8,323 research outputs found
The Fast Heuristic Algorithms and Post-Processing Techniques to Design Large and Low-Cost Communication Networks
It is challenging to design large and low-cost communication networks. In
this paper, we formulate this challenge as the prize-collecting Steiner Tree
Problem (PCSTP). The objective is to minimize the costs of transmission routes
and the disconnected monetary or informational profits. Initially, we note that
the PCSTP is MAX SNP-hard. Then, we propose some post-processing techniques to
improve suboptimal solutions to PCSTP. Based on these techniques, we propose
two fast heuristic algorithms: the first one is a quasilinear time heuristic
algorithm that is faster and consumes less memory than other algorithms; and
the second one is an improvement of a stateof-the-art polynomial time heuristic
algorithm that can find high-quality solutions at a speed that is only inferior
to the first one. We demonstrate the competitiveness of our heuristic
algorithms by comparing them with the state-of-the-art ones on the largest
existing benchmark instances (169 800 vertices and 338 551 edges). Moreover, we
generate new instances that are even larger (1 000 000 vertices and 10 000 000
edges) to further demonstrate their advantages in large networks. The
state-ofthe-art algorithms are too slow to find high-quality solutions for
instances of this size, whereas our new heuristic algorithms can do this in
around 6 to 45s on a personal computer. Ultimately, we apply our
post-processing techniques to update the bestknown solution for a notoriously
difficult benchmark instance to show that they can improve near-optimal
solutions to PCSTP. In conclusion, we demonstrate the usefulness of our
heuristic algorithms and post-processing techniques for designing large and
low-cost communication networks
An odyssey into local refinement and multilevel preconditioning III: Implementation and numerical experiments
In this paper, we examine a number of additive and multiplicative multilevel iterative methods and preconditioners in the setting of two-dimensional local mesh refinement. While standard multilevel methods are effective for uniform refinement-based discretizations of elliptic equations, they tend to be less effective for algebraic systems, which arise from discretizations on locally refined meshes, losing their optimal behavior in both storage and computational complexity. Our primary focus here is on Bramble, Pasciak, and Xu (BPX)-style additive and multiplicative multilevel preconditioners, and on various stabilizations of the additive and multiplicative hierarchical basis (HB) method, and their use in the local mesh refinement setting. In parts I and II of this trilogy, it was shown that both BPX and wavelet stabilizations of HB have uniformly bounded condition numbers on several classes of locally refined two- and three-dimensional meshes based on fairly standard (and easily implementable) red and red-green mesh refinement algorithms. In this third part of the trilogy, we describe in detail the implementation of these types of algorithms, including detailed discussions of the data structures and traversal algorithms we employ for obtaining optimal storage and computational complexity in our implementations. We show how each of the algorithms can be implemented using standard data types, available in languages such as C and FORTRAN, so that the resulting algorithms have optimal (linear) storage requirements, and so that the resulting multilevel method or preconditioner can be applied with optimal (linear) computational costs. We have successfully used these data structure ideas for both MATLAB and C implementations using the FEtk, an open source finite element software package. We finish the paper with a sequence of numerical experiments illustrating the effectiveness of a number of BPX and stabilized HB variants for several examples requiring local refinement
Optimal Assembly for High Throughput Shotgun Sequencing
We present a framework for the design of optimal assembly algorithms for
shotgun sequencing under the criterion of complete reconstruction. We derive a
lower bound on the read length and the coverage depth required for
reconstruction in terms of the repeat statistics of the genome. Building on
earlier works, we design a de Brujin graph based assembly algorithm which can
achieve very close to the lower bound for repeat statistics of a wide range of
sequenced genomes, including the GAGE datasets. The results are based on a set
of necessary and sufficient conditions on the DNA sequence and the reads for
reconstruction. The conditions can be viewed as the shotgun sequencing analogue
of Ukkonen-Pevzner's necessary and sufficient conditions for Sequencing by
Hybridization.Comment: 26 pages, 18 figure
Potential Maximal Clique Algorithms for Perfect Phylogeny Problems
Kloks, Kratsch, and Spinrad showed how treewidth and minimum-fill, NP-hard
combinatorial optimization problems related to minimal triangulations, are
broken into subproblems by block subgraphs defined by minimal separators. These
ideas were expanded on by Bouchitt\'e and Todinca, who used potential maximal
cliques to solve these problems using a dynamic programming approach in time
polynomial in the number of minimal separators of a graph. It is known that
solutions to the perfect phylogeny problem, maximum compatibility problem, and
unique perfect phylogeny problem are characterized by minimal triangulations of
the partition intersection graph. In this paper, we show that techniques
similar to those proposed by Bouchitt\'e and Todinca can be used to solve the
perfect phylogeny problem with missing data, the two- state maximum
compatibility problem with missing data, and the unique perfect phylogeny
problem with missing data in time polynomial in the number of minimal
separators of the partition intersection graph
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