def create_model(seed=None):
global model
#create vocabulary to show representations in gui
if nengo_gui_on:
vocab_angles = spa.Vocabulary(D)
for name in [0, 3, 7, 12, 18, 25, 33, 42]:
#vocab_angles.add('D' + str(name), np.linalg.norm(compressed_im_cued[name+90])) #take mean across phases
v = compressed_im_cued[name + 90]
nrm = np.linalg.norm(v)
if nrm > 0:
v /= nrm
vocab_angles.add('D' + str(name), v) #take mean across phases
v = np.dot(imagearr[-1, :] / 50, U_cued[:, :D])
nrm = np.linalg.norm(v)
if nrm > 0:
v /= nrm
vocab_angles.add('Impulse', v)
#model = nengo.Network(seed=seed)
model = spa.SPA(seed=seed)
with model:
#input nodes
inputNode_cued = nengo.Node(input_func_cued, label='input_cued')
reactivate = nengo.Node(reactivate_func, label='reactivate')
#sensory ensemble
sensory_cued = nengo.Ensemble(Ns,
D,
encoders=e_cued,
intercepts=Uniform(0.01, .1),
radius=1,
label='sensory_cued')
nengo.Connection(inputNode_cued,
sensory_cued,
transform=U_cued[:, :D].T)
#memory ensemble
memory_cued = nengo.Ensemble(Nm,
D,
neuron_type=stpLIF(),
intercepts=Uniform(0.01, .1),
radius=1,
label='memory_cued')
nengo.Connection(reactivate,
memory_cued.neurons) #potential reactivation
nengo.Connection(sensory_cued, memory_cued, transform=.1) #.1)
#recurrent STSP connection
nengo.Connection(memory_cued,
memory_cued,
transform=1,
learning_rule_type=STP(),
solver=nengo.solvers.LstsqL2(weights=True))
#comparison represents sin, cosine of theta of both sensory and memory ensemble
comparison_cued = nengo.Ensemble(Nc,
dimensions=4,
radius=math.sqrt(2),
intercepts=Uniform(.01, 1),
label='comparison_cued')
nengo.Connection(sensory_cued,
comparison_cued[:2],
eval_points=compressed_im_cued[0:-1],
function=sincos.T)
nengo.Connection(memory_cued,
comparison_cued[2:],
eval_points=compressed_im_cued[0:-1],
function=sincos.T)
#decision represents the difference in theta decoded from the sensory and memory ensembles
decision_cued = nengo.Ensemble(n_neurons=Nd,
dimensions=1,
radius=45,
label='decision_cued')
nengo.Connection(comparison_cued,
decision_cued,
eval_points=ep,
scale_eval_points=False,
function=arctan_func)
#same for uncued
if uncued:
inputNode_uncued = nengo.Node(input_func_uncued,
label='input_uncued')
sensory_uncued = nengo.Ensemble(Ns,
D,
encoders=e_uncued,
intercepts=Uniform(0.01, .1),
radius=1,
label='sensory_uncued')
nengo.Connection(inputNode_uncued,
sensory_uncued,
transform=U_uncued[:, :D].T)
memory_uncued = nengo.Ensemble(Nm,
D,
neuron_type=stpLIF(),
intercepts=Uniform(0.01, .1),
radius=1,
label='memory_uncued')
nengo.Connection(sensory_uncued, memory_uncued, transform=.1)
nengo.Connection(memory_uncued,
memory_uncued,
transform=1,
learning_rule_type=STP(),
solver=nengo.solvers.LstsqL2(weights=True))
comparison_uncued = nengo.Ensemble(Nd,
dimensions=4,
radius=math.sqrt(2),
intercepts=Uniform(.01, 1),
label='comparison_uncued')
nengo.Connection(memory_uncued,
comparison_uncued[2:],
eval_points=compressed_im_uncued[0:-1],
function=sincos.T)
nengo.Connection(sensory_uncued,
comparison_uncued[:2],
eval_points=compressed_im_uncued[0:-1],
function=sincos.T)
decision_uncued = nengo.Ensemble(n_neurons=Nd,
dimensions=1,
radius=45,
label='decision_uncued')
nengo.Connection(comparison_uncued,
decision_uncued,
eval_points=ep,
scale_eval_points=False,
function=arctan_func)
#decode for gui
if nengo_gui_on:
model.sensory_decode = spa.State(D,
vocab=vocab_angles,
subdimensions=12,
label='sensory_decode')
for ens in model.sensory_decode.all_ensembles:
ens.neuron_type = nengo.Direct()
nengo.Connection(sensory_cued,
model.sensory_decode.input,
synapse=None)
model.memory_decode = spa.State(D,
vocab=vocab_angles,
subdimensions=12,
label='memory_decode')
for ens in model.memory_decode.all_ensembles:
ens.neuron_type = nengo.Direct()
nengo.Connection(memory_cued,
model.memory_decode.input,
synapse=None)
#probes
if not (nengo_gui_on):
if store_representations: #sim 1 trials 1-100
#p_dtheta_cued=nengo.Probe(decision_cued, synapse=0.01)
model.p_mem_cued = nengo.Probe(memory_cued, synapse=0.01)
#p_sen_cued=nengo.Probe(sensory_cued, synapse=0.01)
if uncued:
model.p_mem_uncued = nengo.Probe(memory_uncued,
synapse=0.01)
if store_spikes_and_resources: #sim 1 trial 1
model.p_spikes_mem_cued = nengo.Probe(memory_cued.neurons,
'spikes')
model.p_res_cued = nengo.Probe(memory_cued.neurons,
'resources')
model.p_cal_cued = nengo.Probe(memory_cued.neurons, 'calcium')
if uncued:
model.p_spikes_mem_uncued = nengo.Probe(
memory_uncued.neurons, 'spikes')
model.p_res_uncued = nengo.Probe(memory_uncued.neurons,
'resources')
model.p_cal_uncued = nengo.Probe(memory_uncued.neurons,
'calcium')
if store_decisions: #sim 2
model.p_dec_cued = nengo.Probe(decision_cued, synapse=0.01)
#Setup the environment
import matplotlib.pyplot as plt
import random
import math
import nengo
from nengo import spa
# Number of dimensions for the SPs
dimensions = 64
# Make a model object with the SPA network
model = spa.SPA(label='Task')
with model:
# Initial the three visual perceptual memory component and one working memory component.
model.vision1 = spa.State(dimensions=dimensions,
neurons_per_dimension=100,
feedback=0.7)
model.vision2 = spa.State(dimensions=dimensions,
neurons_per_dimension=100,
feedback=0.7)
model.cue = spa.Buffer(dimensions=dimensions, neurons_per_dimension=100)
model.representation = spa.Memory(dimensions=dimensions,
neurons_per_dimension=100)
# Specify the action mapping and attention function
actions = spa.Actions(
'dot(cue, LEFT) --> vision1=vision1*2',
'dot(cue, RIGHT) --> vision2=vision2*2',
)
cortical_actions = spa.Actions('representation=vision1+vision2', )
def model(self, p):
vocab = spa.Vocabulary(p.D)
items = []
fan = []
assert p.M % 6 == 0
for i in range(p.M / 6):
for j in range(3):
pp = vocab.parse('X%d+Y%d+%g*Q' %
(6 * i + j, 6 * i + j, p.common))
pp.normalize()
vocab.add('P%d' % (3 * i + j), pp)
items.append(pp.v)
fan.append(1)
for j, v in enumerate(['AB', 'CB', 'AC']):
pp = vocab.parse('%s%d+%s%d+%g*Q' %
(v[0], i, v[1], i, p.common))
pp.normalize()
vocab.add('P%d_2' % (3 * i + j), pp)
items.append(pp.v)
fan.append(2)
rng = np.random.RandomState(seed=p.seed)
order = np.arange(len(items))
rng.shuffle(order)
items = [items[o] for o in order]
fan = [fan[o] for o in order]
self.fan = fan
model = spa.SPA()
with model:
model.cue = spa.State(p.D, vocab=vocab)
if p.noise > 0:
for ens in model.cue.all_ensembles:
ens.noise = nengo.processes.WhiteNoise(
dist=nengo.dists.Gaussian(0, std=p.noise))
model.mem = nengo.networks.EnsembleArray(n_neurons=50,
n_ensembles=len(items))
for ens in model.mem.all_ensembles:
ens.encoders = nengo.dists.Choice([[1]])
ens.intercepts = nengo.dists.Uniform(0, 1)
nengo.Connection(model.mem.output,
model.mem.input,
transform=np.eye(len(items)) - 1,
synapse=p.syn)
nengo.Connection(model.cue.output,
model.mem.input,
transform=np.array(items),
synapse=p.input_syn)
mem_activity = nengo.Node(None, size_in=1)
for ens in model.mem.all_ensembles:
nengo.Connection(ens.neurons,
mem_activity,
transform=np.ones((1, ens.n_neurons)),
synapse=None)
self.p_activity = nengo.Probe(mem_activity, synapse=0.01)
class Env(nengo.Node):
def __init__(self, items):
self.items = items
self.index = 0
self.switch_time = 0
self.times = []
self.correct = []
super(Env, self).__init__(self.func,
size_in=len(items),
size_out=p.D)
def func(self, t, x):
if t > self.switch_time + p.min_time + p.t_zero:
values = list(sorted(x))
if values[-2] < 1e-3 or t > (self.switch_time + p.timeout):
self.correct.append(np.argmax(x) == self.index)
self.index = (self.index + 1) % len(self.items)
self.times.append(t - self.switch_time)
self.switch_time = t
if len(self.times) >= len(self.items) and not p.gui:
raise FinishedException()
if t < self.switch_time + p.t_zero:
return np.zeros(p.D)
else:
return self.items[self.index]
with model:
self.env = Env(items)
nengo.Connection(self.env, model.cue.input, synapse=None)
nengo.Connection(model.mem.output, self.env, synapse=0.005)
return model
def generate(input_signal, alpha=1000.0):
beta = alpha / 4.0
# Read in the class mean for numbers from vision network
weights_data = np.load('models/mnist_vision_data/params.npz')
weights = weights_data['Wc']
means_data = np.load('models/mnist_vision_data/class_means.npz')
means = np.matrix(1.0 / means_data['means'])
sps = np.multiply(weights.T, means.T)[:10]
sps_labels = [
'ZERO', 'ONE', 'TWO', 'THREE', 'FOUR',
'FIVE', 'SIX', 'SEVEN', 'EIGHT', 'NINE']
dimensions = weights.shape[0]
# generate the Function Space
forces, _, _ = forcing_functions.load_folder(
'models/handwriting_trajectories', rhythmic=True,
alpha=alpha, beta=beta)
# make an array out of all the possible functions we want to represent
force_space = np.vstack(forces)
# use this array as our space to perform svd over
fs = nengo.FunctionSpace(space=force_space, n_basis=10)
# store the weights for each trajectory
weights_x = []
weights_y = []
for ii in range(len(forces)):
forces = force_space[ii*2:ii*2+2]
# load up the forces to be output by the forcing function
# calculate the corresponding weights over the basis functions
weights_x.append(np.dot(fs.basis.T, forces[0]))
weights_y.append(np.dot(fs.basis.T, forces[1]))
# Create our vocabularies
rng = np.random.RandomState(0)
vocab_vision = Vocabulary(dimensions=dimensions, rng=rng)
vocab_dmp_weights_x = Vocabulary(dimensions=fs.n_basis, rng=rng)
vocab_dmp_weights_y = Vocabulary(dimensions=fs.n_basis, rng=rng)
for label, sp, wx, wy in zip(
sps_labels, sps, weights_x, weights_y):
vocab_vision.add(
label, np.array(sp)[0] / np.linalg.norm(np.array(sp)[0]))
vocab_dmp_weights_x.add(label, wx)
vocab_dmp_weights_y.add(label, wy)
net = spa.SPA()
# net.config[nengo.Ensemble].neuron_type = nengo.Direct()
with net:
# --------------------- Inputs --------------------------
# def input_func(t):
# return vocab_vision.parse(input_signal).v
# net.input = nengo.Node(input_func, label='input')
net.input = spa.State(dimensions, subdimensions=10,
vocab=vocab_vision)
number = nengo.Node(output=[0], label='number')
# ------------------- Point Attractors --------------------
net.x = point_attractor.generate(
n_neurons=1000, alpha=alpha, beta=beta)
net.y = point_attractor.generate(
n_neurons=1000, alpha=alpha, beta=beta)
# -------------------- Oscillators ----------------------
kick = nengo.Node(nengo.utils.functions.piecewise({0: 1, .05: 0}),
label='kick')
osc = oscillator.generate(net, n_neurons=2000, speed=.05)
osc.label = 'oscillator'
nengo.Connection(kick, osc[0])
# ------------------- Forcing Functions --------------------
net.assoc_mem_x = spa.AssociativeMemory(
input_vocab=vocab_vision,
output_vocab=vocab_dmp_weights_x,
wta_output=False)
nengo.Connection(net.input.output, net.assoc_mem_x.input)
net.assoc_mem_y = spa.AssociativeMemory(
input_vocab=vocab_vision,
output_vocab=vocab_dmp_weights_y,
wta_output=False)
nengo.Connection(net.input.output, net.assoc_mem_y.input)
# -------------------- Product for decoding -----------------------
net.product_x = nengo.Network('Product X')
nengo.networks.Product(n_neurons=1000,
dimensions=fs.n_basis,
net=net.product_x,
input_magnitude=1.0)
net.product_y = nengo.Network('Product Y')
nengo.networks.Product(n_neurons=1000,
dimensions=fs.n_basis,
net=net.product_y,
input_magnitude=1.0)
# get the largest basis function value for normalization
max_basis = np.max(fs.basis*fs.scale)
domain = np.linspace(-np.pi, np.pi, fs.basis.shape[0])
domain_cossin = np.array([np.cos(domain), np.sin(domain)]).T
for ff, product in zip([net.assoc_mem_x.output,
net.assoc_mem_y.output],
[net.product_x, net.product_y]):
for ii in range(fs.n_basis):
# find the value of a basis function at a value of (x, y)
target_function = nengo.utils.connection.target_function(
domain_cossin, fs.basis[:, ii]*fs.scale/max_basis)
nengo.Connection(osc, product.B[ii], **target_function)
# multiply the value of each basis function at x by its weight
nengo.Connection(ff, product.A)
nengo.Connection(net.product_x.output, net.x.input[1],
transform=np.ones((1, fs.n_basis)) * max_basis,
synapse=None)
nengo.Connection(net.product_y.output, net.y.input[1],
transform=np.ones((1, fs.n_basis)) * max_basis,
synapse=None)
# -------------------- Output ------------------------------
net.output = nengo.Node(size_in=2, label='output')
nengo.Connection(net.x.output, net.output[0])
nengo.Connection(net.y.output, net.output[1])
# create a node to give a plot of the represented function
ff_plot = fs.make_plot_node(domain=domain, lines=2,
ylim=[-1000000, 1000000])
nengo.Connection(net.assoc_mem_x.output,
ff_plot[:fs.n_basis], synapse=0.1)
nengo.Connection(net.assoc_mem_y.output,
ff_plot[fs.n_basis:], synapse=0.1)
return net
# this is for creating a new type of object in the environment
class Food(grid.ContinuousAgent):
color = 'green'
shape = 'circle'
# now we actuall make the world
world = grid.World(Cell, map=map, directions=4)
body = grid.ContinuousAgent()
world.add(body, x=2, y=4, dir=1)
world.add(Food(), x=5, y=2)
#world.add(Food(), x=3, y=6)
D = 32
vocab = spa.Vocabulary(D)
model = spa.SPA(label="SearchFood")
class State(nengo.Node):
def __init__(self, body):
self.body = body
super(State, self).__init__(self.update)
def compute_angle_and_distance(self, obj):
angle = (body.dir-1) * 2 * np.pi / 4
dy = obj.y - self.body.y
dx = obj.x - self.body.x
obj_angle = np.arctan2(dy, dx)
theta = angle - obj_angle
dist = np.sqrt(dy**2 + dx**2)
import nengo
from nengo import spa
### Step 1: Create the model
# Notice that when you specify actions, you're determining which modules are connected to which. For example, by having a mapping that depends on the state of cortex, you are determining that the cortex and basal ganglia must be connected. As well, when you specify that the result of the action changes the state of cortex, then you are determining that thalamus must be connected to cortex.
#
# In[ ]:
# Number of dimensions for the Semantic Pointers
dimensions = 16
# Make a model object with the SPA network
model = spa.SPA(label='Routed_Sequence')
with model:
# Specify the modules to be used
model.cortex = spa.Buffer(dimensions=dimensions)
model.vision = spa.Buffer(dimensions=dimensions)
# Specify the action mapping
actions = spa.Actions('dot(vision, START) --> cortex = vision',
'dot(cortex, A) --> cortex = B',
'dot(cortex, B) --> cortex = C',
'dot(cortex, C) --> cortex = D',
'dot(cortex, D) --> cortex = E',
'dot(cortex, E) --> cortex = A')
model.bg = spa.BasalGanglia(actions=actions)
model.thal = spa.Thalamus(model.bg)
# top-right shows the utility (similarity) of the current basal ganglia input
# (i.e., state) with the possible vocabulary vectors.
# You can see that in this model, even though the input is applied for 400ms, it
# doesn't prevent the activation of the second and subsequent rules in the
# sequence.
#Setup the environment
import nengo
from nengo import spa #import spa related packages
#Number of dimensions for the Semantic Pointers
dimensions = 16
#Make a model object with the SPA network
model = spa.SPA(label='Routed_Sequence', seed=20)
with model:
#Specify the modules to be used
model.state = spa.State(dimensions=dimensions,
feedback=1,
feedback_synapse=0.01)
model.vision = spa.State(dimensions=dimensions)
#Specify the action mapping
actions = spa.Actions('dot(vision, START) --> state = vision',
'dot(state, A) --> state = B',
'dot(state, B) --> state = C',
'dot(state, C) --> state = D',
'dot(state, D) --> state = E',
'dot(state, E) --> state = A')
def create_model(p):
model = spa.SPA()
if p.direct:
model.config[nengo.Ensemble].neuron_type = nengo.Direct()
force_neurons_cfg = nengo.Config(nengo.Ensemble)
force_neurons_cfg[nengo.Ensemble].neuron_type = nengo.LIF()
else:
force_neurons_cfg = model.config
with model:
# control
model.control_net = nengo.Network()
with model.control_net:
#assuming the model knows which hand to use (which was blocked)
model.hand_input = nengo.Node(get_hand)
model.target_hand = spa.State(p.Dmid,
vocab=vocab_motor,
feedback=1)
nengo.Connection(model.hand_input,
model.target_hand.input,
synapse=None)
model.attend = spa.State(p.D, vocab=vocab_attend,
feedback=.5) # vocab_attend
model.goal = spa.State(p.Dlow, vocab=vocab_goal,
feedback=.7) # current goal
if p.do_vision:
from nengo_extras.vision import Gabor, Mask
### vision ###
# set up network parameters
n_vis = X_train.shape[1] # nr of pixels, dimensions of network
n_hid = 1000 # nr of gabor encoders/neurons
# random state to start
rng = np.random.RandomState(9)
encoders = Gabor().generate(
n_hid, (4, 4),
rng=rng) # gabor encoders, 11x11 apparently, why?
encoders = Mask(
(14,
90)).populate(encoders, rng=rng,
flatten=True) # use them on part of the image
model.visual_net = nengo.Network()
with model.visual_net:
#represent currently attended item
model.attended_item = nengo.Node(present_item2, size_in=p.D)
nengo.Connection(model.attend.output, model.attended_item)
model.vision_gabor = nengo.Ensemble(
n_hid,
n_vis,
eval_points=X_train,
# neuron_type=nengo.LIF(),
neuron_type=nengo.AdaptiveLIF(
tau_n=.01, inc_n=.05
), #to get a better fit, use more realistic neurons that adapt to input
intercepts=nengo.dists.Uniform(-0.1, 0.1),
#intercepts=nengo.dists.Choice([-0.5]), #should we comment this out? not sure what's happening
#max_rates=nengo.dists.Choice([100]),
encoders=encoders)
#recurrent connection (time constant 500 ms)
# strength = 1 - (100/500) = .8
zeros = np.zeros_like(X_train)
nengo.Connection(
model.vision_gabor,
model.vision_gabor,
synapse=0.005, #.1
eval_points=np.vstack(
[X_train, zeros,
np.random.randn(*X_train.shape)]),
transform=.5)
model.visual_representation = nengo.Ensemble(n_hid,
dimensions=p.Dmid)
model.visconn = nengo.Connection(
model.vision_gabor,
model.visual_representation,
synapse=0.005, #was .005
eval_points=X_train,
function=train_targets,
solver=nengo.solvers.LstsqL2(reg=0.01))
nengo.Connection(model.attended_item,
model.vision_gabor,
synapse=.02) #.03) #synapse?
# display attended item, only in gui
if p.gui:
# show what's being looked at
model.display_attended = nengo.Node(
display_func,
size_in=model.attended_item.size_out) # to show input
nengo.Connection(model.attended_item,
model.display_attended,
synapse=None)
#add node to plot total visual activity
model.visual_activation = nengo.Node(None, size_in=1)
nengo.Connection(model.vision_gabor.neurons,
model.visual_activation,
transform=np.ones((1, n_hid)),
synapse=None)
else:
model.visual_net = nengo.Network()
with model.visual_net:
model.fake_vision = nengo.Node(fake_vision, size_in=p.D)
nengo.Connection(model.attend.output, model.fake_vision)
### central cognition ###
##### Concepts #####
model.concepts = spa.AssociativeMemory(
vocab_all_words, #vocab_concepts,
wta_output=True,
wta_inhibit_scale=1, #was 1
#default_output_key='NONE', #what to say if input doesn't match
threshold=0.3
) # how strong does input need to be for it to recognize
if p.do_vision:
nengo.Connection(
model.visual_representation,
model.concepts.input,
transform=.8 * vision_mapping
) #not too fast to concepts, might have to be increased to have model react faster to first word.
else:
nengo.Connection(model.fake_vision,
model.concepts.input,
transform=.8,
synapse=0.025)
#concepts accumulator
with force_neurons_cfg:
model.concepts_evidence = spa.State(
1, feedback=1, feedback_synapse=0.005
) #the lower the synapse, the faster it accumulates (was .1)
concepts_evidence_scale = 2.5
nengo.Connection(model.concepts.am.elem_output,
model.concepts_evidence.input,
transform=concepts_evidence_scale * np.ones(
(1, model.concepts.am.elem_output.size_out)),
synapse=0.005)
#concepts switch
model.do_concepts = spa.AssociativeMemory(vocab_reset,
default_output_key='CLEAR',
threshold=.2)
nengo.Connection(
model.do_concepts.am.ensembles[-1],
model.concepts_evidence.all_ensembles[0].neurons,
transform=np.ones(
(model.concepts_evidence.all_ensembles[0].n_neurons, 1)) * -10,
synapse=0.005)
###### Visual Representation ######
model.vis_pair = spa.State(
p.D, vocab=vocab_all_words, feedback=1.0, feedback_synapse=.05
) #was 2, 1.6 works ok, but everything gets activated.
model.p_vis_pair = nengo.Probe(model.vis_pair.output, synapse=0.01)
if p.do_familiarity:
assert p.do_motor
##### Familiarity #####
# Assoc Mem with Learned Words
# - familiarity signal should be continuous over all items, so no wta
model.dm_learned_words = spa.AssociativeMemory(vocab_learned_words,
threshold=.2)
nengo.Connection(model.dm_learned_words.output,
model.dm_learned_words.input,
transform=.4,
synapse=.02)
# Familiarity Accumulator
with force_neurons_cfg:
model.familiarity = spa.State(
1, feedback=.9,
feedback_synapse=0.1) #fb syn influences speed of acc
#familiarity_scale = 0.2 #keep stable for negative fam
# familiarity accumulator switch
model.do_fam = spa.AssociativeMemory(vocab_reset,
default_output_key='CLEAR',
threshold=.2)
# reset
nengo.Connection(
model.do_fam.am.ensembles[-1],
model.familiarity.all_ensembles[0].neurons,
transform=np.ones(
(model.familiarity.all_ensembles[0].n_neurons, 1)) * -10,
synapse=0.005)
#first a sum to represent summed similarity
model.summed_similarity = nengo.Ensemble(n_neurons=100,
dimensions=1)
nengo.Connection(
model.dm_learned_words.am.elem_output,
model.summed_similarity,
transform=np.ones(
(1, model.dm_learned_words.am.elem_output.size_out
))) #take sum
#then a connection to accumulate this summed sim
def familiarity_acc_transform(summed_sim):
fam_scale = .5
fam_threshold = 0 #actually, kind of bias
fam_max = 1
return fam_scale * (2 * ((summed_sim - fam_threshold) /
(fam_max - fam_threshold)) - 1)
nengo.Connection(model.summed_similarity,
model.familiarity.input,
function=familiarity_acc_transform)
##### Recollection & Representation #####
model.dm_pairs = spa.AssociativeMemory(
vocab_learned_pairs,
wta_output=True) #input_keys=list_of_pairs
nengo.Connection(model.dm_pairs.output,
model.dm_pairs.input,
transform=.5,
synapse=.05)
#representation
rep_scale = 0.5
model.representation = spa.State(p.D,
vocab=vocab_all_words,
feedback=1.0)
with force_neurons_cfg:
model.rep_filled = spa.State(
1, feedback=.9,
feedback_synapse=.1) #fb syn influences speed of acc
model.do_rep = spa.AssociativeMemory(vocab_reset,
default_output_key='CLEAR',
threshold=.2)
nengo.Connection(
model.do_rep.am.ensembles[-1],
model.rep_filled.all_ensembles[0].neurons,
transform=np.ones(
(model.rep_filled.all_ensembles[0].n_neurons, 1)) * -10,
synapse=0.005)
nengo.Connection(model.representation.output,
model.rep_filled.input,
transform=rep_scale *
np.reshape(sum(vocab_learned_pairs.vectors),
((1, p.D))))
###### Comparison #####
model.comparison = spa.Compare(p.D,
vocab=vocab_all_words,
neurons_per_multiply=500,
input_magnitude=.3)
#turns out comparison is not an accumulator - we also need one of those.
with force_neurons_cfg:
model.comparison_accumulator = spa.State(
1, feedback=.9,
feedback_synapse=0.05) #fb syn influences speed of acc
model.do_compare = spa.AssociativeMemory(
vocab_reset, default_output_key='CLEAR', threshold=.2)
#reset
nengo.Connection(
model.do_compare.am.ensembles[-1],
model.comparison_accumulator.all_ensembles[0].neurons,
transform=np.ones(
(model.comparison_accumulator.all_ensembles[0].n_neurons,
1)) * -10,
synapse=0.005)
#error because we apply a function to a 'passthrough' node, inbetween ensemble as a solution:
model.comparison_result = nengo.Ensemble(n_neurons=100,
dimensions=1)
nengo.Connection(model.comparison.output, model.comparison_result)
def comparison_acc_transform(comparison):
comparison_scale = .6
comparison_threshold = 0 #actually, kind of bias
comparison_max = .6
return comparison_scale * (2 * (
(comparison - comparison_threshold) /
(comparison_max - comparison_threshold)) - 1)
nengo.Connection(model.comparison_result,
model.comparison_accumulator.input,
function=comparison_acc_transform)
if p.do_motor:
#motor
model.motor_net = nengo.Network()
with model.motor_net:
#input multiplier
model.motor_input = spa.State(p.Dmid, vocab=vocab_motor)
#higher motor area (SMA?)
model.motor = spa.State(p.Dmid, vocab=vocab_motor, feedback=.7)
#connect input multiplier with higher motor area
nengo.Connection(model.motor_input.output,
model.motor.input,
synapse=.1,
transform=2)
#finger area
model.fingers = spa.AssociativeMemory(
vocab_fingers,
input_keys=['L1', 'L2', 'R1', 'R2'],
wta_output=True)
nengo.Connection(model.fingers.output,
model.fingers.input,
synapse=0.1,
transform=0.3) #feedback
#conncetion between higher order area (hand, finger), to lower area
nengo.Connection(model.motor.output,
model.fingers.input,
transform=.25 * motor_mapping) #was .2
#finger position (spinal?)
model.finger_pos = nengo.networks.EnsembleArray(n_neurons=50,
n_ensembles=4)
nengo.Connection(model.finger_pos.output,
model.finger_pos.input,
synapse=0.1,
transform=0.8) #feedback
#connection between finger area and finger position
nengo.Connection(model.fingers.am.elem_output,
model.finger_pos.input,
transform=1.0 *
np.diag([0.55, .54, .56, .55])) #fix these
actions = dict(
#wait & start
a_aa_wait='dot(goal,WAIT) - .9 --> goal=0',
a_attend_item1=
'dot(goal,DO_TASK) - .0 --> goal=RECOG, attend=ITEM1, do_concepts=GO',
#attend words
b_attending_item1=
'dot(goal,RECOG) + dot(attend,ITEM1) - concepts_evidence - .3 --> goal=RECOG, attend=ITEM1, do_concepts=GO', # vis_pair=2.5*(ITEM1*concepts)',
c_attend_item2=
'dot(goal,RECOG) + dot(attend,ITEM1) + concepts_evidence - 1.6 --> goal=RECOG2, attend=ITEM2, vis_pair=3*(ITEM1*concepts)',
d_attending_item2=
'dot(goal,RECOG2+RECOG) + dot(attend,ITEM2) - concepts_evidence - .4 --> goal=RECOG2, attend=ITEM2, do_concepts=GO',
e_start_familiarity=
'dot(goal,RECOG2) + dot(attend,ITEM2) + concepts_evidence - 1.8 --> goal=FAMILIARITY, vis_pair=1.9*(ITEM2*concepts)',
)
if p.do_familiarity:
actions[
'd_attending_item2'] += ', dm_learned_words=1.0*(~ITEM1*vis_pair)'
actions[
'e_start_familiarity'] += ', do_fam=GO, dm_learned_words=2.0*(~ITEM1*vis_pair+~ITEM2*vis_pair)'
actions.update(
dict(
#judge familiarity
f_accumulate_familiarity=
'1.1*dot(goal,FAMILIARITY) - 0.2 --> goal=FAMILIARITY-RECOG2, do_fam=GO, dm_learned_words=.8*(~ITEM1*vis_pair+~ITEM2*vis_pair)',
g_respond_unfamiliar=
'dot(goal,FAMILIARITY) - familiarity - .5*dot(fingers,L1+L2+R1+R2) - .6 --> goal=RESPOND_MISMATCH-FAMILIARITY, do_fam=GO, motor_input=1.6*(target_hand+MIDDLE)',
#g2_respond_familiar = 'dot(goal,FAMILIARITY) + familiarity - .5*dot(fingers,L1+L2+R1+R2) - .6 --> goal=RESPOND, do_fam=GO, motor_input=1.6*(target_hand+INDEX)',
#recollection & representation
h_recollection=
'dot(goal,FAMILIARITY) + familiarity - .5*dot(fingers,L1+L2+R1+R2) - .6 --> goal=RECOLLECTION-FAMILIARITY, dm_pairs = vis_pair',
i_representation=
'dot(goal,RECOLLECTION) - rep_filled - .1 --> goal=RECOLLECTION, dm_pairs = vis_pair, representation=3*dm_pairs, do_rep=GO',
#comparison & respond
j_10_compare_word1=
'dot(goal,RECOLLECTION+1.4*COMPARE_ITEM1) + rep_filled - .9 --> goal=COMPARE_ITEM1-RECOLLECTION, do_rep=GO, do_compare=GO, comparison_A = ~ITEM1*vis_pair, comparison_B = ~ITEM1*representation',
k_11_match_word1=
'dot(goal,COMPARE_ITEM1) + comparison_accumulator - .7 --> goal=COMPARE_ITEM2-COMPARE_ITEM1, do_rep=GO, comparison_A = ~ITEM1*vis_pair, comparison_B = ~ITEM1*representation',
l_12_mismatch_word1=
'dot(goal,COMPARE_ITEM1) + .4 * dot(goal,RESPOND_MISMATCH) - comparison_accumulator - .7 --> goal=RESPOND_MISMATCH-COMPARE_ITEM1, do_rep=GO, motor_input=1.6*(target_hand+MIDDLE), do_compare=GO, comparison_A = ~ITEM1*vis_pair, comparison_B = ~ITEM1*representation',
compare_word2=
'dot(goal,COMPARE_ITEM2) - .5 --> goal=COMPARE_ITEM2, do_compare=GO, comparison_A = ~ITEM2*vis_pair, comparison_B = ~ITEM2*representation',
m_match_word2=
'dot(goal,COMPARE_ITEM2) + comparison_accumulator - .7 --> goal=RESPOND_MATCH-COMPARE_ITEM2, motor_input=1.6*(target_hand+INDEX), do_compare=GO, comparison_A = ~ITEM2*vis_pair, comparison_B = ~ITEM2*representation',
n_mismatch_word2=
'dot(goal,COMPARE_ITEM2) - comparison_accumulator - dot(fingers,L1+L2+R1+R2)- .7 --> goal=RESPOND_MISMATCH-COMPARE_ITEM2, motor_input=1.6*(target_hand+MIDDLE),do_compare=GO, comparison_A = ~ITEM2*vis_pair, comparison_B = ~ITEM2*representation',
#respond
o_respond_match=
'dot(goal,RESPOND_MATCH) - .1 --> goal=RESPOND_MATCH, motor_input=1.6*(target_hand+INDEX)',
p_respond_mismatch=
'dot(goal,RESPOND_MISMATCH) - .1 --> goal=RESPOND_MISMATCH, motor_input=1.6*(target_hand+MIDDLE)',
#finish
x_response_done=
'dot(goal,RESPOND_MATCH) + dot(goal,RESPOND_MISMATCH) + 2*dot(fingers,L1+L2+R1+R2) - .7 --> goal=2*END',
y_end=
'dot(goal,END)-.1 --> goal=END-RESPOND_MATCH-RESPOND_MISMATCH',
z_threshold='.05 --> goal=0'
#possible to match complete buffer, ie is representation filled?
# motor_input=1.5*target_hand+MIDDLE,
))
with force_neurons_cfg:
model.bg = spa.BasalGanglia(spa.Actions(**actions))
with force_neurons_cfg:
model.thalamus = spa.Thalamus(model.bg)
model.p_bg_input = nengo.Probe(model.bg.input)
model.p_thal_output = nengo.Probe(model.thalamus.actions.output,
synapse=0.01)
#probes
if p.do_motor:
model.pr_motor_pos = nengo.Probe(
model.finger_pos.output,
synapse=.01) #raw vector (dimensions x time)
model.pr_motor = nengo.Probe(model.fingers.output, synapse=.01)
#model.pr_motor1 = nengo.Probe(model.motor.output, synapse=.01)
#if not p.gui:
# model.pr_vision_gabor = nengo.Probe(model.vision_gabor.neurons,synapse=.005) #do we need synapse, or should we do something with the spikes
# model.pr_familiarity = nengo.Probe(model.dm_learned_words.am.elem_output,synapse=.01) #element output, don't include default
# model.pr_concepts = nengo.Probe(model.concepts.am.elem_output, synapse=.01) # element output, don't include default
#multiply spikes with the connection weights
#input
model.input = spa.Input(goal=goal_func)
if p.gui:
vocab_actions = spa.Vocabulary(model.bg.output.size_out)
for i, action in enumerate(model.bg.actions.actions):
vocab_actions.add(action.name.upper(),
np.eye(model.bg.output.size_out)[i])
model.actions = spa.State(model.bg.output.size_out,
subdimensions=model.bg.output.size_out,
vocab=vocab_actions)
nengo.Connection(model.thalamus.output, model.actions.input)
for net in model.networks:
if net.label is not None and net.label.startswith('channel'):
net.label = ''
return model
def create_model(D=512, incl_interoception=False, query=False):
vocabulary = sim.Experiment()
# Create semantic pointers in each network
spa_voc = utils.create_spa_vocabulary(vocabulary, randomize=True, D=D)
# Episodic and affect integrate two vocabularies
input_episodic = utils.add_vocabularies(spa_voc, 'sensory', 'conceptualization')
input_affect = utils.add_vocabularies(spa_voc, 'episodic', 'interoception')
with spa.SPA('POEM') as model:
# Sensory
model._sensory = spa.State(D, vocab=spa_voc['sensory'])
# Episodic
episodic_output_keys = utils.keys_from_input(input_episodic.keys)
zoo_idx = input_episodic.keys.index('Conceptualization_ZOO')
episodic_output_keys[zoo_idx] = '2*ZOO-2*GLASS-2*SNAKE'
model._episodic = Memory(input_vocab=input_episodic,
output_vocab=spa_voc['episodic'],
input_keys=input_episodic.keys,
output_keys=episodic_output_keys,
wta_output=True,
wta_inhibit_scale=0.1,
threshold_output=True)
ep_output_vectors = np.array([spa_voc['episodic'].parse(key).v for key in\
episodic_output_keys], ndmin=2)
if query:
model.query = spa.State(D, vocab=spa_voc['sensory'])
model.bind = spa.Bind(D, invert_b=True)
nengo.Connection(model.bind.output, model._episodic.input,
transform=3)
nengo.Connection(model._sensory.input, model.bind.A)
nengo.Connection(model.query.input, model.bind.B)
else:
nengo.Connection(model._sensory.output, model._episodic.input,
transform=3) # 3 because inputs set by cloud are
# not normalized
# Language
model._language = Memory(input_vocab=spa_voc['episodic'],
output_vocab=spa_voc['language'])
nengo.Connection(model._episodic.am.elem_output, model._language.input,
transform=ep_output_vectors.T)
# Conceptualization
model._conceptualization = Memory(input_vocab=spa_voc['language'],
output_vocab=spa_voc['conceptualization'],
wta_output=True,
wta_synapse=.05,
threshold_output=True,
wta_inhibit_scale=.3)
trans_mat = vocabulary.custom_transform(spa_voc['language'], D=D)
nengo.Connection(model._language.output, model._conceptualization.input,
transform=trans_mat.T, synapse=0.01)
nengo.Connection(model._conceptualization.output, model._episodic.input,
synapse=0.3)
# Interoception
if incl_interoception:
model._interoception = spa.State(D, vocab=spa_voc['interoception'])
# Affect: EPA expressions at the output
input_words = utils.keys_from_input(input_affect.keys)
epa_expressions_words = utils.get_epa_expression(input_words)
model._affect = Memory(input_vocab=input_affect,
output_vocab=spa_voc['affect'],
input_keys=input_affect.keys,
output_keys=epa_expressions_words,
wta_output=False,
threshold=0.4)
if incl_interoception:
nengo.Connection(model._interoception.output, model._affect.input,
transform=1.)
print(input_affect.keys)
# Emotion detection network (comment if not needed)
model.active = nengo.Ensemble(n_neurons=200, dimensions=3)
model.emotion_present = nengo.Ensemble(n_neurons=50, dimensions=1)
nengo.Connection(model._affect.output[[0, 1, 2]], model.active)
nengo.Connection(model.active, model.emotion_present, function=lambda x: np.sum(x**2))
nengo.Connection(model._episodic.output, model._affect.input)
# Executive: EPA expressions at the input
emotion_tags = spa_voc['executive'].keys
epa_expressions = utils.get_epa_expression(emotion_tags)
model._executive = Memory(input_vocab=spa_voc['affect'],
output_vocab=spa_voc['executive'],
input_keys=epa_expressions,
output_keys=emotion_tags,
threshold=0.8)
nengo.Connection(model._affect.output, model._executive.input,
transform=3)
return model, spa_voc
def _test_sequence(Simulator, plt, seed, outfile, prune_passthrough):
dimensions = 32
subdimensions = 16
T = 4.0
seq_length = 6
with spa.SPA(seed=seed) as model:
model.state = spa.Memory(dimensions=dimensions,
subdimensions=subdimensions)
seq_actions = [
'dot(state,A%d) --> state=A%d' % (i, (i + 1) % seq_length)
for i in range(seq_length)
]
model.bg = spa.BasalGanglia(spa.Actions(*seq_actions))
model.thal = spa.Thalamus(model.bg)
def stim_state(t):
if t < 0.1:
return 'A0'
else:
return '0'
model.input = spa.Input(state=stim_state)
p_state = nengo.Probe(model.state.state.output, synapse=0.01)
if 'spinnaker' in Simulator.__module__:
nengo_spinnaker.add_spinnaker_params(model.config)
model.config[
model.input.input_nodes['state']].function_of_time = True
vocab = model.get_input_vocab('state')
if prune_passthrough:
model = remove_passthrough_nodes(model)
sim = Simulator(model)
sim.run(T)
t = sim.trange()
data = sim.data[p_state]
ideal = np.array([vocab.parse('A%d' % i).v for i in range(seq_length)])
dotp = np.dot(data, ideal.T)
best = np.argmax(dotp, axis=1)
delta = np.diff(best)
indexes = np.where(delta != 0)
# [:, 1:] ignores the first transition, which is meaningless
delta_t = np.diff(indexes)[:, 1:] * 0.001
mean = np.mean(delta_t)
std = np.std(delta_t)
outfile.write('"n_neurons": %d,\n' % sum(e.n_neurons
for e in model.all_ensembles))
outfile.write('"simtime": %f,\n' % T)
outfile.write('"timing_mean": %f,\n' % mean)
outfile.write('"timing_std": %f,\n' % std)
figsize = (onecolumn, 4.0) if horizontal else (onecolumn * 2, 3.0)
setup(figsize=figsize,
palette_args={
'palette': "cubehelix",
'n_colors': 6
})
plt.plot(t[t < 1.0], dotp[t < 1.0])
for transition in t[indexes[0]]:
plt.axvline(transition, c='0.5', lw=1, ls=':')
plt.ylabel('Similarity to item')
plt.xlabel('Time (s)')
plt.xlim(right=1.0)
sns.despine()
if prune_passthrough:
plt.saveas = 'results-4.svg'
else:
plt.saveas = 'results-5.svg'
if hasattr(sim, 'close'):
sim.close()
[r_2, r_22, 0.2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
vects['input3'].append(
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, r_3, r_32, r_3, r_3])
dimensions = 16 #number of dimensions for semantic pointers
# change these slightly to create individual variation
vocab = spa.Vocabulary(dimensions, randomize=False)
# vocab.add('ON_1',[1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0])
# vocab.add('ON_2',[0.4,0.4,0.2,0,0,0,0,0,0,0,0,0,0,0,0,0])
# vocab.add('REST',[0,0,0,0,0,0,0,0,0,0,0,0,0.25,0.25,0.25,0.25])
vocab.add('ON_1', vects['input1'][subject])
vocab.add('ON_2', vects['input2'][subject])
vocab.add('REST', vects['input3'][subject])
model = spa.SPA(dimensions, vocabs=vocab)
with model:
model.cortex = spa.Buffer(dimensions=dimensions)
#print model.get_default_vocab(dimensions).parse("ON_1")
#action mapping
actions = spa.Actions(
'dot(cortex, ON_1) --> cortex = ON_1',
'dot(cortex, ON_2) --> cortex = ON_2',
'dot(cortex, REST) --> cortex = REST',
)
model.bg = spa.BasalGanglia(actions=actions)
model.thal = spa.Thalamus(model.bg)
##########################
import matplotlib.pyplot as plt
import nengo
from nengo import spa
# ## Create the model
#
# Notice that when you specify actions, you're determining which modules are connected to which. For example, by having a mapping that depends on the state of cortex, you are determining that the cortex and basal ganglia must be connected. As well, when you specify that the result of the action changes the state of cortex, then you are determining that thalamus must be connected to cortex.
# In[ ]:
# Number of dimensions for the Semantic Pointers
dimensions = 128
# Make a model object with the SPA network
model = spa.SPA(label='Controlled_Question_Answering')
with model:
# Specify the modules to be used
model.vision = spa.Buffer(dimensions=dimensions, neurons_per_dimension=100)
model.motor = spa.Buffer(dimensions=dimensions, neurons_per_dimension=100)
model.memory = spa.Memory(dimensions=dimensions,
neurons_per_dimension=100,
synapse=0.1)
# Specify the action mapping
actions = spa.Actions(
'dot(vision, STATEMENT) --> memory = vision',
'dot(vision, QUESTION) --> motor = ~vision*memory',
)
model.bg = spa.BasalGanglia(actions=actions)
def __init__(self,
mapping,
D_category=16,
D_items=16,
threshold=0.4,
learning_rate=1e-4):
model = spa.SPA()
self.model = model
self.mapping = mapping
self.vocab_category = spa.Vocabulary(D_category)
self.vocab_items = spa.Vocabulary(D_items)
self.vocab_items_temp = spa.Vocabulary(D_items)
for k in sorted(
mapping.keys()): #allocating verctors for categories name
self.vocab_category.parse(k)
for v in mapping[k]: # allocating vectors to the items
self.vocab_items.parse(v)
with model:
model.category = spa.State(D_category, vocab=self.vocab_category)
model.items = spa.State(D_items,
vocab=self.vocab_items,
subdimensions=64)
#encoders = ens.encoders.sample(n=ens.n_neurons, d=D)
n_neuron = model.items.state_ensembles.all_ensembles[0].n_neurons
encoders = model.items.state_ensembles.all_ensembles[
0].encoders.sample(n=n_neuron, d=D_items)
related = 0.5
w = 1.0 / related - 1
count = 1
for k in sorted(mapping.keys()[:4]): #Practiced Category
for item in mapping[k][:2]: #low freq items
for i in range((count - 1) * 50, count * 50):
encoders[i] = -self.vocab_items.parse(
item).v + w * encoders[i]
encoders[i] = encoders[i] / np.linalg.norm(encoders[i])
count = count + 1
model.items.state_ensembles.all_ensembles[0].encoders = encoders
def learned(x):
cats = np.dot(self.vocab_category.vectors, x)
best_index = np.argmax(
cats
) #takes the category which has the largest projection of x
if cats[best_index] < threshold:
return self.vocab_items.parse('0').v
else: #generate the sum vector
k = self.vocab_category.keys[best_index]
total = '+'.join(self.mapping[k])
v = self.vocab_items.parse(total).v
return v / (2 * np.linalg.norm(v))
c = nengo.Connection(
model.category.all_ensembles[0],
model.items.input,
function=learned,
learning_rule_type=nengo.PES(learning_rate=learning_rate))
model.error = spa.State(D_items, vocab=self.vocab_items)
nengo.Connection(model.items.output, model.error.input)
nengo.Connection(model.error.output, c.learning_rule)
self.stim_category_value = np.zeros(D_category)
self.stim_category = nengo.Node(self.stim_category)
nengo.Connection(self.stim_category,
model.category.input,
synapse=None)
self.stim_correct_value = np.zeros(D_items)
self.stim_correct = nengo.Node(self.stim_correct)
nengo.Connection(self.stim_correct,
model.error.input,
synapse=None,
transform=-1)
self.stim_stoplearn_value = np.zeros(1)
self.stim_stoplearn = nengo.Node(self.stim_stoplearn)
for ens in model.error.all_ensembles:
nengo.Connection(self.stim_stoplearn,
ens.neurons,
synapse=None,
transform=-10 * np.ones((ens.n_neurons, 1)))
self.stim_justmemorize_value = np.zeros(1)
self.stim_justmemorize = nengo.Node(self.stim_justmemorize)
for ens in model.items.all_ensembles:
nengo.Connection(self.stim_justmemorize,
ens.neurons,
synapse=None,
transform=-10 * np.ones((ens.n_neurons, 1)))
self.probe_items = nengo.Probe(model.items.output, synapse=0.01)
self.sim = nengo.Simulator(self.model)
# random locations
rng_items = np.random.RandomState(seed=args.item_seed)
locs = rng_items.uniform(0, 10, size=(7, 2))
items = OrderedDict({
"Tree": locs[0, :],
"Pond": locs[1, :],
"Well": locs[2, :],
"Rock": locs[3, :],
"Reed": locs[4, :],
"Lake": locs[5, :],
"Bush": locs[6, :]
})
shape = (10, 10)
model = spa.SPA(seed=seed)
action_vocab = spa.Vocabulary(3, randomize=False)
item_vocab = spa.Vocabulary(D, randomize=randomize)
# item_vocab = spa.Vocabulary(len(items), randomize=True)
"""
keys = np.array([[1,0,0,0],
[0,1,0,0],
[0,0,1,0],
[0,0,0,1],
])
"""
keys = np.eye(len(items))
vocab_goal.parse(
'START+RETRIEVE+COMPARE+RESPOND+DONE+START_COUNTING+UPDATE_RESULT+STORE_RESULT+UPDATE_COUNT+STORE_COUNT+COMPARE_COUNT'
)
#vocab reset
vocab_reset = spa.Vocabulary(Dlow, rng=rng_vocabs)
vocab_reset.parse('CLEAR+GO')
#vocab_motor
vocab_motor = spa.Vocabulary(Dlow, rng=rng_vocabs)
vocab_motor.parse('YES')
vocab_motor.parse('NO')
###### Model #######
model = spa.SPA(seed=fseed)
with model:
#Vision & Goal
model.vision = spa.State(D, vocab=vocab_concepts) #visual input
model.goalnet = nengo.Network(seed=fseed)
with model.goalnet:
model.goal = spa.State(Dlow, vocab=vocab_goal,
feedback=.5) #goal state #.75
model.count = spa.State(
D, vocab=vocab_concepts, feedback=.8,
feedback_synapse=.05) #the number of counts taken
model.target = spa.State(D, vocab=vocab_concepts,
feedback=1) #target answer from vision
def SyllableSequence(n_per_d, syllable_d, syllables,
difference_gain=15, n_positions=7,
threshold_memories=True, add_default_output=True,
rng=np.random, net=None):
if net is None:
net = spa.SPA("Syllable sequence")
assert isinstance(net, spa.SPA), "Network must be a SPA instance."
vocab = spa.Vocabulary(dimensions=syllable_d,
rng=rng,
unitary=['INC', 'POS1'])
vocab.parse('INC + POS1')
for i in range(2, n_positions+1):
vocab.add('POS%d' % i, vocab.parse('POS%d * INC' % (i-1)))
vocab.parse(" + ".join(syllables))
syll_vocab = vocab.create_subset(syllables)
net.vocab = vocab
with net:
# --- Input sequence
net.sequence = spa.State(dimensions=syllable_d,
neurons_per_dimension=n_per_d)
# --- Input gated memories iterate through position vectors
net.pos_curr = InputGatedMemory(
n_per_d, dimensions=syllable_d, difference_gain=difference_gain)
net.pos_next = InputGatedMemory(
n_per_d, dimensions=syllable_d, difference_gain=difference_gain)
# Switch from current to next with reciprocal connections
nengo.Connection(net.pos_curr.output, net.pos_next.input)
nengo.Connection(net.pos_next.output, net.pos_curr.input,
transform=vocab['INC'].get_convolution_matrix())
# Switching depends on gate; get gate input elsewhere
net.gate = nengo.Node(size_in=1)
# pos gets gate
nengo.Connection(net.gate, net.pos_curr.gate, synapse=None)
# pos_next gets 1 - gate
net.gate_bias = nengo.Node(output=1)
nengo.Connection(net.gate_bias, net.pos_next.gate, synapse=None)
nengo.Connection(net.gate, net.pos_next.gate,
transform=-1, synapse=None)
# --- Get syllables with unbinding
net.bind = CircularConvolution(
n_per_d, syllable_d, invert_a=False, invert_b=True)
net.bind_next = CircularConvolution(
n_per_d, syllable_d, invert_a=False, invert_b=True)
nengo.Connection(net.sequence.output, net.bind.A)
nengo.Connection(net.sequence.output, net.bind_next.A)
nengo.Connection(net.pos_curr.output, net.bind.B)
nengo.Connection(net.pos_next.output, net.bind_next.B,
transform=vocab['INC'].get_convolution_matrix())
# --- Clean up noisy syllables with associative memories
net.syllable = spa.AssociativeMemory(
syll_vocab, wta_output=True, threshold_output=threshold_memories)
net.syllable_next = spa.AssociativeMemory(
syll_vocab, wta_output=True, threshold_output=threshold_memories)
nengo.Connection(net.bind.output, net.syllable.input)
nengo.Connection(net.bind_next.output, net.syllable_next.input)
if add_default_output:
default = np.zeros(syllable_d)
net.syllable.am.add_default_output_vector(default)
net.syllable_next.am.add_default_output_vector(default)
return net
import nengo
import nengo.spa as spa
D = 16
model = spa.SPA(seed=1)
with model:
model.a = spa.Buffer(dimensions=D)
model.b = spa.Buffer(dimensions=D)
model.c = spa.Buffer(dimensions=D)
model.cortical = spa.Cortical(spa.Actions('c = a+b', ))
model.input = spa.Input(
a='A',
b=(lambda t: 'C*~A' if (t % 0.1 < 0.05) else 'D*~A'),
)
if __name__ == '__main__':
import nengo_gui
nengo_gui.Viz(__file__).start()
import nengo
import nengo.spa as spa
import numpy as np
import time
dimensions = 32
vocab = spa.Vocabulary(dimensions)
model = spa.SPA(label='ActionExchange')
"""
class ActionState(nengo.Node):
def __init__(self):
self.action = "WAIT"
super(ActionState, self).__init__(self.update)
def parse_action(t, action):
turn = vocab.parse("TURN").v
wait = vocab.parse("WAIT").v
if np.dot(action, turn) > np.dot(action, wait):
self.turn()
return "WAIT"
def turn():
time.sleep(2)
pass
def update(self, t):
if self.action == "TURN":
self.turn()
# vecotors A and B).
# Setup the environment
import nengo
import nengo.spa as spa
from nengo.spa import Vocabulary
import numpy as np
D = 32 # the dimensionality of the vectors
#Creating a vocabulary
rng = np.random.RandomState(0)
vocab = Vocabulary(dimensions=D, rng=rng)
vocab.add('C', vocab.parse('A * B'))
model = spa.SPA(label="structure", vocabs=[vocab])
with model:
model.A = spa.State(D)
model.B = spa.State(D)
model.C = spa.State(D, feedback=1)
model.Sum = spa.State(D)
actions = spa.Actions(
'C = A * B',
'Sum = A',
'Sum = B'
)
model.cortical = spa.Cortical(actions)
#Input
def model(self, p):
vis_items = ['FATIGUE', 'WHISKEY']
vis_vocab = spa.Vocabulary(p.D)
self.vis_items = vis_items
self.vis_vocab = vis_vocab
result_vocab_items = ['SAME']
input_items = ['PUSH']
action_items = ['F1']
self.result_vocab_items = result_vocab_items
self.input_items = input_items
self.action_items = action_items
##### Vision and motor system #########
import vision_system as v
import motor_system as m
reload(v)
reload(m)
directory = '/home/stacy/github/visual-categorization/assoc_recog_s/images/'
image_list = v.load_images(directory, items=vis_items)
output_list = v.vector_gen_function(vis_items, vocab=vis_vocab)
self.directory = directory
self.image_list = image_list
self.output_list = output_list
model = spa.SPA(label='MAIN')
with model:
model.vision_system = v.make_vision_system(
image_list,
output_list,
n_neurons=500,
AIT_V1_strength=p.AIT_V1_strength,
AIT_r_transform=p.AIT_r_transform,
V1_r_transform=p.V1_r_transform)
model.concept = spa.State(p.D, vocab=vis_vocab)
nengo.Connection(model.vision_system.AIT, model.concept.input)
model.compare = spa.Compare(p.D)
model.wm = spa.State(p.D, vocab=vis_vocab)
model.result = spa.State(p.D, feedback=p.result_feedback)
nengo.Connection(model.concept.output,
model.compare.inputA,
synapse=0.01)
nengo.Connection(model.wm.output, model.compare.inputB)
vocab = model.get_input_vocab('result')
nengo.Connection(model.compare.output,
model.result.input,
transform=p.compare_to_result_strength *
np.array([vocab.parse('SAME').v]).T)
def result_to_motor(in_vocab, out_vocab):
mapping = np.zeros((p.D, p.D))
for i in range(len(input_items)):
mapping += np.outer(
in_vocab.parse(result_vocab_items[i]).v,
out_vocab.parse(input_items[i]).v)
transform = mapping.T
return transform
model.motor_system = m.make_motor_system(
input_items,
action_items,
motor_feedback=p.motor_feedback,
motor_transform=p.motor_transform,
finger_feedback=p.finger_feedback,
motor_to_fingers_strength=p.motor_to_fingers_strength)
nengo.Connection(model.result.output,
model.motor_system.motor_input.input,
transform=result_to_motor(
vocab, model.motor_system.motor_vocab))
def present_func(t):
if t < 1:
index = 0
else:
index = 1
return image_list[index]
stim = nengo.Node(present_func)
nengo.Connection(stim, model.vision_system.presentation_node)
stim_wm = nengo.Node(
model.get_input_vocab('wm').parse('FATIGUE').v)
nengo.Connection(stim_wm, model.wm.input)
self.V1_probe = nengo.Probe(model.vision_system.V1)
self.AIT_probe = nengo.Probe(model.vision_system.AIT,
synapse=0.005)
self.PFC_probe = nengo.Probe(model.compare.output, synapse=0.005)
self.PMC_probe = nengo.Probe(model.result.output, synapse=0.005)
self.MC_probe = nengo.Probe(model.motor_system.motor.output,
synapse=0.005)
self.finger_probe = nengo.Probe(model.motor_system.fingers.output,
synapse=0.005)
self.final_probe = nengo.Probe(
model.motor_system.finger_pos.output, synapse=0.005)
self.mymodel = model
return model
import nengo
import nengo.spa as spa
import numpy as np
D = 32
vocab = spa.Vocabulary(D)
food_vocab = spa.Vocabulary(D)
sub_vocab = spa.Vocabulary(D)
model = spa.SPA(label="Find Food")
with model:
def starter(t):
if t < 0.05:
return "START_FIND_FOOD"
else:
return "0"
def food_exist_func(t):
if t < 0.5:
return "NO_FOOD"
else:
return "FOOD"
def food_close_func(t):
if t < 1:
return "NO_FOOD"
else:
return "CLOSE"
import nengo.spa as spa
from nengo.spa import Vocabulary
import numpy as np
D = 32 # the dimensionality of the vectors
rng = np.random.RandomState(7)
vocab = Vocabulary(dimensions=D, rng=rng, max_similarity=0.1)
#Adding semantic pointers to the vocabulary
CIRCLE = vocab.parse('CIRCLE')
BLUE = vocab.parse('BLUE')
RED = vocab.parse('RED')
SQUARE = vocab.parse('SQUARE')
ZERO = vocab.add('ZERO', [0] * D)
model = spa.SPA(label="Question Answering", vocabs=[vocab])
with model:
model.A = spa.State(D, label="color")
model.B = spa.State(D, label="shape")
model.C = spa.State(D, label="cue")
model.D = spa.State(D, label="bound")
model.E = spa.State(D, label="output")
actions = spa.Actions(
'D = A * B',
'E = D * ~C',
)
model.cortical = spa.Cortical(actions)
# Test binding output
import nengo
import nengo.spa as spa
import numpy as np
dimensions = 32
vocab = spa.Vocabulary(dimensions)
model = spa.SPA(label='Play_w_input')
def my_output(t, x):
# How similar is x to STOP?
eat = np.dot(x, vocab.parse('STOP').v)
return eat
def my_input():
pass
with model:
model.subgoal = spa.State(dimensions, vocab)
model.food = spa.State(dimensions, vocab)
model.food_percept = spa.State(dimensions,
vocab,
feedback=1,
feedback_synapse=0.1)
model.now_state = spa.State(dimensions,
# The book describes that the results of the model can be seen through the
# visualizer in Nengo 1.4 GUI which has a "Utility" box and the "Rules" box.
# Note that the bottom-right graph shows the same information as seen in the
# "Rules" box and top-right graph shows the same information as seen in the
# "Utility" box.
#Setup the environment
import nengo
from nengo import spa #import spa related packages
#Number of dimensions for the Semantic Pointers
dimensions = 16
#Make a model with the SPA network
model = spa.SPA(label='Sequence')
with model:
#Creating a working memory/cortical element
model.state = spa.State(dimensions=dimensions,
feedback=1,
feedback_synapse=0.01)
#Specifying the action mappings (rules) for BG and Thal
actions = spa.Actions('dot(state, A) --> state = B',
'dot(state, B) --> state = C',
'dot(state, C) --> state = D',
'dot(state, D) --> state = E',
'dot(state, E) --> state = A')
#Creating the BG and Thalamus components that confirm to the specified rules
model.BG = spa.BasalGanglia(actions=actions)
def create_model(seed=None):
#create vocabulary to show representations in gui
if nengo_gui_on:
vocab_angles = spa.Vocabulary(D)
for name in [0, 3, 7, 12, 18, 25, 33, 42]:
#vocab_angles.add('D' + str(name), np.linalg.norm(compressed_im_cued[name+90])) #take mean across phases
v = compressed_im_cued[name + 90]
nrm = np.linalg.norm(v)
if nrm > 0:
v /= nrm
vocab_angles.add('D' + str(name), v) #take mean across phases
v = np.dot(imagearr[-1, :] / 50, U_cued[:, :D])
nrm = np.linalg.norm(v)
if nrm > 0:
v /= nrm
vocab_angles.add('Impulse', v)
#model = nengo.Network(seed=seed)
model = spa.SPA(seed=seed)
with model:
#input nodes
if not batch_processing:
model.inputNode_cued = nengo.Node(input_func_cued,
label='input_cued')
model.reactivate = nengo.Node(reactivate_func, label='reactivate')
elif batch_processing:
model.inputNode_cued = nengo.Node(np.zeros(128 * 128))
model.reactivate = nengo.Node(np.zeros(Nm))
#eye ensemble
eye_cued = nengo.Ensemble(Ns,
D,
encoders=e_cued,
intercepts=Uniform(0.01, 0.1),
radius=1,
label='eye_cued',
seed=seed)
nengo.Connection(model.inputNode_cued,
eye_cued,
transform=U_cued[:, :D].T)
#sensory ensemble
sensory_cued = nengo.Ensemble(Ns,
D,
encoders=e_cued,
intercepts=Uniform(0.01, .1),
radius=1,
label='sensory_cued')
conn_cued = nengo.Connection(
eye_cued, sensory_cued,
function=lambda x: x) #default: identity function
if nengo_gui_on:
with nengo.Simulator(network=model,
progress_bar=False) as sim_cued:
weights_cued = sim_cued.data[conn_cued].weights
model.connections.remove(conn_cued)
elif not (nengo_gui_on):
with nengo_dl.Simulator(
network=model, progress_bar=False,
device=device) as sim_cued: #, device=device
weights_cued = sim_cued.data[conn_cued].weights
model.connections.remove(conn_cued)
Ncluster = 1 # number of neurons per cluster
clusters = np.arange(0, Ns, Ncluster)
#parameters for gamma distribution where k=shape, theta=scale and mean=k*theta -> theta=mean/k
# wanted distribution: lowest value 51ms and mean value 141 ms (Lamme & Roelfsema (2000))
k, mean = 2, 0.090 #(mean_synapse - lowest_synapse) #subtract lowest synapse from mean so distribution starts at 0
theta = mean / k
shift = 0.051
weights_trans = 1.50
rec_trans = 0.30
noise_sd = 0.010
if uncued:
# Build second simulation to fetch weights before making the large amount of connections between eye_cued and sensory_cued, place all
# of uncued model inside this if statement to keep code close together
if not batch_processing:
model.inputNode_uncued = nengo.Node(input_func_uncued,
label='input_first')
elif batch_processing:
model.inputNode_uncued = nengo.Node(np.zeros(128 * 128))
eye_uncued = nengo.Ensemble(Ns,
D,
encoders=e_uncued,
intercepts=Uniform(0.01, 0.1),
radius=1,
label='eye_uncued',
seed=seed)
nengo.Connection(model.inputNode_uncued,
eye_uncued,
transform=U_uncued[:, :D].T)
sensory_uncued = nengo.Ensemble(Ns,
D,
encoders=e_uncued,
intercepts=Uniform(0.01, .1),
radius=1,
label='sensory_uncued')
conn_uncued = nengo.Connection(
eye_uncued, sensory_uncued,
function=lambda x: x) #default: identity function
if nengo_gui_on:
with nengo.Simulator(network=model,
progress_bar=False) as sim_uncued:
weights_uncued = sim_uncued.data[conn_uncued].weights
model.connections.remove(conn_uncued)
elif not (nengo_gui_on):
with nengo_dl.Simulator(
network=model, progress_bar=False,
device=device) as sim_uncued: #device=device
weights_uncued = sim_uncued.data[conn_uncued].weights
model.connections.remove(conn_uncued)
synapse_uncued = np.random.gamma(k, theta, clusters.size) + shift
for i in range(clusters.size):
begin = clusters[i]
end = (begin + Ncluster)
nengo.Connection(eye_uncued.neurons[begin:end],
sensory_uncued,
transform=weights_uncued[:, begin:end] *
weights_trans,
synapse=synapse_uncued[i])
nengo.Connection(sensory_uncued,
eye_uncued,
transform=rec_trans,
solver=nengo.solvers.LstsqL2(weights=True),
synapse=0.200)
noise_uncued = nengo.processes.WhiteNoise(
dist=Gaussian(0, noise_sd))
memory_uncued = nengo.Ensemble(Nm,
D,
neuron_type=stpLIF(),
intercepts=Uniform(0.01, .1),
noise=noise_uncued,
radius=1,
label='memory_uncued')
nengo.Connection(sensory_uncued, memory_uncued, transform=0.1)
nengo.Connection(memory_uncued,
memory_uncued,
transform=1,
learning_rule_type=STP(),
solver=nengo.solvers.LstsqL2(weights=True))
comparison_uncued = nengo.Ensemble(Nd,
dimensions=4,
radius=math.sqrt(2),
intercepts=Uniform(.01, 1),
label='comparison_uncued')
nengo.Connection(memory_uncued,
comparison_uncued[2:],
eval_points=compressed_im_uncued[0:-1],
function=sincos.T)
nengo.Connection(sensory_uncued,
comparison_uncued[:2],
eval_points=compressed_im_uncued[0:-1],
function=sincos.T)
decision_uncued = nengo.Ensemble(n_neurons=Nd,
dimensions=1,
radius=45,
label='decision_uncued')
nengo.Connection(comparison_uncued,
decision_uncued,
eval_points=ep,
scale_eval_points=False,
function=arctan_func)
### cued ###
synapse_cued = np.random.gamma(k, theta, clusters.size) + shift
for i in range(clusters.size):
begin = clusters[i]
end = (begin + Ncluster)
nengo.Connection(eye_cued.neurons[begin:end],
sensory_cued,
transform=weights_cued[:, begin:end] *
weights_trans,
synapse=synapse_cued[i])
nengo.Connection(sensory_cued,
eye_cued,
transform=rec_trans,
solver=nengo.solvers.LstsqL2(weights=True),
synapse=0.200)
#memory ensemble
noise_cued = nengo.processes.WhiteNoise(dist=Gaussian(0, noise_sd))
memory_cued = nengo.Ensemble(Nm,
D,
neuron_type=stpLIF(),
intercepts=Uniform(0.01, .1),
noise=noise_cued,
radius=1,
label='memory_cued')
nengo.Connection(sensory_cued, memory_cued, transform=0.1)
nengo.Connection(model.reactivate,
memory_cued.neurons) #potential reactivation
#recurrent STSP connection
nengo.Connection(memory_cued,
memory_cued,
transform=1,
learning_rule_type=STP(),
solver=nengo.solvers.LstsqL2(weights=True))
#comparison represents sin, cosine of theta of both sensory and memory ensemble
comparison_cued = nengo.Ensemble(Nc,
dimensions=4,
radius=math.sqrt(2),
intercepts=Uniform(.01, 1),
label='comparison_cued')
nengo.Connection(sensory_cued,
comparison_cued[:2],
eval_points=compressed_im_cued[0:-1],
function=sincos.T)
nengo.Connection(memory_cued,
comparison_cued[2:],
eval_points=compressed_im_cued[0:-1],
function=sincos.T)
#decision represents the difference in theta decoded from the sensory and memory ensembles
decision_cued = nengo.Ensemble(n_neurons=Nd,
dimensions=1,
radius=45,
label='decision_cued')
nengo.Connection(comparison_cued,
decision_cued,
eval_points=ep,
scale_eval_points=False,
function=arctan_func)
#decode for gui
if nengo_gui_on:
model.sensory_decode = spa.State(D,
vocab=vocab_angles,
subdimensions=12,
label='sensory_decode')
for ens in model.sensory_decode.all_ensembles:
ens.neuron_type = nengo.Direct()
nengo.Connection(sensory_cued,
model.sensory_decode.input,
synapse=None)
model.memory_decode = spa.State(D,
vocab=vocab_angles,
subdimensions=12,
label='memory_decode')
for ens in model.memory_decode.all_ensembles:
ens.neuron_type = nengo.Direct()
nengo.Connection(memory_cued,
model.memory_decode.input,
synapse=None)
#probes
if not (nengo_gui_on):
if store_representations: #sim 1 trials 1-100
model.p_mem_cued = nengo.Probe(memory_cued, synapse=0.05)
model.p_mem_uncued = nengo.Probe(memory_uncued, synapse=0.05)
if store_spikes_and_resources: #sim 1 trial 1
model.p_spikes_mem_cued = nengo.Probe(memory_cued.neurons,
'spikes')
model.p_res_cued = nengo.Probe(memory_cued.neurons,
'resources')
model.p_cal_cued = nengo.Probe(memory_cued.neurons, 'calcium')
model.p_spikes_mem_uncued = nengo.Probe(
memory_uncued.neurons, 'spikes')
model.p_res_uncued = nengo.Probe(memory_uncued.neurons,
'resources')
model.p_cal_uncued = nengo.Probe(memory_uncued.neurons,
'calcium')
if store_decisions: #sim 2
model.p_dec_cued = nengo.Probe(decision_cued, synapse=0.01)
if store_memory:
model.p_mem_cued_raw = nengo.Probe(memory_cued.neurons,
'output',
synapse=0.05)
model.p_mem_uncued_raw = nengo.Probe(memory_uncued.neurons,
'output',
synapse=0.05)
return model
def __init__(self,
mapping,
threshold=0.2,
learning_rate=1e-4,
DimVocab=256,
subdimensions=32,
learned_function_scale=2.0):
model = spa.SPA()
self.model = model
self.mapping = mapping
#self.vocab_category = spa.Vocabulary(D_category)
#self.vocab_items = spa.Vocabulary(D_items)
self.VocabUnified = spa.Vocabulary(DimVocab)
for k in sorted(
mapping.keys()): #allocating verctors for categories name
self.VocabUnified.parse(k)
for v in mapping[k]: # allocating vectors to the items
self.VocabUnified.parse(v)
with model:
model.cue = spa.State(DimVocab,
vocab=self.VocabUnified,
subdimensions=subdimensions)
model.target = spa.State(DimVocab,
vocab=self.VocabUnified,
subdimensions=subdimensions)
c = []
n_sub = len(model.cue.state_ensembles.ea_ensembles)
for i in range(n_sub):
cues = []
targets = []
for cue, vals in mapping.items():
for val in vals:
cues.append(
self.VocabUnified.parse(cue).v[i *
subdimensions:(i +
1) *
subdimensions])
targets.append(
self.VocabUnified.parse(val).v / n_sub *
learned_function_scale)
cues.append(
self.VocabUnified.parse(val).v[i *
subdimensions:(i +
1) *
subdimensions])
targets.append(
self.VocabUnified.parse(cue).v / n_sub *
learned_function_scale)
cc = nengo.Connection(
model.cue.all_ensembles[i],
model.target.input,
learning_rule_type=nengo.PES(learning_rate=learning_rate),
**nengo.utils.connection.target_function(cues, targets))
cc.eval_points = cues
cc.function = targets
c.append(cc)
print i
#model.error = spa.State(D_items, vocab=self.vocab_items)
#nengo.Connection(model.items.output, model.error.input)
#nengo.Connection(model.error.output, c.learning_rule)
#I am not sure how this implements the learning
model.error = spa.State(DimVocab,
vocab=self.VocabUnified,
subdimensions=subdimensions)
nengo.Connection(model.target.output, model.error.input)
print 'the loop ended, right?'
for cc in c:
nengo.Connection(model.error.output, cc.learning_rule)
self.stim_cue_value = np.zeros(DimVocab) #?
self.stim_cue = nengo.Node(self.stim_cue_fun) #?
nengo.Connection(self.stim_cue, model.cue.input, synapse=None)
self.stim_correct_value = np.zeros(DimVocab)
self.stim_correct = nengo.Node(self.stim_correct)
nengo.Connection(self.stim_correct,
model.error.input,
synapse=None,
transform=-1)
self.stim_stoplearn_value = np.zeros(1)
self.stim_stoplearn = nengo.Node(self.stim_stoplearn)
for ens in model.error.all_ensembles:
nengo.Connection(self.stim_stoplearn,
ens.neurons,
synapse=None,
transform=-10 * np.ones((ens.n_neurons, 1)))
self.stim_justmemorize_value = np.zeros(1)
self.stim_justmemorize = nengo.Node(self.stim_justmemorize)
for ens in model.target.all_ensembles: #?
nengo.Connection(self.stim_justmemorize,
ens.neurons,
synapse=None,
transform=-10 * np.ones((ens.n_neurons, 1)))
self.probe_target = nengo.Probe(model.target.output, synapse=0.01)
if __name__ != '__builtin__':
self.sim = nengo.Simulator(self.model)
import nengo.spa as spa
from nengo.spa import Vocabulary
import numpy as np
D = 64 # the dimensionality of the vectors
rng = np.random.RandomState(15)
vocab = Vocabulary(dimensions=D, rng=rng, max_similarity=0.1)
#Adding semantic pointers to the vocabulary
CIRCLE=vocab.parse('CIRCLE')
BLUE=vocab.parse('BLUE')
RED=vocab.parse('RED')
SQUARE=vocab.parse('SQUARE')
ZERO=vocab.add('ZERO', [0]*D)
model = spa.SPA(label="Question Answering with Control", vocabs=[vocab])
with model:
model.visual = spa.State(D)
model.motor = spa.State(D)
model.memory = spa.State(D, feedback=1, feedback_synapse=0.1)
actions = spa.Actions(
'dot(visual, STATEMENT) --> memory=visual',
'dot(visual, QUESTION) --> motor = memory * ~visual'
)
model.bg = spa.BasalGanglia(actions)
model.thalamus = spa.Thalamus(model.bg)
#function for providing visual input
def generate(input_signal, alpha=1000.0):
beta = alpha / 4.0
# generate the Function Space
forces, _, goals = forcing_functions.load_folder(
'models/locomotion_trajectories',
rhythmic=True,
alpha=alpha,
beta=beta)
# make an array out of all the possible functions we want to represent
force_space = np.vstack(forces)
# use this array as our space to perform svd over
fs = nengo.FunctionSpace(space=force_space, n_basis=10)
# store the weights for each movement
weights_a = [] # ankle
weights_k = [] # knee
weights_h = [] # hip
# NOTE: things are added to weights based on the order files are read
for ii in range(int(len(goals) / 6)):
forces = force_space[ii * 6:ii * 6 + 6]
# load up the forces to be output by the forcing function
# calculate the corresponding weights over the basis functions
weights_a.append(
np.hstack([
np.dot(fs.basis.T, forces[0]), # ankle 1
np.dot(fs.basis.T, forces[1])
])) # ankle 2
weights_h.append(
np.hstack([
np.dot(fs.basis.T, forces[2]), # hip 1
np.dot(fs.basis.T, forces[3])
])) # hip 2
weights_k.append(
np.hstack([
np.dot(fs.basis.T, forces[4]), # knee 1
np.dot(fs.basis.T, forces[5])
])) # knee 2
# Create our vocabularies
sps_labels = ['GALLOP', 'RUNNING', 'WALKING']
rng = np.random.RandomState(0)
dimensions = 50 # some arbitrary number
vocab_input = Vocabulary(dimensions=dimensions, rng=rng)
vocab_dmp_weights_a = Vocabulary(dimensions=fs.n_basis * 2, rng=rng)
vocab_dmp_weights_k = Vocabulary(dimensions=fs.n_basis * 2, rng=rng)
vocab_dmp_weights_h = Vocabulary(dimensions=fs.n_basis * 2, rng=rng)
for ii, (label, wa, wk,
wh) in enumerate(zip(sps_labels, weights_a, weights_k,
weights_h)):
vocab_input.parse(label) # randomly generate input vector
vocab_dmp_weights_a.add(label, wa)
vocab_dmp_weights_k.add(label, wk)
vocab_dmp_weights_h.add(label, wh)
net = spa.SPA()
net.config[nengo.Ensemble].neuron_type = nengo.LIFRate()
with net:
config = nengo.Config(nengo.Ensemble)
config[nengo.Ensemble].neuron_type = nengo.Direct()
with config:
# --------------------- Inputs --------------------------
# def input_func(t):
# return vocab_input.parse(input_signal).v
# net.input = nengo.Node(input_func)
net.input = spa.State(dimensions,
subdimensions=10,
vocab=vocab_input)
# ------------------- Point Attractors --------------------
zero = nengo.Node([0])
net.a1 = point_attractor.generate(n_neurons=1000,
alpha=alpha,
beta=beta)
nengo.Connection(zero, net.a1.input[0], synapse=None)
net.a2 = point_attractor.generate(n_neurons=1000,
alpha=alpha,
beta=beta)
nengo.Connection(zero, net.a1.input[0], synapse=None)
net.k1 = point_attractor.generate(n_neurons=1000,
alpha=alpha,
beta=beta)
nengo.Connection(zero, net.k1.input[0], synapse=None)
net.k2 = point_attractor.generate(n_neurons=1000,
alpha=alpha,
beta=beta)
nengo.Connection(zero, net.k2.input[0], synapse=None)
net.h1 = point_attractor.generate(n_neurons=1000,
alpha=alpha,
beta=beta)
nengo.Connection(zero, net.h1.input[0], synapse=None)
net.h2 = point_attractor.generate(n_neurons=1000,
alpha=alpha,
beta=beta)
nengo.Connection(zero, net.h2.input[0], synapse=None)
# -------------------- Oscillators ----------------------
kick = nengo.Node(nengo.utils.functions.piecewise({
0: 1,
.05: 0
}),
label='kick')
osc = oscillator.generate(net, n_neurons=3000, speed=.01)
osc.label = 'oscillator'
nengo.Connection(kick, osc[0])
# ------------------- Forcing Functions --------------------
with config:
net.assoc_mem_a = spa.AssociativeMemory(
input_vocab=vocab_input,
output_vocab=vocab_dmp_weights_a,
wta_output=False)
nengo.Connection(net.input.output, net.assoc_mem_a.input)
net.assoc_mem_k = spa.AssociativeMemory(
input_vocab=vocab_input,
output_vocab=vocab_dmp_weights_k,
wta_output=False)
nengo.Connection(net.input.output, net.assoc_mem_k.input)
net.assoc_mem_h = spa.AssociativeMemory(
input_vocab=vocab_input,
output_vocab=vocab_dmp_weights_h,
wta_output=False)
nengo.Connection(net.input.output, net.assoc_mem_h.input)
# -------------------- Product for decoding -----------------------
product_a1 = nengo.Network('Product A1')
nengo.networks.Product(n_neurons=1000,
dimensions=fs.n_basis,
net=product_a1)
product_a2 = nengo.Network('Product A2')
nengo.networks.Product(n_neurons=1000,
dimensions=fs.n_basis,
net=product_a2)
product_h1 = nengo.Network('Product H1')
nengo.networks.Product(n_neurons=1000,
dimensions=fs.n_basis,
net=product_h1)
product_h2 = nengo.Network('Product H2')
nengo.networks.Product(n_neurons=1000,
dimensions=fs.n_basis,
net=product_h2)
product_k1 = nengo.Network('Product K1')
nengo.networks.Product(n_neurons=1000,
dimensions=fs.n_basis,
net=product_k1)
product_k2 = nengo.Network('Product K2')
nengo.networks.Product(n_neurons=1000,
dimensions=fs.n_basis,
net=product_k2)
# get the largest basis function value for normalization
max_basis = np.max(fs.basis * fs.scale)
domain = np.linspace(-np.pi, np.pi, fs.basis.shape[0])
domain_cossin = np.array([np.cos(domain), np.sin(domain)]).T
for ff, product in zip([
net.assoc_mem_a.output[:fs.n_basis],
net.assoc_mem_a.output[fs.n_basis:],
net.assoc_mem_k.output[:fs.n_basis],
net.assoc_mem_k.output[fs.n_basis:],
net.assoc_mem_h.output[:fs.n_basis],
net.assoc_mem_h.output[fs.n_basis:]
], [
product_a1, product_a2, product_k1, product_k2, product_h1,
product_h2
]):
for ii in range(fs.n_basis):
# find the value of a basis function at a value of (x, y)
target_function = nengo.utils.connection.target_function(
domain_cossin, fs.basis[:, ii] * fs.scale / max_basis)
nengo.Connection(osc, product.B[ii], **target_function)
# multiply the value of each basis function at x by its weight
nengo.Connection(ff, product.A)
nengo.Connection(product_a1.output,
net.a1.input[1],
transform=np.ones((1, fs.n_basis)) * max_basis)
nengo.Connection(product_a2.output,
net.a2.input[1],
transform=np.ones((1, fs.n_basis)) * max_basis)
nengo.Connection(product_k1.output,
net.k1.input[1],
transform=np.ones((1, fs.n_basis)) * max_basis)
nengo.Connection(product_k2.output,
net.k2.input[1],
transform=np.ones((1, fs.n_basis)) * max_basis)
nengo.Connection(product_h1.output,
net.h1.input[1],
transform=np.ones((1, fs.n_basis)) * max_basis)
nengo.Connection(product_h2.output,
net.h2.input[1],
transform=np.ones((1, fs.n_basis)) * max_basis)
# -------------------- Output ------------------------------
net.output = nengo.Node(size_in=6, label='output')
nengo.Connection(net.a1.output, net.output[0], synapse=0.01)
nengo.Connection(net.a2.output, net.output[1], synapse=0.01)
nengo.Connection(net.k1.output, net.output[2], synapse=0.01)
nengo.Connection(net.k2.output, net.output[3], synapse=0.01)
nengo.Connection(net.h1.output, net.output[4], synapse=0.01)
nengo.Connection(net.h2.output, net.output[5], synapse=0.01)
# add in the goal offsets
nengo.Connection(net.assoc_mem_a.output[[-2, -1]],
net.output[[0, 1]],
synapse=None)
nengo.Connection(net.assoc_mem_k.output[[-2, -1]],
net.output[[2, 3]],
synapse=None)
nengo.Connection(net.assoc_mem_h.output[[-2, -1]],
net.output[[4, 5]],
synapse=None)
# create a node to give a plot of the represented function
ff_plot_a = fs.make_plot_node(domain=domain,
lines=2,
ylim=[-1000000, 1000000])
nengo.Connection(net.assoc_mem_a.output, ff_plot_a, synapse=0.1)
ff_plot_k = fs.make_plot_node(domain=domain,
lines=2,
ylim=[-1000000, 1000000])
nengo.Connection(net.assoc_mem_k.output, ff_plot_k, synapse=0.1)
ff_plot_h = fs.make_plot_node(domain=domain,
lines=2,
ylim=[-1000000, 1000000])
nengo.Connection(net.assoc_mem_h.output, ff_plot_h, synapse=0.1)
return net
import nengo
import nengo.spa as spa
import numpy as np
D = 256 # options: 64, 128, 256, 384, 512
D_space = 256 # options: 64, 128, 256, 384, 512
vocab_space = spa.Vocabulary(D_space)
model = spa.SPA()
with model:
model.rule = spa.State(D_space, vocab=vocab_space)
model.objs = spa.State(D_space, feedback=1, vocab=vocab_space)
model.status = spa.State(32)
speed = 0.3
separation = 0.3
strength = 0.4
model.subjx = spa.Compare(D_space)
model.subjy = spa.Compare(D_space)
model.objx = spa.Compare(D_space)
model.objy = spa.Compare(D_space)
for ens in model.all_ensembles:
ens.neuron_type = nengo.Direct()
def create_model(seed=None,
memory_item_first=None,
probe_first=None,
memory_item_second=None,
probe_second=None,
Ns=None,
D=None,
Nm=None,
Nc=None,
Nd=None,
e_first=None,
U_first=None,
compressed_im_first=None,
e_second=None,
U_second=None,
compressed_im_second=None,
store_representations=None,
store_decisions=None,
store_spikes_and_resources=None):
# global model
#create vocabulary to show representations in gui
# if nengo_gui_on:
# vocab_angles = spa.Vocabulary(D)
# for name in [0, 5, 10, 16, 24, 32, 40]:
# #vocab_angles.add('D' + str(name), np.linalg.norm(compressed_im_first[name+90])) #take mean across phases
# v = compressed_im_first[name+90]
# nrm = np.linalg.norm(v)
# if nrm > 0:
# v /= nrm
# vocab_angles.add('D' + str(name), v) #take mean across phases
# v = np.dot(imagearr[-1,:]/50, U_first[:,:D])
# nrm = np.linalg.norm(v)
# if nrm > 0:
# v /= nrm
# vocab_angles.add('Impulse', v)
input_partial_first = partial(input_func_first,
memory_item_first=memory_item_first,
probe_first=probe_first)
input_partial_second = partial(input_func_second,
memory_item_second=memory_item_second,
probe_second=probe_second)
react_partial = partial(reactivate_func, Nm=Nm)
#model = nengo.Network(seed=seed)
model = spa.SPA(seed=seed)
with model:
#input nodes
inputNode_first = nengo.Node(input_partial_first, label='input_first')
#sensory ensemble
sensory_first = nengo.Ensemble(Ns,
D,
encoders=e_first,
intercepts=Uniform(0.01, .1),
radius=1,
label='sensory_first')
nengo.Connection(inputNode_first,
sensory_first,
transform=U_first[:, :D].T)
#memory ensemble
memory_first = nengo.Ensemble(Nm,
D,
neuron_type=stpLIF(),
intercepts=Uniform(0.01, .1),
radius=1,
label='memory_first')
nengo.Connection(sensory_first, memory_first, transform=.1) #.1)
#recurrent STSP connection
nengo.Connection(memory_first,
memory_first,
transform=1,
learning_rule_type=STP(),
solver=nengo.solvers.LstsqL2(weights=True))
#comparison represents sin, cosine of theta of both sensory and memory ensemble
comparison_first = nengo.Ensemble(Nc,
dimensions=4,
radius=math.sqrt(2),
intercepts=Uniform(.01, 1),
label='comparison_first')
nengo.Connection(sensory_first,
comparison_first[:2],
eval_points=compressed_im_first[0:-1],
function=sincos.T)
nengo.Connection(memory_first,
comparison_first[2:],
eval_points=compressed_im_first[0:-1],
function=sincos.T)
#decision represents the difference in theta decoded from the sensory and memory ensembles
decision_first = nengo.Ensemble(n_neurons=Nd,
dimensions=1,
radius=45,
label='decision_first')
nengo.Connection(comparison_first,
decision_first,
eval_points=ep,
scale_eval_points=False,
function=arctan_func)
#same for secondary module
inputNode_second = nengo.Node(input_partial_second,
label='input_second')
reactivate = nengo.Node(react_partial, label='reactivate')
sensory_second = nengo.Ensemble(Ns,
D,
encoders=e_second,
intercepts=Uniform(0.01, .1),
radius=1,
label='sensory_second')
nengo.Connection(inputNode_second,
sensory_second,
transform=U_second[:, :D].T)
memory_second = nengo.Ensemble(Nm,
D,
neuron_type=stpLIF(),
intercepts=Uniform(0.01, .1),
radius=1,
label='memory_second')
nengo.Connection(sensory_second, memory_second, transform=.1)
nengo.Connection(reactivate,
memory_second.neurons) #potential reactivation
nengo.Connection(memory_second,
memory_second,
transform=1,
learning_rule_type=STP(),
solver=nengo.solvers.LstsqL2(weights=True))
comparison_second = nengo.Ensemble(Nd,
dimensions=4,
radius=math.sqrt(2),
intercepts=Uniform(.01, 1),
label='comparison_second')
nengo.Connection(memory_second,
comparison_second[2:],
eval_points=compressed_im_second[0:-1],
function=sincos.T)
nengo.Connection(sensory_second,
comparison_second[:2],
eval_points=compressed_im_second[0:-1],
function=sincos.T)
decision_second = nengo.Ensemble(n_neurons=Nd,
dimensions=1,
radius=45,
label='decision_second')
nengo.Connection(comparison_second,
decision_second,
eval_points=ep,
scale_eval_points=False,
function=arctan_func)
# #decode for gui
# if nengo_gui_on:
# model.sensory_decode = spa.State(D, vocab=vocab_angles, subdimensions=12, label='sensory_decode')
# for ens in model.sensory_decode.all_ensembles:
# ens.neuron_type = nengo.Direct()
# nengo.Connection(sensory_first, model.sensory_decode.input,synapse=None)
# model.memory_decode = spa.State(D, vocab=vocab_angles, subdimensions=12, label='memory_decode')
# for ens in model.memory_decode.all_ensembles:
# ens.neuron_type = nengo.Direct()
# nengo.Connection(memory_first, model.memory_decode.input,synapse=None)
#probes
if not (nengo_gui_on):
if store_representations: #sim 1 trials 1-100
model.p_mem_first = nengo.Probe(memory_first, synapse=0.01)
model.p_mem_second = nengo.Probe(memory_second, synapse=0.01)
model.p_sens_first = nengo.Probe(sensory_first, synapse=0.01)
model.p_sens_second = nengo.Probe(sensory_second, synapse=0.01)
if store_spikes_and_resources: #sim 1 trial 1
model.p_spikes_mem_first = nengo.Probe(memory_first.neurons,
'spikes')
model.p_res_first = nengo.Probe(memory_first.neurons,
'resources')
model.p_cal_first = nengo.Probe(memory_first.neurons,
'calcium')
model.p_spikes_mem_second = nengo.Probe(
memory_second.neurons, 'spikes')
model.p_res_second = nengo.Probe(memory_second.neurons,
'resources')
model.p_cal_second = nengo.Probe(memory_second.neurons,
'calcium')
if store_decisions: #sim 2
model.p_dec_first = nengo.Probe(decision_first, synapse=0.01)
model.p_dec_second = nengo.Probe(decision_second, synapse=0.01)
return model