def bsem(
items,
factors,
paths,
beta=0,
nu_sd=2.5,
alpha_sd=2.5,
d_beta=2.5,
corr_items=False,
corr_factors=False,
g_eta=100,
l_eta=1,
beta_beta=1,
):
r"""Constructs Bayesian SEM.
Args:
items (np.array): Array of item data.
factors (np.array): Factor design.
paths (np.array): Array of directed factor paths.
beta (:obj:`float` or `'estimate'`, optional): Standard deviation of normal
prior on cross loadings. If `'estimate'`, beta is estimated from the data.
nu_sd (:obj:`float`, optional): Standard deviation of normal prior on item
intercepts.
alpha_sd (:obj:`float`, optional): Standard deviation of normal prior on factor
intercepts.
d_beta (:obj:`float`, optional): Scale parameter of half-Cauchy prior on factor
standard deviation.
corr_factors (:obj:`bool`, optional): Allow correlated factors.
corr_items (:obj:`bool`, optional): Allow correlated items.
g_eta (:obj:`float`, optional): Shape parameter of LKJ prior on residual item
correlation matrix.
l_eta (:obj:`float`, optional): Shape parameter of LKJ prior on factor
correlation matrix.
beta_beta (:obj:`float`, optional): Beta parameter of beta prior on beta.
Returns:
None: Places model in context.
"""
# get numbers of cases, items, and factors
n, p = items.shape
p_, m = factors.shape
assert p == p_, "Mismatch between data and factor-loading matrices"
assert paths.shape == (m, m), "Paths matrix has wrong shape"
I = tt.eye(m, m)
# place priors on item and factor intercepts
nu = pm.Normal(name=r"$\nu$",
mu=0,
sd=nu_sd,
shape=p,
testval=items.mean(axis=0))
alpha = pm.Normal(name=r"$\alpha$",
mu=0,
sd=alpha_sd,
shape=m,
testval=np.zeros(m))
# place priors on unscaled factor loadings
Phi = pm.Normal(name=r"$\Phi$",
mu=0,
sd=1,
shape=factors.shape,
testval=factors)
# place priors on paths
B = tt.zeros(paths.shape)
npths = np.sum(paths, axis=None)
print(npths)
if npths > 0:
b = pm.Normal(name=r"$b$",
mu=0,
sd=1,
shape=npths,
testval=np.ones(npths))
# create the paths matrix
k = 0
for i in range(m):
for j in range(m):
if paths[i, j] == 1:
B = tt.set_subtensor(B[i, j], b[k])
k += 1
Gamma = pm.Deterministic("$\Gamma$", B)
# create masking matrix for factor loadings
if isinstance(beta, str):
assert beta == "estimate", f"Don't know what to do with '{beta}'"
beta = pm.Beta(name=r"$\beta$", alpha=1, beta=beta_beta, testval=0.1)
M = (1 - np.asarray(factors)) * beta + np.asarray(factors)
# create scaled factor loadings
Lambda = pm.Deterministic(r"$\Lambda$", Phi * M)
# determine item means
mu = nu + matrix_dot(Lambda, alpha)
# place priors on item standard deviations
D = pm.HalfCauchy(name=r"$D$",
beta=d_beta,
shape=p,
testval=items.std(axis=0))
# place priors on item correlations
f = pm.Lognormal.dist(sd=0.25)
if not corr_items:
Omega = np.eye(p)
else:
G = pm.LKJCholeskyCov(name=r"$G$", eta=g_eta, n=p, sd_dist=f)
ch1 = pm.expand_packed_triangular(p, G, lower=True)
K = tt.dot(ch1, ch1.T)
sd1 = tt.sqrt(tt.diag(K))
Omega = pm.Deterministic(r"$\Omega$", K / sd1[:, None] / sd1[None, :])
# determine residual item variances and covariances
Theta = pm.Deterministic(r"$\Theta$", D[None, :] * Omega * D[:, None])
# place priors on factor correlations
if not corr_factors:
Psi = np.eye(m)
else:
L = pm.LKJCholeskyCov(name=r"$L$", eta=l_eta, n=m, sd_dist=f)
ch = pm.expand_packed_triangular(m, L, lower=True)
Gamma = tt.dot(ch, ch.T)
sd = tt.sqrt(tt.diag(Gamma))
Psi = pm.Deterministic(r"$\Psi$", Gamma / sd[:, None] / sd[None, :])
# determine variances and covariances of items
A = matrix_inverse(I - Gamma)
C = matrix_inverse(I - Gamma.T)
Sigma = matrix_dot(Lambda, A, Psi, C, Lambda.T) + Theta
# place priors on observations
pm.MvNormal(name="$Y$",
mu=mu,
cov=Sigma,
observed=items,
shape=items.shape)
def bcfab(items, factors, paths, nu_sd=2.5, alpha_sd=2.5):
r"""Constructs a Bayesian CFA model in "binomial form".
Args:
items (np.array): Data.
factors (np.array): Factor design matrix.
paths (np.array): Paths design matrix.
nu_sd (:obj:`float`, optional): Standard deviation of normal prior on item
intercepts.
alpha_sd (:obj:`float`, optional): Standard deviation of normal prior on factor
intercepts.
Returns:
None: Places model in context.
"""
# get numbers of cases, items, and factors
n, p = items.shape
p_, m = factors.shape
assert p == p_, "Mismatch between data and factor-loading matrices"
# priors on item intercepts
nu = pm.Normal(name=r"$\nu$", mu=0, sd=nu_sd, shape=p, testval=np.zeros(p))
# priors on factor intercepts
alpha = pm.Normal(name=r"$\alpha$",
mu=0,
sd=alpha_sd,
shape=m,
testval=np.zeros(m))
# priors on factor loadings
l = np.asarray(factors).sum()
lam = pm.Normal(name=r"$\lambda$",
mu=0,
sd=1,
shape=l,
testval=np.zeros(l))
# loading matrix
Lambda = tt.zeros(factors.shape)
k = 0
for i, j in product(range(p), range(m)):
if factors[i, j] == 1:
Lambda = tt.inc_subtensor(Lambda[i, j], lam[k])
k += 1
pm.Deterministic(name=r"$\Lambda$", var=Lambda)
# priors on paths
g = np.asarray(paths).sum()
gam = pm.Normal(name=r"$\gamma$", mu=0, sd=1, shape=g, testval=np.zeros(g))
# path matrix
Gamma = tt.zeros(paths.shape)
k = 0
for i, j in product(range(m), range(m)):
if paths[i, j] == 1:
Gamma = tt.inc_subtensor(Gamma[i, j], gam[k])
k += 1
pm.Deterministic(name=r"$\Gamma$", var=Gamma)
# priors on factor residuals
zeta = pm.Normal(name=r"$\zeta$", mu=0, sigma=1, shape=(n, m), testval=0)
# latent variables
I = np.eye(m)
Pi = pm.math.sigmoid(nu + matrix_dot(
matrix_dot((alpha + zeta), matrix_inverse(I - Gamma.T)), Lambda.T))
# observations
pm.Binomial(name="$Y$",
p=Pi,
n=items.max(axis=0),
observed=items,
shape=items.shape)
def bcfa(Y, M):
r"""Constructs a Bayesian confirmatory factor analysis (BCFA) model.
Args:
Y (numpy.ndarray): An $n \times p$ matrix of data where $n$ is the sample size
and $p$ is the number of manifest variables.
M (numpy.ndarray): An $p \times m$ matrix to describe model structure where $m$
is the number of latent variables.
Notes:
$$\mathbf{Y}$$ probably should be standardized first if you are using continuous
data.
Entries in $\mathbf{M}$ should be [0, 1].
$\mathbf{M}_{(i,j)}$ represents the variance of the normal prior placed on the
regression coefficient from the $j$th latent variable to the $i$th manifest
variable. Values of 0 remove the coefficient from the model entirely, 1
represents a "full-strength" coefficient, and values (0, 1) are for
cross-loadings.
Returns:
None: Model is placed in the context.
"""
# counts
n, p = Y.shape
p_, m = M.shape
assert p == p_, "M is the wrong shape"
# intercepts for manifest variables
sd = max(np.abs(Y.mean()).max() * 2.5, 2.5)
nu = pm.Normal(name=r"$\nu$", mu=0, sd=sd, shape=p, testval=Y.mean())
# unscaled regression coefficients
Phi = pm.Normal(name=r"$\Phi$", mu=0, sd=1, shape=M.shape, testval=M)
# scaled regression coefficients
Lambda = pm.Deterministic(r"$\Lambda$", Phi * np.sqrt(M))
# intercepts for latent variables
alpha = pm.Normal(name=r"$\alpha$", mu=0, sd=2.5, shape=m, testval=0)
# means of manifest variables
mu = nu + matrix_dot(Lambda, alpha)
# standard deviations of manifest variables
D = pm.HalfCauchy(name=r"$D$", beta=2.5, shape=p, testval=Y.std())
# correlations between manifest variables
Omega = np.eye(p)
# covariance matrix for manifest variables
Theta = pm.Deterministic(r"$\Theta$", D[None, :] * Omega * D[:, None])
# covariance matrix on latent variables
f = pm.Lognormal.dist(sd=0.25)
L = pm.LKJCholeskyCov(name=r"$L$", eta=1, n=m, sd_dist=f)
ch = pm.expand_packed_triangular(m, L, lower=True)
Gamma = tt.dot(ch, ch.T)
sd = tt.sqrt(tt.diag(Gamma))
Psi = pm.Deterministic(r"$\Psi$", Gamma / sd[:, None] / sd[None, :])
# covariance of manifest variables
Sigma = matrix_dot(Lambda, Psi, Lambda.T) + Theta
# observations
pm.MvNormal(name="Y", mu=mu, cov=Sigma, observed=Y, shape=Y.shape)
def bcfam(items, factors, paths, nu_sd=2.5, alpha_sd=2.5, d_beta=2.5):
r"""Constructs a Bayesian CFA model in "multivariate form".
Args:
items (np.array): Data.
factors (np.array): Factor design matrix.
paths (np.array): Paths design matrix.
nu_sd (:obj:`float`, optional): Standard deviation of normal prior on item
intercepts.
alpha_sd (:obj:`float`, optional): Standard deviation of normal prior on factor
intercepts.
d_beta (:obj:`float`, optional): Scale parameter of half-Cauchy prior on factor
standard deviation.
Returns:
None: Places model in context.
"""
# get numbers of cases, items, and factors
n, p = items.shape
p_, m = factors.shape
assert p == p_, "Mismatch between data and factor-loading matrices"
# priors on item intercepts
nu = pm.Normal(name=r"$\nu$",
mu=0,
sd=nu_sd,
shape=p,
testval=items.mean(axis=0))
# priors on factor intercepts
alpha = pm.Normal(name=r"$\alpha$",
mu=0,
sd=alpha_sd,
shape=m,
testval=np.zeros(m))
# priors on factor loadings
l = np.asarray(factors).sum()
lam = pm.Normal(name=r"$\lambda$", mu=0, sd=1, shape=l, testval=np.ones(l))
# loading matrix
Lambda = tt.zeros(factors.shape)
k = 0
for i, j in product(range(p), range(m)):
if factors[i, j] == 1:
Lambda = tt.inc_subtensor(Lambda[i, j], lam[k])
k += 1
pm.Deterministic(name=r"$\Lambda$", var=Lambda)
# item means
mu = nu + matrix_dot(Lambda, alpha)
# item residual covariance matrix
d = pm.HalfCauchy(name=r"$\sqrt{\theta}$",
beta=d_beta,
shape=p,
testval=items.std(axis=0))
Theta = tt.diag(d)**2
# factor covariance matrix
Psi = I = np.eye(m)
# priors on paths
g = np.asarray(paths).sum()
gam = pm.Normal(name=r"$\gamma$", mu=0, sd=1, shape=g, testval=np.ones(g))
# path matrix
Gamma = tt.zeros(paths.shape)
k = 0
for i, j in product(range(m), range(m)):
if paths[i, j] == 1:
Gamma = tt.inc_subtensor(Gamma[i, j], gam[k])
k += 1
pm.Deterministic(name=r"$\Gamma$", var=Gamma)
# item covariance matrix
Sigma = (matrix_dot(
Lambda,
matrix_inverse(I - Gamma),
Psi,
matrix_inverse(I - Gamma.T),
Lambda.T,
) + Theta)
# observations
pm.MvNormal(name="$Y$",
mu=mu,
cov=Sigma,
observed=items,
shape=items.shape)
def n_star_inference(n_stars,
iteration,
elem_err=False,
n_init=20000,
n_samples=1000,
max_stars=100):
## Define which stars to use
these_stars = np.arange(max_stars)[iteration * n_stars:(iteration + 1) *
n_stars]
## Load in mock dataset
mock_data = np.load(mock_data_file) #dataset
mu_times = mock_data.f.obs_time[these_stars] #time of birth
sigma_times = mock_data.f.obs_time_err[these_stars] #error on age
all_els = mock_data.f.elements
full_abundances = mock_data.f.abundances[
these_stars] # chemical element abundances for data
full_errors = mock_data.f.abundance_errs[
these_stars] # error on abundances
# Filter out correct elements:
els = ['C', 'Fe', 'He', 'Mg', 'N', 'Ne', 'O', 'Si'] # TNG elements
n_els = len(els)
el_indices = np.zeros(len(els), dtype=int)
for e, el in enumerate(els):
for j in range(len(all_els)):
if els[e] == str(all_els[j]):
el_indices[e] = j
break
if j == len(all_els) - 1:
print("Failed to find element %s" % el)
obs_abundances = full_abundances[:, el_indices]
obs_errors = full_errors[:, el_indices]
# Now standardize dataset
norm_data = (obs_abundances - output_mean) / output_std
norm_sd = obs_errors / output_std
data_obs = norm_data.ravel()
data_sd = np.asarray(norm_sd).ravel()
std_times_mean = (mu_times - input_mean[-1]) / input_std[-1]
std_times_width = sigma_times / input_std[-1]
# Define stacked local priors
Local_prior_mean = np.vstack([
np.hstack([std_Theta_prior_mean, std_times_mean[i]])
for i in range(n_stars)
])
Local_prior_sigma = np.vstack([
np.hstack([std_Theta_prior_width, std_times_width[i]])
for i in range(n_stars)
])
# Bound variables to ensure they don't exit the training parameter space
lowBound = tt._shared(np.asarray([-5, std_log_SFR_crit, -5, std_min_time]))
upBound = tt._shared(np.asarray([5, 5, 5, std_max_time]))
# Create stacked mean and variances
loc_mean = np.hstack([
np.asarray(std_Theta_prior_mean).reshape(1, -1) *
np.ones([n_stars, 1]),
std_times_mean.reshape(-1, 1)
])
loc_std = np.hstack([
np.asarray(std_Theta_prior_width).reshape(1, -1) *
np.ones([n_stars, 1]),
std_times_width.reshape(-1, 1)
])
# Share theano variables
w0 = tt._shared(w_array_0)
b0 = tt._shared(b_array_0)
w1 = tt._shared(w_array_1)
b1 = tt._shared(b_array_1)
ones_tensor = tt.ones([n_stars, 1])
b0_all = ma.matrix_dot(ones_tensor, b0)
b1_all = ma.matrix_dot(ones_tensor, b1)
# Define PyMC3 Model
simple_model = pm.Model()
with simple_model:
# Define priors
Lambda = pm.Normal('Std-Lambda',
mu=std_Lambda_prior_mean,
sd=std_Lambda_prior_width,
shape=(1, len(std_Lambda_prior_mean)))
Locals = pm.Normal(
'Std-Local',
mu=loc_mean,
sd=loc_std,
shape=loc_mean.shape,
transform=pm.distributions.transforms.Interval(lowBound, upBound),
)
TimeSq = tt.reshape(Locals[:, -1]**2., (n_stars, 1))
TruLa = pm.Deterministic('Lambda',
Lambda * input_std[:2] + input_mean[:2])
TruTh = pm.Deterministic(
'Thetas', Locals[:, :3] * input_std[2:5] + input_mean[2:5])
TruTi = pm.Deterministic(
'Times', Locals[:, -1] * input_std[-1] + input_mean[-1])
## NEURAL NET
Lambda_all = ma.matrix_dot(ones_tensor, Lambda)
InputVariables = ma.concatenate([Lambda_all, Locals, TimeSq], axis=1)
layer1 = ma.matrix_dot(InputVariables, w0) + b0_all
output = ma.matrix_dot(ma.tanh(layer1), w1) + b1_all
if elem_err:
# ERRORS
#element_error = pm.Normal('Element-Error',mu=-2,sd=1,shape=(1,n_els))
element_error = pm.HalfCauchy('Std-Element-Error',
beta=0.01 / output_std,
shape=(1, n_els))
TruErr = pm.Deterministic('Element-Error',
element_error * output_std)
stacked_error = ma.matrix_dot(ones_tensor, element_error)
tot_error = ma.sqrt(
stacked_error**2. +
norm_sd**2.) # NB this is all standardized by output_std here
else:
tot_error = norm_sd # NB: all quantities are standardized here
predictions = pm.Deterministic("Predicted-Abundances",
output * output_std + output_mean)
# Define likelihood function (unravelling output to make a multivariate gaussian)
likelihood = pm.Normal('likelihood',
mu=output.ravel(),
sd=tot_error.ravel(),
observed=norm_data.ravel())
# Now sample
init_time = ttime.time()
with simple_model:
samples = pm.sample(draws=n_samples,
chains=chains,
cores=cores,
tune=tune,
nuts_kwargs={'target_accept': 0.9},
init='advi+adapt_diag',
n_init=n_init)
end_time = ttime.time() - init_time
def construct_output(samples):
Lambda = samples.get_values('Lambda')[:, 0, :]
Thetas = samples.get_values('Thetas')[:, :, :]
Times = samples.get_values('Times')[:, :]
predictions = samples.get_values('Predicted-Abundances')[:, :, :]
if elem_err:
Errs = samples.get_values('Element-Error')[:, 0, :]
return Lambda, Thetas, Times, Errs, predictions
else:
return Lambda, Thetas, Times, predictions
print("Finished after %.2f seconds" % end_time)
if elem_err:
Lambda, Thetas, Times, Errs, predictions = construct_output(samples)
return Lambda, Thetas, Times, end_time, Errs, predictions
else:
Lambda, Thetas, Times, predictions = construct_output(samples)
return Lambda, Thetas, Times, end_time, predictions