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The study of epidemic models plays an important role in mathematical epidemiology. There are many researches on epidemic models using ordinary differential equations, partial differential equations or stochastic differential equations. In…
Recent work has shown that different theoretical approaches to the dynamics of the Susceptible-Infected-Susceptible (SIS) model for epidemics lead to qualitatively different estimates for the position of the epidemic threshold in networks.…
In this paper we apply a methodology introduced in Navarro Jimenez et al (2016) in the framework of chemical reaction networks to perform a global sensitivity analysis on simulations of a continuous-time Markov chain model motivated by…
Data assimilation methods aim at estimating the state of a system by combining observations with a physical model. When sequential data assimilation is considered, the joint distribution of the latent state and the observations is described…
The epidemic spreading on arbitrary complex networks is studied in SIR (Susceptible Infected Recovered) compartment model. We propose our implementation of a Naive SIR algorithm for epidemic simulation spreading on networks that uses data…
We consider a stochastic Susceptible-Exposed-Infected-Recovered (SEIR) epidemiological model with a contact rate that fluctuates seasonally. Through the use of a nonlinear, stochastic projection, we are able to analytically determine the…
Model parameter inference is a universal problem across science. This challenge is particularly pronounced in developmental biology, where faithful mechanistic descriptions require spatial-stochastic models with numerous parameters, yet…
We present a modelling framework for the spreading of epidemics on temporal networks from which both the individual-based and pair-based models can be recovered. The proposed temporal pair-based model that is systematically derived from…
The effect of spatial correlations on the spread of infectious diseases was investigated using a stochastic SIR (Susceptible-Infective-Recovered) model on complex networks. It was found that in addition to the reduction of the effective…
Compartmental models provide simple and efficient tools to analyze the relevant transmission processes during an outbreak, to produce short-term forecasts or transmission scenarios, and to assess the impact of vaccination campaigns.…
We propose a generative model and an inference scheme for epidemic processes on dynamic, adaptive contact networks. Network evolution is formulated as a link-Markovian process, which is then coupled to an individual-level stochastic SIR…
We develop a stochastic epidemic model progressing over dynamic networks, where infection rates are heterogeneous and may vary with individual-level covariates. The joint dynamics are modeled as a continuous-time Markov chain such that…
The growing literature on the propagation of COVID-19 relies on various dynamic SIR-type models (Susceptible-Infected-Recovered) which yield model-dependent results. For transparency and ease of comparing the results, we introduce a common…
We propose a method for inference on moderately high-dimensional, nonlinear, non-Gaussian, partially observed Markov process models for which the transition density is not analytically tractable. Markov processes with intractable transition…
In this study, a new and natural way of constructing a stochastic Susceptible-Infected-Susceptible (SIS) model is proposed. This approach is natural in the sense that the disease transmission rate, $\beta$, is substituted with a generic,…
We study the stochastic susceptible-infected-recovered (SIR) model with time-dependent forcing using analytic techniques which allow us to disentangle the interaction of stochasticity and external forcing. The model is formulated as a…
We describe a class of algorithms for evaluating posterior moments of certain Bayesian linear regression models with a normal likelihood and a normal prior on the regression coefficients. The proposed methods can be used for hierarchical…
We predict the future course of ongoing susceptible-infected-susceptible (SIS) epidemics on regular, Erd\H{o}s-R\'{e}nyi and Barab\'asi-Albert networks. It is known that the contact network influences the spread of an epidemic within a…
We demonstrate an approach to replicate and forecast the spread of the SARS-CoV-2 (COVID-19) pandemic using the toolkit of probabilistic programming languages (PPLs). Our goal is to study the impact of various modeling assumptions and…
We propose a simple SIR model in order to investigate the impact of various confinement strategies on a most virulent epidemic. Our approach is motivated by the current COVID-19 pandemic. The main hypothesis is the existence of two…