def run():
# Load the config file, which is assumed to live in
# the same directory as this script.
local_dir = os.path.dirname(__file__)
config = Config(os.path.join(local_dir, 'xor2_config'))
# For spiking networks
config.output_nodes = 2
pop = population.Population(config)
pop.epoch(eval_fitness, 500)
winner = pop.most_fit_genomes[-1]
print 'Number of evaluations: %d' % winner.ID
# Verify network output against training data.
print '\nBest network output:'
net = iznn.create_phenotype(winner)
for inputData, outputData in zip(INPUTS, OUTPUTS):
for j in range(MAX_TIME):
output = net.advance([x * 10 for x in inputData])
if output != [False, False]:
break
if output[0] and not output[1]: # Network answered 1
print "%r expected %d got 1" % (inputData, outputData)
elif not output[0] and output[1]: # Network answered 0
print "%r expected %d got 0" % (inputData, outputData)
else:
print "%r expected %d got ?" % (inputData, outputData)
# Visualize the winner network and plot statistics.
visualize.plot_stats(pop.most_fit_genomes, pop.avg_fitness_scores)
visualize.plot_species(pop.species_log)
visualize.draw_net(winner, view=True)
def check_add_connection(genome_type, feed_forward):
local_dir = os.path.dirname(__file__)
config = Config(os.path.join(local_dir, 'test_configuration'))
config.input_nodes = 3
config.output_nodes = 4
config.hidden_nodes = 5
config.feedforward = feed_forward
N = config.input_nodes + config.hidden_nodes + config.output_nodes
connections = {}
for a in range(100):
g = genome_type.create_unconnected(a, config)
g.add_hidden_nodes(config.hidden_nodes)
for b in range(1000):
g.mutate_add_connection()
for c in g.conn_genes.values():
connections[c.key] = connections.get(c.key, 0) + 1
# TODO: The connections should be returned to the caller and checked
# against the constraints/assumptions particular to the network type.
for i in range(N):
values = []
for j in range(N):
values.append(connections.get((i, j), 0))
print("{0:2d}: {1}".format(i, " ".join("{0:3d}".format(x) for x in values)))
def run():
# Load the config file, which is assumed to live in
# the same directory as this script.
local_dir = os.path.dirname(__file__)
config = Config(os.path.join(local_dir, 'xor2_config'))
# For this network, we use two output neurons and use the difference between
# the "time to first spike" to determine the network response. There are
# probably a great many different choices one could make for an output encoding,
# and this choice may not be the best for tackling a real problem.
config.output_nodes = 2
pop = population.Population(config)
pop.run(eval_fitness, 200)
print('Number of evaluations: {0}'.format(pop.total_evaluations))
# Display the winning genome.
winner = pop.statistics.best_genome()
print('\nBest genome:\n{!s}'.format(winner))
# Show output of the most fit genome against training data.
winner = pop.statistics.best_genome()
print('\nBest genome:\n{!s}'.format(winner))
print('\nBest network output:')
net = iznn.create_phenotype(winner, *iz_params)
dt = iz_params[-1]
for inputData, outputData in zip(xor_inputs, xor_outputs):
neuron_data = {}
for i, n in net.neurons.items():
neuron_data[i] = []
# Reset the network, apply the XOR inputs, and run for the maximum allowed time.
net.reset()
net.set_inputs(inputData)
t0 = None
t1 = None
v0 = None
v1 = None
num_steps = int(max_time / dt)
for j in range(num_steps):
t = dt * j
output = net.advance()
# Capture the time and neuron membrane potential for later use if desired.
for i, n in net.neurons.items():
neuron_data[i].append((t, n.v))
# Remember time and value of the first output spikes from each neuron.
if t0 is None and output[0] > 0:
t0, v0 = neuron_data[net.outputs[0]][-2]
if t1 is None and output[1] > 0:
t1, v1 = neuron_data[net.outputs[1]][-2]
response = compute_output(t0, t1)
print(inputData, response)
def run():
# Load the config file, which is assumed to live in
# the same directory as this script.
local_dir = os.path.dirname(__file__)
config = Config(os.path.join(local_dir, 'xor2_config'))
# For this network, we use two output neurons and use the difference between
# the "time to first spike" to determine the network response. There are
# probably a great many different choices one could make for an output encoding,
# and this choice may not be the best for tackling a real problem.
config.output_nodes = 2
pop = population.Population(config)
pop.run(eval_fitness, 200)
print('Number of evaluations: {0}'.format(pop.total_evaluations))
# Visualize the winner network and plot statistics.
winner = pop.statistics.best_genome()
node_names = {0: 'A', 1: 'B', 2: 'Out1', 3: 'Out2'}
visualize.draw_net(winner, view=True, node_names=node_names)
visualize.plot_stats(pop.statistics)
visualize.plot_species(pop.statistics)
# Verify network output against training data.
print('\nBest network output:')
net = iznn.create_phenotype(winner, *iz_params)
sum_square_error, simulated = simulate(winner)
# Create a plot of the traces out to the max time for each set of inputs.
plt.figure(figsize=(12, 12))
for r, (inputData, outputData, t0, t1, v0, v1, neuron_data) in enumerate(simulated):
response = compute_output(t0, t1)
print("{0!r} expected {1:.3f} got {2:.3f}".format(inputData, outputData, response))
axes = plt.subplot(4, 1, r + 1)
plt.title("Traces for XOR input {{{0:.1f}, {1:.1f}}}".format(*inputData), fontsize=12)
for i, s in neuron_data.items():
if i in net.outputs:
t, v = zip(*s)
plt.plot(t, v, "-", label="neuron {0:d}".format(i))
# Circle the first peak of each output.
circle0 = patches.Ellipse((t0, v0), 1.0, 10.0, color='r', fill=False)
circle1 = patches.Ellipse((t1, v1), 1.0, 10.0, color='r', fill=False)
axes.add_artist(circle0)
axes.add_artist(circle1)
plt.ylabel("Potential (mv)", fontsize=10)
plt.ylim(-100, 50)
plt.tick_params(labelsize=8)
plt.grid()
plt.xlabel("Time (in ms)", fontsize=10)
plt.tight_layout(pad=0.4, w_pad=0.5, h_pad=1.0)
plt.savefig("traces.png", dpi=90)
plt.show()
def run():
# Load the config file, which is assumed to live in
# the same directory as this script.
local_dir = os.path.dirname(__file__)
config = Config(os.path.join(local_dir, 'xor2_config'))
# For this network, we use two output neurons and use the difference between
# the "time to first spike" to determine the network response. There are
# probably a great many different choices one could make for an output encoding,
# and this choice may not be the best for tackling a real problem.
config.output_nodes = 2
pop = population.Population(config)
pop.run(eval_fitness, 200)
print('Number of evaluations: {0}'.format(pop.total_evaluations))
# Display the winning genome.
winner = pop.statistics.best_genome()
print('\nBest genome:\n{!s}'.format(winner))
# Show output of the most fit genome against training data.
winner = pop.statistics.best_genome()
print('\nBest genome:\n{!s}'.format(winner))
print('\nBest network output:')
# Create a network of "fast spiking" Izhikevich neurons, simulation time step 0.25 millisecond.
net = iznn.create_phenotype(winner, **neuron_params)
for inputData, outputData in zip(xor_inputs, xor_outputs):
neuron_data = {}
for i, n in net.neurons.items():
neuron_data[i] = []
# Reset the network, apply the XOR inputs, and run for the maximum allowed time.
net.reset()
net.set_inputs(inputData)
t0 = None
t1 = None
num_steps = int(max_time / dt)
for j in range(num_steps):
t = dt * j
output = net.advance(dt)
# Capture the time and neuron membrane potential for later use if desired.
for i, n in net.neurons.items():
neuron_data[i].append((t, n.v))
# Remember time and value of the first output spikes from each neuron.
if t0 is None and output[0] > 0:
t0, v0 = neuron_data[net.outputs[0]][-2]
if t1 is None and output[1] > 0:
t1, v1 = neuron_data[net.outputs[1]][-2]
response = compute_output(t0, t1)
print(inputData, response)
def run():
# Load the config file, which is assumed to live in
# the same directory as this script.
local_dir = os.path.dirname(__file__)
config = Config(os.path.join(local_dir, 'xor2_config'))
# For this network, we use two output neurons and use the difference between
# the "time to first spike" to determine the network response. There are
# probably a great many different choices one could make for an output encoding,
# and this choice may not be the best for tackling a real problem.
config.output_nodes = 2
pop = population.Population(config)
pop.epoch(eval_fitness, 200)
winner = pop.most_fit_genomes[-1]
print('Number of evaluations: %d' % winner.ID)
# Visualize the winner network and plot statistics.
visualize.plot_stats(pop.most_fit_genomes, pop.avg_fitness_scores)
visualize.plot_species(pop.species_log)
visualize.draw_net(winner, view=True)
# Verify network output against training data.
print('\nBest network output:')
net = iznn.create_phenotype(winner, *iz_params)
error, simulated = simulate(winner)
# Create a plot of the traces out to the max time for each set of inputs.
plt.figure(figsize=(12,12))
for r, (inputData, outputData, t0, t1, neuron_data) in enumerate(simulated):
response = compute_output(t0, t1)
print("%r expected %.3f got %.3f" % (inputData, outputData, response))
plt.subplot(4, 1, r + 1)
plt.title("Traces for XOR input {%.1f, %.1f}" % inputData, fontsize=12)
for i, s in neuron_data.items():
if i not in net.inputs:
t, v = zip(*s)
plt.plot(t, v, "-", label="neuron %d" % i)
plt.ylabel("Potential (mv)", fontsize=10)
plt.ylim(-100, 50)
plt.tick_params(axis='both', labelsize=8)
plt.grid()
plt.xlabel("Time (in ms)", fontsize=10)
plt.tight_layout(pad=0.4, w_pad=0.5, h_pad=1.0)
plt.savefig("traces.png", dpi=90)
plt.show()
def run():
# Load the config file, which is assumed to live in
# the same directory as this script.
local_dir = os.path.dirname(__file__)
config = Config(os.path.join(local_dir, 'xor2_config'))
# For this network, we use two output neurons and use the difference between
# the "time to first spike" to determine the network response. There are
# probably a great many different choices one could make for an output encoding,
# and this choice may not be the best for tackling a real problem.
config.output_nodes = 2
pop = population.Population(config)
pop.run(eval_fitness, 200)
print('Number of evaluations: {0}'.format(pop.total_evaluations))
# Visualize the winner network and plot statistics.
winner = pop.statistics.best_genome()
node_names = {0: 'A', 1: 'B', 2: 'Out1', 3: 'Out2'}
visualize.draw_net(winner, view=True, node_names=node_names)
visualize.plot_stats(pop.statistics)
visualize.plot_species(pop.statistics)
# Verify network output against training data.
print('\nBest network output:')
net = iznn.create_phenotype(winner, *iz_params)
sum_square_error, simulated = simulate(winner)
# Create a plot of the traces out to the max time for each set of inputs.
plt.figure(figsize=(12, 12))
for r, (inputData, outputData, t0, t1, v0, v1,
neuron_data) in enumerate(simulated):
response = compute_output(t0, t1)
print("{0!r} expected {1:.3f} got {2:.3f}".format(
inputData, outputData, response))
axes = plt.subplot(4, 1, r + 1)
plt.title(
"Traces for XOR input {{{0:.1f}, {1:.1f}}}".format(*inputData),
fontsize=12)
for i, s in neuron_data.items():
if i in net.outputs:
t, v = zip(*s)
plt.plot(t, v, "-", label="neuron {0:d}".format(i))
# Circle the first peak of each output.
circle0 = patches.Ellipse((t0, v0), 1.0, 10.0, color='r', fill=False)
circle1 = patches.Ellipse((t1, v1), 1.0, 10.0, color='r', fill=False)
axes.add_artist(circle0)
axes.add_artist(circle1)
plt.ylabel("Potential (mv)", fontsize=10)
plt.ylim(-100, 50)
plt.tick_params(labelsize=8)
plt.grid()
plt.xlabel("Time (in ms)", fontsize=10)
plt.tight_layout(pad=0.4, w_pad=0.5, h_pad=1.0)
plt.savefig("traces.png", dpi=90)
plt.show()
def test_iznn_evolve():
"""This is a stripped-down copy of the XOR2 spiking example."""
# Network inputs and expected outputs.
xor_inputs = ((0, 0), (0, 1), (1, 0), (1, 1))
xor_outputs = (0, 1, 1, 0)
# Maximum amount of simulated time (in milliseconds) to wait for the network to produce an output.
max_time = 50.0
def compute_output(t0, t1):
'''Compute the network's output based on the "time to first spike" of the two output neurons.'''
if t0 is None or t1 is None:
# If one of the output neurons failed to fire within the allotted time,
# give a response which produces a large error.
return -1.0
else:
# If the output neurons fire within 1.0 milliseconds of each other,
# the output is 1, and if they fire more than 11 milliseconds apart,
# the output is 0, with linear interpolation between 1 and 11 milliseconds.
response = 1.1 - 0.1 * abs(t0 - t1)
return max(0.0, min(1.0, response))
def simulate(genome):
# Create a network of Izhikevich neurons based on the given genome.
net = iznn.create_phenotype(genome, **iznn.THALAMO_CORTICAL_PARAMS)
dt = 0.25
sum_square_error = 0.0
simulated = []
for inputData, outputData in zip(xor_inputs, xor_outputs):
neuron_data = {}
for i, n in net.neurons.items():
neuron_data[i] = []
# Reset the network, apply the XOR inputs, and run for the maximum allowed time.
net.reset()
net.set_inputs(inputData)
t0 = None
t1 = None
v0 = None
v1 = None
num_steps = int(max_time / dt)
for j in range(num_steps):
t = dt * j
output = net.advance(dt)
# Capture the time and neuron membrane potential for later use if desired.
for i, n in net.neurons.items():
neuron_data[i].append((t, n.v))
# Remember time and value of the first output spikes from each neuron.
if t0 is None and output[0] > 0:
t0, v0 = neuron_data[net.outputs[0]][-2]
if t1 is None and output[1] > 0:
t1, v1 = neuron_data[net.outputs[1]][-2]
response = compute_output(t0, t1)
sum_square_error += (response - outputData) ** 2
simulated.append(
(inputData, outputData, t0, t1, v0, v1, neuron_data))
return sum_square_error, simulated
def eval_fitness(genomes):
for genome in genomes:
sum_square_error, simulated = simulate(genome)
genome.fitness = 1 - sum_square_error
# Load the config file, which is assumed to live in
# the same directory as this script.
local_dir = os.path.dirname(__file__)
config = Config(os.path.join(local_dir, 'test_configuration'))
# TODO: This is a little hackish, but will a user ever want to do it?
# If so, provide a convenience method on Config for it.
for i, tc in enumerate(config.type_config['DefaultStagnation']):
if tc[0] == 'species_fitness_func':
config.type_config['DefaultStagnation'][i] = (tc[0], 'median')
# For this network, we use two output neurons and use the difference between
# the "time to first spike" to determine the network response. There are
# probably a great many different choices one could make for an output encoding,
# and this choice may not be the best for tackling a real problem.
config.output_nodes = 2
pop = population.Population(config)
pop.run(eval_fitness, 10)
print('Number of evaluations: {0}'.format(pop.total_evaluations))
# Visualize the winner network and plot statistics.
winner = pop.statistics.best_genome()
# Verify network output against training data.
print('\nBest network output:')
net = iznn.create_phenotype(winner, **iznn.RESONATOR_PARAMS)
sum_square_error, simulated = simulate(winner)
repr(winner)
str(winner)
for g in winner.node_genes:
repr(g)
str(g)
for g in winner.conn_genes:
repr(g)
str(g)
def test_iznn_evolve():
"""This is a stripped-down copy of the XOR2 spiking example."""
# Network inputs and expected outputs.
xor_inputs = ((0, 0), (0, 1), (1, 0), (1, 1))
xor_outputs = (0, 1, 1, 0)
# Maximum amount of simulated time (in milliseconds) to wait for the network to produce an output.
max_time = 50.0
def compute_output(t0, t1):
'''Compute the network's output based on the "time to first spike" of the two output neurons.'''
if t0 is None or t1 is None:
# If one of the output neurons failed to fire within the allotted time,
# give a response which produces a large error.
return -1.0
else:
# If the output neurons fire within 1.0 milliseconds of each other,
# the output is 1, and if they fire more than 11 milliseconds apart,
# the output is 0, with linear interpolation between 1 and 11 milliseconds.
response = 1.1 - 0.1 * abs(t0 - t1)
return max(0.0, min(1.0, response))
def simulate(genome):
# Create a network of Izhikevich neurons based on the given genome.
net = iznn.create_phenotype(genome, **iznn.THALAMO_CORTICAL_PARAMS)
dt = 0.25
sum_square_error = 0.0
simulated = []
for inputData, outputData in zip(xor_inputs, xor_outputs):
neuron_data = {}
for i, n in net.neurons.items():
neuron_data[i] = []
# Reset the network, apply the XOR inputs, and run for the maximum allowed time.
net.reset()
net.set_inputs(inputData)
t0 = None
t1 = None
v0 = None
v1 = None
num_steps = int(max_time / dt)
for j in range(num_steps):
t = dt * j
output = net.advance(dt)
# Capture the time and neuron membrane potential for later use if desired.
for i, n in net.neurons.items():
neuron_data[i].append((t, n.v))
# Remember time and value of the first output spikes from each neuron.
if t0 is None and output[0] > 0:
t0, v0 = neuron_data[net.outputs[0]][-2]
if t1 is None and output[1] > 0:
t1, v1 = neuron_data[net.outputs[1]][-2]
response = compute_output(t0, t1)
sum_square_error += (response - outputData)**2
simulated.append(
(inputData, outputData, t0, t1, v0, v1, neuron_data))
return sum_square_error, simulated
def eval_fitness(genomes):
for genome in genomes:
sum_square_error, simulated = simulate(genome)
genome.fitness = 1 - sum_square_error
# Load the config file, which is assumed to live in
# the same directory as this script.
local_dir = os.path.dirname(__file__)
config = Config(os.path.join(local_dir, 'test_configuration'))
# TODO: This is a little hackish, but will a user ever want to do it?
# If so, provide a convenience method on Config for it.
for i, tc in enumerate(config.type_config['DefaultStagnation']):
if tc[0] == 'species_fitness_func':
config.type_config['DefaultStagnation'][i] = (tc[0], 'median')
# For this network, we use two output neurons and use the difference between
# the "time to first spike" to determine the network response. There are
# probably a great many different choices one could make for an output encoding,
# and this choice may not be the best for tackling a real problem.
config.output_nodes = 2
pop = population.Population(config)
pop.run(eval_fitness, 10)
print('Number of evaluations: {0}'.format(pop.total_evaluations))
# Visualize the winner network and plot statistics.
winner = pop.statistics.best_genome()
# Verify network output against training data.
print('\nBest network output:')
net = iznn.create_phenotype(winner, **iznn.RESONATOR_PARAMS)
sum_square_error, simulated = simulate(winner)
repr(winner)
str(winner)
for g in winner.node_genes:
repr(g)
str(g)
for g in winner.conn_genes:
repr(g)
str(g)