def stable_model():
zero = torch.zeros(2)
a = pyro.sample("a", dist.Normal(0, 1))
b = pyro.sample("b", dist.LogNormal(0, 1))
c = pyro.sample("c", dist.Stable(1.5, 0.0, b, a))
d = pyro.sample("d", dist.Stable(1.5, 0.0, b, 0.0), obs=a)
e = pyro.sample("e", dist.Stable(1.5, 0.1, b, a))
f = pyro.sample("f", dist.Stable(1.5, 0.1, b, 0.0), obs=a)
g = pyro.sample("g", dist.Stable(1.5, zero, b, a).to_event(1))
h = pyro.sample("h", dist.Stable(1.5, zero, b, 0).to_event(1), obs=a)
i = pyro.sample(
"i",
dist.TransformedDistribution(dist.Stable(1.5, 0, b, a),
dist.transforms.ExpTransform()),
)
j = pyro.sample(
"j",
dist.TransformedDistribution(dist.Stable(1.5, 0, b, a),
dist.transforms.ExpTransform()),
obs=a.exp(),
)
k = pyro.sample(
"k",
dist.TransformedDistribution(dist.Stable(
1.5, zero, b, a), dist.transforms.ExpTransform()).to_event(1),
)
l = pyro.sample(
"l",
dist.TransformedDistribution(dist.Stable(
1.5, zero, b, a), dist.transforms.ExpTransform()).to_event(1),
obs=a.exp() + zero,
)
return a, b, c, d, e, f, g, h, i, j, k, l
def model(self, zero_data, covariates):
with pyro.plate("batch", len(zero_data), dim=-2):
zero_data = pyro.subsample(zero_data, event_dim=1)
covariates = pyro.subsample(covariates, event_dim=1)
loc = zero_data[..., :1, :]
scale = pyro.sample("scale", dist.LogNormal(loc, 1).to_event(1))
with self.time_plate:
jumps = pyro.sample("jumps", dist.Normal(0, scale).to_event(1))
prediction = jumps.cumsum(-2)
duration, obs_dim = zero_data.shape[-2:]
noise_dist = dist.LinearHMM(
dist.Stable(1.9, 0).expand([obs_dim]).to_event(1),
torch.eye(obs_dim),
dist.Stable(1.9, 0).expand([obs_dim]).to_event(1),
torch.eye(obs_dim),
dist.Stable(1.9, 0).expand([obs_dim]).to_event(1),
duration=duration,
)
rep = StableReparam()
with poutine.reparam(
config={"residual": LinearHMMReparam(rep, rep, rep)}):
self.predict(noise_dist, prediction)
def test_additive(stability, skew0, skew1, scale0, scale1):
num_samples = 10000
d0 = dist.Stable(stability, skew0, scale0, coords="S")
d1 = dist.Stable(stability, skew1, scale1, coords="S")
expected = d0.sample([num_samples]) + d1.sample([num_samples])
scale = (scale0**stability + scale1**stability)**(1 / stability)
skew = ((skew0 * scale0**stability + skew1 * scale1**stability) /
(scale0**stability + scale1**stability))
d = dist.Stable(stability, skew, scale, coords="S")
actual = d.sample([num_samples])
assert ks_2samp(expected, actual).pvalue > 0.05
def model():
stability = pyro.sample("stability", dist.Uniform(1.0, 2.0))
trans_skew = pyro.sample("trans_skew", dist.Uniform(-1.0, 1.0))
obs_skew = pyro.sample("obs_skew", dist.Uniform(-1.0, 1.0))
scale = pyro.sample("scale", dist.Gamma(3, 1))
# We use separate plates because the .cumsum() op breaks independence.
with pyro.plate("time1", len(data)):
dz = pyro.sample("dz", dist.Stable(stability, trans_skew))
z = dz.cumsum(-1)
with pyro.plate("time2", len(data)):
y = pyro.sample("y", dist.Stable(stability, obs_skew, scale, z))
pyro.sample("x", dist.Poisson(y.abs()), obs=data)
def test_sample(alpha, beta):
num_samples = 100
d = dist.Stable(alpha, beta, coords="S")
def sampler(size):
# Temporarily increase radius to test hole-patching logic.
# Scipy doesn't handle values of alpha very close to 1.
try:
old = pyro.distributions.stable.RADIUS
pyro.distributions.stable.RADIUS = 0.02
return d.sample([size])
finally:
pyro.distributions.stable.RADIUS = old
def cdf(x):
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", category=IntegrationWarning)
result = levy_stable.cdf(x, alpha, beta)
# Scipy has only an experimental .cdf() function for alpha=1, beta!=0.
# It sometimes passes and sometimes xfails.
if w and alpha == 1 and beta != 0:
pytest.xfail(reason="scipy.stats.levy_stable.cdf is unstable")
return result
assert kstest(sampler, cdf, N=num_samples).pvalue > 0.1
def model(self, zero_data, covariates):
duration,data_dim = zero_data.shape
feature_dim = covariates.size(-1)
drift_stability = pyro.sample("drift_stability", dist.Uniform(1, 2))
drift_scale = pyro.sample("drift_scale", dist.LogNormal(-20, 5))
with pyro.plate("item", data_dim, dim=-2):
bias = pyro.sample("bias", dist.Normal(5.0, 10.0))
with pyro.plate('features',feature_dim,dim=-1):
weight = pyro.sample("weight", dist.Normal(0.0, 5))
# We'll sample a time-global scale parameter outside the time plate,
# then time-local iid noise inside the time plate.
with self.time_plate:
# We combine two different reparameterizers: the inner SymmetricStableReparam
# is needed for the Stable site, and the outer LocScaleReparam is optional but
# appears to improve inference.
with poutine.reparam(config={"drift": LocScaleReparam()}):
with poutine.reparam(config={"drift": SymmetricStableReparam()}):
drift = pyro.sample("drift",
dist.Stable(drift_stability, 0, drift_scale))
motion = drift.cumsum(-1) # A Brownian motion.
# The prediction now includes three terms.
regression = torch.matmul(covariates, weight[...,None])
prediction = motion + bias + regression.sum(axis=-1)
prediction = prediction.unsqueeze(-1).transpose(-1, -3)
# Finally we can construct a noise distribution.
# We will share parameters across all time series.
obs_scale = pyro.sample("obs_scale", dist.LogNormal(-5, 5))
noise_dist = dist.Normal(loc=0.0, scale=obs_scale.unsqueeze(-1))
self.predict(noise_dist, prediction)
def test_sample(alpha, beta):
num_samples = 100
d = dist.Stable(alpha, beta)
def sampler(size):
# Temporarily increase radius to test hole-patching logic.
# Scipy doesn't handle values of alpha very close to 1.
try:
old = pyro.distributions.stable.RADIUS
pyro.distributions.stable.RADIUS = 0.02
x = d.sample([size])
finally:
pyro.distributions.stable.RADIUS = old
# Convert from Nolan's parametrization S^0 to scipy parametrization S.
if alpha == 1:
z = x
else:
z = x + beta * np.tan(np.pi / 2 * alpha)
return z
def cdf(x):
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always", category=IntegrationWarning)
result = levy_stable.cdf(x, alpha, beta)
# Scipy has only an experimental .cdf() function for alpha=1, beta!=0.
# It sometimes passes and sometimes xfails.
if w and alpha == 1 and beta != 0:
pytest.xfail(reason="scipy.stats.levy_stable.cdf is unstable")
return result
stat, pvalue = kstest(sampler, cdf, N=num_samples)
assert pvalue > 0.1, pvalue
def test_mean(stability, skew, scale, coords):
loc = torch.randn(10)
d = dist.Stable(stability, skew, scale, loc, coords=coords)
if stability <= 1:
assert torch.isnan(d.mean).all()
else:
expected = d.sample((100000, )).mean(0)
assert_close(d.mean, expected, atol=0.1)
def test_variance(stability, scale):
skew = dist.Uniform(-1, 1).sample((10, ))
loc = torch.randn(10)
d = dist.Stable(stability, skew, scale, loc)
if stability < 2:
assert torch.isinf(d.variance).all()
else:
expected = d.sample((100000, )).var(0)
assert_close(d.variance, expected, rtol=0.02)
def test_shape(sample_shape, batch_shape):
stability = torch.empty(batch_shape).uniform_(0, 2).requires_grad_()
skew = torch.empty(batch_shape).uniform_(-1, 1).requires_grad_()
scale = torch.randn(batch_shape).exp().requires_grad_()
loc = torch.randn(batch_shape).requires_grad_()
d = dist.Stable(stability, skew, scale, loc)
assert d.batch_shape == batch_shape
x = d.rsample(sample_shape)
assert x.shape == sample_shape + batch_shape
x.sum().backward()
def test_sample_2(alpha, beta):
num_samples = 10000
d = dist.Stable(alpha, beta, coords="S")
# Temporarily increase radius to test hole-patching logic.
# Scipy doesn't handle values of alpha very close to 1.
try:
old = pyro.distributions.stable.RADIUS
pyro.distributions.stable.RADIUS = 0.02
actual = d.sample([num_samples])
finally:
pyro.distributions.stable.RADIUS = old
actual = d.sample([num_samples])
expected = levy_stable.rvs(alpha, beta, size=num_samples)
assert ks_2samp(expected, actual).pvalue > 0.05
def model(self, zero_data, covariates):
duration, data_dim = zero_data.shape
# Let's model each time series as a Levy stable process, and share process parameters
# across time series. To do that in Pyro, we'll declare the shared random variables
# outside of the "origin" plate:
drift_stability = pyro.sample("drift_stability", dist.Uniform(1, 2))
drift_scale = pyro.sample("drift_scale", dist.LogNormal(-20, 5))
with pyro.plate("origin", data_dim, dim=-2):
# Now inside of the origin plate we sample drift and seasonal components.
# All the time series inside the "origin" plate are independent,
# given the drift parameters above.
with self.time_plate:
# We combine two different reparameterizers: the inner SymmetricStableReparam
# is needed for the Stable site, and the outer LocScaleReparam is optional but
# appears to improve inference.
with poutine.reparam(config={"drift": LocScaleReparam()}):
with poutine.reparam(config={"drift": SymmetricStableReparam()}):
drift = pyro.sample("drift",
dist.Stable(drift_stability, 0, drift_scale))
with pyro.plate("hour_of_week", 24 * 7, dim=-1):
seasonal = pyro.sample("seasonal", dist.Normal(0, 5))
# Now outside of the time plate we can perform time-dependent operations like
# integrating over time. This allows us to create a motion with slow drift.
seasonal = periodic_repeat(seasonal, duration, dim=-1)
motion = drift.cumsum(dim=-1) # A Levy stable motion to model shocks.
prediction = motion + seasonal
# Next we do some reshaping. Pyro's forecasting framework assumes all data is
# multivariate of shape (duration, data_dim), but the above code uses an "origins"
# plate that is left of the time_plate. Our prediction starts off with shape
assert prediction.shape[-2:] == (data_dim, duration)
# We need to swap those dimensions but keep the -2 dimension intact, in case Pyro
# adds sample dimensions to the left of that.
prediction = prediction.unsqueeze(-1).transpose(-1, -3)
assert prediction.shape[-3:] == (1, duration, data_dim), prediction.shape
# Finally we can construct a noise distribution.
# We will share parameters across all time series.
obs_scale = pyro.sample("obs_scale", dist.LogNormal(-5, 5))
noise_dist = dist.Normal(0, obs_scale.unsqueeze(-1))
self.predict(noise_dist, prediction)
def model(self, zero_data, covariates):
data_dim = zero_data.size(-1)
feature_dim = covariates.size(-1)
bias = pyro.sample("bias", dist.Normal(5.0, 10.0).expand((data_dim,)).to_event(1))
weight = pyro.sample("weight", dist.Normal(0.0, 5).expand((feature_dim,)).to_event(1))
# We'll sample a time-global scale parameter outside the time plate,
# then time-local iid noise inside the time plate.
drift_scale = pyro.sample("drift_scale",
dist.LogNormal(0, 5.0).expand((1,)).to_event(1))
with self.time_plate:
# We'll use a reparameterizer to improve variational fit. The model would still be
# correct if you removed this context manager, but the fit appears to be worse.
with poutine.reparam(config={"drift": LocScaleReparam()}):
drift = pyro.sample("drift", dist.Normal(zero_data.double(), drift_scale.double()).to_event(1))
# After we sample the iid "drift" noise we can combine it in any time-dependent way.
# It is important to keep everything inside the plate independent and apply dependent
# transforms outside the plate.
motion = drift.cumsum(-2) # A Brownian motion.
# The prediction now includes three terms.
prediction = motion + bias + (weight * covariates).sum(-1, keepdim=True)
assert prediction.shape[-2:] == zero_data.shape
# The next part of the model creates a likelihood or noise distribution.
# Again we'll be Bayesian and write this as a probabilistic program with
# priors over parameters.
stability = pyro.sample("noise_stability", dist.Uniform(1, 2).expand((1,)).to_event(1))
skew = pyro.sample("noise_skew", dist.Uniform(-1, 1).expand((1,)).to_event(1))
scale = pyro.sample("noise_scale", dist.LogNormal(-5, 5).expand((1,)).to_event(1))
noise_dist = dist.Stable(stability, skew, scale)
# We need to use a reparameterizer to handle the Stable distribution.
# Note "residual" is the name of Pyro's internal sample site in self.predict().
with poutine.reparam(config={"residual": StableReparam()}):
self.predict(noise_dist, prediction)
def model():
stability = pyro.sample("stability", dist.Uniform(0., 2.))
skew = pyro.sample("skew", dist.Uniform(-1., 1.))
y = pyro.sample("z", dist.Stable(stability, skew))
pyro.sample("x", dist.Poisson(y.abs()), obs=torch.tensor(1.))
def random_stable(shape, stability, skew=None):
if skew is None:
skew = dist.Uniform(-1, 1).sample(shape)
scale = torch.rand(shape).exp()
loc = torch.randn(shape)
return dist.Stable(stability, skew, scale, loc)
def model():
with pyro.plate_stack("plates", shape):
with pyro.plate("particles", 200000):
return pyro.sample("x", dist.Stable(stability, 0, scale, loc))
def model():
return pyro.sample("x", dist.Stable(stability, skew))
def model():
with poutine.reparam(config={"x": Reparam()}):
with pyro.plate("plate", 10):
return pyro.sample("x", dist.Stable(1.5, 0))
def test_normal(loc, scale):
num_samples = 100000
expected = dist.Normal(loc, scale).sample([num_samples])
actual = dist.Stable(2, 0, scale * 0.5**0.5, loc).sample([num_samples])
assert_close(actual.mean(), expected.mean(), atol=0.01)
assert_close(actual.std(), expected.std(), atol=0.01)
def random_stable(stability, skew_scale_loc_shape):
skew = dist.Uniform(-1, 1).sample(skew_scale_loc_shape)
scale = torch.rand(skew_scale_loc_shape).exp()
loc = torch.randn(skew_scale_loc_shape)
return dist.Stable(stability, skew, scale, loc)
def model():
with pyro.plate("particles", 20000):
return pyro.sample("x", dist.Stable(stability, skew))
