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21
Excluding Symmetries in ConstraintBased Search
, 1999
"... . We introduce a new method for excluding symmetries in constraint based search. To our knowledge, it is the rst declarative method that can be applied to arbitrary symmetries. Our method is based on the notion of symmetric constraints, which are used in our modication of a general constraint ba ..."
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Cited by 91 (5 self)
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. We introduce a new method for excluding symmetries in constraint based search. To our knowledge, it is the rst declarative method that can be applied to arbitrary symmetries. Our method is based on the notion of symmetric constraints, which are used in our modication of a general constraint based search algorithm. The method does not inuence the search strategy. Furthermore, it can be used with either the full set of symmetries, or with an subset of all symmetries. We proof correctness, completeness and symmetry exclusion properties of our method. We then show how to apply the method in the special case of geometric symmetries (rotations and reections) and permutation symmetries. Furthermore, we give results from practical applications. 1 Introduction In many search problems, one is faced with the existence of symmetries. Symmetries give rise to many dierent solutions found by the search procedure, which are all considered to be "similar". Often, one is not intereste...
Symmetry Breaking in Constraint Programming
 Proceedings of ECAI2000
, 2000
"... We describe a method for symmetry breaking during search (SBDS) in constraint programming. It has the great advantage of not interfering with heuristic choices. It guarantees to return a unique solution from each set of symmetrically equivalent ones, which is the one found first by the variable and ..."
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Cited by 89 (11 self)
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We describe a method for symmetry breaking during search (SBDS) in constraint programming. It has the great advantage of not interfering with heuristic choices. It guarantees to return a unique solution from each set of symmetrically equivalent ones, which is the one found first by the variable and value ordering heuristics. We describe an implementation of SBDS in ILOG Solver, and applications to low autocorrelation binary sequences and the nqueens problem. We discuss how SBDS can be applied when there are too many symmetries to reason with individually, and give applications in graph colouring and Ramsey theory.
Symmetry Breaking During Search in Constraint Programming
 Proceedings ECAI'2000
, 1999
"... We introduce a method for symmetry breaking during search (SBDS) in constraint programming. It has the great advantage of not interfering with heuristic choices. It guarantees to return a unique solution from each set of symmetrically equivalent ones, which is the one found first by the variable ..."
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Cited by 55 (14 self)
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We introduce a method for symmetry breaking during search (SBDS) in constraint programming. It has the great advantage of not interfering with heuristic choices. It guarantees to return a unique solution from each set of symmetrically equivalent ones, which is the one found first by the variable and value ordering heuristics. We prove this claim, describe a general implementation of SBDS in ILOG Solver, and describe applications to low autocorrelation binary sequences and the nqueens problem. We discuss a version of SBDS that can be applied when there are too many symmetries to reason with individually, and give applications in graph colouring and Ramsey theory. 1 Introduction Many constraint satisfaction problems (CSPs) contain symmetries, so that for every solution, there are equivalent solutions. Symmetries divide the set of possible assignments into equivalence classes. Each class contains either only solutions or no solutions. When finding all solutions to a CSP, it is...
Programming Constraint Services
, 2002
"... This thesis presents design, application, implementation, and evaluation of computation spaces as abstractions for programming constraint services at a high level. Spaces are seamlessly integrated into a concurrent programming language and make constraintbased computations compatible with concurrenc ..."
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Cited by 22 (1 self)
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This thesis presents design, application, implementation, and evaluation of computation spaces as abstractions for programming constraint services at a high level. Spaces are seamlessly integrated into a concurrent programming language and make constraintbased computations compatible with concurrency through encapsulation. Spaces are applied
Constraint reasoning over strings
 In Proceedings of the 9th International Conference on the Principles and Practices of Constraint Programming
, 2003
"... Abstract. This paper discusses an approach to representing and reasoning about constraints over strings. We discuss how many string domains can often be concisely represented using regular languages, and how constraints over strings, and domain operations on sets of strings, can be carried out using ..."
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Cited by 20 (5 self)
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Abstract. This paper discusses an approach to representing and reasoning about constraints over strings. We discuss how many string domains can often be concisely represented using regular languages, and how constraints over strings, and domain operations on sets of strings, can be carried out using this representation. 1
Approximate Protein Folding in the HP Side Chain Model on Extended Cubic Lattices
 Lecture Notes in Computer Science 1643: Proceedings of the 7th Annual European Symposium on Algorithms
, 1998
"... One of the most important open problems in computational molecular biology is the prediction of the conformation of a protein based on its amino acid sequence. In this paper, we design approximation algorithms for structure prediction in the socalled HP side chain model. The major drawback of the s ..."
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Cited by 18 (0 self)
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One of the most important open problems in computational molecular biology is the prediction of the conformation of a protein based on its amino acid sequence. In this paper, we design approximation algorithms for structure prediction in the socalled HP side chain model. The major drawback of the standard HP side chain model is the bipartiteness of the cubic lattice. To eliminate this drawback, we introduce the extended cubic lattice which extends the cubic lattice by diagonals in the plane. For this lattice, we present two linear algorithms with approximation ratios of 59=70 and 37=42, respectively. The second algorithm is designed for a `natural' subclass of proteins, which covers more than 99:5% of all sequenced proteins. This is the first time that a protein structure prediction algorithm is designed for a `natural' subclass of all combinatorially possible sequences. ii 1 Introduction One of the most important open problems in molecular biology is the prediction of the spatial...
PSICO: Solving Protein Structures with Constraint Programming and Optimisation
 Constraints
, 2002
"... Abstract. In this paper we propose PSICO (Processing Structural Information with Constraint programming and Optimisation) as a constraintbased approach to determining protein structures compatible with distance constraints obtained from Nuclear Magnetic Resonance (NMR) data. We compare the performa ..."
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Cited by 17 (2 self)
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Abstract. In this paper we propose PSICO (Processing Structural Information with Constraint programming and Optimisation) as a constraintbased approach to determining protein structures compatible with distance constraints obtained from Nuclear Magnetic Resonance (NMR) data. We compare the performance of our proposed algorithm with DYANA ("Dynamics algorithm for NMR applications”) an existing commercial application based on simulated annealing. On a test case with experimental data on the dimeric protein Desulforedoxin, the method proposed here supplied similar results in less than 10 minutes compared to approximately 10 hours of computation time for DYANA. Although the quality of results can still be improved, this shows that CP technology can greatly reduce computation time, a major advantage because structural NMR technique generally demands multiple runs of structural computation.
Applying constraint programming to protein structure determination
 Principles and Practice of Constraint Programming
, 1999
"... Abstract. In this paper, we propose a constraintbased approach to determining protein structures compatible with distance constraints obtained from Nuclear Magnetic Resonance (NMR) data. We compare the performance of our proposed algorithm with DYANA ("Dynamics algorithm for NMR applicatio ..."
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Cited by 16 (4 self)
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Abstract. In this paper, we propose a constraintbased approach to determining protein structures compatible with distance constraints obtained from Nuclear Magnetic Resonance (NMR) data. We compare the performance of our proposed algorithm with DYANA (&quot;Dynamics algorithm for NMR applications ” [1]) an existing commercial application based on simulated annealing. For our test case, computation time for DYANA was more than six hours, whereas the method we propose produced similar results in 8 minutes, so we show that the application of Constraint Programming (CP) technology can greatly reduce computation time. This is a major advantage because this NMR technique generally demands multiple runs of structural computation. 1
Excluding Symmetries in Concurrent Constraint Programming
 In Proceedings of CP99, LNCS 1520
, 1998
"... Introduction In many problems (especially those concerned with combinatorial search), nondeterminism naturally arises in an concurrent constraintbased formulation in form of disjunctive constraints. To check consistency of disjunctive constraints, one needs to perform search by splitting the const ..."
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Cited by 11 (0 self)
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Introduction In many problems (especially those concerned with combinatorial search), nondeterminism naturally arises in an concurrent constraintbased formulation in form of disjunctive constraints. To check consistency of disjunctive constraints, one needs to perform search by splitting the constraint store into local computation stores. In formulizing disjunctive constraints, an important problem is to eliminate symmetries which arise from this kind of formulation. The symmetries give rise to many different solutions found by the search procedure, which are all considered to be "similar". Consider for example constraint problems, where finite domain variables have a geometric interpretation such as in the Nqueens problem or the squaretiling problem (where set of squares of given sizes must fit exactly into a fixed square). A newer and more complex problem is the lattice protein structure prediction problem [2]. In this case, different solutions are symmetric if they can be
An Upper Bound for Number of Contacts in the HPModel on the FaceCenteredCubic Lattice (FCC)
, 2000
"... . Lattice protein models are a major tool for investigating principles of protein folding. For this purpose, one needs an algorithm that is guaranteed to nd the minimal energy conformation in some lattice model (at least for some sequences). So far, there are only algorithm that can nd optimal c ..."
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Cited by 4 (2 self)
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. Lattice protein models are a major tool for investigating principles of protein folding. For this purpose, one needs an algorithm that is guaranteed to nd the minimal energy conformation in some lattice model (at least for some sequences). So far, there are only algorithm that can nd optimal conformations in the cubic lattice. In the more interesting case of the facecenteredcubic lattice (FCC), which is more proteinlike, there are no results. One of the reasons is that for nding optimal conformations, one usually applies a branchandbound technique, and there are no reasonable bounds known for the FCC. We will give such a bound for Dill's HPmodel on the FCC. 1 Introduction Simplied protein models such as lattice models are used to investigate the protein folding problem, the major unsolved problem in computational biology. An important representative of lattice models is the HPmodel, which has been introduced by [7]. In this model, the 20 letter alphabet of amino...