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.

In typical classification tasks, we seek a function which assigns a label to a single object. Kernel-based approaches, such as support vector machines (SVMs), which maximize the margin of confidence of the classifier, are the method of choice for many such tasks. Their popularity stems both from the ability to use high-dimensional feature spaces, and from their strong theoretical guarantees. However, many real-world tasks involve sequential, spatial, or structured data, where multiple labels must be assigned. Existing kernel-based methods ignore structure in the problem, assigning labels independently to each object, losing much useful information. Conversely, probabilistic graphical models, such as Markov networks, can represent correlations between labels, by exploiting problem structure, but cannot handle high-dimensional feature spaces, and lack strong theoretical generalization guarantees. In this paper, we present a new framework that combines the advantages of both approaches: Maximum margin Markov (M 3) networks incorporate both kernels, which efficiently deal with high-dimensional features, and the ability to capture correlations in structured data. We present an efficient algorithm for learning M 3 networks based on a compact quadratic program formulation. We provide a new theoretical bound for generalization in structured domains. Experiments on the task of handwritten character recognition and collective hypertext classification demonstrate very significant gains over previous approaches. 1

Declarative queries are proving to be an attractive paradigm for interacting with networks of wireless sensors. The metaphor that "the sensornet is a database" is problematic, however, because sensors do not exhaustively represent the data in the real world. In order to map the raw sensor readings onto physical reality, a model of that reality is required to complement the readings. In this paper, we enrich interactive sensor querying with statistical modeling techniques. We demonstrate that such models can help provide answers that are both more meaningful, and, by introducing approximations with probabilistic confidences, significantly more efficient to compute in both time and energy. Utilizing the combination of a model and live data acquisition raises the challenging optimization problem of selecting the best sensor readings to acquire, balancing the increase in the confidence of our answer against the communication and data acquisition costs in the network. We describe an exponential time algorithm for finding the optimal solution to this optimization problem, and a polynomial-time heuristic for identifying solutions that perform well in practice. We evaluate our approach on several real-world sensor-network data sets, taking into account the real measured data and communication quality, demonstrating that our model-based approach provides a high-fidelity representation of the real phenomena and leads to significant performance gains versus traditional data acquisition techniques.

Particle filters (PFs) are powerful sampling-based inference/learning algorithms for dynamic Bayesian networks (DBNs). They allow us to treat, in a principled way, any type of probability distribution, nonlinearity and non-stationarity. They have appeared in several fields under such names as “condensation”, “sequential Monte Carlo” and “survival of the fittest”. In this paper, we show how we can exploit the structure of the DBN to increase the efficiency of particle filtering, using a technique known as Rao-Blackwellisation. Essentially, this samples some of the variables, and marginalizes out the rest exactly, using the Kalman filter, HMM filter, junction tree algorithm, or any other finite dimensional optimal filter. We show that Rao-Blackwellised particle filters (RBPFs) lead to more accurate estimates than standard PFs. We demonstrate RBPFs on two problems, namely non-stationary online regression with radial basis function networks and robot localization and map building. We also discuss other potential application areas and provide references to some Þnite dimensional optimal filters.

Most current statistical natural language processing models use only local features so as to permit dynamic programming in inference, but this makes them unable to fully account for the long distance structure that is prevalent in language use. We show how to solve this dilemma with Gibbs sampling, a simple Monte Carlo method used to perform approximate inference in factored probabilistic models. By using simulated annealing in place of Viterbi decoding in sequence models such as HMMs, CMMs, and CRFs, it is possible to incorporate non-local structure while preserving tractable inference. We use this technique to augment an existing CRF-based information extraction system with long-distance dependency models, enforcing label consistency and extraction template consistency constraints. This technique results in an error reduction of up to 9 % over state-of-the-art systems on two established information extraction tasks. 1

We present a new part-of-speech tagger that demonstrates the following ideas: (i) explicit use of both preceding and following tag contexts via a dependency network representation, (ii) broad use of lexical features, including jointly conditioning on multiple consecutive words, (iii) effective use of priors in conditional loglinear models, and (iv) fine-grained modeling of unknown word features. Using these ideas together, the resulting tagger gives a 97.24% accuracy on the Penn Treebank WSJ, an error reduction of 4.4% on the best previous single automatically learned tagging result.

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.

Simultaneous Localization and Mapping (SLAM) is a fundamental problem in mobile robotics: while a robot navigates in an unknown environment, it must incrementally build a map of its surroundings and localize itself within that map. Traditional approaches to the problem are based upon Kalman filters, but suffer from complexity issues: the size of the belief state and the time complexity of the filtering operation grow quadratically in the size of the map. This paper presents a filtering technique that maintains a tractable approximation of the filtered belief state as a thin junction tree. The junction tree grows under measurement and motion updates and is periodically "thinned" to remain tractable via efficient maximum likelihood projections. When applied to the SLAM problem, these thin junction tree filters have a linear-space belief state representation, and use a linear-time filtering operation. Further approximation can yield a constant-time filtering operation, at the expense of delaying the incorporation of observations into the majority of the map. Experiments on a suite of SLAM problems validate the approach.

Probabilistic databases have received considerable attention recently due to the need for storing uncertain data produced by many real world applications. The widespread use of probabilistic databases is hampered by two limitations: (1) current probabilistic databases make simplistic assumptions about the data (e.g., complete independence among tuples) that make it difficult to use them in applications that naturally produce correlated data, and (2) most probabilistic databases can only answer a restricted subset of the queries that can be expressed using traditional query languages. We address both these limitations by proposing a framework that can represent not only probabilistic tuples, but also correlations that may be present among them. Our proposed framework naturally lends itself to the possible world semantics thus preserving the precise query semantics extant in current probabilistic databases. We develop an efficient strategy for query evaluation over such probabilistic databases by casting the query processing problem as an inference problem in an appropriately constructed probabilistic graphical model. We present several optimizations specific to probabilistic databases that enable efficient query evaluation. We validate our approach by presenting an experimental evaluation that illustrates the effectiveness of our techniques at answering various queries using real and synthetic datasets. 1