Linear implementations of the efficient coding hypothesis, such as independent component analysis (ICA) and sparse coding models, have provided functional explanations for properties of simple cells in V1 [1, 2]. These models, however, ignore the nonlinear behavior of neurons and fail to match individual and population properties of neural receptive fields in subtle but important ways. Hierarchical models, including Gaussian Scale Mixtures [3, 4] and other generative statistical models [5, 6], can capture higher-order regularities in natural images and explain nonlinear aspects of neural processing such as normalization and context effects [6,7]. Previously, it had been assumed that the lower level representation is independent of the hierarchy, and had been fixed when training these models. Here we examine the optimal lower-level representations derived in the context of a hierarchical model and find that the resulting representations are strikingly different from those based on linear models. Unlike the the basis functions and filters learned by ICA or sparse coding, these functions individually more closely resemble simple cell receptive fields and collectively span a broad range of spatial scales. Our work unifies several related approaches and observations about natural image structure and suggests that hierarchical models might yield better representations of image structure throughout the hierarchy.

There have been many graph-based approaches for semi-supervised classification. One problem is that of hyperparameter learning: performance depends greatly on the hyperparameters of the similarity graph, transformation of the graph Laplacian and the noise model. We present a Bayesian framework for learning hyperparameters for graph-based semisupervised classification. Given some labeled data, which can contain inaccurate labels, we pose the semi-supervised classification as an inference problem over the unknown labels. Expectation Propagation is used for approximate inference and the mean of the posterior is used for classification. The hyperparameters are learned using EM for evidence maximization. We also show that the posterior mean can be written in terms of the kernel matrix, providing a Bayesian classifier to classify new points. Tests on synthetic and real datasets show cases where there are significant improvements in performance over the existing approaches.

We present a competitive analysis of some nonparametric Bayesian algorithms in a worst-case online learning setting, where no probabilistic assumptions about the generation of the data are made. We consider models which use a Gaussian process prior (over the space of all functions) and provide bounds on the regret (under the log loss) for commonly used nonparametric Bayesian algorithms -- including Gaussian regression and logistic regression -- which show how these algorithms can perform favorably under rather general conditions. These bounds explicitly handle the infinite dimensionality of these nonparametric classes in a natural way. We also make formal connections to the minimax and minimum description length (MDL) framework. Here, we show precisely how Bayesian Gaussian regression is a minimax strategy.

For this purpose, we propose a stochastic procedure, the mirror descent, which performs gradient descent in the dual space. The generated estimates are additionally averaged in a recursive fashion with specific weights. Mirror descent algorithms have been developed in different contexts and they are known to be particularly efficient in high dimensional problems. Moreover their implementation is adapted to the online setting. The main result of the paper is the upper bound on the convergence rate for the generalization error.

Integrate-and-Fire-type models are usually criticized because of their simplicity. On the other hand, the Integrate-and-Fire model is the basis of most of the theoretical studies on spiking neuron models. Here, we develop a sequential procedure to quantitatively evaluate an equivalent Integrate-and-Fire-type model based on intracellular recordings of cortical pyramidal neurons. We find that the resulting effective model is sufficient to predict the spike train of the real pyramidal neuron with high accuracy. In in vivo-like regimes, predicted and recorded traces are almost indistinguishable and a significant part of the spikes can be predicted at the correct timing. Slow processes like spike-frequency adaptation are shown to be a key feature in this context since they are necessary for the model to connect between different driving regimes.

We introduce a new model of genetic diversity which summarizes a large input dataset into an epitome, a short sequence or a small set of short sequences of probability distributions capturing many overlapping subsequences from the dataset. The epitome as a representation has already been used in modeling real-valued signals, such as images and audio. The discrete sequence model we introduce in this paper targets applications in genetics, from multiple alignment to recombination and mutation inference. In our experiments, we concentrate on modeling the diversity of HIV where the epitome emerges as a natural model for producing relatively small vaccines covering a large number of immune system targets known as epitopes. Our experiments show that the epitome includes more epitopes than other vaccine designs of similar length, including cocktails of consensus strains, phylogenetic tree centers, and observed strains. We also discuss epitome designs that take into account uncertainty about T-cell cross reactivity and epitope presentation. In our experiments, we find that vaccine optimization is fairly robust to these uncertainties.

This paper presents a new framework based on walks in a graph for analysis and inference in Gaussian graphical models. The key idea is to decompose correlations between variables as a sum over all walks between those variables in the graph. The weight of each walk is given by a product of edgewise partial correlations. We provide a walk-sum interpretation of Gaussian belief propagation in trees and of the approximate method of loopy belief propagation in graphs with cycles. This perspective leads to a better understanding of Gaussian belief propagation and of its convergence in loopy graphs.

Spectral clustering enjoys its success in both data clustering and semisupervised learning. But, most spectral clustering algorithms cannot handle multi-class clustering problems directly. Additional strategies are needed to extend spectral clustering algorithms to multi-class clustering problems. Furthermore, most spectral clustering algorithms employ hard cluster membership, which is likely to be trapped by the local optimum. In this paper, we present a new spectral clustering algorithm, named "Soft Cut". It improves the normalized cut algorithm by introducing soft membership, and can be efficiently computed using a bound optimization algorithm. Our experiments with a variety of datasets have shown the promising performance of the proposed clustering algorithm.

Multiple visual cues are used by the visual system to analyze a scene; achromatic cues include luminance, texture, contrast and motion. Singlecell recordings have shown that the mammalian visual cortex contains neurons that respond similarly to scene structure (e.g., orientation of a boundary), regardless of the cue type conveying this information. This paper shows that cue-invariant response properties of simple-and complex-type cells can be learned from natural image data in an unsupervised manner. In order to do this, we also extend a previous conceptual model of cue invariance so that it can be applied to model simple-and complex-cell responses. Our results relate cue-invariant response properties to natural image statistics, thereby showing how the statistical modeling approach can be used to model processing beyond the elemental response properties visual neurons. This work also demonstrates how to learn, from natural image data, more sophisticated feature detectors than those based on changes in mean luminance, thereby paving the way for new data-driven approaches to image processing and computer vision.

We develop an approach for estimation with Gaussian Markov processes that imposes a smoothness prior while allowing for discontinuities. Instead of propagating information laterally between neighboring nodes in a graph, we study the posterior distribution of the hidden nodes as a whole--how it is perturbed by invoking discontinuities, or weakening the edges, in the graph. We show that the resulting computation amounts to feed-forward fan-in operations reminiscent of V1 neurons. Moreover, using suitable matrix preconditioners, the incurred matrix inverse and determinant can be approximated, without iteration, in the same computational style. Simulation results illustrate the merits of this approach.