def test_bug170030378(self):
n_item = 50
n_rater = 7
stream = test_util.test_seed_stream()
weight = self.evaluate(
tfd.Sample(tfd.Dirichlet([0.25, 0.25]), n_item).sample(seed=stream()))
mixture_dist = tfd.Categorical(probs=weight) # batch_shape=[50]
rater_sensitivity = self.evaluate(
tfd.Sample(tfd.Beta(5., 1.), n_rater).sample(seed=stream()))
rater_specificity = self.evaluate(
tfd.Sample(tfd.Beta(2., 5.), n_rater).sample(seed=stream()))
probs = tf.stack([rater_sensitivity, rater_specificity])[None, ...]
components_dist = tfd.BatchBroadcast( # batch_shape=[50, 2]
tfd.Independent(tfd.Bernoulli(probs=probs),
reinterpreted_batch_ndims=1),
[50, 2])
obs_dist = tfd.MixtureSameFamily(mixture_dist, components_dist)
observed = self.evaluate(obs_dist.sample(seed=stream()))
mixture_logp = obs_dist.log_prob(observed)
expected_logp = tf.math.reduce_logsumexp(
tf.math.log(weight) + components_dist.distribution.log_prob(
observed[:, None, ...]),
axis=-1)
self.assertAllClose(expected_logp, mixture_logp)
def testSigmoidBetaTargetConservation(self):
# Not inverting the sigmoid bijector makes a kooky distribution, but nuts
# should still conserve it (with a smaller step size).
sigmoid_beta_dist = tfb.Identity(tfb.Sigmoid())(
tfd.Beta(concentration0=1., concentration1=2.))
self.evaluate(assert_univariate_target_conservation(
self, sigmoid_beta_dist, step_size=0.02))
def new(params,
event_shape=(),
alpha_activation=tf.nn.softplus,
beta_activation=tf.nn.softplus,
clip_for_stable=True,
validate_args=False,
name="BetaLayer"):
r"""Create the distribution instance from a `params` vector."""
params = tf.convert_to_tensor(value=params, name='params')
alpha_activation = parse_activation(alpha_activation, 'tf')
beta_activation = parse_activation(beta_activation, 'tf')
event_shape = dist_util.expand_to_vector(
tf.convert_to_tensor(value=event_shape,
name='event_shape',
dtype=tf.int32),
tensor_name='event_shape',
)
output_shape = tf.concat(
[tf.shape(input=params)[:-1], event_shape],
axis=0,
)
# alpha, beta
concentration1, concentration0 = tf.split(params, 2, axis=-1)
concentration1 = alpha_activation(concentration1)
concentration0 = beta_activation(concentration0)
if clip_for_stable:
concentration0 = tf.clip_by_value(concentration0, 1e-3, 1e3)
concentration1 = tf.clip_by_value(concentration1, 1e-3, 1e3)
return tfd.Independent(
tfd.Beta(concentration1=tf.reshape(concentration1, output_shape),
concentration0=tf.reshape(concentration0, output_shape),
validate_args=validate_args),
reinterpreted_batch_ndims=tf.size(input=event_shape),
name=name,
)
def testLogitBetaTargetConservation(self):
logit_beta_dist = tfb.Invert(tfb.Sigmoid())(tfd.Beta(
concentration0=1., concentration1=2.))
self.evaluate(
assert_univariate_target_conservation(self,
logit_beta_dist,
step_size=0.2))
def testBetaTargetConservation(self):
# Not that we expect NUTS to do a good job without an unconstraining
# bijector, but...
beta_dist = tfd.Beta(concentration0=1., concentration1=2.)
self.evaluate(
assert_univariate_target_conservation(self,
beta_dist,
step_size=1e-3))
def testMode(self):
dist = self._cls()(tfd.Beta(concentration1=[5., 10.],
concentration0=15.,
validate_args=True),
tfb.Shift(2., validate_args=True)(tfb.Scale(
10., validate_args=True)),
validate_args=True)
self.assertAllClose(2. + 10. * dist.distribution.mode(),
self.evaluate(dist.mode()),
atol=0.,
rtol=1e-6)
def test_support_works_correctly_with_HMC(self):
num_results = 2000
target = tfd.Beta(concentration1=self.dtype(1.),
concentration0=self.dtype(10.))
transformed_hmc = tfp.mcmc.TransformedTransitionKernel(
inner_kernel=tfp.mcmc.HamiltonianMonteCarlo(
target_log_prob_fn=tf.function(target.log_prob,
autograph=False),
step_size=1.64,
num_leapfrog_steps=2,
seed=_maybe_seed(55)),
bijector=tfb.Sigmoid())
# Recall, tfp.mcmc.sample_chain calls
# transformed_hmc.bootstrap_results too.
states, kernel_results = tfp.mcmc.sample_chain(
num_results=num_results,
# The initial state is used by inner_kernel.bootstrap_results.
# Note the input is *after* bijector.forward.
current_state=self.dtype(0.25),
kernel=transformed_hmc,
num_burnin_steps=200,
num_steps_between_results=1,
parallel_iterations=1)
self.assertEqual(num_results,
tf.compat.dimension_value(states.shape[0]))
sample_mean = tf.reduce_mean(states, axis=0)
sample_var = tf.reduce_mean(tf.math.squared_difference(
states, sample_mean),
axis=0)
[
sample_mean_,
sample_var_,
is_accepted_,
true_mean_,
true_var_,
] = self.evaluate([
sample_mean,
sample_var,
kernel_results.inner_results.is_accepted,
target.mean(),
target.variance(),
])
self.assertAllClose(true_mean_, sample_mean_, atol=0.06, rtol=0.)
self.assertAllClose(true_var_, sample_var_, atol=0.01, rtol=0.1)
self.assertNear(0.6, is_accepted_.mean(), err=0.05)
def stochastic_volatility_prior_fn(num_timesteps):
"""Generative process for the stochastic volatility model."""
persistence_of_volatility = yield Root(
tfb.Shift(-1.)(tfb.Scale(2.)(tfd.Beta(
concentration1=20.,
concentration0=1.5,
name='persistence_of_volatility'))))
mean_log_volatility = yield Root(
tfd.Cauchy(loc=0., scale=5., name='mean_log_volatility'))
white_noise_shock_scale = yield Root(
tfd.HalfCauchy(loc=0., scale=2., name='white_noise_shock_scale'))
_ = yield tfd.JointDistributionCoroutine(functools.partial(
autoregressive_series_fn,
num_timesteps=num_timesteps,
mean=mean_log_volatility,
noise_scale=white_noise_shock_scale,
persistence=persistence_of_volatility),
name='log_volatility')
def test_support_works_correctly_with_rwm(self):
num_results = 500
target = tfd.Beta(
concentration1=self.dtype(1.),
concentration0=self.dtype(10.))
transformed_rwm = tfp.mcmc.TransformedTransitionKernel(
inner_kernel=tfp.mcmc.RandomWalkMetropolis(
target_log_prob_fn=tf.function(target.log_prob, autograph=False),
new_state_fn=tfp.mcmc.random_walk_normal_fn(scale=1.5)),
bijector=tfb.Sigmoid())
# Recall, tfp.mcmc.sample_chain calls
# transformed_hmc.bootstrap_results too.
states = tfp.mcmc.sample_chain(
num_results=num_results,
# The initial state is used by inner_kernel.bootstrap_results.
# Note the input is *after* bijector.forward.
current_state=self.dtype(0.25),
kernel=transformed_rwm,
num_burnin_steps=200,
num_steps_between_results=1,
trace_fn=None,
seed=test_util.test_seed())
self.assertEqual(num_results, tf.compat.dimension_value(states.shape[0]))
sample_mean = tf.reduce_mean(states, axis=0)
sample_var = tf.reduce_mean(
tf.math.squared_difference(states, sample_mean), axis=0)
[
sample_mean_,
sample_var_,
true_mean_,
true_var_,
] = self.evaluate([
sample_mean,
sample_var,
target.mean(),
target.variance(),
])
self.assertAllClose(true_mean_, sample_mean_,
atol=0.15, rtol=0.)
self.assertAllClose(true_var_, sample_var_,
atol=0.03, rtol=0.2)
def test_support_works_correctly_with_MALA(self):
num_results = 2000
target = tfd.Beta(concentration1=self.dtype(1.),
concentration0=self.dtype(10.))
transformed_mala = tfp.mcmc.TransformedTransitionKernel(
inner_kernel=tfp.mcmc.MetropolisAdjustedLangevinAlgorithm(
target_log_prob_fn=tf.function(target.log_prob,
autograph=False),
step_size=1.,
seed=_maybe_seed(test_util.test_seed())),
bijector=tfb.Sigmoid())
# Recall, tfp.mcmc.sample_chain calls
# transformed_hmc.bootstrap_results too.
states, _ = tfp.mcmc.sample_chain(
num_results=num_results,
# The initial state is used by inner_kernel.bootstrap_results.
# Note the input is *after* bijector.forward.
current_state=self.dtype(0.25),
kernel=transformed_mala,
num_burnin_steps=200,
num_steps_between_results=1,
parallel_iterations=1)
self.assertEqual(num_results,
tf.compat.dimension_value(states.shape[0]))
sample_mean = tf.reduce_mean(states, axis=0)
sample_var = tf.reduce_mean(tf.math.squared_difference(
states, sample_mean),
axis=0)
[
sample_mean_,
sample_var_,
true_mean_,
true_var_,
] = self.evaluate([
sample_mean,
sample_var,
target.mean(),
target.variance(),
])
self.assertAllClose(true_mean_, sample_mean_, atol=0.06, rtol=0.)
self.assertAllClose(true_var_, sample_var_, atol=0.01, rtol=0.1)
def test_batch_slicing(self):
# pylint: disable=bad-whitespace
d = tfd.JointDistributionNamed(dict(
s=tfd.Exponential(rate=[10, 12, 14]),
n=lambda s: tfd.Normal(loc=0, scale=s),
x=lambda: tfd.Beta(concentration0=[3, 2, 1], concentration1=1)),
validate_args=True)
# pylint: enable=bad-whitespace
d0, d1 = d[:1], d[1:]
x0 = d0.sample(seed=test_util.test_seed())
x1 = d1.sample(seed=test_util.test_seed())
self.assertLen(x0, 3)
self.assertEqual([1], x0['s'].shape)
self.assertEqual([1], x0['n'].shape)
self.assertEqual([1], x0['x'].shape)
self.assertLen(x1, 3)
self.assertEqual([2], x1['s'].shape)
self.assertEqual([2], x1['n'].shape)
self.assertEqual([2], x1['x'].shape)
def __body(w_, e_, mask, b):
e = math_ops.cast(distributions.Beta((self.__mf - 1.0) / 2.0,
(self.__mf - 1.0) / 2.0).
sample(shape, seed=seed), dtype=self.dtype)
u = random_ops.random_uniform(shape, dtype=self.dtype, seed=seed)
w = (1.0 - (1.0 + b) * e) / (1.0 - (1.0 - b) * e)
x = (1.0 - b) / (1.0 + b)
c = self.scale * x + (self.__mf - 1) * math_ops.log1p(-x**2)
tmp = tf.clip_by_value(x * w, 0, 1 - 1e-16)
reject = gen_math_ops.less(((self.__mf - 1.0) * math_ops.log(1.0 - tmp) +
self.scale * w - c),
math_ops.log(u))
accept = gen_math_ops.logical_not(reject)
w_ = array_ops.where(gen_math_ops.logical_and(mask, accept), w, w_)
e_ = array_ops.where(gen_math_ops.logical_and(mask, accept), e, e_)
mask = array_ops.where(gen_math_ops.logical_and(mask, accept),
reject, mask)
return w_, e_, mask, b
def mk_sigmoid_beta():
beta = tfd.Beta(concentration0=1., concentration1=2.)
# Not inverting the sigmoid bijector makes a kooky distribution, but
# nuts should still conserve it (with a smaller step size).
return tfb.Sigmoid()(beta)
def mk_logit_beta():
beta = tfd.Beta(concentration0=1., concentration1=2.)
return tfb.Invert(tfb.Sigmoid())(beta)