mbi 1.0.0__tar.gz

mbi-1.0.0/LICENSE

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mbi-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: mbi
+Version: 1.0.0
+Summary: Marginal-based estimation and inference (with applications to differential privacy)
+Author-email: Ryan McKenna <rmckenna21@gmail.com>
+License: Apache License 2.0
+Project-URL: Homepage, https://github.com/ryan112358/mbi
+Project-URL: Repository, https://github.com/ryan112358/mbi
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: attrs
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: pandas
+Requires-Dist: networkx
+Requires-Dist: jax
+Requires-Dist: jaxlib
+Requires-Dist: chex
+Requires-Dist: optax
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytype; extra == "dev"
+Requires-Dist: parameterized; extra == "dev"
+Requires-Dist: yapf; extra == "dev"
+Requires-Dist: pylint; extra == "dev"
+Requires-Dist: pydocstyle; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Requires-Dist: myst-parser; extra == "docs"
+Dynamic: license-file
+
+## MBI: Marginal-Based Estimation and Inference
+**(with applications to differential privacy)**
+
+<img src="pgm-logo.png" alt="drawing" width="123"/>
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5548533.svg)](https://doi.org/10.5281/zenodo.5548533)
+[![Continuous integration](https://github.com/ryan112358/private-pgm/actions/workflows/main.yml/badge.svg)](https://github.com/ryan112358/private-pgm/actions/workflows/main.yml)
+[![Documentation Status](https://app.readthedocs.org/projects/private-pgm/badge/?version=latest)](https://private-pgm.readthedocs.io/en/latest/)
+
+![Metrics for ryan112358/private-pgm repository](https://raw.githubusercontent.com/ryan112358/ryan112358/main/metrics.private-pgm.svg)
+
+
+Documentation has been moved to
+[https://private-pgm.readthedocs.io/en/latest/](https://private-pgm.readthedocs.io/en/latest/)!

mbi-1.0.0/README.md

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+## MBI: Marginal-Based Estimation and Inference
+**(with applications to differential privacy)**
+
+<img src="pgm-logo.png" alt="drawing" width="123"/>
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5548533.svg)](https://doi.org/10.5281/zenodo.5548533)
+[![Continuous integration](https://github.com/ryan112358/private-pgm/actions/workflows/main.yml/badge.svg)](https://github.com/ryan112358/private-pgm/actions/workflows/main.yml)
+[![Documentation Status](https://app.readthedocs.org/projects/private-pgm/badge/?version=latest)](https://private-pgm.readthedocs.io/en/latest/)
+
+![Metrics for ryan112358/private-pgm repository](https://raw.githubusercontent.com/ryan112358/ryan112358/main/metrics.private-pgm.svg)
+
+
+Documentation has been moved to
+[https://private-pgm.readthedocs.io/en/latest/](https://private-pgm.readthedocs.io/en/latest/)!

mbi-1.0.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "mbi"
+version = "1.0.0"
+description = "Marginal-based estimation and inference (with applications to differential privacy)"
+authors = [
+    {name = "Ryan McKenna", email = "rmckenna21@gmail.com"},
+]
+license = {text = "Apache License 2.0"}
+readme = "README.md"
+requires-python = ">=3.9"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+    "attrs",
+    "numpy",
+    "scipy",
+    "pandas",
+    "networkx",
+    "jax",
+    "jaxlib",
+    "chex",
+    "optax",
+]
+
+[project.urls]
+Homepage = "https://github.com/ryan112358/mbi"
+Repository = "https://github.com/ryan112358/mbi"
+
+[project.optional-dependencies]
+dev = [
+    "pytest",
+    "pytype",
+    "parameterized",
+    "yapf",
+    "pylint",
+    "pydocstyle",
+]
+docs = [
+    "sphinx",
+    "sphinx-rtd-theme",
+    "myst-parser",
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]

mbi-1.0.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

mbi-1.0.0/src/mbi/__init__.py

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+"""Main entry point for the mbi package.
+
+This module exposes the core classes and submodules of the mbi library,
+making them available for direct import. It simplifies access to functionalities
+like data representation (Domain, Dataset), factor manipulation (Factor),
+and various estimation and oracle modules.
+"""
+from . import callbacks, estimation, junction_tree, marginal_oracles
+from .clique_vector import CliqueVector
+from .dataset import Dataset
+from .domain import Domain
+from .estimation import Estimator
+from .factor import Factor, Projectable
+from .marginal_loss import LinearMeasurement, MarginalLossFn
+from .marginal_oracles import MarginalOracle
+from .markov_random_field import MarkovRandomField
+
+Clique = tuple[str, ...]
+
+__all__ = [
+    'Domain',
+    'Dataset',
+    'Factor',
+    'Clique',
+    'CliqueVector',
+    'LinearMeasurement',
+    'MarginalLossFn',
+    'MarkovRandomField',
+    'Projectable',
+    'MarginalOracle',
+    'Estimator',
+    'estimation',
+    'callbacks',
+    'junction_tree',
+    'marginal_oracles',
+]

mbi-1.0.0/src/mbi/approximate_oracles.py

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+"""Approximate marginal oracles with convex counting numbers.
+
+See the paper ["Relaxed Marginal Consistency for Differentially Private Query Answering"](https://arxiv.org/pdf/2109.06153) for more details.
+
+This file implements one approximate marginal inference oracle: Convex-GBP
+with fixed counting numbers of 1.0 for all regions.  We experimented with
+others, but do not officially support them in this library.  If interested,
+please see the following snapshot of this repository:
+
+https://github.com/ryan112358/private-pgm/tree/approx-experiments-snapshot
+
+Pull requests are welcome to add support for other approximate oracles.
+"""
+
+import functools
+import itertools
+from typing import Any, Protocol, TypeAlias
+
+import jax
+import networkx as nx
+from scipy.cluster.hierarchy import DisjointSet
+
+from .clique_vector import CliqueVector
+from .domain import Domain
+from .factor import Factor
+
+Clique: TypeAlias = tuple[str, ...]
+
+# pylint: disable
+
+
+class StatefulMarginalOracle(Protocol):
+    """
+    Defines the callable signature for stateful marginal oracle functions.
+
+    A stateful marginal oracle computes (approximate) marginals from
+    log-space potentials while also managing an internal state, often
+    for optimization in iterative algorithms (e.g., preserving messages
+    in message passing).
+    """
+    def __call__(
+        self,
+        potentials: CliqueVector,
+        total: float = 1.0,
+        state: Any = None,
+        mesh: jax.sharding.Mesh | None = None
+    ) -> tuple[CliqueVector, Any]:
+        """
+        Computes marginals from log-space potentials and manages state.
+
+        Args:
+            potentials: A CliqueVector representing the log-space potentials
+                of a graphical model.
+            total: The normalization factor, typically the total number of
+                records or a probability sum. Defaults to 1.0.
+            state: An optional argument to pass state between calls.
+                The oracle may use this state and return an updated version.
+            mesh: Specifies how the computation will be sharded across devices.
+
+        Returns:
+            A tuple containing:
+                - CliqueVector: The computed marginals.
+                - Any: The updated state.
+        """
+        ...
+
+
+def build_graph(domain: Domain, cliques: list[tuple[str, ...]]) -> ...:
+    """Builds the region graph for convex generalized belief propagation."""
+    # Hard-code minimal=True, convex=True
+    # Counting numbers = 1 for all regions
+    # Alg 11.3 of Koller & Friedman
+    regions = set(cliques)
+    size = 0
+    while len(regions) > size:
+        size = len(regions)
+        for r1, r2 in itertools.combinations(regions, 2):
+            z = tuple(sorted(set(r1) & set(r2)))
+            if len(z) > 0 and not z in regions:
+                regions.update({z})
+
+    G = nx.DiGraph()
+    G.add_nodes_from(regions)
+    for r1 in regions:
+        for r2 in regions:
+            if set(r2) < set(r1) and not any(
+                set(r2) < set(r3) and set(r3) < set(r1) for r3 in regions
+            ):
+                G.add_edge(r1, r2)
+
+    H = G.reverse()
+    G1, H1 = nx.transitive_closure(G), nx.transitive_closure(H)
+
+    children = {r: list(G.neighbors(r)) for r in regions}
+    parents = {r: list(H.neighbors(r)) for r in regions}
+    descendants = {r: list(G1.neighbors(r)) for r in regions}
+    ancestors = {r: list(H1.neighbors(r)) for r in regions}
+    forebears = {r: set([r] + ancestors[r]) for r in regions}
+    downp = {r: set([r] + descendants[r]) for r in regions}
+
+    min_edges = []
+    for r in regions:
+        ds = DisjointSet()
+        for u in parents[r]:
+            ds.add(u)
+        for u, v in itertools.combinations(parents[r], 2):
+            uv = set(ancestors[u]) & set(ancestors[v])
+            if len(uv) > 0:
+                ds.merge(u, v)
+        canonical = set()
+        for u in parents[r]:
+            canonical.update({ds[u]})
+        min_edges.extend([(u, r) for u in canonical])
+
+    G = nx.DiGraph()
+    G.add_nodes_from(regions)
+    G.add_edges_from(min_edges)
+
+    H = G.reverse()
+    G1, H1 = nx.transitive_closure(G), nx.transitive_closure(H)
+
+    children = {r: list(G.neighbors(r)) for r in regions}
+    parents = {r: list(H.neighbors(r)) for r in regions}
+
+    messages = {}
+    message_order = []
+    for ru in sorted(regions, key=len):
+        for rd in children[ru]:
+            message_order.append((ru, rd))
+            messages[ru, rd] = Factor.zeros(domain.project(rd))
+            messages[rd, ru] = Factor.zeros(domain.project(rd))  # only for hazan et al
+
+    return regions, cliques, messages, message_order, parents, children
+
+_State = dict[tuple[Clique, Clique], Factor]
+
+@functools.partial(jax.jit, static_argnames=['mesh', 'iters'])
+def convex_generalized_belief_propagation(
+    potentials: CliqueVector,
+    total: float = 1,
+    state: _State | None = None,
+    mesh: jax.sharding.Mesh | None = None,
+    iters: int = 1,
+    damping: float = 0.5,
+) -> tuple[CliqueVector, _State]:
+    """Convex generalized belief propagation for approximmate marginal inference.
+
+        The algorithms implements the Algorithm 2 in our paper
+        ["Relaxed Marginal Consistency for Differentially Private Query Answering"](https://arxiv.org/pdf/2109.06153), which itself is based on the paper titled
+        ["Tightening Fractional Covering Upper Bounds on the Partition
+    Function for High-Order Region Graphs"](https://arxiv.org/pdf/1210.4881).
+
+    Args:
+        potentials: A CliqueVector object containing the potentials of the graphical model.
+        total: The total number of records in the dataset.
+        state: The state of the message passing algorithm (i.e., the messages).  Useful when
+            calling this within an iterative procedure for warm starting purposes.
+        mesh: Specifies how the computation will be sharded across machines.
+        iters: The number of iterations to run the algorithm.
+        damping: The damping factor for the messages.
+
+    Returns:
+        A CliqueVector of pseudo-marginals for the cliques in the graphical model.
+    """
+    potentials = potentials.apply_sharding(mesh)
+    domain, cliques = potentials.domain, potentials.cliques
+    # We might need or want a sharding constraint on messages here
+    regions, cliques, messages, message_order, parents, children = build_graph(
+        domain, cliques
+    )
+    if state is not None:
+        messages = state
+
+    # Hardcode assumption that counting numbers are 1.0 for all regions.
+    pot = potentials.expand(regions)
+
+    cc = {}
+    for r in regions:
+        for p in parents[r]:
+            cc[p, r] = 1 / (1 + len(parents[r]))
+
+    for _ in range(iters):
+        new = {}
+        for r in regions:
+            for p in parents[r]:
+                new[p, r] = (
+                    (
+                        pot[p]
+                        + sum(messages[c, p] for c in children[p] if c != r)
+                        - sum(messages[p, p1] for p1 in parents[p])
+                    )
+                    .project(r, log=True)
+                    .normalize(log=True)
+                    .apply_sharding(mesh)
+                )
+
+        for r in regions:
+            for p in parents[r]:
+                new[r, p] = (
+                    cc[p, r]
+                    * (
+                        pot[r]
+                        + sum(messages[c, r] for c in children[r])
+                        + sum(messages[p1, r] for p1 in parents[r])
+                    )
+                    - messages[p, r]
+                ).normalize(log=True).apply_sharding(mesh)
+
+        # Damping is not described in paper, but is needed to get convergence for dense graphs
+        rho = damping
+        for p in regions:
+            for r in children[p]:
+                messages[p, r] = rho * messages[p, r] + (1.0 - rho) * new[p, r]
+                messages[r, p] = rho * messages[r, p] + (1.0 - rho) * new[r, p]
+        mu = {}
+        for r in cliques:
+            mu[r] = (
+                (
+                    pot[r]
+                    + sum(messages[c, r] for c in children[r])
+                    - sum(messages[r, p] for p in parents[r])
+                )
+                .normalize(total, log=True)
+                .exp()
+                .apply_sharding(mesh)
+            )
+
+    return CliqueVector(domain, cliques, mu), messages

mbi-1.0.0/src/mbi/callbacks.py

@@ -0,0 +1,91 @@
+"""Defines callback mechanisms for monitoring optimization processes.
+
+This module provides a `Callback` class that can be used to track and log
+various metrics during iterative algorithms, such as those used in estimating
+marginals. It logs loss values and other relevant statistics.
+"""
+import attr
+import jax
+import pandas as pd
+
+from . import marginal_loss
+from .clique_vector import CliqueVector
+from .factor import Projectable
+from .marginal_loss import LinearMeasurement
+
+
+def _pad(string: str, length: int):
+    """Pads a string with spaces on both sides to a target length."""
+    if len(string) > length:
+        return string[:length]
+    left_pad = (length - len(string)) // 2
+    right_pad = length - len(string) - left_pad
+    return " " * left_pad + string + " " * right_pad
+
+
+@attr.dataclass
+class Callback:
+    loss_fns: dict[str, marginal_loss.MarginalLossFn]
+    frequency: int = 50
+    # Internal state
+    _step: int = 0
+    _logs: list = attr.field(factory=list)
+
+    def __call__(self, marginals: CliqueVector):
+        if self._step == 0:
+            header = "|".join([_pad(x, 12) for x in ["step", *self.loss_fns.keys()]])
+            print(header)
+            print("=" * len(header))
+        if self._step % self.frequency == 0:
+            row = [self.loss_fns[key](marginals) for key in self.loss_fns]
+            self._logs.append([self._step] + row)
+            padded_step = str(self._step) + " " * (9 - len(str(self._step)))
+            print(padded_step, *[("%.6f" % v)[:6] for v in row], sep="   |   ")
+        self._step += 1
+
+    @property
+    def summary(self):
+        return pd.DataFrame(
+            columns=["step"] + list(self.loss_fns.keys()), data=self._logs
+        ).astype(float)
+
+
+def default(
+    measurements: list[LinearMeasurement],
+    data: Projectable | None = None,
+    frequency: int = 50,
+) -> Callback:
+    """Creates a default Callback with standard loss functions (L1/L2 Loss/Error, Primal Feas)."""
+    loss_fns = {}
+    # Measures distance between input marginals and noisy marginals.
+    loss_fns["L2 Loss"] = marginal_loss.from_linear_measurements(
+        measurements, norm="l2", normalize=True
+    )
+    loss_fns["L1 Loss"] = marginal_loss.from_linear_measurements(
+        measurements,
+        norm="l1",
+        normalize=True,
+    )
+
+    if data is not None:
+        # Measures distance between input marginals and true marginals.
+        ground_truth = [
+            LinearMeasurement(
+                M.query(data.project(M.clique)),
+                clique=M.clique,
+                stddev=1,
+                query=M.query,
+            )
+            for M in measurements
+        ]
+        loss_fns["L2 Error"] = marginal_loss.from_linear_measurements(
+            ground_truth, norm="l2", normalize=True
+        )
+        loss_fns["L1 Error"] = marginal_loss.from_linear_measurements(
+            ground_truth, norm="l1", normalize=True
+        )
+
+    loss_fns = {key: jax.jit(loss_fns[key].__call__) for key in loss_fns}
+    loss_fns["Primal Feas"] = jax.jit(marginal_loss.primal_feasibility)
+
+    return Callback(loss_fns, frequency)