Complete local search with memory

Neighborhood search heuristics like local search and its variants are some of the most popular approaches to solve discrete optimization problems of moderate to large size. Apart from tabu search, most of these heuristics are memoryless. In this paper we introduce a new neighborhood search heuristic that makes effctive use of memory structures in a way that is different from tabu search. We report computational experiments with this heuristic on the traveling salesperson problem and the subset sum problem.

MICA: desktop software for comprehensive searching of DNA databases

BACKGROUND: Molecular biologists work with DNA databases that often include entire genomes. A common requirement is to search a DNA database to find exact matches for a nondegenerate or partially degenerate query. The software programs available for such purposes are normally designed to run on remote servers, but an appealing alternative is to work with DNA databases stored on local computers. We describe a desktop software program termed MICA (K-Mer Indexing with Compact Arrays) that allows large DNA databases to be searched efficiently using very little memory. RESULTS: MICA rapidly indexes a DNA database. On a Macintosh G5 computer, the complete human genome could be indexed in about 5 minutes. The indexing algorithm recognizes all 15 characters of the DNA alphabet and fully captures the information in any DNA sequence, yet for a typical sequence of length L, the index occupies only about 2L bytes. The index can be searched to return a complete list of exact matches for a nondegenerate or partially degenerate query of any length. A typical search of a long DNA sequence involves reading only a small fraction of the index into memory. As a result, searches are fast even when the available RAM is limited. CONCLUSION: MICA is suitable as a search engine for desktop DNA analysis software

Randomized heuristics for the Capacitated Clustering Problem

In this paper, we investigate the adaptation of the Greedy Randomized Adaptive Search Procedure (GRASP) and Iterated Greedy methodologies to the Capacitated Clustering Problem (CCP). In particular, we focus on the effect of the balance between randomization and greediness on the performance of these multi-start heuristic search methods when solving this NP-hard problem. The former is a memory-less approach that constructs independent solutions, while the latter is a memory-based method that constructs linked solutions, obtained by partially rebuilding previous ones. Both are based on the combination of greediness and randomization in the constructive process, and coupled with a subsequent local search phase. We propose these two multi-start methods and their hybridization and compare their performance on the CCP. Additionally, we propose a heuristic based on the mathematical programming formulation of this problem, which constitutes a so-called matheuristic. We also implement a classical randomized method based on simulated annealing to complete the picture of randomized heuristics. Our extensive experimentation reveals that Iterated Greedy performs better than GRASP in this problem, and improved outcomes are obtained when both methods are hybridized and coupled with the matheuristic. In fact, the hybridization is able to outperform the best approaches previously published for the CCP. This study shows that memory-based construction is an effective mechanism within multi-start heuristic search techniques

Combinatorial optimization and metaheuristics

Today, combinatorial optimization is one of the youngest and most active areas of discrete mathematics. It is a branch of optimization in applied mathematics and computer science, related to operational research, algorithm theory and computational complexity theory. It sits at the intersection of several fields, including artificial intelligence, mathematics and software engineering. Its increasing interest arises for the fact that a large number of scientific and industrial problems can be formulated as abstract combinatorial optimization problems, through graphs and/or (integer) linear programs. Some of these problems have polynomial-time (“efficient”) algorithms, while most of them are NP-hard, i.e. it is not proved that they can be solved in polynomial-time. Mainly, it means that it is not possible to guarantee that an exact solution to the problem can be found and one has to settle for an approximate solution with known performance guarantees. Indeed, the goal of approximate methods is to find “quickly” (reasonable run-times), with “high” probability, provable “good” solutions (low error from the real optimal solution). In the last 20 years, a new kind of algorithm commonly called metaheuristics have emerged in this class, which basically try to combine heuristics in high level frameworks aimed at efficiently and effectively exploring the search space. This report briefly outlines the components, concepts, advantages and disadvantages of different metaheuristic approaches from a conceptual point of view, in order to analyze their similarities and differences. The two very significant forces of intensification and diversification, that mainly determine the behavior of a metaheuristic, will be pointed out. The report concludes by exploring the importance of hybridization and integration methods