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.

Important inference problems in statistical physics, computer vision, error-correcting coding theory, and artificial intelligence can all be reformulated as the computation of marginal probabilities on factor graphs. The belief propagation (BP) algorithm is an efficient way to solve these problems that is exact when the factor graph is a tree, but only approximate when the factor graph has cycles. We show that BP fixed points correspond to the stationary points of the Bethe approximation of the free energy for a factor graph. We explain how to obtain regionbased free energy approximations that improve the Bethe approximation, and corresponding generalized belief propagation (GBP) algorithms. We emphasize the conditions a free energy approximation must satisfy in order to be a “valid ” or “maxent-normal ” approximation. We describe the relationship between four different methods that can be used to generate valid approximations: the “Bethe method, ” the “junction graph method, ” the “cluster variation method, ” and the “region graph method.” Finally, we explain how to tell whether a region-based approximation, and its corresponding GBP algorithm, is likely to be accurate, and describe empirical results showing that GBP can significantly outperform BP.

In applications of graphical models arising in fields such as computer vision, the hidden variables of interest are most naturally specified by continuous, non--Gaussian distributions. However, due to the limitations of existing inf#6F6F3 algorithms, it is of#]k necessary tof#3# coarse, discrete approximations to such models. In this paper, we develop a nonparametric belief propagation (NBP) algorithm, which uses stochastic methods to propagate kernel--based approximations to the true continuous messages. Each NBP message update is based on an efficient sampling procedure which can accomodate an extremely broad class of potentialf#l3]k[[z3 allowing easy adaptation to new application areas. We validate our method using comparisons to continuous BP for Gaussian networks, and an application to the stereo vision problem.

The Bayes Net Toolbox (BNT) is an open-source Matlab package for directed graphical models. BNT supports many kinds of nodes (probability distributions), exact and approximate inference, parameter and structure learning, and static and dynamic models. BNT is widely used in teaching and research: the web page has received over 28,000 hits since May 2000. In this paper, we discuss a broad spectrum of issues related to graphical models (directed and undirected), and describe, at a high-level, how BNT was designed to cope with them all. We also compare BNT to other software packages for graphical models, and to the nascent OpenBayes effort.

this paper, we propose a Bayesian theory of hierarchical cortical computation based both on (a) the mathematical and computational ideas of computer vision and pattern the- ory and on (b) recent neurophysiological experimental evidence. We ,2 have proposed that Grenander's pattern theory 3 could potentially model the brain as a generafive model in such a way that feedback serves to disambiguate and 'explain away' the earlier representa- tion. The Helmholtz machine 4, 5 was an excellent step towards approximating this proposal, with feedback implementing priors. Its development, however, was rather limited, dealing only with binary images. Moreover, its feedback mechanisms were engaged only during the learning of the feedforward connections but not during perceptual inference, though the Gibbs sampling process for inference can potentially be interpreted as top-down feedback disambiguating low level representations? Rao and Ballard's predictive coding/Kalman filter model 6 did integrate generafive feedback in the perceptual inference process, but it was primarily a linear model and thus severely limited in practical utility. The data-driven Markov Chain Monte Carlo approach of Zhu and colleagues 7, 8 might be the most successful recent application of this proposal in solving real and difficult computer vision problems using generafive models, though its connection to the visual cortex has not been explored. Here, we bring in a powerful and widely applicable paradigm from artificial intelligence and computer vision to propose some new ideas about the algorithms of visual cortical process- ing and the nature of representations in the visual cortex. We will review some of our and others' neurophysiological experimental data to lend support to these ideas

We develop an approach for computing provably exact maximum a posteriori (MAP) configurations for a subclass of problems on graphs with cycles. By decomposing the original problem into a convex combination of tree-structured problems, we obtain an upper bound on the optimal value of the original problem (i.e., the log probability of the MAP assignment) in terms of the combined optimal values of the tree problems. We prove that this upper bound is met with equality if and only if the tree problems share an optimal configuration in common. An important implication is that any such shared configuration must also be a MAP configuration for the original problem. Next we present and analyze two methods for attempting to obtain tight upper bounds: (a) a tree-reweighted messagepassing algorithm that is related to but distinct from the max-product (min-sum) algorithm; and (b) a tree-relaxed linear program (LP), which is derived from the Lagrangian dual of the upper bounds. Finally, we discuss the conditions that govern when the relaxation is tight, in which case the MAP configuration can be obtained. The analysis described here generalizes naturally to convex combinations of hypertree-structured distributions.

We develop and analyze methods for computing provably optimal maximum a posteriori (MAP) configurations for a subclass of Markov random fields defined on graphs with cycles. By decomposing the original distribution into a convex combination of tree-structured distributions, we obtain an upper bound on the optimal value of the original problem (i.e., the log probability of the MAP assignment) in terms of the combined optimal values of the tree problems. We prove that this upper bound is tight if and only if all the tree distributions share an optimal configuration in common. An important implication is that any such shared configuration must also be a MAP configuration for the original distribution. Next we develop two approaches to attempting to obtain tight upper bounds: (a) a tree-relaxed linear program (LP), which is derived from the Lagrangian dual of the upper bounds; and (b) a tree-reweighted max-product messagepassing algorithm that is related to but distinct from the max-product algorithm. In this way, we establish a connection between a certain LP relaxation of the modefinding problem, and a reweighted form of the max-product (min-sum) message-passing algorithm.

We present a tree-based reparameterization framework that provides a new conceptual view of a large class of algorithms for computing approximate marginals in graphs with cycles. This class includes the belief propagation or sum-product algorithm [39, 36], as well as a rich set of variations and extensions of belief propagation. Algorithms in this class can be formulated as a sequence of reparameterization updates, each of which entails re-factorizing a portion of the distribution corresponding to an acyclic subgraph (i.e., a tree). The ultimate goal is to obtain an alternative but equivalent factorization using functions that represent (exact or approximate) marginal distributions on cliques of the graph. Our framework highlights an important property of BP and the entire class of reparameterization algorithms: the distribution on the full graph is not changed. The perspective of tree-based updates gives rise to a simple and intuitive characterization of the fixed points in terms of tree consistency. We develop interpretations of these results in terms of information geometry. The invariance of the distribution, in conjunction with the fixed point characterization, enables us to derive an exact relation between the exact marginals on an arbitrary graph with cycles, and the approximations provided by belief propagation, and more broadly, any algorithm that minimizes the Bethe free energy. We also develop bounds on this approximation error, which illuminate the conditions that govern their accuracy. Finally, we show how the reparameterization perspective extends naturally to more structured approximations (e.g., Kikuchi and variants [52, 37]) that operate over higher order cliques.

Probabilistic models have been adopted for many computer vision applications, however inference in highdimensional spaces remains problematic. As the statespace of a model grows, the dependencies between the dimensions lead to an exponential growth in computation when performing inference. Many common computer vision problems naturally map onto the graphical model framework; the representation is a graph where each node contains a portion of the state-space and there is an edge between two nodes only if they are not independent conditional on the other nodes in the graph. When this graph is sparsely connected, belief propagation algorithms can turn an exponential inference computation into one which is linear in the size of the graph. However belief propagation is only applicable when the variables in the nodes are discrete-valued or jointly represented by a single multivariate Gaussian distribution, and this rules out many computer vision applications.

We present an unsupervised algorithm for registering 3D surface scans of an object undergoing significant deformations. Our algorithm does not need markers, nor does it assume prior knowledge about object shape, the dynamics of its deformation, or scan alignment. The algorithm registers two meshes by optimizing a joint probabilistic model over all point-topoint correspondences between them. This model enforces preservation of local mesh geometry, as well as more global constraints that capture the preservation of geodesic distance between corresponding point pairs. The algorithm applies even when one of the meshes is an incomplete range scan; thus, it can be used to automatically fill in the remaining surfaces for this partial scan, even if those surfaces were previously only seen in a different configuration. We evaluate the algorithm on several real-world datasets, where we demonstrate good results in the presence of significant movement of articulated parts and non-rigid surface deformation. Finally, we show that the output of the algorithm can be used for compelling computer graphics tasks such as interpolation between two scans of a non-rigid object and automatic recovery of articulated object models. 1