| | Models | Description |
| 1. |
A dendritic disinhibitory circuit mechanism for pathway-specific gating (Yang et al. 2016)
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"While reading a book in a noisy café, how does your brain ‘gate in’ visual information while filtering out auditory stimuli? Here we propose a mechanism for such flexible routing of information flow in a complex brain network (pathway-specific gating), tested using a network model of pyramidal neurons and three classes of interneurons with connection probabilities constrained by data. We find that if inputs from different pathways cluster on a pyramidal neuron dendrite, a pathway can be gated-on by a disinhibitory circuit motif. ..." |
| 2. |
Composite spiking network/neural field model of Parkinsons (Kerr et al 2013)
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This code implements a composite model of Parkinson's disease (PD). The
composite model consists of a leaky integrate-and-fire spiking neuronal
network model being driven by output from a neural field model (instead
of the more usual white noise drive). Three different sets of parameters
were used for the field model: one with basal ganglia parameters based
on data from healthy individuals, one based on data from individuals
with PD, and one purely thalamocortical model. The aim of this model is
to explore how the different dynamical patterns in each each of these
field models affects the activity in the network model. |
| 3. |
Convergence regulates synchronization-dependent AP transfer in feedforward NNs (Sailamul et al 2017)
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We study how synchronization-dependent spike transfer can be affected by the structure of convergent feedforward wiring.
We implemented computer simulations of model neural networks: a source and a target layer connected with different types of convergent wiring rules. In the Gaussian-Gaussian (GG) model, both the connection probability and the strength are given as Gaussian distribution as a function of spatial distance. In the Uniform-Constant (UC) and Uniform-Exponential (UE) models, the connection probability density is a uniform constant within a certain range, but the connection strength is set as a constant value or an exponentially decaying function, respectively.
Then we examined how the spike transfer function is modulated under these conditions, while static or synchronized input patterns were introduced to simulate different levels of feedforward spike synchronization.
We observed that the synchronization-dependent modulation of the transfer function appeared noticeably different for each convergence condition. The modulation of the spike transfer function was largest in the UC model, and smallest in the UE model. Our analysis showed that this difference was induced by the different spike weight distributions that was generated from convergent synapses in each model.
Our results suggest that the structure of the feedforward convergence is a crucial factor for correlation-dependent spike control, thus must be considered important to understand the mechanism of information transfer in the brain. |
| 4. |
Cortical oscillations and the basal ganglia (Fountas & Shanahan 2017)
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"Although brain oscillations involving the basal ganglia (BG) have been
the target of extensive research, the main focus lies
disproportionally on oscillations generated within the BG circuit
rather than other sources, such as cortical areas. We remedy this here
by investigating the influence of various cortical frequency bands on
the intrinsic effective connectivity of the BG, as well as the role of
the latter in regulating cortical behaviour. To do this, we construct
a detailed neural model of the complete BG circuit based on fine-tuned
spiking neurons, with both electrical and chemical synapses as well as
short-term plasticity between structures. As a measure of effective
connectivity, we estimate information transfer between nuclei by means
of transfer entropy. Our model successfully reproduces firing and
oscillatory behaviour found in both the healthy and Parkinsonian
BG. We found that, indeed, effective connectivity changes dramatically
for different cortical frequency bands and phase offsets, which are
able to modulate (or even block) information flow in the three major
BG pathways. ..." |
| 5. |
Ketamine disrupts theta modulation of gamma in a computer model of hippocampus (Neymotin et al 2011)
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"Abnormalities in oscillations have been suggested to play a role in schizophrenia.
We studied theta-modulated gamma oscillations in a computer model of hippocampal CA3 in vivo with and
without simulated application of ketamine, an NMDA receptor antagonist and psychotomimetic.
Networks of 1200 multi-compartment neurons (pyramidal, basket and oriens-lacunosum moleculare,
OLM, cells) generated theta and gamma oscillations from intrinsic network dynamics: basket cells
primarily generated gamma and amplified theta, while OLM cells strongly contributed to theta.
..." |
| 6. |
Microsaccades and synchrony coding in the retina (Masquelier et al. 2016)
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We show that microsaccades (MS) enable efficient synchrony-based coding among the primate retinal ganglion cells (RGC). We find that each MS causes certain RGCs to fire synchronously, namely those whose receptive fields contain contrast edges after the MS. The emitted synchronous spike volley thus rapidly transmits the most salient edges of the stimulus. We demonstrate that the readout could be done rapidly by simple coincidence-detector neurons, and that the required connectivity could emerge spontaneously with spike timing-dependent plasticity. |
| 7. |
Modelling platform of the cochlear nucleus and other auditory circuits (Manis & Compagnola 2018)
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"Models of the auditory brainstem have been an invaluable tool for testing hypotheses about auditory information processing and for highlighting the most important gaps in the experimental literature. Due to the complexity of the auditory brainstem, and indeed most brain circuits, the dynamic behavior of the system may be difficult to predict without a detailed, biologically realistic computational model. Despite the sensitivity of models to their exact construction and parameters, most prior models of the cochlear nucleus have incorporated only a small subset of the known biological properties. This confounds the interpretation of modelling results and also limits the potential future uses of these models, which require a large effort to develop. To address these issues, we have developed a general purpose, bio-physically detailed model of the cochlear nucleus for use both in testing hypotheses about cochlear nucleus function and also as an input to models of downstream auditory nuclei. The model implements conductance-based Hodgkin-Huxley representations of cells using a Python-based interface to the NEURON simulator. ..." |
| 8. |
Prosthetic electrostimulation for information flow repair in a neocortical simulation (Kerr 2012)
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This model is an extension of a model ( http://modeldb.yale.edu/138379 ) recently published in Frontiers in Computational Neuroscience. This model consists of 4700 event-driven, rule-based neurons, wired according to anatomical data, and driven by both white-noise synaptic inputs and a sensory signal recorded from a rat thalamus. Its purpose is to explore the effects of cortical damage, along with the repair of this damage via a neuroprosthesis. |
| 9. |
Relative spike time coding and STDP-based orientation selectivity in V1 (Masquelier 2012)
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Phenomenological spiking model of the cat early visual system. We show how natural vision can drive spike time correlations on sufficiently fast time scales to lead to the acquisition of orientation-selective V1 neurons through STDP. This is possible without reference times such as stimulus onsets, or saccade landing times. But even when such reference times are available, we demonstrate that the relative spike times encode the images more robustly than the absolute ones. |
| 10. |
Sensitivity of noisy neurons to coincident inputs (Rossant et al. 2011)
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"Two distant or coincident spikes are injected into a noisy balanced leaky integrate-and-fire neuron. The PSTH of the neuron in response to these inputs is calculated along with the extra number of spikes in the two cases. This number is higher for the coincident spikes, showing the sensitivity of a noisy neuron to coincident inputs." |
| 11. |
Simulated cortical color opponent receptive fields self-organize via STDP (Eguchi et al., 2014)
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"...
In this work, we address the problem of understanding the cortical processing of color information with a possible mechanism of the development of the patchy distribution of color selectivity via computational modeling.
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Our model of the early visual system consists of multiple topographically-arranged layers of excitatory and inhibitory neurons, with sparse intra-layer connectivity and feed-forward connectivity between layers.
Layers are arranged based on anatomy of early visual pathways, and include a retina, lateral geniculate nucleus, and layered neocortex.
...
After training with natural images, the neurons display heightened sensitivity to specific colors.
..." |
| 12. |
Single neuron properties shape chaos and signal transmission in random NNs (Muscinelli et al 2019)
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"While most models of randomly connected neural networks assume single-neuron models with simple dynamics, neurons in the brain exhibit complex intrinsic dynamics over multiple timescales. We analyze how the dynamical properties of single neurons and recurrent connections interact to shape the effective dynamics in large randomly connected networks. A novel dynamical mean-field theory for strongly connected networks of multi-dimensional rate neurons shows that the power spectrum of the network activity in the chaotic phase emerges from a nonlinear sharpening of the frequency response function of single neurons. For the case of two-dimensional rate neurons with strong adaptation, we find that the network exhibits a state of “resonant chaos”, characterized by robust, narrow-band stochastic oscillations. The coherence of stochastic oscillations is maximal at the onset of chaos and their correlation time scales with the adaptation timescale of single units. Surprisingly, the resonance frequency can be predicted from the properties of isolated neurons, even in the presence of heterogeneity in the adaptation parameters. In the presence of these internally-generated chaotic fluctuations, the transmission of weak, low-frequency signals is strongly enhanced by adaptation, whereas signal transmission is not influenced by adaptation in the non-chaotic regime. Our theoretical framework can be applied to other mechanisms at the level of single neurons, such as synaptic filtering, refractoriness or spike synchronization. These results advance our understanding of the interaction between the dynamics of single units and recurrent connectivity, which is a fundamental step toward the description of biologically realistic neural networks." |
| 13. |
STDP allows fast rate-modulated coding with Poisson-like spike trains (Gilson et al. 2011)
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The model demonstrates that a neuron equipped with STDP robustly detects repeating rate patterns among its afferents, from which the spikes are generated on the fly using inhomogenous Poisson sampling, provided those rates have narrow temporal peaks (10-20ms) - a condition met by many experimental Post-Stimulus Time Histograms (PSTH). |
| 14. |
Synaptic information transfer in computer models of neocortical columns (Neymotin et al. 2010)
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We sought to measure how the activity of the network alters information flow from inputs to output patterns.
Information handling by the network reflected the degree of internal connectivity. ...
With greater connectivity strength, the recurrent network translated activity and information due to contribution of activity from intrinsic network dynamics.
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At still higher internal synaptic strength, the network corrupted the external information, producing a state where little external information came through.
The association of increased information retrieved from the network with increased gamma power supports the notion of gamma oscillations playing a role in information processing."
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