46,103 research outputs found

    To Index or Not to Index: Optimizing Exact Maximum Inner Product Search

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    Exact Maximum Inner Product Search (MIPS) is an important task that is widely pertinent to recommender systems and high-dimensional similarity search. The brute-force approach to solving exact MIPS is computationally expensive, thus spurring recent development of novel indexes and pruning techniques for this task. In this paper, we show that a hardware-efficient brute-force approach, blocked matrix multiply (BMM), can outperform the state-of-the-art MIPS solvers by over an order of magnitude, for some -- but not all -- inputs. In this paper, we also present a novel MIPS solution, MAXIMUS, that takes advantage of hardware efficiency and pruning of the search space. Like BMM, MAXIMUS is faster than other solvers by up to an order of magnitude, but again only for some inputs. Since no single solution offers the best runtime performance for all inputs, we introduce a new data-dependent optimizer, OPTIMUS, that selects online with minimal overhead the best MIPS solver for a given input. Together, OPTIMUS and MAXIMUS outperform state-of-the-art MIPS solvers by 3.2×\times on average, and up to 10.9×\times, on widely studied MIPS datasets.Comment: 12 pages, 8 figures, 2 table

    An efficient multi-scale Green's Functions Reaction Dynamics scheme

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    Molecular Dynamics - Green's Functions Reaction Dynamics (MD-GFRD) is a multiscale simulation method for particle dynamics or particle-based reaction-diffusion dynamics that is suited for systems involving low particle densities. Particles in a low-density region are just diffusing and not interacting. In this case one can avoid the costly integration of microscopic equations of motion, such as molecular dynamics (MD), and instead turn to an event-based scheme in which the times to the next particle interaction and the new particle positions at that time can be sampled. At high (local) concentrations, however, e.g. when particles are interacting in a nontrivial way, particle positions must still be updated with small time steps of the microscopic dynamical equations. The efficiency of a multi-scale simulation that uses these two schemes largely depends on the coupling between them and the decisions when to switch between the two scales. Here we present an efficient scheme for multi-scale MD-GFRD simulations. It has been shown that MD-GFRD schemes are more efficient than brute-force molecular dynamics simulations up to a molar concentration of 102μM10^{2}\mu M. In this paper, we show that the choice of the propagation domains has a relevant impact on the computational performance. Domains are constructed using a local optimization of their sizes and a minimal domain size is proposed. The algorithm is shown to be more efficient than brute-force Brownian dynamics simulations up to a molar concentration of 103μM10^{3}\mu M and is up to an order of magnitude more efficient compared with previous MD-GFRD schemes

    Faster tuple lattice sieving using spherical locality-sensitive filters

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    To overcome the large memory requirement of classical lattice sieving algorithms for solving hard lattice problems, Bai-Laarhoven-Stehl\'{e} [ANTS 2016] studied tuple lattice sieving, where tuples instead of pairs of lattice vectors are combined to form shorter vectors. Herold-Kirshanova [PKC 2017] recently improved upon their results for arbitrary tuple sizes, for example showing that a triple sieve can solve the shortest vector problem (SVP) in dimension dd in time 20.3717d+o(d)2^{0.3717d + o(d)}, using a technique similar to locality-sensitive hashing for finding nearest neighbors. In this work, we generalize the spherical locality-sensitive filters of Becker-Ducas-Gama-Laarhoven [SODA 2016] to obtain space-time tradeoffs for near neighbor searching on dense data sets, and we apply these techniques to tuple lattice sieving to obtain even better time complexities. For instance, our triple sieve heuristically solves SVP in time 20.3588d+o(d)2^{0.3588d + o(d)}. For practical sieves based on Micciancio-Voulgaris' GaussSieve [SODA 2010], this shows that a triple sieve uses less space and less time than the current best near-linear space double sieve.Comment: 12 pages + references, 2 figures. Subsumed/merged into Cryptology ePrint Archive 2017/228, available at https://ia.cr/2017/122

    Approximating the least hypervolume contributor: NP-hard in general, but fast in practice

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    The hypervolume indicator is an increasingly popular set measure to compare the quality of two Pareto sets. The basic ingredient of most hypervolume indicator based optimization algorithms is the calculation of the hypervolume contribution of single solutions regarding a Pareto set. We show that exact calculation of the hypervolume contribution is #P-hard while its approximation is NP-hard. The same holds for the calculation of the minimal contribution. We also prove that it is NP-hard to decide whether a solution has the least hypervolume contribution. Even deciding whether the contribution of a solution is at most (1+\eps) times the minimal contribution is NP-hard. This implies that it is neither possible to efficiently find the least contributing solution (unless P=NPP = NP) nor to approximate it (unless NP=BPPNP = BPP). Nevertheless, in the second part of the paper we present a fast approximation algorithm for this problem. We prove that for arbitrarily given \eps,\delta>0 it calculates a solution with contribution at most (1+\eps) times the minimal contribution with probability at least (1−δ)(1-\delta). Though it cannot run in polynomial time for all instances, it performs extremely fast on various benchmark datasets. The algorithm solves very large problem instances which are intractable for exact algorithms (e.g., 10000 solutions in 100 dimensions) within a few seconds.Comment: 22 pages, to appear in Theoretical Computer Scienc

    Sampling Sparse Signals on the Sphere: Algorithms and Applications

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    We propose a sampling scheme that can perfectly reconstruct a collection of spikes on the sphere from samples of their lowpass-filtered observations. Central to our algorithm is a generalization of the annihilating filter method, a tool widely used in array signal processing and finite-rate-of-innovation (FRI) sampling. The proposed algorithm can reconstruct KK spikes from (K+K)2(K+\sqrt{K})^2 spatial samples. This sampling requirement improves over previously known FRI sampling schemes on the sphere by a factor of four for large KK. We showcase the versatility of the proposed algorithm by applying it to three different problems: 1) sampling diffusion processes induced by localized sources on the sphere, 2) shot noise removal, and 3) sound source localization (SSL) by a spherical microphone array. In particular, we show how SSL can be reformulated as a spherical sparse sampling problem.Comment: 14 pages, 8 figures, submitted to IEEE Transactions on Signal Processin

    Dynamical model of DNA-protein interaction: effect of protein charge distribution and mechanical properties

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    The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of single beads. In this paper, we first compare the results obtained with the updated model with those of the original one and then use it to investigate several aspects of the dynamics of DNA sampling, which could not be accounted for by the original model. These aspects include the effect on the speed of DNA sampling of the regularity and/or randomness of the protein charge distribution, the charge and location of the search site, and the shape and deformability of the protein. We also discuss the efficiency of facilitated diffusion, that is, the extent to which the combination of 1D sliding along the DNA and 3D diffusion in the cell can lead to faster sampling than pure 3D diffusion of the protein.Comment: accepted in JC
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