Belief propagation (BP) is an increasingly popular method of perform- ing approximate inference on arbitrary graphical models. At times, even further approximations are required, whether from quantization or other simplified message representations or from stochastic approxima- tion methods. Introducing such errors into the BP message computations has the potential to adversely affect the solution obtained. We analyze this effect with respect to a particular measure of message error, and show bounds on the accumulation of errors in the system. This leads both to convergence conditions and error bounds in traditional and approximate BP message passing.

Alternative splicing (AS) is an important and frequent step in mammalian gene expression that allows a single gene to specify multiple products, and is crucial for the regulation of fundamental biological processes. The extent of AS regulation, and the mechanisms involved, are not well un- derstood. We have developed a custom DNA microarray platform for surveying AS levels on a large scale. We present here a generative model for the AS Array Platform (GenASAP) and demonstrate its utility for quantifying AS levels in different mouse tissues. Learning is performed using a variational expectation maximization algorithm, and the parame- ters are shown to correctly capture expected AS trends.

This paper analyzes generalization of the classic Rescorla-Wagner (R- W) learning algorithm and studies their relationship to Maximum Like- lihood estimation of causal parameters. We prove that the parameters of two popular causal models, P and P C, can be learnt by the same generalized linear Rescorla-Wagner (GLRW) algorithm provided gener- icity conditions apply. We characterize the fixed points of these GLRW algorithms and calculate the fluctuations about them, assuming that the input is a set of i.i.d. We describe how to determine convergence conditions and calculate conver- gence rates for the GLRW algorithms under these conditions.

It has been demonstrated that basic aspects of human visual motion per- ception are qualitatively consistent with a Bayesian estimation frame- work, 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 vari- ance, and that the prior distribution on velocity exhibits significantly heavier tails than a Gaussian, and approximately follows a power-law function.

In this paper we present a framework for using multi-layer per- ceptron (MLP) networks in nonlinear generative models trained by variational Bayesian learning. The nonlinearity is handled by linearizing it using a Gauss–Hermite quadrature at the hidden neu- rons. The method can be used to derive nonlinear coun- terparts for linear algorithms such as factor analysis, independent component/factor analysis and state-space models. This is demon- strated with a nonlinear factor analysis experiment in which even 20 sources can be estimated from a real world speech data set.

Log-concavity is an important property in the context of optimization, Laplace approximation, and sampling; Bayesian methods based on Gaus- sian 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 in- tensity 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.

We propose a new method for estimating intrinsic dimension of a dataset derived by applying the principle of maximum likelihood to the distances between close neighbors. We derive the estimator by a Poisson process approximation, assess its bias and variance theo- retically and by simulations, and apply it to a number of simulated and real datasets. We also show it has the best overall performance compared with two other intrinsic dimension estimators.

Choice-based conjoint analysis builds models of consumer preferences over products with answers gathered in questionnaires. Our main goal is to bring tools from the machine learning community to solve this prob- lem more efficiently. Thus, we propose two algorithms to quickly and accurately estimate consumer preferences. Conjoint analysis (also called trade-off analysis) is one of the most popular marketing re- search technique used to determine which features a new product should have, by conjointly measuring consumers trade-offs between discretized1 attributes. In this paper, we will fo- cus on the choice-based conjoint analysis (CBC) framework [11] since it is both widely used and realistic: at each question in the survey, the consumer is asked to choose one product from several.

We present a novel method for learning with Gaussian process regres- sion in a hierarchical Bayesian framework. In a first step, kernel matri- ces 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 Nystrom 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.

A new distance measure between probability density functions (pdfs) is introduced, which we refer to as the Laplacian pdf dis- tance. The Laplacian pdf distance exhibits a remarkable connec- tion to Mercer kernel based learning theory via the Parzen window technique for density estimation. In a kernel feature space defined by the eigenspectrum of the Laplacian data matrix, this pdf dis- tance is shown to measure the cosine of the angle between cluster mean vectors. The Laplacian data matrix, and hence its eigenspec- trum, can be obtained automatically based on the data at hand, by optimal Parzen window selection. We show that the Laplacian pdf distance has an interesting interpretation as a risk function connected to the probability of error.