Laurent Perrinet

PyNN: A Common Interface for Neuronal Network Simulators

Computational neuroscience has produced a diversity of software for simulations of networks of spiking neurons, with both negative and positive consequences. On the one hand, each simulator uses its own programming or configuration language, leading to considerable difficulty in porting models from one simulator to another. This impedes communication between investigators and makes it harder to reproduce and build on the work of others. On the other hand, simulation results can be cross-checked between different simulators, giving greater confidence in their correctness, and each simulator has different optimizations, so the most appropriate simulator can be chosen for a given modelling task. A common programming interface to multiple simulators would reduce or eliminate the problems of simulator diversity while retaining the benefits. PyNN is such an interface, making it possible to write a simulation script once, using the Python programming language, and run it without modification on any supported simulator (currently NEURON, NEST, PCSIM, Brian and the Heidelberg VLSI neuromorphic hardware). PyNN increases the productivity of neuronal network modelling by providing high-level abstraction, by promoting code sharing and reuse, and by providing a foundation for simulator-agnostic analysis, visualization and data-management tools. PyNN increases the reliability of modelling studies by making it much easier to check results on multiple simulators. PyNN is open-source software and is available from http://neuralensemble.org/PyNN.

Perceptions as Hypotheses: Saccades as Experiments

If perception corresponds to hypothesis testing (Gregory, 1980); then visual searches might be construed as experiments that generate sensory data. In this work, we explore the idea that saccadic eye movements are optimal experiments, in which data are gathered to test hypotheses or beliefs about how those data are caused. This provides a plausible model of visual search that can be motivated from the basic principles of self-organized behavior: namely, the imperative to minimize the entropy of hidden states of the world and their sensory consequences. This imperative is met if agents sample hidden states of the world efficiently. This efficient sampling of salient information can be derived in a fairly straightforward way, using approximate Bayesian inference and variational free-energy minimization. Simulations of the resulting active inference scheme reproduce sequential eye movements that are reminiscent of empirically observed saccades and provide some counterintuitive insights into the way that sensory evidence is accumulated or assimilated into beliefs about the world.

Self-Invertible 2D Log-Gabor Wavelets

Orthogonal and biorthogonal wavelets became very popular image processing tools but exhibit major drawbacks, namely a poor resolution in orientation and the lack of translation invariance due to aliasing between subbands. Alternative multiresolution transforms which specifically solve these drawbacks have been proposed. These transforms are generally overcomplete and consequently offer large degrees of freedom in their design. At the same time their optimization gets a challenging task. We propose here the construction of log-Gabor wavelet transforms which allow exact reconstruction and strengthen the excellent mathematical properties of the Gabor filters. Two major improvements on the previous Gabor wavelet schemes are proposed: first the highest frequency bands are covered by narrowly localized oriented filters. Secondly, the set of filters cover uniformly the Fourier domain including the highest and lowest frequencies and thus exact reconstruction is achieved using the same filters in both the direct and the inverse transforms (which means that the transform is self-invertible). The present transform not only achieves important mathematical properties, it also follows as much as possible the knowledge on the receptive field properties of the simple cells of the Primary Visual Cortex (V1) and on the statistics of natural images. Compared to the state of the art, the log-Gabor wavelets show excellent ability to segregate the image information (e.g. the contrast edges) from spatially incoherent Gaussian noise by hard thresholding, and then to represent image features through a reduced set of large magnitude coefficients. Such characteristics make the transform a promising tool for processing natural images.

Networks of integrate-and-fire neurons using Rank Order Coding B: Spike timing dependent plasticity and emergence of orientation selectivity

Abstract Rank Order Coding is an alternative to conventional rate coding schemes that uses the order in which a neurons inputs fire to encode information. In a visual system framework, we simulated the asynchronous waves of retinal spikes produced in response to natural scenes and used them to stimulate integrate-and-fire V1 neurons that implemented a standard learning rule based on spike timing. After propagating thousands of images, orientation like receptive fields arise in these neurons despite the fact that the input neurons never fired more than once. We also analyze the biological plausibility of such a network.

Functional consequences of correlated excitatory and inhibitory conductances in cortical networks

Neurons in the neocortex receive a large number of excitatory and inhibitory synaptic inputs. Excitation and inhibition dynamically balance each other, with inhibition lagging excitation by only few milliseconds. To characterize the functional consequences of such correlated excitation and inhibition, we studied models in which this correlation structure is induced by feedforward inhibition (FFI). Simple circuits show that an effective FFI changes the integrative behavior of neurons such that only synchronous inputs can elicit spikes, causing the responses to be sparse and precise. Further, effective FFI increases the selectivity for propagation of synchrony through a feedforward network, thereby increasing the stability to background activity. Last, we show that recurrent random networks with effective inhibition are more likely to exhibit dynamical network activity states as have been observed in vivo. Thus, when a feedforward signal path is embedded in such recurrent network, the stabilizing effect of effective inhibition creates an suitable substrate for signal propagation. In conclusion, correlated excitation and inhibition support the notion that synchronous spiking may be important for cortical processing.

Coding static natural images using spiking event times: do neurons Cooperate?

To understand possible strategies of temporal spike coding in the central nervous system, we study functional neuromimetic models of visual processing for static images. We will first present the retinal model which was introduced by Van Rullen and Thorpe and which represents the multiscale contrast values of the image using an orthonormal wavelet transform. These analog values activate a set of spiking neurons which each fire once to produce an asynchronous wave of spikes. According to this model, the image may be progressively reconstructed from this spike wave thanks to regularities in the statistics of the coefficients determined with natural images. Here, we study mathematically how the quality of information transmission carried by this temporal representation varies over time. In particular, we study how these regularities can be used to optimize information transmission by using a form of temporal cooperation of neurons to code analog values. The original model used wavelet transforms that are close to orthogonal. However, the selectivity of realistic neurons overlap, and we propose an extension of the previous model by adding a spatial cooperation between filters. This model extends the previous scheme for arbitrary-and possibly nonorthogonal-representations of features in the images. In particular, we compared the performance of increasingly over-complete representations in the retina. Results show that this algorithm provides an efficient spike coding strategy for low-level visual processing which may adapt to the complexity of the visual input.

Smooth pursuit and visual occlusion: active inference and oculomotor control in schizophrenia.

This paper introduces a model of oculomotor control during the smooth pursuit of occluded visual targets. This model is based upon active inference, in which subjects try to minimise their (proprioceptive) prediction error based upon posterior beliefs about the hidden causes of their (exteroceptive) sensory input. Our model appeals to a single principle – the minimisation of variational free energy – to provide Bayes optimal solutions to the smooth pursuit problem. However, it tries to accommodate the cardinal features of smooth pursuit of partially occluded targets that have been observed empirically in normal subjects and schizophrenia. Specifically, we account for the ability of normal subjects to anticipate periodic target trajectories and emit pre-emptive smooth pursuit eye movements – prior to the emergence of a target from behind an occluder. Furthermore, we show that a single deficit in the postsynaptic gain of prediction error units (encoding the precision of posterior beliefs) can account for several features of smooth pursuit in schizophrenia: namely, a reduction in motor gain and anticipatory eye movements during visual occlusion, a paradoxical improvement in tracking unpredicted deviations from target trajectories and a failure to recognise and exploit regularities in the periodic motion of visual targets. This model will form the basis of subsequent (dynamic causal) models of empirical eye tracking measurements, which we hope to validate, using psychopharmacology and studies of schizophrenia.

Bayesian modeling of dynamic motion integration

The quality of the representation of an objects motion is limited by the noise in the sensory input as well as by an intrinsic ambiguity due to the spatial limitation of the visual motion analyzers (aperture problem). Perceptual and oculomotor data demonstrate that motion processing of extended objects is initially dominated by the local 1D motion cues, related to the objects edges and orthogonal to them, whereas 2D information, related to terminators (or edge-endings), takes progressively over and leads to the final correct representation of global motion. A Bayesian framework accounting for the sensory noise and general expectancies for object velocities has proven successful in explaining several experimental findings concerning early motion processing [Weiss, Y., Adelson, E., 1998. Slow and smooth: a Bayesian theory for the combination of local motion signals in human vision. MIT Technical report, A.I. Memo 1624]. In particular, these models provide a qualitative account for the initial bias induced by the 1D motion cue. However, a complete functional model, encompassing the dynamical evolution of object motion perception, including the integration of different motion cues, is still lacking. Here we outline several experimental observations concerning human smooth pursuit of moving objects and more particularly the time course of its initiation phase, which reflects the ongoing motion integration process. In addition, we propose a recursive extension of the Bayesian model, motivated and constrained by our oculomotor data, to describe the dynamical integration of 1D and 2D motion information. We compare the model predictions for object motion tracking with human oculomotor recordings.

More is not always better: adaptive gain control explains dissociation between perception and action

Moving objects generate motion information at different scales, which are processed in the visual system with a bank of spatiotemporal frequency channels. It is not known how the brain pools this information to reconstruct object speed and whether this pooling is generic or adaptive; that is, dependent on the behavioral task. We used rich textured motion stimuli of varying bandwidths to decipher how the human visual motion system computes object speed in different behavioral contexts. We found that, although a simple visuomotor behavior such as short-latency ocular following responses takes advantage of the full distribution of motion signals, perceptual speed discrimination is impaired for stimuli with large bandwidths. Such opposite dependencies can be explained by an adaptive gain control mechanism in which the divisive normalization pool is adjusted to meet the different constraints of perception and action.

The behavioral receptive field underlying motion integration for primate tracking eye movements

Short-latency ocular following are reflexive, tracking eye movements that are observed in human and non-human primates in response to a sudden and brief translation of the image. Initial, open-loop part of the eye acceleration reflects many of the properties attributed to low-level motion processing. We review a very large set of behavioral data demonstrating several key properties of motion detection and integration stages and their dynamics. We propose that these properties can be modeled as a behavioral receptive field exhibiting linear and nonlinear mechanisms responsible for context-dependent spatial integration and gain control. Functional models similar to that used for describing neuronal properties of receptive fields can then be applied successfully.