The bootstrap has become a popular method for exploring model (structure) uncertainty. Our experiments with artificial and realworld datademonstrate that the graphs learned from bootstrap samples can be severely biased towards too complex graphical models. Accountingfor this bias is hence essential, e.g., when exploring model uncertainty. We find that this bias is intimately tied to (well-known) spurious dependences induced by the bootstrap. The leading-order bias-correction equals one half of Akaike's penalty for model complexity. We demonstrate the effect of this simple bias-correction in our experiments. We also relate this bias to the bias of the plugin estimator for entropy, as well as to the difference betweenthe expected test and training errors of a graphical model, which asymptotically equals Akaike's penalty (rather than one half).

We present a novel method for approximate inference in Bayesian models andregularized risk functionals. It is based on the propagation of mean and variance derived from the Laplace approximation of conditional probabilitiesin 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 itis 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 clustersof 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.

We consider the question of how well a given distribution can be approximated withprobabilistic 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 thethreshold 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. Andindeed, 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 componentanalysis (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 constrainsthe mappings to be linear the model is equivalent to PCA, we then extend the model by considering less restrictive covariance functions whichallow 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.

While the mixture approach is intriguing, neither of [8, 9] compare their model to other methods.

We describe a nonparametric Bayesian approach to generalizing from few labeled examples, guided by a larger set of unlabeled objects and the assumption of a latent tree-structure to the domain. The tree (or a distribution over trees) may be inferred using the unlabeled data. A prior over concepts generated by a mutation process on the inferred tree(s) allows efficient computation of the optimal Bayesian classification function fromthe labeled examples. We test our approach on eight real-world datasets.

Recently, relevance vector machines (RVM) have been fashioned from a sparse Bayesian learning (SBL) framework to perform supervised learning usinga weight prior that encourages sparsity of representation. The methodology incorporates an additional set of hyperparameters governing theprior, one for each weight, and then adopts a specific approximation tothe full marginalization over all weights and hyperparameters. Despite its empirical success however, no rigorous motivation for this particular approximation is currently available. To address this issue, we demonstrate that SBL can be recast as the application of a rigorous variational approximationto the full model by expressing the prior in a dual form. This formulation obviates the necessity of assuming any hyperpriors andleads to natural, intuitive explanations of why sparsity is achieved in practice.

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 structurein 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.