Related papers: Revealing patterns in HIV viral load data and clas…
The World Health Organization (WHO) guidelines for monitoring the effectiveness of HIV treatment in resource-limited settings (RLS) are mostly based on clinical and immunological markers (e.g., CD4 cell counts). Recent research indicates…
Purpose: The use of cumulative measures of exposure to raised HIV viral load (viremia copy-years) is an increasingly common in HIV prevention and treatment epidemiology due to the high biological plausibility. We sought to estimate the…
Assessment of circulating CD4 count change over time in HIV-infected subjects on antiretroviral therapy (ART) is a central component of disease monitoring. The increasing number of HIV-infected subjects starting therapy and the limited…
Viral sequence classification is an important task in pathogen detection, epidemiological surveys and evolutionary studies. Statistical learning methods are widely used to classify and identify viral sequences in samples from environments.…
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…
Modeling viral dynamics in HIV/AIDS studies has resulted in a deep understanding of pathogenesis of HIV infection from which novel antiviral treatment guidance and strategies have been derived. Viral dynamics models based on nonlinear…
Motivated by the challenge of using DNA-seq data to identify viruses in human blood samples, we propose a novel classification algorithm called "Radial Distance Weighted Discrimination" (or Radial DWD). This classifier is designed for…
Background. Several studies have used phylogenetics to investigate Human Immunodeficiency Virus (HIV) transmission among Men who have Sex with Men (MSMs) in Montreal, Quebec, Canada, revealing many transmission clusters. The Quebec HIV…
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…
Retaining persons living with HIV (PLWH) in medical care is paramount to preventing new transmissions of the virus and allowing PLWH to live normal and healthy lifespans. Maintaining regular appointments with an HIV provider and taking…
Estimating new HIV infections is significant yet challenging due to the difficulty in distinguishing between recent and long-term infections. We demonstrate that HIV recency status (recent v.s. long-term) could be determined from the…
Linear discriminant analysis (LDA) is a well-known method for multiclass classification and dimensionality reduction. However, in general, ordinary LDA does not achieve high prediction accuracy when observations in some classes are…
Motivation: HIV is difficult to treat because its virus mutates at a high rate and mutated viruses easily develop resistance to existing drugs. If the relationships between mutations and drug resistances can be determined from historical…
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…
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…
This paper describes a novel approach to modeling homphily, i.e. the tendency of nodes that share (or differ in) certain attributes to be linked; we consider dynamic networks in which nodes can be added over time but not removed. Our…
Key populations at high risk of HIV infection are critical for understanding and monitoring HIV epidemics, but global estimation is hampered by sparse, uneven data. We analyze data from 199 countries for female sex workers (FSW), men who…
Human immunodeficiency virus (HIV-1 or simply HIV) induces a persistent infection, which in the absence of treatment leads to AIDS and death in almost all infected individuals. HIV infection elicits a vigorous immune response starting about…
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…
We study the large sample behavior of a convex clustering framework, which minimizes the sample within cluster sum of squares under an~$\ell_1$ fusion constraint on the cluster centroids. This recently proposed approach has been gaining in…