11,757 research outputs found

    The use of genetic algorithms to maximize the performance of a partially lined screened room

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    This paper shows that it is possible to use genetic algorithms to optimize the layout of ferrite tile absorber in a partially lined screened enclosure to produce a "best" performance. The enclosure and absorber are modeled using TLM modeling techniques and the performance is determined by comparison with theoretical normalized site attenuation of free space. The results show that it is possible to cover just 80% of the surface of the enclosure with ferrite absorber and obtain a response which is within +/-4 dB of the free space response between 40 and 200 MHz

    An efficient memetic, permutation-based evolutionary algorithm for real-world train timetabling

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    Train timetabling is a difficult and very tightly constrained combinatorial problem that deals with the construction of train schedules. We focus on the particular problem of local reconstruction of the schedule following a small perturbation, seeking minimisation of the total accumulated delay by adapting times of departure and arrival for each train and allocation of resources (tracks, routing nodes, etc.). We describe a permutation-based evolutionary algorithm that relies on a semi-greedy heuristic to gradually reconstruct the schedule by inserting trains one after the other following the permutation. This algorithm can be hybridised with ILOG commercial MIP programming tool CPLEX in a coarse-grained manner: the evolutionary part is used to quickly obtain a good but suboptimal solution and this intermediate solution is refined using CPLEX. Experimental results are presented on a large real-world case involving more than one million variables and 2 million constraints. Results are surprisingly good as the evolutionary algorithm, alone or hybridised, produces excellent solutions much faster than CPLEX alone

    Computational Complexity Results for Genetic Programming and the Sorting Problem

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    Genetic Programming (GP) has found various applications. Understanding this type of algorithm from a theoretical point of view is a challenging task. The first results on the computational complexity of GP have been obtained for problems with isolated program semantics. With this paper, we push forward the computational complexity analysis of GP on a problem with dependent program semantics. We study the well-known sorting problem in this context and analyze rigorously how GP can deal with different measures of sortedness.Comment: 12 page

    Understanding Algorithm Performance on an Oversubscribed Scheduling Application

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    The best performing algorithms for a particular oversubscribed scheduling application, Air Force Satellite Control Network (AFSCN) scheduling, appear to have little in common. Yet, through careful experimentation and modeling of performance in real problem instances, we can relate characteristics of the best algorithms to characteristics of the application. In particular, we find that plateaus dominate the search spaces (thus favoring algorithms that make larger changes to solutions) and that some randomization in exploration is critical to good performance (due to the lack of gradient information on the plateaus). Based on our explanations of algorithm performance, we develop a new algorithm that combines characteristics of the best performers; the new algorithms performance is better than the previous best. We show how hypothesis driven experimentation and search modeling can both explain algorithm performance and motivate the design of a new algorithm

    Simultaneous identification of specifically interacting paralogs and inter-protein contacts by Direct-Coupling Analysis

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    Understanding protein-protein interactions is central to our understanding of almost all complex biological processes. Computational tools exploiting rapidly growing genomic databases to characterize protein-protein interactions are urgently needed. Such methods should connect multiple scales from evolutionary conserved interactions between families of homologous proteins, over the identification of specifically interacting proteins in the case of multiple paralogs inside a species, down to the prediction of residues being in physical contact across interaction interfaces. Statistical inference methods detecting residue-residue coevolution have recently triggered considerable progress in using sequence data for quaternary protein structure prediction; they require, however, large joint alignments of homologous protein pairs known to interact. The generation of such alignments is a complex computational task on its own; application of coevolutionary modeling has in turn been restricted to proteins without paralogs, or to bacterial systems with the corresponding coding genes being co-localized in operons. Here we show that the Direct-Coupling Analysis of residue coevolution can be extended to connect the different scales, and simultaneously to match interacting paralogs, to identify inter-protein residue-residue contacts and to discriminate interacting from noninteracting families in a multiprotein system. Our results extend the potential applications of coevolutionary analysis far beyond cases treatable so far.Comment: Main Text 19 pages Supp. Inf. 16 page
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