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The probability-scale residual (PSR) is well defined across a wide variety of variable types and models, making it useful for studies of HIV/AIDS. In this manuscript, we highlight some of the properties of the PSR and illustrate its…

As the global HIV pandemic enters its fourth decade, increasing numbers of surveillance sites have been established which allows countries to look into the epidemics at a finer scale, e.g. at sub-national levels. Currently, the epidemic…

Reports from the Health Department in the Philippines show that cases of Human Immunodeficiency Virus (HIV) are increasing despite management and control efforts by the government. Worldwide, the Philippines has one of the fastest growing…

When modelling HIV epidemics, it is important to incorporate set-point viral load and its heritability. As set-point viral load distributions can differ significantly amongst epidemics, it is imperative to account for the observed local…

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 rates of escape and reversion in response to selection pressure arising from the host immune system, notably the cytotoxic T-lymphocyte (CTL) response, are key factors determining the evolution of HIV. Existing methods for estimating…

Efficient screening and early diagnosis of HIV are critical for reducing onward transmission. Although large scale laboratory testing is not feasible, the widespread adoption of Electronic Health Records (EHRs) offers new opportunities to…

Chronic infections of the human immunodeficiency virus (HIV) create a very complex co-evolutionary process, where the virus tries to escape the continuously adapting host immune system. Quantitative details of this process are largely…

This paper presents an impact assessment for the imputation of missing data. The data set used is HIV Seroprevalence data from an antenatal clinic study survey performed in 2001. Data imputation is performed through five methods: Random…

Motivation: In predicting HIV therapy outcomes, a critical clinical question is whether using historical information can enhance predictive capabilities compared with current or latest available data analysis. This study analyses whether…

Viral deep-sequencing data play a crucial role toward understanding disease transmission network flows, because the higher resolution of these data compared to standard Sanger sequencing provide evidence into the direction of infectious…

Dynamic models have been successfully used in producing estimates of HIV epidemics at national level, due to their epidemiological nature and their ability to simultaneously estimate prevalence, incidence, and mortality rates. Recently, HIV…

In this article, we propose a network spread model for HIV epidemics, wherein each individual is represented by a node of the transmission network and the edges are the connections between individuals along which the infection may spread.…

Multiple mechanisms in the HIV lifecycle play a role in its ability to evade therapy and become a chronic, difficult-to-treat infection. Within its major cellular target, the activated T cell, many steps occur between viral entry and viral…

Given a collection of features available for inclusion in a predictive model, it may be of interest to quantify the relative importance of a subset of features for the prediction task at hand. For example, in HIV vaccine trials, participant…

This article introduces novel methodologies for estimating contextual exposure to HIV population viral load using GPS data. We propose a comprehensive analytical framework comprising (i) local (grid-cell level) estimation of HIV population…

The past decade has seen tremendous progress in the development of biomedical agents that are effective as pre-exposure prophylaxis (PrEP) for HIV prevention. To expand the choice of products and delivery methods, new medications and…

Methods are lacking to handle the problem of survival analysis in the presence of an interval-censored covariate, specifically the case in which the conditional hazard of the primary event of interest depends on the occurrence of a…

Missing data is a recurrent issue in epidemiology where the infection process may be partially observed. Approximate Bayesian Computation, an alternative to data imputation methods such as Markov Chain Monte Carlo integration, is proposed…

Social context plays an important role in perpetuating or reducing HIV risk behaviors. This study analyzed the network and individual attributes that were associated with the likelihood that people who inject drugs (PWID) will engage in HIV…