update experimental synapse models

Author: chaoming0625

brainpy/__init__.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = "2.3.6"
+__version__ = "2.3.7"
 
 
 # fundamental supporting modules
@@ -61,20 +61,23 @@
                      experimental,
                      )
 from brainpy._src.dyn.base import not_pass_shared
-from brainpy._src.dyn.base import (DynamicalSystem,
-                                   DynamicalSystemNS,
+from brainpy._src.dyn.base import (DynamicalSystem as DynamicalSystem,
                                    Container as Container,
                                    Sequential as Sequential,
                                    Network as Network,
                                    NeuGroup as NeuGroup,
-                                   NeuGroupNS as NeuGroupNS,
                                    SynConn as SynConn,
                                    SynOut as SynOut,
                                    SynSTP as SynSTP,
                                    SynLTP as SynLTP,
                                    TwoEndConn as TwoEndConn,
                                    CondNeuGroup as CondNeuGroup,
                                    Channel as Channel)
+from brainpy._src.dyn.base import (DynamicalSystemNS as DynamicalSystemNS,
+                                   NeuGroupNS as NeuGroupNS)
+from brainpy._src.dyn.synapses_v2.base import (SynOutNS as SynOutNS,
+                                               SynSTPNS as SynSTPNS,
+                                               SynConnNS as SynConnNS, )
 from brainpy._src.dyn.transform import (LoopOverTime as LoopOverTime,)
 from brainpy._src.dyn.runners import (DSRunner as DSRunner)  # runner
 from brainpy._src.dyn.context import share, Delay

brainpy/_src/dyn/synapses_v2/abstract_synapses.py

@@ -298,3 +298,106 @@ def update(self, pre_spike, post_v=None):
       return self.out(post_vs, post_v)
     else:
       return post_vs
+
+
+class Alpha(DualExponential):
+  r"""Alpha synapse model.
+
+  **Model Descriptions**
+
+  The analytical expression of alpha synapse is given by:
+
+  .. math::
+
+      g_{syn}(t)= g_{max} \frac{t-t_{s}}{\tau} \exp \left(-\frac{t-t_{s}}{\tau}\right).
+
+  While, this equation is hard to implement. So, let's try to convert it into the
+  differential forms:
+
+  .. math::
+
+      \begin{aligned}
+      &g_{\mathrm{syn}}(t)= g_{\mathrm{max}} g \\
+      &\frac{d g}{d t}=-\frac{g}{\tau}+h \\
+      &\frac{d h}{d t}=-\frac{h}{\tau}+\delta\left(t_{0}-t\right)
+      \end{aligned}
+
+  **Model Examples**
+
+  .. plot::
+    :include-source: True
+
+    >>> 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.Alpha(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()
+
+  Parameters
+  ----------
+  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 :math:`\mathrm{delay\_time / dt}`.
+  tau_decay: float, ArrayType
+    The time constant of the synaptic decay 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.
+  """
+
+  def __init__(
+      self,
+      conn: Union[TwoEndConnector, ArrayType, Dict[str, ArrayType]],
+      out: Optional[SynOutNS] = None,
+      stp: Optional[SynSTPNS] = None,
+      comp_method: str = 'dense',
+      g_max: Union[float, ArrayType, Initializer, Callable] = 1.,
+      tau_decay: Union[float, ArrayType] = 10.0,
+      method: str = 'exp_auto',
+
+      # other parameters
+      name: str = None,
+      mode: bm.Mode = None,
+  ):
+    super().__init__(conn=conn,
+                     comp_method=comp_method,
+                     g_max=g_max,
+                     tau_decay=tau_decay,
+                     tau_rise=tau_decay,
+                     method=method,
+                     out=out,
+                     stp=stp,
+                     name=name,
+                     mode=mode)
+

brainpy/_src/dyn/synapses_v2/base.py

@@ -10,12 +10,12 @@
 from brainpy.types import ArrayType
 
 
-class SynConn(DynamicalSystemNS):
+class SynConnNS(DynamicalSystemNS):
   def __init__(
       self,
       conn: TwoEndConnector,
-      out: Optional['SynOut'] = None,
-      stp: Optional['SynSTP'] = None,
+      out: Optional['SynOutNS'] = None,
+      stp: Optional['SynSTPNS'] = None,
       name: str = None,
       mode: bm.Mode = None,
   ):
@@ -28,8 +28,8 @@ def __init__(
     self.post_size = conn.post_size
     self.pre_num = conn.pre_num
     self.post_num = conn.post_num
-    assert out is None or isinstance(out, SynOut)
-    assert stp is None or isinstance(stp, SynSTP)
+    assert out is None or isinstance(out, SynOutNS)
+    assert stp is None or isinstance(stp, SynSTPNS)
     self.out = out
     self.stp = stp
 
@@ -118,15 +118,15 @@ def _syn2post_with_dense(self, syn_value, syn_weight, conn_mat):
     return post_vs
 
 
-class SynOut(DynamicalSystemNS):
+class SynOutNS(DynamicalSystemNS):
   def update(self, post_g, post_v):
     raise NotImplementedError
 
   def reset_state(self, batch_size: Optional[int] = None):
     pass
 
 
-class SynSTP(DynamicalSystemNS):
+class SynSTPNS(DynamicalSystemNS):
   """Base class for synaptic short-term plasticity."""
 
   def update(self, pre_spike):

brainpy/_src/dyn/synapses_v2/others.py

@@ -0,0 +1,86 @@
+
+from typing import Union, Optional
+
+import brainpy.math as bm
+from brainpy._src.dyn.base import DynamicalSystemNS
+from brainpy._src.dyn.context import share
+from brainpy.check import is_float, is_integer
+
+
+class PoissonInput(DynamicalSystemNS):
+  """Poisson Input.
+
+  Adds independent Poisson input to a target variable. For large
+  numbers of inputs, this is much more efficient than creating a
+  `PoissonGroup`. The synaptic events are generated randomly during the
+  simulation and are not preloaded and stored in memory. All the inputs must
+  target the same variable, have the same frequency and same synaptic weight.
+  All neurons in the target variable receive independent realizations of
+  Poisson spike trains.
+
+  Parameters
+  ----------
+  num_input: int
+    The number of inputs.
+  freq: float
+    The frequency of each of the inputs. Must be a scalar.
+  weight: float
+    The synaptic weight. Must be a scalar.
+  """
+
+  def __init__(
+      self,
+      target_shape,
+      num_input: int,
+      freq: Union[int, float],
+      weight: Union[int, float],
+      seed: Optional[int] = None,
+      mode: bm.Mode = None,
+      name: str = None
+  ):
+    super(PoissonInput, self).__init__(name=name, mode=mode)
+
+    # check data
+    is_integer(num_input, 'num_input', min_bound=1)
+    is_float(freq, 'freq', min_bound=0., allow_int=True)
+    is_float(weight, 'weight', allow_int=True)
+    assert self.mode.is_parent_of(bm.NonBatchingMode, bm.BatchingMode)
+
+    # parameters
+    self.target_shape = target_shape
+    self.num_input = num_input
+    self.freq = freq
+    self.weight = weight
+    self.seed = seed
+    self.rng = bm.random.default_rng(seed)
+
+  def update(self):
+    p = self.freq * share.dt / 1e3
+    a = self.num_input * p
+    b = self.num_input * (1 - p)
+    if isinstance(share.dt, (int, float)):  # dt is not in tracing
+      if (a > 5) and (b > 5):
+        inp = self.rng.normal(a, b * p, self.target_shape)
+      else:
+        inp = self.rng.binomial(self.num_input, p, self.target_shape)
+
+    else:  # dt is in tracing
+      inp = bm.cond((a > 5) * (b > 5),
+                    lambda _: self.rng.normal(a, b * p, self.target_shape),
+                    lambda _: self.rng.binomial(self.num_input, p, self.target_shape),
+                    None,
+                    dyn_vars=self.rng)
+    return inp * self.weight
+
+  def __repr__(self):
+    names = self.__class__.__name__
+    return f'{names}(shape={self.target_shape}, num_input={self.num_input}, freq={self.freq}, weight={self.weight})'
+
+  def reset_state(self, batch_size=None):
+    pass
+
+  def reset(self, batch_size=None):
+    self.rng.seed(self.seed)
+    self.reset_state(batch_size)
+
+

brainpy/experimental.py

@@ -1,9 +1,4 @@
 
-from brainpy._src.dyn.synapses_v2.base import (
-  SynConn as SynConn,
-  SynOut as SynOut,
-  SynSTP as SynSTP,
-)
 from brainpy._src.dyn.synapses_v2.syn_plasticity import (
   STD as STD,
   STP as STP,
@@ -13,5 +8,11 @@
   COBA as COBA,
 )
 from brainpy._src.dyn.synapses_v2.abstract_synapses import (
-  Exponential as Exponential,
+  Exponential,
+  DualExponential,
+  Alpha,
+)
+from brainpy._src.dyn.synapses_v2.others import (
+  PoissonInput,
 )
+