Source code for pyro.primitives

from __future__ import absolute_import, division, print_function

import copy
import warnings
from collections import OrderedDict
from contextlib import contextmanager
from inspect import isclass

import pyro.distributions as dist
import pyro.infer as infer
import pyro.poutine as poutine
from pyro.params import param_with_module_name
from pyro.poutine.plate_messenger import PlateMessenger
from pyro.poutine.runtime import _MODULE_NAMESPACE_DIVIDER, _PYRO_PARAM_STORE, am_i_wrapped, apply_stack, effectful
from pyro.poutine.subsample_messenger import SubsampleMessenger
from pyro.util import deep_getattr, set_rng_seed  # noqa: F401

[docs]def get_param_store(): """ Returns the ParamStore """ return _PYRO_PARAM_STORE
[docs]def clear_param_store(): """ Clears the ParamStore. This is especially useful if you're working in a REPL. """ return _PYRO_PARAM_STORE.clear()
_param = effectful(_PYRO_PARAM_STORE.get_param, type="param")
[docs]def param(name, *args, **kwargs): """ Saves the variable as a parameter in the param store. To interact with the param store or write to disk, see `Parameters <parameters.html>`_. :param name: name of parameter :returns: parameter """ kwargs["name"] = name return _param(name, *args, **kwargs)
[docs]def sample(name, fn, *args, **kwargs): """ Calls the stochastic function `fn` with additional side-effects depending on `name` and the enclosing context (e.g. an inference algorithm). See `Intro I <>`_ and `Intro II <>`_ for a discussion. :param name: name of sample :param fn: distribution class or function :param obs: observed datum (optional; should only be used in context of inference) optionally specified in kwargs :param dict infer: Optional dictionary of inference parameters specified in kwargs. See inference documentation for details. :returns: sample """ obs = kwargs.pop("obs", None) infer = kwargs.pop("infer", {}).copy() # check if stack is empty # if stack empty, default behavior (defined here) if not am_i_wrapped(): if obs is not None: warnings.warn("trying to observe a value outside of inference at " + name, RuntimeWarning) return obs return fn(*args, **kwargs) # if stack not empty, apply everything in the stack? else: # initialize data structure to pass up/down the stack msg = { "type": "sample", "name": name, "fn": fn, "is_observed": False, "args": args, "kwargs": kwargs, "value": None, "infer": infer, "scale": 1.0, "mask": None, "cond_indep_stack": (), "done": False, "stop": False, "continuation": None } # handle observation if obs is not None: msg["value"] = obs msg["is_observed"] = True # apply the stack and return its return value apply_stack(msg) return msg["value"]
[docs]class plate(PlateMessenger): """ Construct for conditionally independent sequences of variables. ``plate`` can be used either sequentially as a generator or in parallel as a context manager (formerly ``irange`` and ``iarange``, respectively). Sequential :class:`plate` is similar to :py:func:`range` in that it generates a sequence of values. Vectorized :class:`plate` is similar to :func:`torch.arange` in that it yields an array of indices by which other tensors can be indexed. :class:`plate` differs from :func:`torch.arange` in that it also informs inference algorithms that the variables being indexed are conditionally independent. To do this, :class:`plate` is a provided as context manager rather than a function, and users must guarantee that all computation within an :class:`plate` context is conditionally independent:: with plate("name", size) as ind: # conditionally independent stuff with ind... Additionally, :class:`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 a ``torch.arange(0, size)``. If ``0 < subsample_size <= size`` this yields a single random batch of indices of size ``subsample_size`` and scales all log likelihood terms by ``size/batch_size``, within this context. .. warning:: This is only correct if all computation is conditionally independent within the context. :param str name: A unique name to help inference algorithms match :class:`plate` sites between models and guides. :param int size: Optional size of the collection being subsampled (like `stop` in builtin `range`). :param int subsample_size: Size of minibatches used in subsampling. Defaults to `size`. :param subsample: Optional custom subsample for user-defined subsampling schemes. If specified, then `subsample_size` will be set to `len(subsample)`. :type subsample: Anything supporting `len()`. :param int dim: 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 enclosing ``plate`` contexts. :param bool use_cuda: 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``. :param str device: 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. :return: A reusabe context manager yielding a single 1-dimensional :class:`torch.Tensor` of indices. Examples: .. doctest:: :hide: >>> loc, scale = torch.tensor(0.), torch.tensor(1.) >>> data = torch.randn(100) >>> z = dist.Bernoulli(0.5).sample((100,)) >>> # 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 user-defined 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. """ pass
class iarange(plate): def __init__(self, *args, **kwargs): warnings.warn("pyro.iarange is deprecated; use pyro.plate instead", DeprecationWarning) super(iarange, self).__init__(*args, **kwargs) class irange(SubsampleMessenger): def __init__(self, *args, **kwargs): warnings.warn("pyro.irange is deprecated; use pyro.plate instead", DeprecationWarning) super(irange, self).__init__(*args, **kwargs)
[docs]def module(name, nn_module, update_module_params=False): """ 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. :param name: name of module :type name: str :param nn_module: the module to be registered with Pyro :type nn_module: torch.nn.Module :param update_module_params: determines whether Parameters in the PyTorch module get overridden with the values found in the ParamStore (if any). Defaults to `False` :type load_from_param_store: bool :returns: torch.nn.Module """ assert hasattr(nn_module, "parameters"), "module has no parameters" assert _MODULE_NAMESPACE_DIVIDER not in name, "improper module name, since contains %s" %\ _MODULE_NAMESPACE_DIVIDER if isclass(nn_module): raise NotImplementedError("pyro.module does not support class constructors for " + "the argument nn_module") target_state_dict = OrderedDict() for param_name, param_value in nn_module.named_parameters(): # register the parameter in the module with pyro # this only does something substantive if the parameter hasn't been seen before full_param_name = param_with_module_name(name, param_name) returned_param = param(full_param_name, param_value) if param_value._cdata != returned_param._cdata: target_state_dict[param_name] = returned_param if target_state_dict and update_module_params: # WARNING: this is very dangerous. better method? for _name, _param in nn_module.named_parameters(): is_param = False name_arr = _name.rsplit('.', 1) if len(name_arr) > 1: mod_name, param_name = name_arr[0], name_arr[1] else: is_param = True mod_name = _name if _name in target_state_dict.keys(): if not is_param: deep_getattr(nn_module, mod_name)._parameters[param_name] = target_state_dict[_name] else: nn_module._parameters[mod_name] = target_state_dict[_name] return nn_module
[docs]def random_module(name, nn_module, prior, *args, **kwargs): """ Places a prior over the parameters of the module `nn_module`. Returns a distribution (callable) over `nn.Module`s, which upon calling returns a sampled `nn.Module`. See the `Bayesian Regression tutorial <>`_ for an example. :param name: name of pyro module :type name: str :param nn_module: the module to be registered with pyro :type nn_module: torch.nn.Module :param prior: 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 """ assert hasattr(nn_module, "parameters"), "Module is not a NN module." # register params in param store lifted_fn = poutine.lift(module, prior=prior) def _fn(): nn_copy = copy.deepcopy(nn_module) # update_module_params must be True or the lifted module will not update local params return lifted_fn(name, nn_copy, update_module_params=True, *args, **kwargs) return _fn
[docs]def enable_validation(is_validate=True): """ 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. :param bool is_validate: (optional; defaults to True) whether to enable validation checks. """ dist.enable_validation(is_validate) infer.enable_validation(is_validate) poutine.enable_validation(is_validate)
[docs]@contextmanager def validation_enabled(is_validate=True): """ Context manager that is useful when temporarily enabling/disabling validation checks. :param bool is_validate: (optional; defaults to True) temporary validation check override. """ infer_validation_status = infer.is_validation_enabled() distribution_validation_status = dist.is_validation_enabled() poutine_validation_status = poutine.is_validation_enabled() try: enable_validation(is_validate) yield finally: dist.enable_validation(distribution_validation_status) infer.enable_validation(infer_validation_status) poutine.enable_validation(poutine_validation_status)