Implement pyro.ops.streaming module

docs/source/ops.rst

@@ -93,6 +93,14 @@ Statistical Utilities
     :show-inheritance:
     :member-order: bysource
 
+Streaming Statistics
+--------------------
+
+.. automodule:: pyro.ops.streaming
+    :members:
+    :undoc-members:
+    :show-inheritance:
+    :member-order: bysource
 
 State Space Model and GP Utilities
 ----------------------------------

pyro/ops/streaming.py

@@ -0,0 +1,277 @@
+# Copyright Contributors to the Pyro project.
+# SPDX-License-Identifier: Apache-2.0
+
+import copy
+from abc import ABC, abstractmethod
+from collections import defaultdict
+from typing import Any, Callable, Dict, Hashable, Union
+
+import torch
+
+from pyro.ops.welford import WelfordCovariance
+
+
+class StreamingStats(ABC):
+    """
+    Abstract base class for streamable statistics of trees of tensors.
+
+    Derived classes must implelement :meth:`update`, :meth:`merge`, and
+    :meth:`get`.
+    """
+
+    @abstractmethod
+    def update(self, sample) -> None:
+        """
+        Update state from a single sample.
+
+        This mutates ``self`` and returns nothing. Updates should be
+        independent of order, i.e. samples should be exchangeable.
+
+        :param sample: A sample value which is a nested dictionary of
+            :class:`torch.Tensor` leaves. This can have arbitrary nesting and
+            shape shape, but assumes shape is constant across calls to
+            ``.update()``.
+        """
+        raise NotImplementedError
+
+    @abstractmethod
+    def merge(self, other) -> "StreamingStats":
+        """
+        Select two aggregate statistics, e.g. from different MCMC chains.
+
+        This is a pure function: it returns a new :class:`StreamingStats`
+        object and does not modify either ``self`` or ``other``.
+
+        :param other: Another streaming stats instance of the same type.
+        """
+        assert isinstance(other, type(self))
+        raise NotImplementedError
+
+    @abstractmethod
+    def get(self) -> Any:
+        """
+        Return the aggregate statistic.
+        """
+        raise NotImplementedError
+
+
+class CountStats(StreamingStats):
+    """
+    Statistic tracking only the number of samples.
+
+    For example::
+
+        >>> stats = CountStats()
+        >>> stats.update(torch.randn(3, 3))
+        >>> stats.get()
+        {'count': 1}
+    """
+
+    def __init__(self):
+        self.count = 0
+        super().__init__()
+
+    def update(self, sample) -> None:
+        self.count += 1
+
+    def merge(self, other: "CountStats") -> "CountStats":
+        assert isinstance(other, type(self))
+        result = CountStats()
+        result.count = self.count + other.count
+        return result
+
+    def get(self) -> Dict[str, int]:
+        """
+        :returns: A dictionary with keys ``count: int``.
+        :rtype: dict
+        """
+        return {"count": self.count}
+
+
+class StatsOfDict(StreamingStats):
+    """
+    Statistics of samples that are dictionaries with constant set of keys.
+
+    For example the following are equivalent::
+
+        # Version 1. Hand encode statistics.
+        >>> a_stats = CountStats()
+        >>> b_stats = CountMeanStats()
+        >>> a_stats.update(torch.tensor(0.))
+        >>> b_stats.update(torch.tensor([1., 2.]))
+        >>> summary = {"a": a_stats.get(), "b": b_stats.get()}
+
+        # Version 2. Collect samples into dictionaries.
+        >>> stats = StatsOfDict({"a": CountStats, "b": CountMeanStats})
+        >>> stats.update({"a": torch.tensor(0.), "b": torch.tensor([1., 2.])})
+        >>> summary = stats.get()
+        >>> summary
+        {'a': {'count': 1}, 'b': {'count': 1, 'mean': tensor([1., 2.])}}
+
+    :param default: Default type of statistics of values of the dictionary.
+        Defaults to the inexpensive :class:`CountStats`.
+    :param dict types: Dictionary mapping key to type of statistic that should
+        be recorded for values corresponding to that key.
+    """
+
+    def __init__(
+        self,
+        types: Dict[Hashable, Callable[[], StreamingStats]] = {},
+        default: Callable[[], StreamingStats] = CountStats,
+    ):
+        self.stats: Dict[Hashable, StreamingStats] = defaultdict(default)
+        self.stats.update({k: v() for k, v in types.items()})
+        super().__init__()
+
+    def update(self, sample: Dict[Hashable, Any]) -> None:
+        for k, v in sample.items():
+            self.stats[k].update(v)
+
+    def merge(self, other: "StatsOfDict") -> "StatsOfDict":
+        assert isinstance(other, type(self))
+        result = copy.deepcopy(self)
+        for k in set(self.stats).union(other.stats):
+            if k not in self.stats:
+                result.stats[k] = copy.deepcopy(other.stats[k])
+            elif k in other.stats:
+                result.stats[k] = self.stats[k].merge(other.stats[k])
+        return result
+
+    def get(self) -> Dict[Hashable, Any]:
+        """
+        :returns: A dictionary of statistics. The keys of this dictionary are
+            the same as the keys of the samples from which this object is
+            updated.
+        :rtype: dict
+        """
+        return {k: v.get() for k, v in self.stats.items()}
+
+
+class StackStats(StreamingStats):
+    """
+    Statistic collecting a stream of tensors into a single stacked tensor.
+    """
+
+    def __init__(self):
+        self.samples = []
+
+    def update(self, sample: torch.Tensor) -> None:
+        assert isinstance(sample, torch.Tensor)
+        self.samples.append(sample)
+
+    def merge(self, other: "StackStats") -> "StackStats":
+        assert isinstance(other, type(self))
+        result = StackStats()
+        result.samples = self.samples + other.samples
+        return result
+
+    def get(self) -> Dict[str, Union[int, torch.Tensor]]:
+        """
+        :returns: A dictionary with keys ``count: int`` and (if any samples
+            have been collected) ``samples: torch.Tensor``.
+        :rtype: dict
+        """
+        if not self.samples:
+            return {"count": 0}
+        return {"count": len(self.samples), "samples": torch.stack(self.samples)}
+
+
+class CountMeanStats(StreamingStats):
+    """
+    Statistic tracking the count and mean of a single :class:`torch.Tensor`.
+    """
+
+    def __init__(self):
+        self.count = 0
+        self.mean = 0
+        super().__init__()
+
+    def update(self, sample: torch.Tensor) -> None:
+        assert isinstance(sample, torch.Tensor)
+        self.count += 1
+        self.mean += (sample.detach() - self.mean) / self.count
+
+    def merge(self, other: "CountMeanStats") -> "CountMeanStats":
+        assert isinstance(other, type(self))
+        result = CountMeanStats()
+        result.count = self.count + other.count
+        p = self.count / max(result.count, 1)
+        q = other.count / max(result.count, 1)
+        result.mean = p * self.mean + q * other.mean
+        return result
+
+    def get(self) -> Dict[str, Union[int, torch.Tensor]]:
+        """
+        :returns: A dictionary with keys ``count: int`` and (if any samples
+            have been collected) ``mean: torch.Tensor``.
+        :rtype: dict
+        """
+        if self.count == 0:
+            return {"count": 0}
+        return {"count": self.count, "mean": self.mean}
+
+
+class CountMeanVarianceStats(StreamingStats):
+    """
+    Statistic tracking the count, mean, and (diagonal) variance of a single
+    :class:`torch.Tensor`.
+    """
+
+    def __init__(self):
+        self.shape = None
+        self.welford = WelfordCovariance(diagonal=True)
+        super().__init__()
+
+    def update(self, sample: torch.Tensor) -> None:
+        assert isinstance(sample, torch.Tensor)
+        if self.shape is None:
+            self.shape = sample.shape
+        assert sample.shape == self.shape
+        self.welford.update(sample.detach().reshape(-1))
+
+    def merge(self, other: "CountMeanVarianceStats") -> "CountMeanVarianceStats":
+        assert isinstance(other, type(self))
+        if self.shape is None:
+            return copy.deepcopy(other)
+        if other.shape is None:
+            return copy.deepcopy(self)
+        result = copy.deepcopy(self)
+        res = result.welford
+        lhs = self.welford
+        rhs = other.welford
+        res.n_samples = lhs.n_samples + rhs.n_samples
+        lhs_weight = lhs.n_samples / res.n_samples
+        rhs_weight = rhs.n_samples / res.n_samples
+        res._mean = lhs_weight * lhs._mean + rhs_weight * rhs._mean
+        res._m2 = (
+            lhs._m2
+            + rhs._m2
+            + (lhs.n_samples * rhs.n_samples / res.n_samples)
+            * (lhs._mean - rhs._mean) ** 2
+        )
+        return result
+
+    def get(self) -> Dict[str, Union[int, torch.Tensor]]:
+        """
+        :returns: A dictionary with keys ``count: int`` and (if any samples
+            have been collected) ``mean: torch.Tensor`` and ``variance:
+            torch.Tensor``.
+        :rtype: dict
+        """
+        if self.shape is None:
+            return {"count": 0}
+        count = self.welford.n_samples
+        mean = self.welford._mean.reshape(self.shape)
+        variance = self.welford.get_covariance(regularize=False).reshape(self.shape)
+        return {"count": count, "mean": mean, "variance": variance}
+
+
+# Note this is ordered logically for sphinx rather than alphabetically.
+__all__ = [
+    "StreamingStats",
+    "StatsOfDict",
+    "StackStats",
+    "CountStats",
+    "CountMeanStats",
+    "CountMeanVarianceStats",
+]

setup.cfg

@@ -35,43 +35,45 @@ column_limit = 120
 python_version = 3.6
 warn_return_any = True
 warn_unused_configs = True
+warn_incomplete_stub = True
 
 # Per-module options:
 
 [mypy-pyro._version.*]
 ignore_errors = True
-warn_incomplete_stub = True
 
 [mypy-pyro.contrib.*]
 ignore_errors = True
-warn_incomplete_stub = True
 
 [mypy-pyro.distributions.*]
 ignore_errors = True
-warn_incomplete_stub = True
 warn_unused_ignores = True
 
 [mypy-pyro.generic.*]
 ignore_errors = True
-warn_incomplete_stub = True
 warn_unused_ignores = True
 
 [mypy-pyro.infer.*]
 ignore_errors = True
-warn_incomplete_stub = True
 warn_unused_ignores = True
 
 [mypy-pyro.nn.*]
 ignore_errors = True
-warn_incomplete_stub = True
 warn_unused_ignores = True
 
-[mypy-pyro.ops.*]
+[mypy-pyro.ops.einsum]
+ignore_errors = True
+warn_unused_ignores = True
+
+[mypy-pyro.ops.contract]
+ignore_errors = True
+warn_unused_ignores = True
+
+[mypy-pyro.ops.tensor_utils]
 ignore_errors = True
 warn_unused_ignores = True
 
 [mypy-pyro.optm.*]
-warn_incomplete_stub = True
 warn_unused_ignores = True
 
 [mypy-pyro.params.*]
@@ -83,5 +85,4 @@ ignore_errors = True
 
 [mypy-pyro.util.*]
 ignore_errors = True
-warn_incomplete_stub = True
 warn_unused_ignores = True

tests/common.py

@@ -225,7 +225,7 @@ def assert_close(actual, expected, atol=1e-7, rtol=0, msg=''):
         assert set(actual.keys()) == set(expected.keys())
         for key, x_val in actual.items():
             assert_close(x_val, expected[key], atol=atol, rtol=rtol,
-                         msg='At key{}: {} vs {}'.format(key, x_val, expected[key]))
+                         msg='At key {}: {} vs {}'.format(repr(key), x_val, expected[key]))
     elif isinstance(actual, str):
         assert actual == expected, msg
     elif is_iterable(actual) and is_iterable(expected):