Statistical applications in fields such as bioinformatics, information retrieval, speech processing, image processing and communications often involve large-scale models in which thousands or millions of random variables are linked in complex ways. Graphical models provide a general methodology for approaching these problems, and indeed many of the models developed by researchers in these applied fields are instances of the general graphical model formalism. We review some of the basic ideas underlying graphical models, including the algorithmic ideas that allow graphical models to be deployed in large-scale data analysis problems. We also present examples of graphical models in bioinformatics, error-control coding and language processing. Key words and phrases: Probabilistic graphical models, junction tree algorithm, sum-product algorithm, Markov chain Monte Carlo, variational inference, bioinformatics, error-control coding.

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 bio-sequence 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) linear-Gaussian. 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 Rao-Blackwellised 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.

The notion of treewidth has seen to be a powerful vehicle for many graph algorithmic studies. This survey paper wants to give an overview of many classes of graphs that can be seen to have a uniform upper bound on the treewidth of graphs in the class. Also, some mutual relations between such classes are discussed.

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This is the nineteenth edition of a (usually) quarterly column that covers new developments in the theory of NP-completeness. 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 NP-Completeness,’ ’ 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, cross-references will be given to that book and the list of problems (NP-complete and harder) presented there. Readers who have results they would like mentioned (NP-hardness, PSPACE-hardness, polynomial-time-solvability, etc.) or open problems they would like publicized, should

In this paper we study the properties of the class of head-cycle-free extended disjunctive logic programs (HEDLPs), which includes, as a special case, all nondisjunctive extended logic programs. We show that any propositional HEDLP can be mapped in polynomial time into a propositional theory such that each model of the latter corresponds to an answer set, as defined by stable model semantics, of the former. Using this mapping, we show that many queries over HEDLPs can be determined by solving propositional satisfiability problems. Our mapping has several important implications: It establishes the NP-completeness of this class of disjunctive logic programs; it allows existing algorithms and tractable subsets for the satisfiability problem to be used in logic programming; it facilitates evaluation of the expressive power of disjunctive logic programs; and it leads to the discovery of useful similarities between stable model semantics and Clark's predicate completion. 1 Introduction ...

A new method is proposed for exploiting causal independencies in exact Bayesian network inference.

This paper gives an overview of several results and techniques for graphs algorithms that compute the treewidth of a graph or that solve otherwise intractable problems when restricted graphs with bounded treewidth more efficiently. Also, several results on graph minors are reviewed.

In this paper, we describe an abstract framework and axioms under which exact local computation of marginals is possible. The primitive objects of the framework are variables and valuations. The primitive operators of the framework are combination and marginalization. These operate on valuations. We state three axioms for these operators and we derive the possibility of local computation from the axioms. Next, we describe a propagation scheme for computing marginals of a valuation when we have a factorization of the valuation on a hypertree. Finally we show how the problem of computing marginals of joint probability distributions and joint belief functions fits the general framework. 1.

The paper presents an algorithm called directional resolution, a variation on the original Davis-Putnam algorithm, and analyzes its worst-case behavior as a function of the topological structure of propositional theories. The concepts of induced width and diversity are shown to play a key role in bounding the complexity of the procedure. The importance of our analysis lies in highlighting structure-based tractable classes of satisfiability and in providing theoretical guarantees on the time and space complexity of the algorithm. Contrary to previous assessments, we show that for many theories directional resolution could be an effective procedure. Our empirical tests confirm theoretical prediction, showing that on problems with a special structure, namely k-tree embeddings (e.g. chains, (k,m)-trees), directional resolution greatly outperforms one of the most effective satisfiability algorithms known to date, the popular Davis-Putnam procedure. Furthermore, combining a bounded...