A Denotational Semantics for SPARC TSO

The SPARC TSO weak memory model is defined axiomatically, with a non-compositional formulation that makes modular reasoning about programs difficult. Our denotational approach uses pomsets to provide a compositional semantics capturing exactly the behaviours permitted by SPARC TSO. It uses buffered states and an inductive definition of execution to assign an input-output meaning to pomsets. We show that our denotational account is sound and complete relative to the axiomatic account, that is, that it captures exactly the behaviours permitted by the axiomatic account. Our compositional approach facilitates the study of SPARC TSO and supports modular analysis of program behaviour

The K giant stars from the LAMOST survey data I: identification, metallicity, and distance

We present a support vector machine classifier to identify the K giant stars from the LAMOST survey directly using their spectral line features. The completeness of the identification is about 75% for tests based on LAMOST stellar parameters. The contamination in the identified K giant sample is lower than 2.5%. Applying the classification method to about 2 million LAMOST spectra observed during the pilot survey and the first year survey, we select 298,036 K giant candidates. The metallicities of the sample are also estimated with uncertainty of $0.13\sim0.29$\,dex based on the equivalent widths of Mg$_{\rm b}$ and iron lines. A Bayesian method is then developed to estimate the posterior probability of the distance for the K giant stars, based on the estimated metallicity and 2MASS photometry. The synthetic isochrone-based distance estimates have been calibrated using 7 globular clusters with a wide range of metallicities. The uncertainty of the estimated distance modulus at $K=11$\,mag, which is the median brightness of the K giant sample, is about 0.6\,mag, corresponding to $\sim30$% in distance. As a scientific verification case, the trailing arm of the Sagittarius stream is clearly identified with the selected K giant sample. Moreover, at about 80\,kpc from the Sun, we use our K giant stars to confirm a detection of stream members near the apo-center of the trailing tail. These rediscoveries of the features of the Sagittarius stream illustrate the potential of the LAMOST survey for detecting substructures in the halo of the Milky Way.Comment: 24 pages, 20 figures, submitted to Ap

PocketPicker: analysis of ligand binding-sites with shape descriptors

Background Identification and evaluation of surface binding-pockets and occluded cavities are initial steps in protein structure-based drug design. Characterizing the active site's shape as well as the distribution of surrounding residues plays an important role for a variety of applications such as automated ligand docking or in situ modeling. Comparing the shape similarity of binding site geometries of related proteins provides further insights into the mechanisms of ligand binding. Results We present PocketPicker, an automated grid-based technique for the prediction of protein binding pockets that specifies the shape of a potential binding-site with regard to its buriedness. The method was applied to a representative set of protein-ligand complexes and their corresponding apo-protein structures to evaluate the quality of binding-site predictions. The performance of the pocket detection routine was compared to results achieved with the existing methods CAST, LIGSITE, LIGSITEcs, PASS and SURFNET. Success rates PocketPicker were comparable to those of LIGSITEcs and outperformed the other tools. We introduce a descriptor that translates the arrangement of grid points delineating a detected binding-site into a correlation vector. We show that this shape descriptor is suited for comparative analyses of similar binding-site geometry by examining induced-fit phenomena in aldose reductase. This new method uses information derived from calculations of the buriedness of potential binding-sites. Conclusions The pocket prediction routine of PocketPicker is a useful tool for identification of potential protein binding-pockets. It produces a convenient representation of binding-site shapes including an intuitive description of their accessibility. The shape-descriptor for automated classification of binding-site geometries can be used as an additional tool complementing elaborate manual inspections

Asynchronous Partial Overlay: A New Algorithm for Solving Distributed Constraint Satisfaction Problems

Distributed Constraint Satisfaction (DCSP) has long been considered an important problem in multi-agent systems research. This is because many real-world problems can be represented as constraint satisfaction and these problems often present themselves in a distributed form. In this article, we present a new complete, distributed algorithm called Asynchronous Partial Overlay (APO) for solving DCSPs that is based on a cooperative mediation process. The primary ideas behind this algorithm are that agents, when acting as a mediator, centralize small, relevant portions of the DCSP, that these centralized subproblems overlap, and that agents increase the size of their subproblems along critical paths within the DCSP as the problem solving unfolds. We present empirical evidence that shows that APO outperforms other known, complete DCSP techniques

The Baryon Oscillation Spectroscopic Survey of SDSS-III

The Baryon Oscillation Spectroscopic Survey (BOSS) is designed to measure the scale of baryon acoustic oscillations (BAO) in the clustering of matter over a larger volume than the combined efforts of all previous spectroscopic surveys of large scale structure. BOSS uses 1.5 million luminous galaxies as faint as i=19.9 over 10,000 square degrees to measure BAO to redshifts z<0.7. Observations of neutral hydrogen in the Lyman alpha forest in more than 150,000 quasar spectra (g<22) will constrain BAO over the redshift range 2.15<z<3.5. Early results from BOSS include the first detection of the large-scale three-dimensional clustering of the Lyman alpha forest and a strong detection from the Data Release 9 data set of the BAO in the clustering of massive galaxies at an effective redshift z = 0.57. We project that BOSS will yield measurements of the angular diameter distance D_A to an accuracy of 1.0% at redshifts z=0.3 and z=0.57 and measurements of H(z) to 1.8% and 1.7% at the same redshifts. Forecasts for Lyman alpha forest constraints predict a measurement of an overall dilation factor that scales the highly degenerate D_A(z) and H^{-1}(z) parameters to an accuracy of 1.9% at z~2.5 when the survey is complete. Here, we provide an overview of the selection of spectroscopic targets, planning of observations, and analysis of data and data quality of BOSS.Comment: 49 pages, 16 figures, accepted by A

Automated physical classification in the SDSS DR10. A catalogue of candidate Quasars

We discuss whether modern machine learning methods can be used to characterize the physical nature of the large number of objects sampled by the modern multi-band digital surveys. In particular, we applied the MLPQNA (Multi Layer Perceptron with Quasi Newton Algorithm) method to the optical data of the Sloan Digital Sky Survey - Data Release 10, investigating whether photometric data alone suffice to disentangle different classes of objects as they are defined in the SDSS spectroscopic classification. We discuss three groups of classification problems: (i) the simultaneous classification of galaxies, quasars and stars; (ii) the separation of stars from quasars; (iii) the separation of galaxies with normal spectral energy distribution from those with peculiar spectra, such as starburst or starforming galaxies and AGN. While confirming the difficulty of disentangling AGN from normal galaxies on a photometric basis only, MLPQNA proved to be quite effective in the three-class separation. In disentangling quasars from stars and galaxies, our method achieved an overall efficiency of 91.31% and a QSO class purity of ~95%. The resulting catalogue of candidate quasars/AGNs consists of ~3.6 million objects, of which about half a million are also flagged as robust candidates, and will be made available on CDS VizieR facility.Comment: Accepted for publication by MNRAS, 13 pages, 6 figure