Probabilistic modeling of correlated neural population firing activity is central to understanding the neural code and building practical decoding algorithms. No parametric models currently exist for modeling multivariate correlated neural data and the high dimensional nature of the data makes fully nonparametric methods impractical. To address these problems we propose an energy-based model in which the joint probability of neural activity is represented using learned functions of the 1D marginal histograms of the data. The parameters of the model are learned using contrastive divergence and an optimization procedure for finding appropriate marginal directions. We evaluate the method using real data recorded from a population of motor cortical neurons. In particular, we model the joint probability of population spiking times and 2D hand position and show that the likelihood of test data under our model is significantly higher than under other models. These results suggest that our model captures correlations in the firing activity. Our rich probabilistic model of neural population activity is a step towards both measurement of the importance of correlations in neural coding and improved decoding of population activity.

We present a conditional temporal probabilistic framework for reconstructing 3D human motion in monocular video based on descriptors encoding image silhouette observations. For computational efficiency we restrict visual inference to low-dimensional kernel induced nonlinear state spaces. Our methodology (kBME) combines kernel PCA-based nonlinear dimensionality reduction (kPCA) and Conditional Bayesian Mixture of Experts (BME) in order to learn complex multivalued predictors between observations and model hidden states. This is necessary for accurate, inverse, visual perception inferences, where several probable, distant 3D solutions exist due to noise or the uncertainty of monocular perspective projection. Low-dimensional models are appropriate because many visual processes exhibit strong nonlinear correlations in both the image observations and the target, hidden state variables. The learned predictors are temporally combined within a conditional graphical model in order to allow a principled propagation of uncertainty. We study several predictors and empirically show that the proposed algorithm positively compares with techniques based on regression, Kernel Dependency Estimation (KDE) or PCA alone, and gives results competitive to those of high-dimensional mixture predictors at a fraction of their computational cost. We show that the method successfully reconstructs the complex 3D motion of humans in real monocular video sequences.

This paper introduces Gaussian Process Dynamical Models (GPDM) for nonlinear time series analysis. A GPDM comprises a low-dimensional latent space with associated dynamics, and a map from the latent space to an observation space.

We show how to learn a Mahanalobis distance metric for k-nearest neighbor (kNN) classification by semidefinite programming. The metric is trained with the goal that the k-nearest neighbors always belong to the same class while examples from different classes are separated by a large margin. On seven data sets of varying size and difficulty, we find that metrics trained in this way lead to significant improvements in kNN classification--for example, achieving a test error rate of 1.3% on the MNIST handwritten digits. As in support vector machines (SVMs), the learning problem reduces to a convex optimization based on the hinge loss. Unlike learning in SVMs, however, our framework requires no modification or extension for problems in multiway (as opposed to binary) classification.

We propose a simple clustering framework on graphs encoding pairwise data similarities. Unlike usual similarity-based methods, the approach softly assigns data to clusters in a probabilistic way. More importantly, a hierarchical clustering is naturally derived in this framework to gradually merge lower-level clusters into higher-level ones. A random walk analysis indicates that the algorithm exposes clustering structures in various resolutions, i.e., a higher level statistically models a longer-term diffusion on graphs and thus discovers a more global clustering structure. Finally we provide very encouraging experimental results.

We introduce a technique for dimensionality estimation based on the notion of quantization dimension, which connects the asymptotic optimal quantization error for a probability distribution on a manifold to its intrinsic dimension. The definition of quantization dimension yields a family of estimation algorithms, whose limiting case is equivalent to a recent method based on packing numbers. Using the formalism of high-rate vector quantization, we address issues of statistical consistency and analyze the behavior of our scheme in the presence of noise.

Reinforcement learning by direct policy gradient estimation is attractive in theory but in practice leads to notoriously ill-behaved optimization problems. We improve its robustness and speed of convergence with stochastic meta-descent, a gain vector adaptation method that employs fast Hessian-vector products. In our experiments the resulting algorithms outperform previously employed online stochastic, offline conjugate, and natural policy gradient methods.

This makes Gaussian process regression too slow for large datasets. In this paper, we present a fast approximation method, based on kd-trees, that significantly reduces both the prediction and the training times of Gaussian process regression.

We describe a hierarchy of motif-based kernels for multiple alignments of biological sequences, particularly suitable to process regulatory regions of genes. The kernels incorporate progressively more information, with the most complex kernel accounting for a multiple alignment of orthologous regions, the phylogenetic tree relating the species, and the prior knowledge that relevant sequence patterns occur in conserved motif blocks. These kernels can be used in the presence of a library of known transcription factor binding sites, or de novo by iterating over all k-mers of a given length. In the latter mode, a discriminative classifier built from such a kernel not only recognizes a given class of promoter regions, but as a side effect simultaneously identifies a collection of relevant, discriminative sequence motifs. We demonstrate the utility of the motif-based multiple alignment kernels by using a collection of aligned promoter regions from five yeast species to recognize classes of cell-cycle regulated genes.

An increasing number of projects in neuroscience requires the statistical analysis of high dimensional data sets, as, for instance, in predicting behavior from neural firing or in operating artificial devices from brain recordings in brain-machine interfaces. Linear analysis techniques remain prevalent in such cases, but classical linear regression approaches are often numerically too fragile in high dimensions. In this paper, we address the question of whether EMG data collected from arm movements of monkeys can be faithfully reconstructed with linear approaches from neural activity in primary motor cortex (M1). To achieve robust data analysis, we develop a full Bayesian approach to linear regression that automatically detects and excludes irrelevant features in the data, regularizing against overfitting. In comparison with ordinary least squares, stepwise regression, partial least squares, LASSO regression and a brute force combinatorial search for the most predictive input features in the data, we demonstrate that the new Bayesian method offers a superior mixture of characteristics in terms of regularization against overfitting, computational efficiency and ease of use, demonstrating its potential as a drop-in replacement for other linear regression techniques. As neuroscientific results, our analyses demonstrate that EMG data can be well predicted from M1 neurons, further opening the path for possible real-time interfaces between brains and machines.