Related papers: Bayesian mixture models for phylogenetic source at…
Recent work has focused attention on statistical inference for the population distribution of the number of sexual partners based on survey data. The characteristics of these distributions are of interest as components of mathematical…
This article introduces epidemia, an R package for Bayesian, regression-oriented modeling of infectious diseases. The implemented models define a likelihood for all observed data while also explicitly modeling transmission dynamics: an…
The problem of missing values in multivariable time series is a key challenge in many applications such as clinical data mining. Although many imputation methods show their effectiveness in many applications, few of them are designed to…
Detecting the origin of information or infection spread in networks is a fundamental challenge with applications in misinformation tracking, epidemiology, and beyond. We study the multi-source detection problem: given snapshot observations…
Network--based epidemic models that account for heterogeneous contact patterns are extensively used to predict and control the diffusion of infectious diseases. We use census and survey data to reconstruct a geo--referenced and…
Infectious diseases are studied to understand their spreading mechanisms, to evaluate control strategies and to predict the risk and course of future outbreaks. Because people only interact with a small number of individuals, and because…
The vast majority of models for the spread of communicable diseases are parametric in nature and involve underlying assumptions about how the disease spreads through a population. In this article we consider the use of Bayesian…
The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…
In this paper, a scale mixture of Normal distributions model is developed for classification and clustering of data having outliers and missing values. The classification method, based on a mixture model, focuses on the introduction of…
We present a proof-of-concept of a model comparison approach for analyzing spatio-temporal observations of interacting populations. Our model variants are a collection of structurally similar Bayesian networks. Their distinct Noisy-Or…
To combat the HIV/AIDS pandemic effectively, targeted interventions among certain key populations play a critical role. Examples of such key populations include sex workers, people who inject drugs, and men who have sex with men. While…
Identifying viral pathogens and characterizing their transmission is essential to developing effective public health measures in response to a pandemic. Phylogenetics, though currently the most popular tool used to characterize the likely…
RNA virus populations will undergo processes of mutation and selection resulting in a mixed population of viral particles. High throughput sequencing of a viral population subsequently contains a mixed signal of the underlying clones. We…
Due to its ability to summarise 'real-time' epidemic behaviour, the time-dependent reproduction number, Rt, is a useful metric for tracking pathogen transmission and quantifying the effects of interventions during infectious disease…
Understanding age-group dynamics of infectious diseases is a fundamental issue for both scientific study and policymaking. Age-structure epidemic models were developed in order to study and improve our understanding of these dynamics. By…
Infectious disease spread is a multi-scale process composed of within-host (biological) and between-host (social) drivers and disentangling them from each other is a central challenge in epidemiology. Here, we introduce VIBES, a multi-scale…
Mathematical models of infectious diseases, which are in principle analytically tractable, use two general approaches. The first approach, generally known as compartmental modeling, addresses the time evolution of disease propagation at the…
We study the problem of estimating the origin of an epidemic outbreak -- given a contact network and a snapshot of epidemic spread at a certain time, determine the infection source. Finding the source is important in different contexts of…
The time-dependent reproduction number Rt can be used to track pathogen transmission and to assess the efficacy of interventions. This quantity can be estimated by fitting renewal equation models to time series of infectious disease case…
Mathematical epidemiological models have a broad use, including both qualitative and quantitative applications. With the increasing availability of data, large-scale quantitative disease spread models can nowadays be formulated. Such models…