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The spread of COVID-19 has been greatly impacted by regulatory policies and behavior patterns that vary across counties, states, and countries. Population-level dynamics of COVID-19 can generally be described using a set of ordinary…

Applications · Statistics 2022-04-11 Joshua P. Keller , Tianjian Zhou , Andee Kaplan , G. Brooke Anderson , Wen Zhou

Timely estimation of the current value for COVID-19 reproduction factor $R$ has become a key aim of efforts to inform management strategies. $R$ is an important metric used by policy-makers in setting mitigation levels and is also important…

Populations and Evolution · Quantitative Biology 2020-05-26 Carlo R. Contaldi

In the recent COVID-19 pandemic, a wide range of epidemiological modelling approaches have been used to predict the effective reproduction number, R(t), and other COVID-19 related measures such as the daily rate of exponential growth, r(t).…

Applications · Statistics 2021-08-13 T. Maishman , S. Schaap , D. S. Silk , S. J. Nevitt , D. C. Woods , V. E. Bowman

We investigate the problem of estimating the distribution of the individual reproduction number governing the COVID-19 pandemic. Under the assumption that this random variable follows a Negative Binomial distribution, we focus on…

Applications · Statistics 2021-01-21 Alexander Braumann , Jonas Krampe , Jens-Peter Kreiss , Efstathios Paparoditis

In this paper, we use a Bayesian method to estimate the effective reproduction number (R(t)), in the context of monitoring the time evolution of the COVID-19 pandemic in Brazil at different geographic levels. The focus of this study is to…

Applications · Statistics 2023-06-05 Edson Porto da Silva , Antônio Marcus Nogueira Lima

In this paper, we estimate epidemiological data of the COVID-19 pandemic in Hungary using only the daily number of hospitalized patients, and applying well-known techniques from systems and control theory. We use a previously published and…

Populations and Evolution · Quantitative Biology 2021-05-11 Balazs Csutak , Peter Polcz , Gabor Szederkenyi

The recent COVID-19 pandemic has shown that when the reproduction number is high and there are no proper measurements in place, the number of infected people can increase dramatically in a short time, producing a phenomenon that many…

Populations and Evolution · Quantitative Biology 2022-09-20 Jonathan A. Chávez Casillas

The outbreak of Coronavirus Disease 2019 (COVID-19) is an ongoing pandemic affecting over 200 countries and regions. Inference about the transmission dynamics of COVID-19 can provide important insights into the speed of disease spread and…

Methodology · Statistics 2020-07-06 Tianjian Zhou , Yuan Ji

It is widely accepted that the number of reported cases during the first stages of the COVID-19 pandemic severely underestimates the number of actual cases. We leverage delay embedding theorems of Whitney and Takens and use Gaussian Process…

Quantitative Methods · Quantitative Biology 2022-02-02 G. A. Kevrekidis , Z. Rapti , Y. Drossinos , P. G. Kevrekidis , M. A. Barmann , Q. Y. Chen , J. Cuevas-Maraver

Two stochastic models are proposed to describe the evolution of the COVID-19 pandemic. In the first model the population is partitioned into four compartments: susceptible $S$, infected $I$, removed $R$ and dead people $D$. In order to have…

Populations and Evolution · Quantitative Biology 2021-09-16 Fabiana Calleri , Giovanni Nastasi , Vittorio Romano

Motivated by the recent outbreak of coronavirus (COVID-19), we propose a stochastic model of epidemic temporal growth and mitigation based on a time-modulated Hawkes process. The model is sufficiently rich to incorporate specific…

Populations and Evolution · Quantitative Biology 2021-03-18 Michele Garetto , Emilio Leonardi , Giovanni Luca Torrisi

Approaches to the calculation of the full state vector of a larger epidemiological model for the spread of COVID-19 in Sweden at the initial time instant from available data and with a simplified dynamical model are proposed and evaluated.…

Systems and Control · Electrical Eng. & Systems 2020-07-20 Håkan Runvik , Alexander Medvedev , Robin Eriksson , Stefan Engblom

COVID-19 pandemic has brought to the fore epidemiological models which, though describing a wealth of behaviors, have previously received little attention in signal processing literature. In this work, a generalized time-varying…

Methodology · Statistics 2025-08-13 Barbara Pascal , Samuel Vaiter

Daily pandemic surveillance, often achieved through the estimation of the reproduction number, constitutes a critical challenge for national health authorities to design countermeasures. In an earlier work, we proposed to formulate the…

Signal Processing · Electrical Eng. & Systems 2022-06-29 Barbara Pascal , Patrice Abry , Nelly Pustelnik , Stéphane G. Roux , Rémi Gribonval , Patrick Flandrin

The investment of time and resources for better strategies and methodologies to tackle a potential pandemic is key to deal with potential outbreaks of new variants or other viruses in the future. In this work, we recreated the scene of a…

Machine Learning · Computer Science 2021-04-22 Andrés L. Suárez-Cetrulo , Ankit Kumar , Luis Miralles-Pechuán

Monitoring the Covid19 pandemic constitutes a critical societal stake that received considerable research efforts. The intensity of the pandemic on a given territory is efficiently measured by the reproduction number, quantifying the rate…

Machine Learning · Computer Science 2023-04-19 Gersende Fort , Barbara Pascal , Patrice Abry , Nelly Pustelnik

The role of epidemiological models is crucial for informing public health officials during a public health emergency, such as the COVID-19 pandemic. However, traditional epidemiological models fail to capture the time-varying effects of…

Methodology · Statistics 2022-06-17 Adam Spannaus , Theodore Papamarkou , Samantha Erwin , J. Blair Christian

Branching process inspired models are widely used to estimate the effective reproduction number -- a useful summary statistic describing an infectious disease outbreak -- using counts of new cases. Case data is a real-time indicator of…

Methodology · Statistics 2023-10-03 Isaac H. Goldstein , Jon Wakefield , Volodymyr M. Minin

Phenomenological and deterministic models are often used for the estimation of transmission parameters in an epidemic and for the prediction of its growth trajectory. Such analyses are usually based on single peak outbreak dynamics. In…

Populations and Evolution · Quantitative Biology 2022-01-20 D. P. Mahapatra , S. Triambak

Basic and instantaneous reproduction numbers, "R" _"0" and "R" _"t" , are important metrics to assess progress of an epidemic and effectiveness of preventative interventions undertaken, and also to estimate coverage needed for vaccination.…

Populations and Evolution · Quantitative Biology 2025-11-07 Derek Marsh