The intent of this notebook is to help TFP 0.12.1 "come to life" via some small snippets - little demos of things you can achieve with TFP.
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Installs & imports
!pip3 install -qU tensorflow==2.4.0 tensorflow_probability==0.12.1 tensorflow-datasets inference_gym
import tensorflow as tf
import tensorflow_probability as tfp
assert '0.12' in tfp.__version__, tfp.__version__
assert '2.4' in tf.__version__, tf.__version__
physical_devices = tf.config.list_physical_devices('CPU')
tf.config.set_logical_device_configuration(
physical_devices[0],
[tf.config.LogicalDeviceConfiguration(),
tf.config.LogicalDeviceConfiguration()])
tfd = tfp.distributions
tfb = tfp.bijectors
tfpk = tfp.math.psd_kernels
import matplotlib.pyplot as plt
import numpy as np
import scipy.interpolate
import IPython
import seaborn as sns
from inference_gym import using_tensorflow as gym
import logging
Bijectors
Glow
A bijector from the paper Glow: Generative Flow with Invertible 1x1 Convolutions, by Kingma and Dhariwal.
Here is how to draw an image from a distribution (note that the distribution has not "learned" anything here).
image_shape = (32, 32, 4) # 32 x 32 RGBA image
glow = tfb.Glow(output_shape=image_shape,
coupling_bijector_fn=tfb.GlowDefaultNetwork,
exit_bijector_fn=tfb.GlowDefaultExitNetwork)
pz = tfd.Sample(tfd.Normal(0., 1.), tf.reduce_prod(image_shape))
# Calling glow on distribution p(z) creates our glow distribution over images.
px = glow(pz)
# Take samples from the distribution to get images from your dataset.
image = px.sample(1)[0].numpy()
# Rescale to [0, 1].
image = (image - image.min()) / (image.max() - image.min())
plt.imshow(image);
RayleighCDF
Bijector for the Rayleigh distribution's CDF. One use is sampling from the Rayleigh distribution, by taking uniform samples, then passing them through the inverse of the CDF.
bij = tfb.RayleighCDF()
uniforms = tfd.Uniform().sample(10_000)
plt.hist(bij.inverse(uniforms), bins='auto');
Ascending() replaces Invert(Ordered())
x = tfd.Normal(0., 1.).sample(5)
print(tfb.Ascending()(x))
print(tfb.Invert(tfb.Ordered())(x))
tf.Tensor([1.9363368 2.650928 3.4936204 4.1817293 5.6920815], shape=(5,), dtype=float32) WARNING:tensorflow:From <ipython-input-5-1406b9939c00>:3: Ordered.__init__ (from tensorflow_probability.python.bijectors.ordered) is deprecated and will be removed after 2021-01-09. Instructions for updating: `Ordered` bijector is deprecated; please use `tfb.Invert(tfb.Ascending())` instead. tf.Tensor([1.9363368 2.650928 3.4936204 4.1817293 5.6920815], shape=(5,), dtype=float32)
Add low arg: Softplus(low=2.)
x = tf.linspace(-4., 4., 100)
for low in (-1., 0., 1.):
bij = tfb.Softplus(low=low)
plt.plot(x, bij(x));
tfb.ScaleMatvecLinearOperatorBlock supports blockwise LinearOperator, multi-part args
op_1 = tf.linalg.LinearOperatorDiag(diag=[1., -1., 3.])
op_2 = tf.linalg.LinearOperatorFullMatrix([[12., 5.], [-1., 3.]])
scale = tf.linalg.LinearOperatorBlockDiag([op_1, op_2], is_non_singular=True)
bij = tfb.ScaleMatvecLinearOperatorBlock(scale)
bij([[1., 2., 3.], [0., 1.]])
WARNING:tensorflow:From /usr/local/lib/python3.6/dist-packages/tensorflow/python/ops/linalg/linear_operator_block_diag.py:223: LinearOperator.graph_parents (from tensorflow.python.ops.linalg.linear_operator) is deprecated and will be removed in a future version. Instructions for updating: Do not call `graph_parents`. [<tf.Tensor: shape=(3,), dtype=float32, numpy=array([ 1., -2., 9.], dtype=float32)>, <tf.Tensor: shape=(2,), dtype=float32, numpy=array([5., 3.], dtype=float32)>]
Distributions
Skellam
Distribution over differences of two Poisson RVs. Note that samples from this distribution can be negative.
x = tf.linspace(-5., 10., 10 - -5 + 1)
rates = (4, 2)
for i, rate in enumerate(rates):
plt.bar(x - .3 * (1 - i), tfd.Poisson(rate).prob(x), label=f'Poisson({rate})', alpha=0.5, width=.3)
plt.bar(x.numpy() + .3, tfd.Skellam(*rates).prob(x).numpy(), color='k', alpha=0.25, width=.3,
label=f'Skellam{rates}')
plt.legend();
JointDistributionCoroutine[AutoBatched] produce namedtuple-like samples
Explicitly specify sample_dtype=[...] for the old tuple behavior.
@tfd.JointDistributionCoroutineAutoBatched
def model():
x = yield tfd.Normal(0., 1., name='x')
y = x + 4.
yield tfd.Normal(y, 1., name='y')
draw = model.sample(10_000)
plt.hist(draw.x, bins='auto', alpha=0.5)
plt.hist(draw.y, bins='auto', alpha=0.5);
WARNING:tensorflow:Note that RandomStandardNormal inside pfor op may not give same output as inside a sequential loop. WARNING:tensorflow:Note that RandomStandardNormal inside pfor op may not give same output as inside a sequential loop.
VonMisesFisher supports dim > 5, entropy()
The von Mises-Fisher distribution is a distribution on the \(n-1\) dimensional sphere in \(\mathbb{R}^n\).
dist = tfd.VonMisesFisher([0., 1, 0, 1, 0, 1], concentration=1.)
draws = dist.sample(3)
print(dist.entropy())
tf.reduce_sum(draws ** 2, axis=1) # each draw has length 1
tf.Tensor(3.3533673, shape=(), dtype=float32) <tf.Tensor: shape=(3,), dtype=float32, numpy=array([1.0000002 , 0.99999994, 1.0000001 ], dtype=float32)>
ExpGamma, ExpInverseGamma
log_rate parameter added to Gamma.
Numerical improvements when sampling low-concentration Beta, Dirichlet & friends. Implicit reparameterization gradients in all cases.
plt.figure(figsize=(10, 3))
plt.subplot(121)
plt.hist(tfd.Beta(.02, .02).sample(10_000), bins='auto')
plt.title('Beta(.02, .02)')
plt.subplot(122)
plt.title('GamX/(GamX+GamY) [the old way]')
g = tfd.Gamma(.02, 1); s0, s1 = g.sample(10_000), g.sample(10_000)
plt.hist(s0 / (s0 + s1), bins='auto')
plt.show()
plt.figure(figsize=(10, 3))
plt.subplot(121)
plt.hist(tfd.ExpGamma(.02, 1.).sample(10_000), bins='auto')
plt.title('ExpGamma(.02, 1)')
plt.subplot(122)
plt.hist(tfb.Log()(tfd.Gamma(.02, 1.)).sample(10_000), bins='auto')
plt.title('tfb.Log()(Gamma(.02, 1)) [the old way]');
JointDistribution*AutoBatched support reproducible sampling (with length-2 tuple/Tensor seeds)
@tfd.JointDistributionCoroutineAutoBatched
def model():
x = yield tfd.Normal(0, 1, name='x')
y = yield tfd.Normal(x + 4, 1, name='y')
print(model.sample(seed=(1, 2)))
print(model.sample(seed=(1, 2)))
StructTuple( x=<tf.Tensor: shape=(), dtype=float32, numpy=-0.59835213>, y=<tf.Tensor: shape=(), dtype=float32, numpy=6.2380724> ) StructTuple( x=<tf.Tensor: shape=(), dtype=float32, numpy=-0.59835213>, y=<tf.Tensor: shape=(), dtype=float32, numpy=6.2380724> )
KL(VonMisesFisher || SphericalUniform)
# Build vMFs with the same mean direction, batch of increasing concentrations.
vmf = tfd.VonMisesFisher(tf.math.l2_normalize(tf.random.normal([10])),
concentration=[0., .1, 1., 10.])
# KL increases with concentration, since vMF(conc=0) == SphericalUniform.
print(tfd.kl_divergence(vmf, tfd.SphericalUniform(10)))
tf.Tensor([4.7683716e-07 4.9877167e-04 4.9384594e-02 2.4844694e+00], shape=(4,), dtype=float32)
parameter_properties
Distribution classes now expose a parameter_properties(dtype=tf.float32, num_classes=None) class method, which can enable automated construction of many classes of distributions.
print('Gamma:', tfd.Gamma.parameter_properties())
print('Categorical:', tfd.Categorical.parameter_properties(dtype=tf.float64, num_classes=7))
Gamma: {'concentration': ParameterProperties(event_ndims=0, shape_fn=<function ParameterProperties.<lambda> at 0x7ff6bbfcdd90>, default_constraining_bijector_fn=<function Gamma._parameter_properties.<locals>.<lambda> at 0x7ff6afd95510>, is_preferred=True), 'rate': ParameterProperties(event_ndims=0, shape_fn=<function ParameterProperties.<lambda> at 0x7ff6bbfcdd90>, default_constraining_bijector_fn=<function Gamma._parameter_properties.<locals>.<lambda> at 0x7ff6afd95ea0>, is_preferred=False), 'log_rate': ParameterProperties(event_ndims=0, shape_fn=<function ParameterProperties.<lambda> at 0x7ff6bbfcdd90>, default_constraining_bijector_fn=<class 'tensorflow_probability.python.bijectors.identity.Identity'>, is_preferred=True)}
Categorical: {'logits': ParameterProperties(event_ndims=1, shape_fn=<function Categorical._parameter_properties.<locals>.<lambda> at 0x7ff6afd95510>, default_constraining_bijector_fn=<class 'tensorflow_probability.python.bijectors.identity.Identity'>, is_preferred=True), 'probs': ParameterProperties(event_ndims=1, shape_fn=<function Categorical._parameter_properties.<locals>.<lambda> at 0x7ff6afdc91e0>, default_constraining_bijector_fn=<class 'tensorflow_probability.python.bijectors.softmax_centered.SoftmaxCentered'>, is_preferred=False)}
experimental_default_event_space_bijector
Now accepts additional args pinning some distribution parts.
@tfd.JointDistributionCoroutineAutoBatched
def model():
scale = yield tfd.Gamma(1, 1, name='scale')
obs = yield tfd.Normal(0, scale, name='obs')
model.experimental_default_event_space_bijector(obs=.2).forward(
[tf.random.uniform([3], -2, 2.)])
StructTuple( scale=<tf.Tensor: shape=(3,), dtype=float32, numpy=array([0.6630705, 1.5401832, 1.0777743], dtype=float32)> )
JointDistribution.experimental_pin
Pins some joint distribution parts, returning JointDistributionPinned object representing the joint unnormalized density.
Working with the experimental_default_event_space_bijector, this makes doing variational inference or MCMC with sensible defaults much more straightforward. In the below example, the first two lines of sample make running MCMC a breeze.
dist = tfd.JointDistributionSequential([
tfd.HalfNormal(1.),
lambda scale: tfd.Normal(0., scale, name='observed')])
@tf.function
def sample():
bij = dist.experimental_default_event_space_bijector(observed=1.)
target_log_prob = dist.experimental_pin(observed=1.).unnormalized_log_prob
kernel = tfp.mcmc.TransformedTransitionKernel(
tfp.mcmc.HamiltonianMonteCarlo(target_log_prob,
step_size=0.6,
num_leapfrog_steps=16),
bijector=bij)
return tfp.mcmc.sample_chain(500,
current_state=tf.ones([8]), # multiple chains
kernel=kernel,
trace_fn=None)
draws = sample()
fig, (hist, trace) = plt.subplots(ncols=2, figsize=(16, 3))
trace.plot(draws, alpha=0.5)
for col in tf.transpose(draws):
sns.kdeplot(col, ax=hist);
tfd.NegativeBinomial.experimental_from_mean_dispersion
Alternative parameterization. Email tfprobability@tensorflow.org or send us a PR to add similar class methods for other distributions.
nb = tfd.NegativeBinomial.experimental_from_mean_dispersion(30., .01)
plt.hist(nb.sample(10_000), bins='auto');
tfp.experimental.distribute
DistributionStrategy-aware joint distributions, allowing for cross-device likelihood computations. Sharded Independent and Sample distributions.
# Note: 2-logical devices are configured in the install/import cell at top.
strategy = tf.distribute.MirroredStrategy()
assert strategy.num_replicas_in_sync == 2
@tfp.experimental.distribute.JointDistributionCoroutine
def model():
root = tfp.experimental.distribute.JointDistributionCoroutine.Root
group_scale = yield root(tfd.Sample(tfd.Exponential(1), 3, name='group_scale'))
_ = yield tfp.experimental.distribute.ShardedSample(tfd.Independent(tfd.Normal(0, group_scale), 1),
sample_shape=[4], name='x')
seed1, seed2 = tfp.random.split_seed((1, 2))
@tf.function
def sample(seed):
return model.sample(seed=seed)
xs = strategy.run(sample, (seed1,))
print("""
Note that the global latent `group_scale` is shared across devices, whereas
the local `x` is sampled independently on each device.
""")
print('sample:', xs)
print('another sample:', strategy.run(sample, (seed2,)))
@tf.function
def log_prob(x):
return model.log_prob(x)
print("""
Note that each device observes the same log_prob (local latent log_probs are
summed across devices).
""")
print('log_prob:', strategy.run(log_prob, (xs,)))
@tf.function
def grad_log_prob(x):
return tfp.math.value_and_gradient(model.log_prob, x)[1]
print("""
Note that each device observes the same log_prob gradient (local latents have
independent gradients, global latents have gradients aggregated across devices).
""")
print('grad_log_prob:', strategy.run(grad_log_prob, (xs,)))
WARNING:tensorflow:There are non-GPU devices in `tf.distribute.Strategy`, not using nccl allreduce.
INFO:tensorflow:Using MirroredStrategy with devices ('/job:localhost/replica:0/task:0/device:CPU:0', '/job:localhost/replica:0/task:0/device:CPU:1')
Note that the global latent `group_scale` is shared across devices, whereas
the local `x` is sampled independently on each device.
sample: StructTuple(
group_scale=PerReplica:{
0: <tf.Tensor: shape=(3,), dtype=float32, numpy=array([2.6355493, 1.1805456, 1.245112 ], dtype=float32)>,
1: <tf.Tensor: shape=(3,), dtype=float32, numpy=array([2.6355493, 1.1805456, 1.245112 ], dtype=float32)>
},
x=PerReplica:{
0: <tf.Tensor: shape=(2, 3), dtype=float32, numpy=
array([[-0.90548456, 0.7675636 , 0.27627748],
[-0.3475989 , 2.0194046 , -1.2531326 ]], dtype=float32)>,
1: <tf.Tensor: shape=(2, 3), dtype=float32, numpy=
array([[ 3.251305 , -0.5790973 , 0.42745453],
[-1.562331 , 0.3006323 , 0.635732 ]], dtype=float32)>
}
)
another sample: StructTuple(
group_scale=PerReplica:{
0: <tf.Tensor: shape=(3,), dtype=float32, numpy=array([2.41133 , 0.10307606, 0.5236566 ], dtype=float32)>,
1: <tf.Tensor: shape=(3,), dtype=float32, numpy=array([2.41133 , 0.10307606, 0.5236566 ], dtype=float32)>
},
x=PerReplica:{
0: <tf.Tensor: shape=(2, 3), dtype=float32, numpy=
array([[-3.2476294 , 0.07213175, -0.39536062],
[-1.2319602 , -0.05505352, 0.06356457]], dtype=float32)>,
1: <tf.Tensor: shape=(2, 3), dtype=float32, numpy=
array([[ 5.6028705 , 0.11919801, -0.48446828],
[-1.5938259 , 0.21123725, 0.28979057]], dtype=float32)>
}
)
Note that each device observes the same log_prob (local latent log_probs are
summed across devices).
INFO:tensorflow:Reduce to /job:localhost/replica:0/task:0/device:CPU:0 then broadcast to ('/job:localhost/replica:0/task:0/device:CPU:0', '/job:localhost/replica:0/task:0/device:CPU:1').
log_prob: PerReplica:{
0: tf.Tensor(-25.05747, shape=(), dtype=float32),
1: tf.Tensor(-25.05747, shape=(), dtype=float32)
}
Note that each device observes the same log_prob gradient (local latents have
independent gradients, global latents are aggregated across devices).
INFO:tensorflow:Reduce to /job:localhost/replica:0/task:0/device:CPU:0 then broadcast to ('/job:localhost/replica:0/task:0/device:CPU:0', '/job:localhost/replica:0/task:0/device:CPU:1').
INFO:tensorflow:Reduce to /job:localhost/replica:0/task:0/device:CPU:0 then broadcast to ('/job:localhost/replica:0/task:0/device:CPU:0', '/job:localhost/replica:0/task:0/device:CPU:1').
grad_log_prob: StructTuple(
group_scale=PerReplica:{
0: <tf.Tensor: shape=(3,), dtype=float32, numpy=array([-1.7555585, -1.2928739, -3.0554674], dtype=float32)>,
1: <tf.Tensor: shape=(3,), dtype=float32, numpy=array([-1.7555585, -1.2928739, -3.0554674], dtype=float32)>
},
x=PerReplica:{
0: <tf.Tensor: shape=(2, 3), dtype=float32, numpy=
array([[ 0.13035832, -0.5507428 , -0.17820862],
[ 0.05004217, -1.4489648 , 0.80831426]], dtype=float32)>,
1: <tf.Tensor: shape=(2, 3), dtype=float32, numpy=
array([[-0.46807498, 0.41551432, -0.27572307],
[ 0.22492138, -0.21570992, -0.41006932]], dtype=float32)>
}
)
PSD Kernels
GeneralizedMatern
The GeneralizedMatern positive-semidefinite kernel generalizes MaternOneHalf, MAterhThreeHalves, and MaternFiveHalves.
gm = tfpk.GeneralizedMatern(df=[0.5, 1.5, 2.5], length_scale=1., amplitude=0.5)
m1 = tfpk.MaternOneHalf(length_scale=1., amplitude=0.5)
m2 = tfpk.MaternThreeHalves(length_scale=1., amplitude=0.5)
m3 = tfpk.MaternFiveHalves(length_scale=1., amplitude=0.5)
xs = tf.linspace(-1.5, 1.5, 100)
gm_matrix = gm.matrix([[0.]], xs[..., tf.newaxis])
plt.plot(xs, gm_matrix[0][0])
plt.plot(xs, m1.matrix([[0.]], xs[..., tf.newaxis])[0])
plt.show()
plt.plot(xs, gm_matrix[1][0])
plt.plot(xs, m2.matrix([[0.]], xs[..., tf.newaxis])[0])
plt.show()
plt.plot(xs, gm_matrix[2][0])
plt.plot(xs, m3.matrix([[0.]], xs[..., tf.newaxis])[0])
plt.show()
Parabolic (Epanechnikov)
epa = tfpk.Parabolic()
xs = tf.linspace(-1.05, 1.05, 100)
plt.plot(xs, epa.matrix([[0.]], xs[..., tf.newaxis])[0]);
VI
build_asvi_surrogate_posterior
Automatically construct a structured surrogate posterior for VI in a way that incorporates the graphical structure of the prior distribution. This utilizes the method described in the paper Automatic Structured Variational Inference (https://arxiv.org/abs/2002.00643).
# Import a Brownian Motion model from TFP's inference gym.
model = gym.targets.BrownianMotionMissingMiddleObservations()
prior = model.prior_distribution()
ground_truth = ground_truth = model.sample_transformations['identity'].ground_truth_mean
target_log_prob = lambda *values: model.log_likelihood(values) + prior.log_prob(values)
This models a Brownian Motion process with a Gaussian observation model. It consists of 30 timesteps, but the middle 10 timesteps are unobservable.
locs[0] ~ Normal(loc=0, scale=innovation_noise_scale)
for t in range(1, num_timesteps):
locs[t] ~ Normal(loc=locs[t - 1], scale=innovation_noise_scale)
for t in range(num_timesteps):
observed_locs[t] ~ Normal(loc=locs[t], scale=observation_noise_scale)
The goal is to infer the values of locs from noisy observations (observed_locs). Since the middle 10 timesteps are unobservable, observed_locs are NaN values at timesteps [10,19].
# The observed loc values in the Brownian Motion inference gym model
OBSERVED_LOC = np.array([
0.21592641, 0.118771404, -0.07945447, 0.037677474, -0.27885845, -0.1484156,
-0.3250906, -0.22957903, -0.44110894, -0.09830782, np.nan, np.nan, np.nan,
np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, -0.8786016,
-0.83736074, -0.7384849, -0.8939254, -0.7774566, -0.70238715, -0.87771565,
-0.51853573, -0.6948214, -0.6202789
]).astype(dtype=np.float32)
# Plot the prior and the likelihood observations
plt.figure()
plt.title('Brownian Motion Prior Samples and Observations')
num_samples = 15
prior_samples = prior.sample(num_samples)
plt.plot(prior_samples, c='blue', alpha=0.1)
plt.plot(prior_samples[0][0], label="Prior Samples", c='blue', alpha=0.1)
plt.scatter(x=range(30),y=OBSERVED_LOC, c='black', alpha=0.5, label="Observations")
plt.legend(bbox_to_anchor=(1.05, 1), borderaxespad=0.);
logging.getLogger('tensorflow').setLevel(logging.ERROR) # suppress pfor warnings
# Construct and train an ASVI Surrogate Posterior.
asvi_surrogate_posterior = tfp.experimental.vi.build_asvi_surrogate_posterior(prior)
asvi_losses = tfp.vi.fit_surrogate_posterior(target_log_prob,
asvi_surrogate_posterior,
optimizer=tf.optimizers.Adam(learning_rate=0.1),
num_steps=500)
logging.getLogger('tensorflow').setLevel(logging.NOTSET)
# Construct and train a Mean-Field Surrogate Posterior.
factored_surrogate_posterior = tfp.experimental.vi.build_factored_surrogate_posterior(event_shape=prior.event_shape)
factored_losses = tfp.vi.fit_surrogate_posterior(target_log_prob,
factored_surrogate_posterior,
optimizer=tf.optimizers.Adam(learning_rate=0.1),
num_steps=500)
logging.getLogger('tensorflow').setLevel(logging.ERROR) # suppress pfor warnings
# Sample from the posteriors.
asvi_posterior_samples = asvi_surrogate_posterior.sample(num_samples)
factored_posterior_samples = factored_surrogate_posterior.sample(num_samples)
logging.getLogger('tensorflow').setLevel(logging.NOTSET)
Both the ASVI and the mean-field surrogate posterior distributions have converged, and the ASVI surrogate posterior had a lower final loss (negative ELBO value).
# Plot the loss curves.
plt.figure()
plt.title('Loss Curves for ASVI vs Mean-Field Surrogate Posteriors')
plt.plot(asvi_losses, c='orange', label='ASVI', alpha = 0.4)
plt.plot(factored_losses, c='green', label='Mean-Field', alpha = 0.4)
plt.ylim(-50, 300)
plt.legend(bbox_to_anchor=(1.3, 1), borderaxespad=0.);
The samples from the posteriors highlight how nicely the ASVI surrogate posterior captures the uncertainty for the timesteps without observations. On the other hand, the mean-field surrogate posterior struggles to capture the true uncertainty.
# Plot samples from the ASVI and Mean-Field Surrogate Posteriors.
plt.figure()
plt.title('Posterior Samples from ASVI vs Mean-Field Surrogate Posterior')
plt.plot(asvi_posterior_samples, c='orange', alpha = 0.25)
plt.plot(asvi_posterior_samples[0][0], label='ASVI Surrogate Posterior', c='orange', alpha = 0.25)
plt.plot(factored_posterior_samples, c='green', alpha = 0.25)
plt.plot(factored_posterior_samples[0][0], label='Mean-Field Surrogate Posterior', c='green', alpha = 0.25)
plt.scatter(x=range(30),y=OBSERVED_LOC, c='black', alpha=0.5, label='Observations')
plt.plot(ground_truth, c='black', label='Ground Truth')
plt.legend(bbox_to_anchor=(1.585, 1), borderaxespad=0.);
MCMC
ProgressBarReducer
Visualize progress of the sampler. (May have a nominal performance penalty; not currently supported under JIT compilation.)
kernel = tfp.mcmc.HamiltonianMonteCarlo(lambda x: -x**2 / 2, .05, 20)
pbar = tfp.experimental.mcmc.ProgressBarReducer(100)
kernel = tfp.experimental.mcmc.WithReductions(kernel, pbar)
plt.hist(tf.reshape(tfp.mcmc.sample_chain(100, current_state=tf.ones([128]), kernel=kernel, trace_fn=None), [-1]), bins='auto')
pbar.bar.close()
99%|█████████▉| 99/100 [00:03<00:00, 27.37it/s]
sample_sequential_monte_carlo supports reproducible sampling
initial_state = tf.random.uniform([4096], -2., 2.)
def smc(seed):
return tfp.experimental.mcmc.sample_sequential_monte_carlo(
prior_log_prob_fn=lambda x: -x**2 / 2,
likelihood_log_prob_fn=lambda x: -(x-1.)**2 / 2,
current_state=initial_state,
seed=seed)[1]
plt.hist(smc(seed=(12, 34)), bins='auto');plt.show()
print(smc(seed=(12, 34))[:10])
print('different:', smc(seed=(10, 20))[:10])
print('same:', smc(seed=(12, 34))[:10])
tf.Tensor( [ 0.665834 0.9892149 0.7961128 1.0016634 -1.000767 -0.19461267 1.3070581 1.127177 0.9940303 0.58239716], shape=(10,), dtype=float32) different: tf.Tensor( [ 1.3284367 0.4374407 1.1349089 0.4557473 0.06510283 -0.08954388 1.1735026 0.8170528 0.12443061 0.34413314], shape=(10,), dtype=float32) same: tf.Tensor( [ 0.665834 0.9892149 0.7961128 1.0016634 -1.000767 -0.19461267 1.3070581 1.127177 0.9940303 0.58239716], shape=(10,), dtype=float32)
Added streaming computations of variance, covariance, Rhat
Note, the interfaces to these have changed somewhat in tfp-nightly.
def cov_to_ellipse(t, cov, mean):
"""Draw a one standard deviation ellipse from the mean, according to cov."""
diag = tf.linalg.diag_part(cov)
a = 0.5 * tf.reduce_sum(diag)
b = tf.sqrt(0.25 * (diag[0] - diag[1])**2 + cov[0, 1]**2)
major = a + b
minor = a - b
theta = tf.math.atan2(major - cov[0, 0], cov[0, 1])
x = (tf.sqrt(major) * tf.cos(theta) * tf.cos(t) -
tf.sqrt(minor) * tf.sin(theta) * tf.sin(t))
y = (tf.sqrt(major) * tf.sin(theta) * tf.cos(t) +
tf.sqrt(minor) * tf.cos(theta) * tf.sin(t))
return x + mean[0], y + mean[1]
fig, axes = plt.subplots(nrows=4, ncols=5, figsize=(14, 8),
sharex=True, sharey=True, constrained_layout=True)
t = tf.linspace(0., 2 * np.pi, 200)
tot = 10
cov = 0.1 * tf.eye(2) + 0.9 * tf.ones([2, 2])
mvn = tfd.MultivariateNormalTriL(loc=[1., 2.],
scale_tril=tf.linalg.cholesky(cov))
for ax in axes.ravel():
rv = tfp.experimental.stats.RunningCovariance(
num_samples=0., mean=tf.zeros(2), sum_squared_residuals=tf.zeros((2, 2)),
event_ndims=1)
for idx, x in enumerate(mvn.sample(tot)):
rv = rv.update(x)
ax.plot(*cov_to_ellipse(t, rv.covariance(), rv.mean),
color='k', alpha=(idx + 1) / tot)
ax.plot(*cov_to_ellipse(t, mvn.covariance(), mvn.mean()), 'r')
fig.suptitle("Twenty tries to approximate the red covariance with 10 draws");
Math, stats
Bessel functions: ive, kve, log-ive
xs = tf.linspace(0.5, 20., 100)
ys = tfp.math.bessel_ive([[0.5], [1.], [np.pi], [4.]], xs)
zs = tfp.math.bessel_kve([[0.5], [1.], [2.], [np.pi]], xs)
for i in range(4):
plt.plot(xs, ys[i])
plt.show()
for i in range(4):
plt.plot(xs, zs[i])
plt.show()
Optional weights arg to tfp.stats.histogram
edges = tf.linspace(-4., 4, 31)
samps = tfd.TruncatedNormal(0, 1, -4, 4).sample(100_000, seed=(123, 456))
_, (ax1, ax2) = plt.subplots(1, 2, figsize=(10, 3))
ax1.bar(edges[:-1], tfp.stats.histogram(samps, edges))
ax1.set_title('samples histogram')
ax2.bar(edges[:-1], tfp.stats.histogram(samps, edges, weights=1 / tfd.Normal(0, 1).prob(samps)))
ax2.set_title('samples, weighted by inverse p(sample)');
tfp.math.erfcinv
x = tf.linspace(-3., 3., 10)
y = tf.math.erfc(x)
z = tfp.math.erfcinv(y)
print(x)
print(z)
tf.Tensor( [-3. -2.3333333 -1.6666666 -1. -0.33333325 0.3333335 1. 1.666667 2.3333335 3. ], shape=(10,), dtype=float32) tf.Tensor( [-3.0002644 -2.3333426 -1.6666666 -0.9999997 -0.3333332 0.33333346 0.9999999 1.6666667 2.3333335 3.0000002 ], shape=(10,), dtype=float32)