The coding of information by neural populations depends critically on the statistical dependencies between neuronal responses. However, there is no simple model that combines the observations that (1) marginal distributions over single-neuron spike counts are often approximately Poisson; and (2) joint distributions over the responses of multiple neurons are often strongly dependent. Here, we show that both marginal and joint properties of neural responses can be captured using Poisson copula models. Copulas are joint distributions that allow random variables with arbitrary marginals to be combined while incorporating arbitrary dependencies between them. Different copulas capture different kinds of dependencies, allowing for a richer and more detailed description of dependencies than traditional summary statistics, such as correlation coefficients. We explore a variety of Poisson copula models for joint neural response distributions, and derive an efficient maximum likelihood procedure for estimating them. We apply these models to neuronal data collected in and macaque motor cortex, and quantify the improvement in coding accuracy afforded by incorporating the dependency structure between pairs of neurons.

``How is information decoded in the brain?'' is one of the most difficult and important questions in neuroscience. Whether neural correlation is important or not in decoding neural activities is of special interest. We have developed a general framework for investigating how far the decoding process in the brain can be simplified. First, we hierarchically construct simplified probabilistic models of neural responses that ignore more than $K$th-order correlations by using a maximum entropy principle. Then, we compute how much information is lost when information is decoded using the simplified models, i.e., ``mismatched decoders''. We introduce an information theoretically correct quantity for evaluating the information obtained by mismatched decoders. We applied our proposed framework to spike data for vertebrate retina. We used 100-ms natural movies as stimuli and computed the information contained in neural activities about these movies. We found that the information loss is negligibly small in population activities of ganglion cells even if all orders of correlation are ignored in decoding. We also found that if we assume stationarity for long durations in the information analysis of dynamically changing stimuli like natural movies, pseudo correlations seem to carry a large portion of the information.

The synchronous brain activity measured via MEG (or EEG) can be interpreted as arising from a collection (possibly large) of current dipoles or sources located throughout the cortex. Estimating the number, location, and orientation of these sources remains a challenging task, one that is significantly compounded by the effects of source correlations and the presence of interference from spontaneous brain activity, sensor noise, and other artifacts. This paper derives an empirical Bayesian method for addressing each of these issues in a principled fashion. The resulting algorithm guarantees descent of a cost function uniquely designed to handle unknown orientations and arbitrary correlations. Robust interference suppression is also easily incorporated. In a restricted setting, the proposed method is shown to have theoretically zero bias estimating both the location and orientation of multi-component dipoles even in the presence of correlations, unlike a variety of existing Bayesian localization methods or common signal processing techniques such as beamforming and sLORETA. Empirical results on both simulated and real data sets verify the efficacy of this approach.

We propose a novel hierarchical, nonlinear model that predicts brain activity in area V1 evoked by natural images. In the study reported here brain activity was measured by means of functional magnetic resonance imaging (fMRI), a noninvasive technique that provides an indirect measure of neural activity pooled over a small volume (~ 2mm cube) of brain tissue. Our model, which we call the SpAM V1 model, is based on the reasonable assumption that fMRI measurements reflect the (possibly nonlinearly) pooled, rectified output of a large population of simple and complex cells in V1. It has a hierarchical filtering stage that consists of three layers: model simple cells, model complex cells, and a third layer in which the complex cells are linearly pooled (called “pooled-complex” cells). The pooling stage then obtains the measured fMRI signals as a sparse additive model (SpAM) in which a sparse nonparametric (nonlinear) combination of model complex cell and model pooled-complex cell outputs are summed. Our results show that the SpAM V1 model predicts fMRI responses evoked by natural images better than a benchmark model that only provides linear pooling of model complex cells. Furthermore, the spatial receptive fields, frequency tuning and orientation tuning curves of the SpAM V1 model estimated for each voxel appears to be consistent with the known properties of V1, and with previous analyses of this data set. A visualization procedure applied to the SpAM V1 model shows that most of the nonlinear pooling consists of simple compressive or saturating nonlinearities.

The odor transduction process has a large time constant and is susceptible to various types of noise. Therefore, the olfactory code at the sensor/receptor level is in general a slow and highly variable indicator of the input odor in both natural and artificial situations. Insects overcome this problem by using a neuronal device in their Antennal Lobe (AL), which transforms the identity code of olfactory receptors to a spatio-temporal code. This transformation improves the decision of the Mushroom Bodies (MBs), the subsequent classifier, in both speed and accuracy.Here we propose a rate model based on two intrinsic mechanisms in the insect AL, namely integration and inhibition. Then we present a MB classifier model that resembles the sparse and random structure of insect MB. A local Hebbian learning procedure governs the plasticity in the model. These formulations not only help to understand the signal conditioning and classification methods of insect olfactory systems, but also can be leveraged in synthetic problems. Among them, we consider here the discrimination of odor mixtures from pure odors. We show on a set of records from metal-oxide gas sensors that the cascade of these two new models facilitates fast and accurate discrimination of even highly imbalanced mixtures from pure odors.

A new spike feature extraction algorithm which enables realtime spike sorting and facilitates miniaturized microchip implementation is presented. The proposed algorithm has been evaluated on synthesized waveforms and experimentally recorded sequences from different animals. When compared with many spike sorting approaches our algorithm demonstrates significantly improved speed, accuracy and allows unsupervised execution. A preliminary hardware implementation has been realized using an integrated microchip interfaced with a personal computer.

Bandpass filtering, orientation selectivity, and contrast gain control are prominent features of sensory coding at the level of V1 simple cells. While the effect of bandpass filtering and orientation selectivity can be assessed within a linear model, contrast gain control is an inherently nonlinear computation. Here we employ the class of $L_p$ elliptically contoured distributions to investigate the extent to which the two features---orientation selectivity and contrast gain control---are suited to model the statistics of natural images. Within this framework we find that contrast gain control can play a significant role for the removal of redundancies in natural images. Orientation selectivity, in contrast, has only a very limited potential for redundancy reduction.

A crucial part of developing mathematical models of how the brain works is the quantification of their success. One of the most widely-used metrics yields the percentage of the variance in the data that is explained by the model. Unfortunately, this metric is biased due to the intrinsic variability in the data. This variability is in principle unexplainable by the model. We derive a simple analytical modification of the traditional formula that significantly improves its accuracy (as measured by bias) with similar or better precision (as measured by mean-square error) in estimating the true underlying Variance Explained by the model class. Our estimator advances on previous work by a) accounting for the uncertainty in the noise estimate, b) accounting for overfitting due to free model parameters mitigating the need for a separate validation data set and c) adding a conditioning term. We apply our new estimator to binocular disparity tuning curves of a set of macaque V1 neurons and find that on a population level almost all of the variance unexplained by Gabor functions is attributable to noise.

We propose a novel application of Formal Concept Analysis (FCA) to neural decoding: instead of just trying to figure out which stimulus was presented, we demonstrate how to explore the semantic relationships between 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 area STSa, using an exact Bayesian approach to construct the formal context needed by FCA. Prominent features of the resulting concept lattices are discussed, including indications for a product-of-experts code in real neurons.

A visual attention system should respond placidly when common stimuli are presented, while at the same time keep alert to anomalous visual inputs. In this paper, a dynamic visual attention model based on the rarity of features is proposed. We introduce the Incremental Coding Length (ICL) to measure the perspective entropy gain of each feature. The objective of our model is to maximize the entropy of the sampled visual features. In order to optimize energy consumption, the limit amount of energy of the system is re-distributed amongst features according to their Incremental Coding Length. By selecting features with large coding length increments, the computational system can achieve attention selectivity in both static and dynamic scenes. We demonstrate that the proposed model achieves superior accuracy in comparison to mainstream approaches in static saliency map generation. Moreover, we also show that our model captures several less-reported dynamic visual search behaviors, such as attentional swing and inhibition of return.