Quasi-Newton Methods for Markov Chain Monte Carlo

The performance of Markov chain Monte Carlo methods is often sensitive to the scaling and correlations between the random variables of interest. An important source of information about the local correlation and scale is given by the Hessian matrix of the target distribution, but this is often either computationally expensive or infeasible. In this paper we propose MCMC samplers that make use of quasi-Newton approximations, which approximate the Hessian of the target distribution from previous samples and gradients generated by the sampler. A key issue is that MCMC samplers that depend on the history of previous states are in general not valid. We address this problem by using limited memory quasi-Newton methods, which depend only on a fixed window of previous samples. On several real world datasets, we show that the quasi-Newton sampler is more effective than standard Hamiltonian Monte Carlo at a fraction of the cost of MCMC methods that require higher-order derivatives.

Hybrid Epidemics - A Case Study on Computer Worm Conficker

Conficker is a computer worm that erupted on the Internet in 2008. It is unique in combining three different spreading strategies: local probing, neighbourhood probing, and global probing. We propose a mathematical model that combines three modes of spreading, local, neighbourhood and global to capture the worm's spreading behaviour. The parameters of the model are inferred directly from network data obtained during the first day of the Conifcker epidemic. The model is then used to explore the trade-off between spreading modes in determining the worm's effectiveness. Our results show that the Conficker epidemic is an example of a critically hybrid epidemic, in which the different modes of spreading in isolation do not lead to successful epidemics. Such hybrid spreading strategies may be used beneficially to provide the most effective strategies for promulgating information across a large population. When used maliciously, however, they can present a dangerous challenge to current internet security protocols

Risks to human and animal health related to the presence of deoxynivalenol and its acetylated and modified forms in food and feed

Peer reviewedPublisher PD

Risks for public health related to the presence of tetrodotoxin (TTX) and TTX analogues in marine bivalves and gastropods

Peer reviewedPublisher PD

LeoTask: a fast, flexible and reliable framework for computational research

LeoTask is a Java library for computation-intensive and time-consuming research tasks. It automatically executes tasks in parallel on multiple CPU cores on a computing facility. It uses a configuration file to enable automatic exploration of parameter space and flexible aggregation of results, and therefore allows researchers to focus on programming the key logic of a computing task. It also supports reliable recovery from interruptions, dynamic and cloneable networks, and integration with the plotting software Gnuplot

Distrofia vulvar crônica sempre a mesma?

Trabalho de Conclusão de Curso - Universidade Federal de Santa Catarina, Centro de Ciências da Saúde, Departamento de Tocoginecologia, Curso de Medicina, Florianópolis, 199

Hybrid spreading mechanisms and T cell activation shape the dynamics of HIV-1 infection

HIV-1 can disseminate between susceptible cells by two mechanisms: cell-free infection following fluid-phase diffusion of virions and by highly-efficient direct cell-to-cell transmission at immune cell contacts. The contribution of this hybrid spreading mechanism, which is also a characteristic of some important computer worm outbreaks, to HIV-1 progression in vivo remains unknown. Here we present a new mathematical model that explicitly incorporates the ability of HIV-1 to use hybrid spreading mechanisms and evaluate the consequences for HIV-1 pathogenenesis. The model captures the major phases of the HIV-1 infection course of a cohort of treatment naive patients and also accurately predicts the results of the Short Pulse Anti-Retroviral Therapy at Seroconversion (SPARTAC) trial. Using this model we find that hybrid spreading is critical to seed and establish infection, and that cell-to-cell spread and increased CD4+ T cell activation are important for HIV-1 progression. Notably, the model predicts that cell-to-cell spread becomes increasingly effective as infection progresses and thus may present a considerable treatment barrier. Deriving predictions of various treatments' influence on HIV-1 progression highlights the importance of earlier intervention and suggests that treatments effectively targeting cell-to-cell HIV-1 spread can delay progression to AIDS. This study suggests that hybrid spreading is a fundamental feature of HIV infection, and provides the mathematical framework incorporating this feature with which to evaluate future therapeutic strategies

Efectos del cambio climático en la distribución de zonas de vida en Centroamérica

Se evaluó el impacto del cambio climático en la distribución de zonas de vida en Centroamérica, a partir de escenarios climáticos generados con un modelo regional. Mediante capas de información climática (WorldClim) y dos escenarios de cambio climático desarrollados por el modelo regional PRECIS con los escenarios A2 y B1 del IPCC, se generó un mapa actual de zonas de vida de Holdridge para Centroamérica y se modeló el cambio de zonas para el clima promedio futuro (2011-2040). Las zonas de vida con mayor representación territorial actual fueron el bosque húmedo tropical, el bosque seco tropical y el bosque húmedo premontano. En ambos escenarios, la mayoría de las zonas de vida sufrieron un cambio hacia otras de piso altitudinal más bajo y provincias de humedad más secas; el cambio más drástico se dio en el escenario A2. Las zonas de vida más afectadas fueron el páramo pluvial subalpino y el bosque seco premontano. El modelaje de las zonas de vida ante escenarios de cambio climático arroja información sobre el grado de sensibilidad de ecosistemas presentes en la región y permite diseñar estrategias de conservación encaminadas a proteger las regiones más amenazadas. (Résumé d'auteur