doi: 10.1371/journal.pcbi.1002211.
Epub 2011 Nov 3.
Neural dynamics as sampling: a model for stochastic computation in recurrent networks of spiking neurons
Affiliations
- PMID: 22096452
- PMCID: PMC3207943
- DOI: 10.1371/journal.pcbi.1002211
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Neural dynamics as sampling: a model for stochastic computation in recurrent networks of spiking neurons
PLoS Comput Biol.
2011 Nov.
Abstract
The organization of computations in networks of spiking neurons in the brain is still largely unknown, in particular in view of the inherently stochastic features of their firing activity and the experimentally observed trial-to-trial variability of neural systems in the brain. In principle there exists a powerful computational framework for stochastic computations, probabilistic inference by sampling, which can explain a large number of macroscopic experimental data in neuroscience and cognitive science. But it has turned out to be surprisingly difficult to create a link between these abstract models for stochastic computations and more detailed models of the dynamics of networks of spiking neurons. Here we create such a link and show that under some conditions the stochastic firing activity of networks of spiking neurons can be interpreted as probabilistic inference via Markov chain Monte Carlo (MCMC) sampling. Since common methods for MCMC sampling in distributed systems, such as Gibbs sampling, are inconsistent with the dynamics of spiking neurons, we introduce a different approach based on non-reversible Markov chains that is able to reflect inherent temporal processes of spiking neuronal activity through a suitable choice of random variables. We propose a neural network model and show by a rigorous theoretical analysis that its neural activity implements MCMC sampling of a given distribution, both for the case of discrete and continuous time. This provides a step towards closing the gap between abstract functional models of cortical computation and more detailed models of networks of spiking neurons.
Conflict of interest statement
The authors have declared that no competing interests exist.
Figures
The figure shows a schematic of the transition operator 
for the internal state variable 
of a spiking neuron 
with an absolute refractory period. The neuron can fire in the resting state 
and in the last refractory state 
.
for the internal state variable of a spiking neuron with an absolute refractory period. The neuron can fire in the resting state and in the last refractory state .
The figure shows the transition operator 
, refractory functions 
and activation functions 
for the neuron model with relative refractory mechanism. (A) Transition probabilities of the internal variable 
given by 
. (B) Three examples of possible refractory functions 
. They assume value 
when the neuron cannot spike, and return to value 
(full readiness to fire again) with different time courses. The value of 
at intermediate time points regulates the current probability of firing of neuron 
(see A). The x-axis is equivalent to the number of time steps since last spike (running from 0 to 
from left to right). (C) Associated activation functions 
according to (11). (D) Spike trains produced by the resulting three different neuron models with (hypothetical) membrane potentials that jump at time 
from a constant low value to a constant high value. Black horizontal bars indicate spikes, and the active states 
are indicated by gray shaded areas of duration 
after each spike. It can be seen from this example that different refractory mechanisms give rise to different spiking dynamics.
, refractory functions and activation functions for the neuron model with relative refractory mechanism. (A) Transition probabilities of the internal variable given by . (B) Three examples of possible refractory functions . They assume value when the neuron cannot spike, and return to value (full readiness to fire again) with different time courses. The value of at intermediate time points regulates the current probability of firing of neuron (see A). The x-axis is equivalent to the number of time steps since last spike (running from 0 to from left to right). (C) Associated activation functions according to (11). (D) Spike trains produced by the resulting three different neuron models with (hypothetical) membrane potentials that jump at time from a constant low value to a constant high value. Black horizontal bars indicate spikes, and the active states are indicated by gray shaded areas of duration after each spike. It can be seen from this example that different refractory mechanisms give rise to different spiking dynamics.
(A) Spike raster of the network. (B) Traces of internal state variables of a neuron (# 26, indicated by orange spikes in A). The rich interaction of the network gives rise to rapidly changing membrane potentials and instantaneous firing rates. (C) Joint distribution of 5 neurons (gray shaded area in A) obtained by the spiking neural network and Gibbs sampling from the same distribution. Active states 
are indicated by a black dot, using one row for each neuron 
, the columns list all 
possible states 
of these 
neurons. The tight match between both distributions suggests that the spiking network represents the target probability distribution 
with high accuracy.
are indicated by a black dot, using one row for each neuron , the columns list all possible states of these neurons. The tight match between both distributions suggests that the spiking network represents the target probability distribution with high accuracy.
(A) Typical visual stimuli for the left and right eye in binocular rivalry experiments. (B) Tuning curve of a neuron with preferred orientation 
. (C) Distribution of dominance durations in the trained network under ambiguous input. The red curve shows the Gamma distribution with maximum likelihood on the data. (D) 2-dimensional projection (via population vector) of the distribution 
encoded in the spiking network showing that it strongly favors coherent global states of arbitrary orientation to incoherent ones (corresponding to population vectors of small magnitude). (E) 2-dimensional projection of the bimodal posterior distribution under an ambiguous input consisting of two different orientations reminiscent of the stimuli shown in A. The black trace shows the temporal evolution of the network state 
for 500 ms around a perceptual switch. (F) Network states at 3 time points 
marked in E. Neurons that fired in the preceding 20 ms (see gray bar in G) are plotted in the color of their preferred orientation. Inactive neurons are shown in white. While states 
and 
represent rather coherent orientations, 
shows an incoherent state corresponding to a perceptual switch. Clamped neurons (which the posterior is condition on) are marked by a black dot. (G) Spike raster of the unclamped neurons during a 500 ms epoch marked by the black trace in E. Gray bars indicate the 20 ms time intervals that define the network states shown in F. Altogether this figure shows that a theoretically rigorous probabilistic inference process can be carried out by a network of spiking neurons with a spike raster that is similar to generic recorded data.
. (C) Distribution of dominance durations in the trained network under ambiguous input. The red curve shows the Gamma distribution with maximum likelihood on the data. (D) 2-dimensional projection (via population vector) of the distribution encoded in the spiking network showing that it strongly favors coherent global states of arbitrary orientation to incoherent ones (corresponding to population vectors of small magnitude). (E) 2-dimensional projection of the bimodal posterior distribution under an ambiguous input consisting of two different orientations reminiscent of the stimuli shown in A. The black trace shows the temporal evolution of the network state for 500 ms around a perceptual switch. (F) Network states at 3 time points marked in E. Neurons that fired in the preceding 20 ms (see gray bar in G) are plotted in the color of their preferred orientation. Inactive neurons are shown in white. While states and represent rather coherent orientations, shows an incoherent state corresponding to a perceptual switch. Clamped neurons (which the posterior is condition on) are marked by a black dot. (G) Spike raster of the unclamped neurons during a 500 ms epoch marked by the black trace in E. Gray bars indicate the 20 ms time intervals that define the network states shown in F. Altogether this figure shows that a theoretically rigorous probabilistic inference process can be carried out by a network of spiking neurons with a spike raster that is similar to generic recorded data.
(A) Shown is the membrane potential histogram of a typical neuron during sampling. The data is that of neuron 
from the simulation shown in Figure 3 (the membrane potential and spike trace of 
are highlighted in Figure 3). (B) The plot shows the ISI distribution of a typical neuron (again 
from Figure 3) during sampling. The distribution is roughly gamma-shaped, reminiscent of experimentally observed ISI distributions. (C) A scatter plot of the coefficient of variation (CV) versus the average interspike interval (ISI) of each neuron taken from the simulation shown in Figure 3. The value of neuron 
from Figure 3 is marked by a cross. The simulated data is in accordance with experimentally observed data.
from the simulation shown in Figure 3 (the membrane potential and spike trace of are highlighted in Figure 3). (B) The plot shows the ISI distribution of a typical neuron (again from Figure 3) during sampling. The distribution is roughly gamma-shaped, reminiscent of experimentally observed ISI distributions. (C) A scatter plot of the coefficient of variation (CV) versus the average interspike interval (ISI) of each neuron taken from the simulation shown in Figure 3. The value of neuron from Figure 3 is marked by a cross. The simulated data is in accordance with experimentally observed data.
The figure shows a histogram of the Kullback-Leibler divergence between 
different Boltzmann distributions over K = 10 variables (with parameters randomly drawn, see setup of Figure 3) and approximations stemming from different neural sampling networks. Networks with absolute refractory mechanism provide the best approximation (as expected from theoretical guarantees). Networks consisting of neurons with relative refractory mechanisms, with only “locally” correct sampling, also provide a close fit to the true distribution (see inset) compared to a fully factorized approximation (assuming correct marginals and independent variables). Furthermore, it can be seen that sampling networks with more realistic, alpha-shaped, additive PSPs still fit the true distribution reasonably well.
different Boltzmann distributions over K = 10 variables (with parameters randomly drawn, see setup of Figure 3) and approximations stemming from different neural sampling networks. Networks with absolute refractory mechanism provide the best approximation (as expected from theoretical guarantees). Networks consisting of neurons with relative refractory mechanisms, with only “locally” correct sampling, also provide a close fit to the true distribution (see inset) compared to a fully factorized approximation (assuming correct marginals and independent variables). Furthermore, it can be seen that sampling networks with more realistic, alpha-shaped, additive PSPs still fit the true distribution reasonably well.
(A) The upper panel shows the shape of a single PSP elicited at time 
. The lower panel shows the time course of the refractory function 
caused by a single spike of neuron 
at 
. The grey-shaded area of length 
indicates the interval of neuron 
being active (i.e., 
) due to a single spike of neuron 
at time 
. (B) Shown is the probability distribution of 5 out of 40 neurons. The plot is similar to Figure 3C, however it is generated with a sampling network that features alpha-shaped, additive PSPs. It can be seen that the network still produces a reasonable approximation to the true Boltzmann distribution (determined by Gibbs sampling).
. The lower panel shows the time course of the refractory function caused by a single spike of neuron at . The grey-shaded area of length indicates the interval of neuron being active (i.e., ) due to a single spike of neuron at time . (B) Shown is the probability distribution of 5 out of 40 neurons. The plot is similar to Figure 3C, however it is generated with a sampling network that features alpha-shaped, additive PSPs. It can be seen that the network still produces a reasonable approximation to the true Boltzmann distribution (determined by Gibbs sampling).References
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