Bayesian Inference from Composite Likelihoods, with an Application to Spatial Extremes

Composite likelihoods are increasingly used in applications where the full likelihood is analytically unknown or computationally prohibitive. Although the maximum composite likelihood estimator has frequentist properties akin to those of the usual maximum likelihood estimator, Bayesian inference based on composite likelihoods has yet to be explored. In this paper we investigate the use of the Metropolis--Hastings algorithm to compute a pseudo-posterior distribution based on the composite likelihood. Two methodologies for adjusting the algorithm are presented and their performance on approximating the true posterior distribution is investigated using simulated data sets and real data on spatial extremes of rainfall

The interplay of sedimentation and crystallization in hard-sphere suspensions

We study crystal nucleation under the influence of sedimentation in a model of colloidal hard spheres via Brownian Dynamics simulations. We introduce two external fields acting on the colloidal fluid: a uniform gravitational field (body force), and a surface field imposed by pinning a layer of equilibrium particles (rough wall). We show that crystal nucleation is suppressed in proximity of the wall due to the slowing down of the dynamics, and that the spatial range of this effect is governed by the static length scale of bond orientational order. For distances from the wall larger than this length scale, the nucleation rate is greatly enhanced by the process of sedimentation, since it leads to a higher volume fraction, or a higher degree of supercooling, near the bottom. The nucleation stage is similar to the homogeneous case, with nuclei being on average spherical and having crystalline planes randomly oriented in space. The growth stage is instead greatly affected by the symmetry breaking introduced by the gravitation field, with a slowing down of the attachment rate due to density gradients, which in turn cause nuclei to grow faster laterally. Our findings suggest that the increase of crystal nucleation in higher density regions might be the cause of the large discrepancy in the crystal nucleation rate of hard spheres between experiments and simulations, on noting that the gravitational effects in previous experiments are not negligible.Comment: 16 pages, 15 figures, 2 tables; Soft Matter (2013

Combinatorial Generation of Test Suites

Testgen is a computer program that generates suites of input and configuration vectors for testing other software or software/hardware systems. As systems become ever more complex, often, there is not enough time to test systems against all possible combinations of inputs and configurations, so test engineers need to be selective in formulating test plans. Testgen helps to satisfy this need: In response to a test-suite-requirement-specification model, it generates a minimal set of test vectors that satisfies all the requirements

Process-based models in Eucalyptus plantation management : reality and perspectives

Yield prediction in commercial forestry has been dominated by empirical modelling. Increasingly, however, process-based models are finding application either in support or instead of these traditional models. In this paper we draw the new forestry demands and how these models can answer different kinds of questions such as forest productivity in planted areas and new plantation, water-use, carbon sequestration and effects of climate change on forest production. In this paper we review current performance against management needs, concentrating in particular on the application of the 3-PG (Landsberg and Waring, 1997) and CABALA (Battaglia et al., 2004) process-based models. In general we find that process-based models have met many of the expectations of a decade ago. The paper briefly indicates new opportunities of process-based models in the area of wood properties and wood products prediction and in the area of forest health assessment.___________________________________La predicción de rendimientos en la silvicultura comercial ha estado dominada hasta ahora por el empleo de técnicas de modelización empíricas. Sin embargo, los modelos basados en procesos se están utilizando cada vez más como suplementos o incluso sustitutos de los tradicionales. En este artículo apuntamos nuevas demandas forestales y la forma en que los nuevos modelos pueden dar respuesta a diferentes cuestiones como la productividad forestal tanto en zonas plantadas como en nuevas plantaciones, el uso del agua, el secuestro de carbono y los efectos del cambio climático en la producción forestal. Asimismo, valoramos la eficacia de los modelos frente a las necesidades actuales de gestión, sobre todo en lo relativo a la aplicación de dos modelos basados en procesos: 3-PG (Landsberg y Waring, 1997) y CABALA (Battaglia et al., 2004). En general, los modelos de este tipo han colmado muchas de las expectativas que suscitaron hace una década. En este artículo se esbozan nuevas aplicaciones para estos modelos en cuanto a la predicción de propiedades y productos de la madera, así como a la valoración de la salud de los bosques

Frequent expansion of Plasmodium vivax Duffy Binding Protein in Ethiopia and its epidemiological significance.

Plasmodium vivax invasion of human erythrocytes depends on the Duffy Binding Protein (PvDBP) which interacts with the Duffy antigen. PvDBP copy number has been recently shown to vary between P. vivax isolates in Sub-Saharan Africa. However, the extent of PvDBP copy number variation, the type of PvDBP multiplications, as well as its significance across broad samples are still unclear. We determined the prevalence and type of PvDBP duplications, as well as PvDBP copy number variation among 178 Ethiopian P. vivax isolates using a PCR-based diagnostic method, a novel quantitative real-time PCR assay and whole genome sequencing. For the 145 symptomatic samples, PvDBP duplications were detected in 95 isolates, of which 81 had the Cambodian and 14 Malagasy-type PvDBP duplications. PvDBP varied from 1 to >4 copies. Isolates with multiple PvDBP copies were found to be higher in symptomatic than asymptomatic infections. For the 33 asymptomatic samples, PvDBP was detected with two copies in two of the isolates, and both were the Cambodian-type PvDBP duplication. PvDBP copy number in Duffy-negative heterozygotes was not significantly different from that in Duffy-positives, providing no support for the hypothesis that increased copy number is a specific association with Duffy-negativity, although the number of Duffy-negatives was small and further sampling is required to test this association thoroughly

A UV to Mid-IR Study of AGN Selection

We classify the spectral energy distributions (SEDs) of 431,038 sources in the 9 sq. deg Bootes field of the NOAO Deep Wide-Field Survey (NDWFS). There are up to 17 bands of data available per source, including ultraviolet (GALEX), optical (NDWFS), near-IR (NEWFIRM), and mid-infrared (IRAC/MIPS) data, as well as spectroscopic redshifts for ~20,000 objects, primarily from the AGN and Galaxy Evolution Survey (AGES). We fit galaxy, AGN, stellar, and brown dwarf templates to the observed SEDs, which yield spectral classes for the Galactic sources and photometric redshifts and galaxy/AGN luminosities for the extragalactic sources. The photometric redshift precision of the galaxy and AGN samples are sigma/(1+z)=0.040 and sigma/(1+z)=0.169, respectively, with the worst 5% outliers excluded. Based on the reduced chi-squared of the SED fit for each SED model, we are able to distinguish between Galactic and extragalactic sources for sources brighter than I=23.5. We compare the SED fits for a galaxy-only model and a galaxy+AGN model. Using known X-ray and spectroscopic AGN samples, we confirm that SED fitting can be successfully used as a method to identify large populations of AGN, including spatially resolved AGN with significant contributions from the host galaxy and objects with the emission line ratios of "composite" spectra. We also use our results to compare to the X-ray, mid-IR, optical color and emission line ratio selection techniques. For an F-ratio threshold of F>10 we find 16,266 AGN candidates brighter than I=23.5 and a surface density of ~1900 AGN per deg^2.Comment: Submitted to ApJ, 35 pages, 17 figures, 2 table