def collapsed_predict(self, Z_new, full_output=True, full_cov=False):
"""
Predict the multinomial probability vector at a grid of points, Z_new
by first integrating out the value of psi at the data, Z_test, given
omega and the kernel parameters.
"""
assert len(self.data_list) == 1, "Must have one data list in order to predict."
data = self.data_list[0]
Z = data["Z"]
assert Z_new is not None and Z_new.ndim == 2 and Z_new.shape[1] == self.D
M_new = Z_new.shape[0]
# Compute the kernel for Z_news
C = self.kernel.K(Z, Z)
Cnn = self.kernel.K(Z_new, Z_new)
Cnv = self.kernel.K(Z_new, Z)
# Predict the psis
mu_psis_new = np.zeros((self.K-1, M_new))
Sig_psis_new = np.zeros((self.K-1, M_new, M_new))
for k in xrange(self.K-1):
sys.stdout.write(".")
sys.stdout.flush()
# Throw out inputs where N[:,k] == 0
Omegak = data["omega"][:,k]
kappak = data["kappa"][:,k]
# Set the precision for invalid points to zero
Omegak[Omegak == 0] = 1e-16
# Account for the mean from the omega potentials
y = kappak/Omegak - self.mu[k]
# The y's are noisy observations at inputs Z
# with diagonal covariace Omegak^{-1}
Cvv_noisy = C + np.diag(1./Omegak)
Lvv_noisy = np.linalg.cholesky(Cvv_noisy)
# Compute the conditional mean given noisy observations
psik_pred = Cnv.dot(dpotrs(Lvv_noisy, y, lower=True)[0])
# Save these into the combined arrays
mu_psis_new[k] = psik_pred + self.mu[k]
if full_cov:
Sig_psis_new[k] = Cnn - Cnv.dot(dpotrs(Lvv_noisy, Cnv.T, lower=True)[0])
sys.stdout.write("\n")
sys.stdout.flush()
# Convert these to pis
pis_new = psi_to_pi(mu_psis_new)
if full_output:
return pis_new, mu_psis_new, Sig_psis_new
else:
return pis_new
def collapsed_predict(self, Z_new, full_output=True, full_cov=False):
"""
Predict the multinomial probability vector at a grid of points, Z_new
by first integrating out the value of psi at the data, Z_test, given
omega and the kernel parameters.
"""
assert len(self.data_list) == 1, "Must have one data list in order to predict."
data = self.data_list[0]
Z = data["Z"]
assert Z_new is not None and Z_new.ndim == 2 and Z_new.shape[1] == self.D
M_new = Z_new.shape[0]
# Compute the kernel for Z_news
C = self.kernel.K(Z, Z)
Cnn = self.kernel.K(Z_new, Z_new)
Cnv = self.kernel.K(Z_new, Z)
# Predict the psis
mu_psis_new = np.zeros((self.K-1, M_new))
Sig_psis_new = np.zeros((self.K-1, M_new, M_new))
for k in range(self.K-1):
sys.stdout.write(".")
sys.stdout.flush()
# Throw out inputs where N[:,k] == 0
Omegak = data["omega"][:,k]
kappak = data["kappa"][:,k]
# Set the precision for invalid points to zero
Omegak[Omegak == 0] = 1e-16
# Account for the mean from the omega potentials
y = kappak/Omegak - self.mu[k]
# The y's are noisy observations at inputs Z
# with diagonal covariace Omegak^{-1}
Cvv_noisy = C + np.diag(1./Omegak)
Lvv_noisy = np.linalg.cholesky(Cvv_noisy)
# Compute the conditional mean given noisy observations
psik_pred = Cnv.dot(dpotrs(Lvv_noisy, y, lower=True)[0])
# Save these into the combined arrays
mu_psis_new[k] = psik_pred + self.mu[k]
if full_cov:
Sig_psis_new[k] = Cnn - Cnv.dot(dpotrs(Lvv_noisy, Cnv.T, lower=True)[0])
sys.stdout.write("\n")
sys.stdout.flush()
# Convert these to pis
pis_new = psi_to_pi(mu_psis_new)
if full_output:
return pis_new, mu_psis_new, Sig_psis_new
else:
return pis_new
def solve_cholesky(A, B):
"""
Solve the system Mx=B where A is the lower-triangular cholesky
decomposition of the matrix M.
"""
X, _ = lapack.dpotrs(A, B, lower=1)
return X
def solve_cholesky(A, B):
"""
Solve the system Mx=B where A is the lower-triangular cholesky
decomposition of the matrix M.
"""
X, _ = lapack.dpotrs(A, B, lower=1)
return X
def __init__(self, X, Y, tuning):
self.X = X
self.Y = Y
self.tuning = tuning
self.K_uf = tuning(X).T
KK = self.K_uf.dot(self.K_uf.T)
Ky = self.K_uf.dot(Y)
self.w_mean = dpotrs(dpotrf(KK)[0],
Ky)[0] # faster than np.linalg.solve(KK, Ky)
if np.any(np.isnan(self.w_mean)):
try:
self.w_mean = np.linalg.solve(KK, Ky)
except:
jitter = np.diag(KK).mean() * 1e-6
num_tries = 1
while num_tries <= 5 and np.isfinite(jitter):
try:
self.w_mean = np.linalg.solve(
KK + np.eye(KK.shape[0]) * jitter, Ky)
except:
jitter *= 10
finally:
num_tries += 1
self.wb_var = np.transpose([
scipy.optimize.nnls(
np.vstack([self._SNRinv(X), np.ones(len(X))]).T,
(self.mean(X) - Y)[:, a]**2)[0] for a in range(Y.shape[1])
])
self.Gaussian_noise = Foo()
self.variance, self.Gaussian_noise.variance = self.wb_var
def LML_se(self,theta,returnGradients=False):
self.setTheta(theta)
K,r = self.cov(self.X,retr=True)
Ky = K.copy()
Ky += np.eye(self.X.shape[0])*self.var_n + np.eye(self.X.shape[0])*1e-8
L = self.cholSafe(Ky)
WlogDet = 2.*np.sum(np.log(np.diag(L)))
alpha, status = dpotrs(L, self.Y, lower=1)
dataFit = - np.sum(alpha * self.Y)
modelComplexity = -self.Y.shape[1] * WlogDet
normalizer = -self.Y.size * log2pi
logMarginalLikelihood = 0.5*(dataFit + modelComplexity + normalizer)
if returnGradients == False:
return logMarginalLikelihood
else:
Wi, status = dpotri(-L, lower=1)
Wi = np.asarray(Wi)
# copy bottom triangle to top triangle
triu = np.triu_indices_from(Wi,k=1)
Wi[triu] = Wi.T[triu]
# dL = change in LML, dK is change in Kernel(K)
dL_dK = 0.5 * (np.dot(alpha,alpha.T) - self.Y.shape[1] * Wi)
dL_dVarn = np.diag(dL_dK).sum()
varfGradient = np.sum(K* dL_dK)/self.var_f
dK_dr = -r*K
dL_dr = dK_dr * dL_dK
lengthscaleGradient = -np.sum(dL_dr*r)/self.charLen
grads = np.array([varfGradient, lengthscaleGradient, dL_dVarn])
return logMarginalLikelihood, grads
def pd_solve(a, b):
""" Fast matrix solve for positive definite matrix a"""
L, info = dpotrf(a)
if info == 0:
return dpotrs(L, b)[0]
else:
return np.linalg.solve(a, b)
def predict(self, Z_new, full_output=True, full_cov=False):
"""
Predict the multinomial probability vector at a grid of points, Z
:param Z_new:
:return:
"""
assert len(self.data_list
) == 1, "Must have one data list in order to predict."
data = self.data_list[0]
M = data["M"]
Z = data["Z"]
assert Z_new is not None and Z_new.ndim == 2 and Z_new.shape[
1] == self.D
M_new = Z_new.shape[0]
# Compute the kernel for Z_news
C = self.kernel.K(Z, Z)
Cvv = C + np.diag(1e-6 * np.ones(M))
Lvv = np.linalg.cholesky(Cvv)
Cnn = self.kernel.K(Z_new, Z_new)
# Compute the kernel between the new and valid points
Cnv = self.kernel.K(Z_new, Z)
# Predict the psis
mu_psis_new = np.zeros((self.K, M_new))
Sig_psis_new = np.zeros((self.K, M_new, M_new))
for k in xrange(self.K):
sys.stdout.write(".")
sys.stdout.flush()
psik = data["psi"][:, k]
# Compute the predictive parameters
y = solve_triangular(Lvv, psik, lower=True)
x = solve_triangular(Lvv.T, y, lower=False)
psik_pred = Cnv.dot(x)
# Save these into the combined arrays
mu_psis_new[k] = psik_pred + self.mu[k]
if full_cov:
# Sig_pred = Cnn - Cnv.dot(np.linalg.solve(Cvv, Cnv.T))
Sig_psis_new[k] = Cnn - Cnv.dot(
dpotrs(Lvv, Cnv.T, lower=True)[0])
sys.stdout.write("\n")
sys.stdout.flush()
# Convert these to pis
pis_new = np.array([ln_psi_to_pi(psi) for psi in mu_psis_new])
if full_output:
return pis_new, mu_psis_new, Sig_psis_new
else:
return pis_new
def dpotrs(A, B, lower=0):
"""
Wrapper for lapack dpotrs function
:param A: Matrix A
:param B: Matrix B
:param lower: is matrix lower (true) or upper (false)
:returns:
"""
return lapack.dpotrs(A, B, lower=lower)
def dpotrs(A, B, lower=0):
"""Wrapper for lapack dpotrs function
:param A: Matrix A
:param B: Matrix B
:param lower: is matrix lower (true) or upper (false)
:returns:
"""
return lapack.dpotrs(A, B, lower=lower)
def dpotrs(A, B, lower=1):
"""
Wrapper for lapack dpotrs function
:param A: Matrix A
:param B: Matrix B
:param lower: is matrix lower (true) or upper (false)
:returns:
"""
A = force_F_ordered(A)
return lapack.dpotrs(A, B, lower=lower)
def dpotrs(A, B, lower=1):
"""
Wrapper for lapack dpotrs function
:param A: Matrix A
:param B: Matrix B
:param lower: is matrix lower (true) or upper (false)
:returns:
"""
A = force_F_ordered(A)
return lapack.dpotrs(A, B, lower=lower)
def cho_solve(chol, y):
"""
Solves the systems chol * chol^T * x = y
:param cov: np.array(nxn)
:param y: np.array(n)
:return: np.array(n)
"""
chol = np.asfortranarray(chol)
return lapack.dpotrs(chol, y, lower=1)[0]
def predict(self, Z_new, full_output=True, full_cov=False):
"""
Predict the multinomial probability vector at a grid of points, Z
:param Z_new:
:return:
"""
assert len(self.data_list) == 1, "Must have one data list in order to predict."
data = self.data_list[0]
M = data["M"]
Z = data["Z"]
assert Z_new is not None and Z_new.ndim == 2 and Z_new.shape[1] == self.D
M_new = Z_new.shape[0]
# Compute the kernel for Z_news
C = self.kernel.K(Z, Z)
Cvv = C + np.diag(1e-6 * np.ones(M))
Lvv = np.linalg.cholesky(Cvv)
Cnn = self.kernel.K(Z_new, Z_new)
# Compute the kernel between the new and valid points
Cnv = self.kernel.K(Z_new, Z)
# Predict the psis
mu_psis_new = np.zeros((self.K, M_new))
Sig_psis_new = np.zeros((self.K, M_new, M_new))
for k in xrange(self.K):
sys.stdout.write(".")
sys.stdout.flush()
psik = data["psi"][:,k]
# Compute the predictive parameters
y = solve_triangular(Lvv, psik, lower=True)
x = solve_triangular(Lvv.T, y, lower=False)
psik_pred = Cnv.dot(x)
# Save these into the combined arrays
mu_psis_new[k] = psik_pred + self.mu[k]
if full_cov:
# Sig_pred = Cnn - Cnv.dot(np.linalg.solve(Cvv, Cnv.T))
Sig_psis_new[k] = Cnn - Cnv.dot(dpotrs(Lvv, Cnv.T, lower=True)[0])
sys.stdout.write("\n")
sys.stdout.flush()
# Convert these to pis
pis_new = np.array([ln_psi_to_pi(psi) for psi in mu_psis_new])
if full_output:
return pis_new, mu_psis_new, Sig_psis_new
else:
return pis_new
def _solve_cholesky(L, b, lower=True):
'''
Solves `Ax = b` given the Cholesky decomposition of `A` using `dpotrs`
'''
if any(i == 0 for i in b.shape):
return np.zeros(b.shape, dtype=float)
x, info = dpotrs(L, b, lower=lower)
if info < 0:
raise ValueError('The %s-th argument has an illegal value.' % -info)
return x
def sample_gaussian(mu=None,Sigma=None,J=None,h=None):
mean_params = mu is not None and Sigma is not None
info_params = J is not None and h is not None
assert mean_params or info_params
if not any_none(mu,Sigma):
return np.random.multivariate_normal(mu,Sigma)
else:
from scipy.linalg.lapack import dpotrs
L = np.linalg.cholesky(J)
x = np.random.randn(h.shape[0])
return scipy.linalg.solve_triangular(L,x,lower=True,trans='T') \
+ dpotrs(L,h,lower=True)[0]
def sample_gaussian(mu=None,Sigma=None,J=None,h=None):
# Copied from pybasicbayes
mean_params = mu is not None and Sigma is not None
info_params = J is not None and h is not None
assert mean_params or info_params
if mu is not None and Sigma is not None:
return np.random.multivariate_normal(mu,Sigma)
else:
L = np.linalg.cholesky(J)
x = np.random.randn(h.shape[0])
return solve_triangular(L,x,lower=True,trans='T') \
+ dpotrs(L,h,lower=True)[0]
def solve_psd(A,
b,
chol=None,
lower=True,
overwrite_b=False,
overwrite_A=False):
if chol is None:
return lapack.dposv(A,
b,
overwrite_b=overwrite_b,
overwrite_a=overwrite_A)[1]
else:
return lapack.dpotrs(chol, b, lower, overwrite_b)[0]
def sample_gaussian(mu=None, Sigma=None, J=None, h=None):
mean_params = mu is not None and Sigma is not None
info_params = J is not None and h is not None
assert mean_params or info_params
if mu is not None and Sigma is not None:
return np.random.multivariate_normal(mu, Sigma)
else:
from scipy.linalg.lapack import dpotrs
L = np.linalg.cholesky(J)
x = np.random.randn(h.shape[0])
return solve_triangular(L,x,lower=True,trans='T') \
+ dpotrs(L,h,lower=True)[0]
def _marginal_likelihood(A_col, J_prior, h_prior, J_post, h_post):
"""
Compute the marginal likelihood as the ratio of log normalizers
"""
Aeff = np.concatenate(([1], np.repeat(A_col, B))).astype(np.bool)
# Extract the entries for which A=1
J0 = J_prior[np.ix_(Aeff, Aeff)]
h0 = h_prior[Aeff]
Jp = J_post[np.ix_(Aeff, Aeff)]
hp = h_post[Aeff]
# Compute the marginal likelihood
L0 = np.linalg.cholesky(J0)
Lp = np.linalg.cholesky(Jp)
ml = 0
ml -= np.sum(np.log(np.diag(Lp)))
ml += np.sum(np.log(np.diag(L0)))
ml += 0.5 * hp.T.dot(dpotrs(Lp, hp, lower=True)[0])
ml -= 0.5 * h0.T.dot(dpotrs(L0, h0, lower=True)[0])
return ml
def _marginal_likelihood(A_col, J_prior, h_prior, J_post, h_post):
"""
Compute the marginal likelihood as the ratio of log normalizers
"""
Aeff = np.concatenate(([1], np.repeat(A_col, B))).astype(np.bool)
# Extract the entries for which A=1
J0 = J_prior[np.ix_(Aeff, Aeff)]
h0 = h_prior[Aeff]
Jp = J_post[np.ix_(Aeff, Aeff)]
hp = h_post[Aeff]
# Compute the marginal likelihood
L0 = np.linalg.cholesky(J0)
Lp = np.linalg.cholesky(Jp)
ml = 0
ml -= np.sum(np.log(np.diag(Lp)))
ml += np.sum(np.log(np.diag(L0)))
ml += 0.5*hp.T.dot(dpotrs(Lp, hp, lower=True)[0])
ml -= 0.5*h0.T.dot(dpotrs(L0, h0, lower=True)[0])
return ml
def update(self, x, y):
"""Update the model with a single input/output sample."""
assert x.shape[0] == self.n
assert y.shape[0] == self.p
pred_y = self.predict(x)
xp = self.mapping.evaluate(x)
self.B += numpy.outer(xp, y)
choluprk1(self.L, xp)
#self.L, cvec, svec = dchud(self.L, xp)
self.W, info = dpotrs(self.L, self.B)
assert info == 0
return pred_y
def _marginal_likelihood(self, J_prior, h_prior, J_post, h_post):
"""
Compute the marginal likelihood as the ratio of log normalizers
"""
a = np.concatenate((np.repeat(self.a, self.B), [1])).astype(np.bool)
# Extract the entries for which A=1
J0 = J_prior[np.ix_(a, a)]
h0 = h_prior[a]
Jp = J_post[np.ix_(a, a)]
hp = h_post[a]
# This relates to the mean/covariance parameterization as follows
# log |C| = log |J^{-1}| = -log |J|
# and
# mu^T C^{-1} mu = mu^T h
# = mu C^{-1} C h
# = h^T C h
# = h^T J^{-1} h
# ml = 0
# ml -= 0.5*np.linalg.slogdet(Jp)[1]
# ml += 0.5*np.linalg.slogdet(J0)[1]
# ml += 0.5*hp.dot(np.linalg.solve(Jp, hp))
# ml -= 0.5*h0.T.dot(np.linalg.solve(J0, h0))
# Now compute it even faster using the Cholesky!
L0 = np.linalg.cholesky(J0)
Lp = np.linalg.cholesky(Jp)
ml = 0
ml -= np.sum(np.log(np.diag(Lp)))
ml += np.sum(np.log(np.diag(L0)))
ml += 0.5 * hp.T.dot(dpotrs(Lp, hp, lower=True)[0])
ml -= 0.5 * h0.T.dot(dpotrs(L0, h0, lower=True)[0])
return ml
def _marginal_likelihood(self, J_prior, h_prior, J_post, h_post):
"""
Compute the marginal likelihood as the ratio of log normalizers
"""
a = np.concatenate((np.repeat(self.a, self.B), [1])).astype(np.bool)
# Extract the entries for which A=1
J0 = J_prior[np.ix_(a, a)]
h0 = h_prior[a]
Jp = J_post[np.ix_(a, a)]
hp = h_post[a]
# This relates to the mean/covariance parameterization as follows
# log |C| = log |J^{-1}| = -log |J|
# and
# mu^T C^{-1} mu = mu^T h
# = mu C^{-1} C h
# = h^T C h
# = h^T J^{-1} h
# ml = 0
# ml -= 0.5*np.linalg.slogdet(Jp)[1]
# ml += 0.5*np.linalg.slogdet(J0)[1]
# ml += 0.5*hp.dot(np.linalg.solve(Jp, hp))
# ml -= 0.5*h0.T.dot(np.linalg.solve(J0, h0))
# Now compute it even faster using the Cholesky!
L0 = np.linalg.cholesky(J0)
Lp = np.linalg.cholesky(Jp)
ml = 0
ml -= np.sum(np.log(np.diag(Lp)))
ml += np.sum(np.log(np.diag(L0)))
ml += 0.5*hp.T.dot(dpotrs(Lp, hp, lower=True)[0])
ml -= 0.5*h0.T.dot(dpotrs(L0, h0, lower=True)[0])
return ml
def resample_psi(self, verbose=False):
for data in self.data_list:
# import pdb; pdb.set_trace()
M = data["M"]
Z = data["Z"]
# Invert once for all k
if "C_inv" in data:
C_inv = data["C_inv"]
else:
C = self.kernel.K(Z)
C += 1e-6 * np.eye(M)
C_inv = np.linalg.inv(C)
# Compute the posterior covariance
psi = np.zeros((M, self.K - 1))
for k in xrange(self.K - 1):
if verbose:
sys.stdout.write(".")
sys.stdout.flush()
# Throw out inputs where N[:,k] == 0
Omegak = data["omega"][:, k]
kappak = data["kappa"][:, k]
# Set the precision for invalid points to zero
Omegak[Omegak == 0] = 1e-32
# Account for the mean
lkhd_mean = kappak / Omegak - self.mu[k]
# Compute the posterior parameters
L_post = np.linalg.cholesky(C_inv + np.diag(Omegak))
mu_post = dpotrs(L_post, Omegak * lkhd_mean, lower=True)[0]
# Go through each GP and resample psi given the likelihood
rand_vec = np.random.randn(M)
psi[:, k] = mu_post + solve_triangular(
L_post, rand_vec, lower=True, trans='T')
assert np.all(np.isfinite(psi[:, k]))
if verbose:
sys.stdout.write("\n")
sys.stdout.flush()
data["psi"] = psi
def _sample_gaussian(self, J, h):
"""Copied from Linderman's `PyPolyaGamma`, who copied `pybasicbayes`.
We actually want to compute
V = inv(J)
m = V @ h
s ~ Normal(m, V)
This function handles that computation more efficiently. See:
https://stats.stackexchange.com/questions/32169/
"""
L = np.linalg.cholesky(J)
x = self.rng.randn(h.shape[0])
A = solve_triangular(L, x, lower=True, trans='T')
B = dpotrs(L, h, lower=True)[0]
return A + B
def resample_psi(self, verbose=False):
for data in self.data_list:
# import pdb; pdb.set_trace()
M = data["M"]
Z = data["Z"]
# Invert once for all k
if "C_inv" in data:
C_inv = data["C_inv"]
else:
C = self.kernel.K(Z)
C += 1e-6 * np.eye(M)
C_inv = np.linalg.inv(C)
# Compute the posterior covariance
psi = np.zeros((M, self.K-1))
for k in xrange(self.K-1):
if verbose:
sys.stdout.write(".")
sys.stdout.flush()
# Throw out inputs where N[:,k] == 0
Omegak = data["omega"][:,k]
kappak = data["kappa"][:,k]
# Set the precision for invalid points to zero
Omegak[Omegak == 0] = 1e-32
# Account for the mean
lkhd_mean = kappak/Omegak - self.mu[k]
# Compute the posterior parameters
L_post = np.linalg.cholesky(C_inv + np.diag(Omegak))
mu_post = dpotrs(L_post, Omegak * lkhd_mean, lower=True)[0]
# Go through each GP and resample psi given the likelihood
rand_vec = np.random.randn(M)
psi[:,k] = mu_post + solve_triangular(L_post, rand_vec, lower=True, trans='T')
assert np.all(np.isfinite(psi[:,k]))
if verbose:
sys.stdout.write("\n")
sys.stdout.flush()
data["psi"] = psi
def solve_cholesky(L, b, lower=True):
'''
Solves the system of equations *Ax = b* given the Cholesky
decomposition of *A*. Uses the routine *dpotrs*.
Parameters
----------
L : (N,N) float array
b : (N,*) float array
'''
if any(i == 0 for i in b.shape):
return np.zeros(b.shape)
x, info = dpotrs(L, b, lower=lower)
if info < 0:
raise ValueError('The %s-th argument has an illegal value.' % (-info))
return x
def mvn_loglike(y, cov):
"""
Evaluate the multivariate-normal log-likelihood for difference vector `y`
and covariance matrix `cov`:
log_p = -1/2*[(y^T).(C^-1).y + log(det(C))] + const.
The likelihood is NOT NORMALIZED, since this does not affect MCMC. The
normalization const = -n/2*log(2*pi), where n is the dimensionality.
Arguments `y` and `cov` MUST be np.arrays with dtype == float64 and shapes
(n) and (n, n), respectively. These requirements are NOT CHECKED.
The calculation follows algorithm 2.1 in Rasmussen and Williams (Gaussian
Processes for Machine Learning).
"""
# Compute the Cholesky decomposition of the covariance.
# Use bare LAPACK function to avoid scipy.linalg wrapper overhead.
L, info = lapack.dpotrf(cov, clean=False)
if info < 0:
raise ValueError(
'lapack dpotrf error: '
'the {}-th argument had an illegal value'.format(-info)
)
elif info < 0:
raise np.linalg.LinAlgError(
'lapack dpotrf error: '
'the leading minor of order {} is not positive definite'
.format(info)
)
# Solve for alpha = cov^-1.y using the Cholesky decomp.
alpha, info = lapack.dpotrs(L, y)
if info != 0:
raise ValueError(
'lapack dpotrs error: '
'the {}-th argument had an illegal value'.format(-info)
)
return -.5*np.dot(y, alpha) - np.log(L.diagonal()).sum()
def block_determinant_add_rows(Pinv, Q, R, S, symm=False):
"""
Compute the determinant of the matrix
A = [[P, Q],
[R, S]]
Given that we already know P^{-1} and det{P}.
We follow the notation of Numerical Recipes S2.7
:param symm: If True, Q=R.T
:return: A^{-1}
"""
# Let A^{-1} = [[Pt, Qt],
# [Rt, St]]
# where t is short for tilde
# Precompute reusable pieces
PiQ = Pinv.dot(Q)
RPi = PiQ.T if symm else R.dot(Pinv)
# Compute the outputs
if symm:
raise Exception("Broken!")
F = S-R.dot(PiQ)
L = np.linalg.cholesky(F)
St = dpotrs(
L, np.eye(F.shape[0]), lower=True)[0]
Rt = -solve_triangular(L, RPi, lower=False)
Pt = Pinv - PiQ.dot(solve_triangular(L, RPi))
Qt = Rt.T
else:
St = np.linalg.inv(S - R.dot(PiQ))
Pt = Pinv + PiQ.dot(St).dot(RPi)
Qt = -PiQ.dot(St)
Rt = Qt.T if symm else -St.dot(RPi)
Ainv = np.vstack([np.hstack((Pt, Qt)),
np.hstack((Rt, St))])
return Ainv
def block_determinant_add_rows(Pinv, Q, R, S, symm=False):
"""
Compute the determinant of the matrix
A = [[P, Q],
[R, S]]
Given that we already know P^{-1} and det{P}.
We follow the notation of Numerical Recipes S2.7
:param symm: If True, Q=R.T
:return: A^{-1}
"""
# Let A^{-1} = [[Pt, Qt],
# [Rt, St]]
# where t is short for tilde
# Precompute reusable pieces
PiQ = Pinv.dot(Q)
RPi = PiQ.T if symm else R.dot(Pinv)
# Compute the outputs
if symm:
raise Exception("Broken!")
F = S - R.dot(PiQ)
L = np.linalg.cholesky(F)
St = dpotrs(L, np.eye(F.shape[0]), lower=True)[0]
Rt = -solve_triangular(L, RPi, lower=False)
Pt = Pinv - PiQ.dot(solve_triangular(L, RPi))
Qt = Rt.T
else:
St = np.linalg.inv(S - R.dot(PiQ))
Pt = Pinv + PiQ.dot(St).dot(RPi)
Qt = -PiQ.dot(St)
Rt = Qt.T if symm else -St.dot(RPi)
Ainv = np.vstack([np.hstack((Pt, Qt)), np.hstack((Rt, St))])
return Ainv
def _sample_beta_and_sigma_y(self):
"""Gibbs sample `beta` and noise parameter `sigma_y`.
"""
phi_X = self.phi(self.X, self.W, add_bias=True)
cov_j = self.B0 + phi_X.T @ phi_X
mu_j = np.tile((self.B0 @ self.b0), (self.J, 1)).T + \
(phi_X.T @ self.Y)
# multi-output generalization of mvn sample code
L = np.linalg.cholesky(cov_j)
Z = self.rng.normal(size=self.beta.shape).T
LZ = solve_triangular(L, Z, lower=True, trans='T')
L_mu = dpotrs(L, mu_j, lower=True)[0]
self.beta[:] = (LZ + L_mu).T
# sample from inverse gamma
a_post = self.gamma_a0 + .5 * self.N
b_post = self.gamma_b0 + .5 * np.diag(
(self.Y.T @ self.Y) + \
(self.b0 @ self.B0 @ self.b0.T) + \
(mu_j.T @ np.linalg.solve(cov_j, mu_j))
)
self.sigma_y = 1. / self.rng.gamma(a_post, 1. / b_post)
def test_cho_solver():
from scipy.linalg.lapack import dpotrs
N = 5
y = np.random.uniform(size=N)
Y = np.random.uniform(size=[N, 2])
a = np.random.uniform(size=[N, N])
a = a.T.dot(a)
L = np.linalg.cholesky(a)
X = cho_solve(L, Y, False)
xa = cho_solve(L, Y[:, 0], False)
xb = cho_solve(L, Y[:, 1], False)
assert np.alltrue(np.isclose(X[:, 0], xa)), "a fails"
assert np.alltrue(np.isclose(X[:, 1], xb)), "b fails"
#with y vec mod (no copy)
#built in
#x1 = cho_solve((L,True),y)
x1 = dpotrs(L, y, 1, 0)
x2 = cho_solve(L, y, False)
#x1 = dpotrs(L,y,1,1)
assert np.all(np.isclose(x1[0], x2))
def __init__(self, X, Y, theta):
theta = theta ** [2,1,2]
[sf2, l2, sn2] = theta
# evaluate RBF kernel for our given X
r = dist.pdist(X) / l2
K = dist.squareform(sf2 * np.exp(-0.5 * r**2))
np.fill_diagonal(K, sf2)
# add in Gaussian noise (+ a bit for numerical stability)
Ky = K.copy()
np.fill_diagonal(Ky, sf2 + sn2 + 1e-8)
# compute the Cholesky factorization of our covariance matrix
LW, info = lapack.dpotrf(Ky, lower=True)
assert info == 0
# calculate lower half of inverse of K (assumes real symmetric positive definite)
Wi, info = lapack.dpotri(LW, lower=True)
assert info == 0
# make symmetric by filling in the upper half
Wi += np.tril(Wi,-1).T
# and solve
alpha, info = lapack.dpotrs(LW, Y, lower=True)
assert info == 0
# save these for later
self.X = X
self.Y = Y
self.theta = theta
self.r = r
self.K = K
self.Ky = Ky
self.LW = LW
self.Wi = Wi
self.alpha = alpha
def __init__(self, X, Y, inducing_inputs, lengthscale):
self.X = X
self.Y = Y
self.inducing_inputs = inducing_inputs
self.lengthscale = lengthscale
self.rectify = rectify
self.kern = GPy.kern.RBF(input_dim=X.shape[1],
variance=1.,
lengthscale=lengthscale,
ARD=True)
K_uf = self.kern.K(inducing_inputs, X)
KK = K_uf.dot(K_uf.T)
Ky = K_uf.dot(Y)
self.w_mean = dpotrs(dpotrf(KK)[0],
Ky)[0] # faster than np.linalg.solve(KK, Ky)
if np.any(np.isnan(self.w_mean)):
try:
self.w_mean = np.linalg.solve(KK, Ky)
except:
jitter = np.diag(KK).mean() * 1e-6
num_tries = 1
while num_tries <= 5 and np.isfinite(jitter):
try:
self.w_mean = np.linalg.solve(
KK + np.eye(KK.shape[0]) * jitter, Ky)
except:
jitter *= 10
finally:
num_tries += 1
self.wb_var = np.transpose([
scipy.optimize.nnls(
np.vstack([self._SNRinv(X), np.ones(len(X))]).T,
(self.mean(X) - Y)[:, a]**2)[0] for a in range(Y.shape[1])
])
self.Gaussian_noise = Foo()
self.variance, self.Gaussian_noise.variance = self.wb_var
def mvn_loglike(y, cov):
"""
Calculate multi-varaite-normal log-likelihood
log_p = -1/2 * [(y^T).(C^-1).y + log(det(C))] + const
To normalize the likelihood, const = -n/2*log(2*pi), which is omitted here
Args:
y -- (n)
cov -- shape (n, n)
Returns:
log_p
"""
L, info = lapack.dpotrf(cov, clean=False)
if info != 0:
raise ValueError('lapack dpotrf error: illegal value for info!')
alpha, info = lapack.dpotrs(L, y)
if info != 0:
raise ValueError(
'lapack dpotrf error: illegal value for info! {}'.format(info))
return -.5 * np.dot(y, alpha) - np.log(L.diagonal()).sum()
def _solve_cholesky(L, b, lower=True):
'''
Solves the system of equations `Ax = b` given the Cholesky decomposition of
`A`. Uses the routine `dpotrs`.
Parameters
----------
L : (n, n) float array
b : (n, *) float array
Returns
-------
(n, *) float array
'''
if any(i == 0 for i in b.shape):
return np.zeros(b.shape)
x, info = dpotrs(L, b, lower=lower)
if info < 0:
raise ValueError('The %s-th argument has an illegal value.' % -info)
return x
def solve_psd(A,b,chol=None,lower=True,overwrite_b=False,overwrite_A=False):
if chol is None:
return lapack.dposv(A,b,overwrite_b=overwrite_b,overwrite_a=overwrite_A)[1]
else:
return lapack.dpotrs(chol,b,lower,overwrite_b)[0]
def kalman_filter(model, return_loglike=False):
# Parameters
dtype = model.dtype
# Kalman filter properties
filter_method = model.filter_method
inversion_method = model.inversion_method
stability_method = model.stability_method
conserve_memory = model.conserve_memory
tolerance = model.tolerance
loglikelihood_burn = model.loglikelihood_burn
# Check for acceptable values
if not filter_method == FILTER_CONVENTIONAL:
warn('The pure Python version of the kalman filter only supports the'
' conventional Kalman filter')
implemented_inv_methods = INVERT_NUMPY | INVERT_UNIVARIATE | SOLVE_CHOLESKY
if not inversion_method & implemented_inv_methods:
warn('The pure Python version of the kalman filter only performs'
' inversion using `numpy.linalg.inv`.')
if not tolerance == 0:
warn('The pure Python version of the kalman filter does not check'
' for convergence.')
# Convergence (this implementation does not consider convergence)
converged = False
period_converged = 0
# Dimensions
nobs = model.nobs
k_endog = model.k_endog
k_states = model.k_states
k_posdef = model.k_posdef
# Allocate memory for variables
filtered_state = np.zeros((k_states, nobs), dtype=dtype)
filtered_state_cov = np.zeros((k_states, k_states, nobs), dtype=dtype)
predicted_state = np.zeros((k_states, nobs+1), dtype=dtype)
predicted_state_cov = np.zeros((k_states, k_states, nobs+1), dtype=dtype)
forecast = np.zeros((k_endog, nobs), dtype=dtype)
forecast_error = np.zeros((k_endog, nobs), dtype=dtype)
forecast_error_cov = np.zeros((k_endog, k_endog, nobs), dtype=dtype)
loglikelihood = np.zeros((nobs+1,), dtype=dtype)
# Selected state covariance matrix
selected_state_cov = (
np.dot(
np.dot(model.selection[:, :, 0],
model.state_cov[:, :, 0]),
model.selection[:, :, 0].T
)
)
# Initial values
if model.initialization == 'known':
initial_state = model._initial_state.astype(dtype)
initial_state_cov = model._initial_state_cov.astype(dtype)
elif model.initialization == 'approximate_diffuse':
initial_state = np.zeros((k_states,), dtype=dtype)
initial_state_cov = (
np.eye(k_states).astype(dtype) * model._initial_variance
)
elif model.initialization == 'stationary':
initial_state = np.zeros((k_states,), dtype=dtype)
initial_state_cov = solve_discrete_lyapunov(
np.array(model.transition[:, :, 0], dtype=dtype),
np.array(selected_state_cov[:, :], dtype=dtype),
)
else:
raise RuntimeError('Statespace model not initialized.')
# Copy initial values to predicted
predicted_state[:, 0] = initial_state
predicted_state_cov[:, :, 0] = initial_state_cov
# print(predicted_state_cov[:, :, 0])
# Setup indices for possibly time-varying matrices
design_t = 0
obs_intercept_t = 0
obs_cov_t = 0
transition_t = 0
state_intercept_t = 0
selection_t = 0
state_cov_t = 0
# Iterate forwards
time_invariant = model.time_invariant
for t in range(nobs):
# Get indices for possibly time-varying arrays
if not time_invariant:
if model.design.shape[2] > 1: design_t = t
if model.obs_intercept.shape[1] > 1: obs_intercept_t = t
if model.obs_cov.shape[2] > 1: obs_cov_t = t
if model.transition.shape[2] > 1: transition_t = t
if model.state_intercept.shape[1] > 1: state_intercept_t = t
if model.selection.shape[2] > 1: selection_t = t
if model.state_cov.shape[2] > 1: state_cov_t = t
# Selected state covariance matrix
if model.selection.shape[2] > 1 or model.state_cov.shape[2] > 1:
selected_state_cov = (
np.dot(
np.dot(model.selection[:, :, selection_t],
model.state_cov[:, :, state_cov_t]),
model.selection[:, :, selection_t].T
)
)
# #### Forecast for time t
# `forecast` $= Z_t a_t + d_t$
#
# *Note*: $a_t$ is given from the initialization (for $t = 0$) or
# from the previous iteration of the filter (for $t > 0$).
forecast[:, t] = (
np.dot(model.design[:, :, design_t], predicted_state[:, t]) +
model.obs_intercept[:, obs_intercept_t]
)
# *Intermediate calculation* (used just below and then once more)
# `tmp1` array used here, dimension $(m \times p)$
# $\\#_1 = P_t Z_t'$
# $(m \times p) = (m \times m) (p \times m)'$
tmp1 = np.dot(predicted_state_cov[:, :, t],
model.design[:, :, design_t].T)
# #### Forecast error for time t
# `forecast_error` $\equiv v_t = y_t -$ `forecast`
forecast_error[:, t] = model.obs[:, t] - forecast[:, t]
# #### Forecast error covariance matrix for time t
# $F_t \equiv Z_t P_t Z_t' + H_t$
forecast_error_cov[:, :, t] = (
np.dot(model.design[:, :, design_t], tmp1) +
model.obs_cov[:, :, obs_cov_t]
)
# Store the inverse
if k_endog == 1 and inversion_method & INVERT_UNIVARIATE:
forecast_error_cov_inv = 1.0 / forecast_error_cov[0, 0, t]
determinant = forecast_error_cov[0, 0, t]
tmp2 = forecast_error_cov_inv * forecast_error[:, t]
tmp3 = forecast_error_cov_inv * model.design[:, :, design_t]
elif inversion_method & SOLVE_CHOLESKY:
U, info = lapack.dpotrf(forecast_error_cov[:, :, t])
determinant = np.product(U.diagonal())**2
tmp2, info = lapack.dpotrs(U, forecast_error[:, t])
tmp3, info = lapack.dpotrs(U, model.design[:, :, design_t])
else:
forecast_error_cov_inv = np.linalg.inv(forecast_error_cov[:, :, t])
determinant = np.linalg.det(forecast_error_cov[:, :, t])
tmp2 = np.dot(forecast_error_cov_inv, forecast_error[:, t])
tmp3 = np.dot(forecast_error_cov_inv, model.design[:, :, design_t])
# #### Filtered state for time t
# $a_{t|t} = a_t + P_t Z_t' F_t^{-1} v_t$
# $a_{t|t} = 1.0 * \\#_1 \\#_2 + 1.0 a_t$
filtered_state[:, t] = (
predicted_state[:, t] + np.dot(tmp1, tmp2)
)
# #### Filtered state covariance for time t
# $P_{t|t} = P_t - P_t Z_t' F_t^{-1} Z_t P_t$
# $P_{t|t} = P_t - \\#_1 \\#_3 P_t$
filtered_state_cov[:, :, t] = (
predicted_state_cov[:, :, t] -
np.dot(
np.dot(tmp1, tmp3),
predicted_state_cov[:, :, t]
)
)
# #### Loglikelihood
loglikelihood[t] = -0.5 * (
np.log((2*np.pi)**k_endog * determinant) +
np.dot(forecast_error[:, t], tmp2)
)
# #### Predicted state for time t+1
# $a_{t+1} = T_t a_{t|t} + c_t$
predicted_state[:, t+1] = (
np.dot(model.transition[:, :, transition_t],
filtered_state[:, t]) +
model.state_intercept[:, state_intercept_t]
)
# #### Predicted state covariance matrix for time t+1
# $P_{t+1} = T_t P_{t|t} T_t' + Q_t^*$
predicted_state_cov[:, :, t+1] = (
np.dot(
np.dot(model.transition[:, :, transition_t],
filtered_state_cov[:, :, t]),
model.transition[:, :, transition_t].T
) + selected_state_cov
)
# Enforce symmetry of predicted covariance matrix
predicted_state_cov[:, :, t+1] = (
predicted_state_cov[:, :, t+1] + predicted_state_cov[:, :, t+1].T
) / 2
if return_loglike:
return np.array(loglikelihood)
else:
kwargs = dict(
(k, v) for k, v in locals().items()
if k in _kalman_filter._fields
)
kwargs['model'] = _statespace(
initial_state=initial_state, initial_state_cov=initial_state_cov
)
kfilter = _kalman_filter(**kwargs)
return FilterResults(model, kfilter)
def kalman_filter(model, return_loglike=False):
# Parameters
dtype = model.dtype
# Kalman filter properties
filter_method = model.filter_method
inversion_method = model.inversion_method
stability_method = model.stability_method
conserve_memory = model.conserve_memory
tolerance = model.tolerance
loglikelihood_burn = model.loglikelihood_burn
# Check for acceptable values
if not filter_method == FILTER_CONVENTIONAL:
warn('The pure Python version of the kalman filter only supports the'
' conventional Kalman filter')
implemented_inv_methods = INVERT_NUMPY | INVERT_UNIVARIATE | SOLVE_CHOLESKY
if not inversion_method & implemented_inv_methods:
warn('The pure Python version of the kalman filter only performs'
' inversion using `numpy.linalg.inv`.')
if not tolerance == 0:
warn('The pure Python version of the kalman filter does not check'
' for convergence.')
# Convergence (this implementation does not consider convergence)
converged = False
period_converged = 0
# Dimensions
nobs = model.nobs
k_endog = model.k_endog
k_states = model.k_states
k_posdef = model.k_posdef
# Allocate memory for variables
filtered_state = np.zeros((k_states, nobs), dtype=dtype)
filtered_state_cov = np.zeros((k_states, k_states, nobs), dtype=dtype)
predicted_state = np.zeros((k_states, nobs + 1), dtype=dtype)
predicted_state_cov = np.zeros((k_states, k_states, nobs + 1), dtype=dtype)
forecast = np.zeros((k_endog, nobs), dtype=dtype)
forecast_error = np.zeros((k_endog, nobs), dtype=dtype)
forecast_error_cov = np.zeros((k_endog, k_endog, nobs), dtype=dtype)
loglikelihood = np.zeros((nobs + 1, ), dtype=dtype)
# Selected state covariance matrix
selected_state_cov = (np.dot(
np.dot(model.selection[:, :, 0], model.state_cov[:, :, 0]),
model.selection[:, :, 0].T))
# Initial values
if model.initialization == 'known':
initial_state = model._initial_state.astype(dtype)
initial_state_cov = model._initial_state_cov.astype(dtype)
elif model.initialization == 'approximate_diffuse':
initial_state = np.zeros((k_states, ), dtype=dtype)
initial_state_cov = (np.eye(k_states).astype(dtype) *
model._initial_variance)
elif model.initialization == 'stationary':
initial_state = np.zeros((k_states, ), dtype=dtype)
initial_state_cov = solve_discrete_lyapunov(
np.array(model.transition[:, :, 0], dtype=dtype),
np.array(selected_state_cov[:, :], dtype=dtype),
)
else:
raise RuntimeError('Statespace model not initialized.')
# Copy initial values to predicted
predicted_state[:, 0] = initial_state
predicted_state_cov[:, :, 0] = initial_state_cov
# print(predicted_state_cov[:, :, 0])
# Setup indices for possibly time-varying matrices
design_t = 0
obs_intercept_t = 0
obs_cov_t = 0
transition_t = 0
state_intercept_t = 0
selection_t = 0
state_cov_t = 0
# Iterate forwards
time_invariant = model.time_invariant
for t in range(nobs):
# Get indices for possibly time-varying arrays
if not time_invariant:
if model.design.shape[2] > 1: design_t = t
if model.obs_intercept.shape[1] > 1: obs_intercept_t = t
if model.obs_cov.shape[2] > 1: obs_cov_t = t
if model.transition.shape[2] > 1: transition_t = t
if model.state_intercept.shape[1] > 1: state_intercept_t = t
if model.selection.shape[2] > 1: selection_t = t
if model.state_cov.shape[2] > 1: state_cov_t = t
# Selected state covariance matrix
if model.selection.shape[2] > 1 or model.state_cov.shape[2] > 1:
selected_state_cov = (np.dot(
np.dot(model.selection[:, :, selection_t],
model.state_cov[:, :, state_cov_t]),
model.selection[:, :, selection_t].T))
# #### Forecast for time t
# `forecast` $= Z_t a_t + d_t$
#
# *Note*: $a_t$ is given from the initialization (for $t = 0$) or
# from the previous iteration of the filter (for $t > 0$).
forecast[:, t] = (
np.dot(model.design[:, :, design_t], predicted_state[:, t]) +
model.obs_intercept[:, obs_intercept_t])
# *Intermediate calculation* (used just below and then once more)
# `tmp1` array used here, dimension $(m \times p)$
# $\\#_1 = P_t Z_t'$
# $(m \times p) = (m \times m) (p \times m)'$
tmp1 = np.dot(predicted_state_cov[:, :, t], model.design[:, :,
design_t].T)
# #### Forecast error for time t
# `forecast_error` $\equiv v_t = y_t -$ `forecast`
forecast_error[:, t] = model.obs[:, t] - forecast[:, t]
# #### Forecast error covariance matrix for time t
# $F_t \equiv Z_t P_t Z_t' + H_t$
forecast_error_cov[:, :,
t] = (np.dot(model.design[:, :, design_t], tmp1) +
model.obs_cov[:, :, obs_cov_t])
# Store the inverse
if k_endog == 1 and inversion_method & INVERT_UNIVARIATE:
forecast_error_cov_inv = 1.0 / forecast_error_cov[0, 0, t]
determinant = forecast_error_cov[0, 0, t]
tmp2 = forecast_error_cov_inv * forecast_error[:, t]
tmp3 = forecast_error_cov_inv * model.design[:, :, design_t]
elif inversion_method & SOLVE_CHOLESKY:
U, info = lapack.dpotrf(forecast_error_cov[:, :, t])
determinant = np.product(U.diagonal())**2
tmp2, info = lapack.dpotrs(U, forecast_error[:, t])
tmp3, info = lapack.dpotrs(U, model.design[:, :, design_t])
else:
forecast_error_cov_inv = np.linalg.inv(forecast_error_cov[:, :, t])
determinant = np.linalg.det(forecast_error_cov[:, :, t])
tmp2 = np.dot(forecast_error_cov_inv, forecast_error[:, t])
tmp3 = np.dot(forecast_error_cov_inv, model.design[:, :, design_t])
# #### Filtered state for time t
# $a_{t|t} = a_t + P_t Z_t' F_t^{-1} v_t$
# $a_{t|t} = 1.0 * \\#_1 \\#_2 + 1.0 a_t$
filtered_state[:, t] = (predicted_state[:, t] + np.dot(tmp1, tmp2))
# #### Filtered state covariance for time t
# $P_{t|t} = P_t - P_t Z_t' F_t^{-1} Z_t P_t$
# $P_{t|t} = P_t - \\#_1 \\#_3 P_t$
filtered_state_cov[:, :, t] = (
predicted_state_cov[:, :, t] -
np.dot(np.dot(tmp1, tmp3), predicted_state_cov[:, :, t]))
# #### Loglikelihood
loglikelihood[t] = -0.5 * (np.log((2 * np.pi)**k_endog * determinant) +
np.dot(forecast_error[:, t], tmp2))
# #### Predicted state for time t+1
# $a_{t+1} = T_t a_{t|t} + c_t$
predicted_state[:,
t + 1] = (np.dot(model.transition[:, :, transition_t],
filtered_state[:, t]) +
model.state_intercept[:, state_intercept_t])
# #### Predicted state covariance matrix for time t+1
# $P_{t+1} = T_t P_{t|t} T_t' + Q_t^*$
predicted_state_cov[:, :, t + 1] = (np.dot(
np.dot(model.transition[:, :, transition_t],
filtered_state_cov[:, :, t]),
model.transition[:, :, transition_t].T) + selected_state_cov)
# Enforce symmetry of predicted covariance matrix
predicted_state_cov[:, :,
t + 1] = (predicted_state_cov[:, :, t + 1] +
predicted_state_cov[:, :, t + 1].T) / 2
if return_loglike:
return np.array(loglikelihood)
else:
kwargs = dict(
(k, v) for k, v in locals().items() if k in _kalman_filter._fields)
kwargs['model'] = _statespace(initial_state=initial_state,
initial_state_cov=initial_state_cov)
kfilter = _kalman_filter(**kwargs)
return FilterResults(model, kfilter)
def lnLL(dy, cov):
L, info = lapack.dpotrf(cov, clean=False)
alpha, info = lapack.dpotrs(L, dy)
return -.5 * np.dot(dy, alpha) - np.log(L.diagonal()).sum()