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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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Typing linear constraints for moding CLP(R) programs

Typing linear constraints for moding CLP(R) programs

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15th International Symposium on Static Analysis

作者： Ruggieri, Salvatore Mesnard, Fred Univ Pisa Dipartimento Informat Corso Italia 40 I-56100 Pisa Italy Univ Reunion IREMIA St Etienne France

ISBN: (纸本)9783540691631

We present a type system for linear constraints over reals and its use in mode analysis of CLP programs. The type system is designed to reason about the properties of definiteness, lower and upper bounds of variables of a linear constraint. Two proof procedures are presented for checking validity of type assertions. The first one considers lower and upper bound types, and it relies on solving homogeneous linear programming problems. The second procedure, which deals with definiteness as well, relies on computing the Minkowski's form of a parameterized polyhedron. The two procedures are sound and complete. We extend the approach to deal with strict inequalities and disequalities. Type assertions are at the basis of moding constraint logic programs. We extend the notion of well-moding from pure logic programming to CLP(R).

关键词： linear constraints polyhedra constraint logic programming well-moding definiteness

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Goal-oriented test data generation for pointer programs

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INFORMATION AND SOFTWARE TECHNOLOGY 2007年第9-10期49卷 1030-1044页

作者： Gotlieb, Arnaud Denmat, Tristan Botella, Bernard INRIA IRISA F-35042 Rennes France THALES AEROSPACE F-78851 Elancourt France

Automatic test data generation leads to the identification of input values on which a selected path or a selected branch is executed within a program (path-oriented vs. goal-oriented methods). In both cases, several approaches based oil constraint solving exist, but in the presence of pointer variables only path-oriented methods have been proposed. Pointers are responsible for the existence of conditional aliasing problems that usually provoke the failure of the goal-oriented test data generation process. In this paper, we propose an overall constraint-based method that exploits the results of an intraprocedural points-to analysis and provides two specific constraint combinators for automatically generating goal-oriented test data. This approach correctly handles multi-levels stack-directed pointers that are mainly used in C programs. The method has been fully implemented in the test data generation tool INKA and first experiences in applying it to a variety of existing programs are presented. (c) 2006 Elsevier B.V. All rights reserved.

关键词： goal-oriented test data generation constraint logic programming static single assignment form pointer variables

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Maxx: Test pattern optimisation with local search over an extended logic

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constraintS 2007年第4期12卷 507-538页

作者： Azevedo, Francisco Univ Nova Lisboa FCT CENTRIA Dept Informat P-2829516 Caparica Portugal

In the electronic computer-aided design area, the test generation problem consists in finding an input vector test for some possible diagnosis (a set of faults) of a digital circuit. Such tests may have some unspecified Primary Inputs (i.e. bits are assigned neither 0 nor 1). In fact, for many purposes, minimally specified tests (or patterns) are preferred. Hence, we have the test pattern optimisation (TPO) problem where the goal is to obtain a test with the maximum number of unspecified bits. In this paper we discuss different modelling approaches and present a TPO tool (Maxx) that substantially outperforms others by combining Branch-and-Bound and local search over distinct models. We apply the usual branch-and-bound search on CLP(FD) over a simple, yet incomplete, logic. A complementary Local Search is performed over an extended model, trying to improve an already computed solution by exploring an extended solution space thanks to the use of an extended logic (too complex for constraint solving). Such extended logic considers sets of dependencies on specified input values, keeping track of sources of unspecified values and their inversion parities. This allows modelling a number of alternative test vectors by unspecification of each possible input bit, thus being able to obtain an improved test vector in linear time. This paper shows, for TPO, that adapting constraint propagation with results obtained from local search outperforms the use of each of these techniques alone, obtaining significantly better results than those obtained with a highly efficient tool based on an integer linear programming formulation on a propositional satisfiability model.

关键词： CLP constraint logic programming PI primary input TG test generation

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Cardinal: A finite sets constraint solver

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constraintS 2007年第1期12卷 93-129页

作者： Azevedo, Francisco Univ Nova Lisboa FCTCENTRIA Dept Informat Monte De Caparica Portugal

In this paper we present Cardinal, a general finite sets constraint solver just made publicly available in ECUPSe constraint System, suitable for combinatorial problem solving by exploiting inferences over sets cardinality. In fact, to deal with set variables and set constraints, existing set constraint solvers are not adequate to handle a number of problems, as they do not actively use important information about the cardinality of the sets, a key feature in such problems. Cardinal is formally presented as a set of rewriting rules on a constraint store and we illustrate its efficiency with experimental results. We show the importance of propagating constraints on sets cardinality, by comparing Cardinal with other solvers. Another contribution of this paper is on modelling: we focus essentially on digital circuits problems, for which we present new modelling approaches and prove that sets alone can be used to model these problems in a clean manner and solve them efficiently using Cardinal. Results on a set of diagnostic problems show that Cardinal obtains a speed up of about two orders of magnitude over Conjunto, a previous available set constraint solver, which uses a more limited amount of constraint propagation on cardinalities. Additionally, to further extend modelling capabilities and efficiency, we generalized Cardinal to actively consider constraints over set functions other than cardinality. The Cardinal version just released allows declaring union, minimum and maximum functions on set variables, and easily constraining those functions, letting Cardinal especial inferences efficiently take care of different problems. We describe such extensions and discuss its potentialities, which promise interesting research directions.

关键词： CLP constraint logic programming PI, primary input TG, test generation

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A model-based design-for-verification approach to checking for deadlock in multi-threaded applications

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INTERNATIONAL JOURNAL OF SOFTWARE ENGINEERING AND KNOWLEDGE ENGINEERING 2007年第2期17卷 207-230页

作者： Sarna-Starosta, Beata Stirewalt, R. E. K. Dillon, Laura K. Michigan State Univ Dept Comp Sci & Engn Software Engn & Network Syst Labs E Lansing MI 48824 USA

This paper explores an approach to design for verification in systems built atop a middleware framework which separates synchronization concerns from the "core-functional logic" of a program. The framework is based on a language-independent compositional model of synchronization contracts, called Szumo, which integrates well with popular OO design artifacts and provides strong guarantees of non-interference for a class of strictly exclusive systems. An approach for extracting models from Szumo design artifacts and analyzing the generated models to detect deadlocks is described. A key decision was to use constraint Handling Rules to express the semantics of synchronization contracts, which allowed a transparent model of the implementation logic.

关键词： concurrency analysis constraint logic programming design for verification

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A model-based design-for-verification approach to checking for deadlock in multi-threaded applications

A model-based design-for-verification approach to checking f...

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18th International Conference on Software Engineering and Knowledge Engineering

作者： Sarna-Starosta, Beata Stirewalt, R. E. K. Dillon, Laura K. Michigan State Univ Dept Comp Sci & Engn Software Engn & Network Syst Labs E Lansing MI 48824 USA

ISBN: (纸本)9781627486606

关键词： concurrency analysis constraint logic programming design for verification

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IBIS: an Interactive Bytecode Inspection System, using symbolic execution and constraint logic programming 03

IBIS: an Interactive Bytecode Inspection System, using symbo...

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Proceedings of the 2nd international conference on Principles and practice of programming in Java

作者： J. Doyle C. Meudec Institute of Technology Carlow Carlow Ireland

ISBN: (纸本)9780954414511

A fundamental area of software engineering that remains a challenge is the delivery of software with the minimum of remaining defects. The principal technique currently used in the software industry for the verification and validation of software is dynamic software testing where the software under consideration is actually executed using test data. The actual generation of test data for the purpose of automated software testing is still however mainly a manual task. This problem is further compounded for Java programmers because testing criteria can be imposed at the Java Bytecode level rather than at the source level. To alleviate these difficulties an Interactive Bytecode Inspection System (IBIS) has been developed that allows examination of the Java Bytecode and the automatic generation and execution of test data.

关键词： automatic tests data generation constraint logic programming Java Bytecode coverage testing logic programming symbolic execution

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Solving nesting problems with non-convex polygons by constraint logic programming

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International Transactions in Operational Research 2003年第6期10卷 651-663页

作者： Carravilla, M.A. Ribeiro, C. Oliveira, J.F. University of Porto Portugal

In this paper an application of constraint logic programming (CLP) to the resolution of nesting problems is presented. Nesting problems are a special case of the cutting and packing problems, in which the pieces generally have non-convex shapes. Because of their combinatorial optimization nature, nesting problems have traditionally been tackled by heuristics and in the recent past by meta-heuristics. When trying to formulate nesting problems as linear programming models, to achieve global optimal solutions, the difficulty of dealing with the disjunction of constraints arises. On the contrary, CLP deals easily with this type of relationships among constraints. A CLP implementation for the nesting problem is described for convex and non-convex shapes. The concept of nofit polygon is used to deal with the geometric constraints inherent to all cutting and packing problems. Computational results are presented. © 2003 Wiley Periodicals, Inc.

关键词： Artificial intelligence constraint logic programming Nesting Packing

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Temporal phylogenetic networks and logic programming

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THEORY AND PRACTICE OF logic programming 2006年第0期6卷 539-558页

作者： Erdem, Esra Lifschitz, Vladimir Ringe, Don Vienna Univ Technol Inst Informat Syst 184 3 A-1040 Vienna Austria Univ Texas Dept Comp Sci Austin TX 78712 USA Univ Penn Dept Linguist Philadelphia PA 19104 USA

The concept of a temporal phylogenetic network is a mathematical model of evolution of a family of natural languages. It takes into account the fact that languages can trade their characteristics with each other when linguistic communities are in contact, and also that a contact is only possible when the languages are spoken at the same time. We show how computational methods of answer set programming and constraint logic programming can be used to generate plausible conjectures about contacts between prehistoric linguistic communities, and illustrate our approach by applying it to the evolutionary history of Indo-European languages.

关键词： phylogenetics historical linguistics Indo-European languages answer set programming constraint logic programming

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