Inference by Minimizing Size, Divergence, or their Sum

We speed up marginal inference by ignoring factors that do not significantly contribute to overall accuracy. In order to pick a suitable subset of factors to ignore, we propose three schemes: minimizing the number of model factors under a bound on the KL divergence between pruned and full models; minimizing the KL divergence under a bound on factor count; and minimizing the weighted sum of KL divergence and factor count. All three problems are solved using an approximation of the KL divergence than can be calculated in terms of marginals computed on a simple seed graph. Applied to synthetic image denoising and to three different types of NLP parsing models, this technique performs marginal inference up to 11 times faster than loopy BP, with graph sizes reduced up to 98%-at comparable error in marginals and parsing accuracy. We also show that minimizing the weighted sum of divergence and size is substantially faster than minimizing either of the other objectives based on the approximation to divergence presented here.Comment: Appears in Proceedings of the Twenty-Sixth Conference on Uncertainty in Artificial Intelligence (UAI2010

Knock-in of Human BACE1 Cleaves Murine APP and Reiterates Alzheimer-like PhenoTypes

Footnotes We thank Roemex and the College for Life Science and Medicine at the University of Aberdeen for their generous support. The authors declare no competing financial interests.Peer reviewedPublisher PD

Crack Surveys of Low-Cracking High-Performance Concrete Bridge Decks in Kansas 2011-2013

Crack densities of Low-Cracking High-Performance Concrete (LC-HPC) bridge decks are compared to crack densities of control decks to investigate the benefits of the LC-HPC specifications developed at the University of Kansas. Specifications for construction of LC-HPC bridge decks are addressed. Bridge deck crack survey procedures are also summarized. Thirteen LC-HPC decks and thirteen control decks are compared by calculating crack densities and noting trends in cracking patterns over time. The results for eight additional decks are also presented. These include three LC-HPC decks, one control deck, and three decks which are considered neither LC-HPC nor control decks. The LC-HPC bridge decks have, with very few exceptions, lower crack densities than the control decks. Cracks are typically transverse above and parallel to the bars in the top layer of reinforcing steel, except at abutments, where cracks propagate longitudinally or perpendicular to the abutment

BANYAN. IV. Fundamental parameters of low-mass star candidates in nearby young stellar kinematic groups - Isochronal Age determination using Magnetic evolutionary models

Based on high resolution optical spectra obtained with ESPaDOnS at CFHT, we determine fundamental parameters (\Teff, R, \Lbol, \logg\ and metallicity) for 59 candidate members of nearby young kinematic groups. The candidates were identified through the BANYAN Bayesian inference method of \citet{2013malo}, which takes into account the position, proper motion, magnitude, color, radial velocity and parallax (when available) to establish a membership probability. The derived parameters are compared to Dartmouth Magnetic evolutionary models and to field stars with the goal to constrain the age of our candidates. We find that, in general, low-mass stars in our sample are more luminous and have inflated radii compared to older stars, a trend expected for pre-main sequence stars. The Dartmouth Magnetic evolutionary models show a good fit to observations of field K and M stars assuming a magnetic field strength of a few kG, as typically observed for cool stars. Using the low-mass members of $\beta$Pictoris moving group, we have re-examined the age inconsistency problem between Lithium Depletion age and isochronal age (Hertzspring-Russell diagram). We find that the inclusion of the magnetic field in evolutionary models increase the isochronal age estimates for the K5V-M5V stars. Using these models and field strengths, we derive an average isochronal age between 15 and 28 Myr and we confirm a clear Lithium Depletion Boundary from which an age of 26$\pm$3~Myr is derived, consistent with previous age estimates based on this method.Comment: Accepted for publication in Ap

Mutant Tau knock-in mice display frontotemporal dementia relevant behaviour and histopathology

Peer reviewedPostprin

Running a Pre-Exascale, Geographically Distributed, Multi-Cloud Scientific Simulation

As we approach the Exascale era, it is important to verify that the existing frameworks and tools will still work at that scale. Moreover, public Cloud computing has been emerging as a viable solution for both prototyping and urgent computing. Using the elasticity of the Cloud, we have thus put in place a pre-exascale HTCondor setup for running a scientific simulation in the Cloud, with the chosen application being IceCube's photon propagation simulation. I.e. this was not a purely demonstration run, but it was also used to produce valuable and much needed scientific results for the IceCube collaboration. In order to reach the desired scale, we aggregated GPU resources across 8 GPU models from many geographic regions across Amazon Web Services, Microsoft Azure, and the Google Cloud Platform. Using this setup, we reached a peak of over 51k GPUs corresponding to almost 380 PFLOP32s, for a total integrated compute of about 100k GPU hours. In this paper we provide the description of the setup, the problems that were discovered and overcome, as well as a short description of the actual science output of the exercise.Comment: 18 pages, 5 figures, 4 tables, to be published in Proceedings of ISC High Performance 202

Clinical use of CCR5 inhibitors in HIV and beyond

Since the discovery of CCR5 as a coreceptor for HIV entry, there has been interest in blockade of the receptor for treatment and prevention of HIV infection. Although several CCR5 antagonists have been evaluated in clinical trials, only maraviroc has been approved for clinical use in the treatment of HIV-infected patients. The efficacy, safety and resistance profile of CCR5 antagonists with a focus on maraviroc are reviewed here along with their usage in special and emerging clinical situations. Despite being approved for use since 2007, the optimal use of maraviroc has yet to be well-defined in HIV and potentially in other diseases. Maraviroc and other CCR5 antagonists have the potential for use in a variety of other clinical situations such as the prevention of HIV transmission, intensification of HIV treatment and prevention of rejection in organ transplantation. The use of CCR5 antagonists may be potentiated by other agents such as rapamycin which downregulate CCR5 receptors thus decreasing CCR5 density. There may even be a role for their use in combination with other entry inhibitors. However, clinical use of CCR5 antagonists may have negative consequences in diseases such as West Nile and Tick-borne encephalitis virus infections. In summary, CCR5 antagonists have great therapeutic potential in the treatment and prevention of HIV as well as future use in novel situations such as organ transplantation. Their optimal use either alone or in combination with other agents will be defined by further investigation