A GPU-based genetic algorithm for the p-median problem

The p-median problem is a well-known NP-hard problem. Many heuristics have been proposed in the literature for this problem. In this paper, we exploit a GPGPU parallel computing platform to present a new genetic algorithm implemented in CUDA and based on a pseudo-Boolean formulation of the p-median problem. We have tested the effectiveness of our algorithm using a Tesla K40 (2880 CUDA cores) on 290 different benchmark instances obtained from OR-Library, discrete location problems benchmark library, and benchmarks introduced in recent publications. The algorithm succeeded in finding optimal solutions for all instances except for two OR-library instances, namely pmed 30 and pmed 40, where better than 99.9% approximations were obtained.     

A memetic genetic algorithm for the vertex p-center problem

Abstract The p-center problem is one of choosing p facilities from a set of candidates to satisfy the demands of n clients in order to minimize the maximum cost between a client and the facility to which it is assigned. In this article, PBS, a population based meta-heuristic for the p-center problem, is described. PBS is a genetic algorithm based meta-heuristic that uses phenotype crossover and directed mutation operators to generate new starting points for a local search. For larger p-center instances, PBS is able to effectively utilize a number of computer processors. It is shown empirically that PBS has comparable performance to state-of-the-art exact and approximate algorithms for a range of p-center benchmark instances.     

Ramsey numbers and an approximation algorithm for the vertex cover problem

Summary We show two results. First we derive an upper bound for the special Ramsey numbers r _k(q) where r _k(q) is the largest number of nodes a graph without odd cycles of length bounded by 2k+1 and without an independent set of size q+1 can have. We prove The proof is constructive and yields an algorithm for computing an independent set of that size. Using this algorithm we secondly describe an O(¦V¦·¦E¦) time bounded approximation algorithm for the vertex cover problem, whose worst case ratio is , for all graphs with at most (2k+3) ^k (2k+2) nodes (e.g. 1.8, if ¦V¦146000).     

A parallel two-list algorithm for the knapsack problem

An n-element knapsack problem has 2ⁿ possible solutions to search over, so a task which can be accomplished in 2″ trials if an exhaustive search is used. Due to the exponential time in solving the knapsack problem, the problem is considered to be very hard. In the past decade, much effort has been done in order to find techniques which could lead to practical algorithms with reasonable running time. In 1994, Chang et al. proposed a brilliant parallel algorithm, which needs O(2^n/8) processors to solve the knapsack problem in O(2^n/2) time; that is, the cost of Chang et al.'s parallel algorithm is O(2^5n/8). In this paper, we propose a parallel algorithm to improve Chang et al.'s parallel algorithm by reducing the time complexity to be O(2^3n/8) under the same O(2^n/8) processors available. Thus, the proposed parallel algorithm has a cost of O(2^n/2). It is an improvement over previous literature. We believe that the proposed parallel algorithm is pragmatically feasible at the moment when multiprocessor systems become more and more popular.     

A parallel algorithm for the integer knapsack problem

A sequential algorithm with complexity O(M²+n) for the integer knapsack problem is presented. M is the capacity of the knapsack, and n the number of objects. The algorithm admits an efficient parallelization on a p-processor ring machine. The corresponding parallel algorithm is O(M²/p+n). The parallel algorithm is compared with a version of the well-known Lee algorithm adapted to the integer knapsack problem. Computational results on both a local area network and a transputer are reported.     

Mean analysis of an online algorithm for the vertex cover problem

In 2005, Demange and Paschos proposed in [M. Demange, V.Th. Paschos, On-line vertex-covering, Theoret. Comput. Sci. 332 (2005) 83-108] an online algorithm (noted LR here) for the classical vertex cover problem. They shown that, for any graph of maximum degree Δ, LR constructs a vertex cover whose size is at most Δ times the optimal one (this bound is tight in the worst case).Very recently, two of the present authors have shown in [F. Delbot, C. Laforest, A better list heuristic for vertex cover, Inform. Process. Lett. 107 (2008) 125-127] that LR has interesting properties (it is a good “list algorithm” and it can easily be distributed). In addition, LR has good experimental behavior in spite of its Δ approximation (or competitive) ratio and the fact that it can be executed without the knowledge of the full instance at the beginning.In this paper we analyze it deeper and we show that LR has good “average” performances: we prove that its mean approximation ratio is strictly less than 2 for any graph and is equal to 1+e−2≈1.13 in paths. LR is then a very interesting algorithm for constructing small vertex covers, despite its bad worst case behavior.     

GPU-based parallel algorithms for sparse nonlinear systems

In this work we describe some parallel algorithms for solving nonlinear systems using CUDA (Compute Unified Device Architecture) over a GPU (Graphics Processing Unit). The proposed algorithms are based on both the Fletcher–Reeves version of the nonlinear conjugate gradient method and a polynomial preconditioner type based on block two-stage methods. Several strategies of parallelization and different storage formats for sparse matrices are discussed. The reported numerical experiments analyze the behavior of these algorithms working in a fine grain parallel environment compared with a thread-based environment.     

A new parallel algorithm for vertex priorities of data flow acyclic digraphs

Data flow acyclic directed graphs (digraph) are widely used to describe the data dependency of mesh-based scientific computing. The parallel execution of such digraphs can approximately depict the flowchart of parallel computing. During the period of parallel execution, vertex priorities are key performance factors. This paper firstly takes the distributed digraph and its resource-constrained parallel scheduling as the vertex priorities model, and then presents a new parallel algorithm for the solution of vertex priorities using the well-known technique of forward–backward iterations. Especially, in each iteration, a more efficient vertex ranking strategy is proposed. In the case of simple digraphs, both theoretical analysis and benchmarks show that the vertex priorities produced by such an algorithm will make the digraph scheduling time converge non-increasingly with the number of iterations. In other cases of non-simple digraphs, benchmarks also show that the new algorithm is superior to many traditional approaches. Embedding the new algorithm into the heuristic framework for the parallel sweeping solution of neutron transport applications, the new vertex priorities improve the performance by 20 % or so while the number of processors scales up from 32 to 2048.     

A parallel multistart algorithm for the closest string problem

In this paper we describe and implement a parallel algorithm to find approximate solutions for the Closest String Problem (CSP). The CSP, also known as Motif Finding problem, has applications in Coding Theory and Computational Biology. The CSP is NP-hard which motivates us to think about heuristics to solve large instances. Several approximation algorithms have been designed for the CSP, but all of them have a poor performance guarantee. Recently some researchers have shown empirically that integer programming techniques can be successfully used to solve moderate-size instances (10–30 strings each of which is 300–800 characters long) of the CSP. However, real-world instances are larger than those tested. In this paper we show how a simple heuristic can be used to find near-optimal solutions to that problem. We implemented a parallel version of this heuristic and report computational experiments on large-scale instances. These results show the effectiveness of our approach.     

A population-based iterated greedy algorithm for the minimum weight vertex cover problem

Given an undirected, vertex-weighted graph, the goal of the minimum weight vertex cover problem is to find a subset of the vertices of the graph such that the subset is a vertex cover and the sum of the weights of its vertices is minimal. This problem is known to be NP-hard and no efficient algorithm is known to solve it to optimality. Therefore, most existing techniques are based on heuristics for providing approximate solutions in a reasonable computation time.Population-based search approaches have shown to be effective for solving a multitude of combinatorial optimization problems. Their advantage can be identified as their ability to find areas of the space containing high quality solutions. This paper proposes a simple and efficient population-based iterated greedy algorithm for tackling the minimum weight vertex cover problem. At each iteration, a population of solutions is established and refined using a fast randomized iterated greedy heuristic based on successive phases of destruction and reconstruction. An extensive experimental evaluation on a commonly used set of benchmark instances shows that our algorithm outperforms current state-of-the-art approaches.     

A combined parallel algorithm for solving the knapsack problem

Parallel implementations of a combined branch-and-bound algorithm for the knapsack problem with one constraint are considered. By the combined algorithm we mean an algorithm in which two methods of branching are implemented, the method based on an estimate of the upper bound and the method of one-sided branching based on the vector. An approach combining parallel implementations of the brunch-and-bound method and the heuristic search is proposed and implemented.     

A global parallel algorithm for the hypergraph transversal problem

We consider the problem of finding all minimal transversals of a hypergraph H⊆V², given by an explicit list of its hyperedges. We give a new decomposition technique for solving the problem with the following advantages: (i) Global parallelism: for certain classes of hypergraphs, e.g., hypergraphs of bounded edge size, and any given integer k, the algorithm outputs k minimal transversals of H in time bounded by polylog(|V|,|H|,k) assuming poly(|V|,|H|,k) number of processors. Except for the case of graphs, none of the previously known algorithms for solving the same problem exhibit this feature. (ii) Using this technique, we also obtain new results on the complexity of generating minimal transversals for new classes of hypergraphs, namely hypergraphs of bounded dual-conformality, and hypergraphs in which every edge intersects every minimal transversal in a bounded number of vertices.     

A parallel improvement algorithm for the bipartite subgraph problem

The authors propose the first parallel improvement algorithm using the maximum neural network model for the bipartite subgraph problem. The goal of this NP-complete problem is to remove the minimum number of edges in a given graph such that the remaining graph is a bipartite graph. A large number of instances have been simulated to verify the proposed algorithm, with the simulation result showing that the algorithm finds a solution within 200 iteration steps and the solution quality is superior to that of the best existing algorithm. The algorithm is extended for the K-partite subgraph problem where no algorithm has been proposed.     

A quality and distance guided hybrid algorithm for the vertex separator problem

This paper presents a quality and distance guided local search (QD-LS) as the diversification strategy for metaheuristics. QD-LS uses an augmented evaluation function which considers both solution quality and distance between the current solution and the best found solution to guide the search towards promising regions of the search space. To evaluate the performance of QD-LS, we propose a quality and distance guided hybrid algorithm (QD-HA) for solving the vertex separator problem. Based on the framework of evolutionary algorithms, QD-HA integrates a basic tabu search procedure with a random greedy recombination operator and QD-LS strategy. Assessed on two sets of 348 common benchmark instances, QD-HA achieves highly competitive results in terms of both solution quality and computational efficiency compared with state-of-the-art algorithms in the literature. Specifically, it improves the previous best known results for 63 out of 244 large instances while matching the best known results for others. The impact of the quality and distance based diversification strategy is also investigated.     

A hybrid metaheuristic approach for the capacitated p-median problem

The capacitated p-median problem (CPMP) seeks to obtain the optimal location of p medians considering distances and capacities for the services to be given by each median. This paper presents an efficient hybrid metaheuristic algorithm by combining a proposed cutting-plane neighborhood structure and a tabu search metaheuristic for the CPMP. In the proposed neighborhood structure to move from the current solution to a neighbor solution, an open median is selected and closed. Then, a linear programming (LP) model is generated by relaxing binary constraints and adding new constraints. The generated LP solution is improved using cutting-plane inequalities. The solution of this strong LP is considered as a new neighbor solution. In order to select an open median to be closed, several strategies are proposed. The neighborhood structure is combined with a tabu search algorithm in the proposed approach. The parameters of the proposed hybrid algorithm are tuned using design of experiments approach. The proposed algorithm is tested on several sets of benchmark instances. The statistical analysis shows efficiency and effectiveness of the hybrid algorithm in comparison with the best approach found in the literature.     

Improved FPT algorithm for feedback vertex set problem in bipartite tournament

We present an O(k³n²+n³) time FPT algorithm for the feedback vertex set problem in a bipartite tournament on n vertices with integral weights. This improves the previously best known O(k^3.12n⁴) time FPT algorithm for the problem.     

A GPU-based parallel method for evolutionary tree construction

Evolutionary trees are widely applied in various applications to show the inferred evolutionary relationships among species or entities. Neighbor-Joining is one solution for data-intensive and time-consuming evolutionary tree construction, with polynomial time complexity. However, its performance becomes poorer with the growth of massive datasets. Graphics Processing Units (GPUs) have brought about new opportunities for these time-consuming applications. Based on its high efficiency, a GPU-based parallel Neighbor-Joining method is proposed, and two efficient parallel mechanisms, data segmentation with asynchronous processing and the minimal chain model with bitonic sort, are put forward to speed up the processing. The experimental results show that an average speedup of 25.1 is achieved and even approximately 30 can be obtained with a sequence dataset ranging from 16,000 to 25,000. Moreover, the proposed parallel mechanisms can be effectively exploited in some other high performance applications.