Markov random fields (MRF's), or undirected graphical models, provide a powerful frameworkfor modeling complex dependencies among random variables. Maximum likelihood learning in MRF's is hard due to the presence of the global normalizing constant. In this paper we consider a class of stochastic approximation algorithmsof the Robbins-Monro type that use Markov chain Monte Carlo to do approximate maximum likelihood learning. We show that using MCMC operators basedon tempered transitions enables the stochastic approximation algorithm to better explore highly multimodal distributions, which considerably improves parameter estimates in large, densely-connected MRF's. Our results on MNIST and NORB datasets demonstrate that we can successfully learn good generative models of high-dimensional, richly structured data that perform well on digit and object recognition tasks.

Finding maximally sparse representations from overcomplete feature dictionaries frequently involves minimizing a cost function composed of a likelihood (or data fit) term and a prior (or penalty function) that favors sparsity. While typically the prior is factorial, here we examine non-factorial alternatives that have a number of desirable properties relevant to sparse estimation and are easily implemented using an efficient, globally-convergent reweighted $\ell_1$ minimization procedure. The first method under consideration arises from the sparse Bayesian learning (SBL) framework. Although based on a highly non-convex underlying cost function, in the context of canonical sparse estimation problems, we prove uniform superiority of this method over the Lasso in that, (i) it can never do worse, and (ii) for any dictionary and sparsity profile, there will always exist cases where it does better. These results challenge the prevailing reliance on strictly convex penalty functions for finding sparse solutions. We then derive a new non-factorial variant with similar properties that exhibits further performance improvements in empirical tests. For both of these methods, as well as traditional factorial analogs, we demonstrate the effectiveness of reweighted $\ell_1$-norm algorithms in handling more general sparse estimation problems involving classification, group feature selection, and non-negativity constraints. As a byproduct of this development, a rigorous reformulation of sparse Bayesian classification (e.g., the relevance vector machine) is derived that, unlike the original, involves no approximation steps and descends a well-defined objective function.

Imaging techniques such as optical imaging of intrinsic signals, 2-photon calcium imaging and voltage sensitive dye imaging can be used to measure the functional organization of visual cortex across different spatial scales. Here, we present Bayesian methods based on Gaussian processes for extracting topographic maps from functional imaging data. In particular, we focus on the estimation of orientation preference maps (OPMs) from intrinsic signal imaging data. We model the underlying map as a bivariate Gaussian process, with a prior covariance function that reflects known properties of OPMs, and a noise covariance adjusted to the data. The posterior mean can be interpreted as an optimally smoothed estimate of the map, and can be used for model based interpolations of the map from sparse measurements. By sampling from the posterior distribution, we can get error bars on statistical properties such as preferred orientations, pinwheel locations or -counts. Finally, the use of an explicit probabilistic model facilitates interpretation of parameters and provides the basis for decoding studies. We demonstrate our model both on simulated data and on intrinsic signaling data from ferret visual cortex.

Almost all successful machine learning algorithms and cognitive models require powerful representations capturing the features that are relevant to a particular problem. We draw on recent work in nonparametric Bayesian statistics to define a rational model of human feature learning that forms a featural representation from raw sensory data without pre-specifying the number of features. By comparing how the human perceptual system and our rational model use distributional and category information to infer feature representations, we seek to identify some of the forces that govern the process by which people separate and combine sensory primitives to form features.

We describe an application of probabilistic modeling and inference technology to the problem of analyzing sensor data in the setting of an intensive care unit (ICU). In particular, we consider the arterial-line blood pressure sensor, which is subject to frequent data artifacts that cause false alarms in the ICU and make the raw data almost useless for automated decision making. The problem is complicated by the fact that the sensor data are averaged over fixed intervals whereas the events causing data artifacts may occur at any time and often have durations significantly shorter than the data collection interval. We show that careful modeling of the sensor, combined with a general technique for detecting sub-interval events and estimating their duration, enables detection of artifacts and accurate estimation of the underlying blood pressure values. Our model's performance identifying artifacts is superior to two other classifiers' and about as good as a physician's.

We present the Gaussian Process Density Sampler (GPDS), an exchangeable generative model for use in nonparametric Bayesian density estimation. Samples drawn from the GPDS are consistent with exact, independent samples from a fixed density function that is a transformation of a function drawn from a Gaussian process prior. Our formulation allows us to infer an unknown density from data using Markov chain Monte Carlo, which gives samples from the posterior distribution over density functions and from the predictive distribution on data space. We can also infer the hyperparameters of the Gaussian process. We compare this density modeling technique to several existing techniques on a toy problem and a skull-reconstruction task.

We propose a novel application of Formal Concept Analysis (FCA) to neural decoding: insteadof just trying to figure out which stimulus was presented, we demonstrate how to explore the semantic relationships in the neural representation of large sets of stimuli. FCA provides a way of displaying and interpreting such relationships via concept lattices. We explore the effects of neural code sparsity on the lattice. We then analyze neurophysiological data from high-level visual cortical areaSTSa, using an exact Bayesian approach to construct the formal context needed by FCA. Prominent features of the resulting concept lattices are discussed, including hierarchical face representation and indications for a product-of-experts code in real neurons.

In a variety of behavioral tasks, subjects exhibit an automatic and apparently sub-optimal sequential effect: they respond more rapidly and accurately to a stimulus if it reinforces a local pattern in stimulus history, such as a string of repetitions or alternations, compared to when it violates such a pattern. This is often the case even if the local trends arise by chance in the context of a randomized design, such that stimulus history has no predictive power. In this work, we use a normative Bayesian framework to examine the hypothesis that such idiosyncrasies may reflect the inadvertent engagement of fundamental mechanisms critical for adapting to changing statistics in the natural environment. We show that prior belief in non-stationarity can induce experimentally observed sequential effects in an otherwise Bayes-optimal algorithm. The Bayesian algorithm is shown to be well approximated by linear-exponential filtering of past observations, a feature also apparent in the behavioral data. We derive an explicit relationship between the parameters and computations of the exact Bayesian algorithm and those of the approximate linear-exponential filter. Since the latter is equivalent to a leaky-integration process, a commonly used model of neuronal dynamics underlying perceptual decision-making and trial-to-trial dependencies, our model provides a principled account of why such dynamics are useful. We also show that near-optimal tuning of the leaky-integration process is possible, using stochastic gradient descent based only on the noisy binary inputs. This is a proof of concept that not only can neurons implement near-optimal prediction based on standard neuronal dynamics, but that they can also learn to tune the processing parameters without explicitly representing probabilities.

We propose a novel bound on single-variable marginal probability distributions in factor graphs with discrete variables. The bound is obtained by propagating local bounds (convex sets of probability distributions) over a subtree of the factor graph, rooted in the variable of interest. By construction, the method not only bounds the exact marginal probability distribution of a variable, but also its approximate Belief Propagation marginal ("belief"). Thus, apart from providing a practical means to calculate bounds on marginals, our contribution also lies in providing a better understanding of the error made by Belief Propagation. We show that our bound outperforms the state-of-the-art on some inference problems arising in medical diagnosis.

In cognitive science, empirical data collected from participants are the arbiters in model selection. Model discrimination thus depends on designing maximally informative experiments. It has been shown that adaptive design optimization (ADO) allows one to discriminate models as efficiently as possible in simulation experiments. In this paper we use ADO in a series of experiments with people to discriminate the Power, Exponential, and Hyperbolic models of memory retention, which has been a long-standing problem in cognitive science, providing an ideal setting in which to test the application of ADO for addressing questions about human cognition. Using an optimality criterion based on mutual information, ADO is able to find designs that are maximally likely to increase our certainty about the true model upon observation of the experiment outcomes. Results demonstrate the usefulness of ADO and also reveal some challenges in its implementation.