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Fast and practical algorithms for planted (l, d) motif search

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2007年第4期4卷 544-552页

作者： Davila, Jaime Balla, Sudha Rajasekaran, Sanguthevar Univ Connecticut Dept Comp Sci & Engn Storrs CT 06269 USA

We consider the planted (l,d) motif search problem, which consists of finding a substring of length l that occurs in a set of input sequences {s(1),...,s(n)} with up to d errors, a problem that arises from the need to find transcription factor-binding sites in genomic information. We propose a sequence of practical algorithms, which start based on the ideas considered in PMS1. These algorithms are exact, have little space requirements, and are able to tackle challenging instances with bigger d, taking less time in the instances reported solved by exact algorithms. In particular, one of the proposed algorithms, PMSprune, is able to solve the challenging instances, such as (17, 6) and (19, 7), which were not previously reported as solved in the literature.

关键词： planted motif search problem challenging instances exact algorithms branch and bound algorithms

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P2P computing for large tree exploration-based exact optimisation

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INTERNATIONAL JOURNAL OF GRID AND UTILITY COMPUTING 2009年第3期1卷 252-260页

作者： Mehdi, M. Mezmaz, M. Melab, N. Talbi, E-G. Bouvry, P. Univ Luxembourg Fac Sci Technol & Commun 6 Rue Coudenhove Kalergi L-1359 Luxembourg Luxembourg INRIA Lille Nord Europe Parc Sci Haute Borne F-59650 Villeneuve Dascq France

The branch and bound (B&B) algorithm is one of the most used methods to solve in an exact way combinatorial optimisation problems. In a previous article, we proposed a new approach of the parallel B&B algorithm for distributed systems using the farmer-worker paradigm. However, the new farmer-worker approach has a disadvantage: some nodes of the B&B tree can be explored by several B&B processes. To prevent this redundant work and speed up, we propose a new P2Papproach inspired from the strategies of existing P2P systems like Napster and JXTA. Validation is performed by experimenting the two approaches on mono-objective flow-shop problem benchmarks using 500 processors belonging to the French national grid, Grid' 5000. The obtained results prove the efficiency of the proposed P2P approach. Indeed, the execution time obtained with the P2P version, even if more communicative, is better than the farmer-worker's one.

关键词： P2P computing exact optimisation flow-shop problem branch and bound algorithms parallel exploration load balancing fault tolerance

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Fast and practical algorithms for planted (l, d) motif search

Fast and practical algorithms for planted (<i>l, d</i>) moti...

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2nd International Workshop on Bioinformatics Research and Applications

作者： Davila, Jaime Balla, Sudha Rajasekaran, Sanguthevar Univ Connecticut Dept Comp Sci & Engn Storrs CT 06269 USA

关键词： planted motif search problem challenging instances exact algorithms branch and bound algorithms

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A general framework for convexity analysis in deterministic global optimization

A general framework for convexity analysis in deterministic ...

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Global Optimization Workshops (GOWs)

作者： Kearfott, Ralph Baker Castille, Jessie Tyagi, Gaurav Univ Louisiana Lafayette Dept Math Lafayette LA 70504 USA Univ Louisiana Lafayette Ctr Adv Comp Studies Lafayette LA 70504 USA

In previous work, we, and also Epperly and Pistikopoulos, proposed an analysis of general nonlinear programs that identified certain variables as convex, not ever needing subdivision, and non-convex, or possibly needing subdivision in branch and bound algorithms. We proposed a specific algorithm, based on a generated computational graph of the problem, for identifying such variables. In our previous work, we identified only independent variables in the computational graph. Here, we examine alternative sets of non-convex variables consisting not just of independent variables, but of a possibly smaller number of intermediate variables. We do so with examples and theorems. We also apply variants of our proposed analysis to the well-known COCONUT Lib-1 test set. If the number of such non-convex variables is sufficiently small, it may be possible to fully subdivide them before analysis of ranges of objective and constraints, thus dispensing totally with the branch and bound process. Advantages to such a non-adaptive process include higher predictability and easier parallizability. We present an algorithm and exploratory results here, with a more complete empirical study in a subsequent paper.

关键词： Automatic verification Non-convexity Automatic differentiation branch and bound algorithms Interval analysis Complete search

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A general framework for convexity analysis in deterministic global optimization

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JOURNAL OF GLOBAL OPTIMIZATION 2013年第3期56卷 765-785页

作者： Kearfott, Ralph Baker Castille, Jessie Tyagi, Gaurav Univ Louisiana Lafayette Dept Math Lafayette LA 70504 USA Univ Louisiana Lafayette Ctr Adv Comp Studies Lafayette LA 70504 USA

关键词： Automatic verification Non-convexity Automatic differentiation branch and bound algorithms Interval analysis Complete search

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Distributed computing task assignment and lightpath establishment (TALE)

Distributed computing task assignment and lightpath establis...

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High-Speed Networks Workshop

作者： Liu, Xin Wei, Wei Yu, Xiang Qiao, Chunming Wang, Ting SUNY Buffalo Dept Comp Sci & Engn Buffalo NY 14260 USA NEC Lab Amer Princeton NJ 08540 USA

ISBN: (纸本)9781424415809

For a future WDM network to efficiently support distributed computing applications that require both execution by multiple geographically separated computing nodes and data transferring between them, traditional approaches to establishing lightpaths between given source destination pairs are not sufficient because a computing task may be executed on any one of several computing nodes having the necessary resources. Therefore, lightpath establishment has to be considered jointly with task assignment to achieve best performance. In this paper, we design and evaluate approaches to the joint optimization of the task assignment and lightpath establishment (TALE) problem. We first formulate the off-line version of the TALE problem and then devise a branch and bound algorithm to obtain the minimum number of wavelengths required to support a set of given jobs. In addition, we propose efficient heuristics to deal with the TALE problem in both off-line and on-line versions. Finally, we demonstrate and compare the performances of proposed heuristics through simulation.

关键词： optical paths Distributed computing wavelength division multiplexing network branch and bound algorithms OFF LINE optimum performance Heuristics

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A Novel Approach for Subgraph Isomorphism Problem on Bipartite Graphs 27

A Novel Approach for Subgraph Isomorphism Problem on Biparti...

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27th Signal Processing and Communications Applications Conference (SIU)

作者： Koca, Mehmet Burak Sevilgen, Fatih Erdogan Gebze Tekn Univ Bilgisayar Muhendisligi Bolumu Kocaeli Turkey

ISBN: (纸本)9781728119045

Subgraph isomorphism problem on specialized graphs is an open research area. Most of the algorithms that had been developed for subgraph isomorphism problem are designed for general graphs. Although, they can be utilized for any graph type, this generic design prevents to take advantages of characteristics of the specialized graphs to burst performance of the subgraph isomorphism search. In this study, we will introduce a novel branch and bound algorithm for subgraph isomorphism problem on bipartite graphs. Bipartite feature of these graphs is utilized to improve search performance by limiting the size of possibility set and by getting rid of backtracking phase of branch and bound technique. Experimental results show that the algorithm provides between 10 and 120 fold better performance results on bipartite graphs when it is compared with the state-of-art algorithms.

关键词： Subgraph isomorphism bipartite graphs branch and bound algorithms

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Efficient Object Localization and Pose Estimation with 3D Wireframe Models

Efficient Object Localization and Pose Estimation with 3D Wi...

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IEEE International Conference on Computer Vision (ICCV)

作者： Yoeruek, Erdem Vidal, Rene Johns Hopkins Univ Ctr Imaging Sci Baltimore MD 21218 USA

ISBN: (纸本)9781479930227

We propose a new and efficient method for 3D object localization and fine-grained 3D pose estimation from a single 2D image. Our approach follows the classical paradigm of matching a 3D model to the 2D observations. Our first contribution is a 3D object model composed of a set of 3D edge primitives learned from 2D object blueprints, which can be viewed as a 3D generalization of HOG features. This model is used to define a matching cost obtained by applying a rigid-body transformation to the 3D object model, projecting it onto the image plane, and matching the projected model to HOG features extracted from the input image. Our second contribution is a very efficient branch-and-bound algorithm for finding the 3D pose that maximizes the matching score. For this, 3D integral images of quantized HOGs are employed to evaluate in constant time the maximum attainable matching scores of individual model primitives. We applied our method to three different datasets of cars and achieved promising results with testing times as low as less than half a second.

关键词： 3D Localization 3D Pose Estimation 3D Wireframe Model Blueprints branch and bound Algorithm Model Matching wire-drawing machine Model matching branch and bound algorithms pose estimation Three Dimensions image plane TESTING TIME two dimentional images

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A BMI based design for robust PID controllers with two-degrees-of-freedom structure

A BMI based design for robust PID controllers with two-degre...

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American Control Conference

作者： Aoyama, J Konishi, K Yamamoto, T Hinamoto, T Hiroshima Univ Grad Sch Engn Dept Artificial Complex Syst Control Higashihiroshima Hiroshima 7398527 Japan

ISBN: (纸本)0780383354

This paper provides a design method for two-degrees-of-freedom I-PD (2DOF-I-PD) controllers including switched PD compensator based on bilinear matrix inequalities (BMIs). Two design specifications based on H-2 norm are formulated in BMIs, and PID parameters can be exactly obtained by solving the BMI problems via branch and bound algorithms. A set of PD compensators can be obtained simultaneously using proposing design method. The most effective parameter is selected out of the set of PD compensator based on the switching criterion which obtained from estimated system conditions using the statistic algorithms. Numerical examples are also shown.

关键词： robust control three-term control PD control control system synthesis compensation H/sup /spl infin// control linear matrix inequalities tree searching statistical analysis bilinear matrix inequalities robust PID controller design two degrees of freedom structure switched PD compensator H/sub 2/ norm PID parameters branch and bound algorithms statistical algorithms branch and bound algorithms Three term control systems Tree searching linear matrix inequalities Proportional derivative control control system synthesis design approach Robust control compensated Statistical methods

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An Optimal Sequence of Tasks for Autonomous Learning Systems

An Optimal Sequence of Tasks for Autonomous Learning Systems

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16th International Conference on Methods and Models in Automation and Robotics (MMAR)

作者： Rudek, Radoslaw Rudek, Agnieszka Skworcow, Piotr Wroclaw Univ Econ Wroclaw Poland Wroclaw Univ Technol Wroclaw Poland De Montfort Univ Water Software Syst Leicester Leics England

ISBN: (纸本)9781457709142

In this paper, we consider an optimal sequence of tasks for systems that improve their performances due to autonomous learning (learning-by-doing). In particular, we focus on a problem of determining sequence of performed tasks for the autonomous learning systems to minimize the total weighted completion times of tasks. Fundamental for the presented approach is that schedule (a sequence of tasks) allows to efficiently utilize learning abilities of the system to optimize its objective, but it does not affect the system itself. To solve the problem, we prove an eliminating property that is used to construct a branch and bound algorithm and present some fast heuristic and metaheuristic methods. An extensive analysis of the efficiency of the proposed algorithms is also provided.

关键词： Religious Missions learning systems branch and bound algorithms

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