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36
Problem Difficulty for Tabu Search in JobShop Scheduling
 Artificial Intelligence
, 2002
"... Tabu search algorithms are among the most effective approaches for solving the jobshop scheduling problem (JSP). Yet, we have little understanding of why these algorithms work so well, and under what conditions. We develop a model of problem difficulty for tabu search in the JSP, borrowing from sim ..."
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Cited by 22 (8 self)
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Tabu search algorithms are among the most effective approaches for solving the jobshop scheduling problem (JSP). Yet, we have little understanding of why these algorithms work so well, and under what conditions. We develop a model of problem difficulty for tabu search in the JSP, borrowing from similar models developed for SAT and other NP  complete problems. We show that the mean distance between random local optima and the nearest optimal solution is highly correlated with the cost of locating optimal solutions to typical, random JSPs. Additionally, this model accounts for the cost of locating suboptimal solutions, and provides an explanation for differences in the relative difficulty of square versus rectangular JSPs. We also identify two important limitations of our model. First, model accuracy is inversely correlated with problem difficulty, and is exceptionally poor for rare, very highcost problem instances. Second, the model is significantly less accurate for structured, nonrandom JSPs. Our results are also likely to be useful in future research on difficulty models of local search in SAT, as local search cost in both SAT and the JSP is largely dictated by the same search space features. Similarly, our research represents the first attempt to quantitatively model the cost of tabu search for any NP complete problem, and may possibly be leveraged in an effort to understand tabu search in problems other than jobshop scheduling.
On the Utility of Redundant Encodings in Mutationbased Evolutionary Search
 In
, 2002
"... A number of recent works in the evolutionary computation eld have suggested that introducing large amounts of genetic redundancy may increase the evolvability of a population in an evolutionary algorithm. These works have variously claimed that the reliability of the search, the nal tness achi ..."
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Cited by 19 (0 self)
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A number of recent works in the evolutionary computation eld have suggested that introducing large amounts of genetic redundancy may increase the evolvability of a population in an evolutionary algorithm. These works have variously claimed that the reliability of the search, the nal tness achieved, the ability to cope with changing environments, and the robustness to high mutation rates, may all be improved by employing this strategy. In this paper we dispute some of these claims, arguing that adding random redundancy cannot be generally useful for optimization purposes. By way of example we report on experiments where a proposed neutral encoding scheme (based on random Boolean networks) is compared to a direct encoding in two mutationonly EAs, at various mutation rates. Our ndings show that with the appropriate choice of perbit mutation rate, the evolvability of populations using the direct encoding is no less than with the redundant one.
Evolution on distributive lattices
 J THEOR BIOL
, 2006
"... We consider the directed evolution of a population after an intervention that has significantly altered the underlying fitness landscape. We model the space of genotypes as a distributive lattice; the fitness landscape is a realvalued function on that lattice. The risk of escape from intervention ..."
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Cited by 16 (9 self)
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We consider the directed evolution of a population after an intervention that has significantly altered the underlying fitness landscape. We model the space of genotypes as a distributive lattice; the fitness landscape is a realvalued function on that lattice. The risk of escape from intervention, i.e., the probability that the population develops an escape mutant before extinction, is encoded in the risk polynomial. Tools from algebraic combinatorics are applied to compute the risk polynomial in terms of the fitness landscape. In an application to the development of drug resistance in HIV, we study the risk of viral escape from treatment with the protease inhibitors ritonavir and indinavir.
Quasiindependence, homology and the unity of type: A topological theory of characters
 J. THEOR. BIOL
, 2002
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An Efficient Local Search Method for Random 3Satisfiability
, 2003
"... We report on some exceptionally good results in the solution of randomly generated 3satisfiability instances using the "recordtorecord travel (RRT)" local search method. When this simple, but lessstudied algorithm is applied to random onemillion variable instances from the problem&apos ..."
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Cited by 10 (4 self)
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We report on some exceptionally good results in the solution of randomly generated 3satisfiability instances using the "recordtorecord travel (RRT)" local search method. When this simple, but lessstudied algorithm is applied to random onemillion variable instances from the problem's satisfiable phase, it seems to find satisfying truth assignments almost always in linear time, with the coefficient of linearity depending on the ratio &alpha; of clauses to variables in the generated instances. RRT has a parameter for tuning "greediness". By lessening greediness, the linear time phase can be extended up to very close to the satisfiability threshold &alpha;_c. Such linear time complexity is typical for randomwalk based local search methods for small values of &alpha;. Previously, however, it has been suspected that these methods necessarily lose their time linearity far below the satisfiability threshold. The only previously introduced algorithm reported to have nearly linear time complexity also close to the satisfiability threshold is the survey propagation (SP) algorithm. However, SP is not a local search method and is more complicated to implement than RRT. Comparative experiments with the WalkSAT local search algorithm show behavior somewhat similar to RRT, but with the linear time phase not extending quite as close to the satisfiability threshold.
The Centrality of
, 1992
"... This Article is brought to you for free and open access by the Biochemistry, Department of at DigitalCommons@University of Nebraska Lincoln. It ..."
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Cited by 10 (4 self)
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This Article is brought to you for free and open access by the Biochemistry, Department of at DigitalCommons@University of Nebraska Lincoln. It
Almost Tight Upper Bound for Finding Fourier Coefficients of Bounded PseudoBoolean Functions
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Folding 3noncrossing RNA pseudoknot structures
 J. Comput. Biol
"... Abstract. In this paper we present a selfcontained analysis and description of the novel ab initio folding algorithm cross, which generates the minimum free energy (mfe), 3noncrossing, σcanonical RNA structure. Here an RNA structure is 3noncrossing if it does not contain more than three mutually ..."
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Abstract. In this paper we present a selfcontained analysis and description of the novel ab initio folding algorithm cross, which generates the minimum free energy (mfe), 3noncrossing, σcanonical RNA structure. Here an RNA structure is 3noncrossing if it does not contain more than three mutually crossing arcs and σcanonical, if each of its stacks has size greater or equal than σ. Our notion of mfestructure is based on a specific concept of pseudoknots and respective loopbased energy parameters. The algorithm decomposes into three parts: the first is the inductive construction of motifs and shadows, the second is the generation of the skeletatrees rooted in irreducible shadows and the third is the saturation of skeleta via context dependent dynamic programming routines. 1. Introduction and