble in order to improve predictive performance across epidemiological targets and populations during infectious disease epidemics. Our findings further suggest that median ensemble methods yield better predictive performance more than ones based on means. Our findings also highlight that forecast consumers should place more weight on incident death forecasts than incident case forecasts at forecast horizons greater than 2 weeks.
Dostawca treści:: Repozytorium Centrum Otwartej Nauki

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