Predicting the 3D structure of protein chains from the linear sequence of amino acids is a fundamental open problem in computational molecular biology [1]. Any approach to the problem must deal with the basic fact that protein structures are translation and rotation invariant. To address this invariance, we have proposed a machine learning approach to protein structure prediction [4] based on the predic- tion of topological representations of proteins, in the form of contact or distance maps. The contact or distance map is a 2D representation of neighborhood rela- tionships consisting of an adjacency matrix at some distance cuto(cid:11) (typically in the range of 6 to 12 (cid:23)A), or a matrix of pairwise Euclidean distances. Fine-grained maps are derived at the amino acid or even atomic level. Coarse maps are obtained by looking at secondary structure elements, such as helices, and the distance between their centers of gravity or, as in the simulations below, the minimal distances be- tween their C(cid:11) atoms.

We describe a method for computing provably exact maximum a poste- riori (MAP) estimates for a subclass of problems on graphs with cycles. The basic idea is to represent the original problem on the graph with cy- cles as a convex combination of tree-structured problems. A convexity argument then guarantees that the optimal value of the original problem (i.e., the log probability of the MAP assignment) is upper bounded by 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 opti- mal configuration in common. An important implication is that any such shared configuration must also be the MAP configuration for the original problem.

Spontaneous facial expressions differ substan- tially from posed expressions, similar to how continuous, spontaneous speech differs from isolated words produced on command. Previous methods for automatic facial expression recognition assumed images were collected in controlled environments in which the subjects delib- erately faced the camera. Since people often nod or turn their heads, automatic recognition of spontaneous facial behavior requires methods for handling out-of-image-plane head rotations. Here we explore an ap- proach based on 3-D warping of images into canonical views. We eval- uated the performance of the approach as a front-end for a spontaneous expression recognition system using support vector machines and hidden Markov models.

The information bottleneck (IB) method is an information-theoretic formulation, this method constructs for clustering problems. Given a joint distribution a new variable that are informative . Maximum likelihood (ML) of mixture models is a standard statistical about approach to clustering problems. In this paper, we ask: how are the two methods related? We define a simple mapping between the IB problem and the ML prob- lem for the multinomial mixture model.

We propose a dynamic Bayesian model for motifs in biopolymer se- quences which captures rich biological prior knowledge and positional dependencies in motif structure in a principled way. Our model posits that the position-specific multinomial parameters for monomer distribu- tion are distributed as a latent Dirichlet-mixture random variable, and the position-specific Dirichlet component is determined by a hidden Markov process. Model parameters can be fit on training motifs using a vari- ational EM algorithm within an empirical Bayesian framework. Varia- tional inference is also used for detecting hidden motifs. Our model im- proves over previous models that ignore biological priors and positional dependence.

In this paper, we propose a Bayesian framework, which constructs shared-state triphone HMMs based on a variational Bayesian approach, and recognizes speech based on the Bayesian prediction classi(cid:2)cation; variational Bayesian estimation and clustering for speech recognition (VBEC). An appropriate model structure with high recognition perfor- mance can be found within a VBEC framework. Unlike conventional methods, including BIC or MDL criterion based on the maximum likeli- hood approach, the proposed model selection is valid in principle, even when there are insuf(cid:2)cient amounts of data, because it does not use an asymptotic assumption. In isolated word recognition experiments, we show the advantage of VBEC over conventional methods, especially when dealing with small amounts of data.

Standard value function approaches to finding policies for Partially Observable Markov Decision Processes (POMDPs) are intractable for large models. The in- tractability of these algorithms is due to a great extent to their generating an optimal policy over the entire belief space. However, in real POMDP problems most belief states are unlikely, and there is a structured, low-dimensional manifold of plausible beliefs embedded in the high-dimensional belief space. We introduce a new method for solving large-scale POMDPs by taking advantage of belief space sparsity. We reduce the dimensionality of the belief space by exponential family Principal Components Analysis [1], which allows us to turn the sparse, high- dimensional belief space into a compact, low-dimensional representation in terms of learned features of the belief state.

In recent years variational methods have become a popular tool for approximate inference and learning in a wide variety of proba- bilistic models. For each new application, however, it is currently necessary (cid:12)rst to derive the variational update equations, and then to implement them in application-speci(cid:12)c code. Each of these steps is both time consuming and error prone. In this paper we describe a general purpose inference engine called VIBES ('Variational Infer- ence for Bayesian Networks') which allows a wide variety of proba- bilistic models to be implemented and solved variationally without recourse to coding. New models are speci(cid:12)ed either through a simple script or via a graphical interface analogous to a drawing package.

The Bayesian paradigm provides a natural and effective means of exploit- ing prior knowledge concerning the time-frequency structure of sound signals such as speech and music--something which has often been over- looked in traditional audio signal processing approaches. Here, after con- structing a Bayesian model and prior distributions capable of taking into account the time-frequency characteristics of typical audio waveforms, we apply Markov chain Monte Carlo methods in order to sample from the resultant posterior distribution of interest. We present speech enhance- ment results which compare favourably in objective terms with standard time-varying filtering techniques (and in several cases yield superior per- formance, both objectively and subjectively); moreover, in contrast to such methods, our results are obtained without an assumption of prior knowledge of the noise power.

We argue that human inductive generalization is best explained in a Bayesian framework, rather than by traditional models based on simi- larity computations. We go beyond previous work on Bayesian concept learning by introducing an unsupervised method for constructing flex- ible hypothesis spaces, and we propose a version of the Bayesian Oc- cam's razor that trades off priors and likelihoods to prevent under- or over-generalization in these flexible spaces. We analyze two published data sets on inductive reasoning as well as the results of a new behavioral study that we have carried out.