We present a novel method for approximate inference in Bayesian models and regularized risk functionals. It is based on the propagation of mean and variance derived from the Laplace approximation of conditional probabilities in factorizing distributions, much akin to Minka's Expectation Propagation. In the jointly normal case, it coincides with the latter and belief propagation, whereas in the general case, it provides an optimization strategy containing Support Vector chunking, the Bayes Committee Machine, and Gaussian Process chunking as special cases.

Discrete Fourier transforms and other related Fourier methods have been practically implementable due to the fast Fourier transform (FFT). However there are many situations where doing fast Fourier transforms without complete data would be desirable. In this paper it is recognised that formulating the FFT algorithm as a belief network allows suitable priors to be set for the Fourier coefficients. Furthermore efficient generalised belief propagation methods between clusters of four nodes enable the Fourier coefficients to be inferred and the missing data to be estimated in near to O(n log n) time, where n is the total of the given and missing data points. This method is compared with a number of common approaches such as setting missing data to zero or to interpolation. It is tested on generated data and for a Fourier analysis of a damaged audio signal.

Rao-Blackwellization is an approximation technique for probabilistic inference that flexibly combines exact inference with sampling. It is useful in models where conditioning on some of the variables leaves a simpler inference problem that can be solved tractably. This paper presents Sample Propagation, an efficient implementation of Rao-Blackwellized approximate inference for a large class of models. Sample Propagation tightly integrates sampling with message passing in a junction tree, and is named for its simple, appealing structure: it walks the clusters of a junction tree, sampling some of the current cluster's variables and then passing a message to one of its neighbors. We discuss the application of Sample Propagation to conditional Gaussian inference problems such as switching linear dynamical systems.

In models that define probabilities via energies, maximum likelihood learning typically involves using Markov Chain Monte Carlo to sample from the model's distribution. If the Markov chain is started at the data distribution, learning often works well even if the chain is only run for a few time steps [3]. But if the data distribution contains modes separated by regions of very low density, brief MCMC will not ensure that different modes have the correct relative energies because it cannot move particles from one mode to another. We show how to improve brief MCMC by allowing long-range moves that are suggested by the data distribution. If the model is approximately correct, these long-range moves have a reasonable acceptance rate.

In applying Hidden Markov Models to the analysis of massive data streams, it is often necessary to use an artificially reduced set of states; this is due in large part to the fact that the basic HMM estimation algorithms have a quadratic dependence on the size of the state set. We present algorithms that reduce this computational bottleneck to linear or near-linear time, when the states can be embedded in an underlying grid of parameters. This type of state representation arises in many domains; in particular, we show an application to traffic analysis at a high-volume Web site.

We describe a Markov chain method for sampling from the distribution of the hidden state sequence in a nonlinear dynamical system, given a sequence of observations. This method updates all states in the sequence simultaneously using an embedded Hidden Markov Model (HMM). An update begins with the creation of "pools" of candidate states at each time. We then define an embedded HMM whose states are indexes within these pools. Using a forward-backward dynamic programming algorithm, we can efficiently choose a state sequence with the appropriate probabilities from the exponentially large number of state sequences that pass through states in these pools. We illustrate the method in a simple one-dimensional example, and in an example showing how an embedded HMM can be used to in effect discretize the state space without any discretization error. We also compare the embedded HMM to a particle smoother on a more substantial problem of inferring human motion from 2D traces of markers.

We present an analysis of concentration-of-expectation phenomena in layered Bayesian networks that use generalized linear models as the local conditional probabilities. This framework encompasses a wide variety of probability distributions, including both discrete and continuous random variables. We utilize ideas from large deviation analysis and the delta method to devise and evaluate a class of approximate inference algorithms for layered Bayesian networks that have superior asymptotic error bounds and very fast computation time.

We consider the question of how well a given distribution can be approximated with probabilistic graphical models. We introduce a new parameter, effective treewidth, that captures the degree of approximability as a tradeoff between the accuracy and the complexity of approximation. We present a simple approach to analyzing achievable tradeoffs that exploits the threshold behavior of monotone graph properties, and provide experimental results that support the approach.

The E-step boils down to computing probabilities of the hidden variables given the observed variables (evidence) and current set of parameters. The M-step then, given these probabilities, yields a new set of parameters guaranteed to increase the likelihood. In Bayesian networks, that will be the focus of this article, the M-step is usually relatively straightforward. A complication may arise in the E-step, when computing the probability of the hidden variables given the evidence becomes intractable. An often used approach is to replace the exact yet intractable inference in the E step with approximate inference, either through sampling or using a deterministic variational method. The use of a "mean-field" variational method in this context leads to an algorithm known as variational EM and can be given theinterpretation of minimizing a free energy with respect to both a tractable approximate distribution (approximate E-step) and the parameters (M-step) [2]. Loopy belief propagation [3] and variants thereof, such as generalized belief propagation [4] and expectation propagation [5], have become popular alternatives to the "mean-field" variational approaches, often yielding somewhat better approximations. And indeed, they can and have been applied for approximate inference in the E-step of the EM algorithm (see e.g.

In this paper we introduce a new underlying probabilistic model for principal component analysis (PCA). Our formulation interprets PCA as a particular Gaussian process prior on a mapping from a latent space to the observed data-space. We show that if the prior's covariance function constrains the mappings to be linear the model is equivalent to PCA, we then extend the model by considering less restrictive covariance functions which allow nonlinear mappings. This more general Gaussian process latent variable model (GPLVM) is then evaluated as an approach to the visualisation of high dimensional data for three different data-sets. Additionally our nonlinear algorithm can be further kernelised leading to'twin kernel PCA' in which a mapping between feature spaces occurs.