10,068 research outputs found

    The pharmacophore kernel for virtual screening with support vector machines

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    We introduce a family of positive definite kernels specifically optimized for the manipulation of 3D structures of molecules with kernel methods. The kernels are based on the comparison of the three-points pharmacophores present in the 3D structures of molecul es, a set of molecular features known to be particularly relevant for virtual screening applications. We present a computationally demanding exact implementation of these kernels, as well as fast approximations related to the classical fingerprint-based approa ches. Experimental results suggest that this new approach outperforms state-of-the-art algorithms based on the 2D structure of mol ecules for the detection of inhibitors of several drug targets

    Searchable Sky Coverage of Astronomical Observations: Footprints and Exposures

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    Sky coverage is one of the most important pieces of information about astronomical observations. We discuss possible representations, and present algorithms to create and manipulate shapes consisting of generalized spherical polygons with arbitrary complexity and size on the celestial sphere. This shape specification integrates well with our Hierarchical Triangular Mesh indexing toolbox, whose performance and capabilities are enhanced by the advanced features presented here. Our portable implementation of the relevant spherical geometry routines comes with wrapper functions for database queries, which are currently being used within several scientific catalog archives including the Sloan Digital Sky Survey, the Galaxy Evolution Explorer and the Hubble Legacy Archive projects as well as the Footprint Service of the Virtual Observatory.Comment: 11 pages, 7 figures, submitted to PAS

    Computation of electromagnetic fields inside three dimensional inhomogeneous dielectrics using a buffered block forward backward algorithm

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    The paper is concerned with the electromagnetic scattering from a three-dimensional inhomogeneous dielectric object. In particular, the paper compares the use of a buffered block forward backward (BBFB) algorithm to the use of the commonly employed weak form of the CG-FFT method for the numerical solution of the resultant electric field integral equation (EFIE). The BBFB method is based on the spatial segmentation of the dielectric into smaller pieces. Results are shown which illustrate the convergence of the algorithm and its superior performance to the CG-FFT

    TetSplat: Real-time Rendering and Volume Clipping of Large Unstructured Tetrahedral Meshes

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    We present a novel approach to interactive visualization and exploration of large unstructured tetrahedral meshes. These massive 3D meshes are used in mission-critical CFD and structural mechanics simulations, and typically sample multiple field values on several millions of unstructured grid points. Our method relies on the pre-processing of the tetrahedral mesh to partition it into non-convex boundaries and internal fragments that are subsequently encoded into compressed multi-resolution data representations. These compact hierarchical data structures are then adaptively rendered and probed in real-time on a commodity PC. Our point-based rendering algorithm, which is inspired by QSplat, employs a simple but highly efficient splatting technique that guarantees interactive frame-rates regardless of the size of the input mesh and the available rendering hardware. It furthermore allows for real-time probing of the volumetric data-set through constructive solid geometry operations as well as interactive editing of color transfer functions for an arbitrary number of field values. Thus, the presented visualization technique allows end-users for the first time to interactively render and explore very large unstructured tetrahedral meshes on relatively inexpensive hardware

    Hierarchical bases for non-hierarchic 3Dtriangular meshes

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    We describe a novel basis of hierarchical, multiscale functions that are linear combinations of standard Rao-Wilton- Glisson (RWG) functions. When the basis is used for discretizing the electric field integral equation (EFIE) for PEC objects it gives rise to a linear system immune from low-frequency breakdown, and well conditioned for dense meshes. The proposed scheme can be applied to any mesh with triangular facets, and therefore it can be used as if it were an algebraic preconditioner. The properties of the new system are confirmed by numerical results that show fast convergence rates of iterative solvers, significantly better than those for the loop-tree basis. As a byproduct of the basis generation, a generalization of the RWG functions to nonsimplex cells is introduced

    A tree-decomposed transfer matrix for computing exact Potts model partition functions for arbitrary graphs, with applications to planar graph colourings

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    Combining tree decomposition and transfer matrix techniques provides a very general algorithm for computing exact partition functions of statistical models defined on arbitrary graphs. The algorithm is particularly efficient in the case of planar graphs. We illustrate it by computing the Potts model partition functions and chromatic polynomials (the number of proper vertex colourings using Q colours) for large samples of random planar graphs with up to N=100 vertices. In the latter case, our algorithm yields a sub-exponential average running time of ~ exp(1.516 sqrt(N)), a substantial improvement over the exponential running time ~ exp(0.245 N) provided by the hitherto best known algorithm. We study the statistics of chromatic roots of random planar graphs in some detail, comparing the findings with results for finite pieces of a regular lattice.Comment: 5 pages, 3 figures. Version 2 has been substantially expanded. Version 3 shows that the worst-case running time is sub-exponential in the number of vertice

    Single-Strip Triangulation of Manifolds with Arbitrary Topology

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    Triangle strips have been widely used for efficient rendering. It is NP-complete to test whether a given triangulated model can be represented as a single triangle strip, so many heuristics have been proposed to partition models into few long strips. In this paper, we present a new algorithm for creating a single triangle loop or strip from a triangulated model. Our method applies a dual graph matching algorithm to partition the mesh into cycles, and then merges pairs of cycles by splitting adjacent triangles when necessary. New vertices are introduced at midpoints of edges and the new triangles thus formed are coplanar with their parent triangles, hence the visual fidelity of the geometry is not changed. We prove that the increase in the number of triangles due to this splitting is 50% in the worst case, however for all models we tested the increase was less than 2%. We also prove tight bounds on the number of triangles needed for a single-strip representation of a model with holes on its boundary. Our strips can be used not only for efficient rendering, but also for other applications including the generation of space filling curves on a manifold of any arbitrary topology.Comment: 12 pages, 10 figures. To appear at Eurographics 200
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