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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)
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)
This paper presents a new approach for exactly solving the Unbounded Knapsack Problem (UKP) and proposes a new bound that was proved to dominate the previous bounds on a special class of UKP instances. Integrating bounds within the framework of sparse dynamic programming led to the creation of an efficient and robust hybrid algorithm, called EDUK2. This(More)