Protein interactions typically arise from a physical interaction of one or more small sites on the surface of the two proteins. Identifying these sites is very important for drug and protein design. In this paper, we propose a computational method based on probabilistic relational model that attempts to address this task using high-throughput protein interaction data and a set of short sequence motifs. We learn the model using the EM algorithm, with a branch-and-bound algorithm as an approximate inference for the E-step. Our method searches for motifs whose presence in a pair of interacting proteins can explain their observed interaction. It also tries to determine which motif pairs have high affinity, and can therefore lead to an interaction. We show that our method is more accurate than others at predicting new protein-protein interactions. More importantly, by examining solved structures of protein complexes, we find that 2/3 of the predicted active motifs correspond to actual interaction sites.

Classification algorithms typically induce population-wide models that are trained to perform well on average on expected future instances. We introduce a Bayesian framework for learning instance-specific models from data that are optimized to predict well for a particular instance. Based on this framework, we present a lazy instance-specific algorithm called ISA that performs selective model averaging over a restricted class of Bayesian networks. On experimental evaluation, this algorithm shows superior performance over model selection. We intend to apply such instance-specific algorithms to improve the performance of patient-specific predictive models induced from medical data.

We propose the hierarchical Dirichlet process (HDP), a nonparametric Bayesian model for clustering problems involving multiple groups of data. Each group of data is modeled with a mixture, with the number of components being open-ended and inferred automatically by the model. Further, components can be shared across groups, allowing dependencies across groups to be modeled effectively as well as conferring generalization to new groups. Such grouped clustering problems occur often in practice, e.g. in the problem of topic discovery in document corpora. We report experimental results on three text corpora showing the effective and superior performance of the HDP over previous models.

It has been demonstrated that basic aspects of human visual motion perception are qualitatively consistent with a Bayesian estimation framework, where the prior probability distribution on velocity favors slow speeds. Here, we present a refined probabilistic model that can account for the typical trial-to-trial variabilities observed in psychophysical speed perception experiments. We also show that data from such experiments can be used to constrain both the likelihood and prior functions of the model. Specifically, we measured matching speeds and thresholds in a two-alternative forced choice speed discrimination task. Parametric fits to the data reveal that the likelihood function is well approximated by a LogNormal distribution with a characteristic contrast-dependent variance, and that the prior distribution on velocity exhibits significantly heavier tails than a Gaussian, and approximately follows a power-law function.

Decision trees are surprisingly adaptive in three important respects: They automatically (1) adapt to favorable conditions near the Bayes decision boundary; (2) focus on data distributed on lower dimensional manifolds; (3) reject irrelevant features. In this paper we examine a decision tree based on dyadic splits that adapts to each of these conditions to achieve minimax optimal rates of convergence. The proposed classifier is the first known to achieve these optimal rates while being practical and implementable.

In the analysis of natural images, Gaussian scale mixtures (GSM) have been used to account for the statistics of filter responses, and to inspire hierarchical cortical representational learning schemes. GSMs pose a critical assignment problem, working out which filter responses were generated by a common multiplicative factor. We present a new approach to solving this assignment problem through a probabilistic extension to the basic GSM, and show how to perform inference in the model using Gibbs sampling. We demonstrate the efficacy of the approach on both synthetic and image data. Understanding the statistical structure of natural images is an important goal for visual neuroscience. Neural representations in early cortical areas decompose images (and likely other sensory inputs) in a way that is sensitive to sophisticated aspects of their probabilistic structure. This structure also plays a key role in methods for image processing and coding. A striking aspect of natural images that has reflections in both top-down and bottom-up modeling is coordination across nearby locations, scales, and orientations. From a topdown perspective, this structure has been modeled using what is known as a Gaussian Scale Mixture model (GSM).

We present a novel method for learning with Gaussian process regression in a hierarchical Bayesian framework. In a first step, kernel matrices on a fixed set of input points are learned from data using a simple and efficient EM algorithm. This step is nonparametric, in that it does not require a parametric form of covariance function. In a second step, kernel functions are fitted to approximate the learned covariance matrix using a generalized Nystr om method, which results in a complex, data driven kernel. We evaluate our approach as a recommendation engine for art images, where the proposed hierarchical Bayesian method leads to excellent prediction performance.

We present a semi-parametric latent variable model based technique for density modelling, dimensionality reduction and visualization. Unlike previous methods, we estimate the latent distribution non-parametrically which enables us to model data generated by an underlying low dimensional, multimodal distribution. In addition, we allow the components of latent variable models to be drawn from the exponential family which makes the method suitable for special data types, for example binary or count data. Simulations on real valued, binary and count data show favorable comparison to other related schemes both in terms of separating different populations and generalization to unseen samples.

Log-concavity is an important property in the context of optimization, Laplace approximation, and sampling; Bayesian methods based on Gaussian process priors have become quite popular recently for classification, regression, density estimation, and point process intensity estimation. Here we prove that the predictive densities corresponding to each of these applications are log-concave, given any observed data. We also prove that the likelihood is log-concave in the hyperparameters controlling the mean function of the Gaussian prior in the density and point process intensity estimation cases, and the mean, covariance, and observation noise parameters in the classification and regression cases; this result leads to a useful parameterization of these hyperparameters, indicating a suitably large class of priors for which the corresponding maximum a posteriori problem is log-concave. Introduction Bayesian methods based on Gaussian process priors have recently become quite popular for machine learning tasks (1). These techniques have enjoyed a good deal of theoretical examination, documenting their learning-theoretic (generalization) properties (2), and developing a variety of efficient computational schemes (e.g., (3-5), and references therein).

We discuss an identification framework for noisy speech mixtures. A block-based generative model is formulated that explicitly incorporates the time-varying harmonic plus noise (H N) model for a number of latent sources observed through noisy convolutive mixtures. All parameters including the pitches of the source signals, the amplitudes and phases of the sources, the mixing filters and the noise statistics are estimated by maximum likelihood, using an EMalgorithm. Exact averaging over the hidden sources is obtained using the Kalman smoother. We show that pitch estimation and source separation can be performed simultaneously. The pitch estimates are compared to laryngograph (EGG) measurements. Artificial and real room mixtures are used to demonstrate the viability of the approach. Intelligible speech signals are re-synthesized from the estimated H N models.