4,672 research outputs found
Correlations in spiking neuronal networks with distance dependent connections
Can the topology of a recurrent spiking network be inferred from observed activity dynamics? Which statistical parameters of network connectivity can be extracted from firing rates, correlations and related measurable quantities? To approach these questions, we analyze distance dependent correlations of the activity in small-world networks of neurons with current-based synapses derived from a simple ring topology. We find that in particular the distribution of correlation coefficients of subthreshold activity can tell apart random networks from networks with distance dependent connectivity. Such distributions can be estimated by sampling from random pairs. We also demonstrate the crucial role of the weight distribution, most notably the compliance with Dales principle, for the activity dynamics in recurrent networks of different types
Mechanisms of Zero-Lag Synchronization in Cortical Motifs
Zero-lag synchronization between distant cortical areas has been observed in
a diversity of experimental data sets and between many different regions of the
brain. Several computational mechanisms have been proposed to account for such
isochronous synchronization in the presence of long conduction delays: Of
these, the phenomenon of "dynamical relaying" - a mechanism that relies on a
specific network motif - has proven to be the most robust with respect to
parameter mismatch and system noise. Surprisingly, despite a contrary belief in
the community, the common driving motif is an unreliable means of establishing
zero-lag synchrony. Although dynamical relaying has been validated in empirical
and computational studies, the deeper dynamical mechanisms and comparison to
dynamics on other motifs is lacking. By systematically comparing
synchronization on a variety of small motifs, we establish that the presence of
a single reciprocally connected pair - a "resonance pair" - plays a crucial
role in disambiguating those motifs that foster zero-lag synchrony in the
presence of conduction delays (such as dynamical relaying) from those that do
not (such as the common driving triad). Remarkably, minor structural changes to
the common driving motif that incorporate a reciprocal pair recover robust
zero-lag synchrony. The findings are observed in computational models of
spiking neurons, populations of spiking neurons and neural mass models, and
arise whether the oscillatory systems are periodic, chaotic, noise-free or
driven by stochastic inputs. The influence of the resonance pair is also robust
to parameter mismatch and asymmetrical time delays amongst the elements of the
motif. We call this manner of facilitating zero-lag synchrony resonance-induced
synchronization, outline the conditions for its occurrence, and propose that it
may be a general mechanism to promote zero-lag synchrony in the brain.Comment: 41 pages, 12 figures, and 11 supplementary figure
Cortical Spike Synchrony as a Measure of Input Familiarity
J.G.O. was supported by the Ministerio de Economia y Competividad and FEDER (Spain, project FIS2015-66503-C3-1-P) and the ICREA Academia programme. E.U. acknowledges support from the Scottish Universities Life Sciences Alliance (SULSA) and HPC-Europa2.Peer reviewedPostprin
Integration of continuous-time dynamics in a spiking neural network simulator
Contemporary modeling approaches to the dynamics of neural networks consider
two main classes of models: biologically grounded spiking neurons and
functionally inspired rate-based units. The unified simulation framework
presented here supports the combination of the two for multi-scale modeling
approaches, the quantitative validation of mean-field approaches by spiking
network simulations, and an increase in reliability by usage of the same
simulation code and the same network model specifications for both model
classes. While most efficient spiking simulations rely on the communication of
discrete events, rate models require time-continuous interactions between
neurons. Exploiting the conceptual similarity to the inclusion of gap junctions
in spiking network simulations, we arrive at a reference implementation of
instantaneous and delayed interactions between rate-based models in a spiking
network simulator. The separation of rate dynamics from the general connection
and communication infrastructure ensures flexibility of the framework. We
further demonstrate the broad applicability of the framework by considering
various examples from the literature ranging from random networks to neural
field models. The study provides the prerequisite for interactions between
rate-based and spiking models in a joint simulation
VIOLA - A multi-purpose and web-based visualization tool for neuronal-network simulation output
Neuronal network models and corresponding computer simulations are invaluable
tools to aid the interpretation of the relationship between neuron properties,
connectivity and measured activity in cortical tissue. Spatiotemporal patterns
of activity propagating across the cortical surface as observed experimentally
can for example be described by neuronal network models with layered geometry
and distance-dependent connectivity. The interpretation of the resulting stream
of multi-modal and multi-dimensional simulation data calls for integrating
interactive visualization steps into existing simulation-analysis workflows.
Here, we present a set of interactive visualization concepts called views for
the visual analysis of activity data in topological network models, and a
corresponding reference implementation VIOLA (VIsualization Of Layer Activity).
The software is a lightweight, open-source, web-based and platform-independent
application combining and adapting modern interactive visualization paradigms,
such as coordinated multiple views, for massively parallel neurophysiological
data. For a use-case demonstration we consider spiking activity data of a
two-population, layered point-neuron network model subject to a spatially
confined excitation originating from an external population. With the multiple
coordinated views, an explorative and qualitative assessment of the
spatiotemporal features of neuronal activity can be performed upfront of a
detailed quantitative data analysis of specific aspects of the data.
Furthermore, ongoing efforts including the European Human Brain Project aim at
providing online user portals for integrated model development, simulation,
analysis and provenance tracking, wherein interactive visual analysis tools are
one component. Browser-compatible, web-technology based solutions are therefore
required. Within this scope, with VIOLA we provide a first prototype.Comment: 38 pages, 10 figures, 3 table
Density-dependence of functional development in spiking cortical networks grown in vitro
During development, the mammalian brain differentiates into specialized
regions with distinct functional abilities. While many factors contribute to
functional specialization, we explore the effect of neuronal density on the
development of neuronal interactions in vitro. Two types of cortical networks,
dense and sparse, with 50,000 and 12,000 total cells respectively, are studied.
Activation graphs that represent pairwise neuronal interactions are constructed
using a competitive first response model. These graphs reveal that, during
development in vitro, dense networks form activation connections earlier than
sparse networks. Link entropy analysis of dense net- work activation graphs
suggests that the majority of connections between electrodes are reciprocal in
nature. Information theoretic measures reveal that early functional information
interactions (among 3 cells) are synergetic in both dense and sparse networks.
However, during later stages of development, previously synergetic
relationships become primarily redundant in dense, but not in sparse networks.
Large link entropy values in the activation graph are related to the domination
of redundant ensembles in late stages of development in dense networks. Results
demonstrate differences between dense and sparse networks in terms of
informational groups, pairwise relationships, and activation graphs. These
differences suggest that variations in cell density may result in different
functional specialization of nervous system tissue in vivo.Comment: 10 pages, 7 figure
Model-free reconstruction of neuronal network connectivity from calcium imaging signals
A systematic assessment of global neural network connectivity through direct
electrophysiological assays has remained technically unfeasible even in
dissociated neuronal cultures. We introduce an improved algorithmic approach
based on Transfer Entropy to reconstruct approximations to network structural
connectivities from network activity monitored through calcium fluorescence
imaging. Based on information theory, our method requires no prior assumptions
on the statistics of neuronal firing and neuronal connections. The performance
of our algorithm is benchmarked on surrogate time-series of calcium
fluorescence generated by the simulated dynamics of a network with known
ground-truth topology. We find that the effective network topology revealed by
Transfer Entropy depends qualitatively on the time-dependent dynamic state of
the network (e.g., bursting or non-bursting). We thus demonstrate how
conditioning with respect to the global mean activity improves the performance
of our method. [...] Compared to other reconstruction strategies such as
cross-correlation or Granger Causality methods, our method based on improved
Transfer Entropy is remarkably more accurate. In particular, it provides a good
reconstruction of the network clustering coefficient, allowing to discriminate
between weakly or strongly clustered topologies, whereas on the other hand an
approach based on cross-correlations would invariantly detect artificially high
levels of clustering. Finally, we present the applicability of our method to
real recordings of in vitro cortical cultures. We demonstrate that these
networks are characterized by an elevated level of clustering compared to a
random graph (although not extreme) and by a markedly non-local connectivity.Comment: 54 pages, 8 figures (+9 supplementary figures), 1 table; submitted
for publicatio
Stimulus-dependent maximum entropy models of neural population codes
Neural populations encode information about their stimulus in a collective
fashion, by joint activity patterns of spiking and silence. A full account of
this mapping from stimulus to neural activity is given by the conditional
probability distribution over neural codewords given the sensory input. To be
able to infer a model for this distribution from large-scale neural recordings,
we introduce a stimulus-dependent maximum entropy (SDME) model---a minimal
extension of the canonical linear-nonlinear model of a single neuron, to a
pairwise-coupled neural population. The model is able to capture the
single-cell response properties as well as the correlations in neural spiking
due to shared stimulus and due to effective neuron-to-neuron connections. Here
we show that in a population of 100 retinal ganglion cells in the salamander
retina responding to temporal white-noise stimuli, dependencies between cells
play an important encoding role. As a result, the SDME model gives a more
accurate account of single cell responses and in particular outperforms
uncoupled models in reproducing the distributions of codewords emitted in
response to a stimulus. We show how the SDME model, in conjunction with static
maximum entropy models of population vocabulary, can be used to estimate
information-theoretic quantities like surprise and information transmission in
a neural population.Comment: 11 pages, 7 figure
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