[math & dyn] add brainpy.math.exprel, and change the code in the …

…corresponding HH neuron models to improve numerical computation accuracy (#557) * merge (#6) * [running] fix multiprocessing bugs (#547) * [running] fix multiprocessing bugs * fix tests * [docs] Fix typo in docs (#549) * ⬆️ Bump conda-incubator/setup-miniconda from 2 to 3 (#551) Bumps [conda-incubator/setup-miniconda](https://github.com/conda-incubator/setup-miniconda) from 2 to 3. - [Release notes](https://github.com/conda-incubator/setup-miniconda/releases) - [Changelog](https://github.com/conda-incubator/setup-miniconda/blob/main/CHANGELOG.md) - [Commits](conda-incubator/setup-miniconda@v2...v3) --- updated-dependencies: - dependency-name: conda-incubator/setup-miniconda dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * updates (#550) * [running] fix multiprocessing bugs * fix tests * [doc] update doc * update * [math] add `brainpy.math.gpu_memory_preallocation()` for controlling GPU memory preallocation * [math] `clear_buffer_memory` support to clear array and compilation both * [dyn] compatible old version of `.reset_state()` function * [setup] update installation info * ``brainpy.math.defjvp`` and ``brainpy.math.XLACustomOp.defjvp`` (#554) * [running] fix multiprocessing bugs * fix tests * [doc] update doc * update * [math] add `brainpy.math.gpu_memory_preallocation()` for controlling GPU memory preallocation * [math] `clear_buffer_memory` support to clear array and compilation both * [dyn] compatible old version of `.reset_state()` function * [setup] update installation info * [install] upgrade dependency * updates * [math] add `brainpy.math.defjvp`, support to define jvp rules for Primitive with multiple results. See examples in `test_ad_support.py` * [math] add `brainpy.math.XLACustomOp.defjvp` * [doc] upgrade `brainpy.math.defjvp` docstring * ⬆️ Bump actions/setup-python from 4 to 5 (#555) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v4...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Sichao He <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [math] add experimental `brainpy.math.exprel` * [delay] move delays in models of `brainpy.synapses` module into new delay register API `DynamicalSystem.register_local_delay()` and `DynamicalSystem.get_local_delay()` * [math & dyn] add `brainpy.math.exprel`, and change the code in the corresponding HH neuron models to improve numerical computation accuracy --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Sichao He <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
brainpy · Dec 10, 2023 · b1e80e8 · b1e80e8
1 parent 5be1834
commit b1e80e8
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Showing 10 changed files with 90 additions and 31 deletions.
diff --git a/brainpy/_src/dyn/neurons/hh.py b/brainpy/_src/dyn/neurons/hh.py
@@ -348,7 +348,8 @@ def __init__(
       self.reset_state(self.mode)
 
   # m channel
-  m_alpha = lambda self, V: 0.1 * (V + 40) / (1 - bm.exp(-(V + 40) / 10))
+  # m_alpha = lambda self, V: 0.1 * (V + 40) / (1 - bm.exp(-(V + 40) / 10))
+  m_alpha = lambda self, V: 1. / bm.exprel(-(V + 40) / 10)
   m_beta = lambda self, V: 4.0 * bm.exp(-(V + 65) / 18)
   m_inf = lambda self, V: self.m_alpha(V) / (self.m_alpha(V) + self.m_beta(V))
   dm = lambda self, m, t, V: self.m_alpha(V) * (1 - m) - self.m_beta(V) * m
@@ -360,7 +361,8 @@ def __init__(
   dh = lambda self, h, t, V: self.h_alpha(V) * (1 - h) - self.h_beta(V) * h
 
   # n channel
-  n_alpha = lambda self, V: 0.01 * (V + 55) / (1 - bm.exp(-(V + 55) / 10))
+  # n_alpha = lambda self, V: 0.01 * (V + 55) / (1 - bm.exp(-(V + 55) / 10))
+  n_alpha = lambda self, V: 0.1 / bm.exprel(-(V + 55) / 10)
   n_beta = lambda self, V: 0.125 * bm.exp(-(V + 65) / 80)
   n_inf = lambda self, V: self.n_alpha(V) / (self.n_alpha(V) + self.n_beta(V))
   dn = lambda self, n, t, V: self.n_alpha(V) * (1 - n) - self.n_beta(V) * n
@@ -383,8 +385,9 @@ def reset_state(self, batch_size=None, **kwargs):
 
   def dV(self, V, t, m, h, n, I):
     I = self.sum_inputs(V, init=I)
-    I_Na = (self.gNa * m ** 3.0 * h) * (V - self.ENa)
-    I_K = (self.gK * n ** 4.0) * (V - self.EK)
+    I_Na = (self.gNa * m * m * m * h) * (V - self.ENa)
+    n2 = n * n
+    I_K = (self.gK * n2 * n2) * (V - self.EK)
     I_leak = self.gL * (V - self.EL)
     dVdt = (- I_Na - I_K - I_leak + I) / self.C
     return dVdt
@@ -516,8 +519,9 @@ class HH(HHLTC):
   """
 
   def dV(self, V, t, m, h, n, I):
-    I_Na = (self.gNa * m ** 3.0 * h) * (V - self.ENa)
-    I_K = (self.gK * n ** 4.0) * (V - self.EK)
+    I_Na = (self.gNa * m * m * m * h) * (V - self.ENa)
+    n2 = n * n
+    I_K = (self.gK * n2 * n2) * (V - self.EK)
     I_leak = self.gL * (V - self.EL)
     dVdt = (- I_Na - I_K - I_leak + I) / self.C
     return dVdt
@@ -680,9 +684,7 @@ def update(self, x=None):
     t = share.load('t')
     dt = share.load('dt')
     x = 0. if x is None else x
-
     V, W = self.integral(self.V, self.W, t, x, dt)
-
     spike = bm.logical_and(self.V < self.V_th, V >= self.V_th)
     self.V.value = V
     self.W.value = W
@@ -930,7 +932,8 @@ def reset_state(self, batch_size=None):
     self.spike = self.init_variable(partial(bm.zeros, dtype=bool), batch_size)
 
   def m_inf(self, V):
-    alpha = -0.1 * (V + 35) / (bm.exp(-0.1 * (V + 35)) - 1)
+    # alpha = -0.1 * (V + 35) / (bm.exp(-0.1 * (V + 35)) - 1)
+    alpha = 1. / bm.exprel(-0.1 * (V + 35))
     beta = 4. * bm.exp(-(V + 60.) / 18.)
     return alpha / (alpha + beta)
 
@@ -941,7 +944,8 @@ def dh(self, h, t, V):
     return self.phi * dhdt
 
   def dn(self, n, t, V):
-    alpha = -0.01 * (V + 34) / (bm.exp(-0.1 * (V + 34)) - 1)
+    # alpha = -0.01 * (V + 34) / (bm.exp(-0.1 * (V + 34)) - 1)
+    alpha = 1. / bm.exprel(-0.1 * (V + 34))
     beta = 0.125 * bm.exp(-(V + 44) / 80)
     dndt = alpha * (1 - n) - beta * n
     return self.phi * dndt

diff --git a/brainpy/_src/dynold/synapses/abstract_models.py b/brainpy/_src/dynold/synapses/abstract_models.py
@@ -114,7 +114,7 @@ def __init__(
     self.g_max, self.conn_mask = self._init_weights(g_max, comp_method=comp_method, sparse_data='csr')
 
     # register delay
-    self.delay_step = self.pre.register_delay("spike", delay_step, self.pre.spike)
+    self.pre.register_local_delay("spike", self.name, delay_step)
 
   def reset_state(self, batch_size=None):
     self.output.reset_state(batch_size)
@@ -124,7 +124,7 @@ def reset_state(self, batch_size=None):
   def update(self, pre_spike=None):
     # pre-synaptic spikes
     if pre_spike is None:
-      pre_spike = self.pre.get_delay_data("spike", self.delay_step)
+      pre_spike = self.pre.get_local_delay("spike", self.name)
     pre_spike = bm.as_jax(pre_spike)
     if self.stop_spike_gradient:
       pre_spike = jax.lax.stop_gradient(pre_spike)
@@ -317,7 +317,7 @@ def __init__(
     self.g = self.syn.g
 
     # delay
-    self.delay_step = self.pre.register_delay("spike", delay_step, self.pre.spike)
+    self.pre.register_local_delay("spike", self.name, delay_step)
 
   def reset_state(self, batch_size=None):
     self.syn.reset_state(batch_size)
@@ -328,7 +328,7 @@ def reset_state(self, batch_size=None):
   def update(self, pre_spike=None):
     # delays
     if pre_spike is None:
-      pre_spike = self.pre.get_delay_data("spike", self.delay_step)
+      pre_spike = self.pre.get_local_delay("spike", self.name)
     pre_spike = bm.as_jax(pre_spike)
     if self.stop_spike_gradient:
       pre_spike = jax.lax.stop_gradient(pre_spike)

diff --git a/brainpy/_src/dynold/synapses/base.py b/brainpy/_src/dynold/synapses/base.py
@@ -296,7 +296,7 @@ def __init__(
                      mode=mode)
 
     # delay
-    self.delay_step = self.pre.register_delay("spike", delay_step, self.pre.spike)
+    self.pre.register_local_delay("spike", self.name, delay_step)
 
     # synaptic dynamics
     self.syn = syn
@@ -317,7 +317,7 @@ def __init__(
 
   def update(self, pre_spike=None, stop_spike_gradient: bool = False):
     if pre_spike is None:
-      pre_spike = self.pre.get_delay_data("spike", self.delay_step)
+      pre_spike = self.pre.get_local_delay("spike", self.name)
     if stop_spike_gradient:
       pre_spike = jax.lax.stop_gradient(pre_spike)
     if self.stp is not None:

diff --git a/brainpy/_src/dynsys.py b/brainpy/_src/dynsys.py
@@ -336,7 +336,7 @@ def _compatible_reset_state(self, *args, **kwargs):
       the_top_layer_reset_state = True
       warnings.warn(
         '''
-    From version >= 2.4.6, the policy of ``.reset_state()`` has been changed. See https://brainpy.tech/docs/tutorial_toolbox/state_saving_and_loading.html for details.
+    From version >= 2.4.6, the policy of ``.reset_state()`` has been changed. See https://brainpy.readthedocs.io/en/latest/tutorial_toolbox/state_saving_and_loading.html for details.
   
     1. If you are resetting all states in a network by calling "net.reset_state(*args, **kwargs)", please use
        "bp.reset_state(net, *args, **kwargs)" function, or "net.reset(*args, **kwargs)". 

diff --git a/brainpy/_src/integrators/ode/exponential.py b/brainpy/_src/integrators/ode/exponential.py
@@ -105,8 +105,6 @@
 .. [2] Hochbruck, M., & Ostermann, A. (2010). Exponential integrators. Acta Numerica, 19, 209-286.
 """
 
-import logging
-
 from functools import wraps
 from brainpy import errors
 from brainpy._src import math as bm
@@ -360,9 +358,7 @@ def integral(*args, **kwargs):
         assert len(args) > 0
         dt = kwargs.pop(C.DT, self.dt)
         linear, derivative = value_and_grad(*args, **kwargs)
-        phi = bm.where(linear == 0.,
-                       bm.ones_like(linear),
-                       (bm.exp(dt * linear) - 1) / (dt * linear))
+        phi = bm.exprel(dt * linear)
         return args[0] + dt * phi * derivative
 
       return [(integral, vars, pars), ]

diff --git a/brainpy/_src/integrators/sde/normal.py b/brainpy/_src/integrators/sde/normal.py
@@ -626,8 +626,7 @@ def integral(*args, **kwargs):
         assert len(args) > 0
         dt = kwargs.pop('dt', self.dt)
         linear, derivative = value_and_grad(*args, **kwargs)
-        linear = bm.as_jax(linear)
-        phi = jnp.where(linear == 0., jnp.ones_like(linear), (jnp.exp(dt * linear) - 1) / (dt * linear))
+        phi = bm.as_jax(bm.exprel(dt * linear))
         return args[0] + dt * phi * derivative
 
       return [(integral, vars, pars), ]

diff --git a/brainpy/_src/math/ndarray.py b/brainpy/_src/math/ndarray.py
@@ -79,7 +79,7 @@ class Array(object):
 
   """
 
-  __slots__ = ('_value', '_keep_sharding')
+  __slots__ = ('_value', )
 
   def __init__(self, value, dtype: Any = None):
     # array value
@@ -132,7 +132,7 @@ def value(self, value):
     if value.dtype != self_value.dtype:
       raise MathError(f"The dtype of the original data is {self_value.dtype}, "
                       f"while we got {value.dtype}.")
-    self._value = value.value if isinstance(value, Array) else value
+    self._value = value
 
   def update(self, value):
     """Update the value of this Array.
@@ -1549,11 +1549,12 @@ def value(self):
     Returns:
       The stored data.
     """
+    v = self._value
     # keep sharding constraints
-    if self._keep_sharding and hasattr(self._value, 'sharding') and (self._value.sharding is not None):
-        return jax.lax.with_sharding_constraint(self._value, self._value.sharding)
+    if self._keep_sharding and hasattr(v, 'sharding') and (v.sharding is not None):
+        return jax.lax.with_sharding_constraint(v, v.sharding)
     # return the value
-    return self._value
+    return v
 
   @value.setter
   def value(self, value):
@@ -1574,6 +1575,6 @@ def value(self, value):
     if value.dtype != self_value.dtype:
       raise MathError(f"The dtype of the original data is {self_value.dtype}, "
                       f"while we got {value.dtype}.")
-    self._value = value.value if isinstance(value, Array) else value
+    self._value = value
 
 
diff --git a/brainpy/_src/math/others.py b/brainpy/_src/math/others.py
@@ -7,14 +7,16 @@
 from jax.tree_util import tree_map
 
 from brainpy import check, tools
+from .compat_numpy import fill_diagonal
 from .environment import get_dt, get_int
 from .ndarray import Array
-from .compat_numpy import fill_diagonal
+from .interoperability import as_jax
 
 __all__ = [
   'shared_args_over_time',
   'remove_diag',
   'clip_by_norm',
+  'exprel',
 ]
 
 
@@ -82,3 +84,38 @@ def f(l):
     return l * clip_norm / jnp.maximum(jnp.sqrt(jnp.sum(l * l, axis=axis, keepdims=True)), clip_norm)
 
   return tree_map(f, t)
+
+
+def _exprel(x, threshold):
+  def true_f(x):
+    x2 = x * x
+    return 1. + x / 2. + x2 / 6. + x2 * x / 24.0  # + x2 * x2 / 120.
+
+  def false_f(x):
+    return (jnp.exp(x) - 1) / x
+
+  # return jax.lax.cond(jnp.abs(x) < threshold, true_f, false_f, x)
+  return jnp.where(jnp.abs(x) <= threshold, 1. + x / 2. + x * x / 6., (jnp.exp(x) - 1) / x)
+
+
+def exprel(x, threshold: float = None):
+  """Relative error exponential, ``(exp(x) - 1)/x``.
+
+  When ``x`` is near zero, ``exp(x)`` is near 1, so the numerical calculation of ``exp(x) - 1`` can
+  suffer from catastrophic loss of precision. ``exprel(x)`` is implemented to avoid the loss of
+  precision that occurs when ``x`` is near zero.
+
+  Args:
+    x: ndarray. Input array. ``x`` must contain real numbers.
+    threshold: float.
+
+  Returns:
+    ``(exp(x) - 1)/x``, computed element-wise.
+  """
+  x = as_jax(x)
+  if threshold is None:
+    if hasattr(x, 'dtype') and x.dtype == jnp.float64:
+      threshold = 1e-8
+    else:
+      threshold = 1e-5
+  return _exprel(x, threshold)
diff --git a/brainpy/_src/math/tests/test_others.py b/brainpy/_src/math/tests/test_others.py
@@ -0,0 +1,21 @@
+
+import brainpy.math as bm
+from scipy.special import exprel
+
+from unittest import TestCase
+
+
+class Test_exprel(TestCase):
+  def test1(self):
+    for x in [1e-4, 1e-5, 1e-6, 1e-7, 1e-8, 1e-9]:
+      print(f'{exprel(x)}, {bm.exprel(x)}, {exprel(x) - bm.exprel(x):.10f}')
+      # self.assertEqual(exprel(x))
+
+  def test2(self):
+    bm.enable_x64()
+    for x in [1e-4, 1e-5, 1e-6, 1e-7, 1e-8, 1e-9]:
+      print(f'{exprel(x)}, {bm.exprel(x)}, {exprel(x) - bm.exprel(x):.10f}')
+      # self.assertEqual(exprel(x))
+
+
+
diff --git a/brainpy/math/others.py b/brainpy/math/others.py
@@ -4,6 +4,7 @@
   shared_args_over_time as shared_args_over_time,
   remove_diag as remove_diag,
   clip_by_norm as clip_by_norm,
+  exprel as exprel,
 )
 
 from brainpy._src.math.object_transform.naming import (