risk-bridge 1.0.1__tar.gz

risk_bridge-1.0.1/LICENSE

@@ -0,0 +1,172 @@
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risk_bridge-1.0.1/PKG-INFO

@@ -0,0 +1,220 @@
+Metadata-Version: 2.4
+Name: risk-bridge
+Version: 1.0.1
+Summary: Risk Bridging through Constrained MLE
+Author: Risk Bridge contributors
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/SaehwanPark/risk-bridge
+Project-URL: Repository, https://github.com/SaehwanPark/risk-bridge
+Project-URL: Issues, https://github.com/SaehwanPark/risk-bridge/issues
+Keywords: risk-modeling,calibration,constrained-optimization,maximum-likelihood,biostatistics
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: comp-builders>=1.0.0
+Requires-Dist: numpy>=2.4.2
+Requires-Dist: pandas>=3.0.1
+Requires-Dist: polars>=1.38.1
+Requires-Dist: rdata>=1.0.0
+Requires-Dist: scikit-learn>=1.8.0
+Requires-Dist: scipy>=1.17.1
+Dynamic: license-file
+
+<p align="center">
+  <img src="assets/risk-bridge-banner.png" alt="Risk Bridge banner" width="100%">
+</p>
+
+# Risk Bridge
+
+Risk Bridge is a Python package for estimating transportable binary-risk models when the available cohorts do not all contain the same information. It combines propensity-score sampling, reference-cohort calibration, maximum likelihood estimation, and constrained maximum likelihood estimation (cMLE) into reproducible simulation and user-data workflows.
+
+Package title: **Risk Bridging through Constrained MLE**.
+
+## Motivation
+
+Risk models often need to be evaluated or adapted across related populations: a target cohort, a source cohort, and a reference cohort. Standard model fitting can drift when covariate distributions, calibration strata, or observed risk markers differ across those cohorts. Risk Bridge provides a repeatable way to compare ordinary ML estimates with calibration-constrained estimates while preserving diagnostics, thresholds, and run metadata.
+
+## Foundation Papers
+
+- > Cao, Y., Ma, W., Zhao, G., McCarthy, A. M., & Chen, J. (2024). A constrained maximum likelihood approach to developing well-calibrated models for predicting binary outcomes. Lifetime Data Analysis, 30(3), 624-648.
+- > Wang, Le., Chen, J. (2026). Developing Accurate Risk Prediction Using Biased Electronic Health Record Data. Manuscript in preparation.
+
+## Key features
+
+- Simulated Scenario 1-3 workflows for reproducible method evaluation.
+- User-data workflow for prepared target, source, and reference CSV datasets.
+- Propensity-score matched and random-sampled source paths.
+- Constrained MLE solver ladder with calibration-violation diagnostics.
+- CSV-first output contract with optional parquet mirrors.
+- Public Python API and `risk-bridge` command-line interface.
+- Unit tests covering preprocessing, calibration, likelihoods, constraints, optimization, metrics, sampling, and pipeline behavior.
+
+## Installation
+
+### From the package index (standard path after publication)
+
+Once the `risk-bridge` package is published:
+
+```bash
+uv add risk-bridge
+# or: pip install risk-bridge
+```
+
+Until the first public upload completes, install from this repository checkout instead.
+
+### From a repository checkout
+
+Risk Bridge is packaged with `uv` and a checked-in lock file. To install `uv`, read [this](https://docs.astral.sh/uv/getting-started/installation/).
+
+```bash
+git clone git@github.com/SaehwanPark/risk-bridge.git
+cd risk-bridge
+uv sync --locked
+```
+
+Run the test suite:
+
+```bash
+uv run pytest
+uv run basedpyright
+```
+
+The orchestration layer uses [`comp-builders`](https://pypi.org/project/comp-builders/) for explicit `Result` composition in recoverable validation paths. `uv sync --locked` installs it from the package index as recorded in `uv.lock`.
+
+## Quick start
+
+Run a small simulated scenario:
+
+```bash
+uv run risk-bridge \
+  --mode simulated \
+  --scenario 2 \
+  --nsim 5 \
+  --n-target 5000 \
+  --n-source 2000 \
+  --n-reference 5000 \
+  --sample-size 500 \
+  --output-root data \
+  --run-label quickstart
+```
+
+Run on prepared CSV datasets:
+
+```bash
+uv run risk-bridge \
+  --mode user-data \
+  --target-csv /path/to/target.csv \
+  --source-csv /path/to/source.csv \
+  --reference-csv /path/to/reference.csv \
+  --y-col label \
+  --z-origin-col z_cont \
+  --z-cat-col z_cat \
+  --x-cols X1,X2,X3,X4 \
+  --sample-size 500 \
+  --nsim 1 \
+  --output-root data \
+  --run-label user_data
+```
+
+For a five-minute setup path, see [QUICKSTART.md](QUICKSTART.md).
+
+## Architecture
+
+```text
+Input cohorts
+  target, source, reference
+        ⬇️
+Preprocessing and schema validation
+        ⬇️
+Calibration artifacts from reference cohort
+  risk strata, external prevalence, X-support
+        ⬇️
+Sampling paths
+  propensity-score matched source + random source
+        ⬇️
+Model fitting
+  ML baseline + cMLE with calibration constraints
+        ⬇️
+Evaluation and exports
+  estimates, ROC metrics, accuracy metrics, diagnostics, metadata
+```
+
+The public CLI delegates to typed configuration objects in `risk_bridge.config`, orchestration in `risk_bridge.runs`, reusable pipeline helpers in `risk_bridge.pipeline`, and numerical components in `risk_bridge.likelihood`, `risk_bridge.constraints`, `risk_bridge.optimize`, and `risk_bridge.metrics`.
+
+## Library usage
+
+```python
+from risk_bridge import UserDataRunConfig, UserDataSchema, run_user_data
+
+run_dir = run_user_data(
+  UserDataRunConfig(
+    target_df=target_df,
+    source_df=source_df,
+    reference_df=reference_df,
+    schema=UserDataSchema(
+      x_cols=("X1", "X2", "X3", "X4"),
+      y_col="label",
+      z_origin_col="z_cont",
+    ),
+    sample_size=500,
+    output_root="data",
+    run_label="hospital_a",
+  )
+)
+print(run_dir)
+```
+
+## Outputs
+
+Each run writes a timestamped directory under `output_root` with `intermediate/` and `final/` folders. Start with these final outputs:
+
+- `final/run_metadata.csv` (includes `schema_version`, currently `1.1.0`)
+- `final/fit_diagnostics.csv`
+- `final/est_cml_psm.csv`
+- `final/calibration_metrics.csv`
+- `final/calibration_residuals.csv`
+- `final/roc_metrics.csv`
+- `final/accuracy_metrics.csv`
+
+## Reproduction
+
+End-to-end regeneration commands for Scenario 2, numerical validation, and the
+synthetic transport second example are in [REPRODUCTION.md](REPRODUCTION.md).
+Cite this software with [CITATION.cff](CITATION.cff); add an archival DOI after
+the Zenodo (or equivalent) deposit.
+
+## Repository layout
+
+```text
+src/risk_bridge/  Python package source
+tests/            Unit tests
+cases/            Privacy-safe replication harnesses
+examples/         Minimal runnable examples
+docs/             Supplementary documentation
+assets/           README visual assets
+```
+
+## Documentation
+
+- [Quickstart](QUICKSTART.md)
+- [Reproduction runbook](REPRODUCTION.md)
+- [User guide](USER_GUIDE.md)
+- [API reference](API_REFERENCE.md)
+- [Architecture overview](ARCHITECTURE.md)
+- [Pipeline architecture](docs/architecture/python_pipeline_analysis.md)
+- [Solver strategy](docs/architecture/python_solver_strategy.md)
+- [Replication cases](cases/README.md)
+- [Changelog](CHANGELOG.md)
+- [Citation](CITATION.cff)
+- [License](LICENSE)
+
+## License
+
+Risk Bridge is released under the Apache License 2.0.

risk_bridge-1.0.1/README.md

@@ -0,0 +1,191 @@
+<p align="center">
+  <img src="assets/risk-bridge-banner.png" alt="Risk Bridge banner" width="100%">
+</p>
+
+# Risk Bridge
+
+Risk Bridge is a Python package for estimating transportable binary-risk models when the available cohorts do not all contain the same information. It combines propensity-score sampling, reference-cohort calibration, maximum likelihood estimation, and constrained maximum likelihood estimation (cMLE) into reproducible simulation and user-data workflows.
+
+Package title: **Risk Bridging through Constrained MLE**.
+
+## Motivation
+
+Risk models often need to be evaluated or adapted across related populations: a target cohort, a source cohort, and a reference cohort. Standard model fitting can drift when covariate distributions, calibration strata, or observed risk markers differ across those cohorts. Risk Bridge provides a repeatable way to compare ordinary ML estimates with calibration-constrained estimates while preserving diagnostics, thresholds, and run metadata.
+
+## Foundation Papers
+
+- > Cao, Y., Ma, W., Zhao, G., McCarthy, A. M., & Chen, J. (2024). A constrained maximum likelihood approach to developing well-calibrated models for predicting binary outcomes. Lifetime Data Analysis, 30(3), 624-648.
+- > Wang, Le., Chen, J. (2026). Developing Accurate Risk Prediction Using Biased Electronic Health Record Data. Manuscript in preparation.
+
+## Key features
+
+- Simulated Scenario 1-3 workflows for reproducible method evaluation.
+- User-data workflow for prepared target, source, and reference CSV datasets.
+- Propensity-score matched and random-sampled source paths.
+- Constrained MLE solver ladder with calibration-violation diagnostics.
+- CSV-first output contract with optional parquet mirrors.
+- Public Python API and `risk-bridge` command-line interface.
+- Unit tests covering preprocessing, calibration, likelihoods, constraints, optimization, metrics, sampling, and pipeline behavior.
+
+## Installation
+
+### From the package index (standard path after publication)
+
+Once the `risk-bridge` package is published:
+
+```bash
+uv add risk-bridge
+# or: pip install risk-bridge
+```
+
+Until the first public upload completes, install from this repository checkout instead.
+
+### From a repository checkout
+
+Risk Bridge is packaged with `uv` and a checked-in lock file. To install `uv`, read [this](https://docs.astral.sh/uv/getting-started/installation/).
+
+```bash
+git clone git@github.com/SaehwanPark/risk-bridge.git
+cd risk-bridge
+uv sync --locked
+```
+
+Run the test suite:
+
+```bash
+uv run pytest
+uv run basedpyright
+```
+
+The orchestration layer uses [`comp-builders`](https://pypi.org/project/comp-builders/) for explicit `Result` composition in recoverable validation paths. `uv sync --locked` installs it from the package index as recorded in `uv.lock`.
+
+## Quick start
+
+Run a small simulated scenario:
+
+```bash
+uv run risk-bridge \
+  --mode simulated \
+  --scenario 2 \
+  --nsim 5 \
+  --n-target 5000 \
+  --n-source 2000 \
+  --n-reference 5000 \
+  --sample-size 500 \
+  --output-root data \
+  --run-label quickstart
+```
+
+Run on prepared CSV datasets:
+
+```bash
+uv run risk-bridge \
+  --mode user-data \
+  --target-csv /path/to/target.csv \
+  --source-csv /path/to/source.csv \
+  --reference-csv /path/to/reference.csv \
+  --y-col label \
+  --z-origin-col z_cont \
+  --z-cat-col z_cat \
+  --x-cols X1,X2,X3,X4 \
+  --sample-size 500 \
+  --nsim 1 \
+  --output-root data \
+  --run-label user_data
+```
+
+For a five-minute setup path, see [QUICKSTART.md](QUICKSTART.md).
+
+## Architecture
+
+```text
+Input cohorts
+  target, source, reference
+        ⬇️
+Preprocessing and schema validation
+        ⬇️
+Calibration artifacts from reference cohort
+  risk strata, external prevalence, X-support
+        ⬇️
+Sampling paths
+  propensity-score matched source + random source
+        ⬇️
+Model fitting
+  ML baseline + cMLE with calibration constraints
+        ⬇️
+Evaluation and exports
+  estimates, ROC metrics, accuracy metrics, diagnostics, metadata
+```
+
+The public CLI delegates to typed configuration objects in `risk_bridge.config`, orchestration in `risk_bridge.runs`, reusable pipeline helpers in `risk_bridge.pipeline`, and numerical components in `risk_bridge.likelihood`, `risk_bridge.constraints`, `risk_bridge.optimize`, and `risk_bridge.metrics`.
+
+## Library usage
+
+```python
+from risk_bridge import UserDataRunConfig, UserDataSchema, run_user_data
+
+run_dir = run_user_data(
+  UserDataRunConfig(
+    target_df=target_df,
+    source_df=source_df,
+    reference_df=reference_df,
+    schema=UserDataSchema(
+      x_cols=("X1", "X2", "X3", "X4"),
+      y_col="label",
+      z_origin_col="z_cont",
+    ),
+    sample_size=500,
+    output_root="data",
+    run_label="hospital_a",
+  )
+)
+print(run_dir)
+```
+
+## Outputs
+
+Each run writes a timestamped directory under `output_root` with `intermediate/` and `final/` folders. Start with these final outputs:
+
+- `final/run_metadata.csv` (includes `schema_version`, currently `1.1.0`)
+- `final/fit_diagnostics.csv`
+- `final/est_cml_psm.csv`
+- `final/calibration_metrics.csv`
+- `final/calibration_residuals.csv`
+- `final/roc_metrics.csv`
+- `final/accuracy_metrics.csv`
+
+## Reproduction
+
+End-to-end regeneration commands for Scenario 2, numerical validation, and the
+synthetic transport second example are in [REPRODUCTION.md](REPRODUCTION.md).
+Cite this software with [CITATION.cff](CITATION.cff); add an archival DOI after
+the Zenodo (or equivalent) deposit.
+
+## Repository layout
+
+```text
+src/risk_bridge/  Python package source
+tests/            Unit tests
+cases/            Privacy-safe replication harnesses
+examples/         Minimal runnable examples
+docs/             Supplementary documentation
+assets/           README visual assets
+```
+
+## Documentation
+
+- [Quickstart](QUICKSTART.md)
+- [Reproduction runbook](REPRODUCTION.md)
+- [User guide](USER_GUIDE.md)
+- [API reference](API_REFERENCE.md)
+- [Architecture overview](ARCHITECTURE.md)
+- [Pipeline architecture](docs/architecture/python_pipeline_analysis.md)
+- [Solver strategy](docs/architecture/python_solver_strategy.md)
+- [Replication cases](cases/README.md)
+- [Changelog](CHANGELOG.md)
+- [Citation](CITATION.cff)
+- [License](LICENSE)
+
+## License
+
+Risk Bridge is released under the Apache License 2.0.

risk_bridge-1.0.1/pyproject.toml

@@ -0,0 +1,69 @@
+[project]
+name = "risk-bridge"
+version = "1.0.1"
+description = "Risk Bridging through Constrained MLE"
+readme = "README.md"
+requires-python = ">=3.11"
+license = "Apache-2.0"
+authors = [
+  { name = "Risk Bridge contributors" },
+]
+keywords = ["risk-modeling", "calibration", "constrained-optimization", "maximum-likelihood", "biostatistics"]
+classifiers = [
+  "Development Status :: 5 - Production/Stable",
+  "Intended Audience :: Science/Research",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Topic :: Scientific/Engineering :: Medical Science Apps.",
+  "Topic :: Scientific/Engineering :: Mathematics",
+]
+dependencies = [
+  "comp-builders>=1.0.0",
+  "numpy>=2.4.2",
+  "pandas>=3.0.1",
+  "polars>=1.38.1",
+  "rdata>=1.0.0",
+  "scikit-learn>=1.8.0",
+  "scipy>=1.17.1",
+]
+
+[project.urls]
+Homepage = "https://github.com/SaehwanPark/risk-bridge"
+Repository = "https://github.com/SaehwanPark/risk-bridge"
+Issues = "https://github.com/SaehwanPark/risk-bridge/issues"
+
+[project.scripts]
+risk-bridge = "risk_bridge.cli:main"
+
+[build-system]
+requires = ["setuptools>=80"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[dependency-groups]
+dev = [
+  "basedpyright>=1.39.6",
+  "matplotlib>=3.11.0",
+  "pytest>=9.0.2",
+]
+
+[tool.basedpyright]
+pythonVersion = "3.11"
+typeCheckingMode = "standard"
+include = [
+  "src/risk_bridge/api.py",
+  "src/risk_bridge/config.py",
+  "src/risk_bridge/pipeline.py",
+  "src/risk_bridge/cli.py",
+  "src/risk_bridge/types.py",
+]
+reportMissingTypeStubs = false
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+
+[tool.uv]
+package = true

risk_bridge-1.0.1/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+