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Epidemic spreading of infectious diseases is ubiquitous and has often considerable impact on public health and economic wealth. The large variability in spatio-temporal patterns of epidemics prohibits simple interventions and demands for a…
We study several bayesian inference problems for irreversible stochastic epidemic models on networks from a statistical physics viewpoint. We derive equations which allow to accurately compute the posterior distribution of the time…
A standard model for epidemics is the SIR model on a graph. We introduce a simple algorithm that uses the early infection times from a sample path of the SIR model to estimate the parameters this model, and we provide a performance…
We consider a time-delayed HIV/AIDS epidemic model with education dissemination and study the asymptotic dynamics of solutions as well as the asymptotic behavior of the endemic equilibrium with respect to the amount of information…
The shape of an epidemic wave in simple epidemic models applies to a homogeneous distribution of infected people in the population. In large inhomogeneous systems, at country-scale for instance, the wave shape is similar except for the…
Evidence-based knowledge of infectious disease burden, including prevalence, incidence, severity and transmission, in different population strata and locations, and possibly in real time, is crucial to the planning and evaluation of public…
The emergence of novel infectious agents presents challenges to statistical models of disease transmission. These challenges arise from limited, poor-quality data and an incomplete understanding of the agent. Moreover, outbreaks manifest…
Identifying a patient's key problems over time is a common task for providers at the point care, yet a complex and time-consuming activity given current electric health records. To enable a problem-oriented summarizer to identify a…
Respondent-driven sampling is a form of link-tracing network sampling, which is widely used to study hard-to-reach populations, often to estimate population proportions. Previous treatments of this process have used a with-replacement…
This article reviews quantitative methods to estimate the basic reproduction number of pandemic influenza, a key threshold quantity to help determine the intensity of interventions required to control the disease. Although it is difficult…
Human to human transmissible infectious diseases spread in a population using human interactions as its transmission vector. The early stages of such an outbreak can be modeled by a graph whose edges encode these interactions between…
Random forests is a state-of-the-art supervised machine learning method which behaves well in high-dimensional settings although some limitations may happen when $p$, the number of predictors, is much larger than the number of observations…
Coalescent theory combined with statistical modeling allows us to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. When sequences are sampled serially through…
This research reports on the relationship and significance of social-economic factors (age, sex, employment status) and modes of HIV/AIDS transmission to the HIV/AIDS spread. Logistic regression model, a form of probabilistic function for…
Compartmental epidemic models with dynamics that evolve over a graph network have gained considerable importance in recent years but analysis of these models is in general difficult due to their complexity. In this paper, we develop two…
Contact-tracing is an essential tool in order to mitigate the impact of pandemic such as the COVID-19. In order to achieve efficient and scalable contact-tracing in real time, digital devices can play an important role. While a lot of…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…
In this work we develop a stochastic model of acute HIV infection, based on the well-known standard model, that allows us to simulate the complex mutation pathways of HIV escape from multiple CTL responses. Under this model, we describe two…
The study of SIS epidemics on networks has stressed the role of the network topology on the spreading process. However, accurate models of SIS epidemics rely on the complete knowledge of the network topology, which is often not available.…
Tuberculosis (TB) and human immunodeficiency virus (HIV) can be considered a deadly human syndemic. In this article, we formulate a model for TB and HIV transmission dynamics. The model considers both TB and acquired immune deficiency…