def __init__(self, model):
""" Initialize the filtered stim model
"""
self.model = model
N = model['N']
prms = model['network']['weight']
self.prior = create_prior(prms['prior'])
# Implement refractory period by having negative mean on self loops
if 'refractory_prior' in prms:
#self.mu[np.diag_indices(N)] = prms['mu_refractory']
self.refractory_prior = create_prior(prms['refractory_prior'])
# Get the upper and lower diagonal indices so that we can evaluate
# the log prob of the refractory weights separately from the
# log prob of the regular weights
self.diags = np.ravel_multi_index(np.diag_indices(N), (N, N))
lower = np.ravel_multi_index(np.tril_indices(N, k=-1), (N, N))
upper = np.ravel_multi_index(np.triu_indices(N, k=1), (N, N))
self.nondiags = np.concatenate((lower, upper))
# Define weight matrix
self.W_flat = T.dvector(name='W')
self.W = T.reshape(self.W_flat, (N, N))
if hasattr(self, 'refractory_prior'):
self.log_p = self.prior.log_p(self.W.take(self.nondiags)) + \
self.refractory_prior.log_p(self.W.take(self.diags))
else:
self.log_p = self.prior.log_p(self.W)
def __init__(self, model):
""" Initialize the filtered stim model
"""
self.model = model
N = model['N']
prms = model['network']['weight']
self.prior = create_prior(prms['prior'])
# Implement refractory period by having negative mean on self loops
if 'refractory_prior' in prms:
#self.mu[np.diag_indices(N)] = prms['mu_refractory']
self.refractory_prior = create_prior(prms['refractory_prior'])
# Get the upper and lower diagonal indices so that we can evaluate
# the log prob of the refractory weights separately from the
# log prob of the regular weights
self.diags = np.ravel_multi_index(np.diag_indices(N), (N,N))
lower = np.ravel_multi_index(np.tril_indices(N,k=-1), (N,N))
upper = np.ravel_multi_index(np.triu_indices(N,k=1), (N,N))
self.nondiags = np.concatenate((lower, upper))
# Define weight matrix
self.W_flat = T.dvector(name='W')
self.W = T.reshape(self.W_flat,(N,N))
if hasattr(self, 'refractory_prior'):
self.log_p = self.prior.log_p(self.W.take(self.nondiags)) + \
self.refractory_prior.log_p(self.W.take(self.diags))
else:
self.log_p = self.prior.log_p(self.W)
def __init__(self, model, loc_model):
self.model = model
self.N = model['N']
self.prms = loc_model
self.name = self.prms['name']
self.N_dims = self.prms['N_dims']
# Create a location prior
self.location_prior = create_prior(self.prms['location_prior'])
# Make sure the sample is of the correct type
from pyglm.components.priors import Categorical, JointCategorical
if isinstance(self.location_prior, (Categorical,JointCategorical)):
self.Lflat = T.lvector('L')
self.dtype = np.int
else:
self.Lflat = T.dvector('L')
self.dtype = np.float
# Latent distance model has NxN_dims matrix of locations Lm
self.Lmatrix = T.reshape(self.Lflat, (self.N, self.N_dims))
self.Lmatrix.name = 'L'
# Define log probability
self.log_p = self.location_prior.log_p(self.Lmatrix)
def __init__(self, model):
self.model = model
self.imp_model = model['impulse']
self.prior = create_prior(self.imp_model['prior'])
# Number of presynaptic neurons
self.N = model['N']
# Get parameters of the prior
# self.mu = self.prms['mu']
# self.sigma = self.prms['sigma']
# Create a basis for the impulse responses response
self.basis = create_basis(self.imp_model['basis'])
(_,self.B) = self.basis.shape
# The basis is interpolated once the data is specified
self.initialize_basis()
# Initialize memory for the filtered spike train
self.ir = theano.shared(name='ir',
value=np.zeros((1,self.N,self.B)))
# Define weights
self.w_ir = T.dvector('w_ir')
# Repeat them (in a differentiable manner) to create a 3-tensor
w_ir2 = T.reshape(self.w_ir, [self.N,self.B])
w_ir3 = T.reshape(self.w_ir, [1,self.N,self.B])
# Make w_ir3 broadcastable in the 1st dim
T.addbroadcast(w_ir3,0)
# Take the elementwise product of the filtered stimulus and
# the repeated weights to get the weighted impulse current along each
# impulse basis dimension. Then sum over bases to get the
# total coupling current from each presynaptic neurons at
# all time points
self.I_imp = T.sum(self.ir*w_ir3, axis=2)
# self.log_p = T.sum(-0.5/self.sigma**2 * (self.w_ir-self.mu)**2)
self.log_p = self.prior.log_p(w_ir2)
# Define a helper variable for the impulse response
# after projecting onto the basis
self.impulse = T.dot(w_ir2, T.transpose(self.ibasis))
def __init__(self, model):
self.model = model
self.imp_model = model['impulse']
self.prior = create_prior(self.imp_model['prior'])
# Number of presynaptic neurons
self.N = model['N']
# Get parameters of the prior
# self.mu = self.prms['mu']
# self.sigma = self.prms['sigma']
# Create a basis for the impulse responses response
self.basis = create_basis(self.imp_model['basis'])
(_, self.B) = self.basis.shape
# The basis is interpolated once the data is specified
self.initialize_basis()
# Initialize memory for the filtered spike train
self.ir = theano.shared(name='ir', value=np.zeros((1, self.N, self.B)))
# Define weights
self.w_ir = T.dvector('w_ir')
# Repeat them (in a differentiable manner) to create a 3-tensor
w_ir2 = T.reshape(self.w_ir, [self.N, self.B])
w_ir3 = T.reshape(self.w_ir, [1, self.N, self.B])
# Make w_ir3 broadcastable in the 1st dim
T.addbroadcast(w_ir3, 0)
# Take the elementwise product of the filtered stimulus and
# the repeated weights to get the weighted impulse current along each
# impulse basis dimension. Then sum over bases to get the
# total coupling current from each presynaptic neurons at
# all time points
self.I_imp = T.sum(self.ir * w_ir3, axis=2)
# self.log_p = T.sum(-0.5/self.sigma**2 * (self.w_ir-self.mu)**2)
self.log_p = self.prior.log_p(w_ir2)
# Define a helper variable for the impulse response
# after projecting onto the basis
self.impulse = T.dot(w_ir2, T.transpose(self.ibasis))
def __init__(self, model, type_model):
self.model = model
self.type_model = type_model
self.name = self.type_model['name']
# There are N neurons to assign types to
self.N = type_model['N']
# There are has R latent types
self.R = self.type_model['R']
# Each neuron has a latent type Y
self.Y = T.lvector('Y')
# A probability of each type with a symmetric Dirichlet prior
self.alpha = T.dvector('alpha')
self.alpha_prior = create_prior(self.type_model['alpha_prior'])
# self.alpha0 = self.prms['alpha0']
# Define log probability
# log_p_alpha = T.sum((self.alpha0 - 1) * T.log(self.alpha))
log_p_alpha = self.alpha_prior.log_p(self.alpha)
log_p_Y = T.sum(T.log(self.alpha[self.Y]))
self.log_p = log_p_alpha + log_p_Y