brainstate 0.0.2.post20241009__py2.py3-none-any.whl → 0.1.0__py2.py3-none-any.whl

brainstate/nn/_dyn_impl/_dynamics_neuron.py

@@ -0,0 +1,290 @@
+# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ==============================================================================
+
+# -*- coding: utf-8 -*-
+
+from __future__ import annotations
+
+from typing import Callable, Optional
+
+import brainunit as u
+import jax
+
+from brainstate import init, surrogate, environ
+from brainstate._state import HiddenState, ShortTermState
+from brainstate.nn._dynamics._dynamics_base import Dynamics
+from brainstate.nn._exp_euler import exp_euler_step
+from brainstate.typing import ArrayLike, Size
+
+__all__ = [
+    'Neuron', 'IF', 'LIF', 'LIFRef', 'ALIF',
+]
+
+
+class Neuron(Dynamics):
+    """
+    Base class for neuronal dynamics.
+
+    All neuron models are differentiable since they use surrogate gradient functions to
+    generate the spiking state.
+    """
+    __module__ = 'brainstate.nn'
+
+    def __init__(
+        self,
+        in_size: Size,
+        spk_fun: Callable = surrogate.InvSquareGrad(),
+        spk_reset: str = 'soft',
+        name: Optional[str] = None,
+    ):
+        super().__init__(in_size, name=name)
+        self.spk_reset = spk_reset
+        self.spk_fun = spk_fun
+
+    def get_spike(self, *args, **kwargs):
+        raise NotImplementedError
+
+
+class IF(Neuron):
+    """
+    Integrate-and-fire neuron model.
+    """
+
+    __module__ = 'brainstate.nn'
+
+    def __init__(
+        self,
+        in_size: Size,
+        R: ArrayLike = 1. * u.ohm,
+        tau: ArrayLike = 5. * u.ms,
+        V_th: ArrayLike = 1. * u.mV,  # should be positive
+        V_initializer: Callable = init.Constant(0. * u.mV),
+        spk_fun: Callable = surrogate.ReluGrad(),
+        spk_reset: str = 'soft',
+        name: str = None,
+    ):
+        super().__init__(in_size, name=name, spk_fun=spk_fun, spk_reset=spk_reset)
+
+        # parameters
+        self.R = init.param(R, self.varshape)
+        self.tau = init.param(tau, self.varshape)
+        self.V_th = init.param(V_th, self.varshape)
+        self.V_initializer = V_initializer
+
+    def init_state(self, batch_size: int = None, **kwargs):
+        self.V = HiddenState(init.param(self.V_initializer, self.varshape, batch_size))
+
+    def reset_state(self, batch_size: int = None, **kwargs):
+        self.V.value = init.param(self.V_initializer, self.varshape, batch_size)
+
+    def get_spike(self, V=None):
+        V = self.V.value if V is None else V
+        v_scaled = (V - self.V_th) / self.V_th
+        return self.spk_fun(v_scaled)
+
+    def update(self, x=0. * u.mA):
+        # reset
+        last_V = self.V.value
+        last_spike = self.get_spike(self.V.value)
+        V_th = self.V_th if self.spk_reset == 'soft' else jax.lax.stop_gradient(last_V)
+        V = last_V - V_th * last_spike
+        # membrane potential
+        dv = lambda v: (-v + self.R * self.sum_current_inputs(x, v)) / self.tau
+        V = exp_euler_step(dv, V)
+        V = self.sum_delta_inputs(V)
+        self.V.value = V
+        return self.get_spike(V)
+
+
+class LIF(Neuron):
+    """
+    Leaky integrate-and-fire neuron model.
+    """
+    __module__ = 'brainstate.nn'
+
+    def __init__(
+        self,
+        in_size: Size,
+        R: ArrayLike = 1. * u.ohm,
+        tau: ArrayLike = 5. * u.ms,
+        V_th: ArrayLike = 1. * u.mV,
+        V_reset: ArrayLike = 0. * u.mV,
+        V_rest: ArrayLike = 0. * u.mV,
+        V_initializer: Callable = init.Constant(0. * u.mV),
+        spk_fun: Callable = surrogate.ReluGrad(),
+        spk_reset: str = 'soft',
+        name: str = None,
+    ):
+        super().__init__(in_size, name=name, spk_fun=spk_fun, spk_reset=spk_reset)
+
+        # parameters
+        self.R = init.param(R, self.varshape)
+        self.tau = init.param(tau, self.varshape)
+        self.V_th = init.param(V_th, self.varshape)
+        self.V_rest = init.param(V_rest, self.varshape)
+        self.V_reset = init.param(V_reset, self.varshape)
+        self.V_initializer = V_initializer
+
+    def init_state(self, batch_size: int = None, **kwargs):
+        self.V = HiddenState(init.param(self.V_initializer, self.varshape, batch_size))
+
+    def reset_state(self, batch_size: int = None, **kwargs):
+        self.V.value = init.param(self.V_initializer, self.varshape, batch_size)
+
+    def get_spike(self, V: ArrayLike = None):
+        V = self.V.value if V is None else V
+        v_scaled = (V - self.V_th) / (self.V_th - self.V_reset)
+        return self.spk_fun(v_scaled)
+
+    def update(self, x=0. * u.mA):
+        last_v = self.V.value
+        lst_spk = self.get_spike(last_v)
+        V_th = self.V_th if self.spk_reset == 'soft' else jax.lax.stop_gradient(last_v)
+        V = last_v - (V_th - self.V_reset) * lst_spk
+        # membrane potential
+        dv = lambda v: (-v + self.V_rest + self.R * self.sum_current_inputs(x, v)) / self.tau
+        V = exp_euler_step(dv, V)
+        V = self.sum_delta_inputs(V)
+        self.V.value = V
+        return self.get_spike(V)
+
+
+class LIFRef(Neuron):
+    """
+    Leaky integrate-and-fire neuron model with refractory period.
+    """
+    __module__ = 'brainstate.nn'
+
+    def __init__(
+        self,
+        in_size: Size,
+        R: ArrayLike = 1. * u.ohm,
+        tau: ArrayLike = 5. * u.ms,
+        tau_ref: ArrayLike = 5. * u.ms,
+        V_th: ArrayLike = 1. * u.mV,
+        V_reset: ArrayLike = 0. * u.mV,
+        V_rest: ArrayLike = 0. * u.mV,
+        V_initializer: Callable = init.Constant(0. * u.mV),
+        spk_fun: Callable = surrogate.ReluGrad(),
+        spk_reset: str = 'soft',
+        name: str = None,
+    ):
+        super().__init__(in_size, name=name, spk_fun=spk_fun, spk_reset=spk_reset)
+
+        # parameters
+        self.R = init.param(R, self.varshape)
+        self.tau = init.param(tau, self.varshape)
+        self.tau_ref = init.param(tau_ref, self.varshape)
+        self.V_th = init.param(V_th, self.varshape)
+        self.V_rest = init.param(V_rest, self.varshape)
+        self.V_reset = init.param(V_reset, self.varshape)
+        self.V_initializer = V_initializer
+
+    def init_state(self, batch_size: int = None, **kwargs):
+        self.V = HiddenState(init.param(self.V_initializer, self.varshape, batch_size))
+        self.last_spike_time = ShortTermState(init.param(init.Constant(-1e7 * u.ms), self.varshape, batch_size))
+
+    def reset_state(self, batch_size: int = None, **kwargs):
+        self.V.value = init.param(self.V_initializer, self.varshape, batch_size)
+        self.last_spike_time.value = init.param(init.Constant(-1e7 * u.ms), self.varshape, batch_size)
+
+    def get_spike(self, V: ArrayLike = None):
+        V = self.V.value if V is None else V
+        v_scaled = (V - self.V_th) / (self.V_th - self.V_reset)
+        return self.spk_fun(v_scaled)
+
+    def update(self, x=0. * u.mA):
+        t = environ.get('t')
+        last_v = self.V.value
+        lst_spk = self.get_spike(last_v)
+        V_th = self.V_th if self.spk_reset == 'soft' else jax.lax.stop_gradient(last_v)
+        last_v = last_v - (V_th - self.V_reset) * lst_spk
+        # membrane potential
+        dv = lambda v: (-v + self.V_rest + self.R * self.sum_current_inputs(x, v)) / self.tau
+        V = exp_euler_step(dv, last_v)
+        V = self.sum_delta_inputs(V)
+        self.V.value = u.math.where(t - self.last_spike_time.value < self.tau_ref, last_v, V)
+        # spike time evaluation
+        lst_spk_time = u.math.where(self.V.value >= self.V_th, environ.get('t'), self.last_spike_time.value)
+        self.last_spike_time.value = jax.lax.stop_gradient(lst_spk_time)
+        return self.get_spike()
+
+
+class ALIF(Neuron):
+    """
+    Adaptive Leaky Integrate-and-Fire (LIF) neuron model.
+    """
+    __module__ = 'brainstate.nn'
+
+    def __init__(
+        self,
+        in_size: Size,
+        R: ArrayLike = 1. * u.ohm,
+        tau: ArrayLike = 5. * u.ms,
+        tau_a: ArrayLike = 100. * u.ms,
+        V_th: ArrayLike = 1. * u.mV,
+        V_reset: ArrayLike = 0. * u.mV,
+        V_rest: ArrayLike = 0. * u.mV,
+        beta: ArrayLike = 0.1 * u.mV,
+        spk_fun: Callable = surrogate.ReluGrad(),
+        spk_reset: str = 'soft',
+        V_initializer: Callable = init.Constant(0. * u.mV),
+        a_initializer: Callable = init.Constant(0.),
+        name: str = None,
+    ):
+        super().__init__(in_size, name=name, spk_fun=spk_fun, spk_reset=spk_reset)
+
+        # parameters
+        self.R = init.param(R, self.varshape)
+        self.tau = init.param(tau, self.varshape)
+        self.tau_a = init.param(tau_a, self.varshape)
+        self.V_th = init.param(V_th, self.varshape)
+        self.V_reset = init.param(V_reset, self.varshape)
+        self.V_rest = init.param(V_rest, self.varshape)
+        self.beta = init.param(beta, self.varshape)
+
+        # functions
+        self.V_initializer = V_initializer
+        self.a_initializer = a_initializer
+
+    def init_state(self, batch_size: int = None, **kwargs):
+        self.V = HiddenState(init.param(self.V_initializer, self.varshape, batch_size))
+        self.a = HiddenState(init.param(self.a_initializer, self.varshape, batch_size))
+
+    def reset_state(self, batch_size: int = None, **kwargs):
+        self.V.value = init.param(self.V_initializer, self.varshape, batch_size)
+        self.a.value = init.param(self.a_initializer, self.varshape, batch_size)
+
+    def get_spike(self, V=None, a=None):
+        V = self.V.value if V is None else V
+        a = self.a.value if a is None else a
+        v_scaled = (V - self.V_th - self.beta * a) / (self.V_th - self.V_reset)
+        return self.spk_fun(v_scaled)
+
+    def update(self, x=0. * u.mA):
+        last_v = self.V.value
+        last_a = self.a.value
+        lst_spk = self.get_spike(last_v, last_a)
+        V_th = self.V_th if self.spk_reset == 'soft' else jax.lax.stop_gradient(last_v)
+        V = last_v - (V_th - self.V_reset) * lst_spk
+        a = last_a + lst_spk
+        # membrane potential
+        dv = lambda v: (-v + self.V_rest + self.R * self.sum_current_inputs(x, v)) / self.tau
+        da = lambda a: -a / self.tau_a
+        V = exp_euler_step(dv, V)
+        a = exp_euler_step(da, a)
+        self.V.value = self.sum_delta_inputs(V)
+        self.a.value = a
+        return self.get_spike(self.V.value, self.a.value)

brainstate/nn/_dyn_impl/_dynamics_neuron_test.py

@@ -0,0 +1,162 @@
+# Copyright 2024 BDP Ecosystem Limited. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ==============================================================================
+
+# -*- coding: utf-8 -*-
+
+from __future__ import annotations
+
+import unittest
+
+import brainunit as u
+import jax
+import jax.numpy as jnp
+
+import brainstate as bst
+from brainstate.nn import IF, LIF, ALIF
+
+
+class TestNeuron(unittest.TestCase):
+    def setUp(self):
+        self.in_size = 10
+        self.batch_size = 5
+        self.time_steps = 100
+
+    def test_neuron_base_class(self):
+        with self.assertRaises(NotImplementedError):
+            bst.nn.Neuron(self.in_size).get_spike()  # Neuron is an abstract base class
+
+    def generate_input(self):
+        return bst.random.randn(self.time_steps, self.batch_size, self.in_size) * u.mA
+
+    def test_if_neuron(self):
+        with bst.environ.context(dt=0.1 * u.ms):
+            neuron = IF(self.in_size)
+            inputs = self.generate_input()
+
+            # Test initialization
+            self.assertEqual(neuron.in_size, (self.in_size,))
+            self.assertEqual(neuron.out_size, (self.in_size,))
+
+            # Test forward pass
+            state = neuron.init_state(self.batch_size)
+
+            for t in range(self.time_steps):
+                out = neuron(inputs[t])
+                self.assertEqual(out.shape, (self.batch_size, self.in_size))
+
+            # Test spike generation
+            v = jnp.linspace(-1, 1, 100) * u.mV
+            spikes = neuron.get_spike(v)
+            self.assertTrue(jnp.all((spikes >= 0) & (spikes <= 1)))
+
+    def test_lif_neuron(self):
+        with bst.environ.context(dt=0.1 * u.ms):
+            tau = 20.0 * u.ms
+            neuron = LIF(self.in_size, tau=tau)
+            inputs = self.generate_input()
+
+            # Test initialization
+            self.assertEqual(neuron.in_size, (self.in_size,))
+            self.assertEqual(neuron.out_size, (self.in_size,))
+            self.assertEqual(neuron.tau, tau)
+
+            # Test forward pass
+            state = neuron.init_state(self.batch_size)
+            call = bst.compile.jit(neuron)
+
+            for t in range(self.time_steps):
+                out = call(inputs[t])
+                self.assertEqual(out.shape, (self.batch_size, self.in_size))
+
+    def test_alif_neuron(self):
+        tau = 20.0 * u.ms
+        tau_ada = 100.0 * u.ms
+        neuron = ALIF(self.in_size, tau=tau, tau_a=tau_ada)
+        inputs = self.generate_input()
+
+        # Test initialization
+        self.assertEqual(neuron.in_size, (self.in_size,))
+        self.assertEqual(neuron.out_size, (self.in_size,))
+        self.assertEqual(neuron.tau, tau)
+        self.assertEqual(neuron.tau_a, tau_ada)
+
+        # Test forward pass
+        neuron.init_state(self.batch_size)
+        call = bst.compile.jit(neuron)
+        with bst.environ.context(dt=0.1 * u.ms):
+            for t in range(self.time_steps):
+                out = call(inputs[t])
+                self.assertEqual(out.shape, (self.batch_size, self.in_size))
+
+    def test_spike_function(self):
+        for NeuronClass in [IF, LIF, ALIF]:
+            neuron = NeuronClass(self.in_size)
+            neuron.init_state()
+            v = jnp.linspace(-1, 1, self.in_size) * u.mV
+            spikes = neuron.get_spike(v)
+            self.assertTrue(jnp.all((spikes >= 0) & (spikes <= 1)))
+
+    def test_soft_reset(self):
+        for NeuronClass in [IF, LIF, ALIF]:
+            neuron = NeuronClass(self.in_size, spk_reset='soft')
+            inputs = self.generate_input()
+            state = neuron.init_state(self.batch_size)
+            call = bst.compile.jit(neuron)
+            with bst.environ.context(dt=0.1 * u.ms):
+                for t in range(self.time_steps):
+                    out = call(inputs[t])
+                    self.assertTrue(jnp.all(neuron.V.value <= neuron.V_th))
+
+    def test_hard_reset(self):
+        for NeuronClass in [IF, LIF, ALIF]:
+            neuron = NeuronClass(self.in_size, spk_reset='hard')
+            inputs = self.generate_input()
+            state = neuron.init_state(self.batch_size)
+            call = bst.compile.jit(neuron)
+            with bst.environ.context(dt=0.1 * u.ms):
+                for t in range(self.time_steps):
+                    out = call(inputs[t])
+                    self.assertTrue(jnp.all((neuron.V.value < neuron.V_th) | (neuron.V.value == 0. * u.mV)))
+
+    def test_detach_spike(self):
+        for NeuronClass in [IF, LIF, ALIF]:
+            neuron = NeuronClass(self.in_size)
+            inputs = self.generate_input()
+            state = neuron.init_state(self.batch_size)
+            call = bst.compile.jit(neuron)
+            with bst.environ.context(dt=0.1 * u.ms):
+                for t in range(self.time_steps):
+                    out = call(inputs[t])
+                    self.assertFalse(jax.tree_util.tree_leaves(out)[0].aval.weak_type)
+
+    def test_keep_size(self):
+        in_size = (2, 3)
+        for NeuronClass in [IF, LIF, ALIF]:
+            neuron = NeuronClass(in_size)
+            self.assertEqual(neuron.in_size, in_size)
+            self.assertEqual(neuron.out_size, in_size)
+
+            inputs = bst.random.randn(self.time_steps, self.batch_size, *in_size) * u.mA
+            state = neuron.init_state(self.batch_size)
+            call = bst.compile.jit(neuron)
+            with bst.environ.context(dt=0.1 * u.ms):
+                for t in range(self.time_steps):
+                    out = call(inputs[t])
+                    self.assertEqual(out.shape, (self.batch_size, *in_size))
+
+
+if __name__ == '__main__':
+    with bst.environ.context(dt=0.1):
+        unittest.main()