Search results for "DYNAMIC PROGRAMMING"
showing 10 items of 61 documents
Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters
2016
Computing alignments between two or more sequences are common operations frequently performed in computational molecular biology. The continuing growth of biological sequence databases establishes the need for their efficient parallel implementation on modern accelerators. This paper presents new approaches to high performance biological sequence database scanning with the Smith-Waterman algorithm and the first stage of progressive multiple sequence alignment based on the ClustalW heuristic on a Xeon Phi-based compute cluster. Our approach uses a three-level parallelization scheme to take full advantage of the compute power available on this type of architecture; i.e. cluster-level data par…
Asymmetry matters: Dynamic half-way points in bidirectional labeling for solving shortest path problems with resource constraints faster
2017
Abstract With their paper “Symmetry helps: Bounded bi-directional dynamic programming for the elementary shortest path problem with resource constraints” [Discrete Optimization 3, 2006, pp. 255–273] Righini and Salani introduced bounded bidirectional dynamic programming (DP) as an acceleration technique for solving variants of the shortest path problem with resource constraints (SPPRC). SPPRCs must be solved iteratively when vehicle routing and scheduling problems are tackled via Lagrangian relaxation or column-generation techniques. Righini and Salani and several subsequent works have shown that bounded bidirectional DP algorithms are often superior to their monodirectional counterparts, s…
Cimo: An efficient 2-phases calculator of multimodal itineraries for real trans-territories based on a dynamic programming
2015
In this work we propose an exact solution for calculating multimodal itinerary. This solution is named Cimo (Calculateur d'Itineraires Multimodaux Ordonnes). Cimo is an exact optimal itineraries' calculator wherein itineraries are sorted, multimodal, and trans-territorial. The solution is based on a dynamic programming algorithm "cut", "price" and "share". This solution is multi-objectives and multi-constraints. Several versions of this algorithm are proposed following a methodological approach that enables evaluation of efficiency and complexity's gain : through theoretical calculus and benchmarks. In the first version of realistic problem, we propose a solution with itineraries calculated…
An FPGA aligner for short read mapping
2012
The rapid growth of short read datasets poses a new challenge to the mapping of short reads to a reference genome in terms of sensitivity and execution speed. In this work, we present a parallel architecture for short read mapping utilizing field programmable gate array (FPGA)-based hardware. The computation intensive semi-global alignment and the hash table lookup operations are mapped onto an FPGA. The proposed Align Core is implemented with a parallel block structure to gain computational efficiency. We present a new parallel block-wise alignment structure to approximate the conventional dynamic programming algorithm. The performance of our FPGA aligner is compared to the GASSST and BWA …
Ancestral Reconstruction and Investigations of Genomic Recombination on some Pentapetalae Chloroplasts
2019
Abstract In this article, we propose a semi-automated method to rebuild genome ancestors of chloroplasts by taking into account gene duplication. Two methods have been used in order to achieve this work: a naked eye investigation using homemade scripts, whose results are considered as a basis of knowledge, and a dynamic programming based approach similar to Needleman-Wunsch. The latter fundamentally uses the Gestalt pattern matching method of sequence matcher to evaluate the occurrences probability of each gene in the last common ancestor of two given genomes. The two approaches have been applied on chloroplastic genomes from Apiales, Asterales, and Fabids orders, the latter belonging to Pe…
Solutions of nonlinear PDEs in the sense of averages
2012
Abstract We characterize p-harmonic functions including p = 1 and p = ∞ by using mean value properties extending classical results of Privaloff from the linear case p = 2 to all pʼs. We describe a class of random tug-of-war games whose value functions approach p-harmonic functions as the step goes to zero for the full range 1 p ∞ .
Neuro-Dynamic Programming for Cooperative Inventory Control
2004
Cost Reduction in Irrigation Networks by an Efficient Use of Pressure Reducing Valves
1992
The cost effective design of hydraulic networks has been traditionally studied from the point of view of the relationship between hydraulic variables and economic parameters, with piping being the main element studied. The reason is clear: the piping is by far the most costly item of a projected network. However it is not usual to find an explicit consideration of the influence that pipe thickness has on the cost of the network because of the added difficulty that this aspect poses to formulating the problem of optimization. In irrigation networks, which are typically branched, it is advisable to place Pressure Reducing Valves (PRV’s) to fulfil three main goals: 1) to control the flow rate …
Some integral type fixed point theorems in Non-Archimedean Menger PM-Spaces with common property (E.A) and application of functional equations in dyn…
2013
In this paper, we prove some integral type common fixed point theorems for weakly compatible mappings in Non-Archimedean Menger PM-spaces employing common property (E.A). Some examples are furnished which demonstrate the validity of our results. We extend our main result to four finite families of self-mappings employing the notion of pairwise commuting. Moreover, we give an application which supports the usability of our main theorem.
On the best Lipschitz extension problem for a discrete distance and the discrete ∞-Laplacian
2012
Abstract This paper concerns the best Lipschitz extension problem for a discrete distance that counts the number of steps. We relate this absolutely minimizing Lipschitz extension with a discrete ∞-Laplacian problem, which arises as the dynamic programming formula for the value function of some e -tug-of-war games. As in the classical case, we obtain the absolutely minimizing Lipschitz extension of a datum f by taking the limit as p → ∞ in a nonlocal p -Laplacian problem.