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For 2-D iteration space tiling, we address the problem of determining the tile parameters that minimize the total execution time under the BSP model. We consider uniform dependency computations, tiled so that (at least) one of the tile boundaries is parallel to the domain boundary. We determine the optimal tile size as a closed form solution. In addition,(More)
Among the measures for quantifying the similarity between three-dimensional (3D) protein structures, maximum contact map overlap (CMO) received sustained attention during the past decade. Despite this, the known algorithms exhibit modest performance and are not applicable for large-scale comparison. This article offers a clear advance in this respect. We(More)
  • Rumen Andonov, Frédéric Raimbault, Patrice Quinton, Fr Ed Eric Raimbault
  • 1993
A systolic algorithm for the dynamic programming approach to the knapsack problem is presented. The algorithm can run on any number of processors and has optimal time speedup and processor eeciency. The running time of the algorithm is (mc=q + m) on a ring of q processors, where c is the knapsack size and m is the number of object types. A new procedure for(More)
Computing the similarity between two protein structures is a crucial task in molecular biology, and has been extensively investigated. Many protein structure comparison methods can be modeled as maximum clique problems in specific k-partite graphs, referred here as alignment graphs. In this paper, we propose a new protein structure comparison method based(More)