We propose a dynamic Bayesian model for motifs in biopolymer sequences 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 distribution 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 variational EM algorithm within an empirical Bayesian framework. Variational inference is also used for detecting hidden motifs. Our model improves over previous models that ignore biological priors and positional dependence. It has much higher sensitivity to motifs during detection and a notable ability to distinguish genuine motifs from false recurring patterns.

We present an account of human concept learning-that is, learning of categories from examples-based on the principle of minimum description length (MDL). In support of this theory, we tested a wide range of two-dimensional concept types, including both regular (simple) and highly irregular (complex) structures, and found the MDL theory to give a good account of subjects' performance. This suggests that the intrinsic complexity ofa concept (that is, its description -length) systematically influences its leamability.

In recent years variational methods have become a popular tool for approximate inference and learning in a wide variety of probabilistic models. For each new application, however, it is currently necessary first to derive the variational update equations, and then to implement them in application-specific 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 Inference for Bayesian Networks') which allows a wide variety of probabilistic models to be implemented and solved variationally without recourse to coding. New models are specified either through a simple script or via a graphical interface analogous to a drawing package. VIBES then automatically generates and solves the variational equations. We illustrate the power and flexibility of VIBES using examples from Bayesian mixture modelling.

Classification trees are one of the most popular types of classifiers, with ease of implementation and interpretation being among their attractive features. Despite the widespread use of classification trees, theoretical analysis of their performance is scarce. In this paper, we show that a new family of classification trees, called dyadic classification trees (DCTs), are near optimal (in a minimax sense) for a very broad range of classification problems. This demonstrates that other schemes (e.g., neural networks, support vector machines) cannot perform significantly better than DCTs in many cases. We also show that this near optimal performance is attained with linear (in the number of training data) complexity growing and pruning algorithms. Moreover, the performance of DCTs on benchmark datasets compares favorably to that of standard CART, which is generally more computationally intensive and which does not possess similar near optimality properties. Our analysis stems from theoretical results on structural risk minimization, on which the pruning rule for DCTs is based.

The extraction of a single high-quality image from a set of lowresolution images is an important problem which arises in fields such as remote sensing, surveillance, medical imaging and the extraction of still images from video. Typical approaches are based on the use of cross-correlation to register the images followed by the inversion of the transformation from the unknown high resolution image to the observed low resolution images, using regularization to resolve the ill-posed nature of the inversion process. In this paper we develop a Bayesian treatment of the super-resolution problem in which the likelihood function for the image registration parameters is based on a marginalization over the unknown high-resolution image. This approach allows us to estimate the unknown point spread function, and is rendered tractable through the introduction of a Gaussian process prior over images. Results indicate a significant improvement over techniques based on MAP (maximum a-posteriori) point optimization of the high resolution image and associated registration parameters. 1 Introduction The task in super-resolution is to combine a set of low resolution images of the same scene in order to obtain a single image of higher resolution. Provided the individual low resolution images have sub-pixel displacements relative to each other, it is possible to extract high frequency details of the scene well beyond the Nyquist limit of the individual source images.

Identity uncertainty is a pervasive problem in real-world data analysis. It arises whenever objects are not labeled with unique identifiers or when those identifiers may not be perceived perfectly. In such cases, two observations may or may not correspond to the same object. In this paper, we consider the problem in the context of citation matching--the problem of deciding which citations correspond to the same publication. Our approach is based on the use of a relational probability model to define a generative model for the domain, including models of author and title corruption and a probabilistic citation grammar. Identity uncertainty is handled by extending standard models to incorporate probabilities over the possible mappings between terms in the language and objects in the domain. Inference is based on Markov chain Monte Carlo, augmented with specific methods for generating efficient proposals when the domain contains many objects. Results on several citation data sets show that the method outperforms current algorithms for citation matching. The declarative, relational nature of the model also means that our algorithm can determine object characteristics such as author names by combining multiple citations of multiple papers.

People routinely make sophisticated causal inferences unconsciously, effortlessly, and from very little data - often from just one or a few observations. We argue that these inferences can be explained as Bayesian computations over a hypothesis space of causal graphical models, shaped by strong top-down prior knowledge in the form of intuitive theories.

We focus on the problem of efficient learning of dependency trees. It is well-known that given the pairwise mutual information coefficients, a minimum-weight spanning tree algorithm solves this problem exactly and in polynomial time. However, for large data-sets it is the construction of the correlation matrix that dominates the running time. We have developed a new spanning-tree algorithm which is capable of exploiting partial knowledge about edge weights. The partial knowledge we maintain is a probabilistic confidence interval on the coefficients, which we derive by examining just a small sample of the data. The algorithm is able to flag the need to shrink an interval, which translates to inspection of more data for the particular attribute pair. Experimental results show running time that is near-constant in the number of records, without significant loss in accuracy of the generated trees. Interestingly, our spanning-tree algorithm is based solely on Tarjan's red-edge rule, which is generally considered a guaranteed recipe for bad performance.

Accurate representation of articulated motion is a challenging problem for machine perception. Several successful tracking algorithms have been developed that model human body as an articulated tree. We propose a learning-based method for creating such articulated models from observations of multiple rigid motions. This paper is concerned with recovering topology of the articulated model, when the rigid motion of constituent segments is known. Our approach is based on finding the Maximum Likelihood tree shaped factorization of the joint probability density function (PDF) of rigid segment motions. The topology of graphical model formed from this factorization corresponds to topology of the underlying articulated body. We demonstrate the performance of our algorithm on both synthetic and real motion capture data.

Missing data is common in real-world datasets and is a problem for many estimation techniques. We have developed a variational Bayesian method to perform Independent Component Analysis (ICA) on high-dimensional data containing missing entries. Missing data are handled naturally in the Bayesian framework by integrating the generative density model. Modeling the distributions of the independent sources with mixture of Gaussians allows sources to be estimated with different kurtosis and skewness. The variational Bayesian method automatically determines the dimensionality of the data and yields an accurate density model for the observed data without overfitting problems. This allows direct probability estimation of missing values in the high dimensional space and avoids dimension reduction preprocessing which is not feasible with missing data.