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Synapse trace #61

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Synapse trace #61

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33c10f2
feat: move trace to synapses
saeedark May 10, 2024
fac2035
fix: Example and bugs
saeedark May 11, 2024
4059992
fix: wrong priority
saeedark May 18, 2024
7f3937a
feat: gap for masks
saeedark May 20, 2024
a0455fb
feat: gap for masks
saeedark May 20, 2024
4518ee2
Merge branch 'synapse-trace' of https://github.com/cnrl/CoNeX into sy…
saeedark May 20, 2024
635d45f
fix: None connection for synapse
saeedark May 24, 2024
67bf34c
style: improvement
saeedark May 25, 2024
a4a517a
style: gap order
saeedark Sep 27, 2024
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172 changes: 172 additions & 0 deletions Example/helpers/mask_example.ipynb
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70 changes: 42 additions & 28 deletions Example/test/layer4.json
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Original file line number Diff line number Diff line change
Expand Up @@ -65,18 +65,6 @@
"init_s": null
}
},
{
"key": 360,
"class": [
"python_callable",
"conex.behaviors.neurons.specs",
"SpikeTrace"
],
"parameters_args": [],
"parameters_kwargs": {
"tau_s": 10.0
}
},
{
"key": 380,
"class": [
Expand All @@ -89,8 +77,7 @@
"max_delay": 1,
"proximal_min_delay": 0,
"distal_min_delay": 0,
"apical_min_delay": 0,
"have_trace": null
"apical_min_delay": 0
}
},
{
Expand Down Expand Up @@ -169,18 +156,6 @@
"init_s": null
}
},
{
"key": 360,
"class": [
"python_callable",
"conex.behaviors.neurons.specs",
"SpikeTrace"
],
"parameters_args": [],
"parameters_kwargs": {
"tau_s": 10.0
}
},
{
"key": 380,
"class": [
Expand All @@ -193,8 +168,7 @@
"max_delay": 1,
"proximal_min_delay": 0,
"distal_min_delay": 0,
"apical_min_delay": 0,
"have_trace": null
"apical_min_delay": 0
}
}
],
Expand Down Expand Up @@ -250,6 +224,16 @@
"parameters_kwargs": {
"current_coef": 1
}
},
{
"key": 420,
"class": [
"python_callable",
"conex.behaviors.synapses.specs",
"PreSpikeCatcher"
],
"parameters_args": [],
"parameters_kwargs": {}
}
],
"device": "cpu",
Expand Down Expand Up @@ -305,6 +289,16 @@
"parameters_kwargs": {
"current_coef": 1
}
},
{
"key": 420,
"class": [
"python_callable",
"conex.behaviors.synapses.specs",
"PreSpikeCatcher"
],
"parameters_args": [],
"parameters_kwargs": {}
}
],
"device": "cpu",
Expand Down Expand Up @@ -360,6 +354,16 @@
"parameters_kwargs": {
"current_coef": 1
}
},
{
"key": 420,
"class": [
"python_callable",
"conex.behaviors.synapses.specs",
"PreSpikeCatcher"
],
"parameters_args": [],
"parameters_kwargs": {}
}
],
"device": "cpu",
Expand Down Expand Up @@ -415,6 +419,16 @@
"parameters_kwargs": {
"current_coef": 1
}
},
{
"key": 420,
"class": [
"python_callable",
"conex.behaviors.synapses.specs",
"PreSpikeCatcher"
],
"parameters_args": [],
"parameters_kwargs": {}
}
],
"device": "cpu",
Expand Down
39 changes: 30 additions & 9 deletions Example/test/mnist.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,11 +20,14 @@
SimpleDendriteStructure,
SimpleDendriteComputation,
LIF,
SpikeTrace,
NeuronAxon,
)
from conex.behaviors.synapses import (
SynapseInit,
PreTrace,
PostTrace,
PreSpikeCatcher,
PostSpikeCatcher,
WeightInitializer,
SimpleDendriticInput,
SimpleSTDP,
Expand Down Expand Up @@ -55,7 +58,6 @@
MNIST_ROOT = "~/Temp/MNIST/"
SENSORY_SIZE_HEIGHT = 28
SENSORY_SIZE_WIDTH = 28 # MNIST's image size
SENSORY_TRACE_TAU_S = 2.7

# Layer 4
L4_EXC_DEPTH = 4
Expand All @@ -66,7 +68,6 @@
L4_EXC_TAU = 10.0
L4_EXC_V_RESET = 0.0
L4_EXC_V_REST = 0.0
L4_EXC_TRACE_TAU = 10.0

L4_INH_SIZE = 576
L4_INH_R = 5.0
Expand Down Expand Up @@ -95,11 +96,18 @@


INP_CC_MODE = "random"
INP_CC_WEIGHT_SHAPE = (4,1,5,5)
INP_CC_WEIGHT_SHAPE = (4, 1, 5, 5)
INP_CC_COEF = 1
INP_CC_A_PLUS = 0.01
INP_CC_A_MINUS = 0.002

L4_EXC_L23_EXC_PRE_TRACE = 10.0
L4_EXC_L23_EXC_POST_TRACE = 10.0


SENSORY_L4_PRE_TRACE = 10.0
SENSORY_L4_POST_TRACE = 10.0


##################################################
# making dataloader
Expand Down Expand Up @@ -134,9 +142,8 @@
sensory_size=NeuronDimension(
depth=1, height=SENSORY_SIZE_HEIGHT, width=SENSORY_SIZE_WIDTH
),
sensory_trace=SENSORY_TRACE_TAU_S,
instance_duration=POISSON_TIME,
output_ports={"data_out": (None,[("sensory_pop", {})])}
output_ports={"data_out": (None, [("sensory_pop", {})])},
)

##################################################
Expand All @@ -159,7 +166,6 @@
v_reset=L4_EXC_V_RESET,
v_rest=L4_EXC_V_REST,
),
SpikeTrace(tau_s=L4_EXC_TRACE_TAU),
NeuronAxon(),
]
),
Expand All @@ -180,7 +186,6 @@
v_reset=L4_INH_V_RESET,
v_rest=L4_INH_V_REST,
),
SpikeTrace(tau_s=L4_INH_TRACE_TAU),
NeuronAxon(),
]
),
Expand All @@ -196,6 +201,7 @@
SynapseInit(),
WeightInitializer(mode=L4_EXC_EXC_MODE),
SimpleDendriticInput(current_coef=L4_EXC_EXC_COEF),
PreSpikeCatcher(),
]
),
)
Expand All @@ -210,6 +216,7 @@
SynapseInit(),
WeightInitializer(mode=L4_EXC_INH_MODE),
SimpleDendriticInput(current_coef=L4_EXC_INH_COEF),
PreSpikeCatcher(),
]
),
)
Expand All @@ -224,6 +231,7 @@
SynapseInit(),
WeightInitializer(mode=L4_INH_EXC_MODE),
SimpleDendriticInput(current_coef=L4_INH_EXC_COEF),
PreSpikeCatcher(),
]
),
)
Expand All @@ -238,6 +246,7 @@
SynapseInit(),
WeightInitializer(mode=L4_INH_INH_MODE),
SimpleDendriticInput(current_coef=L4_INH_INH_COEF),
PreSpikeCatcher(),
]
),
)
Expand Down Expand Up @@ -314,6 +323,10 @@
WeightInitializer(mode=L4_L2_MODE),
SimpleDendriticInput(current_coef=L4_L2_COEF),
SimpleSTDP(a_plus=L4_L2_A_PLUS, a_minus=L4_L2_A_MINUS),
PreSpikeCatcher(),
PostSpikeCatcher(),
PreTrace(tau_s=L4_EXC_L23_EXC_PRE_TRACE),
PostTrace(tau_s=L4_EXC_L23_EXC_POST_TRACE),
]
),
"Proximal",
Expand Down Expand Up @@ -357,9 +370,17 @@
synapsis_behavior=prioritize_behaviors(
[
SynapseInit(),
WeightInitializer(mode=INP_CC_MODE, weight_shape=INP_CC_WEIGHT_SHAPE, kernel_shape=INP_CC_WEIGHT_SHAPE),
WeightInitializer(
mode=INP_CC_MODE,
weight_shape=INP_CC_WEIGHT_SHAPE,
kernel_shape=INP_CC_WEIGHT_SHAPE,
),
Conv2dDendriticInput(current_coef=INP_CC_COEF),
Conv2dSTDP(a_plus=INP_CC_A_PLUS, a_minus=INP_CC_A_MINUS),
PreSpikeCatcher(),
PostSpikeCatcher(),
PreTrace(tau_s=SENSORY_L4_PRE_TRACE),
PostTrace(tau_s=SENSORY_L4_POST_TRACE),
]
),
synaptic_tag="Proximal",
Expand Down
15 changes: 1 addition & 14 deletions conex/behaviors/neurons/axon.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,14 +10,13 @@ class NeuronAxon(Behavior):
"""
Propagate the spikes and apply the delay mechanism.

Note: should be added after fire and trace behavior.
Note: should be added after fire.

Args:
max_delay (int): Maximum delay of all dendrites connected to the neurons. This value determines the delay buffer size.
proximal_min_delay (int): Minimum delay of proximal dendrites. The default is 0.
distal_min_delay (int): Minimum delay of distal dendrites. The default is 0.
apical_min_delay (int): Minimum delay of apical dendrites. The default is 0.
have_trace (boolean): whether to calculate trace or not. None checks if trace is available.
"""

def __init__(
Expand All @@ -27,7 +26,6 @@ def __init__(
proximal_min_delay=0,
distal_min_delay=0,
apical_min_delay=0,
have_trace=None,
**kwargs,
):
super().__init__(
Expand All @@ -36,7 +34,6 @@ def __init__(
proximal_min_delay=proximal_min_delay,
distal_min_delay=distal_min_delay,
apical_min_delay=apical_min_delay,
have_trace=have_trace,
**kwargs,
)

Expand All @@ -45,11 +42,8 @@ def initialize(self, neurons):
self.proximal_min_delay = self.parameter("proximal_min_delay", 0)
self.distal_min_delay = self.parameter("distal_min_delay", 0)
self.apical_min_delay = self.parameter("apical_min_delay", 0)
self.have_trace = self.parameter("have_trace", hasattr(neurons, "trace"))

self.spike_history = neurons.vector_buffer(self.max_delay, dtype=torch.bool)
if self.have_trace:
self.trace_history = neurons.vector_buffer(self.max_delay)

neurons.axon = self

Expand All @@ -70,14 +64,7 @@ def update_min_delay(self, neurons):
def get_spike(self, neurons, delay):
return self.spike_history.gather(0, delay.unsqueeze(0)).squeeze(0)

def get_spike_trace(self, neurons, delay):
return self.trace_history.gather(0, delay.unsqueeze(0)).squeeze(0)

def forward(self, neurons):
self.spike_history = neurons.buffer_roll(
mat=self.spike_history, new=neurons.spikes
)
if self.have_trace:
self.trace_history = neurons.buffer_roll(
mat=self.trace_history, new=neurons.trace
)
26 changes: 0 additions & 26 deletions conex/behaviors/neurons/specs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,32 +28,6 @@ def forward(self, neurons):
neurons.v += neurons.vector(mode=self.mode, scale=self.scale) + self.offset


class SpikeTrace(Behavior):
"""
Calculates the spike trace.

Note : should be placed after Fire behavior.

Args:
tau_s (float): decay term for spike trace. The default is None.
"""

def __init__(self, tau_s, *args, **kwargs):
super().__init__(*args, tau_s=tau_s, **kwargs)

def initialize(self, neurons):
"""
Sets the trace attribute for the neural population.
"""
self.tau_s = self.parameter("tau_s", None, required=True)
neurons.trace = neurons.vector(0.0)

def forward(self, neurons):
"""
Calculates the spike trace of each neuron by adding current spike and decaying the trace so far.
"""
neurons.trace += neurons.spikes
neurons.trace -= (neurons.trace / self.tau_s) * neurons.network.dt


class Fire(Behavior):
Expand Down
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