def FeedforwardDeriv(n_neurons,
dimensions,
tau_fast=0.005,
tau_slow=0.1,
net=None):
if net is None:
net = nengo.Network(label="Derivative (two feedforward connections)")
assert tau_slow > tau_fast, ("tau_fast (%s) must be > tau_slow (%s)" %
(tau_fast, tau_slow))
with net:
net.ea_in = EnsembleArray(n_neurons, n_ensembles=dimensions)
net.ea_out = EnsembleArray(n_neurons, n_ensembles=dimensions)
nengo.Connection(net.ea_in.output,
net.ea_out.input,
synapse=tau_fast,
transform=1. / tau_slow)
nengo.Connection(net.ea_in.output,
net.ea_out.input,
synapse=tau_slow,
transform=-1. / tau_slow)
net.input = net.ea_in.input
net.output = net.ea_out.output
return net
def __init__(self, n_neurons, dimensions, fdbk_synapse=0.1,
conn_synapse=0.005, fdbk_scale=1.0, gate_gain=2.0,
reset_gain=3, **ens_args):
self.input = nengo.Node(size_in=dimensions)
self.output = nengo.Node(size_in=dimensions)
# gate control signal (if gate==0, update stored value, otherwise
# retain stored value)
self.gate = nengo.Node(size_in=1)
# integrator to store value
self.mem = EnsembleArray(n_neurons, dimensions, label="mem",
**ens_args)
# ensemble to gate feedback
self.fdbk = EnsembleArray(n_neurons, dimensions, label="fdbk",
**ens_args)
# ensemble to gate input
self.in_gate = EnsembleArray(n_neurons, dimensions, label="in_gate",
**ens_args)
# calculate gating control signal
self.ctrl = nengo.Ensemble(n_neurons, 1, label="ctrl")
# Connection from mem to fdbk, and from fdbk to mem
nengo.Connection(self.mem.output, self.fdbk.input,
synapse=fdbk_synapse - conn_synapse)
nengo.Connection(self.fdbk.output, self.mem.input,
transform=np.eye(dimensions) * fdbk_scale,
synapse=conn_synapse)
# Connection from input to in_gate, and from in_gate to mem
nengo.Connection(self.input, self.in_gate.input, synapse=None)
nengo.Connection(self.in_gate.output, self.mem.input,
synapse=conn_synapse)
# Connection from gate to ctrl
nengo.Connection(self.gate, self.ctrl, synapse=None)
# Connection from ctrl to fdbk and in_gate
for e in self.fdbk.ensembles:
nengo.Connection(self.ctrl, e.neurons,
function=lambda x: [1 - x[0]],
transform=[[-gate_gain]] * e.n_neurons)
for e in self.in_gate.ensembles:
nengo.Connection(self.ctrl, e.neurons,
transform=[[-gate_gain]] * e.n_neurons)
# Connection from mem to output
nengo.Connection(self.mem.output, self.output, synapse=None)
# reset input (if reset=1, remove all values stored, and set values
# to 0)
self.reset = nengo.Node(size_in=1)
for e in self.mem.ensembles:
nengo.Connection(self.reset, e.neurons,
transform=[[-reset_gain]] * e.n_neurons)
def build_unbind(self, model):
A_input_func = make_func(self, "A_input_vector")
B_input_func = make_func(self, "B_input_vector")
neurons_per_dim = self.neurons_per_dim
radius = self.radius
synapse = self.synapse
dimension = self.dimension
with model:
A_input = nengo.Node(output=A_input_func, size_out=dimension)
B_input = nengo.Node(output=B_input_func, size_out=dimension)
A = EnsembleArray(n_neurons=neurons_per_dim,
n_ensembles=dimension,
label="A",
radius=radius)
B = EnsembleArray(n_neurons=neurons_per_dim,
n_ensembles=dimension,
label="B",
radius=radius)
cconv = CircularConvolution(n_neurons=int(2 * neurons_per_dim),
dimensions=dimension,
invert_b=True)
D = EnsembleArray(n_neurons=neurons_per_dim,
n_ensembles=dimension,
label="D",
radius=radius)
A_output = A.output
B_output = B.output
D_output = D.output
cconv_output = cconv.output
nengo.Connection(A_input, A.input)
nengo.Connection(B_input, B.input)
nengo.Connection(A_output, cconv.A, synapse=synapse)
nengo.Connection(B_output, cconv.B, synapse=synapse)
nengo.Connection(cconv_output, D.input, synapse=synapse)
assoc_synapse = self.assoc_params.synapse
self.D_probe = nengo.Probe(D_output,
'output',
synapse=assoc_synapse)
self.input_probe = nengo.Probe(A_output, 'output', synapse=synapse)
self.D_output = D_output
self.A = A
self.B = B
self.cconv = cconv
self.D = D
def __init__(self,
n_neurons,
dimensions,
feedback=1.0,
difference_gain=1.0,
recurrent_synapse=0.1,
difference_synapse=None,
**kwargs):
if 'net' in kwargs:
raise ObsoleteError("The 'net' argument is no longer supported.")
kwargs.setdefault('label', "Input gated memory")
super(InputGatedMemory, self).__init__(**kwargs)
if difference_synapse is None:
difference_synapse = recurrent_synapse
n_total_neurons = n_neurons * dimensions
with self:
# integrator to store value
self.mem = EnsembleArray(n_neurons, dimensions, label="mem")
nengo.Connection(self.mem.output,
self.mem.input,
transform=feedback,
synapse=recurrent_synapse)
# calculate difference between stored value and input
self.diff = EnsembleArray(n_neurons, dimensions, label="diff")
nengo.Connection(self.mem.output, self.diff.input, transform=-1)
# feed difference into integrator
nengo.Connection(self.diff.output,
self.mem.input,
transform=difference_gain,
synapse=difference_synapse)
# gate difference (if gate==0, update stored value,
# otherwise retain stored value)
self.gate = nengo.Node(size_in=1)
self.diff.add_neuron_input()
nengo.Connection(self.gate,
self.diff.neuron_input,
transform=np.ones((n_total_neurons, 1)) * -10,
synapse=None)
# reset input (if reset=1, remove all values, and set to 0)
self.reset = nengo.Node(size_in=1)
nengo.Connection(self.reset,
self.mem.add_neuron_input(),
transform=np.ones((n_total_neurons, 1)) * -3,
synapse=None)
self.input = self.diff.input
self.output = self.mem.output
def __init__(self, num_func_points, func_value_range=1.0,
func_output_dimensions=1, n_neurons=500, label=None,
seed=None, add_to_container=None):
super(DifferenceFunctionEvaluator, self).__init__(label, seed,
add_to_container)
intercept_interval = 2.0 / (num_func_points - 1)
self.func_output_dimensions = func_output_dimensions
self.n_neurons = n_neurons
with self:
bias_node = nengo.Node(1)
self.func_input = nengo.Node(size_in=1)
self.func_output = nengo.Node(size_in=func_output_dimensions)
self.diff_func_pts = []
self.diff_func_outputs = []
self.func_gate_eas = []
func_domain_inhib_ea = EA(25, num_func_points - 1,
encoders=Choice([[-1]]),
intercepts=Uniform(0,
intercept_interval))
# Generate inhibit signal based of the function domain input value
func_domain_inhib_ea.add_output('const', lambda x: 1)
inhib_trfm = np.array([np.linspace(-1, 1, num_func_points)[:-1] +
intercept_interval / 2.0])
nengo.Connection(bias_node, func_domain_inhib_ea.input,
transform=-1 - inhib_trfm.T)
nengo.Connection(self.func_input,
func_domain_inhib_ea.input,
transform=2 * np.ones((num_func_points - 1, 1)),
synapse=None)
for n in range(func_output_dimensions):
func_gate_ea = EA(n_neurons, num_func_points,
radius=func_value_range)
for i, gate in enumerate(func_gate_ea.all_ensembles[1:]):
nengo.Connection(func_domain_inhib_ea.const[i],
gate.neurons,
transform=[[-5]] * n_neurons)
self.func_gate_eas.append(func_gate_ea)
self.diff_func_pts.append(func_gate_ea.input)
self.diff_func_outputs.append(func_gate_ea.output)
nengo.Connection(func_gate_ea.output, self.func_output[n],
transform=np.ones((1, num_func_points)),
synapse=None)
def build_output(self, model):
assoc_probes = OrderedDict()
threshold_probes = OrderedDict()
assoc_spike_probes = OrderedDict()
synapse = self.assoc_params.synapse
with model:
input = nengo.Node(output=self.assoc_output_func)
output = EnsembleArray(n_neurons=self.neurons_per_dim,
n_ensembles=self.dimension,
label="output",
radius=self.radius)
nengo.Connection(input, output.input, synapse=synapse)
self.output_probe = nengo.Probe(output.output,
'output',
synapse=0.02)
for k in self.probe_keys:
n = nengo.Node(output=self.assoc_memory.probe_func(k))
probe = nengo.Probe(n, synapse=synapse)
threshold_probes[k] = probe
node = nengo.Node(output=self.assoc_memory.spike_func(k))
assoc_spike_probes[k] = nengo.Probe(node, synapse=None)
self.assoc_probes = assoc_probes
self.threshold_probes = threshold_probes
self.assoc_spike_probes = assoc_spike_probes
def make_ens_array(self, **args):
ens_args = dict(args)
ens_args['n_neurons'] = args.get('n_neurons', self.n_neurons_ens)
n_ensembles = ens_args.pop('dimensions', vocab.sp_dim)
ens_args['n_ensembles'] = args.get('n_ensembles', n_ensembles)
ens_args['radius'] = args.get('radius', self.get_optimal_sp_radius())
return EnsembleArray(**ens_args)
def InputGatedMemory(n_neurons, dimensions, feedback=1.0,
difference_gain=1.0, recurrent_synapse=0.1,
difference_synapse=None, net=None):
"""Stores a given vector in memory, with input controlled by a gate."""
if net is None:
net = nengo.Network(label="Input Gated Memory")
if difference_synapse is None:
difference_synapse = recurrent_synapse
n_total_neurons = n_neurons * dimensions
with net:
# integrator to store value
net.mem = EnsembleArray(n_neurons, dimensions, label="mem")
nengo.Connection(net.mem.output, net.mem.input,
transform=feedback,
synapse=recurrent_synapse)
# calculate difference between stored value and input
net.diff = EnsembleArray(n_neurons, dimensions, label="diff")
nengo.Connection(net.mem.output, net.diff.input, transform=-1)
# feed difference into integrator
nengo.Connection(net.diff.output, net.mem.input,
transform=difference_gain,
synapse=difference_synapse)
# gate difference (if gate==0, update stored value,
# otherwise retain stored value)
net.gate = nengo.Node(size_in=1)
net.diff.add_neuron_input()
nengo.Connection(net.gate, net.diff.neuron_input,
transform=np.ones((n_total_neurons, 1)) * -10,
synapse=None)
# reset input (if reset=1, remove all values, and set to 0)
net.reset = nengo.Node(size_in=1)
nengo.Connection(net.reset, net.mem.add_neuron_input(),
transform=np.ones((n_total_neurons, 1)) * -3,
synapse=None)
net.input = net.diff.input
net.output = net.mem.output
return net
def delayed_synapse():
a = 0.1 # desired delay
b = 0.01 # synapse delay
tau = 0.01 # recurrent tau
hz = 15 # input frequency
t = 1.0 # simulation time
dt = 0.00001 # simulation timestep
order = 6 # order of pade approximation
tau_probe = 0.02
dexp_synapse = DoubleExp(tau, tau / 5)
sys_lambert = lambert_delay(a, b, tau, order - 1, order)
synapse = (cont2discrete(Lowpass(tau), dt=dt) *
DiscreteDelay(int(b / dt)))
n_neurons = 2000
neuron_type = PerfectLIF()
A, B, C, D = sys_lambert.observable.transform(5*np.eye(order)).ss
sys_normal = PadeDelay(a, order)
assert len(sys_normal) == order
with Network(seed=0) as model:
stim = Node(output=WhiteSignal(t, high=hz, y0=0))
x = EnsembleArray(n_neurons / order, len(A), neuron_type=neuron_type)
output = Node(size_in=1)
Connection(x.output, x.input, transform=A, synapse=synapse)
Connection(stim, x.input, transform=B, synapse=synapse)
Connection(x.output, output, transform=C, synapse=None)
Connection(stim, output, transform=D, synapse=None)
lowpass_delay = LinearNetwork(
sys_normal, n_neurons_per_ensemble=n_neurons / order,
synapse=tau, input_synapse=tau,
dt=None, neuron_type=neuron_type, radii=1.0)
Connection(stim, lowpass_delay.input, synapse=None)
dexp_delay = LinearNetwork(
sys_normal, n_neurons_per_ensemble=n_neurons / order,
synapse=dexp_synapse, input_synapse=dexp_synapse,
dt=None, neuron_type=neuron_type, radii=1.0)
Connection(stim, dexp_delay.input, synapse=None)
p_stim = Probe(stim, synapse=tau_probe)
p_output_delayed = Probe(output, synapse=tau_probe)
p_output_lowpass = Probe(lowpass_delay.output, synapse=tau_probe)
p_output_dexp = Probe(dexp_delay.output, synapse=tau_probe)
with Simulator(model, dt=dt, seed=0) as sim:
sim.run(t)
return (a, dt, sim.trange(), sim.data[p_stim],
sim.data[p_output_delayed], sim.data[p_output_lowpass],
sim.data[p_output_dexp])
def make_ens_array(self, **args):
ens_args = dict(args)
ens_args['radius'] = args.get('radius', 1)
ens_args['ens_dimensions'] = args.get('ens_dimensions',
self.ens_array_subdim)
n_ensembles = (ens_args.pop('dimensions', vocab.sp_dim) //
ens_args['ens_dimensions'])
ens_args['n_neurons'] = (args.get('n_neurons', self.n_neurons_ens) *
ens_args['ens_dimensions'])
ens_args['n_ensembles'] = args.get('n_ensembles', n_ensembles)
return EnsembleArray(**ens_args)
def IntermediateDeriv(n_neurons, dimensions, tau=0.1, net=None):
if net is None:
net = nengo.Network(label="Derivative (intermediate ensemble)")
with net:
net.ea_in = EnsembleArray(n_neurons, n_ensembles=dimensions)
net.ea_interm = EnsembleArray(n_neurons, n_ensembles=dimensions)
net.ea_out = EnsembleArray(n_neurons, n_ensembles=dimensions)
nengo.Connection(net.ea_in.output, net.ea_interm.input, synapse=tau)
nengo.Connection(net.ea_in.output,
net.ea_out.input,
synapse=tau,
transform=1. / tau)
nengo.Connection(net.ea_interm.output,
net.ea_out.input,
synapse=tau,
transform=-1. / tau)
net.input = net.ea_in.input
net.output = net.ea_out.output
return net
def Product(n_neurons, dimensions, input_magnitude=1):
encoders = nengo.dists.Choice([[1, 1], [1, -1], [-1, 1], [-1, -1]])
product = EnsembleArray(n_neurons,
n_ensembles=dimensions,
ens_dimensions=2,
encoders=encoders,
radius=input_magnitude * np.sqrt(2))
with product:
product.A = nengo.Node(size_in=dimensions, label="A")
product.B = nengo.Node(size_in=dimensions, label="B")
nengo.Connection(product.A, product.input[::2], synapse=None)
nengo.Connection(product.B, product.input[1::2], synapse=None)
# Remove default output
for conn in list(product.connections):
if conn.post is product.output:
product.connections.remove(conn)
product.nodes.remove(product.output)
# Add product output
product.output = product.add_output('product',
lambda x: x[0] * x[1],
synapse=None)
return product
def __init__(self, n_neurons, dimensions, mem_synapse=0.1, fdbk_scale=1.0,
difference_gain=1.0, gate_gain=10, reset_gain=3,
**mem_args):
self.input = nengo.Node(size_in=dimensions)
self.output = nengo.Node(size_in=dimensions)
# integrator to store value
self.mem = EnsembleArray(n_neurons, dimensions, label="mem",
**mem_args)
nengo.Connection(self.mem.output, self.mem.input, synapse=mem_synapse,
transform=np.eye(dimensions) * fdbk_scale)
# calculate difference between stored value and input
self.diff = EnsembleArray(n_neurons, dimensions, label="diff")
nengo.Connection(self.input, self.diff.input, synapse=None)
nengo.Connection(self.mem.output, self.diff.input,
transform=np.eye(dimensions) * -1)
# feed difference into integrator
nengo.Connection(self.diff.output, self.mem.input,
transform=np.eye(dimensions) * difference_gain,
synapse=mem_synapse)
# gate difference (if gate==0, update stored value,
# otherwise retain stored value)
self.gate = nengo.Node(size_in=1)
for e in self.diff.ensembles:
nengo.Connection(self.gate, e.neurons,
transform=[[-gate_gain]] * e.n_neurons)
# reset input (if reset=1, remove all values stored, and set values
# to 0)
self.reset_node = nengo.Node(size_in=1)
for e in self.mem.ensembles:
nengo.Connection(self.reset_node, e.neurons,
transform=[[-reset_gain]] * e.n_neurons)
nengo.Connection(self.mem.output, self.output, synapse=None)
def build_output(self, model):
with model:
self.output = EnsembleArray(n_neurons=self.neurons_per_dim,
n_ensembles=self.dimension,
label="output",
radius=self.radius)
output_output = self.output.output
self.output_probe = nengo.Probe(output_output,
'output',
synapse=0.02)
def Cepstra(n_neurons, n_freqs, n_cepstra, net=None):
if net is None:
net = nengo.Network("Cepstra")
with net:
net.input = nengo.Node(size_in=n_freqs, label="input")
net.out_ea = EnsembleArray(n_neurons, n_ensembles=n_cepstra)
nengo.Connection(net.input,
net.out_ea.input,
synapse=None,
transform=idct(n_freqs, n_cepstra))
net.output = net.out_ea.output
return net
def Product(n_neurons, dimensions, input_magnitude=1):
encoders = nengo.dists.Choice([[1, 1], [1, -1], [-1, 1], [-1, -1]])
product = EnsembleArray(n_neurons, n_ensembles=dimensions,
ens_dimensions=2,
encoders=encoders,
radius=input_magnitude * np.sqrt(2))
with product:
product.A = nengo.Node(size_in=dimensions, label="A")
product.B = nengo.Node(size_in=dimensions, label="B")
nengo.Connection(product.A, product.input[::2], synapse=None)
nengo.Connection(product.B, product.input[1::2], synapse=None)
# Remove default output
for conn in list(product.connections):
if conn.post is product.output:
product.connections.remove(conn)
product.nodes.remove(product.output)
# Add product output
product.output = product.add_output(
'product', lambda x: x[0] * x[1], synapse=None)
return product
def build_syllables(self, net):
assert len(self.syllables) > 0, "No syllables added"
# Make a readout for the production info coming from the DMPs
intercepts = Exponential(0.15, self.production_info.threshold, 1)
net.production_info = EnsembleArray(self.production_info.n_per_d,
n_ensembles=48,
encoders=Choice([[1]]),
intercepts=intercepts,
radius=1.1)
net.syllables = []
dt = self.trial.dt
for syllable in self.syllables:
forcing_f, gesture_ix = traj2func(syllable.trajectory, dt=dt)
forcing_f.__name__ = syllable.label
dmp = RhythmicDMP(forcing_f=forcing_f,
freq=syllable.freq,
**self.syllable.kwargs())
nengo.Connection(dmp.output, net.production_info.input[gesture_ix])
net.syllables.append(dmp)
def VectorNormalize(min_mag, max_mag, dimensions, radius_scale=1.0,
n_neurons_norm=50, n_neurons_prod=150,
norm_error_per_dimension=0.0003,
subtract_scale=1, net=None):
if net is None:
net = nengo.Network(label="Vector Normalize")
max_radius_scale = max_mag * radius_scale
norm_sub_in_low = min_mag ** 2
norm_sub_in_high = max_mag ** 2
norm_sub_in_trfm = scale_trfm(norm_sub_in_low, norm_sub_in_high)
norm_sub_in_bias = scale_bias(norm_sub_in_low, norm_sub_in_high)
norm_sub_in_bias_offset = -(norm_error_per_dimension * dimensions)
prod_a_trfm = 1.0 / max_radius_scale
prod_b_low = 1.0 - 1.0 / min_mag
prod_b_high = 1.0 - 1.0 / max_mag
prod_b_trfm = scale_trfm(prod_b_low, prod_b_high)
prod_b_bias = scale_bias(prod_b_low, prod_b_high)
def norm_sub_func(x, nsit=norm_sub_in_trfm, nsib=norm_sub_in_bias,
pbt=prod_b_trfm, pbb=prod_b_bias):
return norm_subtract_func(x, nsit, nsib, pbt, pbb)
def prod_func(x, y, pat=prod_a_trfm, pbt=prod_b_trfm, pbb=prod_b_bias):
return prod_out_func(x, y, pat, 0, pbt, pbb)
with net:
net.input = nengo.Node(size_in=dimensions)
net.output = nengo.Node(size_in=dimensions)
bias_node = nengo.Node(1)
# Ensemble array to represent input vector and to compute vector
# norm
norm_array = EnsembleArray(n_neurons_norm, dimensions,
radius=max_radius_scale)
norm_array.add_output('squared', lambda x: x ** 2)
nengo.Connection(net.input, norm_array.input)
# Ensemble to calculate amount of magnitude to be subtracted
# i.e. (1 - 1 / np.linalg.norm(input))
norm_subtract_ens = nengo.Ensemble(n_neurons_norm, 1,
n_eval_points=5000)
nengo.Connection(norm_array.squared, norm_subtract_ens,
transform=np.ones((1, dimensions)) * norm_sub_in_trfm)
nengo.Connection(bias_node, norm_subtract_ens,
transform=norm_sub_in_bias + norm_sub_in_bias_offset)
# Product network to compute product between input vector and
# magnitude to be subtracted
prod_array = Product(n_neurons_prod, dimensions)
for e in prod_array.product.ensembles:
e.n_eval_points = 5000
prod_array.product.add_output('prod2', lambda x: prod_func(x[0], x[1]))
prod_array.prod2 = prod_array.product.prod2
nengo.Connection(norm_array.output, prod_array.A,
transform=prod_a_trfm)
nengo.Connection(norm_subtract_ens, prod_array.B,
function=norm_sub_func,
transform=np.ones((dimensions, 1)))
# Output connections
nengo.Connection(norm_array.output, net.output)
nengo.Connection(prod_array.prod2, net.output,
transform=-subtract_scale)
return net
def InputGatedMemory(n_neurons, dimensions, feedback=1.0,
difference_gain=1.0, recurrent_synapse=0.1,
difference_synapse=None, net=None):
"""Stores a given vector in memory, with input controlled by a gate.
Parameters
----------
n_neurons : int
Number of neurons per dimension in the vector.
dimensions : int
Dimensionality of the vector.
feedback : float, optional (Default: 1.0)
Strength of the recurrent connection from the memory to itself.
difference_gain : float, optional (Default: 1.0)
Strength of the connection from the difference ensembles to the
memory ensembles.
recurrent_synapse : float, optional (Default: 0.1)
difference_synapse : Synapse (Default: None)
If None, ...
net : Network, optional (Default: None)
A network in which the network components will be built.
This is typically used to provide a custom set of Nengo object
defaults through modifying ``net.config``.
Returns
-------
net : Network
The newly built memory network, or the provided ``net``.
Attributes
----------
net.diff : EnsembleArray
Represents the difference between the desired vector and
the current vector represented by ``mem``.
net.gate : Node
With input of 0, the network is not gated, and ``mem`` will be updated
to minimize ``diff``. With input greater than 0, the network will be
increasingly gated such that ``mem`` will retain its current value,
and ``diff`` will be inhibited.
net.input : Node
The desired vector.
net.mem : EnsembleArray
Integrative population that stores the vector.
net.output : Node
The vector currently represented by ``mem``.
net.reset : Node
With positive input, the ``mem`` population will be inhibited,
effectively wiping out the vector currently being remembered.
"""
if net is None:
net = nengo.Network(label="Input Gated Memory")
if difference_synapse is None:
difference_synapse = recurrent_synapse
n_total_neurons = n_neurons * dimensions
with net:
# integrator to store value
net.mem = EnsembleArray(n_neurons, dimensions, label="mem")
nengo.Connection(net.mem.output, net.mem.input,
transform=feedback,
synapse=recurrent_synapse)
# calculate difference between stored value and input
net.diff = EnsembleArray(n_neurons, dimensions, label="diff")
nengo.Connection(net.mem.output, net.diff.input, transform=-1)
# feed difference into integrator
nengo.Connection(net.diff.output, net.mem.input,
transform=difference_gain,
synapse=difference_synapse)
# gate difference (if gate==0, update stored value,
# otherwise retain stored value)
net.gate = nengo.Node(size_in=1)
net.diff.add_neuron_input()
nengo.Connection(net.gate, net.diff.neuron_input,
transform=np.ones((n_total_neurons, 1)) * -10,
synapse=None)
# reset input (if reset=1, remove all values, and set to 0)
net.reset = nengo.Node(size_in=1)
nengo.Connection(net.reset, net.mem.add_neuron_input(),
transform=np.ones((n_total_neurons, 1)) * -3,
synapse=None)
net.input = net.diff.input
net.output = net.mem.output
return net
def Visual_Transform_Network(vis_vocab,
vis_am_threshold,
vis_am_input_scale,
copy_draw_trfms_x,
copy_draw_trfms_y,
mtr_vocab,
mtr_sp_scale_factor,
net=None,
net_label='VIS TRFM'):
if net is None:
net = nengo.Network(label=net_label)
with net:
# ----------------------- Inputs and Outputs --------------------------
net.input = nengo.Node(size_in=vis_vocab.dimensions)
net.output = nengo.Node(size_in=mtr_vocab.dimensions)
# ------------------ Digit (Answer) Classification --------------------
# Takes digit semantic pointer from visual wm and identifies
# appropriate digit classification
# - Generates: Digit class (I - 1) used for inhibition.
# - Default output vectors inhibits all.
# Note: threshold is halved to compenstate (sort of) for drift in the
# visual WM system
digit_classify = \
cfg.make_assoc_mem(vis_vocab.vectors[:len(mtr_vocab.keys), :],
np.ones((len(mtr_vocab.keys),
len(mtr_vocab.keys))) -
np.eye(len(mtr_vocab.keys)),
threshold=vis_am_threshold,
label='DIGIT CLASSIFY')
digit_classify.add_default_output_vector(np.ones(len(mtr_vocab.keys)))
nengo.Connection(net.input,
digit_classify.input,
transform=vis_am_input_scale,
synapse=None)
# --------------------- Motor SP Transformation -----------------------
if len(mtr_vocab.keys) != copy_draw_trfms_x.shape[0]:
raise ValueError('Transform System - Number of motor pointers',
' does not match number of given copydraw',
' transforms.')
# ------------------ Motor SP Transform ensembles ---------------------
for n in range(len(mtr_vocab.keys)):
mtr_path_dim = mtr_vocab.dimensions // 2
# Motor SP contains both X and Y information, so motor path dim is
# half that of the SP dim
# trfm_x = convert_func_2_diff_func(copy_draw_trfms_x[n])
# trfm_y = convert_func_2_diff_func(copy_draw_trfms_y[n])
trfm_x = np.array(copy_draw_trfms_x[n])
trfm_y = np.array(copy_draw_trfms_y[n])
trfm_ea = EnsembleArray(n_neurons=cfg.n_neurons_ens,
n_ensembles=mtr_vocab.dimensions,
radius=mtr_sp_scale_factor)
cfg.make_inhibitable(trfm_ea)
nengo.Connection(net.input,
trfm_ea.input[:mtr_path_dim],
transform=trfm_x.T,
synapse=None)
nengo.Connection(net.input,
trfm_ea.input[mtr_path_dim:],
transform=trfm_y.T,
synapse=None)
# Class output is inverted (i.e. if class is 3, it's [1, 1, 0, 1])
# So transform here is just the identity
inhib_trfm = np.zeros((1, len(mtr_vocab.keys)))
inhib_trfm[0, n] = 1
nengo.Connection(digit_classify.output,
trfm_ea.inhibit,
transform=inhib_trfm)
nengo.Connection(trfm_ea.output, net.output, synapse=None)
return net
def __init__(self, n_neurons, dimensions, mem_synapse=0.1,
fdbk_transform=1.0, input_transform=1.0, difference_gain=1.0,
gate_gain=3, reset_value=None, cleanup_values=None,
wta_output=False, wta_inhibit_scale=1,
label=None, seed=None, add_to_container=None, **mem_args):
super(InputGatedCleanupMemory, self).__init__(label, seed,
add_to_container)
if cleanup_values is None:
raise ValueError('InputGatedCleanupMemory - cleanup_values must' +
' be defined.')
else:
cleanup_values = np.matrix(cleanup_values)
# Keep copy of network parameters
self.n_neurons = n_neurons
self.dimensions = dimensions
self.gate_gain = gate_gain
self.input_transform = np.dot(input_transform, cleanup_values)
self.mem_synapse = mem_synapse
self.mem_args = copy(mem_args)
cu_args = copy(mem_args)
cu_args['radius'] = 1
cu_args['encoders'] = Choice([[1]])
cu_args['intercepts'] = Uniform(0.5, 1)
cu_args['eval_points'] = Uniform(0.6, 1.3)
cu_args['n_eval_points'] = 5000
with self:
self.input = nengo.Node(size_in=dimensions)
self.output = nengo.Node(size_in=dimensions)
self.mem = EnsembleArray(n_neurons, cleanup_values.shape[0],
label="mem", **cu_args)
self.mem.add_output('thresh', function=lambda x: 1)
nengo.Connection(self.mem.thresh, self.mem.input,
synapse=mem_synapse)
if wta_output:
nengo.Connection(self.mem.output, self.mem.input,
transform=(np.eye(cleanup_values.shape[0])
- 1) * wta_inhibit_scale)
# calculate difference between stored value and input
diff_args = copy(mem_args)
diff_args['radius'] = 1
self.diff = EnsembleArray(n_neurons, cleanup_values.shape[0],
label="diff", **diff_args)
self.diff_input = self.diff.input
nengo.Connection(self.input, self.diff.input, synapse=None,
transform=self.input_transform)
nengo.Connection(self.mem.output, self.diff.input, transform=-1)
# feed difference into integrator
nengo.Connection(self.diff.output, self.mem.input,
transform=difference_gain, synapse=mem_synapse)
# connect cleanup to output
nengo.Connection(self.mem.thresh, self.output,
transform=cleanup_values.T, synapse=None)
# gate difference (if gate==0, update stored value,
# otherwise retain stored value)
self.gate = nengo.Ensemble(n_neurons, 1, encoders=Choice([[1]]),
intercepts=Uniform(0.5, 1))
for e in self.diff.ensembles:
nengo.Connection(self.gate, e.neurons,
transform=[[-gate_gain]] * e.n_neurons)
# No indenty! Not supposed to be within network context
if reset_value is not None:
make_resettable(self, reset_value)
class InputGatedMemory(nengo.Network):
"""Stores a given vector in memory, with input controlled by a gate.
Parameters
----------
n_neurons : int
Number of neurons per dimension in the vector.
dimensions : int
Dimensionality of the vector.
feedback : float, optional
Strength of the recurrent connection from the memory to itself.
difference_gain : float, optional
Strength of the connection from the difference ensembles to the
memory ensembles.
recurrent_synapse : float, optional
difference_synapse : Synapse
If None, ...
**kwargs
Keyword arguments passed through to ``nengo.Network``
like 'label' and 'seed'.
Attributes
----------
diff : EnsembleArray
Represents the difference between the desired vector and
the current vector represented by ``mem``.
gate : Node
With input of 0, the network is not gated, and ``mem`` will be updated
to minimize ``diff``. With input greater than 0, the network will be
increasingly gated such that ``mem`` will retain its current value,
and ``diff`` will be inhibited.
input : Node
The desired vector.
mem : EnsembleArray
Integrative population that stores the vector.
output : Node
The vector currently represented by ``mem``.
reset : Node
With positive input, the ``mem`` population will be inhibited,
effectively wiping out the vector currently being remembered.
"""
def __init__(self,
n_neurons,
dimensions,
feedback=1.0,
difference_gain=1.0,
recurrent_synapse=0.1,
difference_synapse=None,
**kwargs):
if 'net' in kwargs:
raise ObsoleteError("The 'net' argument is no longer supported.")
kwargs.setdefault('label', "Input gated memory")
super().__init__(**kwargs)
if difference_synapse is None:
difference_synapse = recurrent_synapse
n_total_neurons = n_neurons * dimensions
with self:
# integrator to store value
self.mem = EnsembleArray(n_neurons, dimensions, label="mem")
nengo.Connection(self.mem.output, self.mem.input,
transform=feedback,
synapse=recurrent_synapse)
# calculate difference between stored value and input
self.diff = EnsembleArray(n_neurons, dimensions, label="diff")
nengo.Connection(self.mem.output, self.diff.input, transform=-1)
# feed difference into integrator
nengo.Connection(self.diff.output, self.mem.input,
transform=difference_gain,
synapse=difference_synapse)
# gate difference (if gate==0, update stored value,
# otherwise retain stored value)
self.gate = nengo.Node(size_in=1)
self.diff.add_neuron_input()
nengo.Connection(self.gate, self.diff.neuron_input,
transform=np.ones((n_total_neurons, 1)) * -10,
synapse=None)
# reset input (if reset=1, remove all values, and set to 0)
self.reset = nengo.Node(size_in=1)
nengo.Connection(self.reset, self.mem.add_neuron_input(),
transform=np.ones((n_total_neurons, 1)) * -3,
synapse=None)
self.input = self.diff.input
self.output = self.mem.output
def InputGatedMemory(n_neurons,
n_neurons_diff,
dimensions,
feedback=1.0,
difference_gain=1.0,
recurrent_synapse=0.1,
difference_synapse=None,
net=None,
**kwargs):
"""Stores a given vector in memory, with input controlled by a gate.
Parameters
----------
n_neurons : int
Number of neurons per dimension in the vector.
dimensions : int
Dimensionality of the vector.
feedback : float, optional (Default: 1.0)
Strength of the recurrent connection from the memory to itself.
difference_gain : float, optional (Default: 1.0)
Strength of the connection from the difference ensembles to the
memory ensembles.
recurrent_synapse : float, optional (Default: 0.1)
difference_synapse : Synapse (Default: None)
If None, ...
kwargs
Keyword arguments passed through to ``nengo.Network``.
Returns
-------
net : Network
The newly built memory network, or the provided ``net``.
Attributes
----------
net.diff : EnsembleArray
Represents the difference between the desired vector and
the current vector represented by ``mem``.
net.gate : Node
With input of 0, the network is not gated, and ``mem`` will be updated
to minimize ``diff``. With input greater than 0, the network will be
increasingly gated such that ``mem`` will retain its current value,
and ``diff`` will be inhibited.
net.input : Node
The desired vector.
net.mem : EnsembleArray
Integrative population that stores the vector.
net.output : Node
The vector currently represented by ``mem``.
net.reset : Node
With positive input, the ``mem`` population will be inhibited,
effectively wiping out the vector currently being remembered.
"""
if net is None:
kwargs.setdefault('label', "Input gated memory")
net = nengo.Network(**kwargs)
else:
warnings.warn("The 'net' argument is deprecated.", DeprecationWarning)
if difference_synapse is None:
difference_synapse = recurrent_synapse
n_total_neurons = n_neurons * dimensions
n_total_neurons_diff = n_neurons_diff * dimensions
with net:
# integrator to store value
mem_net = nengo.Network()
mem_net.config[nengo.Ensemble].encoders = nengo.dists.Choice([[-1.]])
mem_net.config[nengo.Ensemble].radius = 1
mem_net.config[nengo.Ensemble].eval_points = nengo.dists.Uniform(
-1, 0.0)
mem_net.config[nengo.Ensemble].intercepts = nengo.dists.Uniform(
-0.6, 1.)
with mem_net:
net.mem = EnsembleArray(n_neurons, dimensions, label="mem")
nengo.Connection(net.mem.output,
net.mem.input,
transform=feedback,
synapse=recurrent_synapse)
diff_net = nengo.Network()
diff_net.config[nengo.Ensemble].radius = 0.5
diff_net.config[nengo.Ensemble].eval_points = nengo.dists.Uniform(
-0.5, 0.5)
with diff_net:
# calculate difference between stored value and input
net.diff = EnsembleArray(n_neurons_diff, dimensions, label="diff")
nengo.Connection(net.mem.output, net.diff.input, transform=-1)
# feed difference into integrator
nengo.Connection(net.diff.output,
net.mem.input,
transform=difference_gain,
synapse=difference_synapse)
# gate difference (if gate==0, update stored value,
# otherwise retain stored value)
net.gate = nengo.Node(size_in=1)
net.diff.add_neuron_input()
nengo.Connection(net.gate,
net.diff.neuron_input,
transform=np.ones((n_total_neurons_diff, 1)) * -10,
synapse=None)
# reset input (if reset=1, remove all values, and set to 0)
net.reset = nengo.Node(size_in=1)
nengo.Connection(net.reset,
net.mem.add_neuron_input(),
transform=np.ones((n_total_neurons, 1)) * -3,
synapse=None)
net.input = net.diff.input
net.output = net.mem.output
return net
def init_module(self):
bias_node = nengo.Node(1)
# Number of actions in this spaun setup
num_actions = experiment.num_learn_actions
# ------------------- Action detection network ------------------------
# Translates
self.action_input = nengo.Node(size_in=num_actions)
self.bg_utilities_input = nengo.Node(size_in=num_actions)
self.vis_sp_input = nengo.Node(size_in=vocab.sp_dim)
# ------------------- Reward detection network ------------------------
# Translates visual input into reward yes/no signals
# Note: Output of reward_detect is inverted
num_reward_sps = len(vocab.reward.keys)
self.reward_detect = cfg.make_thresh_ens_net(num_ens=num_reward_sps)
nengo.Connection(bias_node,
self.reward_detect.input,
transform=np.ones(num_reward_sps)[:, None])
nengo.Connection(self.vis_sp_input,
self.reward_detect.input,
transform=-vocab.reward.vectors,
synapse=None)
# Calculate positive reward values
self.pos_reward_vals = \
cfg.make_ens_array(n_ensembles=num_actions, radius=1)
nengo.Connection(self.action_input,
self.pos_reward_vals.input,
transform=np.eye(num_actions),
synapse=None)
# Calculate negative reward values
self.neg_reward_vals = \
cfg.make_ens_array(n_ensembles=num_actions, radius=1)
nengo.Connection(self.action_input,
self.neg_reward_vals.input,
transform=np.ones(num_actions) - np.eye(num_actions),
synapse=None)
# Do the appropriate reward cross linking
for i in range(num_actions):
# No reward detect --> disinhibit neg_reward_vals
nengo.Connection(self.reward_detect.output[0],
self.neg_reward_vals.ensembles[i].neurons,
transform=[[-3]] *
self.neg_reward_vals.ensembles[i].n_neurons)
# Yes reward detect --> disinhibit pos_reward_vals
nengo.Connection(self.reward_detect.output[1],
self.pos_reward_vals.ensembles[i].neurons,
transform=[[-3]] *
self.pos_reward_vals.ensembles[i].n_neurons)
# Calculate the utility bias needed (so that the rewards don't send
# the utilities to +inf, -inf)
self.util_vals = EnsembleArray(100,
num_actions,
encoders=Choice([[1]]),
intercepts=Exponential(0.15, 0.3, 1))
nengo.Connection(self.reward_detect.output,
self.util_vals.input,
transform=-np.ones((num_actions, 2)))
nengo.Connection(self.action_input,
self.util_vals.input,
transform=np.ones((num_actions, num_actions)),
synapse=None)
nengo.Connection(self.bg_utilities_input,
self.util_vals.input,
transform=1,
synapse=None)
def test_circularconv(Simulator, nl, dims=4, neurons_per_product=128):
rng = np.random.RandomState(4238)
n_neurons = neurons_per_product
n_neurons_d = 2 * neurons_per_product
radius = 1
a = rng.normal(scale=np.sqrt(1./dims), size=dims)
b = rng.normal(scale=np.sqrt(1./dims), size=dims)
result = circconv(a, b)
assert np.abs(a).max() < radius
assert np.abs(b).max() < radius
assert np.abs(result).max() < radius
# --- model
model = nengo.Network(label="circular convolution")
with model:
model.config[nengo.Ensemble].neuron_type = nl()
inputA = nengo.Node(a)
inputB = nengo.Node(b)
A = EnsembleArray(n_neurons, dims, radius=radius)
B = EnsembleArray(n_neurons, dims, radius=radius)
cconv = nengo.networks.CircularConvolution(
n_neurons_d, dimensions=dims)
res = EnsembleArray(n_neurons, dims, radius=radius)
nengo.Connection(inputA, A.input)
nengo.Connection(inputB, B.input)
nengo.Connection(A.output, cconv.A)
nengo.Connection(B.output, cconv.B)
nengo.Connection(cconv.output, res.input)
A_p = nengo.Probe(A.output, synapse=0.03)
B_p = nengo.Probe(B.output, synapse=0.03)
res_p = nengo.Probe(res.output, synapse=0.03)
# --- simulation
sim = Simulator(model)
sim.run(1.0)
t = sim.trange()
with Plotter(Simulator, nl) as plt:
def plot(actual, probe, title=""):
ref_y = np.tile(actual, (len(t), 1))
sim_y = sim.data[probe]
colors = ['b', 'g', 'r', 'c', 'm', 'y']
for i in range(min(dims, len(colors))):
plt.plot(t, ref_y[:, i], '--', color=colors[i])
plt.plot(t, sim_y[:, i], '-', color=colors[i])
plt.title(title)
plt.subplot(311)
plot(a, A_p, title="A")
plt.subplot(312)
plot(b, B_p, title="B")
plt.subplot(313)
plot(result, res_p, title="Result")
plt.tight_layout()
plt.savefig('test_circularconv.test_circularconv_%d.pdf' % dims)
plt.close()
# --- results
tmask = t > (0.5 + sim.dt/2)
assert sim.data[A_p][tmask].shape == (499, dims)
a_sim = sim.data[A_p][tmask].mean(axis=0)
b_sim = sim.data[B_p][tmask].mean(axis=0)
res_sim = sim.data[res_p][tmask].mean(axis=0)
rtol, atol = 0.1, 0.05
assert np.allclose(a, a_sim, rtol=rtol, atol=atol)
assert np.allclose(b, b_sim, rtol=rtol, atol=atol)
assert rmse(result, res_sim) < 0.075
def __init__(self,
num_func_points,
func_value_range=1.0,
func_output_dimensions=1,
n_neurons=500,
label=None,
seed=None,
add_to_container=None):
super(DifferenceFunctionEvaluator,
self).__init__(label, seed, add_to_container)
intercept_interval = 2.0 / (num_func_points - 1)
self.func_output_dimensions = func_output_dimensions
self.n_neurons = n_neurons
with self:
bias_node = nengo.Node(1)
self.func_input = nengo.Node(size_in=1)
self.func_output = nengo.Node(size_in=func_output_dimensions)
self.diff_func_pts = []
self.diff_func_outputs = []
self.func_gate_eas = []
func_domain_inhib_ea = EA(25,
num_func_points - 1,
encoders=Choice([[-1]]),
intercepts=Uniform(
0, intercept_interval))
# Generate inhibit signal based of the function domain input value
func_domain_inhib_ea.add_output('const', lambda x: 1)
inhib_trfm = np.array([
np.linspace(-1, 1, num_func_points)[:-1] +
intercept_interval / 2.0
])
nengo.Connection(bias_node,
func_domain_inhib_ea.input,
transform=-1 - inhib_trfm.T)
nengo.Connection(self.func_input,
func_domain_inhib_ea.input,
transform=2 * np.ones((num_func_points - 1, 1)),
synapse=None)
for n in range(func_output_dimensions):
func_gate_ea = EA(n_neurons,
num_func_points,
radius=func_value_range)
for i, gate in enumerate(func_gate_ea.all_ensembles[1:]):
nengo.Connection(func_domain_inhib_ea.const[i],
gate.neurons,
transform=[[-5]] * n_neurons)
self.func_gate_eas.append(func_gate_ea)
self.diff_func_pts.append(func_gate_ea.input)
self.diff_func_outputs.append(func_gate_ea.output)
nengo.Connection(func_gate_ea.output,
self.func_output[n],
transform=np.ones((1, num_func_points)),
synapse=None)
def add_cleanup_output(self,
output_name='output',
n_neurons=50,
inhibit_scale=3.5,
replace_output=False):
"""Adds a cleaned outputs to the associative memory network.
Creates a doubled-inhibited ensemble structure to the desired assoc
memory output to perform a cleanup operation on it. Note that using the
'filtered_step_func' utility mapping performs a similar cleanup
operation, but does not do a very good cleanup approximation for
utility values near (+/- 0.2) the threshold value. This function
adds the infrastructure needed to perform the cleanup operation across
the entire range of output values, at the cost of two synaptic delays
and adding (n_neurons * 2 * n_items) additional neurons to the network.
Note: This function creates 2 nodes:
- A node named 'cleaned_<OUTPUT_NAME>' that outputs the cleaned
version of the output vectors.
- A node named 'cleaned_<OUTPUT_NAME>_utilities' that outputs the
utilities of the cleaned output vectors.
Parameters
----------
output_name: string, optional
The name of the input to which the default output vector
should be applied.
n_neurons: int, optional
Number of neurons to use for the ensembles used in the double-
inhibited cleanup network.
inhibit_scale: float, optional
Scaling factor applied to the inhibitory connections between
the ensembles. It is recommended that this value be at
least 1.0 / minimum(assoc memory activation thresholds), and that
the minimum assoc memory activation threshold be at most 0.1.
replace_output: boolean, optional
Flag to indicate whether or not to replace the output object
(e.g. am.output) with the cleaned output node.
"""
cleanup_output_name = '_'.join(
[self.cleanup_output_prefix, output_name])
cleanup_utilities_name = '_'.join([
self.cleanup_output_prefix, output_name, self.utility_output_suffix
])
output_utilities_name = '_'.join(
[output_name, self.utility_output_suffix])
# --- Check if cleanup network has already been created for
# the desired output node
if hasattr(self, cleanup_output_name):
raise ValidationError("Cleanup output already exists for "
"output: '%s'." % output_name,
attr='output_name')
with self.cleanup_ens_config:
# --- Set up the double inhibited ensembles, and make the
# appropriate connections.
self.bias_ens1 = EnsembleArray(n_neurons,
self.n_items,
label=output_name + '_bias_ens1')
self.bias_ens2 = EnsembleArray(n_neurons,
self.n_items,
label=output_name + '_bias_ens2')
utility = getattr(self, output_utilities_name)
nengo.Connection(self.bias_node,
self.bias_ens1.input,
transform=np.ones((self.n_items, 1)),
synapse=None)
nengo.Connection(self.bias_node,
self.bias_ens2.input,
transform=np.ones((self.n_items, 1)),
synapse=None)
nengo.Connection(utility,
self.bias_ens1.input,
transform=-inhibit_scale)
nengo.Connection(self.bias_ens1.output,
self.bias_ens2.input,
transform=-1.0)
# --- Make the output node and connect it
output_vectors = self._output_vectors[output_name]
cleanup_output_node = nengo.Node(size_in=output_vectors.shape[1],
label=cleanup_output_name)
nengo.Connection(self.bias_ens2.output,
cleanup_output_node,
transform=output_vectors.T,
synapse=None)
setattr(self, cleanup_output_name, cleanup_output_node)
setattr(self, cleanup_utilities_name, self.bias_ens2.output)
# --- Replace the original output node (pointer) if required
if replace_output:
setattr(self, output_name, cleanup_output_node)
# --- Make inhibitory connection if inhibit option is set
if self.inhibit is not None:
for e in self.bias_ens2.ensembles:
nengo.Connection(self.inhibit,
e,
transform=-self._inhib_scale,
synapse=None)
# --- Connect default output vector to cleaned outputs
# (if available)
default_vector_ens = getattr(
self, '_'.join([output_name, self.default_ens_suffix]), None)
if default_vector_ens:
default_output_vectors = \
self._default_output_vectors[output_name]
nengo.Connection(default_vector_ens,
cleanup_output_node,
transform=default_output_vectors.T,
synapse=None)
def VectorNormalize(min_mag,
max_mag,
dimensions,
radius_scale=1.0,
n_neurons_norm=50,
n_neurons_prod=150,
norm_error_per_dimension=0.0003,
subtract_scale=1,
net=None):
if net is None:
net = nengo.Network(label="Vector Normalize")
max_radius_scale = max_mag * radius_scale
norm_sub_in_low = min_mag**2
norm_sub_in_high = max_mag**2
norm_sub_in_trfm = scale_trfm(norm_sub_in_low, norm_sub_in_high)
norm_sub_in_bias = scale_bias(norm_sub_in_low, norm_sub_in_high)
norm_sub_in_bias_offset = -(norm_error_per_dimension * dimensions)
prod_a_trfm = 1.0 / max_radius_scale
prod_b_low = 1.0 - 1.0 / min_mag
prod_b_high = 1.0 - 1.0 / max_mag
prod_b_trfm = scale_trfm(prod_b_low, prod_b_high)
prod_b_bias = scale_bias(prod_b_low, prod_b_high)
def norm_sub_func(x,
nsit=norm_sub_in_trfm,
nsib=norm_sub_in_bias,
pbt=prod_b_trfm,
pbb=prod_b_bias):
return norm_subtract_func(x, nsit, nsib, pbt, pbb)
def prod_func(x, y, pat=prod_a_trfm, pbt=prod_b_trfm, pbb=prod_b_bias):
return prod_out_func(x, y, pat, 0, pbt, pbb)
with net:
net.input = nengo.Node(size_in=dimensions)
net.output = nengo.Node(size_in=dimensions)
bias_node = nengo.Node(1)
# Ensemble array to represent input vector and to compute vector
# norm
norm_array = EnsembleArray(n_neurons_norm,
dimensions,
radius=max_radius_scale)
norm_array.add_output('squared', lambda x: x**2)
nengo.Connection(net.input, norm_array.input)
# Ensemble to calculate amount of magnitude to be subtracted
# i.e. (1 - 1 / np.linalg.norm(input))
norm_subtract_ens = nengo.Ensemble(n_neurons_norm,
1,
n_eval_points=5000)
nengo.Connection(norm_array.squared,
norm_subtract_ens,
transform=np.ones((1, dimensions)) * norm_sub_in_trfm)
nengo.Connection(bias_node,
norm_subtract_ens,
transform=norm_sub_in_bias + norm_sub_in_bias_offset)
# Product network to compute product between input vector and
# magnitude to be subtracted
prod_array = Product(n_neurons_prod, dimensions)
for e in prod_array.product.ensembles:
e.n_eval_points = 5000
prod_array.product.add_output('prod2', lambda x: prod_func(x[0], x[1]))
prod_array.prod2 = prod_array.product.prod2
nengo.Connection(norm_array.output,
prod_array.A,
transform=prod_a_trfm)
nengo.Connection(norm_subtract_ens,
prod_array.B,
function=norm_sub_func,
transform=np.ones((dimensions, 1)))
# Output connections
nengo.Connection(norm_array.output, net.output)
nengo.Connection(prod_array.prod2,
net.output,
transform=-subtract_scale)
return net
import nengo
import numpy as np
from nengo.networks import CircularConvolution, EnsembleArray
model = nengo.Network(label="Neural Extraction")
D = 10
num_items = 20
threshold_func = lambda x: 1.0 if x > 0.3 else 0.0
with model:
extract = nengo.Network(label="Extract")
with extract:
a = EnsembleArray(n_neurons=80, n_ensembles=D)
b = EnsembleArray(n_neurons=80, n_ensembles=D)
c = CircularConvolution(n_neurons=80, dimensions=D)
d = EnsembleArray(n_neurons=80, n_ensembles=D)
nengo.Connection(a.output, c.A)
nengo.Connection(b.output, c.B)
nengo.Connection(c.output, d.input)
assoc = nengo.Network(label="Associate")
assoc_nodes = []
with assoc:
assoc_input = nengo.Node(size_in=D)
assoc_output = nengo.Node(size_in=D)
for item in range(num_items):
assoc_nodes.append(nengo.Ensemble(n_neurons=20, dimensions=1))
def test_matrix_mul(self):
N = 100
Amat = np.asarray([[.5, -.5]])
Bmat = np.asarray([[0, -1.], [.7, 0]])
radius = 1
model = nengo.Model('Matrix Multiplication', seed=123)
with model:
A = EnsembleArray(nengo.LIF(N * Amat.size),
Amat.size, radius=radius)
B = EnsembleArray(nengo.LIF(N * Bmat.size),
Bmat.size, radius=radius)
inputA = nengo.Node(output=Amat.ravel())
inputB = nengo.Node(output=Bmat.ravel())
nengo.Connection(inputA, A.input)
nengo.Connection(inputB, B.input)
A_p = nengo.Probe(
A.output, 'output', sample_every=0.01, filter=0.01)
B_p = nengo.Probe(
B.output, 'output', sample_every=0.01, filter=0.01)
C = EnsembleArray(nengo.LIF(N * Amat.size * Bmat.shape[1] * 2),
Amat.size * Bmat.shape[1],
dimensions_per_ensemble=2,
radius=1.5 * radius)
for ens in C.ensembles:
ens.encoders = np.tile([[1, 1], [-1, 1], [1, -1], [-1, -1]],
(ens.n_neurons // 4, 1))
transformA = np.zeros((C.dimensions, Amat.size))
transformB = np.zeros((C.dimensions, Bmat.size))
for i in range(Amat.shape[0]):
for j in range(Amat.shape[1]):
for k in range(Bmat.shape[1]):
tmp = (j + k * Amat.shape[1] + i * Bmat.size)
transformA[tmp * 2][j + i * Amat.shape[1]] = 1
transformB[tmp * 2 + 1][k + j * Bmat.shape[1]] = 1
nengo.Connection(A.output, C.input, transform=transformA)
nengo.Connection(B.output, C.input, transform=transformB)
C_p = nengo.Probe(
C.output, 'output', sample_every=0.01, filter=0.01)
D = EnsembleArray(nengo.LIF(N * Amat.shape[0] * Bmat.shape[1]),
Amat.shape[0] * Bmat.shape[1], radius=radius)
def product(x):
return x[0]*x[1]
transformC = np.zeros((D.dimensions, Bmat.size))
for i in range(Bmat.size):
transformC[i // Bmat.shape[0]][i] = 1
prod = C.add_output("product", product)
nengo.Connection(prod, D.input, transform=transformC)
D_p = nengo.Probe(
D.output, 'output', sample_every=0.01, filter=0.01)
sim = self.Simulator(model)
sim.run(1)
with Plotter(self.Simulator) as plt:
t = sim.trange(dt=0.01)
plt.plot(t, sim.data(D_p))
for d in np.dot(Amat, Bmat).flatten():
plt.axhline(d, color='k')
plt.savefig('test_ensemble_array.test_matrix_mul.pdf')
plt.close()
self.assertTrue(np.allclose(sim.data(A_p)[50:, 0], 0.5,
atol=.1, rtol=.01))
self.assertTrue(np.allclose(sim.data(A_p)[50:, 1], -0.5,
atol=.1, rtol=.01))
self.assertTrue(np.allclose(sim.data(B_p)[50:, 0], 0,
atol=.1, rtol=.01))
self.assertTrue(np.allclose(sim.data(B_p)[50:, 1], -1,
atol=.1, rtol=.01))
self.assertTrue(np.allclose(sim.data(B_p)[50:, 2], .7,
atol=.1, rtol=.01))
self.assertTrue(np.allclose(sim.data(B_p)[50:, 3], 0,
atol=.1, rtol=.01))
Dmat = np.dot(Amat, Bmat)
for i in range(Amat.shape[0]):
for k in range(Bmat.shape[1]):
self.assertTrue(np.allclose(
sim.data(D_p)[-10:, i * Bmat.shape[1] + k],
Dmat[i, k],
atol=0.1, rtol=0.1),
(sim.data(D_p)[-10:, i * Bmat.shape[1] + k], Dmat[i, k]))
def InputGatedMemory(n_neurons,
dimensions,
fdbk_scale=1.0,
gate_gain=10,
difference_gain=1.0,
reset_gain=3,
mem_config=None,
net=None):
"""Stores a given vector in memory, with input controlled by a gate."""
if net is None:
net = nengo.Network(label="Input Gated Memory")
if mem_config is None:
mem_config = nengo.Config(nengo.Connection)
mem_config[nengo.Connection].synapse = nengo.Lowpass(0.1)
n_total_neurons = n_neurons * dimensions
with net:
# integrator to store value
with mem_config:
net.mem = EnsembleArray(n_neurons,
dimensions,
neuron_nodes=True,
label="mem")
nengo.Connection(net.mem.output,
net.mem.input,
transform=fdbk_scale)
# calculate difference between stored value and input
net.diff = EnsembleArray(n_neurons,
dimensions,
neuron_nodes=True,
label="diff")
nengo.Connection(net.mem.output, net.diff.input, transform=-1)
# feed difference into integrator
with mem_config:
nengo.Connection(net.diff.output,
net.mem.input,
transform=difference_gain)
# gate difference (if gate==0, update stored value,
# otherwise retain stored value)
net.gate = nengo.Node(size_in=1)
nengo.Connection(net.gate,
net.diff.neuron_input,
transform=np.ones((n_total_neurons, 1)) * -gate_gain,
synapse=None)
# reset input (if reset=1, remove all values, and set to 0)
net.reset = nengo.Node(size_in=1)
nengo.Connection(net.reset,
net.mem.neuron_input,
transform=np.ones((n_total_neurons, 1)) * -reset_gain,
synapse=None)
net.input = net.diff.input
net.output = net.mem.output
return net
def make_ensarray_func(n_neurons, dimensions, **ens_args):
n_ensembles = ens_args.get('n_ensembles', dimensions)
return EnsembleArray(n_neurons, n_ensembles, **ens_args)
def build(self, input_manager, olfactor=False):
with self:
if olfactor:
N=input_manager.Nodors
odors = Node(input_manager.get_odor_concentrations, size_in=N)
odor_memory = EnsembleArray(n_neurons=100, n_ensembles=N, ens_dimensions=2)
odor_change = EnsembleArray(n_neurons=200, n_ensembles=N, ens_dimensions=1, radius=0.01,
intercepts=dists.Uniform(0, 0.1))
# odor_change_Node = Node(size_in=N)
# print(odor_change.neuron_output[0])
for i in range(N):
Connection(odors[i], odor_memory.ensembles[i][0], transform=[[1]], synapse=0.01)
Connection(odor_memory.ensembles[i][0], odor_memory.ensembles[i][1], transform=1, synapse=1.0)
Connection(odor_memory.ensembles[i][0], odor_change.input[i], transform=1, synapse=0.1)
Connection(odor_memory.ensembles[i][1], odor_change.input[i], transform=-1, synapse=0.1)
# Collect data for plotting
self.p_odor = Probe(odors)
# self.ens_probe = nengo.Probe(ens.output, synapse=0.01)
self.p_change = Probe(odor_change.output)
# self.p_change = odor_change.probes
x = Ensemble(n_neurons=200, dimensions=3, neuron_type=Direct())
y = Ensemble(n_neurons=200, dimensions=3, neuron_type=Direct())
z = Ensemble(n_neurons=200, dimensions=3, neuron_type=Direct())
synapse = 1.0
# synapse=0.1
def linear_oscillator(x):
dr = 1 - x[0] ** 2 - x[1] ** 2
s = 2 * np.pi * x[2] / 2
if s > 0.1:
v = synapse * -x[1] * s + x[0] * dr + x[0]
n = synapse * x[0] * s + x[1] * dr + x[1]
return [v, n]
else:
return [0, 1]
def angular_oscillator(x):
dr = 1 - x[0] ** 2 - x[1] ** 2
s = 2 * np.pi * x[2]
if s > 0.1:
return [synapse * -x[1] * s + x[0] * dr + x[0],
synapse * x[0] * s + x[1] * dr + x[1]]
else:
return [0, 1]
def feeding_oscillator(x):
dr = 1 - x[0] ** 2 - x[1] ** 2
s = 2 * np.pi * x[2]
if s > 0.1:
return [synapse * -x[1] * s + x[0] * dr + x[0],
synapse * x[0] * s + x[1] * dr + x[1]]
else:
return [0, 1]
def oscillator_interference(x):
coup = input_manager.osc_coupling
c0 = coup.crawler_interference_start
cr = 1 - coup.feeder_interference_free_window / np.pi
f0 = coup.crawler_interference_start
fr = 1 - coup.feeder_interference_free_window / np.pi
r = coup.interference_ratio
if x[0] > 0 or x[2] > 0:
v = [x[0], 0, x[2]]
else:
v = x
return v
def crawler(x):
return np.abs(x)*2 * input_manager.scaled_stride_step
def turner(x):
return x * input_manager.turner.get_amp(0)
def feeder(x):
if x > 0.999:
return 1
else:
return 0
Connection(x, x[:2], synapse=synapse, function=linear_oscillator)
Connection(y, y[:2], synapse=synapse, function=angular_oscillator)
Connection(z, z[:2], synapse=synapse, function=feeding_oscillator)
linear_freq_node = Node(input_manager.crawler.get_freq, size_out=1)
angular_freq_node = Node(input_manager.turner.get_freq, size_out=1)
feeding_freq_node = Node(input_manager.feeder.get_freq, size_out=1)
linear_freq = Ensemble(n_neurons=50, dimensions=1, neuron_type=Direct())
angular_freq = Ensemble(n_neurons=50, dimensions=1, neuron_type=Direct())
feeding_freq = Ensemble(n_neurons=50, dimensions=1, neuron_type=Direct())
Connection(linear_freq_node, linear_freq)
Connection(angular_freq_node, angular_freq)
Connection(feeding_freq_node, feeding_freq)
Connection(linear_freq, x[2])
Connection(angular_freq, y[2])
Connection(feeding_freq, z[2])
interference = Ensemble(n_neurons=200, dimensions=3, neuron_type=Direct())
Connection(x[0], interference[0], synapse=0)
Connection(y[0], interference[1], synapse=0)
Connection(z[0], interference[2], synapse=0)
speeds = Ensemble(n_neurons=200, dimensions=3, neuron_type=Direct())
Connection(interference, speeds, synapse=0.01, function=oscillator_interference)
linear_s = Node(size_in=1)
angular_s = Node(size_in=1)
feeding_s = Node(size_in=1)
Connection(speeds[0], linear_s, synapse=0, function=crawler)
Connection(speeds[1], angular_s, synapse=0, function=turner)
Connection(speeds[2], feeding_s, synapse=0, function=feeder)
# Collect data for plotting
self.p_speeds = Probe(speeds)
self.p_linear_s = Probe(linear_s)
self.p_angular_s = Probe(angular_s)
self.p_feeding_s = Probe(feeding_s)
def build_input(self, net):
assert self.trial.trajectory is not None, "Must define trajectory"
net.trajectory = EnsembleArray(80, n_ensembles=48)
# Sneaky: override the net.trajectory.input node output
net.trajectory.input.output = ArrayProcess(self.trial.trajectory)
net.trajectory.input.size_in = 0