46,917 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
Multi-core computation of transfer matrices for strip lattices in the Potts model
The transfer-matrix technique is a convenient way for studying strip lattices
in the Potts model since the compu- tational costs depend just on the periodic
part of the lattice and not on the whole. However, even when the cost is
reduced, the transfer-matrix technique is still an NP-hard problem since the
time T(|V|, |E|) needed to compute the matrix grows ex- ponentially as a
function of the graph width. In this work, we present a parallel
transfer-matrix implementation that scales performance under multi-core
architectures. The construction of the matrix is based on several repetitions
of the deletion- contraction technique, allowing parallelism suitable to
multi-core machines. Our experimental results show that the multi-core
implementation achieves speedups of 3.7X with p = 4 processors and 5.7X with p
= 8. The efficiency of the implementation lies between 60% and 95%, achieving
the best balance of speedup and efficiency at p = 4 processors for actual
multi-core architectures. The algorithm also takes advantage of the lattice
symmetry, making the transfer matrix computation to run up to 2X faster than
its non-symmetric counterpart and use up to a quarter of the original space
Large induced subgraphs via triangulations and CMSO
We obtain an algorithmic meta-theorem for the following optimization problem.
Let \phi\ be a Counting Monadic Second Order Logic (CMSO) formula and t be an
integer. For a given graph G, the task is to maximize |X| subject to the
following: there is a set of vertices F of G, containing X, such that the
subgraph G[F] induced by F is of treewidth at most t, and structure (G[F],X)
models \phi.
Some special cases of this optimization problem are the following generic
examples. Each of these cases contains various problems as a special subcase:
1) "Maximum induced subgraph with at most l copies of cycles of length 0
modulo m", where for fixed nonnegative integers m and l, the task is to find a
maximum induced subgraph of a given graph with at most l vertex-disjoint cycles
of length 0 modulo m.
2) "Minimum \Gamma-deletion", where for a fixed finite set of graphs \Gamma\
containing a planar graph, the task is to find a maximum induced subgraph of a
given graph containing no graph from \Gamma\ as a minor.
3) "Independent \Pi-packing", where for a fixed finite set of connected
graphs \Pi, the task is to find an induced subgraph G[F] of a given graph G
with the maximum number of connected components, such that each connected
component of G[F] is isomorphic to some graph from \Pi.
We give an algorithm solving the optimization problem on an n-vertex graph G
in time O(#pmc n^{t+4} f(t,\phi)), where #pmc is the number of all potential
maximal cliques in G and f is a function depending of t and \phi\ only. We also
show how a similar running time can be obtained for the weighted version of the
problem. Pipelined with known bounds on the number of potential maximal
cliques, we deduce that our optimization problem can be solved in time
O(1.7347^n) for arbitrary graphs, and in polynomial time for graph classes with
polynomial number of minimal separators
Towards Structural Classification of Proteins based on Contact Map Overlap
A multitude of measures have been proposed to quantify the similarity between
protein 3-D structure. Among these measures, contact map overlap (CMO)
maximization deserved sustained attention during past decade because it offers
a fine estimation of the natural homology relation between proteins. Despite
this large involvement of the bioinformatics and computer science community,
the performance of known algorithms remains modest. Due to the complexity of
the problem, they got stuck on relatively small instances and are not
applicable for large scale comparison. This paper offers a clear improvement
over past methods in this respect. We present a new integer programming model
for CMO and propose an exact B &B algorithm with bounds computed by solving
Lagrangian relaxation. The efficiency of the approach is demonstrated on a
popular small benchmark (Skolnick set, 40 domains). On this set our algorithm
significantly outperforms the best existing exact algorithms, and yet provides
lower and upper bounds of better quality. Some hard CMO instances have been
solved for the first time and within reasonable time limits. From the values of
the running time and the relative gap (relative difference between upper and
lower bounds), we obtained the right classification for this test. These
encouraging result led us to design a harder benchmark to better assess the
classification capability of our approach. We constructed a large scale set of
300 protein domains (a subset of ASTRAL database) that we have called Proteus
300. Using the relative gap of any of the 44850 couples as a similarity
measure, we obtained a classification in very good agreement with SCOP. Our
algorithm provides thus a powerful classification tool for large structure
databases
A new exact algorithm for the multi-depot vehicle routing problem under capacity and route length constraints
This article presents an exact algorithm for the multi-depot vehicle routing problem (MDVRP) under capacity and route length constraints. The MDVRP is formulated using a vehicle-flow and a set-partitioning formulation, both of which are exploited at different stages of the algorithm. The lower bound computed with the vehicle-flow formulation is used to eliminate non-promising edges, thus reducing the complexity of the pricing subproblem used to solve the set-partitioning formulation. Several classes of valid inequalities are added to strengthen both formulations, including a new family of valid inequalities used to forbid cycles of an arbitrary length. To validate our approach, we also consider the capacitated vehicle routing problem (CVRP) as a particular case of the MDVRP, and conduct extensive computational experiments on several instances from the literature to show its effectiveness. The computational results show that the proposed algorithm is competitive against stateof-the-art methods for these two classes of vehicle routing problems, and is able to solve to optimality some previously open instances. Moreover, for the instances that cannot be solved by the proposed algorithm, the final lower bounds prove stronger than those obtained by earlier methods
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