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154
MolProbity: allatom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res 35: W375–383
, 2007
"... and nucleic acids ..."
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 231 (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
AND/OR Search Spaces for Graphical Models
, 2004
"... The paper introduces an AND/OR search space perspective for graphical models that include probabilistic networks (directed or undirected) and constraint networks. In contrast to the traditional (OR) search space view, the AND/OR search tree displays some of the independencies present in the gr ..."
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Cited by 122 (47 self)
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The paper introduces an AND/OR search space perspective for graphical models that include probabilistic networks (directed or undirected) and constraint networks. In contrast to the traditional (OR) search space view, the AND/OR search tree displays some of the independencies present in the graphical model explicitly and may sometime reduce the search space exponentially. Indeed, most
Efficient and Constructive Algorithms for the Pathwidth and Treewidth of Graphs
, 1993
"... In this paper we give, for all constants k, l, explicit algorithms, that given a graph G = (V; E) with a treedecomposition of G with treewidth at most l, decide whether the treewidth (or pathwidth) of G is at most k, and if so, find a treedecomposition or (pathdecomposition) of G of width at most ..."
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Cited by 75 (13 self)
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In this paper we give, for all constants k, l, explicit algorithms, that given a graph G = (V; E) with a treedecomposition of G with treewidth at most l, decide whether the treewidth (or pathwidth) of G is at most k, and if so, find a treedecomposition or (pathdecomposition) of G of width at most k, and that use O(V) time. In contrast with previous solutions, our algorithms do not rely on nonconstructive reasoning, and are single exponential in k and l. This result can be combined with a result of Reed [37], yielding explicit O(n log n) algorithms for the problem, given a graph G, to determine whether the treewidth (or pathwidth) of G is at most k, and if so, to find a tree (or path)decomposition of width at most k (k constant). Also, Bodlaender [13] has used the result of this paper to obtain linear time algorithms for these problems. We also show that for all constants k, there exists a polynomial time algorithm, that, when given a graph G = (V; E) with treewidth k, computes the pathwidth of G and a minimum path decomposition of G.
Structured Programs have Small TreeWidth and Good Register Allocation
 Information and Computation
, 1995
"... The register allocation problem for an imperative program is often modelled as the coloring problem of the interference graph of the controlflow graph of the program. The interference graph of a flow graph G is the intersection graph of some connected subgraphs of G. These connected subgraphs repre ..."
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Cited by 66 (1 self)
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The register allocation problem for an imperative program is often modelled as the coloring problem of the interference graph of the controlflow graph of the program. The interference graph of a flow graph G is the intersection graph of some connected subgraphs of G. These connected subgraphs represent the lives, or life times, of variables, so the coloring problem models that two variables with overlapping life times should be in different registers. For general programs with unrestricted gotos, the interference graph can be any graph, and hence we cannot in general color within a factor O(n " ) from optimality unless NP=P. It is shown that if a graph has treewidth k, we can efficiently color any intersection graph of connected subgraphs within a factor (bk=2c + 1) from optimality. Moreover, it is shown that structured (j gotofree) programs, including, for example, short circuit evaluations and multiple exits from loops, have treewidth at most 6. Thus, for every structured progr...
Tractability of Parameterized Completion Problems on Chordal, Strongly Chordal and Proper Interval Graphs
, 1994
"... We study the parameterized complexity of three NPhard graph completion problems. The MINIMUM FILLIN problem is to decide if a graph can be triangulated by adding at most k edges. We develop O(c m) and O(k mn + f(k)) algorithms for this problem on a graph with n vertices and m edges. Here f(k ..."
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Cited by 58 (5 self)
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We study the parameterized complexity of three NPhard graph completion problems. The MINIMUM FILLIN problem is to decide if a graph can be triangulated by adding at most k edges. We develop O(c m) and O(k mn + f(k)) algorithms for this problem on a graph with n vertices and m edges. Here f(k) is exponential in k and the constants hidden by the bigO notation are small and do not depend on k. In particular, this implies that the problem is fixedparameter tractable (FPT). The PROPER
Combinatorial Optimization on Graphs of Bounded Treewidth
, 2007
"... There are many graph problems that can be solved in linear or polynomial time with a dynamic programming algorithm when the input graph has bounded treewidth. For combinatorial optimization problems, this is a useful approach for obtaining fixedparameter tractable algorithms. Starting from trees an ..."
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Cited by 51 (4 self)
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There are many graph problems that can be solved in linear or polynomial time with a dynamic programming algorithm when the input graph has bounded treewidth. For combinatorial optimization problems, this is a useful approach for obtaining fixedparameter tractable algorithms. Starting from trees and seriesparallel graphs, we introduce the concepts of treewidth and tree decompositions, and illustrate the technique with the Weighted Independent Set problem as an example. The paper surveys some of the latest developments, putting an emphasis on applicability, on algorithms that exploit tree decompositions, and on algorithms that determine or approximate treewidth and find tree decompositions with optimal or close to optimal treewidth. Directions for further research and suggestions for further reading are also given.
Treewidth: Computational Experiments
, 2001
"... Many NPhard graph problems can be solved in polynomial time for graphs with bounded treewidth. Equivalent results are known for pathwidth and branchwidth. In recent years, several studies have shown that this result is not only of theoretical interest but can successfully be applied to find (almost ..."
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Cited by 46 (9 self)
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Many NPhard graph problems can be solved in polynomial time for graphs with bounded treewidth. Equivalent results are known for pathwidth and branchwidth. In recent years, several studies have shown that this result is not only of theoretical interest but can successfully be applied to find (almost) optimal solutions or lower bounds for many optimization problems. To apply a tree decomposition approach, the treewidth of the graph has to be determined, independently of the application at hand. Although for fixed k, linear time algorithms exist to solve the decision problem “treewidth < k”, their practical use is very limited. The computational tractability of treewidth has been rarely studied so far. In this paper, we compare four heuristics and two lower bounds for instances from applications such as the frequency assignment problem and the vertex coloring problem. Three of the heuristics are based on wellknown algorithms to recognize triangulated graphs. The fourth heuristic recursively improves a tree decomposition by the computation of minimal separating vertex sets in subgraphs. Lower bounds can be computed from maximal cliques and the minimum degree of induced subgraphs. A computational analysis shows that the treewidth of several graphs can be identified by these methods. For other graphs, however, more sophisticated techniques are necessary.
Star Coloring of Graphs
, 2001
"... A star coloring of an undirected graph G is a proper vertex coloring of G (i.e., no two neighbors are assigned the same color) such that any path of length 3 in G is not bicolored. The star ..."
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Cited by 42 (1 self)
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A star coloring of an undirected graph G is a proper vertex coloring of G (i.e., no two neighbors are assigned the same color) such that any path of length 3 in G is not bicolored. The star
Shortest Paths in Digraphs of Small Treewidth. Part I: Sequential Algorithms
, 1995
"... We consider the problem of preprocessing an nvertex digraph with real edge weights so that subsequent queries for the shortest path or distance between any two vertices can be efficiently answered. We give algorithms that depend on the treewidth of the input graph. When the treewidth is a consta ..."
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Cited by 39 (4 self)
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We consider the problem of preprocessing an nvertex digraph with real edge weights so that subsequent queries for the shortest path or distance between any two vertices can be efficiently answered. We give algorithms that depend on the treewidth of the input graph. When the treewidth is a constant, our algorithms can answer distance queries in O(ff(n)) time after O(n) preprocessing. This improves upon previously known results for the same problem. We also give a dynamic algorithm which, after a change in an edge weight, updates the data structure in time O(n fi ), for any constant 0 ! fi ! 1. Furthermore, an algorithm of independent interest is given: computing a shortest path tree, or finding a negative cycle in linear time.