10,068 research outputs found
The pharmacophore kernel for virtual screening with support vector machines
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
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
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
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
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
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
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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