The linear correlation coefficient is typically used to characterize and analyze dependencies of neural spike counts. Here, we show that the correlation coefficient is in general insufficient to characterize these dependencies. We construct two neuron spike count models with Poisson-like marginals and vary their dependence structure using copulas. To this end, we construct a copula that allows to keep the spike counts uncorrelated while varying their dependence strength. Moreover, we employ a network of leaky integrate-and-fire neurons to investigate whether weakly correlated spike counts with strong dependencies are likely to occur in real networks. We find that the entropy of uncorrelated but dependent spike count distributions can deviate from the corresponding distribution with independent components by more than 25% and that weakly correlated but strongly dependent spike counts are very likely to occur in biological networks. Finally, we introduce a test for deciding whether the dependence structure of distributions with Poisson-like marginals is well characterized by the linear correlation coefficient and verify it for different copula-based models.

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.

We present a probabilistic factor analysis model which can be used for studying spatiotemporal datasets. The spatial and temporal structure is modeled by using Gaussian process priors both for the loading matrix and the factors. The posterior distributions are approximated using the variational Bayesian framework. High computational cost of Gaussian process modeling is reduced by using sparse approximations. Themodel is used to compute the reconstructions of the global sea surface temperatures from a historical dataset. The results suggest that the proposed model can outperform the state-of-the-art reconstruction systems.

The control of neuroprosthetic devices from the activity of motor cortex neurons benefits from learning effects where the function of these neurons is adapted to the control task. It was recently shown that tuning properties of neurons in monkey motor cortex are adapted selectively in order to compensate for an erroneous interpretation of their activity. In particular, it was shown that the tuning curves of those neurons whose preferred directions had been misinterpreted changed more than those of other neurons. In this article, we show that the experimentally observed self-tuning properties of the system can be explained on the basis of a simple learning rule. This learning rule utilizes neuronal noise for exploration and performs Hebbian weight updates that are modulated by a global reward signal. In contrast to most previously proposed reward-modulated Hebbian learning rules, this rule does not require extraneous knowledge about what is noise and what is signal. The learning rule is able to optimize the performance of the model system within biologically realistic periods of time and under high noise levels. When the neuronal noise is fitted to experimental data, the model produces learning effects similar to those found in monkey experiments.

We present a general inference framework for inter-domain Gaussian Processes (GPs), focusing on its usefulness to build sparse GP models. The state-of-the-art sparse GP model introduced by Snelson and Ghahramani in [1] relies on finding a small, representative pseudo data set of m elements (from the same domain as the n available data elements) which is able to explain existing data well, and then uses it to perform inference. This reduces inference and model selection computation time from O(n^3) to O(m^2n), where m << n. Inter-domain GPs can be used to find a (possibly more compact) representative set of features lying in a different domain, at the same computational cost. Being able to specify a different domain for the representative features allows to incorporate prior knowledge about relevant characteristics of data and detaches the functional form of the covariance and basis functions. We will show how previously existing models fit into this framework and will use it to develop two new sparse GP models. Tests on large, representative regression data sets suggest that significant improvement can be achieved, while retaining computational efficiency.

Learning linear combinations of multiple kernels is an appealing strategy when the right choice of features is unknown. Previous approaches to multiple kernel learning (MKL) promote sparse kernel combinations and hence support interpretability. Unfortunately, L1-norm MKL is hardly observed to outperform trivial baselines in practical applications. To allow for robust kernel mixtures, we generalize MKL to arbitrary Lp-norms. We devise new insights on the connection between several existing MKL formulations and develop two efficient interleaved optimization strategies for arbitrary p>1. Empirically, we demonstrate that the interleaved optimization strategies are much faster compared to the traditionally used wrapper approaches. Finally, we apply Lp-norm MKL to real-world problems from computational biology, showing that non-sparse MKL achieves accuracies that go beyond the state-of-the-art.

Many models for computations in recurrent networks of neurons assume that the network state moves from some initial state to some fixed point attractor or limit cycle that represents the output of the computation. However experimental data show that in response to a sensory stimulus the network state moves from its initial state through a trajectory of network states and eventually returns to the initial state, without reaching an attractor or limit cycle in between. This type of network response, where salient information about external stimuli is encoded in characteristic trajectories of continuously varying network states, raises the question how a neural system could compute with such code, and arrive for example at a temporally stable classification of the external stimulus. We show that a known unsupervised learning algorithm, Slow Feature Analysis (SFA), could be an important ingredient for extracting stable information from these network trajectories. In fact, if sensory stimuli are more often followed by another stimulus from the same class than by a stimulus from another class, SFA approaches the classification capability of Fishers Linear Discriminant (FLD), a powerful algorithm for supervised learning. We apply this principle to simulated cortical microcircuits, and show that it enables readout neurons to learn discrimination of spoken digits and detection of repeating firing patterns within a stream of spike trains with the same firing statistics, without requiring any supervision for learning.

Semi-supervised regression based on the graph Laplacian suffers from the fact that the solution is biased towards a constant and the lack of extrapolating power. Outgoing from these observations we propose to use the second-order Hessian energy for semi-supervised regression which overcomes both of these problems, in particular, if the data lies on or close to a low-dimensional submanifold in the feature space, the Hessian energy prefers functions which vary ``linearly with respect to the natural parameters in the data. This property makes it also particularly suited for the task of semi-supervised dimensionality reduction where the goal is to find the natural parameters in the data based on a few labeled points. The experimental result suggest that our method is superior to semi-supervised regression using Laplacian regularization and standard supervised methods and is particularly suited for semi-supervised dimensionality reduction.

The Minimum Description Length (MDL) principle selects the model that has the shortest code for data plus model. We show that for a countable class of models, MDL predictions are close to the true distribution in a strong sense. The result is completely general. No independence, ergodicity, stationarity, identifiability, or other assumption on the model class need to be made. More formally, we show that for any countable class of models, the distributions selected by MDL (or MAP) asymptotically predict (merge with) the true measure in the class in total variation distance.

In this paper we present a novel approach to learn directed acyclic graphs (DAG) and factor models within the same framework while also allowing for model comparison between them. For this purpose, we exploit the connection between factor models and DAGs to propose Bayesian hierarchies based on spike and slab priors to promote sparsity, heavy-tailed priors to ensure identifiability and predictive densities to perform the model comparison. We require identifiability to be able to produce variable orderings leading to valid DAGs and sparsity to learn the structures. The effectiveness of our approach is demonstrated through extensive experiments on artificial and biological data showing that our approach outperform a number of state of the art methods.