brainpy.synapses.DualExponential

class brainpy.synapses.DualExponential(pre, post, conn, stp=None, output=CUBA, comp_method='dense', g_max=1.0, tau_decay=10.0, tau_rise=1.0, delay_step=None, method='exp_auto', name=None, mode=None, stop_spike_gradient=False)

Dual exponential synapse model.

Model Descriptions

The dual exponential synapse model [1], also named as difference of two exponentials model, is given by:

\[g_{\mathrm{syn}}(t)=g_{\mathrm{max}} \frac{\tau_{1} \tau_{2}}{ \tau_{1}-\tau_{2}}\left(\exp \left(-\frac{t-t_{0}}{\tau_{1}}\right) -\exp \left(-\frac{t-t_{0}}{\tau_{2}}\right)\right)\]

where \(\tau_1\) is the time constant of the decay phase, \(\tau_2\) is the time constant of the rise phase, \(t_0\) is the time of the pre-synaptic spike, \(g_{\mathrm{max}}\) is the maximal conductance.

However, in practice, this formula is hard to implement. The equivalent solution is two coupled linear differential equations [2]:

\[\begin{split}\begin{aligned} &g_{\mathrm{syn}}(t)=g_{\mathrm{max}} g * \mathrm{STP} \\ &\frac{d g}{d t}=-\frac{g}{\tau_{\mathrm{decay}}}+h \\ &\frac{d h}{d t}=-\frac{h}{\tau_{\text {rise }}}+ \delta\left(t_{0}-t\right), \end{aligned}\end{split}\]

where \(\mathrm{STP}\) is used to model the short-term plasticity effect of synapses.

Model Examples

>>> import brainpy as bp
>>> from brainpy import neurons, synapses, synouts
>>> import matplotlib.pyplot as plt
>>>
>>> neu1 = neurons.LIF(1)
>>> neu2 = neurons.LIF(1)
>>> syn1 = synapses.DualExponential(neu1, neu2, bp.connect.All2All(), output=synouts.CUBA())
>>> net = bp.Network(pre=neu1, syn=syn1, post=neu2)
>>>
>>> runner = bp.DSRunner(net, inputs=[('pre.input', 25.)], monitors=['pre.V', 'post.V', 'syn.g', 'syn.h'])
>>> runner.run(150.)
>>>
>>> fig, gs = bp.visualize.get_figure(2, 1, 3, 8)
>>> fig.add_subplot(gs[0, 0])
>>> plt.plot(runner.mon.ts, runner.mon['pre.V'], label='pre-V')
>>> plt.plot(runner.mon.ts, runner.mon['post.V'], label='post-V')
>>> plt.legend()
>>>
>>> fig.add_subplot(gs[1, 0])
>>> plt.plot(runner.mon.ts, runner.mon['syn.g'], label='g')
>>> plt.plot(runner.mon.ts, runner.mon['syn.h'], label='h')
>>> plt.legend()
>>> plt.show()

(Source code, png, hires.png, pdf)

Parameters:

• pre (NeuGroup) – The pre-synaptic neuron group.

• post (NeuGroup) – The post-synaptic neuron group.

• conn (optional, ArrayType, dict of (str, ndarray), TwoEndConnector) – The synaptic connections.

• comp_method (str) – The connection type used for model speed optimization. It can be sparse and dense. The default is sparse.

• delay_step (int, ArrayType, Initializer, Callable) – The delay length. It should be the value of \(\mathrm{delay\_time / dt}\).

• tau_decay (float, ArrayArray, ndarray) – The time constant of the synaptic decay phase. [ms]

• tau_rise (float, ArrayArray, ndarray) – The time constant of the synaptic rise phase. [ms]

• g_max (float, ArrayType, Initializer, Callable) – The synaptic strength (the maximum conductance). Default is 1.

• name (str) – The name of this synaptic projection.

• method (str) – The numerical integration methods.

References

[1]

Sterratt, David, Bruce Graham, Andrew Gillies, and David Willshaw. “The Synapse.” Principles of Computational Modelling in Neuroscience. Cambridge: Cambridge UP, 2011. 172-95. Print.

[2]

Roth, A., & Van Rossum, M. C. W. (2009). Modeling Synapses. Computational Modeling Methods for Neuroscientists.

__init__(pre, post, conn, stp=None, output=CUBA, comp_method='dense', g_max=1.0, tau_decay=10.0, tau_rise=1.0, delay_step=None, method='exp_auto', name=None, mode=None, stop_spike_gradient=False)

Methods

__init__(pre, post, conn[, stp, output, ...])
check_post_attrs(*attrs)	Check whether post group satisfies the requirement.
check_pre_attrs(*attrs)	Check whether pre group satisfies the requirement.
clear_input()
cpu()	Move all variable into the CPU device.
cuda()	Move all variables into the GPU device.
dg(g, t, h)
dh(h, t)
get_delay_data(identifier, delay_step, *indices)	Get delay data according to the provided delay steps.
load_state_dict(state_dict[, warn, compatible])	Copy parameters and buffers from state_dict into this module and its descendants.
load_states(filename[, verbose])	Load the model states.
nodes([method, level, include_self])	Collect all children nodes.
register_delay(identifier, delay_step, ...)	Register delay variable.
register_implicit_nodes(*nodes[, node_cls])
register_implicit_vars(*variables[, var_cls])
reset(*args, **kwargs)	Reset function which reset the whole variables in the model.
reset_local_delays([nodes])	Reset local delay variables.
reset_state([batch_size])	Reset function which reset the states in the model.
save_states(filename[, variables])	Save the model states.
state_dict()	Returns a dictionary containing a whole state of the module.
to(device)	Moves all variables into the given device.
tpu()	Move all variables into the TPU device.
train_vars([method, level, include_self])	The shortcut for retrieving all trainable variables.
tree_flatten()	Flattens the object as a PyTree.
tree_unflatten(aux, dynamic_values)	Unflatten the data to construct an object of this class.
unique_name([name, type_])	Get the unique name for this object.
update(tdi[, pre_spike])	The function to specify the updating rule.
update_local_delays([nodes])	Update local delay variables.
vars([method, level, include_self, ...])	Collect all variables in this node and the children nodes.

Attributes

global_delay_data	Global delay data, which stores the delay variables and corresponding delay targets.
mode	Mode of the model, which is useful to control the multiple behaviors of the model.
name	Name of the model.