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27
An Efficient Exact Algorithm for Constraint Bipartite Vertex Cover
"... The "Constraint Bipartite Vertex Cover" problem (CBVC for short) is: given a bipartite graph G with n vertices and two positive integers k 1 ; k 2 , is there a vertex cover taking at most k 1 vertices from one and at most k 2 vertices from the other vertex set of G? CBVC is NPcomplete. It formalize ..."
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Cited by 9 (3 self)
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The "Constraint Bipartite Vertex Cover" problem (CBVC for short) is: given a bipartite graph G with n vertices and two positive integers k 1 ; k 2 , is there a vertex cover taking at most k 1 vertices from one and at most k 2 vertices from the other vertex set of G? CBVC is NPcomplete. It formalizes the spare allocation problem for reconfigurable arrays, an important problem from VLSI manufacturing.
Distributed Sparse Gaussian Elimination And Orthogonal Factorization
 LAPACK WORKING NOTE 64 (UT CS93203)
, 1993
"... We consider the solution of a linear system Ax = b on a distributed memory machine when the matrix A has full rank and is large, sparse and nonsymmetric. We use our Cartesian nested dissection algorithm to compute a fillreducing column ordering of the matrix. We develop algorithms that use the asso ..."
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Cited by 8 (3 self)
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We consider the solution of a linear system Ax = b on a distributed memory machine when the matrix A has full rank and is large, sparse and nonsymmetric. We use our Cartesian nested dissection algorithm to compute a fillreducing column ordering of the matrix. We develop algorithms that use the associated separator tree to estimate the structure of the factor and to distribute and perform numeric computations. When the matrix is nonsymmetric but square, the numeric computations involve Gaussian elimination with row pivoting; when the matrix is overdetermined, roworiented Householder transforms are applied to compute the triangular factor of an orthogonal factorization. We compare the fill incurred by our approach to that incurred by well known sequential methods and report on the performance of our implementation on the Intel iPSC/860.
NPHardness of the Stable Matrix in Unit Interval Family Problem in Discrete Time
 Systems and Control Letters
, 2001
"... We show that to determine if a family of matrices, each with parameters in the unit interval, contains a matrix with all eigenvalues inside the unit circle is an NPhard problem. We also discuss how this problem is closely related to the widespread problem of power control in wireless systems. keywo ..."
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Cited by 8 (4 self)
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We show that to determine if a family of matrices, each with parameters in the unit interval, contains a matrix with all eigenvalues inside the unit circle is an NPhard problem. We also discuss how this problem is closely related to the widespread problem of power control in wireless systems. keywords: Complexity, NPhardness. 1 1
RealTime Properties of Indirect Recursive Porcedures
, 1996
"... The purpose of this paper is to show that indirect recursive procedures can be used for implementing realtime applications without harm, if a few conditions are met. These conditions ensure that upper bounds for space and time requirements can be derived at compile time. Moreover they are simpl ..."
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Cited by 7 (1 self)
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The purpose of this paper is to show that indirect recursive procedures can be used for implementing realtime applications without harm, if a few conditions are met. These conditions ensure that upper bounds for space and time requirements can be derived at compile time. Moreover they are simple enough such that many important recursive algorithms can be implemented. In addition
Some Prospects for Efficient Fixed Parameter Algorithms
 In Proc. of the 25th Conference on Current Trends in Theory and Practice of Informatics (SOFSEM’98), Springer, LNCS 1521
, 1998
"... Recent time has seen quite some progress in the development of exponential time algorithms for NPhard problems, where the base of the exponential term is fairly small. These developments are also tightly related to the theory of fixed parameter tractability. In this incomplete survey, we explain so ..."
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Cited by 6 (0 self)
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Recent time has seen quite some progress in the development of exponential time algorithms for NPhard problems, where the base of the exponential term is fairly small. These developments are also tightly related to the theory of fixed parameter tractability. In this incomplete survey, we explain some basic techniques in the design of efficient fixed parameter algorithms, discuss deficiencies of parameterized complexity theory, and try to point out some future research challenges. The focus of this paper is on the design of efficient algorithms and not on a structural theory of parameterized complexity. Moreover, our emphasis will be laid on two exemplifying issues: Vertex Cover and MaxSat problems. A shorter version of this paper appears as an invited talk in the proceedings of the 25th Conference on Current Trends in Theory and Practice of Informatics (SOFSEM'98), Springer, LNCS , held in Jasna, Slovakia, November 2127, 1998. y Supported by a Feodor Lynen fellowship of the Alex...
A linear time algorithm for finding a maximal planar subgraph based on PCtrees
 of Lecture Notes in Computer Science
, 2005
"... ABSTRACT. Given an undirected graph G, the maximal planar subgraph problem is to determine a planar subgraph H of G such that no edge of GH can be added to H without destroying planarity. Polynomial algorithms have been obtained by Jakayumar, Thulasiraman and Swamy [6] and Wu [9]. O(mlogn) algorith ..."
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Cited by 5 (0 self)
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ABSTRACT. Given an undirected graph G, the maximal planar subgraph problem is to determine a planar subgraph H of G such that no edge of GH can be added to H without destroying planarity. Polynomial algorithms have been obtained by Jakayumar, Thulasiraman and Swamy [6] and Wu [9]. O(mlogn) algorithms were previously given by Di Battista and Tamassia [3] and Cai, Han and Tarjan [2]. A recent O(mα (n)) algorithm was obtained by La Poute [7]. Our algorithm is based on a simple planarity test [5] developed by the author, which is a vertex addition algorithm based on a depthfirstsearch ordering. The planarity test [5] uses no complicated data structure and is conceptually simpler than Hopcroft and Tarjan's path addition and Lempel, Even and Cederbaum's vertex addition approaches. 1 1.
Structural pattern matching of nonribosomal peptides
 BMC STRUCTURAL BIOLOGY  METHODOLOGY ARTICLE
, 2009
"... Background
Nonribosomal peptides (NRPs), bioactive secondary metabolites produced by many microorganisms, show a broad range of important biological activities (e.g. antibiotics, immunosuppressants, antitumor agents). NRPs are mainly composed of amino acids but their primary structure is not always ..."
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Background
Nonribosomal peptides (NRPs), bioactive secondary metabolites produced by many microorganisms, show a broad range of important biological activities (e.g. antibiotics, immunosuppressants, antitumor agents). NRPs are mainly composed of amino acids but their primary structure is not always linear and can contain cycles or branchings. Furthermore, there are several hundred different monomers that can be incorporated into NRPs. The NORINE database, the first resource entirely dedicated to NRPs, currently stores more than 700 NRPs annotated with their monomeric peptide structure encoded by undirected labeled graphs. This opens a way to a systematic analysis of structural patterns occurring in NRPs. Such studies can investigate the functional role of some monomeric chains, or analyse NRPs that have been computationally predicted from the synthetase protein sequence. A basic operation in such analyses is the search for a given structural pattern in the database.
Results
We developed an efficient method that allows for a quick search for a structural pattern in the NORINE database. The method identifies all peptides containing a pattern substructure of a given size. This amounts to solving a variant of the maximum common subgraph problem on pattern and peptide graphs, which is done by computing cliques in an appropriate compatibility graph.
Conclusion
The method has been incorporated into the NORINE database, available at http://bioinfo.lifl.fr/norine. Less than one second is needed to search for a pattern in the entire database.
Maintenance of 2 and 3Connected Components of Graphs, Part I: 2 and 3EdgeConnected Components
, 1990
"... In this paper a data structure is presented to efficiently maintain the 2and 3edgeconnected components of a graph, under insertions of edges in the graph. Starting from an "empty" graph of n nodes, the insertion of e edges takes O(nlogn[ e) time in total. The data structure allows for inserti ..."
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Cited by 4 (0 self)
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In this paper a data structure is presented to efficiently maintain the 2and 3edgeconnected components of a graph, under insertions of edges in the graph. Starting from an "empty" graph of n nodes, the insertion of e edges takes O(nlogn[ e) time in total. The data structure allows for insertions of nodes also (in the same time bounds, taking n as the final number of nodes).
OnLine Graphics Recognition: StateoftheArt
 in GREC 2003: 5th IAPR International Workshop on Graphics Recognition, 2003
, 2003
"... A brief survey on online graphics recognition is presented. We first present some common scenarios and applications of online graphics recognition and then identify major problems and subproblems at three levels: primitive shape recognition, composite graphic object recognition, and document ..."
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A brief survey on online graphics recognition is presented. We first present some common scenarios and applications of online graphics recognition and then identify major problems and subproblems at three levels: primitive shape recognition, composite graphic object recognition, and document recognition and understanding. Representative approaches to these problems are also presented. We also list several open problems at the end.
An efficient implementation of the PCtrees algorithm of shih and hsu’s planarity test
 Institute of Information Science, Academia Sinica
, 2003
"... In Shih & Hsu [9] a simpler planarity test was introduced utilizing a data structure called PCtrees (generalized from PQtrees). In this paper we give an efficient implementation of that linear time algorithm and illustrate in detail how to obtain a Kuratowski subgraph when the given graph is not p ..."
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Cited by 3 (0 self)
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In Shih & Hsu [9] a simpler planarity test was introduced utilizing a data structure called PCtrees (generalized from PQtrees). In this paper we give an efficient implementation of that linear time algorithm and illustrate in detail how to obtain a Kuratowski subgraph when the given graph is not planar, and how to obtain the embedding alongside the testing algorithm. We have implemented the algorithm using LEDA and an object code is available at