Identifying the measurements required to estimate rates of COVID-19 transmission, infection, and detection, using variational data assimilation

@article{Armstrong2020IdentifyingTM,
  title={Identifying the measurements required to estimate rates of COVID-19 transmission, infection, and detection, using variational data assimilation},
  author={Eve Armstrong and Jaline Gerardin and Manuela Runge},
  journal={medRxiv},
  year={2020}
}
We demonstrate the ability of statistical data assimilation to identify the measurements required for accurate state and parameter estimation in an epidemiological model for the novel coronavirus disease COVID-19. Our context is an effort to inform policy regarding social behavior, to mitigate strain on hospital capacity. The model unknowns are taken to be: the time-varying transmission rate, the fraction of exposed cases that require hospitalization, and the time-varying detection… Expand
Agent-based model and data assimilation: Analysis of COVID-19 in Tokyo
In this paper we introduce an agent-based model together with a particle filter approach for studying the spread of COVID-19. Investigations are performed on the metropolis of Tokyo, but otherExpand
FRONTLINE COMMUNITIES AND SARS-COV-2-MULTI-POPULATION MODELING WITH AN ASSESSMENT OF DISPARITY BY RACE/ETHNICITY USING ENSEMBLE DATA ASSIMILATION
TLDR
The results of this work are considered to be a reanalysis of pandemic evolution across differently affected sub-populations which may also be used to improve modeling and forecasts. Expand
Parameter Estimation of an Epidemic Model with State Constraints
We consider a mathematical model with five compartments relevant to depict the feature of a certain type of epidemic transmission. We aim to identify some system parameters by means of a minimizationExpand
An international assessment of the COVID-19 pandemic using ensemble data assimilation
TLDR
This work shows how one can use iterative ensemble smoothers to effectively estimate parameters of an SEIR model with age-classes and compartments of sick, hospitalized, and dead to make accurate short-term predictions of the epidemic development given knowledge of the future effective reproductive number. Expand
An international initiative of predicting the SARS-CoV-2 pandemic using ensemble data assimilation
TLDR
This work demonstrates the efficiency of using iterative ensemble smoothers to estimate the parameters of an SEIR model with age-classes and compartments of sick, hospitalized, and dead and estimates the effective reproductive number as a function of time. Expand

References

SHOWING 1-10 OF 52 REFERENCES
University Center for Systems Science and Engineering. Novel coronavirus cases
  • https: //github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_time_series
  • 2020
An epidemiological modelling approach for COVID-19 via data assimilation
TLDR
An epidemiological model for forecasting and policy evaluation which incorporates new data in real-time through variational data assimilation is proposed and developed, named SITR model, which allows for more granular inference on infection numbers. Expand
Epidemiology and Transmission of COVID-19 in Shenzhen China: Analysis of 391 cases and 1,286 of their close contacts
TLDR
This work shows that heightened surveillance and isolation, particularly contact tracing, reduces the time cases are infectious in the community, thereby reducing R.CoV-2's overall impact, however, its overall impact is uncertain and highly dependent on the number of asymptomatic cases. Expand
Systematic variational method for statistical nonlinear state and parameter estimation.
  • J. Ye, Daniel Rey, +5 authors J. C. Quinn
  • Mathematics, Medicine
  • Physical review. E, Statistical, nonlinear, and soft matter physics
  • 2015
In statistical data assimilation one evaluates the conditional expected values, conditioned on measurements, of interesting quantities on the path of a model through observation and predictionExpand
Predicting the Future: Completing Models of Observed Complex Systems
Through the development of an exact path integral for use in transferring information from observations to a model of the observed system, the author provides a general framework for the discussionExpand
Statistical data assimilation for estimating electrophysiology simultaneously with connectivity within a biological neuronal network.
  • E. Armstrong
  • Computer Science, Medicine
  • Physical review. E
  • 2020
TLDR
This paper offers a proof-of-concept that DA has the potential to inform laboratory designs for estimating properties in small and isolatable functional circuits. Expand
An optimization-based approach to calculating neutrino flavor evolution
Author(s): Armstrong, Eve; Patwardhan, Amol V; Johns, Lucas; Kishimoto, Chad T; Abarbanel, Henry DI; Fuller, George M
Nonlinear statistical data assimilation for HVCRA neurons in the avian song system
Adjoint-based Data Assimilation of an Epidemiology Model for the Covid-19 Pandemic in 2020
TLDR
Data assimilation is used to optimally fit a classical epidemiology model to the Johns Hopkins data of the Covid-19 pandemic to find a solution to a given model which fits the given data in an optimal sense. Expand
Clinical Characteristics of 138 Hospitalized Patients With 2019 Novel Coronavirus-Infected Pneumonia in Wuhan, China.
TLDR
The epidemiological and clinical characteristics of novel coronavirus (2019-nCoV)-infected pneumonia in Wuhan, China, and hospital-associated transmission as the presumed mechanism of infection for affected health professionals and hospitalized patients are described. Expand
...
1
2
3
4
5
...