def __init__(self, model):
"""
Initialize the population of GLMs connected by a network.
"""
self.model = model
self.N = model['N']
# Initialize a list of data sequences
self.data_sequences = []
# Initialize latent variables of the population
self.latent = LatentVariables(model)
# Create a network model to connect the GLMs
self.network = Network(model, self.latent)
# Create a single GLM that is shared across neurons
# This is to simplify the model and reuse parameters.
# Basically it speeds up the gradient calculations since we
# can manually leverage conditional independencies among GLMs
self.glm = Glm(model, self.network, self.latent)
def __init__(self, model):
"""
Initialize the population of GLMs connected by a network.
"""
self.model = model
self.N = model['N']
# TODO: Go through every key in the model and initialize the
# top level components.
# Create a network model to connect the GLMs
self.network = Network(model)
# Create a single GLM that is shared across neurons
# This is to simplify the model and reuse parameters.
# Basically it speeds up the gradient calculations since we
# can manually leverage conditional independencies among GLMs
self.glm = Glm(model, self.network)
def __init__(self, model):
"""
Initialize the population of GLMs connected by a network.
"""
self.model = model
self.N = model['N']
# Initialize a list of data sequences
self.data_sequences = []
# Initialize latent variables of the population
self.latent = LatentVariables(model)
# Create a network model to connect the GLMs
self.network = Network(model, self.latent)
# Create a single GLM that is shared across neurons
# This is to simplify the model and reuse parameters.
# Basically it speeds up the gradient calculations since we
# can manually leverage conditional independencies among GLMs
self.glm = Glm(model, self.network, self.latent)
class Population:
"""
Population connected GLMs.
"""
def __init__(self, model):
"""
Initialize the population of GLMs connected by a network.
"""
self.model = model
self.N = model['N']
# Initialize a list of data sequences
self.data_sequences = []
# Initialize latent variables of the population
self.latent = LatentVariables(model)
# Create a network model to connect the GLMs
self.network = Network(model, self.latent)
# Create a single GLM that is shared across neurons
# This is to simplify the model and reuse parameters.
# Basically it speeds up the gradient calculations since we
# can manually leverage conditional independencies among GLMs
self.glm = Glm(model, self.network, self.latent)
def compute_log_p(self, vars):
""" Compute the log joint probability under a given set of variables
"""
lp = 0.0
lp += self.compute_log_prior(vars)
# Add the likelihood of each data sequence
for data in self.data_sequences:
self.set_data(data)
lp += self.compute_ll(vars)
return lp
def compute_log_prior(self, vars):
""" Compute the log joint probability under a given set of variables
"""
lp = 0.0
# Get set of symbolic variables
syms = self.get_variables()
lp += seval(self.latent.log_p,
syms['latent'],
vars['latent'])
lp += seval(self.network.log_p,
syms['net'],
vars['net'])
for n in range(self.N):
nvars = self.extract_vars(vars, n)
lp += seval(self.glm.log_prior,
syms,
nvars)
return lp
def compute_ll(self, vars):
""" Compute the log likelihood under a given set of variables
"""
ll = 0.0
# Get set of symbolic variables
syms = self.get_variables()
# Add the likelihood from each GLM
for n in range(self.N):
nvars = self.extract_vars(vars, n)
ll += seval(self.glm.ll,
syms,
nvars)
return ll
def eval_state(self, vars):
""" Evaluate the population state expressions given the parameters,
e.g. the stimulus response curves from the basis function weights.
"""
# Get set of symbolic variables
syms = self.get_variables()
# Get the symbolic state expression to evaluate
state_vars = self.get_state()
state = {}
state['latent'] = self._eval_state_helper(syms['latent'],
state_vars['latent'],
vars['latent'])
state['net'] = self._eval_state_helper(syms['net'],
state_vars['net'],
vars['net'])
glm_states = []
for n in np.arange(self.N):
nvars = self.extract_vars(vars, n)
glm_states.append(self._eval_state_helper(syms,
state_vars['glm'],
nvars))
state['glms'] = glm_states
# Finally, evaluate the log probability and the log likelihood
# state['logp'] = self.compute_log_p(vars)
state['logprior'] = self.compute_log_prior(vars)
state['ll'] = self.compute_ll(vars)
state['logp'] = state['ll'] + state['logprior']
return state
def _eval_state_helper(self, syms, d, vars):
""" Helper function to recursively evaluate state variables
"""
state = {}
for (k,v) in d.items():
if isinstance(v,dict):
state[k] = self._eval_state_helper(syms, v, vars)
else:
state[k] = seval(v, syms, vars)
return state
def get_variables(self):
""" Get a list of all variables
"""
v = {}
v['latent'] = self.latent.get_variables()
v['net'] = self.network.get_variables()
v['glm'] = self.glm.get_variables()
return v
def set_hyperparameters(self, model):
""" Set the hyperparameters of the model
"""
self.latent.set_hyperparameters(model)
self.network.set_hyperparameters(model)
self.glm.set_hyperparameters(model)
def sample(self):
"""
Sample parameters of the GLM from the prior
"""
v = {}
v['latent'] = self.latent.sample(v)
v['net'] = self.network.sample(v)
v['glms'] =[]
for n in range(self.N):
xn = self.glm.sample(v)
xn['n'] = n
v['glms'].append(xn)
return v
def extract_vars(self, vals, n):
""" Hacky helper function to extract the variables for only the
n-th GLM.s
"""
newvals = {}
for (k,v) in vals.items():
if k=='glms':
newvals['glm'] = v[n]
else:
newvals[k] = v
return newvals
def get_state(self):
""" Get the 'state' of the system in symbolic Theano variables
"""
state = {}
state['latent'] = self.latent.get_state()
state['net'] = self.network.get_state()
state['glm'] = self.glm.get_state()
return state
def preprocess_data(self, data):
"""
Preprocess the data to compute filtered stimuli, spike trains, etc.
"""
assert isinstance(data, dict), 'Data must be a dictionary'
self.latent.preprocess_data(data)
self.network.preprocess_data(data)
self.glm.preprocess_data(data)
data['preprocessed'] = True
return data
def add_data(self, data, set_as_current_data=True):
"""
Add another data sequence to the population. Recursively call components
to prepare the new data sequence. E.g. the background model may preprocess
the stimulus with a set of basis filters.
"""
# TODO: Figure out how to handle time varying weights with multiple
# data sequences. Maybe we only allow one sequence.
assert isinstance(data, dict), 'Data must be a dictionary'
# Check for spike times in the data array
assert 'S' in data, 'Data must contain an array of spike times'
assert isinstance(data['S'], np.ndarray), 'Spike times must be a numpy array'
if 'preprocessed' not in data or not data['preprocessed']:
data = self.preprocess_data(data)
# Add the data to the list
self.data_sequences.append(data)
# By default, we set this as the current dataset
if set_as_current_data:
self.set_data(data)
def set_data(self, data):
"""
Condition on the data
"""
assert 'preprocessed' in data and data['preprocessed'] == True, \
'Data must be preprocessed before it can be set'
self.latent.set_data(data)
self.network.set_data(data)
self.glm.set_data(data)
def simulate(self, vars, (T_start,T_stop), dt, stim, dt_stim):
""" Simulate spikes from a network of coupled GLMs
:param vars - the variables corresponding to each GLM
:type vars list of N variable vectors
:param dt - time steps to simulate
:rtype TxN matrix of spike counts in each bin
"""
# Initialize the background rates
N = self.model['N']
t = np.arange(T_start, T_stop, dt)
t_ind = np.arange(int(T_start/dt), int(T_stop/dt))
assert len(t) == len(t_ind)
nT = len(t)
# Get set of symbolic variables
syms = self.get_variables()
# Initialize the background rate
X = np.zeros((nT,N))
for n in np.arange(N):
nvars = self.extract_vars(vars, n)
X[:,n] = seval(self.glm.bias_model.I_bias,
syms,
nvars)
# Add stimulus induced currents if given
temp_data = {'S' : np.zeros((nT, N)),
'stim' : stim,
'dt_stim': dt_stim}
self.add_data(temp_data)
for n in np.arange(N):
nvars = self.extract_vars(vars, n)
X[:,n] += seval(self.glm.bkgd_model.I_stim,
syms,
nvars)
print "Max background rate: %s" % str(self.glm.nlin_model.f_nlin(np.amax(X)))
# Remove the temp data from the population data sequences
self.data_sequences.pop()
# Get the impulse response functions
imps = []
for n_post in np.arange(N):
nvars = self.extract_vars(vars, n_post)
imps.append(seval(self.glm.imp_model.impulse,
syms,
nvars))
imps = np.transpose(np.array(imps), axes=[1,0,2])
T_imp = imps.shape[2]
# Debug: compute effective weights
# tt_imp = dt*np.arange(T_imp)
# Weff = np.trapz(imps, tt_imp, axis=2)
# print "Effective impulse weights: "
# print Weff
# Iterate over each time step and generate spikes
S = np.zeros((nT,N))
acc = np.zeros(N)
thr = -np.log(np.random.rand(N))
# TODO: Handle time-varying weights appropriately
time_varying_weights = False
if not time_varying_weights:
At = np.tile(np.reshape(seval(self.network.graph.A,
syms['net'],
vars['net']),
[N,N,1]),
[1,1,T_imp])
Wt = np.tile(np.reshape(seval(self.network.weights.W,
syms['net'],
vars['net']),
[N,N,1]),
[1,1,T_imp])
# Count the number of exceptions arising from more spikes per bin than allowable
n_exceptions = 0
for t in np.arange(nT):
# Update accumulator
if np.mod(t,10000)==0:
print "Iteration %d" % t
# TODO Handle nonlinearities with variables
lam = self.glm.nlin_model.f_nlin(X[t,:])
acc = acc + lam*dt
# Spike if accumulator exceeds threshold
i_spk = acc > thr
S[t,i_spk] += 1
n_spk = np.sum(i_spk)
# Compute the length of the impulse response
t_imp = np.minimum(nT-t-1,T_imp)
# Get the instantaneous connectivity
if time_varying_weights:
# TODO: Really get the time-varying weights
At = np.tile(np.reshape(seval(self.network.graph.A,
syms['net'],
vars['net']),
[N,N,1]),
[1,1,t_imp])
Wt = np.tile(np.reshape(seval(self.network.weights.W,
syms['net'],
vars['net']),
[N,N,1]),
[1,1,t_imp])
# Iterate until no more spikes
# Cap the number of spikes in a time bin
max_spks_per_bin = 10
while n_spk > 0:
if np.any(S[t,:] >= max_spks_per_bin):
n_exceptions += 1
break
# Add weighted impulse response to activation of other neurons)
X[t+1:t+t_imp+1,:] += np.sum(At[i_spk,:,:t_imp] *
Wt[i_spk,:,:t_imp] *
imps[i_spk,:,:t_imp],0).T
# Subtract threshold from the accumulator
acc -= thr*i_spk
acc[acc<0] = 0
# Set new threshold after spike
thr[i_spk] = -np.log(np.random.rand(n_spk))
i_spk = acc > thr
S[t,i_spk] += 1
n_spk = np.sum(i_spk)
#if np.any(S[t,:]>10):
# import pdb
# pdb.set_trace()
# raise Exception("More than 10 spikes in a bin! Decrease variance on impulse weights or decrease simulation bin width.")
# DEBUG:
tt = dt * np.arange(nT)
lam = np.zeros_like(X)
for n in np.arange(N):
lam[:,n] = self.glm.nlin_model.f_nlin(X[:,n])
print "Max firing rate (post sim): %f" % np.max(lam)
E_nS = np.trapz(lam,tt,axis=0)
nS = np.sum(S,0)
print "Sampled %s spikes." % str(nS)
print "Expected %s spikes." % str(E_nS)
if np.any(np.abs(nS-E_nS) > 3*np.sqrt(E_nS)):
print "ERROR: Actual num spikes (%s) differs from expected (%s) by >3 std." % (str(nS),str(E_nS))
print "Number of exceptions arising from multiple spikes per bin: %d" % n_exceptions
return S,X
class Population:
"""
Population connected GLMs.
"""
def __init__(self, model):
"""
Initialize the population of GLMs connected by a network.
"""
self.model = model
self.N = model['N']
# Initialize a list of data sequences
self.data_sequences = []
# Initialize latent variables of the population
self.latent = LatentVariables(model)
# Create a network model to connect the GLMs
self.network = Network(model, self.latent)
# Create a single GLM that is shared across neurons
# This is to simplify the model and reuse parameters.
# Basically it speeds up the gradient calculations since we
# can manually leverage conditional independencies among GLMs
self.glm = Glm(model, self.network, self.latent)
def compute_log_p(self, vars):
""" Compute the log joint probability under a given set of variables
"""
lp = 0.0
lp += self.compute_log_prior(vars)
# Add the likelihood of each data sequence
for data in self.data_sequences:
self.set_data(data)
lp += self.compute_ll(vars)
return lp
def compute_log_prior(self, vars):
""" Compute the log joint probability under a given set of variables
"""
lp = 0.0
# Get set of symbolic variables
syms = self.get_variables()
lp += seval(self.latent.log_p, syms['latent'], vars['latent'])
lp += seval(self.network.log_p, syms['net'], vars['net'])
for n in range(self.N):
nvars = self.extract_vars(vars, n)
lp += seval(self.glm.log_prior, syms, nvars)
return lp
def compute_ll(self, vars):
""" Compute the log likelihood under a given set of variables
"""
ll = 0.0
# Get set of symbolic variables
syms = self.get_variables()
# Add the likelihood from each GLM
for n in range(self.N):
nvars = self.extract_vars(vars, n)
ll += seval(self.glm.ll, syms, nvars)
return ll
def eval_state(self, vars):
""" Evaluate the population state expressions given the parameters,
e.g. the stimulus response curves from the basis function weights.
"""
# Get set of symbolic variables
syms = self.get_variables()
# Get the symbolic state expression to evaluate
state_vars = self.get_state()
state = {}
state['latent'] = self._eval_state_helper(syms['latent'],
state_vars['latent'],
vars['latent'])
state['net'] = self._eval_state_helper(syms['net'], state_vars['net'],
vars['net'])
glm_states = []
for n in np.arange(self.N):
nvars = self.extract_vars(vars, n)
glm_states.append(
self._eval_state_helper(syms, state_vars['glm'], nvars))
state['glms'] = glm_states
# Finally, evaluate the log probability and the log likelihood
# state['logp'] = self.compute_log_p(vars)
state['logprior'] = self.compute_log_prior(vars)
state['ll'] = self.compute_ll(vars)
state['logp'] = state['ll'] + state['logprior']
return state
def _eval_state_helper(self, syms, d, vars):
""" Helper function to recursively evaluate state variables
"""
state = {}
for (k, v) in d.items():
if isinstance(v, dict):
state[k] = self._eval_state_helper(syms, v, vars)
else:
state[k] = seval(v, syms, vars)
return state
def get_variables(self):
""" Get a list of all variables
"""
v = {}
v['latent'] = self.latent.get_variables()
v['net'] = self.network.get_variables()
v['glm'] = self.glm.get_variables()
return v
def set_hyperparameters(self, model):
""" Set the hyperparameters of the model
"""
self.latent.set_hyperparameters(model)
self.network.set_hyperparameters(model)
self.glm.set_hyperparameters(model)
def sample(self):
"""
Sample parameters of the GLM from the prior
"""
v = {}
v['latent'] = self.latent.sample(v)
v['net'] = self.network.sample(v)
v['glms'] = []
for n in range(self.N):
xn = self.glm.sample(v)
xn['n'] = n
v['glms'].append(xn)
return v
def extract_vars(self, vals, n):
""" Hacky helper function to extract the variables for only the
n-th GLM.s
"""
newvals = {}
for (k, v) in vals.items():
if k == 'glms':
newvals['glm'] = v[n]
else:
newvals[k] = v
return newvals
def get_state(self):
""" Get the 'state' of the system in symbolic Theano variables
"""
state = {}
state['latent'] = self.latent.get_state()
state['net'] = self.network.get_state()
state['glm'] = self.glm.get_state()
return state
def preprocess_data(self, data):
"""
Preprocess the data to compute filtered stimuli, spike trains, etc.
"""
assert isinstance(data, dict), 'Data must be a dictionary'
self.latent.preprocess_data(data)
self.network.preprocess_data(data)
self.glm.preprocess_data(data)
data['preprocessed'] = True
return data
def add_data(self, data, set_as_current_data=True):
"""
Add another data sequence to the population. Recursively call components
to prepare the new data sequence. E.g. the background model may preprocess
the stimulus with a set of basis filters.
"""
# TODO: Figure out how to handle time varying weights with multiple
# data sequences. Maybe we only allow one sequence.
assert isinstance(data, dict), 'Data must be a dictionary'
# Check for spike times in the data array
assert 'S' in data, 'Data must contain an array of spike times'
assert isinstance(data['S'],
np.ndarray), 'Spike times must be a numpy array'
if 'preprocessed' not in data or not data['preprocessed']:
data = self.preprocess_data(data)
# Add the data to the list
self.data_sequences.append(data)
# By default, we set this as the current dataset
if set_as_current_data:
self.set_data(data)
def set_data(self, data):
"""
Condition on the data
"""
assert 'preprocessed' in data and data['preprocessed'] == True, \
'Data must be preprocessed before it can be set'
self.latent.set_data(data)
self.network.set_data(data)
self.glm.set_data(data)
def simulate(self, vars, (T_start, T_stop), dt, stim, dt_stim):
""" Simulate spikes from a network of coupled GLMs
:param vars - the variables corresponding to each GLM
:type vars list of N variable vectors
:param dt - time steps to simulate
:rtype TxN matrix of spike counts in each bin
"""
# Initialize the background rates
N = self.model['N']
t = np.arange(T_start, T_stop, dt)
t_ind = np.arange(int(T_start / dt), int(T_stop / dt))
assert len(t) == len(t_ind)
nT = len(t)
# Get set of symbolic variables
syms = self.get_variables()
# Initialize the background rate
X = np.zeros((nT, N))
for n in np.arange(N):
nvars = self.extract_vars(vars, n)
X[:, n] = seval(self.glm.bias_model.I_bias, syms, nvars)
# Add stimulus induced currents if given
temp_data = {'S': np.zeros((nT, N)), 'stim': stim, 'dt_stim': dt_stim}
self.add_data(temp_data)
for n in np.arange(N):
nvars = self.extract_vars(vars, n)
X[:, n] += seval(self.glm.bkgd_model.I_stim, syms, nvars)
print "Max background rate: %s" % str(
self.glm.nlin_model.f_nlin(np.amax(X)))
# Remove the temp data from the population data sequences
self.data_sequences.pop()
# Get the impulse response functions
imps = []
for n_post in np.arange(N):
nvars = self.extract_vars(vars, n_post)
imps.append(seval(self.glm.imp_model.impulse, syms, nvars))
imps = np.transpose(np.array(imps), axes=[1, 0, 2])
T_imp = imps.shape[2]
# Debug: compute effective weights
# tt_imp = dt*np.arange(T_imp)
# Weff = np.trapz(imps, tt_imp, axis=2)
# print "Effective impulse weights: "
# print Weff
# Iterate over each time step and generate spikes
S = np.zeros((nT, N))
acc = np.zeros(N)
thr = -np.log(np.random.rand(N))
# TODO: Handle time-varying weights appropriately
time_varying_weights = False
if not time_varying_weights:
At = np.tile(
np.reshape(
seval(self.network.graph.A, syms['net'], vars['net']),
[N, N, 1]), [1, 1, T_imp])
Wt = np.tile(
np.reshape(
seval(self.network.weights.W, syms['net'], vars['net']),
[N, N, 1]), [1, 1, T_imp])
# Count the number of exceptions arising from more spikes per bin than allowable
n_exceptions = 0
for t in np.arange(nT):
# Update accumulator
if np.mod(t, 10000) == 0:
print "Iteration %d" % t
# TODO Handle nonlinearities with variables
lam = self.glm.nlin_model.f_nlin(X[t, :])
acc = acc + lam * dt
# Spike if accumulator exceeds threshold
i_spk = acc > thr
S[t, i_spk] += 1
n_spk = np.sum(i_spk)
# Compute the length of the impulse response
t_imp = np.minimum(nT - t - 1, T_imp)
# Get the instantaneous connectivity
if time_varying_weights:
# TODO: Really get the time-varying weights
At = np.tile(
np.reshape(
seval(self.network.graph.A, syms['net'], vars['net']),
[N, N, 1]), [1, 1, t_imp])
Wt = np.tile(
np.reshape(
seval(self.network.weights.W, syms['net'],
vars['net']), [N, N, 1]), [1, 1, t_imp])
# Iterate until no more spikes
# Cap the number of spikes in a time bin
max_spks_per_bin = 10
while n_spk > 0:
if np.any(S[t, :] >= max_spks_per_bin):
n_exceptions += 1
break
# Add weighted impulse response to activation of other neurons)
X[t + 1:t + t_imp + 1, :] += np.sum(
At[i_spk, :, :t_imp] * Wt[i_spk, :, :t_imp] *
imps[i_spk, :, :t_imp], 0).T
# Subtract threshold from the accumulator
acc -= thr * i_spk
acc[acc < 0] = 0
# Set new threshold after spike
thr[i_spk] = -np.log(np.random.rand(n_spk))
i_spk = acc > thr
S[t, i_spk] += 1
n_spk = np.sum(i_spk)
#if np.any(S[t,:]>10):
# import pdb
# pdb.set_trace()
# raise Exception("More than 10 spikes in a bin! Decrease variance on impulse weights or decrease simulation bin width.")
# DEBUG:
tt = dt * np.arange(nT)
lam = np.zeros_like(X)
for n in np.arange(N):
lam[:, n] = self.glm.nlin_model.f_nlin(X[:, n])
print "Max firing rate (post sim): %f" % np.max(lam)
E_nS = np.trapz(lam, tt, axis=0)
nS = np.sum(S, 0)
print "Sampled %s spikes." % str(nS)
print "Expected %s spikes." % str(E_nS)
if np.any(np.abs(nS - E_nS) > 3 * np.sqrt(E_nS)):
print "ERROR: Actual num spikes (%s) differs from expected (%s) by >3 std." % (
str(nS), str(E_nS))
print "Number of exceptions arising from multiple spikes per bin: %d" % n_exceptions
return S, X