def __init__(self, mu, spread, flip_at_least_one=True):
if not type(mu) is numpy.ndarray:
raise TypeError("Mean vector must be a numpy array")
if not len(mu.shape) == 1:
raise ValueError("Mean vector must be a 1D numpy array")
if not len(mu) > 0:
raise ValueError("Mean vector dimension must be positive")
if mu.dtype != numpy.bool8:
raise ValueError("Mean must be a bool8 numpy array")
Distribution.__init__(self, len(mu))
if not type(spread) is float:
raise TypeError("Spread must be a float")
if not (spread > 0. and spread < 1.):
raise ValueError("Spread must be a probability")
if not type(flip_at_least_one) is bool:
raise ValueError("Flip at least one must be a boolean")
self.mu = mu
self.spread = spread
self.flip_at_least_one = flip_at_least_one
def __init__(self, mu, spread, flip_at_least_one=True):
if not type(mu) is numpy.ndarray:
raise TypeError("Mean vector must be a numpy array")
if not len(mu.shape) == 1:
raise ValueError("Mean vector must be a 1D numpy array")
if not len(mu) > 0:
raise ValueError("Mean vector dimension must be positive")
if mu.dtype != numpy.bool8:
raise ValueError("Mean must be a bool8 numpy array")
Distribution.__init__(self, len(mu))
if not type(spread) is float:
raise TypeError("Spread must be a float")
if not (spread > 0. and spread < 1.):
raise ValueError("Spread must be a probability")
if not type(flip_at_least_one) is bool:
raise ValueError("Flip at least one must be a boolean")
self.mu = mu
self.spread = spread
self.flip_at_least_one = flip_at_least_one
def __init__(self,
mu=array([0, 0]),
Sigma=eye(2),
is_cholesky=False,
ell=None):
Distribution.__init__(self, len(Sigma))
assert (len(shape(mu)) == 1)
assert (max(shape(Sigma)) == len(mu))
self.mu = mu
self.ell = ell
if is_cholesky:
self.L = Sigma
if ell == None:
assert (shape(Sigma)[0] == shape(Sigma)[1])
else:
assert (shape(Sigma)[1] == ell)
else:
assert (shape(Sigma)[0] == shape(Sigma)[1])
if ell is not None:
self.L, _, _ = MatrixTools.low_rank_approx(Sigma, ell)
self.L = self.L.T
assert (shape(self.L)[1] == ell)
else:
try:
self.L = cholesky(Sigma)
except LinAlgError:
# some really crude check for PSD (which only corrects for orunding errors
self.L = cholesky(Sigma + eye(len(Sigma)) * 1e-5)
def __init__(self, X, y, n_importance, prior, ridge=None):
Distribution.__init__(self, dimension=shape(X)[1])
self.n_importance = n_importance
self.prior = prior
self.ridge = ridge
self.X = X
self.y = y
def __init__(self, X, y, n_importance, prior, ridge=None):
Distribution.__init__(self, dimension=shape(X)[1])
self.n_importance=n_importance
self.prior=prior
self.ridge=ridge
self.X=X
self.y=y
def __init__(self, amplitude=6, frequency=6, variance=1, radius=10, dimension=2):
Distribution.__init__(self, dimension)
self.amplitude = amplitude
self.frequency = frequency
self.variance = variance
self.radius = radius
assert(dimension >= 2)
def __init__(self, prior=None, logdet_alg="shogun_exact",
solve_method="shogun", shogun_loglevel=2):
Distribution.__init__(self, dimension=2)
self.prior = prior
self.logdet_alg = logdet_alg
self.solve_method = solve_method
LogDetEstimator().io.set_loglevel(shogun_loglevel)
LogDetEstimator().io.set_location_info(1)
def __init__(self, omega, support=None):
Distribution.__init__(self, dimension=None)
assert (abs(sum(omega) - 1) < 1e-6)
if support == None:
support = range(len(omega))
else:
assert (len(omega) == len(support))
self.num_objects = len(omega)
self.omega = omega
self.cdf = np.cumsum(omega)
self.support = support
def __init__(self, omega, support=None):
Distribution.__init__(self, dimension=None)
assert(abs(sum(omega) - 1) < 1e-6)
if support == None:
support = range(len(omega))
else:
assert(len(omega) == len(support))
self.num_objects = len(omega)
self.omega = omega
self.cdf = np.cumsum(omega)
self.support = support
def __init__(self, X, y, n_importance, prior, ridge=None):
Distribution.__init__(self, dimension=shape(X)[1])
self.n_importance=n_importance
self.prior=prior
self.ridge=ridge
self.X=X
self.y=y
# compute alphabet sizes based on number of unique elements for each
# covariate in the cateogrical input data represented as reals
self.alphabet_sizes=array([len(set(X[:,i])) for i in range(X.shape[1])],
dtype=int32)
def __init__(self, X, y, n_importance, prior, ridge=None):
Distribution.__init__(self, dimension=shape(X)[1])
self.n_importance = n_importance
self.prior = prior
self.ridge = ridge
self.X = X
self.y = y
# compute alphabet sizes based on number of unique elements for each
# covariate in the cateogrical input data represented as reals
self.alphabet_sizes = array(
[len(set(X[:, i])) for i in range(X.shape[1])], dtype=int32)
def __init__(self,
prior=None,
logdet_alg="shogun_exact",
solve_method="shogun",
shogun_loglevel=2):
Distribution.__init__(self, dimension=2)
self.prior = prior
self.logdet_alg = logdet_alg
self.solve_method = solve_method
LogDetEstimator().io.set_loglevel(shogun_loglevel)
LogDetEstimator().io.set_location_info(1)
def __init__(self, ps):
if not type(ps) is numpy.ndarray:
raise TypeError("Probability vector must be a numpy array")
Distribution.__init__(self, len(ps))
if not len(ps) > 0:
raise ValueError("Probability vector must contain at least one element")
if not all(ps > 0) and all (ps < 1):
raise ValueError("Probability vector must lie in (0,1)")
self.ps = ps
def __init__(self, dimension=2, num_components=2, components=None, mixing_proportion=None):
Distribution.__init__(self, dimension)
self.num_components = num_components
if (components == None):
self.components = [Gaussian(mu=zeros(self.dimension),Sigma=eye(self.dimension)) for _ in range(self.num_components)]
else:
assert(len(components)==self.num_components)
self.components=components
if (mixing_proportion == None):
self.mixing_proportion=Discrete((1.0/num_components)*ones([num_components]))
else:
assert(num_components==mixing_proportion.num_objects)
self.mixing_proportion = mixing_proportion
def __init__(self,
full_target,
current_state,
schedule="in_turns",
index_block=None):
"""
full_target - Distribution instance on which Gibbs sampling is performed
current_state - Current point of the Gibbs sampler, represented as a
list of arbritary objects.
schedule - Schedule for variables
index_block - If schedule is "in_turns", this can specify the order.
If not specified, arange(dimension) is used
"""
if not type(current_state) is type([]):
raise TypeError("Current state must be a list")
Distribution.__init__(self, len(current_state))
if not isinstance(full_target, Distribution):
raise TypeError("Given full target is not a Distribution")
if index_block is None:
index_block = arange(self.dimension, dtype=numpy.int64)
if not type(schedule) is type(""):
raise TypeError("Schedule must be a string")
if not schedule in FullConditionals.schedules:
raise ValueError("Unknown schedule")
if not type(index_block) is numpy.ndarray:
raise TypeError("Index block must be numpy array")
if not len(index_block.shape) is 1:
raise TypeError("Index block must be 1D numpy array")
if not len(index_block) is self.dimension:
raise ValueError("Index block dimension does not match number of \
Gibbs blocks")
if not index_block.dtype == numpy.int:
raise ValueError("Index block must be integer numpy array")
self.full_target = full_target
self.current_state = current_state
self.schedule = schedule
self.index_block = index_block
# this is the current index of the Gibbs block
# initialise with last, to cause the first sample come from the first
self.current_idx = self.dimension
def __init__(self,
amplitude=6,
frequency=6,
variance=1,
radius=10,
dimension=2):
Distribution.__init__(self, dimension)
self.amplitude = amplitude
self.frequency = frequency
self.variance = variance
self.radius = radius
assert (dimension >= 2)
def __init__(self, W, biasx, biash):
GenericTests.check_type(W,'W',numpy.ndarray,2)
GenericTests.check_type(biasx,'biasx',numpy.ndarray,1)
GenericTests.check_type(biash,'biash',numpy.ndarray,1)
if not biash.shape[0]==W.shape[0]:
raise ValueError("dimensions of W and biash must agree along # of hidden units")
if not biasx.shape[0]==W.shape[1]:
raise ValueError("dimensions of W and biasx must agree along # of visible units")
Distribution.__init__(self, W.shape[1])
self.W = W
self.biasx = biasx
self.biash = biash
self.num_hidden_units = W.shape[0]
def __str__(self):
s = self.__class__.__name__ + "=["
s += "W=" + str(self.W)
s += "bias=" + str(self.bias)
s += ", " + Distribution.__str__(self)
s += "]"
return s
def __str__(self):
s = self.__class__.__name__ + "=["
s += "variance=" + str(self.variance)
s += ", radius=" + str(self.radius)
s += ", " + Distribution.__str__(self)
s += "]"
return s
def __str__(self):
s=self.__class__.__name__+ "=["
s += "components="+ str(self.components)
s += ", mixing_proportion="+ str(self.mixing_proportion)
s += ", " + Distribution.__str__(self)
s += "]"
return s
def __str__(self):
s = self.__class__.__name__ + "=["
s += "bananicity=" + str(self.bananicity)
s += ", V=" + str(self.V)
s += ", " + Distribution.__str__(self)
s += "]"
return s
def __str__(self):
s = self.__class__.__name__ + "=["
s += "mu=" + str(self.mu)
s += ", L=" + str(self.L)
s += ", " + Distribution.__str__(self)
s += "]"
return s
def __str__(self):
s = self.__class__.__name__ + "=["
s += "mu=" + str(self.mu)
s += ", L=" + str(self.L)
s += ", " + Distribution.__str__(self)
s += "]"
return s
def __str__(self):
s = self.__class__.__name__ + "=["
s += "spread=" + str(self.ps)
s += ", flip_at_least_one=" + str(self.flip_at_least_one)
s += ", " + Distribution.__str__(self)
s += "]"
return s
def __str__(self):
s = self.__class__.__name__ + "=["
s += "W=" + str(self.W)
s += "bias=" + str(self.bias)
s += ", " + Distribution.__str__(self)
s += "]"
return s
def __str__(self):
s = self.__class__.__name__ + "=["
s += "bananicity=" + str(self.bananicity)
s += ", V=" + str(self.V)
s += ", " + Distribution.__str__(self)
s += "]"
return s
def __str__(self):
s = self.__class__.__name__ + "=["
s += "spread=" + str(self.ps)
s += ", flip_at_least_one=" + str(self.flip_at_least_one)
s += ", " + Distribution.__str__(self)
s += "]"
return s
def get_plotting_bounds(self):
if self.bananicity == 0.03 and self.V == 100.0:
return [(-20, 20), (-7, 12)]
elif self.bananicity == 0.1 and self.V == 100.0:
return [(-20, 20), (-5, 30)]
else:
return Distribution.get_plotting_bounds(self)
def get_plotting_bounds(self):
if self.bananicity == 0.03 and self.V == 100.0:
return [(-20, 20), (-7, 12)]
elif self.bananicity == 0.1 and self.V == 100.0:
return [(-20, 20), (-5, 30)]
else:
return Distribution.get_plotting_bounds(self)
def __str__(self):
s = self.__class__.__name__ + "=["
s += "components=" + str(self.components)
s += ", mixing_proportion=" + str(self.mixing_proportion)
s += ", " + Distribution.__str__(self)
s += "]"
return s
def __init__(self, full_target, current_state, schedule="in_turns", index_block=None):
"""
full_target - Distribution instance on which Gibbs sampling is performed
current_state - Current point of the Gibbs sampler, represented as a
list of arbritary objects.
schedule - Schedule for variables
index_block - If schedule is "in_turns", this can specify the order.
If not specified, arange(dimension) is used
"""
if not type(current_state) is type([]):
raise TypeError("Current state must be a list")
Distribution.__init__(self, len(current_state))
if not isinstance(full_target, Distribution):
raise TypeError("Given full target is not a Distribution")
if index_block is None:
index_block = arange(self.dimension, dtype=numpy.int64)
if not type(schedule) is type(""):
raise TypeError("Schedule must be a string")
if not schedule in FullConditionals.schedules:
raise ValueError("Unknown schedule")
if not type(index_block) is numpy.ndarray:
raise TypeError("Index block must be numpy array")
if not len(index_block.shape) is 1:
raise TypeError("Index block must be 1D numpy array")
if not len(index_block) is self.dimension:
raise ValueError("Index block dimension does not match number of \
Gibbs blocks")
if not index_block.dtype == numpy.int:
raise ValueError("Index block must be integer numpy array")
self.full_target = full_target
self.current_state = current_state
self.schedule = schedule
self.index_block = index_block
# this is the current index of the Gibbs block
# initialise with last, to cause the first sample come from the first
self.current_idx = self.dimension
def __init__(self, mu, spread, N=3):
GenericTests.check_type(mu, 'mu', numpy.ndarray, 1)
GenericTests.check_type(spread, 'spread', float)
GenericTests.check_type(N, 'N', int)
if mu.dtype != numpy.bool8:
raise ValueError("Mean must be a bool8 numpy array")
Distribution.__init__(self, len(mu))
if not (spread > 0. and spread < 1.):
raise ValueError("Spread must be a probability")
self.mu = mu
self.spread = spread
self.N = N
def __str__(self):
s = self.__class__.__name__ + "=["
s += "mu=" + str(self.mu)
s += "spread=" + str(self.spread)
s += "N=" + str(self.N)
s += ", " + Distribution.__str__(self)
s += "]"
return s
def __str__(self):
s = self.__class__.__name__ + "=["
s += "num_objects=" + str(self.num_objects)
s += ", omega=" + str(self.omega)
s += ", cdf=" + str(self.cdf)
s += ", support=" + str(self.support)
s += ", " + Distribution.__str__(self)
s += "]"
return s
def __str__(self):
s = self.__class__.__name__ + "=["
s += "amplitude=" + str(self.amplitude)
s += ", frequency=" + str(self.frequency)
s += ", variance=" + str(self.variance)
s += ", radius=" + str(self.radius)
s += ", " + Distribution.__str__(self)
s += "]"
return s
def __str__(self):
s = self.__class__.__name__ + "=["
s += "amplitude=" + str(self.amplitude)
s += ", frequency=" + str(self.frequency)
s += ", variance=" + str(self.variance)
s += ", radius=" + str(self.radius)
s += ", " + Distribution.__str__(self)
s += "]"
return s
def __init__(self, W, biasx, biash):
GenericTests.check_type(W, 'W', numpy.ndarray, 2)
GenericTests.check_type(biasx, 'biasx', numpy.ndarray, 1)
GenericTests.check_type(biash, 'biash', numpy.ndarray, 1)
if not biash.shape[0] == W.shape[0]:
raise ValueError(
"dimensions of W and biash must agree along # of hidden units")
if not biasx.shape[0] == W.shape[1]:
raise ValueError(
"dimensions of W and biasx must agree along # of visible units"
)
Distribution.__init__(self, W.shape[1])
self.W = W
self.biasx = biasx
self.biash = biash
self.num_hidden_units = W.shape[0]
def __str__(self):
s = self.__class__.__name__ + "=["
s += "num_objects=" + str(self.num_objects)
s += ", omega=" + str(self.omega)
s += ", cdf=" + str(self.cdf)
s += ", support=" + str(self.support)
s += ", " + Distribution.__str__(self)
s += "]"
return s
def __str__(self):
s = self.__class__.__name__ + "=["
s += "full_target=" + str(self.full_target)
s += ", current_state=" + str(self.current_state)
s += ", schedule=" + str(self.schedule)
s += ", index_block=" + str(self.index_block)
s += ", current_idx=" + str(self.current_idx)
s += ", " + Distribution.__str__(self)
s += "]"
return s
def __str__(self):
s = self.__class__.__name__ + "=["
s += "full_target=" + str(self.full_target)
s += ", current_state=" + str(self.current_state)
s += ", schedule=" + str(self.schedule)
s += ", index_block=" + str(self.index_block)
s += ", current_idx=" + str(self.current_idx)
s += ", " + Distribution.__str__(self)
s += "]"
return s
def get_proposal_points(self, n):
"""
Returns n points which lie on a uniform grid on the "center" of the banana
"""
if self.dimension == 2:
(xmin, xmax), _ = self.get_plotting_bounds()
x1 = linspace(xmin, xmax, n)
x2 = self.bananicity * (x1 ** 2 - self.V)
return array([x1, x2]).T
else:
return Distribution.get_proposal_points(self, n)
def get_proposal_points(self, n):
"""
Returns n points which lie on a uniform grid on the "center" of the banana
"""
if self.dimension == 2:
(xmin, xmax), _ = self.get_plotting_bounds()
x1 = linspace(xmin, xmax, n)
x2 = self.bananicity * (x1**2 - self.V)
return array([x1, x2]).T
else:
return Distribution.get_proposal_points(self, n)
def __init__(self, W, bias):
GenericTests.check_type(W, 'W', numpy.ndarray, 2)
GenericTests.check_type(bias, 'bias', numpy.ndarray, 1)
if not W.shape[0] == W.shape[1]:
raise ValueError("W must be square")
if not bias.shape[0] == W.shape[0]:
raise ValueError("dimensions of W and bias must agree")
if not all(diag(W) == 0):
raise ValueError("W must have zeros along the diagonal")
if not allclose(W, W.T):
raise ValueError("W must be symmetric")
Distribution.__init__(self, W.shape[0])
self.W = W
self.bias = bias
def __init__(self, W, bias):
GenericTests.check_type(W, 'W', numpy.ndarray, 2)
GenericTests.check_type(bias, 'bias', numpy.ndarray, 1)
if not W.shape[0] == W.shape[1]:
raise ValueError("W must be square")
if not bias.shape[0] == W.shape[0]:
raise ValueError("dimensions of W and bias must agree")
if not all(diag(W) == 0):
raise ValueError("W must have zeros along the diagonal")
if not allclose(W, W.T):
raise ValueError("W must be symmetric")
Distribution.__init__(self, W.shape[0])
self.W = W
self.bias = bias
def __init__(self,
dimension=2,
num_components=2,
components=None,
mixing_proportion=None):
Distribution.__init__(self, dimension)
self.num_components = num_components
if (components == None):
self.components = [
Gaussian(mu=zeros(self.dimension), Sigma=eye(self.dimension))
for _ in range(self.num_components)
]
else:
assert (len(components) == self.num_components)
self.components = components
if (mixing_proportion == None):
self.mixing_proportion = Discrete(
(1.0 / num_components) * ones([num_components]))
else:
assert (num_components == mixing_proportion.num_objects)
self.mixing_proportion = mixing_proportion
def get_proposal_points(self, n):
"""
Returns n points which lie on a uniform grid on the "center" of the flower
"""
if self.dimension == 2:
theta = linspace(0, 2 * pi, n)
# sample radius
radius_sample = zeros(n) + self.radius + \
self.amplitude * cos(self.frequency * theta)
# sample points
X = array((cos(theta) * radius_sample, sin(theta) * radius_sample)).T
return X
else:
return Distribution.get_proposal_points(self, n)
def get_proposal_points(self, n):
"""
Returns n points which lie on a uniform grid on the "center" of the flower
"""
if self.dimension == 2:
theta = linspace(0, 2 * pi, n)
# sample radius
radius_sample = zeros(n) + self.radius + \
self.amplitude * cos(self.frequency * theta)
# sample points
X = array(
(cos(theta) * radius_sample, sin(theta) * radius_sample)).T
return X
else:
return Distribution.get_proposal_points(self, n)
def __init__(self, dimension=2, bananicity=0.03, V=100.0):
assert (dimension >= 2)
Distribution.__init__(self, dimension)
self.bananicity = bananicity
self.V = V
def __init__(self, dimension=2, bananicity=0.03, V=100.0):
assert(dimension >= 2)
Distribution.__init__(self, dimension)
self.bananicity = bananicity
self.V = V
def __init__(self, mu=array([0, 0]), Sigma=eye(2), is_cholesky=False, ell=None):
Distribution.__init__(self, len(Sigma))
assert(len(shape(mu)) == 1)
assert(max(shape(Sigma)) == len(mu))
self.mu = mu
self.ell = ell
if is_cholesky:
self.L = Sigma
if ell == None:
assert(shape(Sigma)[0] == shape(Sigma)[1])
else:
assert(shape(Sigma)[1] == ell)
else:
assert(shape(Sigma)[0] == shape(Sigma)[1])
if ell is not None:
self.L, _, _ = MatrixTools.low_rank_approx(Sigma, ell)
self.L = self.L.T
assert(shape(self.L)[1] == ell)
else:
try:
self.L = cholesky(Sigma)
except LinAlgError:
# some really crude check for PSD (which only corrects for orunding errors
self.L = cholesky(Sigma+eye(len(Sigma))*1e-5)
