Pyro DocumentationÂ¶
InstallationÂ¶
Getting StartedÂ¶
 Install Pyro.
 Learn the basic concepts of Pyro: models and inference.
 Dive in to other tutorials and examples.
PrimitivesÂ¶

sample
(name, fn, *args, **kwargs)[source]Â¶ Calls the stochastic function fn with additional sideeffects depending on name and the enclosing context (e.g. an inference algorithm). See Intro I and Intro II for a discussion.
Parameters:  name â€“ name of sample
 fn â€“ distribution class or function
 obs â€“ observed datum (optional; should only be used in context of inference) optionally specified in kwargs
 infer (dict) â€“ Optional dictionary of inference parameters specified in kwargs. See inference documentation for details.
Returns: sample

param
(name, *args, **kwargs)[source]Â¶ Saves the variable as a parameter in the param store. To interact with the param store or write to disk, see Parameters.
Parameters: name â€“ name of parameter Returns: parameter

module
(name, nn_module, update_module_params=False)[source]Â¶ Takes a torch.nn.Module and registers its parameters with the ParamStore. In conjunction with the ParamStore save() and load() functionality, this allows the user to save and load modules.
Parameters:  name (str) â€“ name of module
 nn_module (torch.nn.Module) â€“ the module to be registered with Pyro
 update_module_params â€“ determines whether Parameters in the PyTorch module get overridden with the values found in the ParamStore (if any). Defaults to False
Returns: torch.nn.Module

random_module
(name, nn_module, prior, *args, **kwargs)[source]Â¶ Places a prior over the parameters of the module nn_module. Returns a distribution (callable) over nn.Modules, which upon calling returns a sampled nn.Module.
See the Bayesian Regression tutorial for an example.
Parameters:  name (str) â€“ name of pyro module
 nn_module (torch.nn.Module) â€“ the module to be registered with pyro
 prior â€“ pyro distribution, stochastic function, or python dict with parameter names as keys and respective distributions/stochastic functions as values.
Returns: a callable which returns a sampled module

class
plate
(name, size=None, subsample_size=None, subsample=None, dim=None, use_cuda=None, device=None)[source]Â¶ Construct for conditionally independent sequences of variables.
plate
can be used either sequentially as a generator or in parallel as a context manager (formerlyirange
andiarange
, respectively).Sequential
plate
is similar torange()
in that it generates a sequence of values.Vectorized
plate
is similar totorch.arange()
in that it yields an array of indices by which other tensors can be indexed.plate
differs fromtorch.arange()
in that it also informs inference algorithms that the variables being indexed are conditionally independent. To do this,plate
is a provided as context manager rather than a function, and users must guarantee that all computation within anplate
context is conditionally independent:with plate("name", size) as ind: # ...do conditionally independent stuff with ind...
Additionally,
plate
can take advantage of the conditional independence assumptions by subsampling the indices and informing inference algorithms to scale various computed values. This is typically used to subsample minibatches of data:with plate("data", len(data), subsample_size=100) as ind: batch = data[ind] assert len(batch) == 100
By default
subsample_size=False
and this simply yields atorch.arange(0, size)
. If0 < subsample_size <= size
this yields a single random batch of indices of sizesubsample_size
and scales all log likelihood terms bysize/batch_size
, within this context.Warning
This is only correct if all computation is conditionally independent within the context.
Parameters:  name (str) â€“ A unique name to help inference algorithms match
plate
sites between models and guides.  size (int) â€“ Optional size of the collection being subsampled (like stop in builtin range).
 subsample_size (int) â€“ Size of minibatches used in subsampling. Defaults to size.
 subsample (Anything supporting len().) â€“ Optional custom subsample for userdefined subsampling schemes. If specified, then subsample_size will be set to len(subsample).
 dim (int) â€“ An optional dimension to use for this independence index.
If specified,
dim
should be negative, i.e. should index from the right. If not specified,dim
is set to the rightmost dim that is left of all enclosingplate
contexts.  use_cuda (bool) â€“ DEPRECATED, use the device arg instead.
Optional bool specifying whether to use cuda tensors for subsample
and log_prob. Defaults to
torch.Tensor.is_cuda
.  device (str) â€“ Optional keyword specifying which device to place the results of subsample and log_prob on. By default, results are placed on the same device as the default tensor.
Returns: A reusabe context manager yielding a single 1dimensional
torch.Tensor
of indices.Examples:
>>> # This version declares sequential independence and subsamples data: >>> for i in plate('data', 100, subsample_size=10): ... if z[i]: # Control flow in this example prevents vectorization. ... obs = sample('obs_{}'.format(i), dist.Normal(loc, scale), obs=data[i])
>>> # This version declares vectorized independence: >>> with plate('data'): ... obs = sample('obs', dist.Normal(loc, scale), obs=data)
>>> # This version subsamples data in vectorized way: >>> with plate('data', 100, subsample_size=10) as ind: ... obs = sample('obs', dist.Normal(loc, scale), obs=data[ind])
>>> # This wraps a userdefined subsampling method for use in pyro: >>> ind = torch.randint(0, 100, (10,)).long() # custom subsample >>> with plate('data', 100, subsample=ind): ... obs = sample('obs', dist.Normal(loc, scale), obs=data[ind])
>>> # This reuses two different independence contexts. >>> x_axis = plate('outer', 320, dim=1) >>> y_axis = plate('inner', 200, dim=2) >>> with x_axis: ... x_noise = sample("x_noise", dist.Normal(loc, scale)) ... assert x_noise.shape == (320,) >>> with y_axis: ... y_noise = sample("y_noise", dist.Normal(loc, scale)) ... assert y_noise.shape == (200, 1) >>> with x_axis, y_axis: ... xy_noise = sample("xy_noise", dist.Normal(loc, scale)) ... assert xy_noise.shape == (200, 320)
See SVI Part II for an extended discussion.
 name (str) â€“ A unique name to help inference algorithms match

clear_param_store
()[source]Â¶ Clears the ParamStore. This is especially useful if youâ€™re working in a REPL.

validation_enabled
(*args, **kwds)[source]Â¶ Context manager that is useful when temporarily enabling/disabling validation checks.
Parameters: is_validate (bool) â€“ (optional; defaults to True) temporary validation check override.

enable_validation
(is_validate=True)[source]Â¶ Enable or disable validation checks in Pyro. Validation checks provide useful warnings and errors, e.g. NaN checks, validating distribution arguments and support values, etc. which is useful for debugging. Since some of these checks may be expensive, we recommend turning this off for mature models.
Parameters: is_validate (bool) â€“ (optional; defaults to True) whether to enable validation checks.

trace
(fn=None, ignore_warnings=False)[source]Â¶ Lazy replacement for
torch.jit.trace()
that works with Pyro functions that callpyro.param()
.The actual compilation artifact is stored in the
compiled
attribute of the output. Call diagnostic methods on this attribute.Example:
def model(x): scale = pyro.param("scale", torch.tensor(0.5), constraint=constraints.positive) return pyro.sample("y", dist.Normal(x, scale)) @pyro.ops.jit.trace def model_log_prob_fn(x, y): cond_model = pyro.condition(model, data={"y": y}) tr = pyro.poutine.trace(cond_model).get_trace(x) return tr.log_prob_sum()
InferenceÂ¶
In the context of probabilistic modeling, learning is usually called inference. In the particular case of Bayesian inference, this often involves computing (approximate) posterior distributions. In the case of parameterized models, this usually involves some sort of optimization. Pyro supports multiple inference algorithms, with support for stochastic variational inference (SVI) being the most extensive. Look here for more inference algorithms in future versions of Pyro.
See Intro II for a discussion of inference in Pyro.
SVIÂ¶

class
SVI
(model, guide, optim, loss, loss_and_grads=None, num_samples=10, num_steps=0, **kwargs)[source]Â¶ Bases:
pyro.infer.abstract_infer.TracePosterior
Parameters:  model â€“ the model (callable containing Pyro primitives)
 guide â€“ the guide (callable containing Pyro primitives)
 optim (pyro.optim.PyroOptim) â€“ a wrapper a for a PyTorch optimizer
 loss (pyro.infer.elbo.ELBO) â€“ an instance of a subclass of
ELBO
. Pyro provides three builtin losses:Trace_ELBO
,TraceGraph_ELBO
, andTraceEnum_ELBO
. See theELBO
docs to learn how to implement a custom loss.  num_samples â€“ the number of samples for Monte Carlo posterior approximation
 num_steps â€“ the number of optimization steps to take in
run()
A unified interface for stochastic variational inference in Pyro. The most commonly used loss is
loss=Trace_ELBO()
. See the tutorial SVI Part I for a discussion.
ELBOÂ¶

class
ELBO
(num_particles=1, max_plate_nesting=inf, max_iarange_nesting=None, vectorize_particles=False, strict_enumeration_warning=True, ignore_jit_warnings=False, retain_graph=None)[source]Â¶ Bases:
object
ELBO
is the toplevel interface for stochastic variational inference via optimization of the evidence lower bound.Most users will not interact with this base class
ELBO
directly; instead they will create instances of derived classes:Trace_ELBO
,TraceGraph_ELBO
, orTraceEnum_ELBO
.Parameters:  num_particles â€“ The number of particles/samples used to form the ELBO (gradient) estimators.
 max_plate_nesting (int) â€“ Optional bound on max number of nested
pyro.plate()
contexts. This is only required when enumerating over sample sites in parallel, e.g. if a site setsinfer={"enumerate": "parallel"}
. If omitted, ELBO may guess a valid value by running the (model,guide) pair once, however this guess may be incorrect if model or guide structure is dynamic.  vectorize_particles (bool) â€“ Whether to vectorize the ELBO computation over num_particles. Defaults to False. This requires static structure in model and guide.
 strict_enumeration_warning (bool) â€“ Whether to warn about possible
misuse of enumeration, i.e. that
pyro.infer.traceenum_elbo.TraceEnum_ELBO
is used iff there are enumerated sample sites.  ignore_jit_warnings (bool) â€“ Flag to ignore warnings from the JIT
tracer. When this is True, all
torch.jit.TracerWarning
will be ignored. Defaults to False.  retain_graph (bool) â€“ Whether to retain autograd graph during an SVI step. Defaults to None (False).
References
[1] Automated Variational Inference in Probabilistic Programming David Wingate, Theo Weber
[2] Black Box Variational Inference, Rajesh Ranganath, Sean Gerrish, David M. Blei

class
Trace_ELBO
(num_particles=1, max_plate_nesting=inf, max_iarange_nesting=None, vectorize_particles=False, strict_enumeration_warning=True, ignore_jit_warnings=False, retain_graph=None)[source]Â¶ Bases:
pyro.infer.elbo.ELBO
A trace implementation of ELBObased SVI. The estimator is constructed along the lines of references [1] and [2]. There are no restrictions on the dependency structure of the model or the guide. The gradient estimator includes partial RaoBlackwellization for reducing the variance of the estimator when nonreparameterizable random variables are present. The RaoBlackwellization is partial in that it only uses conditional independence information that is marked by
plate
contexts. For more finegrained RaoBlackwellization, seeTraceGraph_ELBO
.References
 [1] Automated Variational Inference in Probabilistic Programming,
 David Wingate, Theo Weber
 [2] Black Box Variational Inference,
 Rajesh Ranganath, Sean Gerrish, David M. Blei

loss
(model, guide, *args, **kwargs)[source]Â¶ Returns: returns an estimate of the ELBO Return type: float Evaluates the ELBO with an estimator that uses num_particles many samples/particles.

class
JitTrace_ELBO
(num_particles=1, max_plate_nesting=inf, max_iarange_nesting=None, vectorize_particles=False, strict_enumeration_warning=True, ignore_jit_warnings=False, retain_graph=None)[source]Â¶ Bases:
pyro.infer.trace_elbo.Trace_ELBO
Like
Trace_ELBO
but usespyro.ops.jit.compile()
to compileloss_and_grads()
.This works only for a limited set of models:
 Models must have static structure.
 Models must not depend on any global data (except the param store).
 All model inputs that are tensors must be passed in via
*args
.  All model inputs that are not tensors must be passed in via
**kwargs
, and compilation will be triggered once per unique**kwargs
.

class
TraceGraph_ELBO
(num_particles=1, max_plate_nesting=inf, max_iarange_nesting=None, vectorize_particles=False, strict_enumeration_warning=True, ignore_jit_warnings=False, retain_graph=None)[source]Â¶ Bases:
pyro.infer.elbo.ELBO
A TraceGraph implementation of ELBObased SVI. The gradient estimator is constructed along the lines of reference [1] specialized to the case of the ELBO. It supports arbitrary dependency structure for the model and guide as well as baselines for nonreparameterizable random variables. Where possible, conditional dependency information as recorded in the
Trace
is used to reduce the variance of the gradient estimator. In particular two kinds of conditional dependency information are used to reduce variance: the sequential order of samples (z is sampled after y => y does not depend on z)
plate
generators
References
 [1] Gradient Estimation Using Stochastic Computation Graphs,
 John Schulman, Nicolas Heess, Theophane Weber, Pieter Abbeel
 [2] Neural Variational Inference and Learning in Belief Networks
 Andriy Mnih, Karol Gregor

loss
(model, guide, *args, **kwargs)[source]Â¶ Returns: returns an estimate of the ELBO Return type: float Evaluates the ELBO with an estimator that uses num_particles many samples/particles.

loss_and_grads
(model, guide, *args, **kwargs)[source]Â¶ Returns: returns an estimate of the ELBO Return type: float Computes the ELBO as well as the surrogate ELBO that is used to form the gradient estimator. Performs backward on the latter. Num_particle many samples are used to form the estimators. If baselines are present, a baseline loss is also constructed and differentiated.

class
JitTraceGraph_ELBO
(num_particles=1, max_plate_nesting=inf, max_iarange_nesting=None, vectorize_particles=False, strict_enumeration_warning=True, ignore_jit_warnings=False, retain_graph=None)[source]Â¶ Bases:
pyro.infer.tracegraph_elbo.TraceGraph_ELBO
Like
TraceGraph_ELBO
but usestorch.jit.trace()
to compileloss_and_grads()
.This works only for a limited set of models:
 Models must have static structure.
 Models must not depend on any global data (except the param store).
 All model inputs that are tensors must be passed in via
*args
.  All model inputs that are not tensors must be passed in via
**kwargs
, and compilation will be triggered once per unique**kwargs
.

class
BackwardSampleMessenger
(enum_trace, guide_trace)[source]Â¶ Bases:
pyro.poutine.messenger.Messenger
Implements forward filtering / backward sampling for sampling from the joint posterior distribution

class
TraceEnum_ELBO
(num_particles=1, max_plate_nesting=inf, max_iarange_nesting=None, vectorize_particles=False, strict_enumeration_warning=True, ignore_jit_warnings=False, retain_graph=None)[source]Â¶ Bases:
pyro.infer.elbo.ELBO
A trace implementation of ELBObased SVI that supports  exhaustive enumeration over discrete sample sites, and  local parallel sampling over any sample site.
To enumerate over a sample site in the
guide
, mark the site with eitherinfer={'enumerate': 'sequential'}
orinfer={'enumerate': 'parallel'}
. To configure all guide sites at once, useconfig_enumerate()
. To enumerate over a sample site in themodel
, mark the siteinfer={'enumerate': 'parallel'}
and ensure the site does not appear in theguide
.This assumes restricted dependency structure on the model and guide: variables outside of an
plate
can never depend on variables inside thatplate
.
loss
(model, guide, *args, **kwargs)[source]Â¶ Returns: an estimate of the ELBO Return type: float Estimates the ELBO using
num_particles
many samples (particles).

differentiable_loss
(model, guide, *args, **kwargs)[source]Â¶ Returns: a differentiable estimate of the ELBO Return type: torch.Tensor Raises: ValueError â€“ if the ELBO is not differentiable (e.g. is identically zero) Estimates a differentiable ELBO using
num_particles
many samples (particles). The result should be infinitely differentiable (as long as underlying derivatives have been implemented).

loss_and_grads
(model, guide, *args, **kwargs)[source]Â¶ Returns: an estimate of the ELBO Return type: float Estimates the ELBO using
num_particles
many samples (particles). Performs backward on the ELBO of each particle.


class
JitTraceEnum_ELBO
(num_particles=1, max_plate_nesting=inf, max_iarange_nesting=None, vectorize_particles=False, strict_enumeration_warning=True, ignore_jit_warnings=False, retain_graph=None)[source]Â¶ Bases:
pyro.infer.traceenum_elbo.TraceEnum_ELBO
Like
TraceEnum_ELBO
but usespyro.ops.jit.compile()
to compileloss_and_grads()
.This works only for a limited set of models:
 Models must have static structure.
 Models must not depend on any global data (except the param store).
 All model inputs that are tensors must be passed in via
*args
.  All model inputs that are not tensors must be passed in via
**kwargs
, and compilation will be triggered once per unique**kwargs
.

class
TraceMeanField_ELBO
(num_particles=1, max_plate_nesting=inf, max_iarange_nesting=None, vectorize_particles=False, strict_enumeration_warning=True, ignore_jit_warnings=False, retain_graph=None)[source]Â¶ Bases:
pyro.infer.trace_elbo.Trace_ELBO
A trace implementation of ELBObased SVI. This is currently the only ELBO estimator in Pyro that uses analytic KL divergences when those are available.
In contrast to, e.g.,
TraceGraph_ELBO
andTrace_ELBO
this estimator places restrictions on the dependency structure of the model and guide. In particular it assumes that the guide has a meanfield structure, i.e. that it factorizes across the different latent variables present in the guide. It also assumes that all of the latent variables in the guide are reparameterized. This latter condition is satisfied for, e.g., the Normal distribution but is not satisfied for, e.g., the Categorical distribution.Warning
This estimator may give incorrect results if the meanfield condition is not satisfied.
Note for advanced users:
The mean field condition is a sufficient but not necessary condition for this estimator to be correct. The precise condition is that for every latent variable z in the guide, its parents in the model must not include any latent variables that are descendants of z in the guide. Here â€parents in the modelâ€™ and â€descendants in the guideâ€™ is with respect to the corresponding (statistical) dependency structure. For example, this condition is always satisfied if the model and guide have identical dependency structures.

class
JitTraceMeanField_ELBO
(num_particles=1, max_plate_nesting=inf, max_iarange_nesting=None, vectorize_particles=False, strict_enumeration_warning=True, ignore_jit_warnings=False, retain_graph=None)[source]Â¶ Bases:
pyro.infer.trace_mean_field_elbo.TraceMeanField_ELBO
Like
TraceMeanField_ELBO
but usespyro.ops.jit.trace()
to compileloss_and_grads()
.This works only for a limited set of models:
 Models must have static structure.
 Models must not depend on any global data (except the param store).
 All model inputs that are tensors must be passed in via
*args
.  All model inputs that are not tensors must be passed in via
**kwargs
, and compilation will be triggered once per unique**kwargs
.

class
RenyiELBO
(alpha=0, num_particles=2, max_plate_nesting=inf, max_iarange_nesting=None, vectorize_particles=False, strict_enumeration_warning=True)[source]Â¶ Bases:
pyro.infer.elbo.ELBO
An implementation of Renyiâ€™s \(\alpha\)divergence variational inference following reference [1].
In order for the objective to be a strict lower bound, we require \(\alpha \ge 0\). Note, however, that according to reference [1], depending on the dataset \(\alpha < 0\) might give better results. In the special case \(\alpha = 0\), the objective function is that of the important weighted autoencoder derived in reference [2].
Note
Setting \(\alpha < 1\) gives a better bound than the usual ELBO. For \(\alpha = 1\), it is better to use
Trace_ELBO
class because it helps reduce variances of gradient estimations.Warning
Minibatch training is not supported yet.
Parameters:  alpha (float) â€“ The order of \(\alpha\)divergence. Here \(\alpha \neq 1\). Default is 0.
 num_particles â€“ The number of particles/samples used to form the objective (gradient) estimator. Default is 2.
 max_plate_nesting (int) â€“ Bound on max number of nested
pyro.plate()
contexts. Default is infinity.  strict_enumeration_warning (bool) â€“ Whether to warn about possible
misuse of enumeration, i.e. that
TraceEnum_ELBO
is used iff there are enumerated sample sites.
References:
 [1] Renyi Divergence Variational Inference,
 Yingzhen Li, Richard E. Turner
 [2] Importance Weighted Autoencoders,
 Yuri Burda, Roger Grosse, Ruslan Salakhutdinov
ImportanceÂ¶

class
Importance
(model, guide=None, num_samples=None)[source]Â¶ Bases:
pyro.infer.abstract_infer.TracePosterior
Parameters:  model â€“ probabilistic model defined as a function
 guide â€“ guide used for sampling defined as a function
 num_samples â€“ number of samples to draw from the guide (default 10)
This method performs posterior inference by importance sampling using the guide as the proposal distribution. If no guide is provided, it defaults to proposing from the modelâ€™s prior.
Discrete InferenceÂ¶

infer_discrete
(fn=None, first_available_dim=None, temperature=1)[source]Â¶ A poutine that samples discrete sites marked with
site["infer"]["enumerate"] = "parallel"
from the posterior, conditioned on observations.Example:
@infer_discrete(first_available_dim=1, temperature=0) @config_enumerate def viterbi_decoder(data, hidden_dim=10): transition = 0.3 / hidden_dim + 0.7 * torch.eye(hidden_dim) means = torch.arange(float(hidden_dim)) states = [0] for t in pyro.markov(range(len(data))): states.append(pyro.sample("states_{}".format(t), dist.Categorical(transition[states[1]]))) pyro.sample("obs_{}".format(t), dist.Normal(means[states[1]], 1.), obs=data[t]) return states # returns maximum likelihood states
Parameters:  fn â€“ a stochastic function (callable containing Pyro primitive calls)
 first_available_dim (int) â€“ The first tensor dimension (counting from the right) that is available for parallel enumeration. This dimension and all dimensions left may be used internally by Pyro. This should be a negative integer.
 temperature (int) â€“ Either 1 (sample via forwardfilter backwardsample) or 0 (optimize via Viterbilike MAP inference). Defaults to 1 (sample).
Inference UtilitiesÂ¶

class
EmpiricalMarginal
(trace_posterior, sites=None, validate_args=None)[source]Â¶ Bases:
pyro.distributions.empirical.Empirical
Marginal distribution over a single site (or multiple, provided they have the same shape) from the
TracePosterior
â€™s model.Note
If multiple sites are specified, they must have the same tensor shape. Samples from each site will be stacked and stored within a single tensor. See
Empirical
. To hold the marginal distribution of sites having different shapes, useMarginals
instead.Parameters:  trace_posterior (TracePosterior) â€“ a
TracePosterior
instance representing a Monte Carlo posterior.  sites (list) â€“ optional list of sites for which we need to generate the marginal distribution.
 trace_posterior (TracePosterior) â€“ a

class
Marginals
(trace_posterior, sites=None, validate_args=None)[source]Â¶ Bases:
object
Holds the marginal distribution over one or more sites from the
TracePosterior
â€™s model. This is a convenience container class, which can be extended byTracePosterior
subclasses. e.g. for implementing diagnostics.Parameters:  trace_posterior (TracePosterior) â€“ a TracePosterior instance representing a Monte Carlo posterior.
 sites (list) â€“ optional list of sites for which we need to generate the marginal distribution.

empirical
Â¶ A dictionary of sitesâ€™ names and their corresponding
EmpiricalMarginal
distribution.Type: OrderedDict

support
(flatten=False)[source]Â¶ Gets support of this marginal distribution.
Parameters: flatten (bool) â€“ A flag to decide if we want to flatten batch_shape when the marginal distribution is collected from the posterior with num_chains > 1
. Defaults to False.Returns: a dict with keys are sitesâ€™ names and values are sitesâ€™ supports. Return type: OrderedDict

class
TracePosterior
(num_chains=1)[source]Â¶ Bases:
object
Abstract TracePosterior object from which posterior inference algorithms inherit. When run, collects a bag of execution traces from the approximate posterior. This is designed to be used by other utility classes like EmpiricalMarginal, that need access to the collected execution traces.

information_criterion
(pointwise=False)[source]Â¶ Computes information criterion of the model. Currently, returns only â€śWidely Applicable/WatanabeAkaike Information Criterionâ€ť (WAIC) and the corresponding effective number of parameters.
Reference:
[1] Practical Bayesian model evaluation using leaveoneout crossvalidation and WAIC, Aki Vehtari, Andrew Gelman, and Jonah Gabry
Parameters: pointwise (bool) â€“ a flag to decide if we want to get a vectorized WAIC or not. When pointwise=False
, returns the sum.Returns: a dictionary containing values of WAIC and its effective number of parameters. Return type: OrderedDict


class
TracePredictive
(model, posterior, num_samples)[source]Â¶ Bases:
pyro.infer.abstract_infer.TracePosterior
Generates and holds traces from the posterior predictive distribution, given model execution traces from the approximate posterior. This is achieved by constraining latent sites to randomly sampled parameter values from the model execution traces and running the model forward to generate traces with new response (â€ś_RETURNâ€ť) sites.
Parameters:  model â€“ arbitrary Python callable containing Pyro primitives.
 posterior (TracePosterior) â€“ trace posterior instance holding samples from the modelâ€™s approximate posterior.
 num_samples (int) â€“ number of samples to generate.
MCMCÂ¶
MCMCÂ¶

class
MCMC
(kernel, num_samples, warmup_steps=None, num_chains=1, mp_context=None, disable_progbar=False)[source]Â¶ Bases:
pyro.infer.abstract_infer.TracePosterior
Wrapper class for Markov Chain Monte Carlo algorithms. Specific MCMC algorithms are TraceKernel instances and need to be supplied as a
kernel
argument to the constructor.Note
The case of num_chains > 1 uses python multiprocessing to run parallel chains in multiple processes. This goes with the usual caveats around multiprocessing in python, e.g. the model used to initialize the
kernel
must be serializable via pickle, and the performance / constraints will be platform dependent (e.g. only the â€śspawnâ€ť context is available in Windows). This has also not been extensively tested on the Windows platform.Parameters:  kernel â€“ An instance of the
TraceKernel
class, which when given an execution trace returns another sample trace from the target (posterior) distribution.  num_samples (int) â€“ The number of samples that need to be generated, excluding the samples discarded during the warmup phase.
 warmup_steps (int) â€“ Number of warmup iterations. The samples generated during the warmup phase are discarded. If not provided, default is half of num_samples.
 num_chains (int) â€“ Number of MCMC chains to run in parallel. Depending on whether num_chains is 1 or more than 1, this class internally dispatches to either _SingleSampler or _ParallelSampler.
 mp_context (str) â€“ Multiprocessing context to use when num_chains > 1. Only applicable for Python 3.5 and above. Use mp_context=â€ťspawnâ€ť for CUDA.
 disable_progbar (bool) â€“ Disable progress bar and diagnostics update.

marginal
(sites=None)[source]Â¶ Marginalizes latent sites from the sampler.
Parameters: sites (list) â€“ optional list of sites for which we need to generate the marginal distribution. Returns: A MCMCMarginals
class instance.Return type: MCMCMarginals
.
 kernel â€“ An instance of the
HMCÂ¶

class
HMC
(model, step_size=1, trajectory_length=None, num_steps=None, adapt_step_size=True, adapt_mass_matrix=True, full_mass=False, transforms=None, max_plate_nesting=None, jit_compile=False, jit_options=None, ignore_jit_warnings=False, target_accept_prob=0.8)[source]Â¶ Bases:
pyro.infer.mcmc.trace_kernel.TraceKernel
Simple Hamiltonian Monte Carlo kernel, where
step_size
andnum_steps
need to be explicitly specified by the user.References
[1] MCMC Using Hamiltonian Dynamics, Radford M. Neal
Parameters:  model â€“ Python callable containing Pyro primitives.
 step_size (float) â€“ Determines the size of a single step taken by the verlet integrator while computing the trajectory using Hamiltonian dynamics. If not specified, it will be set to 1.
 trajectory_length (float) â€“ Length of a MCMC trajectory. If not
specified, it will be set to
step_size x num_steps
. In casenum_steps
is not specified, it will be set to \(2\pi\).  num_steps (int) â€“ The number of discrete steps over which to simulate
Hamiltonian dynamics. The state at the end of the trajectory is
returned as the proposal. This value is always equal to
int(trajectory_length / step_size)
.  adapt_step_size (bool) â€“ A flag to decide if we want to adapt step_size during warmup phase using Dual Averaging scheme.
 adapt_mass_matrix (bool) â€“ A flag to decide if we want to adapt mass matrix during warmup phase using Welford scheme.
 full_mass (bool) â€“ A flag to decide if mass matrix is dense or diagonal.
 transforms (dict) â€“ Optional dictionary that specifies a transform
for a sample site with constrained support to unconstrained space. The
transform should be invertible, and implement log_abs_det_jacobian.
If not specified and the model has sites with constrained support,
automatic transformations will be applied, as specified in
torch.distributions.constraint_registry
.  max_plate_nesting (int) â€“ Optional bound on max number of nested
pyro.plate()
contexts. This is required if model contains discrete sample sites that can be enumerated over in parallel.  jit_compile (bool) â€“ Optional parameter denoting whether to use the PyTorch JIT to trace the log density computation, and use this optimized executable trace in the integrator.
 jit_options (dict) â€“ A dictionary contains optional arguments for
torch.jit.trace()
function.  ignore_jit_warnings (bool) â€“ Flag to ignore warnings from the JIT
tracer when
jit_compile=True
. Default is False.  target_accept_prob (float) â€“ Increasing this value will lead to a smaller step size, hence the sampling will be slower and more robust. Default to 0.8.
Note
Internally, the mass matrix will be ordered according to the order of the names of latent variables, not the order of their appearance in the model.
Example:
>>> true_coefs = torch.tensor([1., 2., 3.]) >>> data = torch.randn(2000, 3) >>> dim = 3 >>> labels = dist.Bernoulli(logits=(true_coefs * data).sum(1)).sample() >>> >>> def model(data): ... coefs_mean = torch.zeros(dim) ... coefs = pyro.sample('beta', dist.Normal(coefs_mean, torch.ones(3))) ... y = pyro.sample('y', dist.Bernoulli(logits=(coefs * data).sum(1)), obs=labels) ... return y >>> >>> hmc_kernel = HMC(model, step_size=0.0855, num_steps=4) >>> mcmc_run = MCMC(hmc_kernel, num_samples=500, warmup_steps=100).run(data) >>> posterior = mcmc_run.marginal('beta').empirical['beta'] >>> posterior.mean tensor([ 0.9819, 1.9258, 2.9737])

initial_trace
Â¶ Find a valid trace to initiate the MCMC sampler. This is also used as a prototype trace to interconvert between Pyroâ€™s trace object and dict object used by the integrator.

inverse_mass_matrix
Â¶

num_steps
Â¶

step_size
Â¶
NUTSÂ¶

class
NUTS
(model, step_size=1, adapt_step_size=True, adapt_mass_matrix=True, full_mass=False, use_multinomial_sampling=True, transforms=None, max_plate_nesting=None, jit_compile=False, jit_options=None, ignore_jit_warnings=False, target_accept_prob=0.8, max_tree_depth=10)[source]Â¶ Bases:
pyro.infer.mcmc.hmc.HMC
NoUTurn Sampler kernel, which provides an efficient and convenient way to run Hamiltonian Monte Carlo. The number of steps taken by the integrator is dynamically adjusted on each call to
sample
to ensure an optimal length for the Hamiltonian trajectory [1]. As such, the samples generated will typically have lower autocorrelation than those generated by theHMC
kernel. Optionally, the NUTS kernel also provides the ability to adapt step size during the warmup phase.Refer to the baseball example to see how to do Bayesian inference in Pyro using NUTS.
References
 [1] The NoUturn sampler: adaptively setting path lengths in Hamiltonian Monte Carlo,
 Matthew D. Hoffman, and Andrew Gelman.
 [2] A Conceptual Introduction to Hamiltonian Monte Carlo,
 Michael Betancourt
 [3] Slice Sampling,
 Radford M. Neal
Parameters:  model â€“ Python callable containing Pyro primitives.
 step_size (float) â€“ Determines the size of a single step taken by the verlet integrator while computing the trajectory using Hamiltonian dynamics. If not specified, it will be set to 1.
 adapt_step_size (bool) â€“ A flag to decide if we want to adapt step_size during warmup phase using Dual Averaging scheme.
 adapt_mass_matrix (bool) â€“ A flag to decide if we want to adapt mass matrix during warmup phase using Welford scheme.
 full_mass (bool) â€“ A flag to decide if mass matrix is dense or diagonal.
 use_multinomial_sampling (bool) â€“ A flag to decide if we want to sample candidates along its trajectory using â€śmultinomial samplingâ€ť or using â€śslice samplingâ€ť. Slice sampling is used in the original NUTS paper [1], while multinomial sampling is suggested in [2]. By default, this flag is set to True. If it is set to False, NUTS uses slice sampling.
 transforms (dict) â€“ Optional dictionary that specifies a transform
for a sample site with constrained support to unconstrained space. The
transform should be invertible, and implement log_abs_det_jacobian.
If not specified and the model has sites with constrained support,
automatic transformations will be applied, as specified in
torch.distributions.constraint_registry
.  max_plate_nesting (int) â€“ Optional bound on max number of nested
pyro.plate()
contexts. This is required if model contains discrete sample sites that can be enumerated over in parallel.  jit_compile (bool) â€“ Optional parameter denoting whether to use the PyTorch JIT to trace the log density computation, and use this optimized executable trace in the integrator.
 jit_options (dict) â€“ A dictionary contains optional arguments for
torch.jit.trace()
function.  ignore_jit_warnings (bool) â€“ Flag to ignore warnings from the JIT
tracer when
jit_compile=True
. Default is False.  target_accept_prob (float) â€“ Target acceptance probability of step size adaptation scheme. Increasing this value will lead to a smaller step size, so the sampling will be slower but more robust. Default to 0.8.
 max_tree_depth (int) â€“ Max depth of the binary tree created during the doubling scheme of NUTS sampler. Default to 10.
Example:
>>> true_coefs = torch.tensor([1., 2., 3.]) >>> data = torch.randn(2000, 3) >>> dim = 3 >>> labels = dist.Bernoulli(logits=(true_coefs * data).sum(1)).sample() >>> >>> def model(data): ... coefs_mean = torch.zeros(dim) ... coefs = pyro.sample('beta', dist.Normal(coefs_mean, torch.ones(3))) ... y = pyro.sample('y', dist.Bernoulli(logits=(coefs * data).sum(1)), obs=labels) ... return y >>> >>> nuts_kernel = NUTS(model, adapt_step_size=True) >>> mcmc_run = MCMC(nuts_kernel, num_samples=500, warmup_steps=300).run(data) >>> posterior = mcmc_run.marginal('beta').empirical['beta'] >>> posterior.mean tensor([ 0.9221, 1.9464, 2.9228])
DistributionsÂ¶
PyTorch DistributionsÂ¶
Most distributions in Pyro are thin wrappers around PyTorch distributions.
For details on the PyTorch distribution interface, see
torch.distributions.distribution.Distribution
.
For differences between the Pyro and PyTorch interfaces, see
TorchDistributionMixin
.
BernoulliÂ¶

class
Bernoulli
(probs=None, logits=None, validate_args=None)Â¶ Wraps
torch.distributions.bernoulli.Bernoulli
withTorchDistributionMixin
.
BetaÂ¶

class
Beta
(concentration1, concentration0, validate_args=None)Â¶ Wraps
torch.distributions.beta.Beta
withTorchDistributionMixin
.
BinomialÂ¶

class
Binomial
(total_count=1, probs=None, logits=None, validate_args=None)Â¶ Wraps
torch.distributions.binomial.Binomial
withTorchDistributionMixin
.
CategoricalÂ¶

class
Categorical
(probs=None, logits=None, validate_args=None)Â¶ Wraps
torch.distributions.categorical.Categorical
withTorchDistributionMixin
.
CauchyÂ¶

class
Cauchy
(loc, scale, validate_args=None)Â¶ Wraps
torch.distributions.cauchy.Cauchy
withTorchDistributionMixin
.
Chi2Â¶

class
Chi2
(df, validate_args=None)Â¶ Wraps
torch.distributions.chi2.Chi2
withTorchDistributionMixin
.
DirichletÂ¶

class
Dirichlet
(concentration, validate_args=None)Â¶ Wraps
torch.distributions.dirichlet.Dirichlet
withTorchDistributionMixin
.
ExponentialÂ¶

class
Exponential
(rate, validate_args=None)Â¶ Wraps
torch.distributions.exponential.Exponential
withTorchDistributionMixin
.
ExponentialFamilyÂ¶

class
ExponentialFamily
(batch_shape=torch.Size([]), event_shape=torch.Size([]), validate_args=None)Â¶ Wraps
torch.distributions.exp_family.ExponentialFamily
withTorchDistributionMixin
.
FisherSnedecorÂ¶

class
FisherSnedecor
(df1, df2, validate_args=None)Â¶ Wraps
torch.distributions.fishersnedecor.FisherSnedecor
withTorchDistributionMixin
.
GammaÂ¶

class
Gamma
(concentration, rate, validate_args=None)Â¶ Wraps
torch.distributions.gamma.Gamma
withTorchDistributionMixin
.
GeometricÂ¶

class
Geometric
(probs=None, logits=None, validate_args=None)Â¶ Wraps
torch.distributions.geometric.Geometric
withTorchDistributionMixin
.
GumbelÂ¶

class
Gumbel
(loc, scale, validate_args=None)Â¶ Wraps
torch.distributions.gumbel.Gumbel
withTorchDistributionMixin
.
HalfCauchyÂ¶

class
HalfCauchy
(scale, validate_args=None)Â¶ Wraps
torch.distributions.half_cauchy.HalfCauchy
withTorchDistributionMixin
.
HalfNormalÂ¶

class
HalfNormal
(scale, validate_args=None)Â¶ Wraps
torch.distributions.half_normal.HalfNormal
withTorchDistributionMixin
.
IndependentÂ¶

class
Independent
(base_distribution, reinterpreted_batch_ndims, validate_args=None)[source]Â¶ Wraps
torch.distributions.independent.Independent
withTorchDistributionMixin
.
LaplaceÂ¶

class
Laplace
(loc, scale, validate_args=None)Â¶ Wraps
torch.distributions.laplace.Laplace
withTorchDistributionMixin
.
LogNormalÂ¶

class
LogNormal
(loc, scale, validate_args=None)Â¶ Wraps
torch.distributions.log_normal.LogNormal
withTorchDistributionMixin
.
LogisticNormalÂ¶

class
LogisticNormal
(loc, scale, validate_args=None)Â¶ Wraps
torch.distributions.logistic_normal.LogisticNormal
withTorchDistributionMixin
.
LowRankMultivariateNormalÂ¶

class
LowRankMultivariateNormal
(loc, cov_factor, cov_diag, validate_args=None)Â¶ Wraps
torch.distributions.lowrank_multivariate_normal.LowRankMultivariateNormal
withTorchDistributionMixin
.
MultinomialÂ¶

class
Multinomial
(total_count=1, probs=None, logits=None, validate_args=None)Â¶ Wraps
torch.distributions.multinomial.Multinomial
withTorchDistributionMixin
.
MultivariateNormalÂ¶

class
MultivariateNormal
(loc, covariance_matrix=None, precision_matrix=None, scale_tril=None, validate_args=None)[source]Â¶ Wraps
torch.distributions.multivariate_normal.MultivariateNormal
withTorchDistributionMixin
.
NegativeBinomialÂ¶

class
NegativeBinomial
(total_count, probs=None, logits=None, validate_args=None)Â¶ Wraps
torch.distributions.negative_binomial.NegativeBinomial
withTorchDistributionMixin
.
NormalÂ¶

class
Normal
(loc, scale, validate_args=None)Â¶ Wraps
torch.distributions.normal.Normal
withTorchDistributionMixin
.
OneHotCategoricalÂ¶

class
OneHotCategorical
(probs=None, logits=None, validate_args=None)Â¶ Wraps
torch.distributions.one_hot_categorical.OneHotCategorical
withTorchDistributionMixin
.
ParetoÂ¶

class
Pareto
(scale, alpha, validate_args=None)Â¶ Wraps
torch.distributions.pareto.Pareto
withTorchDistributionMixin
.
PoissonÂ¶

class
Poisson
(rate, validate_args=None)Â¶ Wraps
torch.distributions.poisson.Poisson
withTorchDistributionMixin
.
RelaxedBernoulliÂ¶

class
RelaxedBernoulli
(temperature, probs=None, logits=None, validate_args=None)Â¶ Wraps
torch.distributions.relaxed_bernoulli.RelaxedBernoulli
withTorchDistributionMixin
.
RelaxedOneHotCategoricalÂ¶

class
RelaxedOneHotCategorical
(temperature, probs=None, logits=None, validate_args=None)Â¶ Wraps
torch.distributions.relaxed_categorical.RelaxedOneHotCategorical
withTorchDistributionMixin
.
StudentTÂ¶

class
StudentT
(df, loc=0.0, scale=1.0, validate_args=None)Â¶ Wraps
torch.distributions.studentT.StudentT
withTorchDistributionMixin
.
TransformedDistributionÂ¶

class
TransformedDistribution
(base_distribution, transforms, validate_args=None)Â¶ Wraps
torch.distributions.transformed_distribution.TransformedDistribution
withTorchDistributionMixin
.
UniformÂ¶

class
Uniform
(low, high, validate_args=None)Â¶ Wraps
torch.distributions.uniform.Uniform
withTorchDistributionMixin
.
WeibullÂ¶

class
Weibull
(scale, concentration, validate_args=None)Â¶ Wraps
torch.distributions.weibull.Weibull
withTorchDistributionMixin
.
Pyro DistributionsÂ¶
Abstract DistributionÂ¶

class
Distribution
[source]Â¶ Bases:
object
Base class for parameterized probability distributions.
Distributions in Pyro are stochastic function objects with
sample()
andlog_prob()
methods. Distribution are stochastic functions with fixed parameters:d = dist.Bernoulli(param) x = d() # Draws a random sample. p = d.log_prob(x) # Evaluates log probability of x.
Implementing New Distributions:
Derived classes must implement the methods:
sample()
,log_prob()
.Examples:
Take a look at the examples to see how they interact with inference algorithms.

__call__
(*args, **kwargs)[source]Â¶ Samples a random value (just an alias for
.sample(*args, **kwargs)
).For tensor distributions, the returned tensor should have the same
.shape
as the parameters.Returns: A random value. Return type: torch.Tensor

enumerate_support
(expand=True)[source]Â¶ Returns a representation of the parametrized distributionâ€™s support, along the first dimension. This is implemented only by discrete distributions.
Note that this returns support values of all the batched RVs in lockstep, rather than the full cartesian product.
Parameters: expand (bool) â€“ whether to expand the result to a tensor of shape (n,) + batch_shape + event_shape
. If false, the return value has unexpanded shape(n,) + (1,)*len(batch_shape) + event_shape
which can be broadcasted to the full shape.Returns: An iterator over the distributionâ€™s discrete support. Return type: iterator

has_enumerate_support
= FalseÂ¶

has_rsample
= FalseÂ¶

log_prob
(x, *args, **kwargs)[source]Â¶ Evaluates log probability densities for each of a batch of samples.
Parameters: x (torch.Tensor) â€“ A single value or a batch of values batched along axis 0. Returns: log probability densities as a onedimensional Tensor
with same batch size as value and params. The shape of the result should beself.batch_size
.Return type: torch.Tensor

sample
(*args, **kwargs)[source]Â¶ Samples a random value.
For tensor distributions, the returned tensor should have the same
.shape
as the parameters, unless otherwise noted.Parameters: sample_shape (torch.Size) â€“ the size of the iid batch to be drawn from the distribution. Returns: A random value or batch of random values (if parameters are batched). The shape of the result should be self.shape()
.Return type: torch.Tensor

score_parts
(x, *args, **kwargs)[source]Â¶ Computes ingredients for stochastic gradient estimators of ELBO.
The default implementation is correct both for nonreparameterized and for fully reparameterized distributions. Partially reparameterized distributions should override this method to compute correct .score_function and .entropy_term parts.
Parameters: x (torch.Tensor) â€“ A single value or batch of values. Returns: A ScoreParts object containing parts of the ELBO estimator. Return type: ScoreParts

TorchDistributionMixinÂ¶

class
TorchDistributionMixin
[source]Â¶ Bases:
pyro.distributions.distribution.Distribution
Mixin to provide Pyro compatibility for PyTorch distributions.
You should instead use TorchDistribution for new distribution classes.
This is mainly useful for wrapping existing PyTorch distributions for use in Pyro. Derived classes must first inherit from
torch.distributions.distribution.Distribution
and then inherit fromTorchDistributionMixin
.
__call__
(sample_shape=torch.Size([]))[source]Â¶ Samples a random value.
This is reparameterized whenever possible, calling
rsample()
for reparameterized distributions andsample()
for nonreparameterized distributions.Parameters: sample_shape (torch.Size) â€“ the size of the iid batch to be drawn from the distribution. Returns: A random value or batch of random values (if parameters are batched). The shape of the result should be self.shape(). Return type: torch.Tensor

shape
(sample_shape=torch.Size([]))[source]Â¶ The tensor shape of samples from this distribution.
Samples are of shape:
d.shape(sample_shape) == sample_shape + d.batch_shape + d.event_shape
Parameters: sample_shape (torch.Size) â€“ the size of the iid batch to be drawn from the distribution. Returns: Tensor shape of samples. Return type: torch.Size

expand_by
(sample_shape)[source]Â¶ Expands a distribution by adding
sample_shape
to the left side of itsbatch_shape
.To expand internal dims of
self.batch_shape
from 1 to something larger, useexpand()
instead.Parameters: sample_shape (torch.Size) â€“ The size of the iid batch to be drawn from the distribution. Returns: An expanded version of this distribution. Return type: ReshapedDistribution

to_event
(reinterpreted_batch_ndims=None)[source]Â¶ Reinterprets the
n
rightmost dimensions of this distributionsbatch_shape
as event dims, adding them to the left side ofevent_shape
.Example:
>>> [d1.batch_shape, d1.event_shape] [torch.Size([2, 3]), torch.Size([4, 5])] >>> d2 = d1.to_event(1) >>> [d2.batch_shape, d2.event_shape] [torch.Size([2]), torch.Size([3, 4, 5])] >>> d3 = d1.to_event(2) >>> [d3.batch_shape, d3.event_shape] [torch.Size([]), torch.Size([2, 3, 4, 5])]
Parameters: reinterpreted_batch_ndims (int) â€“ The number of batch dimensions to reinterpret as event dimensions. Returns: A reshaped version of this distribution. Return type: pyro.distributions.torch.Independent

mask
(mask)[source]Â¶ Masks a distribution by a zeroone tensor that is broadcastable to the distributions
batch_shape
.Parameters: mask (torch.Tensor) â€“ A zeroone valued float tensor. Returns: A masked copy of this distribution. Return type: MaskedDistribution

TorchDistributionÂ¶

class
TorchDistribution
(batch_shape=torch.Size([]), event_shape=torch.Size([]), validate_args=None)[source]Â¶ Bases:
torch.distributions.distribution.Distribution
,pyro.distributions.torch_distribution.TorchDistributionMixin
Base class for PyTorchcompatible distributions with Pyro support.
This should be the base class for almost all new Pyro distributions.
Note
Parameters and data should be of type
Tensor
and all methods return typeTensor
unless otherwise noted.Tensor Shapes:
TorchDistributions provide a method
.shape()
for the tensor shape of samples:x = d.sample(sample_shape) assert x.shape == d.shape(sample_shape)
Pyro follows the same distribution shape semantics as PyTorch. It distinguishes between three different roles for tensor shapes of samples:
 sample shape corresponds to the shape of the iid samples drawn from the distribution. This is taken as an argument by the distributionâ€™s sample method.
 batch shape corresponds to nonidentical (independent) parameterizations of the distribution, inferred from the distributionâ€™s parameter shapes. This is fixed for a distribution instance.
 event shape corresponds to the event dimensions of the distribution, which is fixed for a distribution class. These are collapsed when we try to score a sample from the distribution via d.log_prob(x).
These shapes are related by the equation:
assert d.shape(sample_shape) == sample_shape + d.batch_shape + d.event_shape
Distributions provide a vectorized
log_prob()
method that evaluates the log probability density of each event in a batch independently, returning a tensor of shapesample_shape + d.batch_shape
:x = d.sample(sample_shape) assert x.shape == d.shape(sample_shape) log_p = d.log_prob(x) assert log_p.shape == sample_shape + d.batch_shape
Implementing New Distributions:
Derived classes must implement the methods
sample()
(orrsample()
if.has_rsample == True
) andlog_prob()
, and must implement the propertiesbatch_shape
, andevent_shape
. Discrete classes may also implement theenumerate_support()
method to improve gradient estimates and set.has_enumerate_support = True
.
AVFMultivariateNormalÂ¶

class
AVFMultivariateNormal
(loc, scale_tril, control_var)[source]Â¶ Bases:
pyro.distributions.torch.MultivariateNormal
Multivariate normal (Gaussian) distribution with transport equation inspired control variates (adaptive velocity fields).
A distribution over vectors in which all the elements have a joint Gaussian density.
Parameters:  loc (torch.Tensor) â€“ Ddimensional mean vector.
 scale_tril (torch.Tensor) â€“ Cholesky of Covariance matrix; D x D matrix.
 control_var (torch.Tensor) â€“ 2 x L x D tensor that parameterizes the control variate; L is an arbitrary positive integer. This parameter needs to be learned (i.e. adapted) to achieve lower variance gradients. In a typical use case this parameter will be adapted concurrently with the loc and scale_tril that define the distribution.
Example usage:
control_var = torch.tensor(0.1 * torch.ones(2, 1, D), requires_grad=True) opt_cv = torch.optim.Adam([control_var], lr=0.1, betas=(0.5, 0.999)) for _ in range(1000): d = AVFMultivariateNormal(loc, scale_tril, control_var) z = d.rsample() cost = torch.pow(z, 2.0).sum() cost.backward() opt_cv.step() opt_cv.zero_grad()

arg_constraints
= {'control_var': Real(), 'loc': Real(), 'scale_tril': LowerTriangular()}Â¶
BetaBinomialÂ¶

class
BetaBinomial
(concentration1, concentration0, total_count=1, validate_args=None)[source]Â¶ Bases:
pyro.distributions.torch_distribution.TorchDistribution
Compound distribution comprising of a betabinomial pair. The probability of success (
probs
for theBinomial
distribution) is unknown and randomly drawn from aBeta
distribution prior to a certain number of Bernoulli trials given bytotal_count
.Parameters: 
arg_constraints
= {'concentration0': GreaterThan(lower_bound=0.0), 'concentration1': GreaterThan(lower_bound=0.0), 'total_count': IntegerGreaterThan(lower_bound=0)}Â¶

concentration0
Â¶

concentration1
Â¶

has_enumerate_support
= TrueÂ¶

mean
Â¶

support
Â¶

variance
Â¶

DeltaÂ¶

class
Delta
(v, log_density=0.0, event_dim=0, validate_args=None)[source]Â¶ Bases:
pyro.distributions.torch_distribution.TorchDistribution
Degenerate discrete distribution (a single point).
Discrete distribution that assigns probability one to the single element in its support. Delta distribution parameterized by a random choice should not be used with MCMC based inference, as doing so produces incorrect results.
Parameters:  v (torch.Tensor) â€“ The single support element.
 log_density (torch.Tensor) â€“ An optional density for this Delta. This
is useful to keep the class of
Delta
distributions closed under differentiable transformation.  event_dim (int) â€“ Optional event dimension, defaults to zero.

arg_constraints
= {'log_density': Real(), 'v': Real()}Â¶

has_rsample
= TrueÂ¶

mean
Â¶

support
= Real()Â¶

variance
Â¶
DirichletMultinomialÂ¶

class
DirichletMultinomial
(concentration, total_count=1, is_sparse=False, validate_args=None)[source]Â¶ Bases:
pyro.distributions.torch_distribution.TorchDistribution
Compound distribution comprising of a dirichletmultinomial pair. The probability of classes (
probs
for theMultinomial
distribution) is unknown and randomly drawn from aDirichlet
distribution prior to a certain number of Categorical trials given bytotal_count
.Parameters:  or torch.Tensor concentration (float) â€“ concentration parameter (alpha) for the Dirichlet distribution.
 or torch.Tensor total_count (int) â€“ number of Categorical trials.
 is_sparse (bool) â€“ Whether to assume value is mostly zero when computing
log_prob()
, which can speed up computation when data is sparse.

arg_constraints
= {'concentration': GreaterThan(lower_bound=0.0), 'total_count': IntegerGreaterThan(lower_bound=0)}Â¶

concentration
Â¶

mean
Â¶

support
Â¶

variance
Â¶
EmpiricalDistributionÂ¶

class
Empirical
(samples, log_weights, validate_args=None)[source]Â¶ Bases:
pyro.distributions.torch_distribution.TorchDistribution
Empirical distribution associated with the sampled data. Note that the shape requirement for log_weights is that its shape must match the leftmost shape of samples. Samples are aggregated along the
aggregation_dim
, which is the rightmost dim of log_weights.Example:
>>> emp_dist = Empirical(torch.randn(2, 3, 10), torch.ones(2, 3)) >>> emp_dist.batch_shape torch.Size([2]) >>> emp_dist.event_shape torch.Size([10])
>>> single_sample = emp_dist.sample() >>> single_sample.shape torch.Size([2, 10]) >>> batch_sample = emp_dist.sample((100,)) >>> batch_sample.shape torch.Size([100, 2, 10])
>>> emp_dist.log_prob(single_sample).shape torch.Size([2]) >>> # Vectorized samples cannot be scored by log_prob. >>> with pyro.validation_enabled(): ... emp_dist.log_prob(batch_sample).shape Traceback (most recent call last): ... ValueError: ``value.shape`` must be torch.Size([2, 10])
Parameters:  samples (torch.Tensor) â€“ samples from the empirical distribution.
 log_weights (torch.Tensor) â€“ log weights (optional) corresponding to the samples.

arg_constraints
= {}Â¶

enumerate_support
(expand=True)[source]Â¶ See
pyro.distributions.torch_distribution.TorchDistribution.enumerate_support()

event_shape
Â¶ See
pyro.distributions.torch_distribution.TorchDistribution.event_shape()

has_enumerate_support
= TrueÂ¶

log_prob
(value)[source]Â¶ Returns the log of the probability mass function evaluated at
value
. Note that this currently only supports scoring values with emptysample_shape
.Parameters: value (torch.Tensor) â€“ scalar or tensor value to be scored.

log_weights
Â¶

mean
Â¶ See
pyro.distributions.torch_distribution.TorchDistribution.mean()

sample
(sample_shape=torch.Size([]))[source]Â¶ See
pyro.distributions.torch_distribution.TorchDistribution.sample()

sample_size
Â¶ Number of samples that constitute the empirical distribution.
Return int: number of samples collected.

support
= Real()Â¶

variance
Â¶ See
pyro.distributions.torch_distribution.TorchDistribution.variance()
GammaPoissonÂ¶

class
GammaPoisson
(concentration, rate, validate_args=None)[source]Â¶ Bases:
pyro.distributions.torch_distribution.TorchDistribution
Compound distribution comprising of a gammapoisson pair, also referred to as a gammapoisson mixture. The
rate
parameter for thePoisson
distribution is unknown and randomly drawn from aGamma
distribution.Note
This can be treated as an alternate parametrization of the
NegativeBinomial
(total_count
,probs
) distribution, with concentration = total_count and rate = (1  probs) / probs.Parameters: 
arg_constraints
= {'concentration': GreaterThan(lower_bound=0.0), 'rate': GreaterThan(lower_bound=0.0)}Â¶

concentration
Â¶

mean
Â¶

rate
Â¶

support
= IntegerGreaterThan(lower_bound=0)Â¶

variance
Â¶

GaussianScaleMixtureÂ¶

class
GaussianScaleMixture
(coord_scale, component_logits, component_scale)[source]Â¶ Bases:
pyro.distributions.torch_distribution.TorchDistribution
Mixture of Normal distributions with zero mean and diagonal covariance matrices.
That is, this distribution is a mixture with K components, where each component distribution is a Ddimensional Normal distribution with zero mean and a Ddimensional diagonal covariance matrix. The K different covariance matrices are controlled by the parameters coord_scale and component_scale. That is, the covariance matrix of the kâ€™th component is given by
Sigma_ii = (component_scale_k * coord_scale_i) ** 2 (i = 1, â€¦, D)
where component_scale_k is a positive scale factor and coord_scale_i are positive scale parameters shared between all K components. The mixture weights are controlled by a Kdimensional vector of softmax logits, component_logits. This distribution implements pathwise derivatives for samples from the distribution. This distribution does not currently support batched parameters.
See reference [1] for details on the implementations of the pathwise derivative. Please consider citing this reference if you use the pathwise derivative in your research.
[1] Pathwise Derivatives for Multivariate Distributions, Martin Jankowiak & Theofanis Karaletsos. arXiv:1806.01856
Note that this distribution supports both even and odd dimensions, but the former should be more a bit higher precision, since it doesnâ€™t use any erfs in the backward call. Also note that this distribution does not support D = 1.
Parameters:  coord_scale (torch.tensor) â€“ Ddimensional vector of scales
 component_logits (torch.tensor) â€“ Kdimensional vector of logits
 component_scale (torch.tensor) â€“ Kdimensional vector of scale multipliers

arg_constraints
= {'component_logits': Real(), 'component_scale': GreaterThan(lower_bound=0.0), 'coord_scale': GreaterThan(lower_bound=0.0)}Â¶

has_rsample
= TrueÂ¶
MaskedMixtureÂ¶

class
MaskedMixture
(mask, component0, component1, validate_args=None)[source]Â¶ Bases:
pyro.distributions.torch_distribution.TorchDistribution
A masked deterministic mixture of two distributions.
This is useful when the mask is sampled from another distribution, possibly correlated across the batch. Often the mask can be marginalized out via enumeration.
Example:
change_point = pyro.sample("change_point", dist.Categorical(torch.ones(len(data) + 1)), infer={'enumerate': 'parallel'}) mask = torch.arange(len(data), dtype=torch.long) >= changepoint with pyro.plate("data", len(data)): pyro.sample("obs", MaskedMixture(mask, dist1, dist2), obs=data)
Parameters:  mask (torch.Tensor) â€“ A byte tensor toggling between
component0
andcomponent1
.  component0 (pyro.distributions.TorchDistribution) â€“ a distribution
for batch elements
mask == 0
.  component1 (pyro.distributions.TorchDistribution) â€“ a distribution
for batch elements
mask == 1
.

arg_constraints
= {}Â¶

has_rsample
Â¶

support
Â¶
 mask (torch.Tensor) â€“ A byte tensor toggling between
MixtureOfDiagNormalsÂ¶

class
MixtureOfDiagNormals
(locs, coord_scale, component_logits)[source]Â¶ Bases:
pyro.distributions.torch_distribution.TorchDistribution
Mixture of Normal distributions with arbitrary means and arbitrary diagonal covariance matrices.
That is, this distribution is a mixture with K components, where each component distribution is a Ddimensional Normal distribution with a Ddimensional mean parameter and a Ddimensional diagonal covariance matrix. The K different component means are gathered into the K x D dimensional parameter locs and the K different scale parameters are gathered into the K x D dimensional parameter coord_scale. The mixture weights are controlled by a Kdimensional vector of softmax logits, component_logits. This distribution implements pathwise derivatives for samples from the distribution.
See reference [1] for details on the implementations of the pathwise derivative. Please consider citing this reference if you use the pathwise derivative in your research. Note that this distribution does not support dimension D = 1.
[1] Pathwise Derivatives for Multivariate Distributions, Martin Jankowiak & Theofanis Karaletsos. arXiv:1806.01856
Parameters:  locs (torch.Tensor) â€“ K x D mean matrix
 coord_scale (torch.Tensor) â€“ K x D scale matrix
 component_logits (torch.Tensor) â€“ Kdimensional vector of softmax logits

arg_constraints
= {'component_logits': Real(), 'coord_scale': GreaterThan(lower_bound=0.0), 'locs': Real()}Â¶

has_rsample
= TrueÂ¶
OMTMultivariateNormalÂ¶

class
OMTMultivariateNormal
(loc, scale_tril)[source]Â¶ Bases:
pyro.distributions.torch.MultivariateNormal
Multivariate normal (Gaussian) distribution with OMT gradients w.r.t. both parameters. Note the gradient computation w.r.t. the Cholesky factor has cost O(D^3), although the resulting gradient variance is generally expected to be lower.
A distribution over vectors in which all the elements have a joint Gaussian density.
Parameters:  loc (torch.Tensor) â€“ Mean.
 scale_tril (torch.Tensor) â€“ Cholesky of Covariance matrix.

arg_constraints
= {'loc': Real(), 'scale_tril': LowerTriangular()}Â¶
RelaxedBernoulliStraightThroughÂ¶

class
RelaxedBernoulliStraightThrough
(temperature, probs=None, logits=None, validate_args=None)[source]Â¶ Bases:
pyro.distributions.torch.RelaxedBernoulli
An implementation of
RelaxedBernoulli
with a straightthrough gradient estimator.This distribution has the following properties:
 The samples returned by the
rsample()
method are discrete/quantized.  The
log_prob()
method returns the log probability of the relaxed/unquantized sample using the GumbelSoftmax distribution.  In the backward pass the gradient of the sample with respect to the parameters of the distribution uses the relaxed/unquantized sample.
References:
 [1] The Concrete Distribution: A Continuous Relaxation of Discrete Random Variables,
 Chris J. Maddison, Andriy Mnih, Yee Whye Teh
 [2] Categorical Reparameterization with GumbelSoftmax,
 Eric Jang, Shixiang Gu, Ben Poole
 The samples returned by the
RelaxedOneHotCategoricalStraightThroughÂ¶

class
RelaxedOneHotCategoricalStraightThrough
(temperature, probs=None, logits=None, validate_args=None)[source]Â¶ Bases:
pyro.distributions.torch.RelaxedOneHotCategorical
An implementation of
RelaxedOneHotCategorical
with a straightthrough gradient estimator.This distribution has the following properties:
 The samples returned by the
rsample()
method are discrete/quantized.  The
log_prob()
method returns the log probability of the relaxed/unquantized sample using the GumbelSoftmax distribution.  In the backward pass the gradient of the sample with respect to the parameters of the distribution uses the relaxed/unquantized sample.
References:
 [1] The Concrete Distribution: A Continuous Relaxation of Discrete Random Variables,
 Chris J. Maddison, Andriy Mnih, Yee Whye Teh
 [2] Categorical Reparameterization with GumbelSoftmax,
 Eric Jang, Shixiang Gu, Ben Poole
 The samples returned by the
RejectorÂ¶

class
Rejector
(propose, log_prob_accept, log_scale)[source]Â¶ Bases:
pyro.distributions.torch_distribution.TorchDistribution
Rejection sampled distribution given an acceptance rate function.
Parameters:  propose (Distribution) â€“ A proposal distribution that samples batched
proposals via
propose()
.rsample()
supports asample_shape
arg only ifpropose()
supports asample_shape
arg.  log_prob_accept (callable) â€“ A callable that inputs a batch of proposals and returns a batch of log acceptance probabilities.
 log_scale â€“ Total log probability of acceptance.

has_rsample
= TrueÂ¶
 propose (Distribution) â€“ A proposal distribution that samples batched
proposals via
VonMisesÂ¶

class
VonMises
(loc, concentration, validate_args=None)[source]Â¶ Bases:
pyro.distributions.torch_distribution.TorchDistribution
A circular von Mises distribution.
This implementation uses polar coordinates. The
loc
andvalue
args can be any real number (to facilitate unconstrained optimization), but are interpreted as angles modulo 2 pi.See
VonMises3D
for a 3D cartesian coordinate cousin of this distribution.Parameters:  loc (torch.Tensor) â€“ an angle in radians.
 concentration (torch.Tensor) â€“ concentration parameter

arg_constraints
= {'concentration': GreaterThan(lower_bound=0.0), 'loc': Real()}Â¶

has_rsample
= FalseÂ¶

mean
Â¶ The provided mean is the circular one.

sample
(**kwargs)[source]Â¶ The sampling algorithm for the von Mises distribution is based on the following paper: Best, D. J., and Nicholas I. Fisher. â€śEfficient simulation of the von Mises distribution.â€ť Applied Statistics (1979): 152157.

support
= Real()Â¶

variance
Â¶ The provided variance is the circular one.
VonMises3DÂ¶

class
VonMises3D
(concentration, validate_args=None)[source]Â¶ Bases:
pyro.distributions.torch_distribution.TorchDistribution
Spherical von Mises distribution.
This implementation combines the direction parameter and concentration parameter into a single combined parameter that contains both direction and magnitude. The
value
arg is represented in cartesian coordinates: it must be a normalized 3vector that lies on the 2sphere.See
VonMises
for a 2D polar coordinate cousin of this distribution.Currently only
log_prob()
is implemented.Parameters: concentration (torch.Tensor) â€“ A combined locationandconcentration vector. The direction of this vector is the location, and its magnitude is the concentration. 
arg_constraints
= {'concentration': Real()}Â¶

support
= Real()Â¶

Transformed DistributionsÂ¶
InverseAutoRegressiveFlowÂ¶

class
InverseAutoregressiveFlow
(autoregressive_nn, log_scale_min_clip=5.0, log_scale_max_clip=3.0)[source]Â¶ Bases:
pyro.distributions.torch_transform.TransformModule
An implementation of Inverse Autoregressive Flow, using Eq (10) from Kingma Et Al., 2016,
\(\mathbf{y} = \mu_t + \sigma_t\odot\mathbf{x}\)where \(\mathbf{x}\) are the inputs, \(\mathbf{y}\) are the outputs, \(\mu_t,\sigma_t\) are calculated from an autoregressive network on \(\mathbf{x}\), and \(\sigma_t>0\).
Together with TransformedDistribution this provides a way to create richer variational approximations.
Example usage:
>>> from pyro.nn import AutoRegressiveNN >>> base_dist = dist.Normal(torch.zeros(10), torch.ones(10)) >>> iaf = InverseAutoregressiveFlow(AutoRegressiveNN(10, [40])) >>> iaf_module = pyro.module("my_iaf", iaf) >>> iaf_dist = dist.TransformedDistribution(base_dist, [iaf]) >>> iaf_dist.sample() tensor([0.4071, 0.5030, 0.7924, 0.2366, 0.2387, 0.1417, 0.0868, 0.1389, 0.4629, 0.0986])
The inverse of the Bijector is required when, e.g., scoring the log density of a sample with TransformedDistribution. This implementation caches the inverse of the Bijector when its forward operation is called, e.g., when sampling from TransformedDistribution. However, if the cached value isnâ€™t available, either because it was already popped from the cache, or an arbitary value is being scored, it will calculate it manually. Note that this is an operation that scales as O(D) where D is the input dimension, and so should be avoided for large dimensional uses. So in general, it is cheap to sample from IAF and score a value that was sampled by IAF, but expensive to score an arbitrary value.
Parameters:  autoregressive_nn (nn.Module) â€“ an autoregressive neural network whose forward call returns a realvalued mean and logitscale as a tuple
 log_scale_min_clip (float) â€“ The minimum value for clipping the log(scale) from the autoregressive NN
 log_scale_max_clip (float) â€“ The maximum value for clipping the log(scale) from the autoregressive NN
References:
1. Improving Variational Inference with Inverse Autoregressive Flow [arXiv:1606.04934] Diederik P. Kingma, Tim Salimans, Rafal Jozefowicz, Xi Chen, Ilya Sutskever, Max Welling
2. Variational Inference with Normalizing Flows [arXiv:1505.05770] Danilo Jimenez Rezende, Shakir Mohamed
3. MADE: Masked Autoencoder for Distribution Estimation [arXiv:1502.03509] Mathieu Germain, Karol Gregor, Iain Murray, Hugo Larochelle

codomain
= Real()Â¶
InverseAutoRegressiveFlowStableÂ¶

class
InverseAutoregressiveFlowStable
(autoregressive_nn, sigmoid_bias=2.0)[source]Â¶ Bases:
pyro.distributions.torch_transform.TransformModule
An implementation of an Inverse Autoregressive Flow, using Eqs (13)/(14) from Kingma Et Al., 2016,
\(\mathbf{y} = \sigma_t\odot\mathbf{x} + (1\sigma_t)\odot\mu_t\)where \(\mathbf{x}\) are the inputs, \(\mathbf{y}\) are the outputs, \(\mu_t,\sigma_t\) are calculated from an autoregressive network on \(\mathbf{x}\), and \(\sigma_t\) is restricted to \([0,1]\).
This variant of IAF is claimed by the authors to be more numerically stable than one using Eq (10), although in practice it leads to a restriction on the distributions that can be represented, presumably since the input is restricted to rescaling by a number on \([0,1]\).
Example usage:
>>> from pyro.nn import AutoRegressiveNN >>> base_dist = dist.Normal(torch.zeros(10), torch.ones(10)) >>> iaf = InverseAutoregressiveFlowStable(AutoRegressiveNN(10, [40])) >>> iaf_module = pyro.module("my_iaf", iaf) >>> iaf_dist = dist.TransformedDistribution(base_dist, [iaf]) >>> iaf_dist.sample() tensor([0.4071, 0.5030, 0.7924, 0.2366, 0.2387, 0.1417, 0.0868, 0.1389, 0.4629, 0.0986])
See InverseAutoregressiveFlow docs for a discussion of the running cost.
Parameters:  autoregressive_nn (nn.Module) â€“ an autoregressive neural network whose forward call returns a realvalued mean and logitscale as a tuple
 sigmoid_bias (float) â€“ bias on the hidden units fed into the sigmoid; default=`2.0`
References:
1. Improving Variational Inference with Inverse Autoregressive Flow [arXiv:1606.04934] Diederik P. Kingma, Tim Salimans, Rafal Jozefowicz, Xi Chen, Ilya Sutskever, Max Welling
2. Variational Inference with Normalizing Flows [arXiv:1505.05770] Danilo Jimenez Rezende, Shakir Mohamed
3. MADE: Masked Autoencoder for Distribution Estimation [arXiv:1502.03509] Mathieu Germain, Karol Gregor, Iain Murray, Hugo Larochelle

codomain
= Real()Â¶
PermuteTransformÂ¶

class
PermuteTransform
(permutation)[source]Â¶ Bases:
torch.distributions.transforms.Transform
A bijection that reorders the input dimensions, that is, multiplies the input by a permutation matrix. This is useful in between
InverseAutoregressiveFlow
transforms to increase the flexibility of the resulting distribution and stabilize learning. Whilst not being an autoregressive transform, the log absolute determinate of the Jacobian is easily calculable as 0. Note that reordering the input dimension between two layers ofInverseAutoregressiveFlow
is not equivalent to reordering the dimension inside the MADE networks that those IAFs use; using a PermuteTransform results in a distribution with more flexibility.Example usage:
>>> from pyro.nn import AutoRegressiveNN >>> from pyro.distributions import InverseAutoregressiveFlow, PermuteTransform >>> base_dist = dist.Normal(torch.zeros(10), torch.ones(10)) >>> iaf1 = InverseAutoregressiveFlow(AutoRegressiveNN(10, [40])) >>> ff = PermuteTransform(torch.randperm(10, dtype=torch.long)) >>> iaf2 = InverseAutoregressiveFlow(AutoRegressiveNN(10, [40])) >>> iaf_dist = dist.TransformedDistribution(base_dist, [iaf1, ff, iaf2]) >>> iaf_dist.sample() tensor([0.4071, 0.5030, 0.7924, 0.2366, 0.2387, 0.1417, 0.0868, 0.1389, 0.4629, 0.0986])
Parameters: permutation (torch.LongTensor) â€“ a permutation ordering that is applied to the inputs. 
bijective
= TrueÂ¶

codomain
= Real()Â¶

log_abs_det_jacobian
(x, y)[source]Â¶ Calculates the elementwise determinant of the log Jacobian, i.e. log(abs([dy_0/dx_0, â€¦, dy_{N1}/dx_{N1}])). Note that this type of transform is not autoregressive, so the log Jacobian is not the sum of the previous expression. However, it turns out itâ€™s always 0 (since the determinant is 1 or +1), and so returning a vector of zeros works.

PlanarFlowÂ¶

class
PlanarFlow
(input_dim)[source]Â¶ Bases:
pyro.distributions.torch_transform.TransformModule
A â€planarâ€™ normalizing flow that uses the transformation
\(\mathbf{y} = \mathbf{x} + \mathbf{u}\tanh(\mathbf{w}^T\mathbf{z}+b)\)where \(\mathbf{x}\) are the inputs, \(\mathbf{y}\) are the outputs, and the learnable parameters are \(b\in\mathbb{R}\), \(\mathbf{u}\in\mathbb{R}^D\), \(\mathbf{w}\in\mathbb{R}^D\) for input dimension \(D\). For this to be an invertible transformation, the condition \(\mathbf{w}^T\mathbf{u}>1\) is enforced.
Together with TransformedDistribution this provides a way to create richer variational approximations.
Example usage:
>>> base_dist = dist.Normal(torch.zeros(10), torch.ones(10)) >>> plf = PlanarFlow(10) >>> plf_module = pyro.module("my_plf", plf) >>> plf_dist = dist.TransformedDistribution(base_dist, [plf]) >>> plf_dist.sample() tensor([0.4071, 0.5030, 0.7924, 0.2366, 0.2387, 0.1417, 0.0868, 0.1389, 0.4629, 0.0986])
The inverse of this transform does not possess an analytical solution and is left unimplemented. However, the inverse is cached when the forward operation is called during sampling, and so samples drawn using planar flow can be scored.
Parameters: input_dim â€“ the dimension of the input (and output) variable. References:
Variational Inference with Normalizing Flows [arXiv:1505.05770] Danilo Jimenez Rezende, Shakir Mohamed

codomain
= Real()Â¶

TransformModuleÂ¶

class
TransformModule
[source]Â¶ Bases:
torch.distributions.transforms.Transform
,torch.nn.modules.module.Module
Transforms with learnable parameters such as normalizing flows should inherit from this class rather than Transform so they are also a subclass of nn.Module and inherit all the useful methods of that class.
ParametersÂ¶
Parameters in Pyro are basically thin wrappers around PyTorch Tensors that carry unique names. As such Parameters are the primary stateful objects in Pyro. Users typically interact with parameters via the Pyro primitive pyro.param. Parameters play a central role in stochastic variational inference, where they are used to represent point estimates for the parameters in parameterized families of models and guides.
ParamStoreÂ¶

class
ParamStoreDict
[source]Â¶ Bases:
object
Global store for parameters in Pyro. This is basically a keyvalue store. The typical user interacts with the ParamStore primarily through the primitive pyro.param.
See Intro Part II for further discussion and SVI Part I for some examples.
Some things to bear in mind when using parameters in Pyro:
 parameters must be assigned unique names
 the init_tensor argument to pyro.param is only used the first time that a given (named) parameter is registered with Pyro.
 for this reason, a user may need to use the clear() method if working in a REPL in order to get the desired behavior. this method can also be invoked with pyro.clear_param_store().
 the internal name of a parameter within a PyTorch nn.Module that has been registered with Pyro is prepended with the Pyro name of the module. so nothing prevents the user from having two different modules each of which contains a parameter named weight. by contrast, a user can only have one toplevel parameter named weight (outside of any module).
 parameters can be saved and loaded from disk using save and load.

setdefault
(name, init_constrained_value, constraint=Real())[source]Â¶ Retrieve a constrained parameter value from the if it exists, otherwise set the initial value. Note that this is a little fancier than
dict.setdefault()
.If the parameter already exists,
init_constrained_tensor
will be ignored. To avoid expensive creation ofinit_constrained_tensor
you can wrap it in alambda
that will only be evaluated if the parameter does not already exist:param_store.get("foo", lambda: (0.001 * torch.randn(1000, 1000)).exp(), constraint=constraints.positive)
Parameters:  name (str) â€“ parameter name
 init_constrained_value (torch.Tensor or callable returning a torch.Tensor) â€“ initial constrained value
 constraint (torch.distributions.constraints.Constraint) â€“ torch constraint object
Returns: constrained parameter value
Return type:

named_parameters
()[source]Â¶ Returns an iterator over
(name, unconstrained_value)
tuples for each parameter in the ParamStore.

get_param
(name, init_tensor=None, constraint=Real())[source]Â¶ Get parameter from its name. If it does not yet exist in the ParamStore, it will be created and stored. The Pyro primitive pyro.param dispatches to this method.
Parameters:  name (str) â€“ parameter name
 init_tensor (torch.Tensor) â€“ initial tensor
 constraint (torch.distributions.constraints.Constraint) â€“ torch constraint
Returns: parameter
Return type:

match
(name)[source]Â¶ Get all parameters that match regex. The parameter must exist.
Parameters: name (str) â€“ regular expression Returns: dict with key param name and value torch Tensor

param_name
(p)[source]Â¶ Get parameter name from parameter
Parameters: p â€“ parameter Returns: parameter name

load
(filename, map_location=None)[source]Â¶ Loads parameters from disk
Note
If using
pyro.module()
on parameters loaded from disk, be sure to set theupdate_module_params
flag:pyro.get_param_store().load('saved_params.save') pyro.module('module', nn, update_module_params=True)
Parameters:  filename (str) â€“ file name to load from
 map_location (function, torch.device, string or a dict) â€“ specifies how to remap storage locations
Neural NetworkÂ¶
The module pyro.nn provides implementations of neural network modules that are useful in the context of deep probabilistic programming. None of these modules is really part of the core language.
AutoRegressiveNNÂ¶

class
AutoRegressiveNN
(input_dim, hidden_dims, param_dims=[1, 1], permutation=None, skip_connections=False, nonlinearity=ReLU())[source]Â¶ Bases:
torch.nn.modules.module.Module
An implementation of a MADElike autoregressive neural network.
Example usage:
>>> x = torch.randn(100, 10) >>> arn = AutoRegressiveNN(10, [50], param_dims=[1]) >>> p = arn(x) # 1 parameters of size (100, 10) >>> arn = AutoRegressiveNN(10, [50], param_dims=[1, 1]) >>> m, s = arn(x) # 2 parameters of size (100, 10) >>> arn = AutoRegressiveNN(10, [50], param_dims=[1, 5, 3]) >>> a, b, c = arn(x) # 3 parameters of sizes, (100, 1, 10), (100, 5, 10), (100, 3, 10)
Parameters:  input_dim (int) â€“ the dimensionality of the input
 hidden_dims (list[int]) â€“ the dimensionality of the hidden units per layer
 param_dims (list[int]) â€“ shape the output into parameters of dimension (p_n, input_dim) for p_n in param_dims when p_n > 1 and dimension (input_dim) when p_n == 1. The default is [1, 1], i.e. output two parameters of dimension (input_dim), which is useful for inverse autoregressive flow.
 permutation (torch.LongTensor) â€“ an optional permutation that is applied to the inputs and controls the order of the autoregressive factorization. in particular for the identity permutation the autoregressive structure is such that the Jacobian is upper triangular. By default this is chosen at random.
 skip_connections (bool) â€“ Whether to add skip connections from the input to the output.
 nonlinearity (torch.nn.module) â€“ The nonlinearity to use in the feedforward network such as torch.nn.ReLU(). Note that no nonlinearity is applied to the final network output, so the output is an unbounded real number.
Reference:
MADE: Masked Autoencoder for Distribution Estimation [arXiv:1502.03509] Mathieu Germain, Karol Gregor, Iain Murray, Hugo Larochelle

class
MaskedLinear
(in_features, out_features, mask, bias=True)[source]Â¶ Bases:
torch.nn.modules.linear.Linear
A linear mapping with a given mask on the weights (arbitrary bias)
Parameters:  in_features (int) â€“ the number of input features
 out_features (int) â€“ the number of output features
 mask (torch.Tensor) â€“ the mask to apply to the in_features x out_features weight matrix
 bias (bool) â€“ whether or not MaskedLinear should include a bias term. defaults to True

create_mask
(input_dim, observed_dim, hidden_dims, permutation, output_dim_multiplier)[source]Â¶ Creates MADE masks for a conditional distribution
Parameters:  input_dim (int) â€“ the dimensionality of the input variable
 observed_dim (int) â€“ the dimensionality of the variable that is conditioned on (for conditional densities)
 hidden_dims (list[int]) â€“ the dimensionality of the hidden layers(s)
 permutation (torch.LongTensor) â€“ the order of the input variables
 output_dim_multiplier (int) â€“ tiles the output (e.g. for when a separate mean and scale parameter are desired)
OptimizationÂ¶
The module pyro.optim provides support for optimization in Pyro. In particular it provides PyroOptim, which is used to wrap PyTorch optimizers and manage optimizers for dynamically generated parameters (see the tutorial SVI Part I for a discussion). Any custom optimization algorithms are also to be found here.
Pyro OptimizersÂ¶

class
PyroOptim
(optim_constructor, optim_args)[source]Â¶ Bases:
object
A wrapper for torch.optim.Optimizer objects that helps with managing dynamically generated parameters.
Parameters:  optim_constructor â€“ a torch.optim.Optimizer
 optim_args â€“ a dictionary of learning arguments for the optimizer or a callable that returns such dictionaries

__call__
(params, *args, **kwargs)[source]Â¶ Parameters: params (an iterable of strings) â€“ a list of parameters Do an optimization step for each param in params. If a given param has never been seen before, initialize an optimizer for it.

get_state
()[source]Â¶ Get state associated with all the optimizers in the form of a dictionary with keyvalue pairs (parameter name, optim state dicts)

AdagradRMSProp
(optim_args)[source]Â¶ A wrapper for an optimizer that is a mashup of
Adagrad
andRMSprop
.

ClippedAdam
(optim_args)[source]Â¶ A wrapper for a modification of the
Adam
optimization algorithm that supports gradient clipping.

class
PyroLRScheduler
(scheduler_constructor, optim_args)[source]Â¶ Bases:
pyro.optim.optim.PyroOptim
A wrapper for torch.optim.lr_scheduler objects that adjust learning rates for dynamically generated parameters.
Parameters:  optim_constructor â€“ a torch.optim.lr_scheduler
 optim_args â€“ a dictionary of learning arguments for the optimizer or a callable that returns such dictionaries. must contain the key â€optimizerâ€™ with pytorch optimizer value
Example:
optimizer = torch.optim.SGD pyro_scheduler = pyro.optim.ExponentialLR({'optimizer': optimizer, 'optim_args': {'lr': 0.01}, 'gamma': 0.1}) svi = SVI(model, guide, pyro_scheduler, loss=TraceGraph_ELBO()) svi.step()
PyTorch OptimizersÂ¶

Adamax
(optim_args)Â¶ Wraps
torch.optim.Adamax
withPyroOptim
.

Adagrad
(optim_args)Â¶ Wraps
torch.optim.Adagrad
withPyroOptim
.

SGD
(optim_args)Â¶ Wraps
torch.optim.SGD
withPyroOptim
.

Adam
(optim_args)Â¶ Wraps
torch.optim.Adam
withPyroOptim
.

Rprop
(optim_args)Â¶ Wraps
torch.optim.Rprop
withPyroOptim
.

ASGD
(optim_args)Â¶ Wraps
torch.optim.ASGD
withPyroOptim
.

RMSprop
(optim_args)Â¶ Wraps
torch.optim.RMSprop
withPyroOptim
.

SparseAdam
(optim_args)Â¶ Wraps
torch.optim.SparseAdam
withPyroOptim
.

Adadelta
(optim_args)Â¶ Wraps
torch.optim.Adadelta
withPyroOptim
.

MultiStepLR
(optim_args)Â¶ Wraps
torch.optim.MultiStepLR
withPyroLRScheduler
.

ReduceLROnPlateau
(optim_args)Â¶ Wraps
torch.optim.ReduceLROnPlateau
withPyroLRScheduler
.

StepLR
(optim_args)Â¶ Wraps
torch.optim.StepLR
withPyroLRScheduler
.

CosineAnnealingLR
(optim_args)Â¶ Wraps
torch.optim.CosineAnnealingLR
withPyroLRScheduler
.

LambdaLR
(optim_args)Â¶ Wraps
torch.optim.LambdaLR
withPyroLRScheduler
.

ExponentialLR
(optim_args)Â¶ Wraps
torch.optim.ExponentialLR
withPyroLRScheduler
.
HigherOrder OptimizersÂ¶

class
MultiOptimizer
[source]Â¶ Bases:
object
Base class of optimizers that make use of higherorder derivatives.
Higherorder optimizers generally use
torch.autograd.grad()
rather thantorch.Tensor.backward()
, and therefore require a different interface from usual Pyro and PyTorch optimizers. In this interface, thestep()
method inputs aloss
tensor to be differentiated, and backpropagation is triggered one or more times inside the optimizer.Derived classes must implement
step()
to compute derivatives and update parameters inplace.Example:
tr = poutine.trace(model).get_trace(*args, **kwargs) loss = tr.log_prob_sum() params = {name: site['value'].unconstrained() for name, site in tr.nodes.items() if site['type'] == 'param'} optim.step(loss, params)

step
(loss, params)[source]Â¶ Performs an inplace optimization step on parameters given a differentiable
loss
tensor.Note that this detaches the updated tensors.
Parameters:  loss (torch.Tensor) â€“ A differentiable tensor to be minimized. Some optimizers require this to be differentiable multiple times.
 params (dict) â€“ A dictionary mapping param name to unconstrained value as stored in the param store.

get_step
(loss, params)[source]Â¶ Computes an optimization step of parameters given a differentiable
loss
tensor, returning the updated values.Note that this preserves derivatives on the updated tensors.
Parameters:  loss (torch.Tensor) â€“ A differentiable tensor to be minimized. Some optimizers require this to be differentiable multiple times.
 params (dict) â€“ A dictionary mapping param name to unconstrained value as stored in the param store.
Returns: A dictionary mapping param name to updated unconstrained value.
Return type:


class
PyroMultiOptimizer
(optim)[source]Â¶ Bases:
pyro.optim.multi.MultiOptimizer
Facade to wrap
PyroOptim
objects in aMultiOptimizer
interface.

class
TorchMultiOptimizer
(optim_constructor, optim_args)[source]Â¶ Bases:
pyro.optim.multi.PyroMultiOptimizer
Facade to wrap
Optimizer
objects in aMultiOptimizer
interface.

class
MixedMultiOptimizer
(parts)[source]Â¶ Bases:
pyro.optim.multi.MultiOptimizer
Container class to combine different
MultiOptimizer
instances for different parameters.Parameters: parts (list) â€“ A list of (names, optim)
pairs, where eachnames
is a list of parameter names, and eachoptim
is aMultiOptimizer
orPyroOptim
object to be used for the named parameters. Together thenames
should partition up all desired parameters to optimize.Raises: ValueError â€“ if any name is optimized by multiple optimizers.

class
Newton
(trust_radii={})[source]Â¶ Bases:
pyro.optim.multi.MultiOptimizer
Implementation of
MultiOptimizer
that performs a Newton update on batched lowdimensional variables, optionally regularizing via a perparametertrust_radius
. Seenewton_step()
for details.The result of
get_step()
will be differentiable, however the updated values fromstep()
will be detached.Parameters: trust_radii (dict) â€“ a dict mapping parameter name to radius of trust region. Missing names will use unregularized Newton update, equivalent to infinite trust radius.
Poutine (Effect handlers)Â¶
Beneath the builtin inference algorithms, Pyro has a library of composable effect handlers for creating new inference algorithms and working with probabilistic programs. Pyroâ€™s inference algorithms are all built by applying these handlers to stochastic functions.
HandlersÂ¶
Poutine is a library of composable effect handlers for recording and modifying the behavior of Pyro programs. These lowerlevel ingredients simplify the implementation of new inference algorithms and behavior.
Handlers can be used as higherorder functions, decorators, or context managers to modify the behavior of functions or blocks of code:
For example, consider the following Pyro program:
>>> def model(x):
... s = pyro.param("s", torch.tensor(0.5))
... z = pyro.sample("z", dist.Normal(x, s))
... return z ** 2
We can mark sample sites as observed using condition
,
which returns a callable with the same input and output signatures as model
:
>>> conditioned_model = poutine.condition(model, data={"z": 1.0})
We can also use handlers as decorators:
>>> @pyro.condition(data={"z": 1.0})
... def model(x):
... s = pyro.param("s", torch.tensor(0.5))
... z = pyro.sample("z", dist.Normal(x, s))
... return z ** 2
Or as context managers:
>>> with pyro.condition(data={"z": 1.0}):
... s = pyro.param("s", torch.tensor(0.5))
... z = pyro.sample("z", dist.Normal(0., s))
... y = z ** 2
Handlers compose freely:
>>> conditioned_model = poutine.condition(model, data={"z": 1.0})
>>> traced_model = poutine.trace(conditioned_model)
Many inference algorithms or algorithmic components can be implemented in just a few lines of code:
guide_tr = poutine.trace(guide).get_trace(...)
model_tr = poutine.trace(poutine.replay(conditioned_model, trace=guide_tr)).get_trace(...)
monte_carlo_elbo = model_tr.log_prob_sum()  guide_tr.log_prob_sum()

block
(fn=None, hide_fn=None, expose_fn=None, hide=None, expose=None, hide_types=None, expose_types=None)[source]Â¶ This handler selectively hides Pyro primitive sites from the outside world. Default behavior: block everything.
A site is hidden if at least one of the following holds:
hide_fn(msg) is True
or(not expose_fn(msg)) is True
msg["name"] in hide
msg["type"] in hide_types
msg["name"] not in expose and msg["type"] not in expose_types
hide
,hide_types
, andexpose_types
are allNone
For example, suppose the stochastic function fn has two sample sites â€śaâ€ť and â€śbâ€ť. Then any effect outside of
BlockMessenger(fn, hide=["a"])
will not be applied to site â€śaâ€ť and will only see site â€śbâ€ť:>>> def fn(): ... a = pyro.sample("a", dist.Normal(0., 1.)) ... return pyro.sample("b", dist.Normal(a, 1.)) >>> fn_inner = trace(fn) >>> fn_outer = trace(block(fn_inner, hide=["a"])) >>> trace_inner = fn_inner.get_trace() >>> trace_outer = fn_outer.get_trace() >>> "a" in trace_inner True >>> "a" in trace_outer False >>> "b" in trace_inner True >>> "b" in trace_outer True
Parameters:  fn â€“ a stochastic function (callable containing Pyro primitive calls)
 hide_fn â€“ function that takes a site and returns True to hide the site or False/None to expose it. If specified, all other parameters are ignored. Only specify one of hide_fn or expose_fn, not both.
 expose_fn â€“ function that takes a site and returns True to expose the site or False/None to hide it. If specified, all other parameters are ignored. Only specify one of hide_fn or expose_fn, not both.
 hide â€“ list of site names to hide
 expose â€“ list of site names to be exposed while all others hidden
 hide_types â€“ list of site types to be hidden
 expose_types â€“ list of site types to be exposed while all others hidden
Returns: stochastic function decorated with a
BlockMessenger

broadcast
(fn=None)[source]Â¶ Automatically broadcasts the batch shape of the stochastic function at a sample site when inside a single or nested plate context. The existing batch_shape must be broadcastable with the size of the
plate
contexts installed in the cond_indep_stack.Notice how model_automatic_broadcast below automates expanding of distribution batch shapes. This makes it easy to modularize a Pyro model as the subcomponents are agnostic of the wrapping
plate
contexts.>>> def model_broadcast_by_hand(): ... with IndepMessenger("batch", 100, dim=2): ... with IndepMessenger("components", 3, dim=1): ... sample = pyro.sample("sample", dist.Bernoulli(torch.ones(3) * 0.5) ... .expand_by(100)) ... assert sample.shape == torch.Size((100, 3)) ... return sample
>>> @poutine.broadcast ... def model_automatic_broadcast(): ... with IndepMessenger("batch", 100, dim=2): ... with IndepMessenger("components", 3, dim=1): ... sample = pyro.sample("sample", dist.Bernoulli(torch.tensor(0.5))) ... assert sample.shape == torch.Size((100, 3)) ... return sample

condition
(fn=None, data=None)[source]Â¶ Given a stochastic function with some sample statements and a dictionary of observations at names, change the sample statements at those names into observes with those values.
Consider the following Pyro program:
>>> def model(x): ... s = pyro.param("s", torch.tensor(0.5)) ... z = pyro.sample("z", dist.Normal(x, s)) ... return z ** 2
To observe a value for site z, we can write
>>> conditioned_model = condition(model, data={"z": torch.tensor(1.)})
This is equivalent to adding obs=value as a keyword argument to pyro.sample(â€śzâ€ť, â€¦) in model.
Parameters:  fn â€“ a stochastic function (callable containing Pyro primitive calls)
 data â€“ a dict or a
Trace
Returns: stochastic function decorated with a
ConditionMessenger

do
(fn=None, data=None)[source]Â¶ Given a stochastic function with some sample statements and a dictionary of values at names, set the return values of those sites equal to the values and hide them from the rest of the stack as if they were hardcoded to those values by using
block
.Consider the following Pyro program:
>>> def model(x): ... s = pyro.param("s", torch.tensor(0.5)) ... z = pyro.sample("z", dist.Normal(x, s)) ... return z ** 2
To intervene with a value for site z, we can write
>>> intervened_model = do(model, data={"z": torch.tensor(1.)})
This is equivalent to replacing z = pyro.sample(â€śzâ€ť, â€¦) with z = value.
Parameters:  fn â€“ a stochastic function (callable containing Pyro primitive calls)
 data â€“ a
dict
or aTrace
Returns: stochastic function decorated with a
BlockMessenger
andpyro.poutine.condition_messenger.ConditionMessenger

enum
(fn=None, first_available_dim=None)[source]Â¶ Enumerates in parallel over discrete sample sites marked
infer={"enumerate": "parallel"}
.Parameters: first_available_dim (int) â€“ The first tensor dimension (counting from the right) that is available for parallel enumeration. This dimension and all dimensions left may be used internally by Pyro. This should be a negative integer.

escape
(fn=None, escape_fn=None)[source]Â¶ Given a callable that contains Pyro primitive calls, evaluate escape_fn on each site, and if the result is True, raise a
NonlocalExit
exception that stops execution and returns the offending site.Parameters:  fn â€“ a stochastic function (callable containing Pyro primitive calls)
 escape_fn â€“ function that takes a partial trace and a site, and returns a boolean value to decide whether to exit at that site
Returns: stochastic function decorated with
EscapeMessenger

infer_config
(fn=None, config_fn=None)[source]Â¶ Given a callable that contains Pyro primitive calls and a callable taking a trace site and returning a dictionary, updates the value of the infer kwarg at a sample site to config_fn(site).
Parameters:  fn â€“ a stochastic function (callable containing Pyro primitive calls)
 config_fn â€“ a callable taking a site and returning an infer dict
Returns: stochastic function decorated with
InferConfigMessenger

lift
(fn=None, prior=None)[source]Â¶ Given a stochastic function with param calls and a prior distribution, create a stochastic function where all param calls are replaced by sampling from prior. Prior should be a callable or a dict of names to callables.
Consider the following Pyro program:
>>> def model(x): ... s = pyro.param("s", torch.tensor(0.5)) ... z = pyro.sample("z", dist.Normal(x, s)) ... return z ** 2 >>> lifted_model = lift(model, prior={"s": dist.Exponential(0.3)})
lift
makesparam
statements behave likesample
statements using the distributions inprior
. In this example, site s will now behave as if it was replaced withs = pyro.sample("s", dist.Exponential(0.3))
:>>> tr = trace(lifted_model).get_trace(0.0) >>> tr.nodes["s"]["type"] == "sample" True >>> tr2 = trace(lifted_model).get_trace(0.0) >>> bool((tr2.nodes["s"]["value"] == tr.nodes["s"]["value"]).all()) False
Parameters:  fn â€“ function whose parameters will be lifted to random values
 prior â€“ prior function in the form of a Distribution or a dict of stochastic fns
Returns: fn
decorated with aLiftMessenger

markov
(fn=None, history=1, keep=False)[source]Â¶ Markov dependency declaration.
This can be used in a variety of ways:  as a context manager  as a decorator for recursive functions  as an iterator for markov chains
Parameters:  history (int) â€“ The number of previous contexts visible from the
current context. Defaults to 1. If zero, this is similar to
pyro.plate
.  keep (bool) â€“ If true, frames are replayable. This is important
when branching: if
keep=True
, neighboring branches at the same level can depend on each other; ifkeep=False
, neighboring branches are independent (conditioned on their shareâ€ť
 history (int) â€“ The number of previous contexts visible from the
current context. Defaults to 1. If zero, this is similar to

mask
(fn=None, mask=None)[source]Â¶ Given a stochastic function with some batched sample statements and masking tensor, mask out some of the sample statements elementwise.
Parameters:  fn â€“ a stochastic function (callable containing Pyro primitive calls)
 mask (torch.ByteTensor) â€“ a
{0,1}
valued masking tensor (1 includes a site, 0 excludes a site)
Returns: stochastic function decorated with a
MaskMessenger

queue
(fn=None, queue=None, max_tries=None, extend_fn=None, escape_fn=None, num_samples=None)[source]Â¶ Used in sequential enumeration over discrete variables.
Given a stochastic function and a queue, return a return value from a complete trace in the queue.
Parameters:  fn â€“ a stochastic function (callable containing Pyro primitive calls)
 queue â€“ a queue data structure like multiprocessing.Queue to hold partial traces
 max_tries â€“ maximum number of attempts to compute a single complete trace
 extend_fn â€“ function (possibly stochastic) that takes a partial trace and a site, and returns a list of extended traces
 escape_fn â€“ function (possibly stochastic) that takes a partial trace and a site, and returns a boolean value to decide whether to exit
 num_samples â€“ optional number of extended traces for extend_fn to return
Returns: stochastic function decorated with poutine logic

replay
(fn=None, trace=None, params=None)[source]Â¶ Given a callable that contains Pyro primitive calls, return a callable that runs the original, reusing the values at sites in trace at those sites in the new trace
Consider the following Pyro program:
>>> def model(x): ... s = pyro.param("s", torch.tensor(0.5)) ... z = pyro.sample("z", dist.Normal(x, s)) ... return z ** 2
replay
makessample
statements behave as if they had sampled the values at the corresponding sites in the trace:>>> old_trace = trace(model).get_trace(1.0) >>> replayed_model = replay(model, trace=old_trace) >>> bool(replayed_model(0.0) == old_trace.nodes["_RETURN"]["value"]) True
Parameters:  fn â€“ a stochastic function (callable containing Pyro primitive calls)
 trace â€“ a
Trace
data structure to replay against  params â€“ dict of names of param sites and constrained values in fn to replay against
Returns: a stochastic function decorated with a
ReplayMessenger

scale
(fn=None, scale=None)[source]Â¶ Given a stochastic function with some sample statements and a positive scale factor, scale the score of all sample and observe sites in the function.
Consider the following Pyro program:
>>> def model(x): ... s = pyro.param("s", torch.tensor(0.5)) ... z = pyro.sample("z", dist.Normal(x, s), obs=1.0) ... return z ** 2
scale
multiplicatively scales the logprobabilities of sample sites:>>> scaled_model = scale(model, scale=0.5) >>> scaled_tr = trace(scaled_model).get_trace(0.0) >>> unscaled_tr = trace(model).get_trace(0.0) >>> bool((scaled_tr.log_prob_sum() == 0.5 * unscaled_tr.log_prob_sum()).all()) True
Parameters:  fn â€“ a stochastic function (callable containing Pyro primitive calls)
 scale â€“ a positive scaling factor
Returns: stochastic function decorated with a
ScaleMessenger

trace
(fn=None, graph_type=None, param_only=None)[source]Â¶ Return a handler that records the inputs and outputs of primitive calls and their dependencies.
Consider the following Pyro program:
>>> def model(x): ... s = pyro.param("s", torch.tensor(0.5)) ... z = pyro.sample("z", dist.Normal(x, s)) ... return z ** 2
We can record its execution using
trace
and use the resulting data structure to compute the logjoint probability of all of the sample sites in the execution or extract all parameters.>>> trace = trace(model).get_trace(0.0) >>> logp = trace.log_prob_sum() >>> params = [trace.nodes[name]["value"].unconstrained() for name in trace.param_nodes]
Parameters:  fn â€“ a stochastic function (callable containing Pyro primitive calls)
 graph_type â€“ string that specifies the kind of graph to construct
 param_only â€“ if true, only records params and not samples
Returns: stochastic function decorated with a
TraceMessenger

config_enumerate
(guide=None, default='parallel', expand=False, num_samples=None)[source]Â¶ Configures enumeration for all relevant sites in a guide. This is mainly used in conjunction with
TraceEnum_ELBO
.When configuring for exhaustive enumeration of discrete variables, this configures all sample sites whose distribution satisfies
.has_enumerate_support == True
. When configuring for local parallel Monte Carlo sampling viadefault="parallel", num_samples=n
, this configures all sample sites. This does not overwrite existing annotationsinfer={"enumerate": ...}
.This can be used as either a function:
guide = config_enumerate(guide)
or as a decorator:
@config_enumerate def guide1(*args, **kwargs): ... @config_enumerate(default="sequential", expand=True) def guide2(*args, **kwargs): ...
Parameters:  guide (callable) â€“ a pyro model that will be used as a guide in
SVI
.  default (str) â€“ Which enumerate strategy to use, one of â€śsequentialâ€ť, â€śparallelâ€ť, or None. Defaults to â€śparallelâ€ť.
 expand (bool) â€“ Whether to expand enumerated sample values. See
enumerate_support()
for details. This only applies to exhaustive enumeration, wherenum_samples=None
. Ifnum_samples
is notNone
, then this samples will always be expanded.  num_samples (int or None) â€“ if not
None
, use local Monte Carlo sampling rather than exhaustive enumeration. This makes sense for both continuous and discrete distributions.
Returns: an annotated guide
Return type: callable
 guide (callable) â€“ a pyro model that will be used as a guide in
TraceÂ¶

class
Trace
(graph_type='flat')[source]Â¶ Bases:
object
Graph data structure denoting the relationships amongst different pyro primitives in the execution trace.
An execution trace of a Pyro program is a record of every call to
pyro.sample()
andpyro.param()
in a single execution of that program. Traces are directed graphs whose nodes represent primitive calls or input/output, and whose edges represent conditional dependence relationships between those primitive calls. They are created and populated bypoutine.trace
.Each node (or site) in a trace contains the name, input and output value of the site, as well as additional metadata added by inference algorithms or user annotation. In the case of
pyro.sample
, the trace also includes the stochastic function at the site, and any observed data added by users.Consider the following Pyro program:
>>> def model(x): ... s = pyro.param("s", torch.tensor(0.5)) ... z = pyro.sample("z", dist.Normal(x, s)) ... return z ** 2
We can record its execution using
pyro.poutine.trace
and use the resulting data structure to compute the logjoint probability of all of the sample sites in the execution or extract all parameters.>>> trace = pyro.poutine.trace(model).get_trace(0.0) >>> logp = trace.log_prob_sum() >>> params = [trace.nodes[name]["value"].unconstrained() for name in trace.param_nodes]
We can also inspect or manipulate individual nodes in the trace.
trace.nodes
contains acollections.OrderedDict
of site names and metadata corresponding tox
,s
,z
, and the return value:>>> list(name for name in trace.nodes.keys()) ["_INPUT", "s", "z", "_RETURN"]
Values of
trace.nodes
are dictionaries of node metadata:>>> trace.nodes["z"] {'type': 'sample', 'name': 'z', 'is_observed': False, 'fn': Normal(), 'value': tensor(0.6480), 'args': (), 'kwargs': {}, 'infer': {}, 'scale': 1.0, 'cond_indep_stack': (), 'done': True, 'stop': False, 'continuation': None}
'infer'
is a dictionary of user or algorithmspecified metadata.'args'
and'kwargs'
are the arguments passed viapyro.sample
tofn.__call__
orfn.log_prob
.'scale'
is used to scale the logprobability of the site when computing the logjoint.'cond_indep_stack'
contains data structures corresponding topyro.plate
contexts appearing in the execution.'done'
,'stop'
, and'continuation'
are only used by Pyroâ€™s internals.Parameters: graph_type (string) â€“ string specifying the kind of trace graph to construct 
add_node
(site_name, **kwargs)[source]Â¶ Parameters: site_name (string) â€“ the name of the site to be added Adds a site to the trace.
Raises an error when attempting to add a duplicate node instead of silently overwriting.

compute_log_prob
(site_filter=<function <lambda>>)[source]Â¶ Compute the sitewise log probabilities of the trace. Each
log_prob
has shape equal to the correspondingbatch_shape
. Eachlog_prob_sum
is a scalar. Both computations are memoized.

compute_score_parts
()[source]Â¶ Compute the batched local score parts at each site of the trace. Each
log_prob
has shape equal to the correspondingbatch_shape
. Eachlog_prob_sum
is a scalar. All computations are memoized.

edges
Â¶

format_shapes
(title='Trace Shapes:', last_site=None)[source]Â¶ Returns a string showing a table of the shapes of all sites in the trace.

log_prob_sum
(site_filter=<function <lambda>>)[source]Â¶ Compute the sitewise log probabilities of the trace. Each
log_prob
has shape equal to the correspondingbatch_shape
. Eachlog_prob_sum
is a scalar. The computation oflog_prob_sum
is memoized.Returns: total log probability. Return type: torch.Tensor

nonreparam_stochastic_nodes
Â¶ Returns: a list of names of sample sites whose stochastic functions are not reparameterizable primitive distributions

observation_nodes
Â¶ Returns: a list of names of observe sites

pack_tensors
(plate_to_symbol=None)[source]Â¶ Computes packed representations of tensors in the trace. This should be called after
compute_log_prob()
orcompute_score_parts()
.

param_nodes
Â¶ Returns: a list of names of param sites

reparameterized_nodes
Â¶ Returns: a list of names of sample sites whose stochastic functions are reparameterizable primitive distributions

stochastic_nodes
Â¶ Returns: a list of names of sample sites

MessengersÂ¶
Messenger objects contain the implementations of the effects exposed by handlers. Advanced users may modify the implementations of messengers behind existing handlers or write new messengers that implement new effects and compose correctly with the rest of the library.
MessengerÂ¶

class
Messenger
[source]Â¶ Bases:
object
Context manager class that modifies behavior and adds side effects to stochastic functions i.e. callables containing Pyro primitive statements.
This is the base Messenger class. It implements the default behavior for all Pyro primitives, so that the joint distribution induced by a stochastic function fn is identical to the joint distribution induced by
Messenger()(fn)
.Class of transformers for messages passed during inference. Most inference operations are implemented in subclasses of this.

classmethod
register
(fn=None, type=None, post=None)[source]Â¶ Parameters:  fn â€“ function implementing operation
 type (str) â€“ name of the operation
(also passed to
effectful()
)  post (bool) â€“ if True, use this operation as postprocess
Dynamically add operations to an effect. Useful for generating wrappers for libraries.
Example:
@SomeMessengerClass.register def some_function(msg) ...do_something... return msg

classmethod
unregister
(fn=None, type=None)[source]Â¶ Parameters:  fn â€“ function implementing operation
 type (str) â€“ name of the operation
(also passed to
effectful()
)
Dynamically remove operations from an effect. Useful for removing wrappers from libraries.
Example:
SomeMessengerClass.unregister(some_function, "name")

classmethod
BlockMessengerÂ¶

class
BlockMessenger
(hide_fn=None, expose_fn=None, hide_all=True, expose_all=False, hide=None, expose=None, hide_types=None, expose_types=None)[source]Â¶ Bases:
pyro.poutine.messenger.Messenger
This Messenger selectively hides Pyro primitive sites from the outside world. Default behavior: block everything. BlockMessenger has a flexible interface that allows users to specify in several different ways which sites should be hidden or exposed.
A site is hidden if at least one of the following holds:
hide_fn(msg) is True
or(not expose_fn(msg)) is True
msg["name"] in hide
msg["type"] in hide_types
msg["name"] not in expose and msg["type"] not in expose_types
hide
,hide_types
, andexpose_types
are allNone
For example, suppose the stochastic function fn has two sample sites â€śaâ€ť and â€śbâ€ť. Then any poutine outside of BlockMessenger(fn, hide=[â€śaâ€ť]) will not be applied to site â€śaâ€ť and will only see site â€śbâ€ť:
>>> def fn(): ... a = pyro.sample("a", dist.Normal(0., 1.)) ... return pyro.sample("b", dist.Normal(a, 1.))
>>> fn_inner = TraceMessenger()(fn) >>> fn_outer = TraceMessenger()(BlockMessenger(hide=["a"])(TraceMessenger()(fn))) >>> trace_inner = fn_inner.get_trace() >>> trace_outer = fn_outer.get_trace() >>> "a" in trace_inner True >>> "a" in trace_outer False >>> "b" in trace_inner True >>> "b" in trace_outer True
See the constructor for details.
Parameters:  hide_fn â€“ function that takes a site and returns True to hide the site or False/None to expose it. If specified, all other parameters are ignored. Only specify one of hide_fn or expose_fn, not both.
 expose_fn â€“ function that takes a site and returns True to expose the site or False/None to hide it. If specified, all other parameters are ignored. Only specify one of hide_fn or expose_fn, not both.
 hide_all (bool) â€“ hide all sites
 expose_all (bool) â€“ expose all sites normally
 hide (list) â€“ list of site names to hide, rest will be exposed normally
 expose (list) â€“ list of site names to expose, rest will be hidden
 hide_types (list) â€“ list of site types to hide, rest will be exposed normally
 expose_types (list) â€“ list of site types to expose normally, rest will be hidden
BroadcastMessengerÂ¶

class
BroadcastMessenger
[source]Â¶ Bases:
pyro.poutine.messenger.Messenger
BroadcastMessenger automatically broadcasts the batch shape of the stochastic function at a sample site when inside a single or nested plate context. The existing batch_shape must be broadcastable with the size of the
plate
contexts installed in the cond_indep_stack.
ConditionMessengerÂ¶

class
ConditionMessenger
(data)[source]Â¶ Bases:
pyro.poutine.messenger.Messenger
Adds values at observe sites to condition on data and override sampling
EscapeMessengerÂ¶

class
EscapeMessenger
(escape_fn)[source]Â¶ Bases:
pyro.poutine.messenger.Messenger
Messenger that does a nonlocal exit by raising a util.NonlocalExit exception
IndepMessengerÂ¶

class
CondIndepStackFrame
[source]Â¶ Bases:
pyro.poutine.indep_messenger.CondIndepStackFrame

vectorized
Â¶


class
IndepMessenger
(name=None, size=None, dim=None, device=None)[source]Â¶ Bases:
pyro.poutine.messenger.Messenger
This messenger keeps track of stack of independence information declared by nested
plate
contexts. This information is stored in acond_indep_stack
at each sample/observe site for consumption byTraceMessenger
.Example:
x_axis = IndepMessenger('outer', 320, dim=1) y_axis = IndepMessenger('inner', 200, dim=2) with x_axis: x_noise = sample("x_noise", dist.Normal(loc, scale).expand_by([320])) with y_axis: y_noise = sample("y_noise", dist.Normal(loc, scale).expand_by([200, 1])) with x_axis, y_axis: xy_noise = sample("xy_noise", dist.Normal(loc, scale).expand_by([200, 320]))

indices
Â¶

LiftMessengerÂ¶

class
LiftMessenger
(prior)[source]Â¶ Bases:
pyro.poutine.messenger.Messenger
Messenger which â€śliftsâ€ť parameters to random samples. Given a stochastic function with param calls and a prior, creates a stochastic function where all param calls are replaced by sampling from prior.
Prior should be a callable or a dict of names to callables.
ReplayMessengerÂ¶

class
ReplayMessenger
(trace=None, params=None)[source]Â¶ Bases:
pyro.poutine.messenger.Messenger
Messenger for replaying from an existing execution trace.
ScaleMessengerÂ¶

class
ScaleMessenger
(scale)[source]Â¶ Bases:
pyro.poutine.messenger.Messenger
This messenger rescales the log probability score.
This is typically used for data subsampling or for stratified sampling of data (e.g. in fraud detection where negatives vastly outnumber positives).
Parameters: scale (float or torch.Tensor) â€“ a positive scaling factor
TraceMessengerÂ¶

class
TraceHandler
(msngr, fn)[source]Â¶ Bases:
object
Execution trace poutine.
A TraceHandler records the input and output to every Pyro primitive and stores them as a site in a Trace(). This should, in theory, be sufficient information for every inference algorithm (along with the implicit computational graph in the Variables?)
We can also use this for visualization.

get_trace
(*args, **kwargs)[source]Â¶ Returns: data structure Return type: pyro.poutine.Trace Helper method for a very common use case. Calls this poutine and returns its trace instead of the functionâ€™s return value.

trace
Â¶


class
TraceMessenger
(graph_type=None, param_only=None)[source]Â¶ Bases:
pyro.poutine.messenger.Messenger
Execution trace messenger.
A TraceMessenger records the input and output to every Pyro primitive and stores them as a site in a Trace(). This should, in theory, be sufficient information for every inference algorithm (along with the implicit computational graph in the Variables?)
We can also use this for visualization.

get_trace
()[source]Â¶ Returns: data structure Return type: pyro.poutine.Trace Helper method for a very common use case. Returns a shallow copy of
self.trace
.

RuntimeÂ¶

exception
NonlocalExit
(site, *args, **kwargs)[source]Â¶ Bases:
exceptions.Exception
Exception for exiting nonlocally from poutine execution.
Used by poutine.EscapeMessenger to return site information.

am_i_wrapped
()[source]Â¶ Checks whether the current computation is wrapped in a poutine. :returns: bool

apply_stack
(initial_msg)[source]Â¶ Execute the effect stack at a single site according to the following scheme:
 For each
Messenger
in the stack from bottom to top, executeMessenger._process_message
with the message; if the message field â€śstopâ€ť is True, stop; otherwise, continue  Apply default behavior (
default_process_message
) to finish remaining site execution  For each
Messenger
in the stack from top to bottom, execute_postprocess_message
to update the message and internal messenger state with the site results  If the message field â€ścontinuationâ€ť is not
None
, call it with the message
Parameters: initial_msg (dict) â€“ the starting version of the trace site Returns: None
 For each

default_process_message
(msg)[source]Â¶ Default method for processing messages in inference.
Parameters: msg â€“ a message to be processed Returns: None

effectful
(fn=None, type=None)[source]Â¶ Parameters:  fn â€“ function or callable that performs an effectful computation
 type (str) â€“ the type label of the operation, e.g. â€śsampleâ€ť
Wrapper for calling
apply_stack()
to apply any active effects.
UtilitiesÂ¶

all_escape
(trace, msg)[source]Â¶ Parameters:  trace â€“ a partial trace
 msg â€“ the message at a Pyro primitive site
Returns: boolean decision value
Utility function that checks if a site is not already in a trace.
Used by EscapeMessenger to decide whether to do a nonlocal exit at a site. Subroutine for approximately integrating out variables for variance reduction.

discrete_escape
(trace, msg)[source]Â¶ Parameters:  trace â€“ a partial trace
 msg â€“ the message at a Pyro primitive site
Returns: boolean decision value
Utility function that checks if a sample site is discrete and not already in a trace.
Used by EscapeMessenger to decide whether to do a nonlocal exit at a site. Subroutine for integrating out discrete variables for variance reduction.

enum_extend
(trace, msg, num_samples=None)[source]Â¶ Parameters:  trace â€“ a partial trace
 msg â€“ the message at a Pyro primitive site
 num_samples â€“ maximum number of extended traces to return.
Returns: a list of traces, copies of input trace with one extra site
Utility function to copy and extend a trace with sites based on the input site whose values are enumerated from the support of the input siteâ€™s distribution.
Used for exact inference and integrating out discrete variables.

mc_extend
(trace, msg, num_samples=None)[source]Â¶ Parameters:  trace â€“ a partial trace
 msg â€“ the message at a Pyro primitive site
 num_samples â€“ maximum number of extended traces to return.
Returns: a list of traces, copies of input trace with one extra site
Utility function to copy and extend a trace with sites based on the input site whose values are sampled from the input siteâ€™s function.
Used for Monte Carlo marginalization of individual sample sites.
Miscellaneous OpsÂ¶
The pyro.ops
module implements tensor utilities
that are mostly independent of the rest of Pyro.
Utilities for HMCÂ¶

class
DualAveraging
(prox_center=0, t0=10, kappa=0.75, gamma=0.05)[source]Â¶ Bases:
object
Dual Averaging is a scheme to solve convex optimization problems. It belongs to a class of subgradient methods which uses subgradients to update parameters (in primal space) of a model. Under some conditions, the averages of generated parameters during the scheme are guaranteed to converge to an optimal value. However, a counterintuitive aspect of traditional subgradient methods is â€śnew subgradients enter the model with decreasing weightsâ€ť (see \([1]\)). Dual Averaging scheme solves that phenomenon by updating parameters using weights equally for subgradients (which lie in a dual space), hence we have the name â€śdual averagingâ€ť.
This class implements a dual averaging scheme which is adapted for Markov chain Monte Carlo (MCMC) algorithms. To be more precise, we will replace subgradients by some statistics calculated during an MCMC trajectory. In addition, introducing some free parameters such as
t0
andkappa
is helpful and still guarantees the convergence of the scheme.References
[1] Primaldual subgradient methods for convex problems, Yurii Nesterov
[2] The NoUturn sampler: adaptively setting path lengths in Hamiltonian Monte Carlo, Matthew D. Hoffman, Andrew Gelman
Parameters:  prox_center (float) â€“ A â€śproxcenterâ€ť parameter introduced in \([1]\) which pulls the primal sequence towards it.
 t0 (float) â€“ A free parameter introduced in \([2]\) that stabilizes the initial steps of the scheme.
 kappa (float) â€“ A free parameter introduced in \([2]\)
that controls the weights of steps of the scheme.
For a small
kappa
, the scheme will quickly forget states from early steps. This should be a number in \((0.5, 1]\).  gamma (float) â€“ A free parameter which controls the speed of the convergence of the scheme.

velocity_verlet
(z, r, potential_fn, inverse_mass_matrix, step_size, num_steps=1, z_grads=None)[source]Â¶ Second order symplectic integrator that uses the velocity verlet algorithm.
Parameters:  z (dict) â€“ dictionary of sample site names and their current values
(type
Tensor
).  r (dict) â€“ dictionary of sample site names and corresponding momenta
(type
Tensor
).  potential_fn (callable) â€“ function that returns potential energy given z
for each sample site. The negative gradient of the function with respect
to
z
determines the rate of change of the corresponding sitesâ€™ momentar
.  inverse_mass_matrix (torch.Tensor) â€“ a tensor \(M^{1}\) which is used to calculate kinetic energy: \(E_{kinetic} = \frac{1}{2}z^T M^{1} z\). Here \(M\) can be a 1D tensor (diagonal matrix) or a 2D tensor (dense matrix).
 step_size (float) â€“ step size for each time step iteration.
 num_steps (int) â€“ number of discrete time steps over which to integrate.
 z_grads (torch.Tensor) â€“ optional gradients of potential energy at current
z
.
Return tuple (z_next, r_next, z_grads, potential_energy): next position and momenta, together with the potential energy and its gradient w.r.t.
z_next
. z (dict) â€“ dictionary of sample site names and their current values
(type
Newton OptimizersÂ¶

newton_step
(loss, x, trust_radius=None)[source]Â¶ Performs a Newton update step to minimize loss on a batch of variables, optionally constraining to a trust region [1].
This is especially usful because the final solution of newton iteration is differentiable wrt the inputs, even when all but the final
x
is detached, due to this methodâ€™s quadratic convergence [2].loss
must be twicedifferentiable as a function ofx
. Ifloss
is2+d
times differentiable, then the return value of this function isd
times differentiable.When
loss
is interpreted as a negative log probability density, then the return valuesmode,cov
of this function can be used to construct a Laplace approximationMultivariateNormal(mode,cov)
.Warning
Take care to detach the result of this function when used in an optimization loop. If you forget to detach the result of this function during optimization, then backprop will propagate through the entire iteration process, and worse will compute two extra derivatives for each step.
Example use inside a loop:
x = torch.zeros(1000, 2) # arbitrary initial value for step in range(100): x = x.detach() # block gradients through previous steps x.requires_grad = True # ensure loss is differentiable wrt x loss = my_loss_function(x) x = newton_step(loss, x, trust_radius=1.0) # the final x is still differentiable
 [1] Yuan, Yaxiang. Iciam. Vol. 99. 2000.
 â€śA review of trust region algorithms for optimization.â€ť ftp://ftp.cc.ac.cn/pub/yyx/papers/p995.pdf
 [2] Christianson, Bruce. Optimization Methods and Software 3.4 (1994)
 â€śReverse accumulation and attractive fixed points.â€ť http://uhra.herts.ac.uk/bitstream/handle/2299/4338/903839.pdf
Parameters:  loss (torch.Tensor) â€“ A scalar function of
x
to be minimized.  x (torch.Tensor) â€“ A dependent variable of shape
(N, D)
whereN
is the batch size andD
is a small number.  trust_radius (float) â€“ An optional trust region trust_radius. The
updated value
mode
of this function will be withintrust_radius
of the inputx
.
Returns: A pair
(mode, cov)
wheremode
is an updated tensor of the same shape as the original valuex
, andcov
is an esitmate of the covariance DxD matrix withcov.shape == x.shape[:1] + (D,D)
.Return type:

newton_step_1d
(loss, x, trust_radius=None)[source]Â¶ Performs a Newton update step to minimize loss on a batch of 1dimensional variables, optionally regularizing to constrain to a trust region.
See
newton_step()
for details.Parameters:  loss (torch.Tensor) â€“ A scalar function of
x
to be minimized.  x (torch.Tensor) â€“ A dependent variable with rightmost size of 1.
 trust_radius (float) â€“ An optional trust region trust_radius. The
updated value
mode
of this function will be withintrust_radius
of the inputx
.
Returns: A pair
(mode, cov)
wheremode
is an updated tensor of the same shape as the original valuex
, andcov
is an esitmate of the covariance 1x1 matrix withcov.shape == x.shape[:1] + (1,1)
.Return type:  loss (torch.Tensor) â€“ A scalar function of

newton_step_2d
(loss, x, trust_radius=None)[source]Â¶ Performs a Newton update step to minimize loss on a batch of 2dimensional variables, optionally regularizing to constrain to a trust region.
See
newton_step()
for details.Parameters:  loss (torch.Tensor) â€“ A scalar function of
x
to be minimized.  x (torch.Tensor) â€“ A dependent variable with rightmost size of 2.
 trust_radius (float) â€“ An optional trust region trust_radius. The
updated value
mode
of this function will be withintrust_radius
of the inputx
.
Returns: A pair
(mode, cov)
wheremode
is an updated tensor of the same shape as the original valuex
, andcov
is an esitmate of the covariance 2x2 matrix withcov.shape == x.shape[:1] + (2,2)
.Return type:  loss (torch.Tensor) â€“ A scalar function of

newton_step_3d
(loss, x, trust_radius=None)[source]Â¶ Performs a Newton update step to minimize loss on a batch of 3dimensional variables, optionally regularizing to constrain to a trust region.
See
newton_step()
for details.Parameters:  loss (torch.Tensor) â€“ A scalar function of
x
to be minimized.  x (torch.Tensor) â€“ A dependent variable with rightmost size of 2.
 trust_radius (float) â€“ An optional trust region trust_radius. The
updated value
mode
of this function will be withintrust_radius
of the inputx
.
Returns: A pair
(mode, cov)
wheremode
is an updated tensor of the same shape as the original valuex
, andcov
is an esitmate of the covariance 3x3 matrix withcov.shape == x.shape[:1] + (3,3)
.Return type:  loss (torch.Tensor) â€“ A scalar function of
Tensor ContractionÂ¶

contract_expression
(equation, *shapes, **kwargs)[source]Â¶ Wrapper around
opt_einsum.contract_expression()
that optionally uses Pyroâ€™s cheap optimizer and optionally caches contraction paths.Parameters: cache_path (bool) â€“ whether to cache the contraction path. Defaults to True.

contract
(equation, *operands, **kwargs)[source]Â¶ Wrapper around
opt_einsum.contract()
that optionally uses Pyroâ€™s cheap optimizer and optionally caches contraction paths.Parameters: cache_path (bool) â€“ whether to cache the contraction path. Defaults to True.

einsum
(equation, *operands, **kwargs)[source]Â¶ Generalized plated sumproduct algorithm via tensor variable elimination.
This generalizes
contract()
in two ways: Multiple outputs are allowed, and intermediate results can be shared.
 Inputs and outputs can be plated along symbols given in
plates
; reductions alongplates
are product reductions.
The best way to understand this function is to try the examples below, which show how
einsum()
calls can be implemented as multiple calls tocontract()
(which is generally more expensive).To illustrate multiple outputs, note that the following are equivalent:
z1, z2, z3 = einsum('ab,bc>a,b,c', x, y) # multiple outputs z1 = contract('ab,bc>a', x, y) z2 = contract('ab,bc>b', x, y) z3 = contract('ab,bc>c', x, y)
To illustrate plated inputs, note that the following are equivalent:
assert len(x) == 3 and len(y) == 3 z = einsum('ab,ai,bi>b', w, x, y, plates='i') z = contract('ab,a,a,a,b,b,b>b', w, *x, *y)
When a sum dimension a always appears with a plate dimension i, then a corresponds to a distinct symbol for each slice of a. Thus the following are equivalent:
assert len(x) == 3 and len(y) == 3 z = einsum('ai,ai>', x, y, plates='i') z = contract('a,b,c,a,b,c>', *x, *y)
When such a sum dimension appears in the output, it must be accompanied by all of its plate dimensions, e.g. the following are equivalent:
assert len(x) == 3 and len(y) == 3 z = einsum('abi,abi>bi', x, y, plates='i') z0 = contract('ab,ac,ad,ab,ac,ad>b', *x, *y) z1 = contract('ab,ac,ad,ab,ac,ad>c', *x, *y) z2 = contract('ab,ac,ad,ab,ac,ad>d', *x, *y) z = torch.stack([z0, z1, z2])
Note that each plate slice through the output is multilinear in all plate slices through all inptus, thus e.g. batch matrix multiply would be implemented without
plates
, so the following are all equivalent:xy = einsum('abc,acd>abd', x, y, plates='') xy = torch.stack([xa.mm(ya) for xa, ya in zip(x, y)]) xy = torch.bmm(x, y)
Among all valid equations, some computations are polynomial in the sizes of the input tensors and other computations are exponential in the sizes of the input tensors. This function raises
NotImplementedError
whenever the computation is exponential.Parameters:  equation (str) â€“ An einsum equation, optionally with multiple outputs.
 operands (torch.Tensor) â€“ A collection of tensors.
 plates (str) â€“ An optional string of plate symbols.
 backend (str) â€“ An optional einsum backend, defaults to â€torchâ€™.
 cache (dict) â€“ An optional
shared_intermediates()
cache.  modulo_total (bool) â€“ Optionally allow einsum to arbitrarily scale each result plate, which can significantly reduce computation. This is safe to set whenever each result plate denotes a nonnormalized probability distribution whose total is not of interest.
Returns: a tuple of tensors of requested shape, one entry per output.
Return type: Raises:  ValueError â€“ if tensor sizes mismatch or an output requests a plated dim without that dimâ€™s plates.
 NotImplementedError â€“ if contraction would have cost exponential in the size of any input tensor.
Statistical UtilitiesÂ¶

gelman_rubin
(input, chain_dim=0, sample_dim=1)[source]Â¶ Computes Rhat over chains of samples. It is required that
input.size(sample_dim) >= 2
andinput.size(chain_dim) >= 2
.Parameters:  input (torch.Tensor) â€“ the input tensor.
 chain_dim (int) â€“ the chain dimension.
 sample_dim (int) â€“ the sample dimension.
Returns torch.Tensor: Rhat of
input
.

split_gelman_rubin
(input, chain_dim=0, sample_dim=1)[source]Â¶ Computes Rhat over chains of samples. It is required that
input.size(sample_dim) >= 4
.Parameters:  input (torch.Tensor) â€“ the input tensor.
 chain_dim (int) â€“ the chain dimension.
 sample_dim (int) â€“ the sample dimension.
Returns torch.Tensor: split Rhat of
input
.

autocorrelation
(input, dim=0)[source]Â¶ Computes the autocorrelation of samples at dimension
dim
.Reference: https://en.wikipedia.org/wiki/Autocorrelation#Efficient_computation
Parameters:  input (torch.Tensor) â€“ the input tensor.
 dim (int) â€“ the dimension to calculate autocorrelation.
Returns torch.Tensor: autocorrelation of
input
.

autocovariance
(input, dim=0)[source]Â¶ Computes the autocovariance of samples at dimension
dim
.Parameters:  input (torch.Tensor) â€“ the input tensor.
 dim (int) â€“ the dimension to calculate autocorrelation.
Returns torch.Tensor: autocorrelation of
input
.

effective_sample_size
(input, chain_dim=0, sample_dim=1)[source]Â¶ Computes effective sample size of input.
Reference:
 [1] Introduction to Markov Chain Monte Carlo,
 Charles J. Geyer
 [2] Stan Reference Manual version 2.18,
 Stan Development Team
Parameters:  input (torch.Tensor) â€“ the input tensor.
 chain_dim (int) â€“ the chain dimension.
 sample_dim (int) â€“ the sample dimension.
Returns torch.Tensor: effective sample size of
input
.

resample
(input, num_samples, dim=0, replacement=False)[source]Â¶ Draws
num_samples
samples frominput
at dimensiondim
.Parameters:  input (torch.Tensor) â€“ the input tensor.
 num_samples (int) â€“ the number of samples to draw from
input
.  dim (int) â€“ dimension to draw from
input
.
Returns torch.Tensor: samples drawn randomly from
input
.

quantile
(input, probs, dim=0)[source]Â¶ Computes quantiles of
input
atprobs
. Ifprobs
is a scalar, the output will be squeezed atdim
.Parameters:  input (torch.Tensor) â€“ the input tensor.
 probs (list) â€“ quantile positions.
 dim (int) â€“ dimension to take quantiles from
input
.
Returns torch.Tensor: quantiles of
input
atprobs
.

pi
(input, prob, dim=0)[source]Â¶ Computes percentile interval which assigns equal probability mass to each tail of the interval.
Parameters:  input (torch.Tensor) â€“ the input tensor.
 prob (float) â€“ the probability mass of samples within the interval.
 dim (int) â€“ dimension to calculate percentile interval from
input
.
Returns torch.Tensor: quantiles of
input
atprobs
.

hpdi
(input, prob, dim=0)[source]Â¶ Computes â€śhighest posterior density intervalâ€ť which is the narrowest interval with probability mass
prob
.Parameters:  input (torch.Tensor) â€“ the input tensor.
 prob (float) â€“ the probability mass of samples within the interval.
 dim (int) â€“ dimension to calculate percentile interval from
input
.
Returns torch.Tensor: quantiles of
input
atprobs
.

waic
(input, log_weights=None, pointwise=False, dim=0)[source]Â¶ Computes â€śWidely Applicable/WatanabeAkaike Information Criterionâ€ť (WAIC) and its corresponding effective number of parameters.
Reference:
[1] WAIC and crossvalidation in Stan, Aki Vehtari, Andrew Gelman
Parameters:  input (torch.Tensor) â€“ the input tensor, which is log likelihood of a model.
 log_weights (torch.Tensor) â€“ weights of samples along
dim
.  dim (int) â€“ the sample dimension of
input
.
Returns tuple: tuple of WAIC and effective number of parameters.
Automatic Guide GenerationÂ¶
The pyro.contrib.autoguide
module provides algorithms to automatically
generate guides from simple models, for use in SVI
.
For example to generate a mean field Gaussian guide:
def model():
...
guide = AutoDiagonalNormal(model) # a mean field guide
svi = SVI(model, guide, Adam({'lr': 1e3}), Trace_ELBO())
Automatic guides can also be combined using pyro.poutine.block()
and
AutoGuideList
.
AutoGuideÂ¶

class
AutoGuide
(model, prefix='auto')[source]Â¶ Bases:
object
Base class for automatic guides.
Derived classes must implement the
__call__()
method.Auto guides can be used individually or combined in an
AutoGuideList
object.Parameters:  model (callable) â€“ a pyro model
 prefix (str) â€“ a prefix that will be prefixed to all param internal sites

__call__
(*args, **kwargs)[source]Â¶ A guide with the same
*args, **kwargs
as the basemodel
.Returns: A dict mapping sample site name to sampled value. Return type: dict
AutoGuideListÂ¶

class
AutoGuideList
(model, prefix='auto')[source]Â¶ Bases:
pyro.contrib.autoguide.AutoGuide
Container class to combine multiple automatic guides.
Example usage:
guide = AutoGuideList(my_model) guide.add(AutoDiagonalNormal(poutine.block(model, hide=["assignment"]))) guide.add(AutoDiscreteParallel(poutine.block(model, expose=["assignment"]))) svi = SVI(model, guide, optim, Trace_ELBO())
Parameters:  model (callable) â€“ a Pyro model
 prefix (str) â€“ a prefix that will be prefixed to all param internal sites

__call__
(*args, **kwargs)[source]Â¶ A composite guide with the same
*args, **kwargs
as the basemodel
.Returns: A dict mapping sample site name to sampled value. Return type: dict
AutoCallableÂ¶

class
AutoCallable
(model, guide, median=<function <lambda>>)[source]Â¶ Bases:
pyro.contrib.autoguide.AutoGuide
AutoGuide
wrapper for simple callable guides.This is used internally for composing autoguides with custom userdefined guides that are simple callables, e.g.:
def my_local_guide(*args, **kwargs): ... guide = AutoGuideList(model) guide.add(AutoDelta(poutine.block(model, expose=['my_global_param'])) guide.add(my_local_guide) # automatically wrapped in an AutoCallable
To specify a median callable, you can instead:
def my_local_median(*args, **kwargs) ... guide.add(AutoCallable(model, my_local_guide, my_local_median))
For more complex guides that need e.g. access to plates, users should instead subclass
AutoGuide
.Parameters:  model (callable) â€“ a Pyro model
 guide (callable) â€“ a Pyro guide (typically over only part of the model)
 median (callable) â€“ an optional callable returning a dict mapping sample site name to computed median tensor.
AutoDeltaÂ¶

class
AutoDelta
(model, prefix='auto')[source]Â¶ Bases:
pyro.contrib.autoguide.AutoGuide
This implementation of
AutoGuide
uses Delta distributions to construct a MAP guide over the entire latent space. The guide does not depend on the modelâ€™s*args, **kwargs
...note:: This class does MAP inference in constrained space.
Usage:
guide = AutoDelta(model) svi = SVI(model, guide, ...)
By default latent variables are randomly initialized by the model. To change this default behavior the user should call
pyro.param()
before beginning inference, with"auto_"
prefixed to the targetd sample site names e.g. for sample sites named â€ślevelâ€ť and â€śconcentrationâ€ť, initialize via:pyro.param("auto_level", torch.tensor([1., 0., 1.])) pyro.param("auto_concentration", torch.ones(k), constraint=constraints.positive)
AutoContinuousÂ¶

class
AutoContinuous
(model, prefix='auto')[source]Â¶ Bases:
pyro.contrib.autoguide.AutoGuide
Base class for implementations of continuousvalued Automatic Differentiation Variational Inference [1].
Each derived class implements its own
get_posterior()
method.Assumes model structure and latent dimension are fixed, and all latent variables are continuous.
Parameters: model (callable) â€“ a Pyro model Reference:
 [1] Automatic Differentiation Variational Inference,
 Alp Kucukelbir, Dustin Tran, Rajesh Ranganath, Andrew Gelman, David M. Blei

__call__
(*args, **kwargs)[source]Â¶ An automatic guide with the same
*args, **kwargs
as the basemodel
.Returns: A dict mapping sample site name to sampled value. Return type: dict

median
(*args, **kwargs)[source]Â¶ Returns the posterior median value of each latent variable.
Returns: A dict mapping sample site name to median tensor. Return type: dict

quantiles
(quantiles, *args, **kwargs)[source]Â¶ Returns posterior quantiles each latent variable. Example:
print(guide.quantiles([0.05, 0.5, 0.95]))
Parameters: quantiles (torch.Tensor or list) â€“ A list of requested quantiles between 0 and 1. Returns: A dict mapping sample site name to a list of quantile values. Return type: dict
AutoMultivariateNormalÂ¶

class
AutoMultivariateNormal
(model, prefix='auto')[source]Â¶ Bases:
pyro.contrib.autoguide.AutoContinuous
This implementation of
AutoContinuous
uses a Cholesky factorization of a Multivariate Normal distribution to construct a guide over the entire latent space. The guide does not depend on the modelâ€™s*args, **kwargs
.Usage:
guide = AutoMultivariateNormal(model) svi = SVI(model, guide, ...)
By default the mean vector is initialized to zero and the Cholesky factor is initialized to the identity. To change this default behavior the user should call
pyro.param()
before beginning inference, e.g.:latent_dim = 10 pyro.param("auto_loc", torch.randn(latent_dim)) pyro.param("auto_scale_tril", torch.tril(torch.rand(latent_dim)), constraint=constraints.lower_cholesky)
AutoDiagonalNormalÂ¶

class
AutoDiagonalNormal
(model, prefix='auto')[source]Â¶ Bases:
pyro.contrib.autoguide.AutoContinuous
This implementation of
AutoContinuous
uses a Normal distribution with a diagonal covariance matrix to construct a guide over the entire latent space. The guide does not depend on the modelâ€™s*args, **kwargs
.Usage:
guide = AutoDiagonalNormal(model) svi = SVI(model, guide, ...)
By default the mean vector is initialized to zero and the scale is initialized to the identity. To change this default behavior the user should call
pyro.param()
before beginning inference, e.g.:latent_dim = 10 pyro.param("auto_loc", torch.randn(latent_dim)) pyro.param("auto_scale", torch.ones(latent_dim), constraint=constraints.positive)
AutoLowRankMultivariateNormalÂ¶

class
AutoLowRankMultivariateNormal
(model, prefix='auto', rank=1)[source]Â¶ Bases:
pyro.contrib.autoguide.AutoContinuous
This implementation of
AutoContinuous
uses a low rank plus diagonal Multivariate Normal distribution to construct a guide over the entire latent space. The guide does not depend on the modelâ€™s*args, **kwargs
.Usage:
guide = AutoLowRankMultivariateNormal(model, rank=10) svi = SVI(model, guide, ...)
By default the
cov_diag
is initialized to 1/2 and thecov_factor
is intialized randomly such thatcov_factor.matmul(cov_factor.t())
is half the identity matrix. To change this default behavior the user should callpyro.param()
before beginning inference, e.g.:latent_dim = 10 pyro.param("auto_loc", torch.randn(latent_dim)) pyro.param("auto_cov_factor", torch.randn(latent_dim, rank))) pyro.param("auto_cov_diag", torch.randn(latent_dim).exp()), constraint=constraints.positive)
Parameters:
AutoIAFNormalÂ¶

class
AutoIAFNormal
(model, hidden_dim=None, prefix='auto')[source]Â¶ Bases:
pyro.contrib.autoguide.AutoContinuous
This implementation of
AutoContinuous
uses a Diagonal Normal distribution transformed via aInverseAutoregressiveFlow
to construct a guide over the entire latent space. The guide does not depend on the modelâ€™s*args, **kwargs
.Usage:
guide = AutoIAFNormal(model, hidden_dim=latent_dim) svi = SVI(model, guide, ...)
Parameters:
AutoLaplaceApproximationÂ¶

class
AutoLaplaceApproximation
(model, prefix='auto')[source]Â¶ Bases:
pyro.contrib.autoguide.AutoContinuous
Laplace approximation (quadratic approximation) approximates the posterior \(\log p(z  x)\) by a multivariate normal distribution in the unconstrained space. Under the hood, it uses Delta distributions to construct a MAP guide over the entire (unconstrained) latent space. Its covariance is given by the inverse of the hessian of \(\log p(x, z)\) at the MAP point of z.
Usage:
delta_guide = AutoLaplaceApproximation(model) svi = SVI(model, delta_guide, ...) # ...then train the delta_guide... guide = delta_guide.laplace_approximation()
By default the mean vector is initialized to zero. To change this default behavior the user should call
pyro.param()
before beginning inference, e.g.:latent_dim = 10 pyro.param("auto_loc", torch.randn(latent_dim))

laplace_approximation
(*args, **kwargs)[source]Â¶ Returns a
AutoMultivariateNormal
instance whose posteriorâ€™s loc and scale_tril are given by Laplace approximation.

AutoDiscreteParallelÂ¶

class
AutoDiscreteParallel
(model, prefix='auto')[source]Â¶ Bases:
pyro.contrib.autoguide.AutoGuide
A discrete meanfield guide that learns a latent discrete distribution for each discrete site in the model.
Automatic Name GenerationÂ¶
The pyro.contrib.autoname
module provides tools for automatically
generating unique, semantically meaningful names for sample sites.

scope
(fn=None, prefix=None, inner=None)[source]Â¶ Parameters:  fn â€“ a stochastic function (callable containing Pyro primitive calls)
 prefix â€“ a string to prepend to sample names (optional if
fn
is provided)  inner â€“ switch to determine where duplicate name counters appear
Returns: fn
decorated with aScopeMessenger
scope
prepends a prefix followed by a/
to the name at a Pyro sample site. It works much like TensorFlowâ€™sname_scope
andvariable_scope
, and can be used as a context manager, a decorator, or a higherorder function.scope
is very useful for aligning compositional models with guides or data.Example:
>>> @scope(prefix="a") ... def model(): ... return pyro.sample("x", dist.Bernoulli(0.5)) ... >>> assert "a/x" in poutine.trace(model).get_trace()
Example:
>>> def model(): ... with scope(prefix="a"): ... return pyro.sample("x", dist.Bernoulli(0.5)) ... >>> assert "a/x" in poutine.trace(model).get_trace()
Scopes compose as expected, with outer scopes appearing before inner scopes in names:
>>> @scope(prefix="b") ... def model(): ... with scope(prefix="a"): ... return pyro.sample("x", dist.Bernoulli(0.5)) ... >>> assert "b/a/x" in poutine.trace(model).get_trace()
When used as a decorator or higherorder function,
scope
will use the name of the input function as the prefix if no userspecified prefix is provided.Example:
>>> @scope ... def model(): ... return pyro.sample("x", dist.Bernoulli(0.5)) ... >>> assert "model/x" in poutine.trace(model).get_trace()

name_count
(fn=None)[source]Â¶ name_count
is a very simple autonaming scheme that simply appends a suffix â€ś__â€ť plus a counter to any name that appears multiple tims in an execution. Only duplicate instances of a name get a suffix; the first instance is not modified.Example:
>>> @name_count ... def model(): ... for i in range(3): ... pyro.sample("x", dist.Bernoulli(0.5)) ... >>> assert "x" in poutine.trace(model).get_trace() >>> assert "x__1" in poutine.trace(model).get_trace() >>> assert "x__2" in poutine.trace(model).get_trace()
name_count
also composes withscope()
by adding a suffix to duplicate scope entrances:Example:
>>> @name_count ... def model(): ... for i in range(3): ... with pyro.contrib.autoname.scope(prefix="a"): ... pyro.sample("x", dist.Bernoulli(0.5)) ... >>> assert "a/x" in poutine.trace(model).get_trace() >>> assert "a__1/x" in poutine.trace(model).get_trace() >>> assert "a__2/x" in poutine.trace(model).get_trace()
Example:
>>> @name_count ... def model(): ... with pyro.contrib.autoname.scope(prefix="a"): ... for i in range(3): ... pyro.sample("x", dist.Bernoulli(0.5)) ... >>> assert "a/x" in poutine.trace(model).get_trace() >>> assert "a/x__1" in poutine.trace(model).get_trace() >>> assert "a/x__2" in poutine.trace(model).get_trace()
Named Data StructuresÂ¶
The pyro.contrib.named
module is a thin syntactic layer on top of Pyro. It
allows Pyro models to be written to look like programs with operating on Python
data structures like latent.x.sample_(...)
, rather than programs with
stringlabeled statements like x = pyro.sample("x", ...)
.
This module provides three container data structures named.Object
,
named.List
, and named.Dict
. These data structures are intended to be
nested in each other. Together they track the address of each piece of data
in each data structure, so that this address can be used as a Pyro site. For
example:
>>> state = named.Object("state")
>>> print(str(state))
state
>>> z = state.x.y.z # z is just a placeholder.
>>> print(str(z))
state.x.y.z
>>> state.xs = named.List() # Create a contained list.
>>> x0 = state.xs.add()
>>> print(str(x0))
state.xs[0]
>>> state.ys = named.Dict()
>>> foo = state.ys['foo']
>>> print(str(foo))
state.ys['foo']
These addresses can now be used inside sample
, observe
and param
statements. These named data structures even provide inplace methods that
alias Pyro statements. For example:
>>> state = named.Object("state")
>>> loc = state.loc.param_(torch.zeros(1, requires_grad=True))
>>> scale = state.scale.param_(torch.ones(1, requires_grad=True))
>>> z = state.z.sample_(dist.Normal(loc, scale))
>>> obs = state.x.sample_(dist.Normal(loc, scale), obs=z)
For deeper examples of how these can be used in model code, see the Tree Data and Mixture examples.
Authors: Fritz Obermeyer, Alexander Rush

class
Object
(name)[source]Â¶ Bases:
object
Object to hold immutable latent state.
This object can serve either as a container for nested latent state or as a placeholder to be replaced by a tensor via a named.sample, named.observe, or named.param statement. When used as a placeholder, Object objects take the place of strings in normal pyro.sample statements.
Parameters: name (str) â€“ The name of the object. Example:
state = named.Object("state") state.x = 0 state.ys = named.List() state.zs = named.Dict() state.a.b.c.d.e.f.g = 0 # Creates a chain of named.Objects.
Warning
This data structure is writeonce: data may be added but may not be mutated or removed. Trying to mutate this data structure may result in silent errors.

sample_
(fn, *args, **kwargs)Â¶ Calls the stochastic function fn with additional sideeffects depending on name and the enclosing context (e.g. an inference algorithm). See Intro I and Intro II for a discussion.
Parameters:  name â€“ name of sample
 fn â€“ distribution class or function
 obs â€“ observed datum (optional; should only be used in context of inference) optionally specified in kwargs
 infer (dict) â€“ Optional dictionary of inference parameters specified in kwargs. See inference documentation for details.
Returns: sample

param_
(*args, **kwargs)Â¶ Saves the variable as a parameter in the param store. To interact with the param store or write to disk, see Parameters.
Parameters: name â€“ name of parameter Returns: parameter


class
List
(name=None)[source]Â¶ Bases:
list
Listlike object to hold immutable latent state.
This must either be given a name when constructed:
latent = named.List("root")
or must be immediately stored in a
named.Object
:latent = named.Object("root") latent.xs = named.List() # Must be bound to a Object before use.
Warning
This data structure is writeonce: data may be added but may not be mutated or removed. Trying to mutate this data structure may result in silent errors.

add
()[source]Â¶ Append one new named.Object.
Returns: a new latent object at the end Return type: named.Object


class
Dict
(name=None)[source]Â¶ Bases:
dict
Dictlike object to hold immutable latent state.
This must either be given a name when constructed:
latent = named.Dict("root")
or must be immediately stored in a
named.Object
:latent = named.Object("root") latent.xs = named.Dict() # Must be bound to a Object before use.
Warning
This data structure is writeonce: data may be added but may not be mutated or removed. Trying to mutate this data structure may result in silent errors.
ScopingÂ¶
pyro.contrib.autoname.scoping
contains the implementation of
pyro.contrib.autoname.scope()
, a tool for automatically appending
a semantically meaningful prefix to names of sample sites.

class
NameCountMessenger
[source]Â¶ Bases:
pyro.poutine.messenger.Messenger
NameCountMessenger
is the implementation ofpyro.contrib.autoname.name_count()

class
ScopeMessenger
(prefix=None, inner=None)[source]Â¶ Bases:
pyro.poutine.messenger.Messenger
ScopeMessenger
is the implementation ofpyro.contrib.autoname.scope()

scope
(fn=None, prefix=None, inner=None)[source]Â¶ Parameters:  fn â€“ a stochastic function (callable containing Pyro primitive calls)
 prefix â€“ a string to prepend to sample names (optional if
fn
is provided)  inner â€“ switch to determine where duplicate name counters appear
Returns: fn
decorated with aScopeMessenger
scope
prepends a prefix followed by a/
to the name at a Pyro sample site. It works much like TensorFlowâ€™sname_scope
andvariable_scope
, and can be used as a context manager, a decorator, or a higherorder function.scope
is very useful for aligning compositional models with guides or data.Example:
>>> @scope(prefix="a") ... def model(): ... return pyro.sample("x", dist.Bernoulli(0.5)) ... >>> assert "a/x" in poutine.trace(model).get_trace()
Example:
>>> def model(): ... with scope(prefix="a"): ... return pyro.sample("x", dist.Bernoulli(0.5)) ... >>> assert "a/x" in poutine.trace(model).get_trace()
Scopes compose as expected, with outer scopes appearing before inner scopes in names:
>>> @scope(prefix="b") ... def model(): ... with scope(prefix="a"): ... return pyro.sample("x", dist.Bernoulli(0.5)) ... >>> assert "b/a/x" in poutine.trace(model).get_trace()
When used as a decorator or higherorder function,
scope
will use the name of the input function as the prefix if no userspecified prefix is provided.Example:
>>> @scope ... def model(): ... return pyro.sample("x", dist.Bernoulli(0.5)) ... >>> assert "model/x" in poutine.trace(model).get_trace()

name_count
(fn=None)[source]Â¶ name_count
is a very simple autonaming scheme that simply appends a suffix â€ś__â€ť plus a counter to any name that appears multiple tims in an execution. Only duplicate instances of a name get a suffix; the first instance is not modified.Example:
>>> @name_count ... def model(): ... for i in range(3): ... pyro.sample("x", dist.Bernoulli(0.5)) ... >>> assert "x" in poutine.trace(model).get_trace() >>> assert "x__1" in poutine.trace(model).get_trace() >>> assert "x__2" in poutine.trace(model).get_trace()
name_count
also composes withscope()
by adding a suffix to duplicate scope entrances:Example:
>>> @name_count ... def model(): ... for i in range(3): ... with pyro.contrib.autoname.scope(prefix="a"): ... pyro.sample("x", dist.Bernoulli(0.5)) ... >>> assert "a/x" in poutine.trace(model).get_trace() >>> assert "a__1/x" in poutine.trace(model).get_trace() >>> assert "a__2/x" in poutine.trace(model).get_trace()
Example:
>>> @name_count ... def model(): ... with pyro.contrib.autoname.scope(prefix="a"): ... for i in range(3): ... pyro.sample("x", dist.Bernoulli(0.5)) ... >>> assert "a/x" in poutine.trace(model).get_trace() >>> assert "a/x__1" in poutine.trace(model).get_trace() >>> assert "a/x__2" in poutine.trace(model).get_trace()
Bayesian Neural NetworksÂ¶
Generalised Linear Mixed ModelsÂ¶
The pyro.contrib.glmm
module provides models and guides for
generalised linear mixed models (GLMM). It also includes the
Normalinversegamma family.
To create a classical Bayesian linear model, use:
from pyro.contrib.glmm import known_covariance_linear_model
# Note: coef is a pvector, observation_sd is a scalar
# Here, p=1 (one feature)
model = known_covariance_linear_model(coef_mean=torch.tensor([0.]),
coef_sd=torch.tensor([10.]),
observation_sd=torch.tensor(2.))
# An n x p design tensor
# Here, n=2 (two observations)
design = torch.tensor(torch.tensor([[1.], [1.]]))
model(design)
A nonlinear link function may be introduced, for instance:
from pyro.contrib.glmm import logistic_regression_model
# No observation_sd is needed for logistic models
model = logistic_regression_model(coef_mean=torch.tensor([0.]),
coef_sd=torch.tensor([10.]))
Random effects may be incorporated as regular Bayesian regression coefficients.
For random effects with a shared covariance matrix, see pyro.contrib.glmm.lmer_model()
.
Gaussian ProcessesÂ¶
See the Gaussian Processes tutorial for an introduction.
ModelsÂ¶
GPModelÂ¶

class
GPModel
(X, y, kernel, mean_function=None, jitter=1e06)[source]Â¶ Bases:
pyro.contrib.gp.parameterized.Parameterized
Base class for Gaussian Process models.
The core of a Gaussian Process is a covariance function \(k\) which governs the similarity between input points. Given \(k\), we can establish a distribution over functions \(f\) by a multivarite normal distribution
\[p(f(X)) = \mathcal{N}(0, k(X, X)),\]where \(X\) is any set of input points and \(k(X, X)\) is a covariance matrix whose entries are outputs \(k(x, z)\) of \(k\) over input pairs \((x, z)\). This distribution is usually denoted by
\[f \sim \mathcal{GP}(0, k).\]Note
Generally, beside a covariance matrix \(k\), a Gaussian Process can also be specified by a mean function \(m\) (which is a zerovalue function by default). In that case, its distribution will be
\[p(f(X)) = \mathcal{N}(m(X), k(X, X)).\]Gaussian Process models are
Parameterized
subclasses. So its parameters can be learned, set priors, or fixed by using corresponding methods fromParameterized
. A typical way to define a Gaussian Process model is>>> X = torch.tensor([[1., 5, 3], [4, 3, 7]]) >>> y = torch.tensor([2., 1]) >>> kernel = gp.kernels.RBF(input_dim=3) >>> kernel.set_prior("variance", dist.Uniform(torch.tensor(0.5), torch.tensor(1.5))) >>> kernel.set_prior("lengthscale", dist.Uniform(torch.tensor(1.0), torch.tensor(3.0))) >>> gpr = gp.models.GPRegression(X, y, kernel)
There are two ways to train a Gaussian Process model:
Using an MCMC algorithm (in module
pyro.infer.mcmc
) onmodel()
to get posterior samples for the Gaussian Processâ€™s parameters. For example:>>> hmc_kernel = HMC(gpr.model) >>> mcmc_run = MCMC(hmc_kernel, num_samples=10) >>> posterior_ls_trace = [] # store lengthscale trace >>> ls_name = "GPR/RBF/lengthscale" >>> for trace, _ in mcmc_run._traces(): ... posterior_ls_trace.append(trace.nodes[ls_name]["value"])
Using a variational inference on the pair
model()
,guide()
:>>> optimizer = torch.optim.Adam(gpr.parameters(), lr=0.01) >>> loss_fn = pyro.infer.TraceMeanField_ELBO().differentiable_loss >>> >>> for i in range(1000): ... svi.step() ... optimizer.zero_grad() ... loss = loss_fn(gpr.model, gpr.guide) ... loss.backward() ... optimizer.step()
To give a prediction on new dataset, simply use
forward()
like any PyTorchtorch.nn.Module
:>>> Xnew = torch.tensor([[2., 3, 1]]) >>> f_loc, f_cov = gpr(Xnew, full_cov=True)
Reference:
[1] Gaussian Processes for Machine Learning, Carl E. Rasmussen, Christopher K. I. Williams
Parameters:  X (torch.Tensor) â€“ A input data for training. Its first dimension is the number of data points.
 y (torch.Tensor) â€“ An output data for training. Its last dimension is the number of data points.
 kernel (Kernel) â€“ A Pyro kernel object, which is the covariance function \(k\).
 mean_function (callable) â€“ An optional mean function \(m\) of this Gaussian process. By default, we use zero mean.
 jitter (float) â€“ A small positive term which is added into the diagonal part of a covariance matrix to help stablize its Cholesky decomposition.

model
()[source]Â¶ A â€śmodelâ€ť stochastic function. If
self.y
isNone
, this method returns mean and variance of the Gaussian Process prior.

guide
()[source]Â¶ A â€śguideâ€ť stochastic function to be used in variational inference methods. It also gives posterior information to the method
forward()
for prediction.

forward
(Xnew, full_cov=False)[source]Â¶ Computes the mean and covariance matrix (or variance) of Gaussian Process posterior on a test input data \(X_{new}\):
\[p(f^* \mid X_{new}, X, y, k, \theta),\]where \(\theta\) are parameters of this model.
Note
Modelâ€™s parameters \(\theta\) together with kernelâ€™s parameters have been learned from a training procedure (MCMC or SVI).
Parameters:  Xnew (torch.Tensor) â€“ A input data for testing. Note that
Xnew.shape[1:]
must be the same asX.shape[1:]
.  full_cov (bool) â€“ A flag to decide if we want to predict full covariance matrix or just variance.
Returns: loc and covariance matrix (or variance) of \(p(f^*(X_{new}))\)
Return type:  Xnew (torch.Tensor) â€“ A input data for testing. Note that

set_data
(X, y=None)[source]Â¶ Sets data for Gaussian Process models.
Some examples to utilize this method are:
Batch training on a sparse variational model:
>>> Xu = torch.tensor([[1., 0, 2]]) # inducing input >>> likelihood = gp.likelihoods.Gaussian() >>> vsgp = gp.models.VariationalSparseGP(X, y, kernel, Xu, likelihood) >>> optimizer = torch.optim.Adam(vsgp.parameters(), lr=0.01) >>> loss_fn = pyro.infer.TraceMeanField_ELBO().differentiable_loss >>> batched_X, batched_y = X.split(split_size=10), y.split(split_size=10) >>> for Xi, yi in zip(batched_X, batched_y): ... optimizer.zero_grad() ... vsgp.set_data(Xi, yi) ... svi.step() ... loss = loss_fn(vsgp.model, vsgp.guide) ... loss.backward() ... optimizer.step()
Making a twolayer Gaussian Process stochastic function:
>>> gpr1 = gp.models.GPRegression(X, None, kernel) >>> Z, _ = gpr1.model() >>> gpr2 = gp.models.GPRegression(Z, y, kernel) >>> def two_layer_model(): ... Z, _ = gpr1.model() ... gpr2.set_data(Z, y) ... return gpr2.model()
References:
[1] Scalable Variational Gaussian Process Classification, James Hensman, Alexander G. de G. Matthews, Zoubin Ghahramani
[2] Deep Gaussian Processes, Andreas C. Damianou, Neil D. Lawrence
Parameters:  X (torch.Tensor) â€“ A input data for training. Its first dimension is the number of data points.
 y (torch.Tensor) â€“ An output data for training. Its last dimension is the number of data points.
GPRegressionÂ¶

class
GPRegression
(X, y, kernel, noise=None, mean_function=None, jitter=1e06)[source]Â¶ Bases:
pyro.contrib.gp.models.model.GPModel
Gaussian Process Regression model.
The core of a Gaussian Process is a covariance function \(k\) which governs the similarity between input points. Given \(k\), we can establish a distribution over functions \(f\) by a multivarite normal distribution
\[p(f(X)) = \mathcal{N}(0, k(X, X)),\]where \(X\) is any set of input points and \(k(X, X)\) is a covariance matrix whose entries are outputs \(k(x, z)\) of \(k\) over input pairs \((x, z)\). This distribution is usually denoted by
\[f \sim \mathcal{GP}(0, k).\]Note
Generally, beside a covariance matrix \(k\), a Gaussian Process can also be specified by a mean function \(m\) (which is a zerovalue function by default). In that case, its distribution will be
\[p(f(X)) = \mathcal{N}(m(X), k(X, X)).\]Given inputs \(X\) and their noisy observations \(y\), the Gaussian Process Regression model takes the form
\[\begin{split}f &\sim \mathcal{GP}(0, k(X, X)),\\ y & \sim f + \epsilon,\end{split}\]where \(\epsilon\) is Gaussian noise.
Note
This model has \(\mathcal{O}(N^3)\) complexity for training, \(\mathcal{O}(N^3)\) complexity for testing. Here, \(N\) is the number of train inputs.
Reference:
[1] Gaussian Processes for Machine Learning, Carl E. Rasmussen, Christopher K. I. Williams
Parameters:  X (torch.Tensor) â€“ A input data for training. Its first dimension is the number of data points.
 y (torch.Tensor) â€“ An output data for training. Its last dimension is the number of data points.
 kernel (Kernel) â€“ A Pyro kernel object, which is the covariance function \(k\).
 noise (torch.Tensor) â€“ Variance of Gaussian noise of this model.
 mean_function (callable) â€“ An optional mean function \(m\) of this Gaussian process. By default, we use zero mean.
 jitter (float) â€“ A small positive term which is added into the diagonal part of a covariance matrix to help stablize its Cholesky decomposition.

forward
(Xnew, full_cov=False, noiseless=True)[source]Â¶ Computes the mean and covariance matrix (or variance) of Gaussian Process posterior on a test input data \(X_{new}\):
\[p(f^* \mid X_{new}, X, y, k, \epsilon) = \mathcal{N}(loc, cov).\]Note
The noise parameter
noise
(\(\epsilon\)) together with kernelâ€™s parameters have been learned from a training procedure (MCMC or SVI).Parameters:  Xnew (torch.Tensor) â€“ A input data for testing. Note that
Xnew.shape[1:]
must be the same asself.X.shape[1:]
.  full_cov (bool) â€“ A flag to decide if we want to predict full covariance matrix or just variance.
 noiseless (bool) â€“ A flag to decide if we want to include noise in the prediction output or not.
Returns: loc and covariance matrix (or variance) of \(p(f^*(X_{new}))\)
Return type:  Xnew (torch.Tensor) â€“ A input data for testing. Note that

iter_sample
(noiseless=True)[source]Â¶ Iteratively constructs a sample from the Gaussian Process posterior.
Recall that at test input points \(X_{new}\), the posterior is multivariate Gaussian distributed with mean and covariance matrix given by
forward()
.This method samples lazily from this multivariate Gaussian. The advantage of this approach is that later query points can depend upon earlier ones. Particularly useful when the querying is to be done by an optimisation routine.
Note
The noise parameter
noise
(\(\epsilon\)) together with kernelâ€™s parameters have been learned from a training procedure (MCMC or SVI).Parameters: noiseless (bool) â€“ A flag to decide if we want to add sampling noise to the samples beyond the noise inherent in the GP posterior. Returns: sampler Return type: function
SparseGPRegressionÂ¶

class
SparseGPRegression
(X, y, kernel, Xu, noise=None, mean_function=None, approx=None, jitter=1e06)[source]Â¶ Bases:
pyro.contrib.gp.models.model.GPModel
Sparse Gaussian Process Regression model.
In
GPRegression
model, when the number of input data \(X\) is large, the covariance matrix \(k(X, X)\) will require a lot of computational steps to compute its inverse (for log likelihood and for prediction). By introducing an additional inducinginput parameter \(X_u\), we can reduce computational cost by approximate \(k(X, X)\) by a lowrank NymstrĂ¶m approximation \(Q\) (see reference [1]), where\[Q = k(X, X_u) k(X,X)^{1} k(X_u, X).\]Given inputs \(X\), their noisy observations \(y\), and the inducinginput parameters \(X_u\), the model takes the form:
\[\begin{split}u & \sim \mathcal{GP}(0, k(X_u, X_u)),\\ f & \sim q(f \mid X, X_u) = \mathbb{E}_{p(u)}q(f\mid X, X_u, u),\\ y & \sim f + \epsilon,\end{split}\]where \(\epsilon\) is Gaussian noise and the conditional distribution \(q(f\mid X, X_u, u)\) is an approximation of
\[p(f\mid X, X_u, u) = \mathcal{N}(m, k(X, X)  Q),\]whose terms \(m\) and \(k(X, X)  Q\) is derived from the joint multivariate normal distribution:
\[[f, u] \sim \mathcal{GP}(0, k([X, X_u], [X, X_u])).\]This class implements three approximation methods:
Deterministic Training Conditional (DTC):
\[q(f\mid X, X_u, u) = \mathcal{N}(m, 0),\]which in turns will imply
\[f \sim \mathcal{N}(0, Q).\]Fully Independent Training Conditional (FITC):
\[q(f\mid X, X_u, u) = \mathcal{N}(m, diag(k(X, X)  Q)),\]which in turns will correct the diagonal part of the approximation in DTC:
\[f \sim \mathcal{N}(0, Q + diag(k(X, X)  Q)).\]Variational Free Energy (VFE), which is similar to DTC but has an additional trace_term in the modelâ€™s log likelihood. This additional term makes â€śVFEâ€ť equivalent to the variational approach in
SparseVariationalGP
(see reference [2]).
Note
This model has \(\mathcal{O}(NM^2)\) complexity for training, \(\mathcal{O}(NM^2)\) complexity for testing. Here, \(N\) is the number of train inputs, \(M\) is the number of inducing inputs.
References:
[1] A Unifying View of Sparse Approximate Gaussian Process Regression, Joaquin QuiĂ±oneroCandela, Carl E. Rasmussen
[2] Variational learning of inducing variables in sparse Gaussian processes, Michalis Titsias
Parameters:  X (torch.Tensor) â€“ A input data for training. Its first dimension is the number of data points.
 y (torch.Tensor) â€“ An output data for training. Its last dimension is the number of data points.
 kernel (Kernel) â€“ A Pyro kernel object, which is the covariance function \(k\).
 Xu (torch.Tensor) â€“ Initial values for inducing points, which are parameters of our model.
 noise (torch.Tensor) â€“ Variance of Gaussian noise of this model.
 mean_function (callable) â€“ An optional mean function \(m\) of this Gaussian process. By default, we use zero mean.
 approx (str) â€“ One of approximation methods: â€śDTCâ€ť, â€śFITCâ€ť, and â€śVFEâ€ť (default).
 jitter (float) â€“ A small positive term which is added into the diagonal part of a covariance matrix to help stablize its Cholesky decomposition.
 name (str) â€“ Name of this model.

forward
(Xnew, full_cov=False, noiseless=True)[source]Â¶ Computes the mean and covariance matrix (or variance) of Gaussian Process posterior on a test input data \(X_{new}\):
\[p(f^* \mid X_{new}, X, y, k, X_u, \epsilon) = \mathcal{N}(loc, cov).\]Note
The noise parameter
noise
(\(\epsilon\)), the inducingpoint parameterXu
, together with kernelâ€™s parameters have been learned from a training procedure (MCMC or SVI).Parameters:  Xnew (torch.Tensor) â€“ A input data for testing. Note that
Xnew.shape[1:]
must be the same asself.X.shape[1:]
.  full_cov (bool) â€“ A flag to decide if we want to predict full covariance matrix or just variance.
 noiseless (bool) â€“ A flag to decide if we want to include noise in the prediction output or not.
Returns: loc and covariance matrix (or variance) of \(p(f^*(X_{new}))\)
Return type:  Xnew (torch.Tensor) â€“ A input data for testing. Note that
VariationalGPÂ¶

class
VariationalGP
(X, y, kernel, likelihood, mean_function=None, latent_shape=None, whiten=False, jitter=1e06)[source]Â¶ Bases:
pyro.contrib.gp.models.model.GPModel
Variational Gaussian Process model.
This model deals with both Gaussian and nonGaussian likelihoods. Given inputs\(X\) and their noisy observations \(y\), the model takes the form
\[\begin{split}f &\sim \mathcal{GP}(0, k(X, X)),\\ y & \sim p(y) = p(y \mid f) p(f),\end{split}\]where \(p(y \mid f)\) is the likelihood.
We will use a variational approach in this model by approximating \(q(f)\) to the posterior \(p(f\mid y)\). Precisely, \(q(f)\) will be a multivariate normal distribution with two parameters
f_loc
andf_scale_tril
, which will be learned during a variational inference process.Note
This model can be seen as a special version of
SparseVariationalGP
model with \(X_u = X\).Note
This model has \(\mathcal{O}(N^3)\) complexity for training, \(\mathcal{O}(N^3)\) complexity for testing. Here, \(N\) is the number of train inputs. Size of variational parameters is \(\mathcal{O}(N^2)\).
Parameters:  X (torch.Tensor) â€“ A input data for training. Its first dimension is the number of data points.
 y (torch.Tensor) â€“ An output data for training. Its last dimension is the number of data points.
 kernel (Kernel) â€“ A Pyro kernel object, which is the covariance function \(k\).
 Likelihood likelihood (likelihood) â€“ A likelihood object.
 mean_function (callable) â€“ An optional mean function \(m\) of this Gaussian process. By default, we use zero mean.
 latent_shape (torch.Size) â€“ Shape for latent processes (batch_shape of
\(q(f)\)). By default, it equals to output batch shape
y.shape[:1]
. For the multiclass classification problems,latent_shape[1]
should corresponse to the number of classes.  whiten (bool) â€“ A flag to tell if variational parameters
f_loc
andf_scale_tril
are transformed by the inverse ofLff
, whereLff
is the lower triangular decomposition of \(kernel(X, X)\). Enable this flag will help optimization.  jitter (float) â€“ A small positive term which is added into the diagonal part of a covariance matrix to help stablize its Cholesky decomposition.

forward
(Xnew, full_cov=False)[source]Â¶ Computes the mean and covariance matrix (or variance) of Gaussian Process posterior on a test input data \(X_{new}\):
\[p(f^* \mid X_{new}, X, y, k, f_{loc}, f_{scale\_tril}) = \mathcal{N}(loc, cov).\]Note
Variational parameters
f_loc
,f_scale_tril
, together with kernelâ€™s parameters have been learned from a training procedure (MCMC or SVI).Parameters:  Xnew (torch.Tensor) â€“ A input data for testing. Note that
Xnew.shape[1:]
must be the same asself.X.shape[1:]
.  full_cov (bool) â€“ A flag to decide if we want to predict full covariance matrix or just variance.
Returns: loc and covariance matrix (or variance) of \(p(f^*(X_{new}))\)
Return type:  Xnew (torch.Tensor) â€“ A input data for testing. Note that
VariationalSparseGPÂ¶

class
VariationalSparseGP
(X, y, kernel, Xu, likelihood, mean_function=None, latent_shape=None, num_data=None, whiten=False, jitter=1e06)[source]Â¶ Bases:
pyro.contrib.gp.models.model.GPModel
Variational Sparse Gaussian Process model.
In
VariationalGP
model, when the number of input data \(X\) is large, the covariance matrix \(k(X, X)\) will require a lot of computational steps to compute its inverse (for log likelihood and for prediction). This model introduces an additional inducinginput parameter \(X_u\) to solve that problem. Given inputs \(X\), their noisy observations \(y\), and the inducinginput parameters \(X_u\), the model takes the form:\[\begin{split}[f, u] &\sim \mathcal{GP}(0, k([X, X_u], [X, X_u])),\\ y & \sim p(y) = p(y \mid f) p(f),\end{split}\]where \(p(y \mid f)\) is the likelihood.
We will use a variational approach in this model by approximating \(q(f,u)\) to the posterior \(p(f,u \mid y)\). Precisely, \(q(f) = p(f\mid u)q(u)\), where \(q(u)\) is a multivariate normal distribution with two parameters
u_loc
andu_scale_tril
, which will be learned during a variational inference process.Note
This model can be learned using MCMC method as in reference [2]. See also
GPModel
.Note
This model has \(\mathcal{O}(NM^2)\) complexity for training, \(\mathcal{O}(M^3)\) complexity for testing. Here, \(N\) is the number of train inputs, \(M\) is the number of inducing inputs. Size of variational parameters is \(\mathcal{O}(M^2)\).
References:
[1] Scalable variational Gaussian process classification, James Hensman, Alexander G. de G. Matthews, Zoubin Ghahramani
[2] MCMC for Variationally Sparse Gaussian Processes, James Hensman, Alexander G. de G. Matthews, Maurizio Filippone, Zoubin Ghahramani
Parameters:  X (torch.Tensor) â€“ A input data for training. Its first dimension is the number of data points.
 y (torch.Tensor) â€“ An output data for training. Its last dimension is the number of data points.
 kernel (Kernel) â€“ A Pyro kernel object, which is the covariance function \(k\).
 Xu (torch.Tensor) â€“ Initial values for inducing points, which are parameters of our model.
 Likelihood likelihood (likelihood) â€“ A likelihood object.
 mean_function (callable) â€“ An optional mean function \(m\) of this Gaussian process. By default, we use zero mean.
 latent_shape (torch.Size) â€“ Shape for latent processes (batch_shape of
\(q(u)\)). By default, it equals to output batch shape
y.shape[:1]
. For the multiclass classification problems,latent_shape[1]
should corresponse to the number of classes.  num_data (int) â€“ The size of full training dataset. It is useful for training this model with minibatch.
 whiten (bool) â€“ A flag to tell if variational parameters
u_loc
andu_scale_tril
are transformed by the inverse ofLuu
, whereLuu
is the lower triangular decomposition of \(kernel(X_u, X_u)\). Enable this flag will help optimization.  jitter (float) â€“ A small positive term which is added into the diagonal part of a covariance matrix to help stablize its Cholesky decomposition.

forward
(Xnew, full_cov=False)[source]Â¶ Computes the mean and covariance matrix (or variance) of Gaussian Process posterior on a test input data \(X_{new}\):
\[p(f^* \mid X_{new}, X, y, k, X_u, u_{loc}, u_{scale\_tril}) = \mathcal{N}(loc, cov).\]Note
Variational parameters
u_loc
,u_scale_tril
, the inducingpoint parameterXu
, together with kernelâ€™s parameters have been learned from a training procedure (MCMC or SVI).Parameters:  Xnew (torch.Tensor) â€“ A input data for testing. Note that
Xnew.shape[1:]
must be the same asself.X.shape[1:]
.  full_cov (bool) â€“ A flag to decide if we want to predict full covariance matrix or just variance.
Returns: loc and covariance matrix (or variance) of \(p(f^*(X_{new}))\)
Return type:  Xnew (torch.Tensor) â€“ A input data for testing. Note that
GPLVMÂ¶

class
GPLVM
(base_model)[source]Â¶ Bases:
pyro.contrib.gp.parameterized.Parameterized
Gaussian Process Latent Variable Model (GPLVM) model.
GPLVM is a Gaussian Process model with its train input data is a latent variable. This model is useful for dimensional reduction of high dimensional data. Assume the mapping from low dimensional latent variable to is a Gaussian Process instance. Then the high dimensional data will play the role of train output
y
and our target is to learn latent inputs which best explainy
. For the purpose of dimensional reduction, latent inputs should have lower dimensions thany
.We follows reference [1] to put a unit Gaussian prior to the input and approximate its posterior by a multivariate normal distribution with two variational parameters:
X_loc
andX_scale_tril
.For example, we can do dimensional reduction on Iris dataset as follows:
>>> # With y as the 2D Iris data of shape 150x4 and we want to reduce its dimension >>> # to a tensor X of shape 150x2, we will use GPLVM.
>>> # First, define the initial values for X parameter: >>> X_init = torch.zeros(150, 2) >>> # Then, define a Gaussian Process model with input X_init and output y: >>> kernel = gp.kernels.RBF(input_dim=2, lengthscale=torch.ones(2)) >>> Xu = torch.zeros(20, 2) # initial inducing inputs of sparse model >>> gpmodule = gp.models.SparseGPRegression(X_init, y, kernel, Xu) >>> # Finally, wrap gpmodule by GPLVM, optimize, and get the "learned" mean of X: >>> gplvm = gp.models.GPLVM(gpmodule) >>> gp.util.train(gplvm) >>> X = gplvm.X
Reference:
[1] Bayesian Gaussian Process Latent Variable Model Michalis K. Titsias, Neil D. Lawrence
Parameters: base_model (GPModel) â€“ A Pyro Gaussian Process model object. Note that base_model.X
will be the initial value for the variational parameterX_loc
.
KernelsÂ¶
KernelÂ¶

class
Kernel
(input_dim, active_dims=None)[source]Â¶ Bases:
pyro.contrib.gp.parameterized.Parameterized
Base class for kernels used in this Gaussian Process module.
Every inherited class should implement a
forward()
pass which takes inputs \(X\), \(Z\) and returns their covariance matrix.To construct a new kernel from the old ones, we can use methods
add()
,mul()
,exp()
,warp()
,vertical_scale()
.References:
[1] Gaussian Processes for Machine Learning, Carl E. Rasmussen, Christopher K. I. Williams
Parameters:  input_dim (int) â€“ Number of feature dimensions of inputs.
 variance (torch.Tensor) â€“ Variance parameter of this kernel.
 active_dims (list) â€“ List of feature dimensions of the input which the kernel acts on.

forward
(X, Z=None, diag=False)[source]Â¶ Calculates covariance matrix of inputs on active dimensionals.
Parameters:  X (torch.Tensor) â€“ A 2D tensor with shape \(N \times input\_dim\).
 Z (torch.Tensor) â€“ An (optional) 2D tensor with shape \(M \times input\_dim\).
 diag (bool) â€“ A flag to decide if we want to return full covariance matrix or just its diagonal part.
Returns: covariance matrix of \(X\) and \(Z\) with shape \(N \times M\)
Return type:
BrownianÂ¶

class
Brownian
(input_dim, variance=None, active_dims=None)[source]Â¶ Bases:
pyro.contrib.gp.kernels.kernel.Kernel
This kernel correponds to a twosided Brownion motion (Wiener process):
\(k(x,z)=\begin{cases}\sigma^2\min(x,z),& \text{if } x\cdot z\ge 0\\ 0, & \text{otherwise}. \end{cases}\)Note that the input dimension of this kernel must be 1.
Reference:
[1] Theory and Statistical Applications of Stochastic Processes, Yuliya Mishura, Georgiy Shevchenko
CombinationÂ¶

class
Combination
(kern0, kern1)[source]Â¶ Bases:
pyro.contrib.gp.kernels.kernel.Kernel
Base class for kernels derived from a combination of kernels.
Parameters:  kern0 (Kernel) â€“ First kernel to combine.
 kern1 (Kernel or numbers.Number) â€“ Second kernel to combine.
ConstantÂ¶
CoregionalizeÂ¶

class
Coregionalize
(input_dim, rank=None, components=None, diagonal=None, active_dims=None)[source]Â¶ Bases:
pyro.contrib.gp.kernels.kernel.Kernel
A kernel for the linear model of coregionalization \(k(x,z) = x^T (W W^T + D) z\) where \(W\) is an
input_dim
byrank
matrix and typicallyrank < input_dim
, andD
is a diagonal matrix.This generalizes the
Linear
kernel to multiple features with a lowrankplusdiagonal weight matrix. The typical use case is for modeling correlations among outputs of a multioutput GP, where outputs are coded as distinct data points with onehot coded features denoting which output each datapoint represents.If only
rank
is specified, the kernel(W W^T + D)
will be randomly initialized to a matrix with expected value the identity matrix.References:
 [1] Mauricio A. Alvarez, Lorenzo Rosasco, Neil D. Lawrence (2012)
 Kernels for VectorValued Functions: a Review
Parameters:  input_dim (int) â€“ Number of feature dimensions of inputs.
 rank (int) â€“ Optional rank. This is only used if
components
is unspecified. If neigherrank
norcomponents
is specified, thenrank
defaults toinput_dim
.  components (torch.Tensor) â€“ An optional
(input_dim, rank)
shaped matrix that maps features torank
many components. If unspecified, this will be randomly initialized.  diagonal (torch.Tensor) â€“ An optional vector of length
input_dim
. If unspecified, this will be set to constant0.5
.  active_dims (list) â€“ List of feature dimensions of the input which the kernel acts on.
 name (str) â€“ Name of the kernel.
CosineÂ¶

class
Cosine
(input_dim, variance=None, lengthscale=None, active_dims=None)[source]Â¶ Bases:
pyro.contrib.gp.kernels.isotropic.Isotropy
Implementation of Cosine kernel:
\(k(x,z) = \sigma^2 \cos\left(\frac{xz}{l}\right).\)Parameters: lengthscale (torch.Tensor) â€“ Lengthscale parameter of this kernel.
DotProductÂ¶
ExponentÂ¶
ExponentialÂ¶
IsotropyÂ¶

class
Isotropy
(input_dim, variance=None, lengthscale=None, active_dims=None)[source]Â¶ Bases:
pyro.contrib.gp.kernels.kernel.Kernel
Base class for a family of isotropic covariance kernels which are functions of the distance \(xz/l\), where \(l\) is the lengthscale parameter.
By default, the parameter
lengthscale
has size 1. To use the isotropic version (different lengthscale for each dimension), make sure thatlengthscale
has size equal toinput_dim
.Parameters: lengthscale (torch.Tensor) â€“ Lengthscale parameter of this kernel.
LinearÂ¶

class
Linear
(input_dim, variance=None, active_dims=None)[source]Â¶ Bases:
pyro.contrib.gp.kernels.dot_product.DotProduct
Implementation of Linear kernel:
\(k(x, z) = \sigma^2 x \cdot z.\)Doing Gaussian Process regression with linear kernel is equivalent to doing a linear regression.
Note
Here we implement the homogeneous version. To use the inhomogeneous version, consider using
Polynomial
kernel withdegree=1
or making aSum
with aConstant
kernel.
Matern32Â¶
Matern52Â¶

class
Matern52
(input_dim, variance=None, lengthscale=None, active_dims=None)[source]Â¶ Bases:
pyro.contrib.gp.kernels.isotropic.Isotropy
Implementation of Matern52 kernel:
\(k(x,z)=\sigma^2\left(1+\sqrt{5}\times\frac{xz}{l}+\frac{5}{3}\times \frac{xz^2}{l^2}\right)\exp\left(\sqrt{5} \times \frac{xz}{l}\right).\)
PeriodicÂ¶

class
Periodic
(input_dim, variance=None, lengthscale=None, period=None, active_dims=None)[source]Â¶ Bases:
pyro.contrib.gp.kernels.kernel.Kernel
Implementation of Periodic kernel:
\(k(x,z)=\sigma^2\exp\left(2\times\frac{\sin^2(\pi(xz)/p)}{l^2}\right),\)where \(p\) is the
period
parameter.References:
[1] Introduction to Gaussian processes, David J.C. MacKay
Parameters:  lengthscale (torch.Tensor) â€“ Length scale parameter of this kernel.
 period (torch.Tensor) â€“ Period parameter of this kernel.
PolynomialÂ¶

class
Polynomial
(input_dim, variance=None, bias=None, degree=1, active_dims=None)[source]Â¶ Bases:
pyro.contrib.gp.kernels.dot_product.DotProduct
Implementation of Polynomial kernel:
\(k(x, z) = \sigma^2(\text{bias} + x \cdot z)^d.\)Parameters:  bias (torch.Tensor) â€“ Bias parameter of this kernel. Should be positive.
 degree (int) â€“ Degree \(d\) of the polynomial.
ProductÂ¶
RBFÂ¶

class
RBF
(input_dim, variance=None, lengthscale=None, active_dims=None)[source]Â¶ Bases:
pyro.contrib.gp.kernels.isotropic.Isotropy
Implementation of Radial Basis Function kernel:
\(k(x,z) = \sigma^2\exp\left(0.5 \times \frac{xz^2}{l^2}\right).\)Note
This kernel also has name Squared Exponential in literature.
RationalQuadraticÂ¶

class
RationalQuadratic
(input_dim, variance=None, lengthscale=None, scale_mixture=None, active_dims=None)[source]Â¶ Bases:
pyro.contrib.gp.kernels.isotropic.Isotropy
Implementation of RationalQuadratic kernel:
\(k(x, z) = \sigma^2 \left(1 + 0.5 \times \frac{xz^2}{\alpha l^2} \right)^{\alpha}.\)Parameters: scale_mixture (torch.Tensor) â€“ Scale mixture (\(\alpha\)) parameter of this kernel. Should have size 1.
SumÂ¶
TransformingÂ¶
VerticalScalingÂ¶
WarpingÂ¶

class
Warping
(kern, iwarping_fn=None, owarping_coef=None)[source]Â¶ Bases:
pyro.contrib.gp.kernels.kernel.Transforming
Creates a new kernel according to
\(k_{new}(x, z) = q(k(f(x), f(z))),\)where \(f\) is an function and \(q\) is a polynomial with nonnegative coefficients
owarping_coef
.We can take advantage of \(f\) to combine a Gaussian Process kernel with a deep learning architecture. For example:
>>> linear = torch.nn.Linear(10, 3) >>> # register its parameters to Pyro's ParamStore and wrap it by lambda >>> # to call the primitive pyro.module each time we use the linear function >>> pyro_linear_fn = lambda x: pyro.module("linear", linear)(x) >>> kernel = gp.kernels.Matern52(input_dim=3, lengthscale=torch.ones(3)) >>> warped_kernel = gp.kernels.Warping(kernel, pyro_linear_fn)
Reference:
[1] Deep Kernel Learning, Andrew G. Wilson, Zhiting Hu, Ruslan Salakhutdinov, Eric P. Xing
Parameters:  iwarping_fn (callable) â€“ An input warping function \(f\).
 owarping_coef (list) â€“ A list of coefficients of the output warping polynomial. These coefficients must be nonnegative.
LikelihoodsÂ¶
LikelihoodÂ¶

class
Likelihood
[source]Â¶ Bases:
pyro.contrib.gp.parameterized.Parameterized
Base class for likelihoods used in Gaussian Process.
Every inherited class should implement a forward pass which takes an input \(f\) and returns a sample \(y\).

forward
(f_loc, f_var, y=None)[source]Â¶ Samples \(y\) given \(f_{loc}\), \(f_{var}\).
Parameters:  f_loc (torch.Tensor) â€“ Mean of latent function output.
 f_var (torch.Tensor) â€“ Variance of latent function output.
 y (torch.Tensor) â€“ Training output tensor.
Returns: a tensor sampled from likelihood
Return type:

BinaryÂ¶

class
Binary
(response_function=None)[source]Â¶ Bases:
pyro.contrib.gp.likelihoods.likelihood.Likelihood
Implementation of Binary likelihood, which is used for binary classification problems.
Binary likelihood uses
Bernoulli
distribution, so the output ofresponse_function
should be in range \((0,1)\). By default, we use sigmoid function.Parameters: response_function (callable) â€“ A mapping to correct domain for Binary likelihood. 
forward
(f_loc, f_var, y=None)[source]Â¶ Samples \(y\) given \(f_{loc}\), \(f_{var}\) according to
\[\begin{split}f & \sim \mathbb{Normal}(f_{loc}, f_{var}),\\ y & \sim \mathbb{Bernoulli}(f).\end{split}\]Note
The log likelihood is estimated using Monte Carlo with 1 sample of \(f\).
Parameters:  f_loc (torch.Tensor) â€“ Mean of latent function output.
 f_var (torch.Tensor) â€“ Variance of latent function output.
 y (torch.Tensor) â€“ Training output tensor.
Returns: a tensor sampled from likelihood
Return type:

GaussianÂ¶

class
Gaussian
(variance=None)[source]Â¶ Bases:
pyro.contrib.gp.likelihoods.likelihood.Likelihood
Implementation of Gaussian likelihood, which is used for regression problems.
Gaussian likelihood uses
Normal
distribution.Parameters: variance (torch.Tensor) â€“ A variance parameter, which plays the role of noise
in regression problems.
forward
(f_loc, f_var, y=None)[source]Â¶ Samples \(y\) given \(f_{loc}\), \(f_{var}\) according to
\[y \sim \mathbb{Normal}(f_{loc}, f_{var} + \epsilon),\]where \(\epsilon\) is the
variance
parameter of this likelihood.Parameters:  f_loc (torch.Tensor) â€“ Mean of latent function output.
 f_var (torch.Tensor) â€“ Variance of latent function output.
 y (torch.Tensor) â€“ Training output tensor.
Returns: a tensor sampled from likelihood
Return type:

MultiClassÂ¶

class
MultiClass
(num_classes, response_function=None)[source]Â¶ Bases:
pyro.contrib.gp.likelihoods.likelihood.Likelihood
Implementation of MultiClass likelihood, which is used for multiclass classification problems.
MultiClass likelihood uses
Categorical
distribution, soresponse_function
should normalize its inputâ€™s rightmost axis. By default, we use softmax function.Parameters:  num_classes (int) â€“ Number of classes for prediction.
 response_function (callable) â€“ A mapping to correct domain for MultiClass likelihood.

forward
(f_loc, f_var, y=None)[source]Â¶ Samples \(y\) given \(f_{loc}\), \(f_{var}\) according to
\[\begin{split}f & \sim \mathbb{Normal}(f_{loc}, f_{var}),\\ y & \sim \mathbb{Categorical}(f).\end{split}\]Note
The log likelihood is estimated using Monte Carlo with 1 sample of \(f\).
Parameters:  f_loc (torch.Tensor) â€“ Mean of latent function output.
 f_var (torch.Tensor) â€“ Variance of latent function output.
 y (torch.Tensor) â€“ Training output tensor.
Returns: a tensor sampled from likelihood
Return type:
PoissonÂ¶

class
Poisson
(response_function=None)[source]Â¶ Bases:
pyro.contrib.gp.likelihoods.likelihood.Likelihood
Implementation of Poisson likelihood, which is used for count data.
Poisson likelihood uses the
Poisson
distribution, so the output ofresponse_function
should be positive. By default, we usetorch.exp()
as response function, corresponding to a logGaussian Cox process.Parameters: response_function (callable) â€“ A mapping to positive real numbers. 
forward
(f_loc, f_var, y=None)[source]Â¶ Samples \(y\) given \(f_{loc}\), \(f_{var}\) according to
\[\begin{split}f & \sim \mathbb{Normal}(f_{loc}, f_{var}),\\ y & \sim \mathbb{Poisson}(\exp(f)).\end{split}\]Note
The log likelihood is estimated using Monte Carlo with 1 sample of \(f\).
Parameters:  f_loc (torch.Tensor) â€“ Mean of latent function output.
 f_var (torch.Tensor) â€“ Variance of latent function output.
 y (torch.Tensor) â€“ Training output tensor.
Returns: a tensor sampled from likelihood
Return type:

ParameterizedÂ¶

class
Parameterized
[source]Â¶ Bases:
torch.nn.modules.module.Module
A wrapper of
torch.nn.Module
whose parameters can be set constraints, set priors.Under the hood, we move parameters to a buffer store and create â€śrootâ€ť parameters which are used to generate that parameterâ€™s value. For example, if we set a contraint to a parameter, an â€śunconstrainedâ€ť parameter will be created, and the constrained value will be transformed from that â€śunconstrainedâ€ť parameter.
By default, when we set a prior to a parameter, an auto Delta guide will be created. We can use the method
autoguide()
to setup other auto guides. To fix a parameter to a specific value, it is enough to turn off its â€śrootâ€ť parametersâ€™requires_grad
flags.Example:
>>> class Linear(Parameterized): ... def __init__(self, a, b): ... super(Linear, self).__init__() ... self.a = Parameter(a) ... self.b = Parameter(b) ... ... def forward(self, x): ... return self.a * x + self.b ... >>> linear = Linear(torch.tensor(1.), torch.tensor(0.)) >>> linear.set_constraint("a", constraints.positive) >>> linear.set_prior("b", dist.Normal(0, 1)) >>> linear.autoguide("b", dist.Normal) >>> assert "a_unconstrained" in dict(linear.named_parameters()) >>> assert "b_loc" in dict(linear.named_parameters()) >>> assert "b_scale_unconstrained" in dict(linear.named_parameters()) >>> assert "a" in dict(linear.named_buffers()) >>> assert "b" in dict(linear.named_buffers()) >>> assert "b_scale" in dict(linear.named_buffers())
Note that by default, data of a parameter is a float
torch.Tensor
(unless we usetorch.set_default_tensor_type()
to change default tensor type). To cast these parameters to a correct data type or GPU device, we can call methods such asdouble()
orcuda()
. Seetorch.nn.Module
for more information.
set_constraint
(name, constraint)[source]Â¶ Sets the constraint of an existing parameter.
Parameters:  name (str) â€“ Name of the parameter.
 constraint (Constraint) â€“ A PyTorch constraint. See
torch.distributions.constraints
for a list of constraints.

set_prior
(name, prior)[source]Â¶ Sets the constraint of an existing parameter.
Parameters:  name (str) â€“ Name of the parameter.
 prior (Distribution) â€“ A Pyro prior distribution.

autoguide
(name, dist_constructor)[source]Â¶ Sets an autoguide for an existing parameter with name
name
(mimic the behavior of modulepyro.contrib.autoguide
).Note
dist_constructor should be one of
Delta
,Normal
, andMultivariateNormal
. More distribution constructor will be supported in the future if needed.Parameters:  name (str) â€“ Name of the parameter.
 dist_constructor â€“ A
Distribution
constructor.

set_mode
(mode)[source]Â¶ Sets
mode
of this object to be able to use its parameters in stochastic functions. Ifmode="model"
, a parameter will get its value from its prior. Ifmode="guide"
, the value will be drawn from its guide.Note
This method automatically sets
mode
for submodules which belong toParameterized
class.Parameters: mode (str) â€“ Either â€śmodelâ€ť or â€śguideâ€ť.

mode
Â¶

UtilÂ¶

conditional
(Xnew, X, kernel, f_loc, f_scale_tril=None, Lff=None, full_cov=False, whiten=False, jitter=1e06)[source]Â¶ Given \(X_{new}\), predicts loc and covariance matrix of the conditional multivariate normal distribution
\[p(f^*(X_{new}) \mid X, k, f_{loc}, f_{scale\_tril}).\]Here
f_loc
andf_scale_tril
are variation parameters of the variational distribution\[q(f \mid f_{loc}, f_{scale\_tril}) \sim p(f  X, y),\]where \(f\) is the function value of the Gaussian Process given input \(X\)
\[p(f(X)) \sim \mathcal{N}(0, k(X, X))\]and \(y\) is computed from \(f\) by some likelihood function \(p(yf)\).
In case
f_scale_tril=None
, we consider \(f = f_{loc}\) and computes\[p(f^*(X_{new}) \mid X, k, f).\]In case
f_scale_tril
is notNone
, we follow the derivation from reference [1]. For the casef_scale_tril=None
, we follow the popular reference [2].References:
[1] Sparse GPs: approximate the posterior, not the model
[2] Gaussian Processes for Machine Learning, Carl E. Rasmussen, Christopher K. I. Williams
Parameters:  Xnew (torch.Tensor) â€“ A new input data.
 X (torch.Tensor) â€“ An input data to be conditioned on.
 kernel (Kernel) â€“ A Pyro kernel object.
 f_loc (torch.Tensor) â€“ Mean of \(q(f)\). In case
f_scale_tril=None
, \(f_{loc} = f\).  f_scale_tril (torch.Tensor) â€“ Lower triangular decomposition of covariance matrix of \(q(f)\)â€s .
 Lff (torch.Tensor) â€“ Lower triangular decomposition of \(kernel(X, X)\) (optional).
 full_cov (bool) â€“ A flag to decide if we want to return full covariance matrix or just variance.
 whiten (bool) â€“ A flag to tell if
f_loc
andf_scale_tril
are already transformed by the inverse ofLff
.  jitter (float) â€“ A small positive term which is added into the diagonal part of a covariance matrix to help stablize its Cholesky decomposition.
Returns: loc and covariance matrix (or variance) of \(p(f^*(X_{new}))\)
Return type:

train
(gpmodule, optimizer=None, loss_fn=None, retain_graph=None, num_steps=1000)[source]Â¶ A helper to optimize parameters for a GP module.
Parameters:  gpmodule (GPModel) â€“ A GP module.
 optimizer (Optimizer) â€“ A PyTorch optimizer instance.
By default, we use Adam with
lr=0.01
.  loss_fn (callable) â€“ A loss function which takes inputs are
gpmodule.model
,gpmodule.guide
, and returns ELBO loss. By default,loss_fn=TraceMeanField_ELBO().differentiable_loss
.  retain_graph (bool) â€“ An optional flag of
torch.autograd.backward
.  num_steps (int) â€“ Number of steps to run SVI.
Returns: a list of losses during the training procedure
Return type:
Mini PyroÂ¶
This file contains a minimal implementation of the Pyro Probabilistic
Programming Language. The API (method signatures, etc.) match that of
the full implementation as closely as possible. This file is independent
of the rest of Pyro, with the exception of the pyro.distributions
module.
An accompanying example that makes use of this implementation can be found at examples/minipyro.py.
Optimal Experiment DesignÂ¶
The pyro.contrib.oed
module provides tools to create optimal experiment
designs for pyro models. In particular, it provides estimators for the
average posterior entropy (APE) criterion.
To estimate the APE for a particular design, use:
def model(design):
...
eig = vi_ape(model, design, ...)
APE can then be minimised using existing optimisers in pyro.optim
.
Expected Information GainÂ¶

vi_ape
(model, design, observation_labels, target_labels, vi_parameters, is_parameters, y_dist=None)[source]Â¶ Estimates the average posterior entropy (APE) loss function using variational inference (VI).
The APE loss function estimated by this method is defined as
\(APE(d)=E_{Y\sim p(y\theta, d)}[H(p(\thetaY, d))]\)where \(H[p(x)]\) is the differential entropy. The APE is related to expected information gain (EIG) by the equation
\(EIG(d)=H[p(\theta)]APE(d)\)in particular, minimising the APE is equivalent to maximising EIG.
Parameters:  model (function) â€“ A pyro model accepting design as only argument.
 design (torch.Tensor) â€“ Tensor representation of design
 observation_labels (list) â€“ A subset of the sample sites present in model. These sites are regarded as future observations and other sites are regarded as latent variables over which a posterior is to be inferred.
 target_labels (list) â€“ A subset of the sample sites over which the posterior entropy is to be measured.
 vi_parameters (dict) â€“ Variational inference parameters which should include:
optim: an instance of
pyro.Optim
, guide: a guide function compatible with model, num_steps: the number of VI steps to make, and loss: the loss function to use for VI  is_parameters (dict) â€“ Importance sampling parameters for the marginal distribution of \(Y\). May include num_samples: the number of samples to draw from the marginal.
 y_dist (pyro.distributions.Distribution) â€“ (optional) the distribution assumed for the response variable \(Y\)
Returns: Loss function estimate
Return type: torch.Tensor

naive_rainforth_eig
(model, design, observation_labels, target_labels=None, N=100, M=10, M_prime=None)[source]Â¶ Naive Rainforth (i.e. Nested Monte Carlo) estimate of the expected information gain (EIG). The estimate is
\[\frac{1}{N}\sum_{n=1}^N \log p(y_n  \theta_n, d)  \log \left(\frac{1}{M}\sum_{m=1}^M p(y_n  \theta_m, d)\right)\]Monte Carlo estimation is attempted for the \(\log p(y  \theta, d)\) term if the parameter M_prime is passed. Otherwise, it is assumed that that \(\log p(y  \theta, d)\) can safely be read from the model itself.
Parameters:  model (function) â€“ A pyro model accepting design as only argument.
 design (torch.Tensor) â€“ Tensor representation of design
 observation_labels (list) â€“ A subset of the sample sites present in model. These sites are regarded as future observations and other sites are regarded as latent variables over which a posterior is to be inferred.
 target_labels (list) â€“ A subset of the sample sites over which the posterior entropy is to be measured.
 N (int) â€“ Number of outer expectation samples.
 M (int) â€“ Number of inner expectation samples for p(yd).
 M_prime (int) â€“ Number of samples for p(y  theta, d) if required.
Returns: EIG estimate
Return type: torch.Tensor

donsker_varadhan_eig
(model, design, observation_labels, target_labels, num_samples, num_steps, T, optim, return_history=False, final_design=None, final_num_samples=None)[source]Â¶ DonskerVaradhan estimate of the expected information gain (EIG).
The DonskerVaradhan representation of EIG is
\[\sup_T E_{p(y, \theta  d)}[T(y, \theta)]  \log E_{p(yd)p(\theta)}[\exp(T(\bar{y}, \bar{\theta}))]\]where \(T\) is any (measurable) function.
This methods optimises the loss function over a prespecified class of functions T.
Parameters:  model (function) â€“ A pyro model accepting design as only argument.
 design (torch.Tensor) â€“ Tensor representation of design
 observation_labels (list) â€“ A subset of the sample sites present in model. These sites are regarded as future observations and other sites are regarded as latent variables over which a posterior is to be inferred.
 target_labels (list) â€“ A subset of the sample sites over which the posterior entropy is to be measured.
 num_samples (int) â€“ Number of samples per iteration.
 num_steps (int) â€“ Number of optimisation steps.
 or torch.nn.Module T (function) â€“ optimisable function T for use in the DonskerVaradhan loss function.
 optim (pyro.optim.Optim) â€“ Optimiser to use.
 return_history (bool) â€“ If True, also returns a tensor giving the loss function at each step of the optimisation.
 final_design (torch.Tensor) â€“ The final design tensor to evaluate at. If None, uses design.
 final_num_samples (int) â€“ The number of samples to use at the final evaluation, If None, uses `num_samples.
Returns: EIG estimate, optionally includes full optimisatio history
Return type: torch.Tensor or tuple

barber_agakov_ape
(model, design, observation_labels, target_labels, num_samples, num_steps, guide, optim, return_history=False, final_design=None, final_num_samples=None)[source]Â¶ BarberAgakov estimate of average posterior entropy (APE).
The BarberAgakov representation of APE is
\(sup_{q}E_{p(y, \theta  d)}[\log q(\theta  y, d)]\)where \(q\) is any distribution on \(\theta\).
This method optimises the loss over a given guide family guide representing \(q\).
Parameters:  model (function) â€“ A pyro model accepting design as only argument.
 design (torch.Tensor) â€“ Tensor representation of design
 observation_labels (list) â€“ A subset of the sample sites present in model. These sites are regarded as future observations and other sites are regarded as latent variables over which a posterior is to be inferred.
 target_labels (list) â€“ A subset of the sample sites over which the posterior entropy is to be measured.
 num_samples (int) â€“ Number of samples per iteration.
 num_steps (int) â€“ Number of optimisation steps.
 guide (function) â€“ guide family for use in the (implicit) posterior estimation. The parameters of guide are optimised to maximise the BarberAgakov objective.
 optim (pyro.optim.Optim) â€“ Optimiser to use.
 return_history (bool) â€“ If True, also returns a tensor giving the loss function at each step of the optimisation.
 final_design (torch.Tensor) â€“ The final design tensor to evaluate at. If None, uses design.
 final_num_samples (int) â€“ The number of samples to use at the final evaluation, If None, uses `num_samples.
Returns: EIG estimate, optionally includes full optimisatio history
Return type: torch.Tensor or tuple

class
EwmaLog
(alpha)[source]Â¶ Logarithm function with exponentially weighted moving average for gradients.
For input inputs this function return
inputs.log()
. However, it computes the gradient as\(\frac{\sum_{t=0}^{T1} \alpha^t}{\sum_{t=0}^{T1} \alpha^t x_{Tt}}\)where \(x_t\) are historical input values passed to this function, \(x_T\) being the most recently seen value.
This gradient may help with numerical stability when the sequence of inputs to the function form a convergent sequence.
TrackingÂ¶
Data AssociationÂ¶

class
MarginalAssignment
(exists_logits, assign_logits, bp_iters=None)[source]Â¶ Computes marginal data associations between objects and detections.
This assumes that each detection corresponds to zero or one object, and each object corresponds to zero or more detections. Specifically this does not assume detections have been partitioned into frames of mutual exclusion as is common in 2D assignment problems.
Parameters:  exists_logits (torch.Tensor) â€“ a tensor of shape
[num_objects]
representing perobject factors for existence of each potential object.  assign_logits (torch.Tensor) â€“ a tensor of shape
[num_detections, num_objects]
representing peredge factors of assignment probability, where each edge denotes that a given detection associates with a single object.  bp_iters (int) â€“ optional number of belief propagation iterations. If
unspecified or
None
an expensive exact algorithm will be used.
Variables:  num_detections (int) â€“ the number of detections
 num_objects (int) â€“ the number of (potentially existing) objects
 exists_dist (pyro.distributions.Bernoulli) â€“ a mean field posterior distribution over object existence.
 assign_dist (pyro.distributions.Categorical) â€“ a mean field posterior
distribution over the object (or None) to which each detection
associates. This has
.event_shape == (num_objects + 1,)
where the final element denotes spurious detection, and.batch_shape == (num_frames, num_detections)
.
 exists_logits (torch.Tensor) â€“ a tensor of shape

class
MarginalAssignmentSparse
(num_objects, num_detections, edges, exists_logits, assign_logits, bp_iters)[source]Â¶ A cheap sparse version of
MarginalAssignment
.Parameters:  num_detections (int) â€“ the number of detections
 num_objects (int) â€“ the number of (potentially existing) objects
 edges (torch.LongTensor) â€“ a
[2, num_edges]
shaped tensor of (detection, object) index pairs specifying feasible associations.  exists_logits (torch.Tensor) â€“ a tensor of shape
[num_objects]
representing perobject factors for existence of each potential object.  assign_logits (torch.Tensor) â€“ a tensor of shape
[num_edges]
representing peredge factors of assignment probability, where each edge denotes that a given detection associates with a single object.  bp_iters (int) â€“ optional number of belief propagation iterations. If
unspecified or
None
an expensive exact algorithm will be used.
Variables:  num_detections (int) â€“ the number of detections
 num_objects (int) â€“ the number of (potentially existing) objects
 exists_dist (pyro.distributions.Bernoulli) â€“ a mean field posterior distribution over object existence.
 assign_dist (pyro.distributions.Categorical) â€“ a mean field posterior
distribution over the object (or None) to which each detection
associates. This has
.event_shape == (num_objects + 1,)
where the final element denotes spurious detection, and.batch_shape == (num_frames, num_detections)
.

class
MarginalAssignmentPersistent
(exists_logits, assign_logits, bp_iters=None, bp_momentum=0.5)[source]Â¶ This computes marginal distributions of a multiframe multiobject data association problem with an unknown number of persistent objects.
The inputs are factors in a factor graph (existence probabilites for each potential object and assignment probabilities for each objectdetection pair), and the outputs are marginal distributions of posterior existence probability of each potential object and posterior assignment probabilites of each objectdetection pair.
This assumes a shared (maximum) number of detections per frame; to handle variable number of detections, simply set corresponding elements of
assign_logits
tofloat('inf')
.Parameters:  exists_logits (torch.Tensor) â€“ a tensor of shape
[num_objects]
representing perobject factors for existence of each potential object.  assign_logits (torch.Tensor) â€“ a tensor of shape
[num_frames, num_detections, num_objects]
representing peredge factors of assignment probability, where each edge denotes that at a given time frame a given detection associates with a single object.  bp_iters (int) â€“ optional number of belief propagation iterations. If
unspecified or
None
an expensive exact algorithm will be used.  bp_momentum (float) â€“ optional momentum to use for belief propagation.
Should be in the interval
[0,1)
.
Variables:  num_frames (int) â€“ the number of time frames
 num_detections (int) â€“ the (maximum) number of detections per frame
 num_objects (int) â€“ the number of (potentially existing) objects
 exists_dist (pyro.distributions.Bernoulli) â€“ a mean field posterior distribution over object existence.
 assign_dist (pyro.distributions.Categorical) â€“ a mean field posterior
distribution over the object (or None) to which each detection
associates. This has
.event_shape == (num_objects + 1,)
where the final element denotes spurious detection, and.batch_shape == (num_frames, num_detections)
.
 exists_logits (torch.Tensor) â€“ a tensor of shape

compute_marginals
(exists_logits, assign_logits)[source]Â¶ This implements exact inference of pairwise marginals via enumeration. This is very expensive and is only useful for testing.
See
MarginalAssignment
for args and problem description.

compute_marginals_bp
(exists_logits, assign_logits, bp_iters)[source]Â¶ This implements approximate inference of pairwise marginals via loopy belief propagation, adapting the approach of [1].
See
MarginalAssignment
for args and problem description. [1] Jason L. Williams, Roslyn A. Lau (2014)
 Approximate evaluation of marginal association probabilities with belief propagation https://arxiv.org/abs/1209.6299

compute_marginals_sparse_bp
(num_objects, num_detections, edges, exists_logits, assign_logits, bp_iters)[source]Â¶ This implements approximate inference of pairwise marginals via loopy belief propagation, adapting the approach of [1].
See
MarginalAssignmentSparse
for args and problem description. [1] Jason L. Williams, Roslyn A. Lau (2014)
 Approximate evaluation of marginal association probabilities with belief propagation https://arxiv.org/abs/1209.6299

compute_marginals_persistent
(exists_logits, assign_logits)[source]Â¶ This implements exact inference of pairwise marginals via enumeration. This is very expensive and is only useful for testing.
See
MarginalAssignmentPersistent
for args and problem description.

compute_marginals_persistent_bp
(exists_logits, assign_logits, bp_iters, bp_momentum=0.5)[source]Â¶ This implements approximate inference of pairwise marginals via loopy belief propagation, adapting the approach of [1], [2].
See
MarginalAssignmentPersistent
for args and problem description. [1] Jason L. Williams, Roslyn A. Lau (2014)
 Approximate evaluation of marginal association probabilities with belief propagation https://arxiv.org/abs/1209.6299
 [2] Ryan Turner, Steven Bottone, Bhargav Avasarala (2014)
 A Complete Variational Tracker https://papers.nips.cc/paper/5572acompletevariationaltracker.pdf
DistributionsÂ¶

class
EKFDistribution
(x0, P0, dynamic_model, measurement_cov, time_steps=1, dt=1.0, validate_args=None)[source]Â¶ Distribution over EKF states. See
EKFState
. Currently only supports log_prob.Parameters:  x0 (torch.Tensor) â€“ PV tensor (mean)
 P0 (torch.Tensor) â€“ covariance
 dynamic_model â€“
DynamicModel
object  measurement_cov (torch.Tensor) â€“ measurement covariance
 time_steps (int) â€“ number time step
 dt (torch.Tensor) â€“ time step

filter_states
(value)[source]Â¶ Returns the ekf states given measurements
Parameters: value (torch.Tensor) â€“ measurement means of shape (time_steps, event_shape)

log_prob
(value)[source]Â¶ Returns the joint log probability of the innovations of a tensor of measurements
Parameters: value (torch.Tensor) â€“ measurement means of shape (time_steps, event_shape)
Dynamic ModelsÂ¶

class
DynamicModel
(dimension, dimension_pv, num_process_noise_parameters=None)[source]Â¶ Dynamic model interface.
Parameters:  dimension â€“ native state dimension.
 dimension_pv â€“ PV state dimension.
 num_process_noise_parameters â€“ process noise parameter space dimension.
This for UKF applications. Can be left as
None
for EKF and most other filters.

dimension
Â¶ Native state dimension access.

dimension_pv
Â¶ PV state dimension access.

num_process_noise_parameters
Â¶ Process noise parameters space dimension access.

forward
(x, dt, do_normalization=True)[source]Â¶ Integrate native state
x
over time intervaldt
.Parameters:  x â€“ current native state. If the DynamicModel is nondifferentiable,
be sure to handle the case of
x
being augmented with process noise parameters.  dt â€“ time interval to integrate over.
 do_normalization â€“ whether to perform normalization on output, e.g., modâ€™ing angles into an interval.
Returns: Native state x integrated dt into the future.
 x â€“ current native state. If the DynamicModel is nondifferentiable,
be sure to handle the case of

geodesic_difference
(x1, x0)[source]Â¶ Compute and return the geodesic difference between 2 native states. This is a generalization of the Euclidean operation
x1  x0
.Parameters:  x1 â€“ native state.
 x0 â€“ native state.
Returns: Geodesic difference between native states
x1
andx2
.

mean2pv
(x)[source]Â¶ Compute and return PV state from native state. Useful for combining state estimates of different types in IMM (Interacting Multiple Model) filtering.
Parameters: x â€“ native state estimate mean. Returns: PV state estimate mean.

cov2pv
(P)[source]Â¶ Compute and return PV covariance from native covariance. Useful for combining state estimates of different types in IMM (Interacting Multiple Model) filtering.
Parameters: P â€“ native state estimate covariance. Returns: PV state estimate covariance.

process_noise_cov
(dt=0.0)[source]Â¶ Compute and return process noise covariance (Q).
Parameters: dt â€“ time interval to integrate over. Returns: Readonly covariance (Q). For a DifferentiableDynamicModel, this is the covariance of the native state x
resulting from stochastic integration (for use with EKF). Otherwise, it is the covariance directly of the process noise parameters (for use with UKF).

class
DifferentiableDynamicModel
(dimension, dimension_pv, num_process_noise_parameters=None)[source]Â¶ DynamicModel for which state transition Jacobians can be efficiently calculated, usu. analytically or by automatic differentiation.

class
Ncp
(dimension, sv2)[source]Â¶ NCP (NearlyConstant Position) dynamic model. May be subclassed, e.g., with CWNV (Continuous White Noise Velocity) or DWNV (Discrete White Noise Velocity).
Parameters:  dimension â€“ native state dimension.
 sv2 â€“ variance of velocity. Usually chosen so that the standard deviation is roughly half of the max velocity one would ever expect to observe.

forward
(x, dt, do_normalization=True)[source]Â¶ Integrate native state
x
over time intervaldt
.Parameters:  x â€“ current native state. If the DynamicModel is nondifferentiable,
be sure to handle the case of
x
being augmented with process noise parameters.  dt â€“ time interval to integrate over. do_normalization: whether to perform normalization on output, e.g., modâ€™ing angles into an interval. Has no effect for this subclass.
Returns: Native state x integrated dt into the future.
 x â€“ current native state. If the DynamicModel is nondifferentiable,
be sure to handle the case of

mean2pv
(x)[source]Â¶ Compute and return PV state from native state. Useful for combining state estimates of different types in IMM (Interacting Multiple Model) filtering.
Parameters: x â€“ native state estimate mean. Returns: PV state estimate mean.

cov2pv
(P)[source]Â¶ Compute and return PV covariance from native covariance. Useful for combining state estimates of different types in IMM (Interacting Multiple Model) filtering.
Parameters: P â€“ native state estimate covariance. Returns: PV state estimate covariance.

class
Ncv
(dimension, sa2)[source]Â¶ NCV (NearlyConstant Velocity) dynamic model. May be subclassed, e.g., with CWNA (Continuous White Noise Acceleration) or DWNA (Discrete White Noise Acceleration).
Parameters:  dimension â€“ native state dimension.
 sa2 â€“ variance of acceleration. Usually chosen so that the standard deviation is roughly half of the max acceleration one would ever expect to observe.

forward
(x, dt, do_normalization=True)[source]Â¶ Integrate native state
x
over time intervaldt
.Parameters:  x â€“ current native state. If the DynamicModel is nondifferentiable,
be sure to handle the case of
x
being augmented with process noise parameters.  dt â€“ time interval to integrate over.
 do_normalization â€“ whether to perform normalization on output, e.g., modâ€™ing angles into an interval. Has no effect for this subclass.
Returns: Native state x integrated dt into the future.
 x â€“ current native state. If the DynamicModel is nondifferentiable,
be sure to handle the case of

mean2pv
(x)[source]Â¶ Compute and return PV state from native state. Useful for combining state estimates of different types in IMM (Interacting Multiple Model) filtering.
Parameters: x â€“ native state estimate mean. Returns: PV state estimate mean.

cov2pv
(P)[source]Â¶ Compute and return PV covariance from native covariance. Useful for combining state estimates of different types in IMM (Interacting Multiple Model) filtering.
Parameters: P â€“ native state estimate covariance. Returns: PV state estimate covariance.

class
NcpContinuous
(dimension, sv2)[source]Â¶ NCP (NearlyConstant Position) dynamic model with CWNV (Continuous White Noise Velocity).
 References:
 â€śEstimation with Applications to Tracking and Navigationâ€ť by Y. Bar Shalom et al, 2001, p.269.
Parameters:  dimension â€“ native state dimension.
 sv2 â€“ variance of velocity. Usually chosen so that the standard deviation is roughly half of the max velocity one would ever expect to observe.

class
NcvContinuous
(dimension, sa2)[source]Â¶ NCV (NearlyConstant Velocity) dynamic model with CWNA (Continuous White Noise Acceleration).
 References:
 â€śEstimation with Applications to Tracking and Navigationâ€ť by Y. Bar Shalom et al, 2001, p.269.
Parameters:  dimension â€“ native state dimension.
 sa2 â€“ variance of acceleration. Usually chosen so that the standard deviation is roughly half of the max acceleration one would ever expect to observe.

class
NcpDiscrete
(dimension, sv2)[source]Â¶ NCP (NearlyConstant Position) dynamic model with DWNV (Discrete White Noise Velocity).
Parameters:  dimension â€“ native state dimension.
 sv2 â€“ variance of velocity. Usually chosen so that the standard deviation is roughly half of the max velocity one would ever expect to observe.
 References:
 â€śEstimation with Applications to Tracking and Navigationâ€ť by Y. Bar Shalom et al, 2001, p.273.

class
NcvDiscrete
(dimension, sa2)[source]Â¶ NCV (NearlyConstant Velocity) dynamic model with DWNA (Discrete White Noise Acceleration).
Parameters:  dimension â€“ native state dimension.
 sa2 â€“ variance of acceleration. Usually chosen so that the standard deviation is roughly half of the max acceleration one would ever expect to observe.
 References:
 â€śEstimation with Applications to Tracking and Navigationâ€ť by Y. Bar Shalom et al, 2001, p.273.

process_noise_cov
(dt=0.0)[source]Â¶ Compute and return cached process noise covariance (Q).
Parameters: dt â€“ time interval to integrate over. Returns: Readonly covariance (Q) of the native state x resulting from stochastic integration (for use with EKF). (Note that this Q, modulo numerical error, has rank dimension/2. So, it is only positive semidefinite.)
Extended Kalman FilterÂ¶

class
EKFState
(dynamic_model, mean, cov, time=None, frame_num=None)[source]Â¶ StateCentric EKF (Extended Kalman Filter) for use with either an NCP (NearlyConstant Position) or NCV (NearlyConstant Velocity) target dynamic model. Stores a target dynamic model, state estimate, and state time. Incoming
Measurement
provide sensor information for updates.Warning
For efficiency, the dynamic model is only shallowcopied. Make a deep copy outside as necessary to protect against unexpected changes.
Parameters:  dynamic_model â€“ target dynamic model.
 mean â€“ mean of target state estimate.
 cov â€“ covariance of target state estimate.
 time â€“ time of state estimate.

dynamic_model
Â¶ Dynamic model access.

dimension
Â¶ Native state dimension access.

mean
Â¶ Native state estimate mean access.

cov
Â¶ Native state estimate covariance access.

dimension_pv
Â¶ PV state dimension access.

time
Â¶ Continuous State time access.

frame_num
Â¶ Discrete State time access.

predict
(dt=None, destination_time=None, destination_frame_num=None)[source]Â¶ Use dynamic model to predict (aka propagate aka integrate) state estimate inplace.
Parameters:  dt â€“ time to integrate over. The state time will be automatically
incremented this amount unless you provide
destination_time
. Usingdestination_time
may be preferable for prevention of roundoff error accumulation.  destination_time â€“ optional value to set continuous state time to after integration. If this is not provided, then destination_frame_num must be.
 destination_frame_num â€“ optional value to set discrete state time to after integration. If this is not provided, then destination_frame_num must be.
 dt â€“ time to integrate over. The state time will be automatically
incremented this amount unless you provide

innovation
(measurement)[source]Â¶ Compute and return the innovation that a measurement would induce if it were used for an update, but donâ€™t actually perform the update. Assumes state and measurement are timealigned. Useful for computing Chi^2 stats and likelihoods.
Parameters: measurement â€“ measurement Returns: Innovation mean and covariance of hypothetical update. Return type: tuple( torch.Tensor
,torch.Tensor
)

log_likelihood_of_update
(measurement)[source]Â¶ Compute and return the likelihood of a potential update, but donâ€™t actually perform the update. Assumes state and measurement are time aligned. Useful for gating and calculating costs in assignment problems for data association.
Param: measurement. Returns: Likelihood of hypothetical update.

update
(measurement)[source]Â¶ Use measurement to update state estimate inplace and return innovation. The innovation is useful, e.g., for evaluating filter consistency or updating model likelihoods when the
EKFState
is part of anIMMFState
.Param: measurement. Returns: EKF State, Innovation mean and covariance.
HashingÂ¶

class
LSH
(radius)[source]Â¶ Implements localitysensitive hashing for lowdimensional euclidean space.
Allows to efficiently find neighbours of a point. Provides 2 guarantees:
 Difference between coordinates of points not returned by
nearby()
and input point is larger thanradius
.  Difference between coordinates of points returned by
nearby()
and input point is smaller than 2radius
.
Example:
>>> radius = 1 >>> lsh = LSH(radius) >>> a = torch.tensor([0.51, 0.51]) # hash(a)=(1,1) >>> b = torch.tensor([0.49, 0.49]) # hash(a)=(0,0) >>> c = torch.tensor([1.0, 1.0]) # hash(b)=(1,1) >>> lsh.add('a', a) >>> lsh.add('b', b) >>> lsh.add('c', c) >>> # even though c is within 2radius of a >>> lsh.nearby('a') {'b'} >>> lsh.nearby('b') {'a', 'c'} >>> lsh.remove('b') >>> lsh.nearby('a') set()
Parameters: radius (float) â€“ Scaling parameter used in hash function. Determines the size of the neighbourhood. 
add
(key, point)[source]Â¶ Adds (
key
,point
) pair to the hash.Parameters:  key â€“ Key used identify
point
.  point (torch.Tensor) â€“ data, should be detached and on cpu.
 key â€“ Key used identify
 Difference between coordinates of points not returned by