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148
Dynamic Bayesian Networks: Representation, Inference and Learning
, 2002
"... Modelling sequential data is important in many areas of science and engineering. Hidden Markov models (HMMs) and Kalman filter models (KFMs) are popular for this because they are simple and flexible. For example, HMMs have been used for speech recognition and biosequence analysis, and KFMs have bee ..."
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Cited by 563 (3 self)
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Modelling sequential data is important in many areas of science and engineering. Hidden Markov models (HMMs) and Kalman filter models (KFMs) are popular for this because they are simple and flexible. For example, HMMs have been used for speech recognition and biosequence analysis, and KFMs have been used for problems ranging from tracking planes and missiles to predicting the economy. However, HMMs
and KFMs are limited in their “expressive power”. Dynamic Bayesian Networks (DBNs) generalize HMMs by allowing the state space to be represented in factored form, instead of as a single discrete random variable. DBNs generalize KFMs by allowing arbitrary probability distributions, not just (unimodal) linearGaussian. In this thesis, I will discuss how to represent many different kinds of models as DBNs, how to perform exact and approximate inference in DBNs, and how to learn DBN models from sequential data.
In particular, the main novel technical contributions of this thesis are as follows: a way of representing
Hierarchical HMMs as DBNs, which enables inference to be done in O(T) time instead of O(T 3), where T is the length of the sequence; an exact smoothing algorithm that takes O(log T) space instead of O(T); a simple way of using the junction tree algorithm for online inference in DBNs; new complexity bounds on exact online inference in DBNs; a new deterministic approximate inference algorithm called factored frontier; an analysis of the relationship between the BK algorithm and loopy belief propagation; a way of
applying RaoBlackwellised particle filtering to DBNs in general, and the SLAM (simultaneous localization
and mapping) problem in particular; a way of extending the structural EM algorithm to DBNs; and a variety of different applications of DBNs. However, perhaps the main value of the thesis is its catholic presentation of the field of sequential data modelling.
A column approximate minimum degree ordering algorithm
, 2000
"... Sparse Gaussian elimination with partial pivoting computes the factorization PAQ = LU of a sparse matrix A, where the row ordering P is selected during factorization using standard partial pivoting with row interchanges. The goal is to select a column preordering, Q, based solely on the nonzero patt ..."
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Cited by 251 (50 self)
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Sparse Gaussian elimination with partial pivoting computes the factorization PAQ = LU of a sparse matrix A, where the row ordering P is selected during factorization using standard partial pivoting with row interchanges. The goal is to select a column preordering, Q, based solely on the nonzero pattern of A such that the factorization remains as sparse as possible, regardless of the subsequent choice of P. The choice of Q can have a dramatic impact on the number of nonzeros in L and U. One scheme for determining a good column ordering for A is to compute a symmetric ordering that reduces fillin in the Cholesky factorization of ATA. This approach, which requires the sparsity structure of ATA to be computed, can be expensive both in
The NPcompleteness column: an ongoing guide
 Journal of Algorithms
, 1985
"... 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 ..."
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Cited by 188 (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
Processor verification using efficient reductions of the logic of uninterpreted functions to propositional logic
 ACM Transactions on Computational Logic
, 1999
"... The logic of equality with uninterpreted functions (EUF) provides a means of abstracting the manipulation of data by a processor when verifying the correctness of its control logic. By reducing formulas in this logic to propositional formulas, we can apply Boolean methods such as Ordered Binary Deci ..."
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Cited by 90 (24 self)
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The logic of equality with uninterpreted functions (EUF) provides a means of abstracting the manipulation of data by a processor when verifying the correctness of its control logic. By reducing formulas in this logic to propositional formulas, we can apply Boolean methods such as Ordered Binary Decision Diagrams (BDDs) and Boolean satisfiability checkers to perform the verification. We can exploit characteristics of the formulas describing the verification conditions to greatly simplify the propositional formulas generated. We identify a class of terms we call "pterms" for which equality comparisons can only be used in monotonically positive formulas. By applying suitable abstractions to the hardware model, we can express the functionality of data values and instruction addresses flowing through an instruction pipeline with pterms. A decision procedure can exploit the restricted uses of pterms by considering only "maximally diverse" interpretations of the associated function symbols...
Decomposing Constraint Satisfaction Problems Using Database Techniques
, 1994
"... There is a very close relationship between constraint satisfaction problems and the satisfaction of joindependencies in a relational database which is due to a common underlying structure, namely a hypergraph. By making that relationship explicit we are able to adapt techniques previously developed ..."
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Cited by 82 (20 self)
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There is a very close relationship between constraint satisfaction problems and the satisfaction of joindependencies in a relational database which is due to a common underlying structure, namely a hypergraph. By making that relationship explicit we are able to adapt techniques previously developed for the study of relational databases to obtain new results for constraint satisfaction problems. In particular, we prove that a constraint satisfaction problem may be decomposed into a number of subproblems precisely when the corresponding hypergraph satisfies a simple condition. We show that combining this decomposition approach with existing algorithms can lead to a significant improvement in efficiency.
Implementation of Interior Point Methods for Large Scale Linear Programming
 in Interior Point Methods in Mathematical Programming
, 1996
"... In the past 10 years the interior point methods (IPM) for linear programming have gained extraordinary interest as an alternative to the sparse simplex based methods. This has initiated a fruitful competition between the two types of algorithms which has lead to very efficient implementations on bot ..."
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Cited by 69 (22 self)
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In the past 10 years the interior point methods (IPM) for linear programming have gained extraordinary interest as an alternative to the sparse simplex based methods. This has initiated a fruitful competition between the two types of algorithms which has lead to very efficient implementations on both sides. The significant difference between interior point and simplex based methods is reflected not only in the theoretical background but also in the practical implementation. In this paper we give an overview of the most important characteristics of advanced implementations of interior point methods. First, we present the infeasibleprimaldual algorithm which is widely considered the most efficient general purpose IPM. Our discussion includes various algorithmic enhancements of the basic algorithm. The only shortcoming of the "traditional" infeasibleprimaldual algorithm is to detect a possible primal or dual infeasibility of the linear program. We discuss how this problem can be solve...
Four Strikes against Physical Mapping of DNA
 JOURNAL OF COMPUTATIONAL BIOLOGY
, 1993
"... Physical Mapping is a central problem in molecular biology ... and the human genome project. The problem is to reconstruct the relative position of fragments of DNA along the genome from information on their pairwise overlaps. We show that four simplified models of the problem lead to NPcomplete ..."
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Cited by 55 (8 self)
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Physical Mapping is a central problem in molecular biology ... and the human genome project. The problem is to reconstruct the relative position of fragments of DNA along the genome from information on their pairwise overlaps. We show that four simplified models of the problem lead to NPcomplete decision problems: Colored unit interval graph completion, the maximum interval (or unit interval) subgraph, the pathwidth of a bipartite graph, and the kconsecutive ones problem for k >= 2. These models have been chosen to reflect various features typical in biological data, including false negative and positive errors, small width of the map and chimericism.
Fast and Effective Algorithms for Graph Partitioning and Sparse Matrix Ordering
 IBM JOURNAL OF RESEARCH AND DEVELOPMENT
, 1996
"... Graph partitioning is a fundamental problem in several scientific and engineering applications. In this paper, we describe heuristics that improve the stateoftheart practical algorithms used in graphpartitioning software in terms of both partitioning speed and quality. An important use of graph ..."
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Cited by 54 (11 self)
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Graph partitioning is a fundamental problem in several scientific and engineering applications. In this paper, we describe heuristics that improve the stateoftheart practical algorithms used in graphpartitioning software in terms of both partitioning speed and quality. An important use of graphpartitioning is in ordering sparse matrices for obtaining direct solutions to sparse systems of linear equations arising in engineering and optimization applications. The experiments reported in this paper show that the use of these heuristics results in a considerable improvement in the quality of sparsematrix orderings over conventional ordering methods, especially for sparse matrices arising in linear programming problems. In addition, our graphpartitioningbased ordering algorithm is more parallelizable than minimumdegreebased ordering algorithms, and it renders the ordered matrix more amenable to parallel factorization.
Probabilistic argumentation systems
 Handbook of Defeasible Reasoning and Uncertainty Management Systems, Volume 5: Algorithms for Uncertainty and Defeasible Reasoning
, 2000
"... Different formalisms for solving problems of inference under uncertainty have been developed so far. The most popular numerical approach is the theory of Bayesian inference [42]. More general approaches are the DempsterShafer theory of evidence [51], and possibility theory [16], which is closely re ..."
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Cited by 53 (33 self)
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Different formalisms for solving problems of inference under uncertainty have been developed so far. The most popular numerical approach is the theory of Bayesian inference [42]. More general approaches are the DempsterShafer theory of evidence [51], and possibility theory [16], which is closely related to fuzzy systems.
Approximating Treewidth, Pathwidth, Frontsize, and Shortest Elimination Tree
, 1995
"... Various parameters of graphs connected to sparse matrix factorization and other applications can be approximated using an algorithm of Leighton et al. that finds vertex separators of graphs. The approximate values of the parameters, which include minimum front size, treewidth, pathwidth, and minimum ..."
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Cited by 52 (4 self)
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Various parameters of graphs connected to sparse matrix factorization and other applications can be approximated using an algorithm of Leighton et al. that finds vertex separators of graphs. The approximate values of the parameters, which include minimum front size, treewidth, pathwidth, and minimum elimination tree height, are no more than O(logn) (minimum front size and treewidth) and O(log^2 n) (pathwidth and minimum elimination tree height) times the optimal values. In addition, we show that unless P = NP there are no absolute approximation algorithms for any of the parameters.