def test_missing():
data = ma.masked_values([1, 2, -1, 4, -1], value=-1)
with Model() as model:
x = Normal('x', 1, 1)
with pytest.warns(ImputationWarning):
Normal('y', x, 1, observed=data)
y_missing, = model.missing_values
assert y_missing.tag.test_value.shape == (2,)
model.logp(model.test_point)
with model:
prior_trace = sample_prior_predictive()
assert {'x', 'y'} <= set(prior_trace.keys())
def test_missing_dual_observations():
with Model() as model:
obs1 = ma.masked_values([1, 2, -1, 4, -1], value=-1)
obs2 = ma.masked_values([-1, -1, 6, -1, 8], value=-1)
beta1 = Normal('beta1', 1, 1)
beta2 = Normal('beta2', 2, 1)
latent = Normal('theta', shape=5)
with pytest.warns(ImputationWarning):
ovar1 = Normal('o1', mu=beta1 * latent, observed=obs1)
with pytest.warns(ImputationWarning):
ovar2 = Normal('o2', mu=beta2 * latent, observed=obs2)
prior_trace = sample_prior_predictive()
assert {'beta1', 'beta2', 'theta', 'o1', 'o2'} <= set(prior_trace.keys())
sample()
def test_missing_pandas():
data = pd.DataFrame([1, 2, numpy.nan, 4, numpy.nan])
with Model() as model:
x = Normal('x', 1, 1)
with pytest.warns(ImputationWarning):
Normal('y', x, 1, observed=data)
y_missing, = model.missing_values
assert y_missing.tag.test_value.shape == (2,)
model.logp(model.test_point)
with model:
prior_trace = sample_prior_predictive()
assert {'x', 'y'} <= set(prior_trace.keys())
def get_garch_model():
r = np.array([28, 8, -3, 7, -1, 1, 18, 12])
sigma1 = np.array([15, 10, 16, 11, 9, 11, 10, 18])
alpha0 = np.array([10, 10, 16, 8, 9, 11, 12, 18])
shape = r.shape
with Model() as garch:
alpha1 = Normal('alpha1', mu=0., sd=1., shape=shape)
BoundedNormal = Bound(Normal, upper=(1 - alpha1))
beta1 = BoundedNormal('beta1', mu=0., sd=1e6, shape=shape)
mu = Normal('mu', mu=0., sd=1e6, shape=shape)
theta = tt.sqrt(alpha0 + alpha1 * tt.pow(r - mu, 2) +
beta1 * tt.pow(sigma1, 2))
Normal('obs', mu, sd=theta, observed=r)
return garch
def test_minibatch():
draws = 3000
mu0 = 1
sd0 = 1
def f(x, a, b, c):
return a*x**2 + b*x + c
a, b, c = 1, 2, 3
batch_size = 50
total_size = batch_size*500
x_train = np.random.uniform(-10, 10, size=(total_size,)).astype('float32')
x_obs = pm.data.Minibatch(x_train, batch_size=batch_size)
y_train = f(x_train, a, b, c) + np.random.normal(size=x_train.shape).astype('float32')
y_obs = pm.data.Minibatch(y_train, batch_size=batch_size)
with Model():
abc = Normal('abc', mu=mu0, sd=sd0, shape=(3,))
x = x_obs
x2 = x**2
o = tt.ones_like(x)
X = tt.stack([x2, x, o]).T
y = X.dot(abc)
pm.Normal('y', mu=y, observed=y_obs)
step_method = pm.SGFS(batch_size=batch_size, step_size=1., total_size=total_size)
trace = pm.sample(draws=draws, step=step_method, init=None, cores=2)
np.testing.assert_allclose(np.mean(trace['abc'], axis=0), np.asarray([a, b, c]), rtol=0.1)
def logp(self, observed):
"""Calculated the log likelihood of the observed streamflow given
simulated streamflow from GR4J"""
simulated = simulate_streamflow(self.precipitation,
self.evaporation,
self.S0,
self.Pr0,
self.R0,
self.x1,
self.x2,
self.x3,
self.x4,
self.x4_limit,
truncate_gradient=self.truncate,
tv_x1=self.tv_x1)
# This restricts likelihood calculations to fewer than len(observed)
# points. This can potentially make for more rapid calculations.
if self.subsample_index is not None:
observed = observed[self.subsample_index]
simulated = simulated[self.subsample_index]
density = Normal.dist(mu=simulated, sd=self.sd)
return tt.sum(density.logp(observed))
def multidimensional_model():
mu = -2.1
tau = 1.3
with Model() as model:
x = Normal('x', mu, tau, shape=(3,2), testval=.1*np.ones((3,2)) )
return model.test_point, model, (mu, tau ** -1)
def multidimensional_model():
mu = -2.1
tau = 1.3
with Model() as model:
Normal("x", mu, tau=tau, shape=(3, 2), testval=0.1 * tt.ones((3, 2)))
return model.test_point, model, (mu, tau**-0.5)
def test_normal_mixture(self):
with Model() as model:
w = Dirichlet('w', np.ones_like(self.norm_w))
mu = Normal('mu', 0., 10., shape=self.norm_w.size)
tau = Gamma('tau', 1., 1., shape=self.norm_w.size)
x_obs = NormalMixture('x_obs',
w,
mu,
tau=tau,
observed=self.norm_x)
step = Metropolis()
trace = sample(5000,
step,
random_seed=self.random_seed,
progressbar=False)
assert_allclose(np.sort(trace['w'].mean(axis=0)),
np.sort(self.norm_w),
rtol=0.1,
atol=0.1)
assert_allclose(np.sort(trace['mu'].mean(axis=0)),
np.sort(self.norm_mu),
rtol=0.1,
atol=0.1)
def simple_model():
mu = -2.1
tau = 1.3
with Model() as model:
x = Normal('x', mu, tau, shape=2, testval=[.1]*2)
return model.test_point, model, (mu, tau ** -1)
def simple_model():
mu = -2.1
tau = 1.3
with Model() as model:
Normal("x", mu, tau=tau, size=2, initval=floatX_array([0.1, 0.1]))
return model.initial_point, model, (mu, tau**-0.5)
def test_linear_component(self):
vars_to_create = {
"sigma", "sigma_interval__", "y_obs", "lm_x0", "lm_Intercept"
}
with Model() as model:
lm = LinearComponent(self.data_linear["x"],
self.data_linear["y"],
name="lm") # yields lm_x0, lm_Intercept
sigma = Uniform("sigma", 0, 20) # yields sigma_interval__
Normal("y_obs", mu=lm.y_est, sigma=sigma,
observed=self.y_linear) # yields y_obs
start = find_MAP(vars=[sigma])
step = Slice(model.vars)
trace = sample(500,
tune=0,
step=step,
start=start,
progressbar=False,
random_seed=self.random_seed)
assert round(abs(np.mean(trace["lm_Intercept"]) - self.intercept),
1) == 0
assert round(abs(np.mean(trace["lm_x0"]) - self.slope), 1) == 0
assert round(abs(np.mean(trace["sigma"]) - self.sd), 1) == 0
assert vars_to_create == set(model.named_vars.keys())
def Update_After_Win(Obs_Sent, X, N, Freq, trace):
# Win Data = change in freqency distribution
Obs_idx = np.argmin(abs(X - Obs_Sent))
Freq[Obs_idx] = Freq[Obs_idx] + 1
#Normalisation
Freq * N / (N + 1)
model = Model()
with model:
# Priors are posteriors from previous iteration
alpha = from_posterior('alpha', trace['alpha'])
beta = from_posterior('beta', trace['beta'])
gamma = from_posterior('gamma', trace['gamma'])
delta = from_posterior('delta', trace['delta'])
#epsilon = from_posterior('epsilon', trace['epsilon'])
Arg_A = np.linalg.norm(X - alpha)
Arg_B = np.linalg.norm(X - beta)
# Expected value of Frequency
mu = gamma * np.exp(-2 * Arg_A**2) + delta * np.exp(-2 * Arg_B**2)
# Likelihood (sampling distribution) of observations
Y_obs = Normal('Y_obs', mu, 1, observed=Freq[Obs_idx])
# draw 100 posterior samples
trace = sample(100, cores=1)
return (trace)
def test_linear_component(self):
vars_to_create = {
'sigma', 'sigma_interval__', 'y_obs', 'lm_x0', 'lm_Intercept'
}
with Model() as model:
lm = LinearComponent(self.data_linear['x'],
self.data_linear['y'],
name='lm') # yields lm_x0, lm_Intercept
sigma = Uniform('sigma', 0, 20) # yields sigma_interval__
Normal('y_obs', mu=lm.y_est, sigma=sigma,
observed=self.y_linear) # yields y_obs
start = find_MAP(vars=[sigma])
step = Slice(model.vars)
trace = sample(500,
tune=0,
step=step,
start=start,
progressbar=False,
random_seed=self.random_seed)
assert round(abs(np.mean(trace['lm_Intercept']) - self.intercept),
1) == 0
assert round(abs(np.mean(trace['lm_x0']) - self.slope), 1) == 0
assert round(abs(np.mean(trace['sigma']) - self.sd), 1) == 0
assert vars_to_create == set(model.named_vars.keys())
def test_expressions(expr):
with Model() as model:
var = expr((10, 10))
Normal('obs', observed=var)
assert var.tag.test_value.shape == (10, 10)
assert len(model.free_RVs) == 3
fit(1)
def test_missing_with_predictors():
predictors = array([0.5, 1, 0.5, 2, 0.3])
data = ma.masked_values([1, 2, -1, 4, -1], value=-1)
with Model() as model:
x = Normal("x", 1, 1)
with pytest.warns(ImputationWarning):
Normal("y", x * predictors, 1, observed=data)
(y_missing, ) = model.missing_values
assert y_missing.tag.test_value.shape == (2, )
model.logp(model.test_point)
with model:
prior_trace = sample_prior_predictive()
assert {"x", "y"} <= set(prior_trace.keys())
def multidimensional_model():
mu = -2.1
tau = 1.3
with Model() as model:
Normal("x", mu, tau=tau, size=(3, 2), initval=0.1 * np.ones((3, 2)))
return model.initial_point, model, (mu, tau**-0.5)
def simple_model():
mu = -2.1
tau = 1.3
with Model() as model:
Normal("x", mu, tau=tau, shape=2, testval=tt.ones(2) * 0.1)
return model.test_point, model, (mu, tau**-0.5)
def simple_model():
mu = 2.
tau = 10.
with Model() as model:
x = Normal('x', mu, tau=tau)
return model
def test_gradient_with_scaling(self):
with pm.Model() as model1:
genvar = generator(gen1())
m = Normal('m')
Normal('n', observed=genvar, total_size=1000)
grad1 = theano.function([m], tt.grad(model1.logpt, m))
with pm.Model() as model2:
m = Normal('m')
shavar = theano.shared(np.ones((1000, 100)))
Normal('n', observed=shavar)
grad2 = theano.function([m], tt.grad(model2.logpt, m))
for i in range(10):
shavar.set_value(np.ones((100, 100)) * i)
g1 = grad1(1)
g2 = grad2(1)
np.testing.assert_almost_equal(g1, g2)
def test_mixture_list_of_normals(self):
with Model() as model:
w = Dirichlet('w', np.ones_like(self.norm_w))
mu = Normal('mu', 0., 10., shape=self.norm_w.size)
tau = Gamma('tau', 1., 1., shape=self.norm_w.size)
Mixture('x_obs', w,
[Normal.dist(mu[0], tau=tau[0]), Normal.dist(mu[1], tau=tau[1])],
observed=self.norm_x)
step = Metropolis()
trace = sample(5000, step, random_seed=self.random_seed, progressbar=False)
assert_allclose(np.sort(trace['w'].mean(axis=0)),
np.sort(self.norm_w),
rtol=0.1, atol=0.1)
assert_allclose(np.sort(trace['mu'].mean(axis=0)),
np.sort(self.norm_mu),
rtol=0.1, atol=0.1)
def test_common_errors(self):
with pm.Model():
with pytest.raises(ValueError) as e:
Normal("n", observed=[[1]], total_size=[2, Ellipsis, 2, 2])
assert "Length of" in str(e.value)
with pytest.raises(ValueError) as e:
Normal("n", observed=[[1]], total_size=[2, 2, 2])
assert "Length of" in str(e.value)
with pytest.raises(TypeError) as e:
Normal("n", observed=[[1]], total_size="foo")
assert "Unrecognized" in str(e.value)
with pytest.raises(TypeError) as e:
Normal("n", observed=[[1]], total_size=["foo"])
assert "Unrecognized" in str(e.value)
with pytest.raises(ValueError) as e:
Normal("n", observed=[[1]], total_size=[Ellipsis, Ellipsis])
assert "Double Ellipsis" in str(e.value)
def test_common_errors(self):
with pm.Model():
with pytest.raises(ValueError) as e:
Normal('n', observed=[[1]], total_size=[2, Ellipsis, 2, 2])
assert 'Length of' in str(e.value)
with pytest.raises(ValueError) as e:
Normal('n', observed=[[1]], total_size=[2, 2, 2])
assert 'Length of' in str(e.value)
with pytest.raises(TypeError) as e:
Normal('n', observed=[[1]], total_size='foo')
assert 'Unrecognized' in str(e.value)
with pytest.raises(TypeError) as e:
Normal('n', observed=[[1]], total_size=['foo'])
assert 'Unrecognized' in str(e.value)
with pytest.raises(ValueError) as e:
Normal('n', observed=[[1]], total_size=[Ellipsis, Ellipsis])
assert 'Double Ellipsis' in str(e.value)
def test_mixture_list_of_normals(self):
with Model() as model:
w = Dirichlet('w', floatX(np.ones_like(self.norm_w)))
mu = Normal('mu', 0., 10., shape=self.norm_w.size)
tau = Gamma('tau', 1., 1., shape=self.norm_w.size)
Mixture('x_obs', w,
[Normal.dist(mu[0], tau=tau[0]), Normal.dist(mu[1], tau=tau[1])],
observed=self.norm_x)
step = Metropolis()
trace = sample(3500, step, random_seed=self.random_seed,
progressbar=False, chains=1)
assert_allclose(np.sort(trace['w'].mean(axis=0)),
np.sort(self.norm_w),
rtol=0.1, atol=0.1)
assert_allclose(np.sort(trace['mu'].mean(axis=0)),
np.sort(self.norm_mu),
rtol=0.1, atol=0.1)
def test_allinmodel():
model1 = Model()
model2 = Model()
with model1:
x1 = Normal("x1", mu=0, sigma=1)
y1 = Normal("y1", mu=0, sigma=1)
with model2:
x2 = Normal("x2", mu=0, sigma=1)
y2 = Normal("y2", mu=0, sigma=1)
starting.allinmodel([x1, y1], model1)
starting.allinmodel([x1], model1)
with raises(ValueError, match=r"Some variables not in the model: \['x2', 'y2'\]"):
starting.allinmodel([x2, y2], model1)
with raises(ValueError, match=r"Some variables not in the model: \['x2'\]"):
starting.allinmodel([x2, y1], model1)
with raises(ValueError, match=r"Some variables not in the model: \['x2'\]"):
starting.allinmodel([x2], model1)
def test_mixture_list_of_normals(self):
with Model() as model:
w = Dirichlet("w", floatX(np.ones_like(self.norm_w)), shape=self.norm_w.size)
mu = Normal("mu", 0.0, 10.0, shape=self.norm_w.size)
tau = Gamma("tau", 1.0, 1.0, shape=self.norm_w.size)
Mixture(
"x_obs",
w,
[Normal.dist(mu[0], tau=tau[0]), Normal.dist(mu[1], tau=tau[1])],
observed=self.norm_x,
)
step = Metropolis()
trace = sample(5000, step, random_seed=self.random_seed, progressbar=False, chains=1)
assert_allclose(np.sort(trace["w"].mean(axis=0)), np.sort(self.norm_w), rtol=0.1, atol=0.1)
assert_allclose(
np.sort(trace["mu"].mean(axis=0)), np.sort(self.norm_mu), rtol=0.1, atol=0.1
)
def test_advi_minibatch():
n = 1000
sd0 = 2.
mu0 = 4.
sd = 3.
mu = -5.
data = sd * np.random.RandomState(0).randn(n) + mu
d = n / sd**2 + 1 / sd0**2
mu_post = (n * np.mean(data) / sd**2 + mu0 / sd0**2) / d
data_t = tt.vector()
data_t.tag.test_value = np.zeros(1, )
with Model() as model:
mu_ = Normal('mu', mu=mu0, sd=sd0, testval=0)
x = Normal('x', mu=mu_, sd=sd, observed=data_t)
minibatch_RVs = [x]
minibatch_tensors = [data_t]
def create_minibatch(data):
while True:
data = np.roll(data, 100, axis=0)
yield (data[:100], )
minibatches = create_minibatch(data)
with model:
advi_fit = advi_minibatch(n=1000,
minibatch_tensors=minibatch_tensors,
minibatch_RVs=minibatch_RVs,
minibatches=minibatches,
total_size=n,
learning_rate=1e-1,
random_seed=1)
np.testing.assert_allclose(advi_fit.means['mu'], mu_post, rtol=0.1)
trace = sample_vp(advi_fit, 10000)
np.testing.assert_allclose(np.mean(trace['mu']), mu_post, rtol=0.4)
np.testing.assert_allclose(np.std(trace['mu']), np.sqrt(1. / d), rtol=0.4)
def test_advi_minibatch():
n = 1000
sd0 = 2.
mu0 = 4.
sd = 3.
mu = -5.
data = sd * np.random.RandomState(0).randn(n) + mu
d = n / sd**2 + 1 / sd0**2
mu_post = (n * np.mean(data) / sd**2 + mu0 / sd0**2) / d
data_t = tt.vector()
data_t.tag.test_value = np.zeros(1, )
with Model() as model:
mu_ = Normal('mu', mu=mu0, sd=sd0, testval=0)
x = Normal('x', mu=mu_, sd=sd, observed=data_t)
# mu = Normal('mu', mu=0, sd=1, testval=0)
# sd = HalfNormal('sd', sd=1)
# n = Normal('n', mu=mu, sd=sd, observed=data_t)
minibatch_RVs = [x]
minibatch_tensors = [data_t]
def create_minibatch(data):
while True:
data = np.roll(data, 100, axis=0)
yield data[:100]
minibatches = [create_minibatch(data)]
means, sds, elbos = advi_minibatch(model=model,
n=1000,
minibatch_tensors=minibatch_tensors,
minibatch_RVs=minibatch_RVs,
minibatches=minibatches,
total_size=n,
learning_rate=1e-1,
seed=1)
np.testing.assert_allclose(means['mu'], mu_post, rtol=0.1)
def test_gradient_with_scaling(self):
with pm.Model() as model1:
genvar = generator(gen1())
m = Normal("m")
Normal("n", observed=genvar, total_size=1000)
grad1 = aesara.function([m.tag.value_var],
at.grad(model1.logpt, m.tag.value_var))
with pm.Model() as model2:
m = Normal("m")
shavar = aesara.shared(np.ones((1000, 100)))
Normal("n", observed=shavar)
grad2 = aesara.function([m.tag.value_var],
at.grad(model2.logpt, m.tag.value_var))
for i in range(10):
shavar.set_value(np.ones((100, 100)) * i)
g1 = grad1(1)
g2 = grad2(1)
np.testing.assert_almost_equal(g1, g2)
def linear_regression(data: Callable, samples=None) -> pm.Model:
x, y = data()
basic_model = pm.Model()
with basic_model:
# Define priors
sigma = HalfCauchy("sigma", beta=10, testval=1.0)
intercept = Normal("Intercept", 0, sigma=20)
x_coeff = Normal("x", 0, sigma=20)
likelihood = Normal("y", mu=intercept + x_coeff * x, sigma=sigma, observed=y)
map = map_estimation(basic_model, method="powell")
if samples is not None:
if not isinstance(samples, int):
raise (ValueError, "samples arg must be int")
elif samples < 50:
raise (ValueError, "samples, must be greater than 50")
else:
trace = pm.sample(samples)
traceplot(trace)
return basic_model, trace
def __init__(self, parent):
self.player = parent
X = np.loadtxt('AWS_collapsed.txt')
X = (X + 1) / 2
Freq = np.zeros(100)
#
for i in X:
Freq[int(np.ceil(i * 100))] += 1
#
X = np.linspace(0, 1, 100)
#
with pm.Model():
# Priors are posteriors from previous iteration
alpha = Normal('alpha', 0.5, 0.5)
beta = Normal('beta', 0.5, 0.5)
gamma = Normal('gamma', 0.5, 0.5)
delta = Normal('delta', 0.5, 0.5)
# self.trace = initialise_prior(X,Freq)
self.trace = pm.backends.text.load('AWS')
def test_normal_mixture_nd(self):
nd, ncomp = 3, 5
with Model() as model0:
mus = Normal('mus', shape=(nd, ncomp))
taus = Gamma('taus', alpha=1, beta=1, shape=(nd, ncomp))
ws = Dirichlet('ws', np.ones(ncomp))
mixture0 = NormalMixture('m', w=ws, mu=mus, tau=taus, shape=nd)
with Model() as model1:
mus = Normal('mus', shape=(nd, ncomp))
taus = Gamma('taus', alpha=1, beta=1, shape=(nd, ncomp))
ws = Dirichlet('ws', np.ones(ncomp))
comp_dist = [Normal.dist(mu=mus[:, i], tau=taus[:, i])
for i in range(ncomp)]
mixture1 = Mixture('m', w=ws, comp_dists=comp_dist, shape=nd)
testpoint = model0.test_point
testpoint['mus'] = np.random.randn(nd, ncomp)
assert_allclose(model0.logp(testpoint), model1.logp(testpoint))
assert_allclose(mixture0.logp(testpoint), mixture1.logp(testpoint))
def build_model():
y = shared(np.array([15, 10, 16, 11, 9, 11, 10, 18], dtype=np.float32))
with Model() as arma_model:
sigma = HalfCauchy('sigma', 5)
theta = Normal('theta', 0, sd=2)
phi = Normal('phi', 0, sd=2)
mu = Normal('mu', 0, sd=10)
err0 = y[0] - (mu + phi * mu)
def calc_next(last_y, this_y, err, mu, phi, theta):
nu_t = mu + phi * last_y + theta * err
return this_y - nu_t
err, _ = scan(fn=calc_next,
sequences=dict(input=y, taps=[-1, 0]),
outputs_info=[err0],
non_sequences=[mu, phi, theta])
Potential('like', Normal.dist(0, sd=sigma).logp(err))
mu, sds, elbo = variational.advi(n=2000)
return arma_model
theta = Normal('theta', 0, sd=2)
phi = Normal('phi', 0, sd=2)
mu = Normal('mu', 0, sd=10)
err0 = y[0] - (mu + phi*mu)
def calc_next(last_y, this_y, err, mu, phi, theta):
nu_t = mu + phi*last_y + theta*err
return this_y - nu_t
err, _ = scan(fn=calc_next,
sequences=dict(input=y, taps=[-1,0]),
outputs_info=[err0],
non_sequences=[mu, phi, theta])
like = Potential('like', Normal.dist(0, sd=sigma).logp(err))
with arma_model:
mu, sds, elbo = variational.advi(n=2000)
def run(n=1000):
if n == "short":
n = 50
with arma_model:
trace = sample(1000)
burn = n/10
traceplot(trace[burn:])
def test_normal_mixture_nd(self, nd, ncomp):
nd = to_tuple(nd)
ncomp = int(ncomp)
comp_shape = nd + (ncomp,)
test_mus = np.random.randn(*comp_shape)
test_taus = np.random.gamma(1, 1, size=comp_shape)
observed = generate_normal_mixture_data(w=np.ones(ncomp)/ncomp,
mu=test_mus,
sd=1/np.sqrt(test_taus),
size=10)
with Model() as model0:
mus = Normal('mus', shape=comp_shape)
taus = Gamma('taus', alpha=1, beta=1, shape=comp_shape)
ws = Dirichlet('ws', np.ones(ncomp))
mixture0 = NormalMixture('m', w=ws, mu=mus, tau=taus, shape=nd,
comp_shape=comp_shape)
obs0 = NormalMixture('obs', w=ws, mu=mus, tau=taus, shape=nd,
comp_shape=comp_shape,
observed=observed)
with Model() as model1:
mus = Normal('mus', shape=comp_shape)
taus = Gamma('taus', alpha=1, beta=1, shape=comp_shape)
ws = Dirichlet('ws', np.ones(ncomp))
comp_dist = [Normal.dist(mu=mus[..., i], tau=taus[..., i],
shape=nd)
for i in range(ncomp)]
mixture1 = Mixture('m', w=ws, comp_dists=comp_dist, shape=nd)
obs1 = Mixture('obs', w=ws, comp_dists=comp_dist, shape=nd,
observed=observed)
with Model() as model2:
# Expected to fail if comp_shape is not provided,
# nd is multidim and it does not broadcast with ncomp. If by chance
# it does broadcast, an error is raised if the mixture is given
# observed data.
# Furthermore, the Mixture will also raise errors when the observed
# data is multidimensional but it does not broadcast well with
# comp_dists.
mus = Normal('mus', shape=comp_shape)
taus = Gamma('taus', alpha=1, beta=1, shape=comp_shape)
ws = Dirichlet('ws', np.ones(ncomp))
if len(nd) > 1:
if nd[-1] != ncomp:
with pytest.raises(ValueError):
NormalMixture('m', w=ws, mu=mus, tau=taus,
shape=nd)
mixture2 = None
else:
mixture2 = NormalMixture('m', w=ws, mu=mus, tau=taus,
shape=nd)
else:
mixture2 = NormalMixture('m', w=ws, mu=mus, tau=taus,
shape=nd)
observed_fails = False
if len(nd) >= 1 and nd != (1,):
try:
np.broadcast(np.empty(comp_shape), observed)
except Exception:
observed_fails = True
if observed_fails:
with pytest.raises(ValueError):
NormalMixture('obs', w=ws, mu=mus, tau=taus,
shape=nd,
observed=observed)
obs2 = None
else:
obs2 = NormalMixture('obs', w=ws, mu=mus, tau=taus,
shape=nd,
observed=observed)
testpoint = model0.test_point
testpoint['mus'] = test_mus
testpoint['taus'] = test_taus
assert_allclose(model0.logp(testpoint), model1.logp(testpoint))
assert_allclose(mixture0.logp(testpoint), mixture1.logp(testpoint))
assert_allclose(obs0.logp(testpoint), obs1.logp(testpoint))
if mixture2 is not None and obs2 is not None:
assert_allclose(model0.logp(testpoint), model2.logp(testpoint))
if mixture2 is not None:
assert_allclose(mixture0.logp(testpoint), mixture2.logp(testpoint))
if obs2 is not None:
assert_allclose(obs0.logp(testpoint), obs2.logp(testpoint))
def test_mixture_of_mixture(self):
if theano.config.floatX == 'float32':
rtol = 1e-4
else:
rtol = 1e-7
nbr = 4
with Model() as model:
# mixtures components
g_comp = Normal.dist(
mu=Exponential('mu_g', lam=1.0, shape=nbr, transform=None),
sigma=1,
shape=nbr)
l_comp = Lognormal.dist(
mu=Exponential('mu_l', lam=1.0, shape=nbr, transform=None),
sigma=1,
shape=nbr)
# weight vector for the mixtures
g_w = Dirichlet('g_w', a=floatX(np.ones(nbr)*0.0000001), transform=None)
l_w = Dirichlet('l_w', a=floatX(np.ones(nbr)*0.0000001), transform=None)
# mixture components
g_mix = Mixture.dist(w=g_w, comp_dists=g_comp)
l_mix = Mixture.dist(w=l_w, comp_dists=l_comp)
# mixture of mixtures
mix_w = Dirichlet('mix_w', a=floatX(np.ones(2)), transform=None)
mix = Mixture('mix', w=mix_w,
comp_dists=[g_mix, l_mix],
observed=np.exp(self.norm_x))
test_point = model.test_point
def mixmixlogp(value, point):
floatX = theano.config.floatX
priorlogp = st.dirichlet.logpdf(x=point['g_w'],
alpha=np.ones(nbr)*0.0000001,
).astype(floatX) + \
st.expon.logpdf(x=point['mu_g']).sum(dtype=floatX) + \
st.dirichlet.logpdf(x=point['l_w'],
alpha=np.ones(nbr)*0.0000001,
).astype(floatX) + \
st.expon.logpdf(x=point['mu_l']).sum(dtype=floatX) + \
st.dirichlet.logpdf(x=point['mix_w'],
alpha=np.ones(2),
).astype(floatX)
complogp1 = st.norm.logpdf(x=value,
loc=point['mu_g']).astype(floatX)
mixlogp1 = logsumexp(np.log(point['g_w']).astype(floatX) +
complogp1,
axis=-1, keepdims=True)
complogp2 = st.lognorm.logpdf(value,
1.,
0.,
np.exp(point['mu_l'])).astype(floatX)
mixlogp2 = logsumexp(np.log(point['l_w']).astype(floatX) +
complogp2,
axis=-1, keepdims=True)
complogp_mix = np.concatenate((mixlogp1, mixlogp2), axis=1)
mixmixlogpg = logsumexp(np.log(point['mix_w']).astype(floatX) +
complogp_mix,
axis=-1, keepdims=True)
return priorlogp, mixmixlogpg
value = np.exp(self.norm_x)[:, None]
priorlogp, mixmixlogpg = mixmixlogp(value, test_point)
# check logp of mixture
assert_allclose(mixmixlogpg, mix.logp_elemwise(test_point),
rtol=rtol)
# check model logp
assert_allclose(priorlogp + mixmixlogpg.sum(),
model.logp(test_point),
rtol=rtol)
# check input and check logp again
test_point['g_w'] = np.asarray([.1, .1, .2, .6])
test_point['mu_g'] = np.exp(np.random.randn(nbr))
priorlogp, mixmixlogpg = mixmixlogp(value, test_point)
assert_allclose(mixmixlogpg, mix.logp_elemwise(test_point),
rtol=rtol)
assert_allclose(priorlogp + mixmixlogpg.sum(),
model.logp(test_point),
rtol=rtol)