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constraint logic programming approach to protein structure prediction -: art. no. 186

BMC BIOINFORMATICS 2004年第1期5卷 186-186页

作者： Dal Palù, A Dovier, A Fogolari, F Univ Udine Dipartimento Matemat & Informat I-33100 Udine Italy Univ Udine Dipartimento Sci & Tecnol Biomed I-33100 Udine Italy

Background: The protein structure prediction problem is one of the most challenging problems in biological sciences. Many approaches have been proposed using database information and/or simplified protein models. The protein structure prediction problem can be cast in the form of an optimization problem. Notwithstanding its importance, the problem has very seldom been tackled by constraint logic programming, a declarative programming paradigm suitable for solving combinatorial optimization problems. Results: constraint logic programming techniques have been applied to the protein structure prediction problem on the face-centered cube lattice model. Molecular dynamics techniques, endowed with the notion of constraint, have been also exploited. Even using a very simplified model, constraint logic programming on the face-centered cube lattice model allowed us to obtain acceptable results for a few small proteins. As a test implementation their (known) secondary structure and the presence of disulfide bridges are used as constraints. Simplified structures obtained in this way have been converted to all atom models with plausible structure. Results have been compared with a similar approach using a well-established technique as molecular dynamics. Conclusions: The results obtained on small proteins show that constraint logic programming techniques can be employed for studying protein simplified models, which can be converted into realistic all atom models. The advantage of constraint logic programming over other, much more explored, methodologies, resides in the rapid software prototyping, in the easy way of encoding heuristics, and in exploiting all the advances made in this research area, e.g. in constraint propagation and its use for pruning the huge search space.

关键词： Molecular Dynamic Simulation Secondary Structure Element constraint logic programming Secondary Structure Information Core Residue

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Hybrid mixed-integer/constraint logic programming strategies for solving scheduling and combinatorial optimization problems

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COMPUTERS & CHEMICAL ENGINEERING 2000年第2-7期24卷 337-343页

作者： Harjunkoski, I Jain, V Grossman, IE Carnegie Mellon Univ Dept Chem Engn Pittsburgh PA 15213 USA

In this paper, we present two methods to overcome the combinatorial complexity when solving large discrete optimization problems. The basic idea relies on combining mixed integer programming (MIP) and constraint logic programming (CLP) to exploit their complementary strengths. These strategies are illustrated in the area of job-shop scheduling and trim-loss problems. Comparisons of the strategies are presented with direct solutions on MIP and CLP problems. (C) 2000 Elsevier Science Ltd. All rights reserved.

关键词： mixed integer programming constraint logic programming hybrid MIP/CLP

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From extended feature models to constraint logic programming

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SCIENCE OF COMPUTER programming 2013年第12期78卷 2295-2312页

作者： Karatas, Ahmet Serkan Oguztuzun, Halit Dogru, Ali Middle E Tech Univ Dept Comp Engn TR-06531 Ankara Turkey

Since feature models for realistic product families may be quite complicated, the automated analysis of feature models is desirable. Although several approaches reported in the literature address this issue, complex cross-tree relationships involving attributes in extended feature models have not been handled. In this article, we introduce a mapping from extended feature models to constraint logic programming over finite domains. This mapping is used to translate into constraint logic programs;basic, cardinality-based and extended feature models, which can include complex cross-tree relationships involving attributes. This translation enables the use of off-the-shelf constraint solvers for the automated analysis of extended feature models involving such complex relationships. We also present the performance results of some well-known analysis operations on an example translated model. (C) 2012 Elsevier B.V. All rights reserved.

关键词： Variability modeling Extended feature model Feature attribute constraint logic programming

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Cane railway scheduling via constraint logic programming: Labelling order and constraints in a real-life application

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ANNALS OF OPERATIONS RESEARCH 2001年第1-4期108卷 193-209页

作者： Martin, F Pinkney, A Yu, XH Univ Cent Queensland Fac Informat & Commun Mackay Qld 4741 Australia

In Australia, cane transport is the largest unit cost in the manufacturing of raw sugar, making up around 35% of the total manufacturing costs. Producing efficient schedules for the cane railways can result in significant cost savings. This paper presents a study using constraint logic programming (CLP) to solve the cane transport scheduling problem. Tailored heuristic labelling order and constraints strategies are proposed and encouraging results of application to several test problems and one real-life case are presented. The preliminary results demonstrate that CLP can be used as an effective tool for solving the cane transport scheduling problem, with a potential decrease in development costs of the scheduling system. It can also be used as an efficient tool for rescheduling tasks which the existing cane transport scheduling system cannot perform well.

关键词： cane railway scheduling constraint logic programming labelling order

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Probabilistic Spatial Reasoning in constraint logic programming 10th

Probabilistic Spatial Reasoning in Constraint Logic Programm...

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10th International Conference on Scalable Uncertainty Management (SUM)

作者： Schultz, Carl Bhatt, Mehul Suchan, Jakob Univ Munster Munster Germany Univ Bremen Bremen Germany DesignSpace Grp Bremen Germany

ISBN: (纸本)9783319458564;9783319458557

In this paper we present a novel framework and full implementation of probabilistic spatial reasoning within a logic programming context. The crux of our approach is extending Probabilistic logic programming (based on distribution semantics) to support reasoning over spatial variables via constraint logic programming. Spatial reasoning is formulated as a numerical optimisation problem, and we implement our approach within ProbLog 1. We demonstrate a range of powerful features beyond what is currently provided by existing probabilistic and spatial reasoning tools.

关键词： Probabilistic logic programming constraint logic programming Declarative spatial reasoning

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Modeling and Optimization of Pickup and Delivery Problem Using constraint logic programming 11th

Modeling and Optimization of Pickup and Delivery Problem Usi...

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11th International Conference on Large-Scale Scientific Computations (LSSC)

作者： Badica, Amelia Badica, Costin Leon, Florin Buligiu, Ion Univ Craiova Craiova Romania Tech Univ Gheorghe Asachi Iasi Iasi Romania

ISBN: (纸本)9783319734415;9783319734408

Our research was conducted in a project that aims to develop an intelligent freight broker agent for providing logistics brokerage services for the efficient allocation of transport resources (vehicles or trucks) to the transport applications. This agent coordinates transportation arrangements of customers (usually shippers and consignees) with resource providers or carriers, following the freight broker business model. The scheduling function of the freight broker agent was formulated as a special type of vehicle routing with pickup and delivery problem. This research is based on our recently proposed declarative model of the freight broker agent using constraint logic programming. This model allows the computation of the feasible transportation schedules. In this paper we augment this model with a declarative representation of optimal schedules and then we show how these optimal schedules can be computed using the ECLiPSe constraint logic programming system.

关键词： Combinatorial optimization Pickup and delivery problem constraint logic programming

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Computation of non-ground disjunctive well-founded semantics with constraint logic programming 2nd

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2nd International Workshop on Non-Monotonic Extensions of logic programming

作者： Dix, J Stolzenburg, F Univ Koblenz Dept Comp Sci D-56075 Koblenz Germany

ISBN: (纸本)3540628436

Impressive work has been done in the last;years concerning the meaning of negation and disjunction in logic programs, but most of this research concentrated on propositional programs only. While it suffices to consider the propositional case for investigating general properties and the overall behaviour of a semantics, we feel that for real applications and for computational purposes an implementation should be able to handle first-order programs without grounding them. In this paper we present a theoretical framework by defining a calculus of program transformations that apply directly to rules with variables and function symbols. Our main results are that (1) this calculus is confluent for arbitrary programs, (2) for finite ground programs it is equivalent to a terminating calculus introduced by Brass and Dir (1995), and (3) it approximates a generalisation of D-WFS for arbitrary programs. We achieve this by transforming program rules into rules with equational constraints thereby using heavily methods and techniques from constraint logic programming. In particular, disconnection-methods play a crucial role. In principle, any constraint theory known from the field of constraint logic programming can be exploited in the context of nonmonotonic reasoning, not only equational constraints over the Herbrand domain. However, the respective constraint solver must be able to treat negative constraints of the considered constraint domain. In summary, this work yields the basis for a general combination of two paradigms: constraint logic programming and non-monotonic reasoning.

关键词： constraint logic programming equational constraints disjunctive logic programming well-founded semantics non-monotonic reasoning

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Selective Unification in constraint logic programming 17

Selective Unification in Constraint Logic Programming

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19th International Symposium on Principles and Practice of Declarative programming (PPDP)

作者： Mesnard, Fred Payet, Etienne Vidal, German Univ Reunion LIM St Denis Reunion France Univ Politecn Valencia DSIC MiST Valencia Spain

ISBN: (纸本)9781450352918

Concolic testing is a well-known validation technique for imperative and object-oriented programs. We have recently introduced an adaptation of this technique to logic programming. At the heart of our framework for concolic testing lies a logic programming specific procedure that we call "selective unification". In this paper, we consider concolic testing in the context of constraint logic programming and extend the notion of selective unification accordingly. We prove that the selective unification problem is generally undecidable for constraint logic programs, and we present a correct and complete algorithm for selective unification in the context of a class of constraint structures.

关键词： constraint logic programming Concolic testing Unification

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Optimizing allocation in floor storage systems for the shoe industry by constraint logic programming

Optimizing allocation in floor storage systems for the shoe ...

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9th International Conference on Intelligent Systems Design and Applications

作者： Meneghetti, Antonella Univ Udine DiEM I-33100 Udine Italy

ISBN: (纸本)9781424447350

Floor storage systems are used in the shoe industry to store fashion products of seasonal collections with low quantity and high variety. Since space is precious and order picking must be sped up, stacking of shoe boxes should be optimized. The problem is modeled by assigning an integer code to each box basing on shoe characteristics (model, material, color, and size) and trying to force similar boxes into near locations to improve pickers' ability of fast order retrieval. The model is encoded in constraint logic programming and solved comparing different strategies, also using Large Neighborhood Search.

关键词： Allocation Floor storage systems Shoe industry constraint logic programming Large Neighborhood Search

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Incremental search in constraint logic programming

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New Generation Computing 1991年第3-4期9卷 257-275页

作者： Van Hentenryck, Pascal Le Provost, Thierry Brown University Providence 02912 RI Box 1910 United States European Computer-industry Research Centre (ECRC) Munich 17 D-8000 Arabellastrasse Germany

Incremental search consists of adding new constraints or deleting old ones once a solution to a search problem has been found. Although incremental search is of primary importance in application areas such as scheduling, planning, trouble shooting, and interactive problem-solving, it is not presently supported by logic programming languages and little research has been devoted to this topic. This paper presents a scheme to deal efficiently with incremental search problems. The scheme allows the incremental addition and deletion of constraints and is based on re-execution, using parts of computation paths stored during previous computations. The scheme has been implemented as part of the constraint logic programming language CHIP and applied to practical problems. It has shown arbitrarily large (i.e. unbounded) speedups compared with previous approaches on practical problems. © 1991 Ohmsha, Ltd. and Springer.

关键词： constraint logic programming Incrementality Reexecution Search

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