相关论文: Improved neighbor list algorithm in molecular simu…

We present an approach to make molecular optimization more efficient. We infer a hypergraph replacement grammar from the ChEMBL database, count the frequencies of particular rules being used to expand particular nonterminals in other rules,…

We present a new approach for solving (minimum disagreement) correlation clustering that results in sublinear algorithms with highly efficient time and space complexity for this problem. In particular, we obtain the following algorithms for…

Among the novel metrics used to study the relative importance of nodes in complex networks, k-core decomposition has found a number of applications in areas as diverse as sociology, proteinomics, graph visualization, and distributed system…

Iterative decoding was not originally introduced as the solution to an optimization problem rendering the analysis of its convergence very difficult. In this paper, we investigate the link between iterative decoding and classical…

Designing molecular structures with desired chemical properties is an essential task in drug discovery and material design. However, finding molecules with the optimized desired properties is still a challenging task due to combinatorial…

Particle-in-cell merging algorithms aim to resample dynamically the six-dimensional phase space occupied by particles without distorting substantially the physical description of the system. Whereas various approaches have been proposed in…

Sorting database tables before compressing them improves the compression rate. Can we do better than the lexicographical order? For minimizing the number of runs in a run-length encoding compression scheme, the best approaches to…

A fast algorithm for the approximation of a low rank LU decomposition is presented. In order to achieve a low complexity, the algorithm uses sparse random projections combined with FFT-based random projections. The asymptotic approximation…

We propose new sequential sorting operations by adapting techniques and methods used for designing parallel sorting algorithms. Although the norm is to parallelize a sequential algorithm to improve performance, we adapt a contrarian…

Numerous algorithms and parallelisations have been developed for short-range particle simulations; however, none are optimally performant for all scenarios. Such a concept led to the prior development of the particle simulation library…

Recent indexing techniques inspired by source coding have been shown successful to index billions of high-dimensional vectors in memory. In this paper, we propose an approach that re-ranks the neighbor hypotheses obtained by these…

The current computer architecture has moved towards the multi/many-core structure. However, the algorithms in the current sequential dense numerical linear algebra libraries (e.g. LAPACK) do not parallelize well on multi/many-core…

Graph search is one of the most successful algorithmic trends in near neighbor search. Several of the most popular and empirically successful algorithms are, at their core, a simple walk along a pruned near neighbor graph. Such algorithms…

Meshless methods approximate operators in a specific node as a weighted sum of values in its neighbours. Higher order approximations of derivatives provide more accurate solutions with better convergence characteristics, but they come at…

The life of the modern world essentially depends on the work of the large artificial homogeneous networks, such as wired and wireless communication systems, networks of roads and pipelines. The support of their effective continuous…

Neighborhood algorithms may take a considerable percentage of computer time in discrete element methods (DEM). While the sort-and-sweep algorithm is ideal in some ways, as it only deal with particles whose relative positions change in one…

Non-negative signals form an important class of sparse signals. Many algorithms have already beenproposed to recover such non-negative representations, where greedy and convex relaxed algorithms are among the most popular methods. One fast…

We present an acceleration method for sequences of large-scale linear systems, such as the ones arising from the numerical solution of time-dependent partial differential equations coupled with algebraic constraints. We discuss different…

Customizable contraction hierarchies are one of the most popular route planning frameworks in practice, due to their simplicity and versatility. In this work, we present a novel algorithm for finding k-nearest neighbors in customizable…

The graph partitioning problem has many applications in scientific computing such as computer aided design, data mining, image compression and other applications with sparse-matrix vector multiplications as a kernel operation. In many cases…