Semi-supervised dimensionality reduction based on partial least squares for visual analysis of high dimensional data

Dimensionality reduction is employed for visual data analysis as a way to obtaining reduced spaces for high dimensional data or to mapping data directly into 2D or 3D spaces. Although techniques have evolved to improve data segregation on reduced or visual spaces, they have limited capabilities for adjusting the results according to user's knowledge. In this paper, we propose a novel approach to handling both dimensionality reduction and visualization of high dimensional data, taking into account user's input. It employs Partial Least Squares (PLS), a statistical tool to perform retrieval of latent spaces focusing on the discriminability of the data. The method employs a training set for building a highly precise model that can then be applied to a much larger data set very effectively. The reduced data set can be exhibited using various existing visualization techniques. The training data is important to code user's knowledge into the loop. However, this work also devises a strategy for calculating PLS reduced spaces when no training data is available. The approach produces increasingly precise visual mappings as the user feeds back his or her knowledge and is capable of working with small and unbalanced training sets.

Strategies in identifying individuals in a segregant population of common bean and implications of genotype x environment interaction in the success of selection

The objective of this study was to compare the BLUP selection method with different selection strategies in F-2:4 and assess the efficiency of this method on the early choice of the best common bean (Phaseolus vulgaris) lines. Fifty-one F-2:4 progenies were produced from a cross between the CVIII8511 x RP-26 lines. A randomized block design was used with 20 replications and one-plant field plots. Character data on plant architecture and grain yield were obtained and then the sum of the standardized variables was estimated for simultaneous selection of both traits. Analysis was carried out by mixed models (BLUP) and the least squares method to compare different selection strategies, like mass selection, stratified mass selection and between and within progeny selection. The progenies selected by BLUP were assessed in advanced generations, always selecting the greatest and smallest sum of the standardized variables. Analyses by the least squares method and BLUP procedure ranked the progenies in the same way. The coincidence of the individuals identified by BLUP and between and within progeny selection was high and of the greatest magnitude when BLUP was compared with mass selection. Although BLUP is the best estimator of genotypic value, its efficiency in the response to long term selection is not different from any of the other methods, because it is also unable to predict the future effect of the progenies x environments interaction. It was inferred that selection success will always depend on the most accurate possible progeny assessment and using alternatives to reduce the progenies x environments interaction effect.

Low-energy electron collisions with glycine

We report cross sections for elastic electron scattering by gas phase glycine (neutral form), obtained with the Schwinger multichannel method. The present results are the first obtained with a new implementation that combines parallelization with OpenMP directives and pseudopotentials. The position of the well known pi* shape resonance ranged from 2.3 eV to 2.8 eV depending on the polarization model and conformer. For the most stable isomer, the present result (2.4 eV) is in fair agreement with electron transmission spectroscopy assignments (1.93 +/- 0.05 eV) and available calculations. Our results also point out a shape resonance around 9.5 eV in the A' symmetry that would be weakly coupled to vibrations of the hydroxyl group. Since electron attachment to a broad and lower lying sigma* orbital located on the OH bond has been suggested the underlying mechanism leading to dissociative electron attachment at low energies, we sought for a shape resonance around similar to 4 eV. Though we obtained cross sections with the target molecule at the equilibrium geometry and with stretched OH bond lengths, least-squares fits to the calculated eigenphase sums did not point out signatures of this anion state (though, in principle, it could be hidden in the large background). The low energy (similar to 1 eV) integral cross section strongly scales as the bond length is stretched, and this could indicate a virtual state pole, since dipole supported bound states are not expected at the geometries addressed here. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.3687345]

Probing the anomalous extinction of four young star clusters: the use of colour-excess, main-sequence fitting and fractal analysis

Aims. We studied four young star clusters to characterise their anomalous extinction or variable reddening and asses whether they could be due to contamination by either dense clouds or circumstellar effects. Methods. We evaluated the extinction law (R-V) by adopting two methods: (i) the use of theoretical expressions based on the colour-excess of stars with known spectral type; and (ii) the analysis of two-colour diagrams, where the slope of the observed colour distribution was compared to the normal distribution. An algorithm to reproduce the zero-age main-sequence (ZAMS) reddened colours was developed to derive the average visual extinction (A(V)) that provides the closest fit to the observational data. The structure of the clouds was evaluated by means of a statistical fractal analysis, designed to compare their geometric structure with the spatial distribution of the cluster members. Results. The cluster NGC 6530 is the only object of our sample affected by anomalous extinction. On average, the other clusters suffer normal extinction, but several of their members, mainly in NGC 2264, seem to have high R-V, probably because of circumstellar effects. The ZAMS fitting provides A(V) values that are in good agreement with those found in the literature. The fractal analysis shows that NGC 6530 has a centrally concentrated distribution of stars that differs from the substructures found in the density distribution of the cloud projected in the A(V) map, suggesting that the original cloud was changed by the cluster formation. However, the fractal dimension and statistical parameters of Berkeley 86, NGC 2244, and NGC 2264 indicate that there is a good cloud-cluster correlation, when compared to other works based on an artificial distribution of points.

Gaussian deconvolution: a useful method for a form-free modeling of scattering data from mono- and multilayered planar systems

A new method for analysis of scattering data from lamellar bilayer systems is presented. The method employs a form-free description of the cross-section structure of the bilayer and the fit is performed directly to the scattering data, introducing also a structure factor when required. The cross-section structure (electron density profile in the case of X-ray scattering) is described by a set of Gaussian functions and the technique is termed Gaussian deconvolution. The coefficients of the Gaussians are optimized using a constrained least-squares routine that induces smoothness of the electron density profile. The optimization is coupled with the point-of-inflection method for determining the optimal weight of the smoothness. With the new approach, it is possible to optimize simultaneously the form factor, structure factor and several other parameters in the model. The applicability of this method is demonstrated by using it in a study of a multilamellar system composed of lecithin bilayers, where the form factor and structure factor are obtained simultaneously, and the obtained results provided new insight into this very well known system.