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MolProbity: allatom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35: W375–383
, 2007
"... and nucleic acids ..."
The monadic secondorder logic of graphs I. Recognizable sets of Finite Graphs
 Information and Computation
, 1990
"... The notion of a recognizable sef offinite graphs is introduced. Every set of finite graphs, that is definable in monadic secondorder logic is recognizable, but not vice versa. The monadic secondorder theory of a contextfree set of graphs is decidable. 0 19W Academic Press. Inc. This paper begins ..."
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Cited by 298 (17 self)
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The notion of a recognizable sef offinite graphs is introduced. Every set of finite graphs, that is definable in monadic secondorder logic is recognizable, but not vice versa. The monadic secondorder theory of a contextfree set of graphs is decidable. 0 19W Academic Press. Inc. This paper begins an investigation of the monadic secondorder logic of graphs and of sets of graphs, using techniques from universal algebra, and the theory of formal languages. (By a graph, we mean a finite directed hyperedgelabelled hypergraph, equipped with a sequence of distinguished vertices.) A survey of this research can be found in Courcelle [ 111. An algebraic structure on the set of graphs (in the above sense) has been proposed by Bauderon and Courcelle [2,7]. The notion of a recognizable set of finite graphs follows, as an instance of the general notion of recognizability introduced by Mezei and Wright in [25]. A graph can also be considered as a logical structure of a certain type. Hence, properties of graphs can be written in firstorder logic or in secondorder logic. It turns out that monadic secondorder logic, where quantifications over sets of vertices and sets of edges are used, is a reasonably powerful logical language (in which many usual graph properties can be written), for which one can obtain decidability results. These decidability results do not hold for secondorder logic, where quantifications over binary relations can also be used. Our main theorem states that every definable set of finite graphs (i.e., every set that is the set of finite graphs satisfying a graph property expressible in monadic secondorder logic) is recognizable. * This work has been supported by the “Programme de Recherches Coordonntes: Mathematiques et Informatique.”
The NPcompleteness column: an ongoing guide
 JOURNAL OF ALGORITHMS
, 1987
"... This is the nineteenth edition of a (usually) quarterly column that covers new developments in the theory of NPcompleteness. The presentation is modeled on that used by M. R. Garey and myself in our book "Computers and Intractability: A Guide to the Theory of NPCompleteness," W. H. Freem ..."
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Cited by 242 (0 self)
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This is the nineteenth edition of a (usually) quarterly column that covers new developments in the theory of NPcompleteness. The presentation is modeled on that used by M. R. Garey and myself in our book "Computers and Intractability: A Guide to the Theory of NPCompleteness," W. H. Freeman & Co., New York, 1979 (hereinafter referred to as "[G&J]"; previous columns will be referred to by their dates). A background equivalent to that provided by [G&J] is assumed, and, when appropriate, crossreferences will be given to that book and the list of problems (NPcomplete and harder) presented there. Readers who have results they would like mentioned (NPhardness, PSPACEhardness, polynomialtimesolvability, etc.) or open problems they would like publicized, should
Algorithms For Vertex Partitioning Problems On Partial kTrees
, 1997
"... In this paper, we consider a large class of vertex partitioning problems and apply to those the theory of algorithm design for problems restricted to partial ktrees. We carefully describe the details of algorithms and analyze their complexity in an attempt to make the algorithms feasible as solutio ..."
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Cited by 56 (5 self)
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In this paper, we consider a large class of vertex partitioning problems and apply to those the theory of algorithm design for problems restricted to partial ktrees. We carefully describe the details of algorithms and analyze their complexity in an attempt to make the algorithms feasible as solutions for practical applications.
Computational properties of argument systems satisfying graphtheoretic constraints
 Artificial Intelligence
, 2007
"... One difficulty that arises in abstract argument systems is that many natural questions regarding argument acceptability are, in general, computationally intractable having been classified as complete for classes such as NP, coNP, and ¢¡ £. In consequence, a number of researchers have considered me ..."
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Cited by 50 (9 self)
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One difficulty that arises in abstract argument systems is that many natural questions regarding argument acceptability are, in general, computationally intractable having been classified as complete for classes such as NP, coNP, and ¢¡ £. In consequence, a number of researchers have considered methods for specialising the structure of such systems so as to identify classes for which efficient decision processes exist. In this paper the effect of a number of graphtheoretic restrictions is considered: ¤partite systems (¤¦¥¨ § ) in which the set of arguments may be partitioned into ¤ sets each of which is conflictfree; systems in which the numbers of attacks originating from and made upon any argument are bounded; planar systems; and, finally, those of ¤bounded treewidth. For the class of bipartite graphs, it is shown that determining the acceptability status of a specific argument can be accomplished in polynomialtime under both credulous and sceptical semantics. In addition we establish the existence of polynomial time methods for systems having bounded treewidth when deciding the following: whether a given (set of) arguments is credulously accepted; if the system has a nonempty preferred extension; has a stable extension; is coherent;
kNLC Graphs and Polynomial Algorithms
"... We introduce the class of knode label controlled (kNLC) graphs and the class of kNLC trees. Each kNLC graph is an undirected treestructured graph, where k is a positive integer. The class of kNLC trees is a proper subset of the class of kNLC graphs. Both classes include many interesting gr ..."
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Cited by 42 (2 self)
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We introduce the class of knode label controlled (kNLC) graphs and the class of kNLC trees. Each kNLC graph is an undirected treestructured graph, where k is a positive integer. The class of kNLC trees is a proper subset of the class of kNLC graphs. Both classes include many interesting graph families. For instance, each partial ktree is a (2 k+1 1)NLC tree and each cograph is a 1NLC graph. Furthermore, we introduce a very general method for the design of polynomial algorithms for NPcomplete graph problems, where the input graphs are restricted to treestructured graphs. We exemplify our method with the simple maxcut problem and the Hamiltonian circuit property on kNLC graphs.
Width parameters beyond treewidth and their applications
 Computer Journal
, 2007
"... Besides the very successful concept of treewidth (see [Bodlaender, H. and Koster, A. (2007) Combinatorial optimisation on graphs of bounded treewidth. These are special issues on Parameterized Complexity]), many concepts and parameters measuring the similarity or dissimilarity of structures compare ..."
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Cited by 40 (0 self)
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Besides the very successful concept of treewidth (see [Bodlaender, H. and Koster, A. (2007) Combinatorial optimisation on graphs of bounded treewidth. These are special issues on Parameterized Complexity]), many concepts and parameters measuring the similarity or dissimilarity of structures compared to trees have been born and studied over the past years. These concepts and parameters have proved to be useful tools in many applications, especially in the design of efficient algorithms. Our presented novel look at the contemporary developments of these ‘width ’ parameters in combinatorial structures delivers—besides traditional treewidth and derived dynamic programming schemes—also a number of other useful parameters like branchwidth, rankwidth (cliquewidth) or hypertreewidth. In this contribution, we demonstrate how ‘width ’ parameters of graphs and generalized structures (such as matroids or hypergraphs), can be used to improve the design of parameterized algorithms and the structural analysis in other applications on an abstract level.
Fixedparameter algorithms for artificial intelligence, constraint satisfaction, and database problems
, 2007
"... We survey the parameterized complexity of problems that arise in artificial intelligence, database theory and automated reasoning. In particular, we consider various parameterizations of the constraint satisfaction problem, the evaluation problem of Boolean conjunctive database queries and the propo ..."
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Cited by 31 (10 self)
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We survey the parameterized complexity of problems that arise in artificial intelligence, database theory and automated reasoning. In particular, we consider various parameterizations of the constraint satisfaction problem, the evaluation problem of Boolean conjunctive database queries and the propositional satisfiability problem. Furthermore, we survey parameterized algorithms for problems arising in the context of the stable model semantics of logic programs, for a number of other problems of nonmonotonic reasoning, and for the computation of cores in data exchange.
I/Oefficient algorithms for graphs of bounded treewidth
 In Proceedings of the 12th Annual ACMSIAM Symposium on Discrete Algorithms (SODA’2001
, 2001
"... We present an algorithm that takes O(sort(N)) I/Os 1 to compute a tree decomposition of width at most k, for any graph G of treewidth at most k and size N. Given such a tree decomposition, we use a dynamic programming framework to solve a wide variety of problems on G in O(N/(DB)) I/Os, including th ..."
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Cited by 16 (5 self)
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We present an algorithm that takes O(sort(N)) I/Os 1 to compute a tree decomposition of width at most k, for any graph G of treewidth at most k and size N. Given such a tree decomposition, we use a dynamic programming framework to solve a wide variety of problems on G in O(N/(DB)) I/Os, including the singlesource shortest path problem and a number of problems that are NPhard on general graphs. The tree decomposition can also be used to obtain an optimal separator decomposition of G. We use such a decomposition to perform depthfirst search in G in O(N/(DB)) I/Os. As important tools that are used in the tree decomposition algorithm, we introduce flippable DAGs and present an algorithm that computes a perfect elimination ordering of a ktree in O(sort(N)) I/Os. The second contribution of our paper, which is of independent interest, is a general and simple framework for obtaining I/Oefficient algorithms for a number of graph problems that can be solved using greedy algorithms in internal memory. We apply this framework in order to obtain an improved algorithm for finding a maximal matching and the first deterministic I/Oefficient algorithm for finding a maximal independent set of an arbitrary graph. Both algorithms take O(sort(V +E)) I/Os. The maximal matching algorithm is used in the tree decomposition algorithm.