metadentify 0.1.0a0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- metadentify-0.1.0a0/.github/workflows/ci.yml +63 -0
- metadentify-0.1.0a0/.github/workflows/publish.yml +44 -0
- metadentify-0.1.0a0/LICENSE +201 -0
- metadentify-0.1.0a0/Makefile +32 -0
- metadentify-0.1.0a0/PKG-INFO +220 -0
- metadentify-0.1.0a0/README.md +179 -0
- metadentify-0.1.0a0/devtools/lint.py +53 -0
- metadentify-0.1.0a0/docs/development.md +94 -0
- metadentify-0.1.0a0/docs/images/cnp_diagram.png +0 -0
- metadentify-0.1.0a0/docs/images/dags_and_curve.png +0 -0
- metadentify-0.1.0a0/docs/images/example_curves_1.png +0 -0
- metadentify-0.1.0a0/docs/images/example_curves_2.png +0 -0
- metadentify-0.1.0a0/docs/images/id_diagram.svg +621 -0
- metadentify-0.1.0a0/docs/images/p_identifiability.png +0 -0
- metadentify-0.1.0a0/docs/installation.md +27 -0
- metadentify-0.1.0a0/docs/publishing.md +213 -0
- metadentify-0.1.0a0/experiments/example_experiment.py +324 -0
- metadentify-0.1.0a0/experiments/example_sweep.yaml +67 -0
- metadentify-0.1.0a0/pyproject.toml +198 -0
- metadentify-0.1.0a0/src/metadentify/__init__.py +0 -0
- metadentify-0.1.0a0/src/metadentify/args.py +59 -0
- metadentify-0.1.0a0/src/metadentify/baselines.py +460 -0
- metadentify-0.1.0a0/src/metadentify/launch_sweep.py +153 -0
- metadentify-0.1.0a0/src/metadentify/mechanisms.py +167 -0
- metadentify-0.1.0a0/src/metadentify/mixture.py +778 -0
- metadentify-0.1.0a0/src/metadentify/modules.py +926 -0
- metadentify-0.1.0a0/src/metadentify/py.typed +0 -0
- metadentify-0.1.0a0/src/metadentify/queries.py +147 -0
- metadentify-0.1.0a0/src/metadentify/run_experiment.py +94 -0
- metadentify-0.1.0a0/src/metadentify/sbatch.py +52 -0
- metadentify-0.1.0a0/src/metadentify/train.py +276 -0
- metadentify-0.1.0a0/src/metadentify/utils.py +49 -0
- metadentify-0.1.0a0/tests/test_placeholder.py +3 -0
- metadentify-0.1.0a0/uv.lock +3909 -0
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# This workflow will install Python dependencies, run tests and lint with a single version of Python
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# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
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name: CI
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on:
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push:
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# Use ["main", "master"] for CI only on the default branch.
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# Use ["**"] for CI on all branches.
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branches: ["main", "master"]
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pull_request:
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branches: ["main", "master"]
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permissions:
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contents: read
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jobs:
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build:
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strategy:
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matrix:
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# Update this as needed:
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# Common platforms: ["ubuntu-latest", "macos-latest", "windows-latest"]
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os: ["ubuntu-latest"]
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python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
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# Linux only by default. Use ${{ matrix.os }} for other OSes.
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runs-on: ${{ matrix.os }}
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steps:
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# Generally following uv docs:
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# https://docs.astral.sh/uv/guides/integration/github/
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- name: Checkout (official GitHub action)
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uses: actions/checkout@v6
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with:
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# Important for versioning plugins:
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fetch-depth: 0
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- name: Install uv (official Astral action)
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uses: astral-sh/setup-uv@v7
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with:
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# Update this as needed:
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version: "0.10.2"
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enable-cache: true
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python-version: ${{ matrix.python-version }}
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- name: Set up Python (using uv)
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run: uv python install
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# Alternately can use the official Python action:
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# - name: Set up Python (using actions/setup-python)
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# uses: actions/setup-python@v5
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# with:
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# python-version: ${{ matrix.python-version }}
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- name: Install all dependencies
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run: uv sync --all-extras
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- name: Run linting
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run: uv run python devtools/lint.py
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- name: Run tests
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run: uv run pytest
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name: Publish to PyPI
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on:
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release:
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types: [published]
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workflow_dispatch: # Enable manual trigger.
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jobs:
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build-and-publish:
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runs-on: ubuntu-latest
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permissions:
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id-token: write # Mandatory for OIDC.
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contents: read
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steps:
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- name: Checkout (official GitHub action)
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uses: actions/checkout@v6
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with:
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fetch-depth: 0
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- name: Install uv (official Astral action)
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uses: astral-sh/setup-uv@v7
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with:
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version: "0.10.2"
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enable-cache: true
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python-version: "3.12"
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- name: Set up Python (using uv)
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run: uv python install
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- name: Install all dependencies
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run: uv sync --all-extras
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- name: Run tests
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run: uv run pytest
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- name: Build package
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run: uv build
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- name: Publish to PyPI
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run: uv publish --trusted-publishing always
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# Although uv is newer and faster, the "official" publishing option is the one from PyPA,
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# which uses twine. If desired, replace `uv publish` with:
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# uses: pypa/gh-action-pypi-publish@release/v1
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Apache License
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Version 2.0, January 2004
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Metadata-Version: 2.4
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Name: metadentify
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Version: 0.1.0a0
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Summary: Meta/in-context/amortized causal inference for computational identifiability
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Project-URL: Repository, https://github.com/lbynum/metadentify
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# `metadentify`: Meta/in-context/amortized causal inference for computational identifiability
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[](https://badge.fury.io/py/metadentify)
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[](https://arxiv.org/abs/ARXIV.ID)
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> Two approaches to identifiability. Mathematical derivation (top) seeks to prove the existence of a unique parameter, analytically in expectation. Computational search (bottom, implemented in this repository) instead defines an empirical search procedure for an estimator and defines 'computational identifiability' as the successful discovery of an estimator, conditional on a prior over parameters, a hypothesis space over estimators, finite samples, and a desired error tolerance.
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This repository contains the official code and resources for the paper [**Computational Identifiability**](https://arxiv.org/abs/ARXIV.ID) (https://arxiv.org/abs/ARXIV.ID).
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## Overview
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A critical step in answering a causal or statistical query from data is determining if there is sufficient information to compute a unique answer. Traditionally, **theoretical identifiability** achieves this mathematically in expectation, often relying on mathematically idealized conditions like asymptotic properties or infinite data.
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This motivates **computational identifiability**, a complemetary notion of identifiability that is computation-bound. Instead of analytical mathematical derivation, it frames identifiability as a finite computational search procedure for an empirical estimator.
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Computational identifiability starts with:
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1. A meta-prior over the parameters in question (e.g., a distribution over structural causal models, or SCMs).
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2. A hypothesis space of possible estimators (e.g., an instantiated Conditional Neural Process, a pre-trained tabular foundation model, etc.).
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For a given finite sample size, error tolerance, and confidence bound, computational identifiability is satisfied if an empirical estimator exists within the hypothesis space that can successfully estimate the query within the desired error margin.
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## Framework & methodology
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To operationalize this search, we generalize the connection between causal effect estimation and meta-learning.
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To meta-learn causal estimators, we define context set $D_c$ of $n$ observations $O=o$ and source labels $S=s$. Source labels can be, e.g., indicators for 'observational,' 'interventional,' 'counterfactual,' etc., corresponding to each type of data available for meta-training. We then define the target set $D_t$ consisting of $m$ query points $X_t=x_t$ and corresponding realized causal query values $\Theta_t = \theta_t$. The meta-model processes these inputs in the style of a conditional neural process (CNP) as pictured in the diagram above (see Section 3.1.1 in the paper for full architecture descriptions).
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> **(a)-(f)** A few example DAGs we consider in the paper. **(Right)** Diagram showing *computational identifiability curves*, visualizing computational identifiability across a range of possible $\epsilon$ values. The empirical (or posterior) probability of identifiability can be read at a given desired error tolerance (see Section 3.2 in the paper for the corresponding algorithm).
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* **Meta-learning causal effect estimators:** We learn mappings from observations and query points to causal query values by training on joint distributions over SCMs, observations, and query values. The `experiments/` folder demonstrates applying this same meta-learning process to several settings.
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* **Architectures:** This repository implements two Conditional Neural Process (CNP) style architectures with conformalized quantile regression to use out-of-the-box (see `modules.py`). The Q-CNP uses mean-pooling and Q-TNP uses attention-based processing.
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* **Posterior estimates:** By using models that support posterior uncertainty, we can directly estimate the **probability of identifiability** for any new data at test-time.
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## Codebase & features
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This package is designed for modularity, scalable training, and easy experimentation.
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### Causal mixtures & `dowhy` integration
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* **`mixture.py`**: This module directly implements the joint-causal-query-mixture distribution used to generate meta-training data (see Definitions 1-6 in the paper for details).
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* **`dowhy` backend**: The codebase natively supports the `dowhy` package (specifically `dowhy.gcm`) as its language for specifying structural causal models. This provides an intuitive and standardized way to experiment with new causal graphs and mechanisms. This allows easy experimentation with **observational, interventional, and counterfactual** data and estimands.
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### Infrastructure & scaling
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The repository is optimized to easily scale up meta-learning experiments with distributed computing environments:
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* **Weights & Biases (W&B):** Fully integrated for experiment tracking and metric logging built into the meta-model (`modules.py`).
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> [!NOTE]
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> Additional features under development. Stay tuned :)
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## Usage examples
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Below are usage examples for computational identifiability experiments. The same `run-experiment` function can be called and routed to different experiment files (e.g., `experiments/example_experiment.py`). The `--log_identifiability` flag can be added to any experiment to log the identifiability curve to W&B for normalized epsilon from 0-2.5. In addition, many other arguments are possible (see `args.py` for a full list of arguments). All runs and sweeps will automatically log to Weights&Biases unless `--disable_wandb` is passed.
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> Identifiability curves from meta-models (the Q-CNP backbone in modules.py) trained on each of the cases in example_experiment.py, as a function of varying dataset size $N$.
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> Identifiability curves from per-dataset estimation methods (implemented in baselines.py) instead of meta-trained models, for each of the cases in example_experiment.py.
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The above figures plot P(identifiability) values from the W&B sweep defined in `example_sweep.yaml`, which automates running `example_experiment.py` across a range of parameters (see below for W&B setup instructions).
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#### Distributed W&B sweeps on SLURM inside a Singularity container
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In this example, we launch a 12-node distributed sweep experiment on SLURM inside a Singularity environment with W&B logging (using the same `experiments/example_sweep.yaml` config):
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python src/metadentify/launch_sweep.py --config experiments/example_sweep.yaml --num_jobs 12
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```
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## Citation
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If you find this code or concept useful in your research, please cite the corresponding papers:
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```
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@article{bynum2026computational,
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title={Computational Identifiability},
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author={Bynum, Lucius EJ and Ranganath, Rajesh and Cho, Kyunghyun},
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journal={arXiv preprint arXiv:ARXIV.ID},
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year={2026}
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}
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@article{bynum2025black,
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title={Black Box Causal Inference: Effect Estimation via Meta Prediction},
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author={Bynum, Lucius EJ and Puli, Aahlad Manas and Herrero-Quevedo, Diego and Nguyen, Nhi and Fernandez-Granda, Carlos and Cho, Kyunghyun and Ranganath, Rajesh},
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journal={arXiv preprint arXiv:2503.05985},
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year={2025}
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}
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```
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Package made with <a href="https://github.com/jlevy/simple-modern-uv" target="_blank"> simple-modern-uv </a>
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