def train(sepal_length, sepal_length_unit_mean_sd,
sepal_width, sepal_width_unit_mean_sd,
petal_length, petal_length_unit_mean_sd,
petal_width, petal_width_unit_mean_sd,
unique_species, species):
# SpiNNaker setup
sim.setup(timestep=1.0, min_delay=1.0, max_delay=10.0,
spinnaker_hostname="192.168.1.1")
# Calculate input rates
input_rates = []
calculate_stim_rates(sepal_length, sepal_length_unit_mean_sd, input_rates, MAX_FREQUENCY)
calculate_stim_rates(sepal_width, sepal_width_unit_mean_sd, input_rates, MAX_FREQUENCY)
calculate_stim_rates(petal_length, petal_length_unit_mean_sd, input_rates, MAX_FREQUENCY)
calculate_stim_rates(petal_width, petal_width_unit_mean_sd, input_rates, MAX_FREQUENCY)
# Calculate class rates
class_rates = []
for u, _ in enumerate(unique_species):
class_rates.append(list((species == u) * MAX_FREQUENCY))
# Build basic network with orthogonal stimulation of both populations
input_populations, class_populations = build_basic_network(input_rates, STIMULUS_TIME,
class_rates, STIMULUS_TIME,
False, 0.0, True, sim)
# Create BCPNN model with weights disabled
bcpnn_synapse = bcpnn.BCPNNSynapse(
tau_zi=BCPNN_TAU_PRIMARY,
tau_zj=BCPNN_TAU_PRIMARY,
tau_p=BCPNN_TAU_ELIGIBILITY,
f_max=MAX_FREQUENCY,
w_max=BCPNN_MAX_WEIGHT,
weights_enabled=False,
plasticity_enabled=True,
weight=0.0)
# Create all-to-all connector to connect inputs to classes
input_class_connector = sim.AllToAllConnector()
# Loop through all pairs of input populations and classes
plastic_connections = []
for (i, c) in itertools.product(input_populations, class_populations):
# Connect input to class with all-to-all plastic synapse
connection = sim.Projection(i, c, input_class_connector, bcpnn_synapse,
receptor_type="excitatory", label="%s-%s" % (i.label, c.label))
plastic_connections.append(connection)
# Run simulation
sim.run(STIMULUS_TIME * len(sepal_length))
# Read biases
# **HACK** investigate where out by 1000 comes from!
learnt_biases = [c.get_data().segments[0].filter(name="bias")[0][-1,:] * 0.001
for c in class_populations]
# Read plastic weights
learnt_weights = [p.get("weight", format="array") for p in plastic_connections]
return learnt_biases, learnt_weights
def test(learnt_weights, learnt_biases):
# SpiNNaker setup
sim.setup(timestep=1.0,
min_delay=1.0,
max_delay=10.0,
spinnaker_hostname="192.168.1.1")
# Generate testing stimuli patters
testing_stimuli_rates = [
[MAX_FREQUENCY, MIN_FREQUENCY, MAX_FREQUENCY, MIN_FREQUENCY],
[MIN_FREQUENCY, MAX_FREQUENCY, MAX_FREQUENCY, MIN_FREQUENCY],
]
# Generate uncertain class stimuli pattern
uncertain_stimuli_rates = [
[MAX_FREQUENCY * 0.5],
[MAX_FREQUENCY * 0.5],
]
# Build basic network
input_populations, class_populations = build_basic_network(
testing_stimuli_rates, TESTING_STIMULUS_TIME, uncertain_stimuli_rates,
TESTING_TIME, True, learnt_biases, False, sim)
# Create BCPNN model with weights disabled
bcpnn_synapse = bcpnn.BCPNNSynapse(tau_zi=BCPNN_TAU_PRIMARY,
tau_zj=BCPNN_TAU_PRIMARY,
tau_p=BCPNN_TAU_ELIGIBILITY,
f_max=MAX_FREQUENCY,
w_max=BCPNN_MAX_WEIGHT,
weights_enabled=True,
plasticity_enabled=False)
for ((i, c),
w) in zip(itertools.product(input_populations, class_populations),
learnt_weights):
# Convert learnt weight matrix into a connection list
connections = convert_weights_to_list(w, 1.0, 7.0)
# Create projections
sim.Projection(i,
c,
sim.FromListConnector(connections),
bcpnn_synapse,
receptor_type="excitatory",
label="%s-%s" % (i.label, c.label))
# Run simulation
sim.run(TESTING_TIME)
# Read spikes from input and class populations
input_data = [i.get_data() for i in input_populations]
class_data = [c.get_data() for c in class_populations]
# End simulation on SpiNNaker
sim.end()
# Return spikes
return input_data, class_data
def test_discrete(connection_weight_filenames, hcu_biases,
ampa_gain, nmda_gain, tau_ca2, i_alpha,
stim_minicolumns, testing_simtime, delay_model,
num_hcu, num_mcu_per_hcu, num_mcu_neurons, record_membrane, **setup_kwargs):
assert len(hcu_biases) == num_hcu, "An array of biases must be provided for each HCU"
assert len(connection_weight_filenames) == (num_hcu ** 2), "A tuple of weight matrix filenames must be provided for each HCU->HCU product"
# Scale parameters to obtain HCU size and synaptic stringth
num_excitatory, num_inhibitory, JE, JI = scale_parameters(num_mcu_per_hcu, num_mcu_neurons)
# Setup simulator and seed RNG
sim.setup(timestep=dt, min_delay=dt, max_delay=7.0 * dt, **setup_kwargs)
rng = NumpyRNG(seed=1)
# Calculate mean firing rate
e_cell_mean_firing_rate = (num_mcu_neurons / num_excitatory) * 20.0
# Build HCUs configured for testing
hcus = [HCU.testing_adaptive(name="%u" % i, sim=sim, rng=rng,
num_excitatory=num_excitatory, num_inhibitory=num_inhibitory, JE=JE, JI=JI,
bias=bias, tau_ca2=tau_ca2, i_alpha=i_alpha,
e_cell_mean_firing_rate=e_cell_mean_firing_rate,
simtime=testing_simtime, record_membrane=record_membrane,
stim_spike_times=generate_discrete_hcu_stimuli(stim_minicolumns, num_excitatory, num_mcu_per_hcu)) for i, bias in enumerate(hcu_biases)]
# **HACK** not actually plastic - just used to force signed weights
bcpnn_synapse = bcpnn.BCPNNSynapse(
tau_zi=tau_syn_ampa_gaba,
tau_zj=tau_syn_ampa_gaba,
tau_p=1000.0,
f_max=20.0,
w_max=JE,
weights_enabled=True,
plasticity_enabled=False)
# Loop through all hcu products and their corresponding connection weight
for connection_weight_filename, ((i_pre, hcu_pre), (i_post, hcu_post)) in zip(connection_weight_filenames, itertools.product(enumerate(hcus), repeat=2)):
# Use delay model to calculate delay
hcu_delay = delay_model(i_pre, i_post)
logger.info("Connecting HCU %u->%u with delay %ums" % (i_pre, i_post, hcu_delay))
# Build connections
HCUConnection.testing(
sim=sim,
pre_hcu=hcu_pre, post_hcu=hcu_post,
ampa_gain=ampa_gain, nmda_gain=nmda_gain,
ampa_synapse=bcpnn_synapse, nmda_synapse=bcpnn_synapse,
connection_weight_filename=connection_weight_filename, delay=hcu_delay)
# Run simulation
sim.run(testing_simtime)
# Read results from HCUs
results = [hcu.read_results() for hcu in hcus]
return results, sim.end
def test(sepal_length, sepal_length_unit_mean_sd,
sepal_width, sepal_width_unit_mean_sd,
petal_length, petal_length_unit_mean_sd,
petal_width, petal_width_unit_mean_sd,
num_species,
learnt_biases, learnt_weights):
# SpiNNaker setup
sim.setup(timestep=1.0, min_delay=1.0, max_delay=10.0,
spinnaker_hostname="192.168.1.1")
# Calculate input rates
input_rates = []
calculate_stim_rates(sepal_length, sepal_length_unit_mean_sd, input_rates, MAX_FREQUENCY)
calculate_stim_rates(sepal_width, sepal_width_unit_mean_sd, input_rates, MAX_FREQUENCY)
calculate_stim_rates(petal_length, petal_length_unit_mean_sd, input_rates, MAX_FREQUENCY)
calculate_stim_rates(petal_width, petal_width_unit_mean_sd, input_rates, MAX_FREQUENCY)
# Generate uncertain class pattern
uncertain_class_rates = [[MAX_FREQUENCY * (1.0 / num_species)]
for s in range(num_species)]
# Build basic network
testing_time = STIMULUS_TIME * len(sepal_length)
input_populations, class_populations = build_basic_network(input_rates, STIMULUS_TIME,
uncertain_class_rates, testing_time,
True, learnt_biases, False, sim)
# Create BCPNN model with weights disabled
bcpnn_synapse = bcpnn.BCPNNSynapse(
tau_zi=BCPNN_TAU_PRIMARY,
tau_zj=BCPNN_TAU_PRIMARY,
tau_p=BCPNN_TAU_ELIGIBILITY,
f_max=MAX_FREQUENCY,
w_max=BCPNN_MAX_WEIGHT,
weights_enabled=True,
plasticity_enabled=False)
for ((i, c), w) in zip(itertools.product(input_populations, class_populations), learnt_weights):
# Convert learnt weight matrix into a connection list
connections = convert_weights_to_list(w, 1.0, 7.0 * (30.0 / float(CLASS_POP_SIZE)))
# Create projections
sim.Projection(i, c, sim.FromListConnector(connections), bcpnn_synapse,
receptor_type="excitatory", label="%s-%s" % (i.label, c.label))
# Run simulation
sim.run(testing_time)
# Read spikes from input and class populations
input_data = [i.get_data() for i in input_populations]
class_data = [c.get_data() for c in class_populations]
# End simulation on SpiNNaker
sim.end()
# Return spikes
return input_data, class_data
def train_discrete(ampa_tau_zi, ampa_tau_zj, nmda_tau_zi, nmda_tau_zj, tau_p,
stim_minicolumns, training_simtime, delay_model,
num_hcu, num_mcu_per_hcu, num_mcu_neurons, **setup_kwargs):
# Scale parameters to obtain HCU size and synaptic stringth
num_excitatory, num_inhibitory, JE, JI = scale_parameters(num_mcu_per_hcu, num_mcu_neurons)
# Setup simulator and seed RNG
sim.setup(timestep=dt, min_delay=dt, max_delay=7.0 * dt, **setup_kwargs)
rng = NumpyRNG(seed=1)
# Calculate mean firing rate
e_cell_mean_firing_rate = 4.0#(float(num_mcu_neurons) / float(num_excitatory)) * 20.0
# Build HCUs configured for training
hcus = [HCU.training(name="%u" % h, sim=sim, rng=rng, simtime=training_simtime,
num_excitatory=num_excitatory, num_inhibitory=num_inhibitory, JE=JE, JI=JI,
intrinsic_tau_z=ampa_tau_zj, intrinsic_tau_p=tau_p,
e_cell_mean_firing_rate=e_cell_mean_firing_rate,
stim_spike_times=generate_discrete_hcu_stimuli(stim_minicolumns, num_excitatory, num_mcu_per_hcu)) for h in range(num_hcu)]
# Loop through all hcu products
connections = []
for (i_pre, hcu_pre), (i_post, hcu_post) in itertools.product(enumerate(hcus), repeat=2):
# Use delay model to calculate delay
hcu_delay = delay_model(i_pre, i_post)
# Build BCPNN models
ampa_synapse = bcpnn.BCPNNSynapse(
tau_zi=ampa_tau_zi,
tau_zj=ampa_tau_zj,
tau_p=tau_p,
f_max=20.0,
w_max=JE,
weights_enabled=False,
plasticity_enabled=True,
weight=0.0,
delay=hcu_delay)
nmda_synapse = bcpnn.BCPNNSynapse(
tau_zi=nmda_tau_zi,
tau_zj=nmda_tau_zj,
tau_p=tau_p,
f_max=20.0,
w_max=JE,
weights_enabled=False,
plasticity_enabled=True,
weight=0.0,
delay=hcu_delay)
logger.info("Connecting HCU %u->%u with delay %ums" % (i_pre, i_post, hcu_delay))
connections.append(HCUConnection.training(
sim=sim, pre_hcu=hcu_pre, post_hcu=hcu_post,
ampa_synapse=ampa_synapse, nmda_synapse=nmda_synapse, rng=rng))
# Run simulation
sim.run(training_simtime)
# Read results from HCUs
hcu_results = [hcu.read_results() for hcu in hcus]
# Read results from inter-hcu connections
connection_results = [c.read_results() for c in connections]
return hcu_results, connection_results, sim.end
def train_discrete(ampa_tau_zi, ampa_tau_zj, nmda_tau_zi, nmda_tau_zj, tau_p,
minicolumn_indices, training_stim_time, training_interval_time,
delay_model, num_hcu, num_mcu_neurons, timer, **setup_kwargs):
# Setup simulator and seed RNG
sim.setup(timestep=dt, min_delay=dt, max_delay=7.0 * dt, **setup_kwargs)
rng = sim.NativeRNG(host_rng=NumpyRNG(seed=1))
# Determine length of each epoch
epoch_duration = training_stim_time + training_interval_time
# Stimulate minicolumns in sequence
stim_minicolumns = [(m, float(i * epoch_duration), 20.0, training_stim_time)
for i, m in enumerate(minicolumn_indices)]
# Calculate length of training required
training_duration = float(len(stim_minicolumns)) * epoch_duration
# Calculate mean firing rate
e_cell_mean_firing_rate = (float(num_mcu_neurons) / float(NE)) * 20.0
# Build HCUs configured for training
hcus = [HCU.training(name="%u" % h, sim=sim, rng=rng, simtime=training_duration,
intrinsic_tau_z=ampa_tau_zj, intrinsic_tau_p=tau_p,
e_cell_mean_firing_rate=e_cell_mean_firing_rate,
stim_spike_times=generate_discrete_hcu_stimuli(stim_minicolumns, num_mcu_neurons)) for h in range(num_hcu)]
# Loop through all hcu products
connections = []
for (i_pre, hcu_pre), (i_post, hcu_post) in itertools.product(enumerate(hcus), repeat=2):
# Use delay model to calculate delay
hcu_delay = delay_model(i_pre, i_post)
# Build BCPNN models
ampa_synapse = bcpnn.BCPNNSynapse(
tau_zi=ampa_tau_zi,
tau_zj=ampa_tau_zj,
tau_p=tau_p,
f_max=20.0,
w_max=JE,
weights_enabled=False,
plasticity_enabled=True,
weight=0.0,
delay=hcu_delay)
nmda_synapse = bcpnn.BCPNNSynapse(
tau_zi=nmda_tau_zi,
tau_zj=nmda_tau_zj,
tau_p=tau_p,
f_max=20.0,
w_max=JE,
weights_enabled=False,
plasticity_enabled=True,
weight=0.0,
delay=hcu_delay)
logger.info("Connecting HCU %u->%u with delay %ums" % (i_pre, i_post, hcu_delay))
connections.append(HCUConnection.training(
sim=sim, pre_hcu=hcu_pre, post_hcu=hcu_post,
ampa_synapse=ampa_synapse, nmda_synapse=nmda_synapse, rng=rng))
logger.info("Build time %gs", timer.diff())
# Run simulation
sim.run(training_duration)
logger.info("Load and run time %gs", timer.diff())
# Read results from HCUs
hcu_results = [hcu.read_results() for hcu in hcus]
# Read results from inter-hcu connections
connection_results = [c.read_results() for c in connections]
return hcu_results, connection_results, sim.end
def train():
# SpiNNaker setup
sim.setup(timestep=1.0,
min_delay=1.0,
max_delay=10.0,
spinnaker_hostname="192.168.1.1")
# Generate orthogonal input stimuli
orthogonal_stimuli_rates = []
num_inputs = len(INPUT_NAMES)
for i in range(num_inputs):
input_stimuli = []
for s in range(TRAINING_TIME / TRAINING_STIMULUS_TIME):
input_stimuli.append(MIN_FREQUENCY if (
s % num_inputs) == i else MAX_FREQUENCY)
orthogonal_stimuli_rates.append(input_stimuli)
# Build basic network with orthogonal stimulation of both populations
input_populations, class_populations = build_basic_network(
orthogonal_stimuli_rates, TRAINING_STIMULUS_TIME,
orthogonal_stimuli_rates, TRAINING_STIMULUS_TIME, False, 0.0, True,
sim)
# Create BCPNN model with weights disabled
bcpnn_synapse = bcpnn.BCPNNSynapse(tau_zi=BCPNN_TAU_PRIMARY,
tau_zj=BCPNN_TAU_PRIMARY,
tau_p=BCPNN_TAU_ELIGIBILITY,
f_max=MAX_FREQUENCY,
w_max=BCPNN_MAX_WEIGHT,
weights_enabled=False,
plasticity_enabled=True,
weight=0.0)
# Create all-to-all conector to connect inputs to classes
input_class_connector = sim.AllToAllConnector()
# Loop through all pairs of input populations and classes
plastic_connections = []
for (i, c) in itertools.product(input_populations, class_populations):
# Connect input to class with all-to-all plastic synapse
connection = sim.Projection(i,
c,
input_class_connector,
bcpnn_synapse,
receptor_type="excitatory",
label="%s-%s" % (i.label, c.label))
plastic_connections.append(connection)
# Run simulation
sim.run(TRAINING_TIME)
# Plot bias evolution
num_classes = len(CLASS_NAMES)
#bias_figure, bias_axes = pylab.subplots()
# **HACK** Extract learnt biases from gsyn channel
learnt_biases = []
plotting_times = range(TRAINING_TIME)
for i, c in enumerate(class_populations):
# Read bias from class
bias = c.get_data().segments[0].filter(name="bias")[0]
'''
# Loop through plotting times to get mean biases
mean_pj = []
for t in plotting_times:
# Slice out the rows for all neurons at this time
time_rows = gsyn[t::TRAINING_TIME]
time_bias = zip(*time_rows)[2]
mean_pj.append(numpy.average(numpy.exp(numpy.divide(time_bias,BCPNN_PHI))))
bias_axes.plot(plotting_times, mean_pj, label=c.label)
'''
# Add final bias column to list
# **HACK** investigate where out by 1000 comes from!
learnt_biases.append(bias[-1, :] * 0.001)
'''
bias_axes.set_title("Mean final bias")
bias_axes.set_ylim((0.0, 1.0))
bias_axes.set_ylabel("Pj")
bias_axes.set_xlabel("Time/ms")
bias_axes.legend()
'''
# Plot weights
weight_figure, weight_axes = pylab.subplots(num_inputs, num_classes)
# Loop through plastic connections
learnt_weights = []
for i, c in enumerate(plastic_connections):
# Extract weights and calculate mean
weights = c.get("weight", format="array")
mean_weight = numpy.average(weights)
# Add weights to list
learnt_weights.append(weights)
# Plot mean weight in each panel
axis = weight_axes[i % num_inputs][i / num_classes]
axis.matshow([[mean_weight]], cmap=pylab.cm.gray)
#axis.set_title("%s: %fuS" % (c.label, mean_weight))
axis.set_title("%u->%u: %f" %
(i % num_inputs, i / num_classes, mean_weight))
axis.get_xaxis().set_visible(False)
axis.get_yaxis().set_visible(False)
# Show figures
pylab.show()
# End simulation on SpiNNaker
sim.end()
# Return learnt weights
return learnt_weights, learnt_biases