The bootstrap has become a popular method for exploring model (structure) uncertainty. Our experiments with artificial and realworld data demonstrate that the graphs learned from bootstrap samples can be severely biased towards too complex graphical models. Accounting for 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 between the expected test and training errors of a graphical model, which asymptotically equals Akaike's penalty (rather than one half).

In this paper we present Discriminative Random Fields (DRF), a discriminative framework for the classification of natural image regions by incorporating neighborhood spatial dependencies in the labels as well as the observed data. The proposed model exploits local discriminative models and allows to relax the assumption of conditional independence of the observed data given the labels, commonly used in the Markov Random Field (MRF) framework. The parameters of the DRF model are learned using penalized maximum pseudo-likelihood method. Furthermore, the form of the DRF model allows the MAP inference for binary classification problems using the graph min-cut algorithms. The performance of the model was verified on the synthetic as well as the real-world images. The DRF model outperforms the MRF model in the experiments.

A general linear response method for deriving improved estimates of correlations in the variational Bayes framework is presented. Three applications are given and it is discussed how to use linear response as a general principle for improving mean field approximations.

Existing source location and recovery algorithms used in magnetoencephalographic imaging generally assume that the source activity at different brain locations is independent or that the correlation structure is known. However, electrophysiological recordings of local field potentials show strong correlations in aggregate activity over significant distances. Indeed, it seems very likely that stimulus-evoked activity would follow strongly correlated time-courses in different brain areas. Here, we present, and validate through simulations, a new approach to source reconstruction in which the correlation between sources is modelled and estimated explicitly by variational Bayesian methods, facilitating accurate recovery of source locations and the time-courses of their activation.

In the problem of probability forecasting the learner's goal is to output, given a training set and a new object, a suitable probability measure on the possible values of the new object's label. An online algorithm for probability forecasting is said to be well-calibrated if the probabilities it outputs agree with the observed frequencies. We give a natural nonasymptotic formalization of the notion of well-calibratedness, which we then study under the assumption of randomness (the object/label pairs are independent and identically distributed). It turns out that, although no probability forecasting algorithm is automatically well-calibrated in our sense, there exists a wide class of algorithms for "multiprobability forecasting" (such algorithms are allowed to output a set, ideally very narrow, of probability measures) which satisfy this property; we call the algorithms in this class "Venn probability machines". Our experimental results demonstrate that a 1-Nearest Neighbor Venn probability machine performs reasonably well on a standard benchmark data set, and one of our theoretical results asserts that a simple Venn probability machine asymptotically approaches the true conditional probabilities regardless, and without knowledge, of the true probability measure generating the examples.

The purpose of this paper is to investigate infinity-sample properties of risk minimization based multi-category classification methods. These methods can be considered as natural extensions to binary large margin classification. We establish conditions that guarantee the infinity-sample consistency of classifiers obtained in the risk minimization framework. Examples are provided for two specific forms of the general formulation, which extend a number of known methods. Using these examples, we show that some risk minimization formulations can also be used to obtain conditional probability estimates for the underlying problem. Such conditional probability information will be useful for statistical inferencing tasks beyond classification.

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 from the labeled examples. We test our approach on eight real-world datasets.

When we model a higher order functions, such as learning and memory, we face a difficulty of comparing neural activities with hidden variables that depend on the history of sensory and motor signals and the dynamics of the network. Here, we propose novel method for estimating hidden variables of a learning agent, such as connection weights from sequences of observable variables. Bayesian estimation is a method to estimate the posterior probability of hidden variables from observable data sequence using a dynamic model of hidden and observable variables. In this paper, we apply particle filter for estimating internal parameters and metaparameters of a reinforcement learning model. We verified the effectiveness of the method using both artificial data and real animal behavioral data.

Loopy belief propagation (BP) has been successfully used in a number of difficult graphical models to find the most probable configuration of the hidden variables. In applications ranging from protein folding to image analysis one would like to find not just the best configuration but rather the top M. While this problem has been solved using the junction tree formalism, in many real world problems the clique size in the junction tree is prohibitively large. In this work we address the problem of finding the M best configurations when exact inference is impossible. We start by developing a new exact inference algorithm for calculating the best configurations that uses only max-marginals. For approximate inference, we replace the max-marginals with the beliefs calculated using max-product BP and generalized BP. We show empirically that the algorithm can accurately and rapidly approximate the M best configurations in graphs with hundreds of variables.

In this paper we obtain convergence bounds for the concentration of Bayesian posterior distributions (around the true distribution) using a novel method that simplifies and enhances previous results. Based on the analysis, we also introduce a generalized family of Bayesian posteriors, and show that the convergence behavior of these generalized posteriors is completely determined by the local prior structure around the true distribution. This important and surprising robustness property does not hold for the standard Bayesian posterior in that it may not concentrate when there exist "bad" prior structures even at places far away from the true distribution.