mosaic-harmonize 0.1.0__tar.gz

mosaic_harmonize-0.1.0/LICENSE

@@ -0,0 +1,190 @@
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mosaic_harmonize-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: mosaic-harmonize
+Version: 0.1.0
+Summary: Multi-site Optimal-transport Shift Alignment with Interval Calibration for clinical data harmonization
+Author-email: Peigen Chen <chenpg5@mail.sysu.edu.cn>
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/chenpg2/mosaic-harmonize
+Project-URL: Repository, https://github.com/chenpg2/mosaic-harmonize
+Project-URL: Documentation, https://github.com/chenpg2/mosaic-harmonize#readme
+Project-URL: Bug Tracker, https://github.com/chenpg2/mosaic-harmonize/issues
+Keywords: harmonization,optimal-transport,conformal-prediction,multi-center,clinical-data,batch-effect,domain-adaptation
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.24
+Requires-Dist: pandas>=2.0
+Requires-Dist: scipy>=1.10
+Requires-Dist: scikit-learn>=1.3
+Provides-Extra: boosting
+Requires-Dist: lightgbm>=4.0; extra == "boosting"
+Requires-Dist: anchorboosting>=0.3; extra == "boosting"
+Provides-Extra: conformal
+Requires-Dist: mapie>=1.0; extra == "conformal"
+Provides-Extra: viz
+Requires-Dist: matplotlib>=3.7; extra == "viz"
+Requires-Dist: seaborn>=0.12; extra == "viz"
+Provides-Extra: full
+Requires-Dist: mosaic-harmonize[boosting,conformal,viz]; extra == "full"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: mosaic-harmonize[full]; extra == "dev"
+Dynamic: license-file
+
+# MOSAIC
+
+**Multi-site Optimal-transport Shift Alignment with Interval Calibration**
+
+[![PyPI](https://img.shields.io/pypi/v/mosaic-harmonize)](https://pypi.org/project/mosaic-harmonize/)
+[![Python](https://img.shields.io/pypi/pyversions/mosaic-harmonize)](https://pypi.org/project/mosaic-harmonize/)
+[![License](https://img.shields.io/badge/license-Apache%202.0-blue)](LICENSE)
+<!-- [![DOI](https://img.shields.io/badge/DOI-10.1038%2Fs41746--XXX-blue)](https://doi.org/10.1038/s41746-XXX) -->
+
+MOSAIC is a Python package for harmonizing clinical tabular data collected across multiple sites. It combines 1-D optimal transport for distribution alignment, anchor regression for domain-robust prediction, and weighted conformal inference for uncertainty quantification. The three components can be used independently or chained through a single pipeline.
+
+The package was developed for multi-center IVF (in vitro fertilization) outcome prediction, but the methods are general and apply to any multi-site clinical or biomedical dataset with batch effects.
+
+## Overview
+
+MOSAIC has three tiers, each usable on its own:
+
+| Tier | Class | What it does |
+|------|-------|-------------|
+| 1. Harmonization | `OTHarmonizer` | Per-feature quantile-based optimal transport mapping to a reference distribution. Reduces cross-center distribution shift while preserving within-center rank order. |
+| 2. Robust learning | `AnchorEstimator` | Wraps any sklearn estimator with anchor regression (via [anchorboosting](https://github.com/mlondschien/anchorboosting)) or V-REx reweighting. Penalizes predictions that rely on center-specific patterns. |
+| 3. Uncertainty | `ConformalCalibrator` | Split conformal prediction with optional covariate-shift correction (Tibshirani et al., NeurIPS 2019). Produces prediction intervals (regression) or prediction sets (classification) with finite-sample coverage guarantees. |
+
+`MOSAICPipeline` chains all three into a single `fit` / `predict` interface.
+
+## Installation
+
+Core (OT harmonization + anchor regression + conformal):
+
+```bash
+pip install mosaic-harmonize
+```
+
+With all optional dependencies (LightGBM, anchorboosting, MAPIE, matplotlib):
+
+```bash
+pip install mosaic-harmonize[full]
+```
+
+Individual extras: `boosting`, `conformal`, `viz`. For development: `dev`.
+
+Requires Python 3.9+.
+
+## Quick start
+
+### Full pipeline
+
+```python
+from mosaic import MOSAICPipeline
+from lightgbm import LGBMRegressor
+
+pipe = MOSAICPipeline(
+    harmonizer="ot",
+    robust_learner="anchor",
+    uncertainty="weighted_conformal",
+    base_estimator=LGBMRegressor(),
+)
+
+# center_ids: array of site labels, one per row
+pipe.fit(X_train, y_train, center_ids=train_centers)
+
+result = pipe.predict(X_test, center_id="new_hospital")
+print(result.prediction)       # point predictions
+print(result.lower, result.upper)  # 90% prediction intervals
+```
+
+### Individual components
+
+```python
+from mosaic import OTHarmonizer, AnchorEstimator, ConformalCalibrator
+
+# Tier 1: align distributions
+ot = OTHarmonizer(n_quantiles=1000, reference="global")
+X_harmonized = ot.fit_transform(X_train, center_ids=train_centers)
+
+# Inspect shift reduction
+print(ot.wasserstein_distances())
+print(ot.feature_shift_report())
+
+# Tier 2: train a domain-robust model
+anchor = AnchorEstimator(base_estimator=LGBMRegressor(), task_type="regression")
+anchor.fit(X_harmonized, y_train, anchors=train_centers)
+print(f"Best gamma: {anchor.best_gamma_}")
+print(f"Cross-center stability: {anchor.stability_score_:.3f}")
+
+# Tier 3: calibrate with conformal prediction
+cal = ConformalCalibrator(method="weighted", alpha=0.10)
+cal.calibrate(anchor, X_cal, y_cal, X_test=X_test)
+result = cal.predict(X_test)
+print(f"Interval widths: {(result.upper - result.lower).mean():.2f}")
+```
+
+### Save and load
+
+```python
+pipe.save("model.mosaic")
+pipe = MOSAICPipeline.load("model.mosaic")
+```
+
+### Register a new center at inference time
+
+```python
+pipe.register_center("hospital_B", X_new_center)
+result = pipe.predict(X_query, center_id="hospital_B")
+```
+
+## API reference
+
+### OTHarmonizer
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `n_quantiles` | int | 1000 | Number of quantile points for the OT map |
+| `features` | list[str] or None | None | Columns to harmonize (None = all numeric) |
+| `reference` | str | "global" | Reference distribution: "global" or a center name |
+| `min_samples` | int | 50 | Minimum non-null samples to build a map |
+
+Methods: `fit(X, center_ids)`, `transform(X, center_id=..., center_ids=...)`, `fit_transform(X, center_ids)`, `wasserstein_distances()`, `feature_shift_report()`.
+
+### AnchorEstimator
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `base_estimator` | sklearn estimator or None | None | Base learner (None = Ridge/LogisticRegression) |
+| `gammas` | list[float] or None | [1.5, 3.0, 7.0] | Anchor penalty strengths to search |
+| `task_type` | str | "auto" | "auto", "regression", "binary", or "multiclass" |
+| `n_vrex_rounds` | int | 5 | V-REx reweighting iterations (fallback mode) |
+
+Methods: `fit(X, y, anchors, X_val=None, y_val=None)`, `predict(X)`, `predict_proba(X)`. Properties: `best_gamma_`, `stability_score_`.
+
+### ConformalCalibrator
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `method` | str | "weighted" | "weighted", "standard", or "lac" |
+| `alpha` | float | 0.10 | Miscoverage level (0.10 = 90% target coverage) |
+
+Methods: `calibrate(model, X_cal, y_cal, X_test=None)`, `predict(X_test)` returning `ConformalResult`.
+
+### MOSAICPipeline
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `harmonizer` | str or None | "ot" | "ot" or None |
+| `robust_learner` | str or None | "anchor" | "anchor" or None |
+| `uncertainty` | str or None | "weighted_conformal" | "weighted_conformal", "standard", "lac", or None |
+| `base_estimator` | sklearn estimator | None | Base learner passed to AnchorEstimator |
+
+Methods: `fit(X_train, y_train, center_ids, X_cal=None, y_cal=None)`, `predict(X, center_id=..., center_ids=...)`, `register_center(name, X_new)`, `diagnose(X, center_id)`, `save(path)`, `load(path)`.
+
+## Benchmarks
+
+Evaluated on a multi-center IVF dataset (334K rows, 5 centers, 15 prediction targets). Full results in `benchmarks/results/`.
+
+### Ablation (Exp 1): each tier adds value
+
+| Target | Baseline R² | +OT | +OT+Anchor | Full MOSAIC |
+|--------|------------|-----|------------|-------------|
+| HCG_Day_E2 | -0.665 | 0.127 | 0.229 | 0.229 |
+| egg_num | 0.210 | 0.205 | 0.352 | 0.352 |
+| HCG_Day_Endo | -0.775 | -0.177 | 0.120 | 0.120 |
+
+OT corrects distribution shift (E2: R² from -0.67 to 0.13). Anchor regression adds further gains for regression targets (egg_num: 0.21 to 0.35).
+
+### Cross-center generalization gap (Exp 2)
+
+On an external test center unseen during training, MOSAIC reduces the validation-to-test performance gap by 42-76% for high-shift features (HCG_Day_E2: 75%, HCG_Day_P: 52%, HCG_Day_Endo: 72%).
+
+### Conformal coverage (Exp 3)
+
+All 11 regression targets achieve 81-93% empirical coverage at the 90% nominal level. Weighted conformal consistently produces narrower intervals than standard split conformal at comparable coverage.
+
+### Comparison with existing methods (Exp 5)
+
+| Feature | No harmonization | Z-score | ComBat | MOSAIC (OT) |
+|---------|-----------------|---------|--------|-------------|
+| HCG_Day_E2 (R²) | -0.665 | 0.069 | -0.383 | 0.127 |
+| Clinical_pregnancy (AUC) | 0.838 | 0.837 | 0.837 | 0.839 |
+| total_Gn (R²) | -0.121 | -0.327 | -0.034 | -0.022 |
+
+MOSAIC outperforms Z-score and ComBat on high-shift features while maintaining comparable performance on low-shift targets.
+
+## Citation
+
+If you use MOSAIC in your research, please cite:
+
+```
+@article{chen2026mosaic,
+  title={MOSAIC: Multi-site Optimal-transport Shift Alignment with Interval
+         Calibration for Clinical Data Harmonization},
+  author={Chen, Peigen},
+  journal={npj Digital Medicine},
+  year={2026},
+  note={Manuscript in preparation}
+}
+```
+
+## License
+
+Apache-2.0. See [LICENSE](LICENSE) for details.

mosaic_harmonize-0.1.0/README.md

@@ -0,0 +1,200 @@
+# MOSAIC
+
+**Multi-site Optimal-transport Shift Alignment with Interval Calibration**
+
+[![PyPI](https://img.shields.io/pypi/v/mosaic-harmonize)](https://pypi.org/project/mosaic-harmonize/)
+[![Python](https://img.shields.io/pypi/pyversions/mosaic-harmonize)](https://pypi.org/project/mosaic-harmonize/)
+[![License](https://img.shields.io/badge/license-Apache%202.0-blue)](LICENSE)
+<!-- [![DOI](https://img.shields.io/badge/DOI-10.1038%2Fs41746--XXX-blue)](https://doi.org/10.1038/s41746-XXX) -->
+
+MOSAIC is a Python package for harmonizing clinical tabular data collected across multiple sites. It combines 1-D optimal transport for distribution alignment, anchor regression for domain-robust prediction, and weighted conformal inference for uncertainty quantification. The three components can be used independently or chained through a single pipeline.
+
+The package was developed for multi-center IVF (in vitro fertilization) outcome prediction, but the methods are general and apply to any multi-site clinical or biomedical dataset with batch effects.
+
+## Overview
+
+MOSAIC has three tiers, each usable on its own:
+
+| Tier | Class | What it does |
+|------|-------|-------------|
+| 1. Harmonization | `OTHarmonizer` | Per-feature quantile-based optimal transport mapping to a reference distribution. Reduces cross-center distribution shift while preserving within-center rank order. |
+| 2. Robust learning | `AnchorEstimator` | Wraps any sklearn estimator with anchor regression (via [anchorboosting](https://github.com/mlondschien/anchorboosting)) or V-REx reweighting. Penalizes predictions that rely on center-specific patterns. |
+| 3. Uncertainty | `ConformalCalibrator` | Split conformal prediction with optional covariate-shift correction (Tibshirani et al., NeurIPS 2019). Produces prediction intervals (regression) or prediction sets (classification) with finite-sample coverage guarantees. |
+
+`MOSAICPipeline` chains all three into a single `fit` / `predict` interface.
+
+## Installation
+
+Core (OT harmonization + anchor regression + conformal):
+
+```bash
+pip install mosaic-harmonize
+```
+
+With all optional dependencies (LightGBM, anchorboosting, MAPIE, matplotlib):
+
+```bash
+pip install mosaic-harmonize[full]
+```
+
+Individual extras: `boosting`, `conformal`, `viz`. For development: `dev`.
+
+Requires Python 3.9+.
+
+## Quick start
+
+### Full pipeline
+
+```python
+from mosaic import MOSAICPipeline
+from lightgbm import LGBMRegressor
+
+pipe = MOSAICPipeline(
+    harmonizer="ot",
+    robust_learner="anchor",
+    uncertainty="weighted_conformal",
+    base_estimator=LGBMRegressor(),
+)
+
+# center_ids: array of site labels, one per row
+pipe.fit(X_train, y_train, center_ids=train_centers)
+
+result = pipe.predict(X_test, center_id="new_hospital")
+print(result.prediction)       # point predictions
+print(result.lower, result.upper)  # 90% prediction intervals
+```
+
+### Individual components
+
+```python
+from mosaic import OTHarmonizer, AnchorEstimator, ConformalCalibrator
+
+# Tier 1: align distributions
+ot = OTHarmonizer(n_quantiles=1000, reference="global")
+X_harmonized = ot.fit_transform(X_train, center_ids=train_centers)
+
+# Inspect shift reduction
+print(ot.wasserstein_distances())
+print(ot.feature_shift_report())
+
+# Tier 2: train a domain-robust model
+anchor = AnchorEstimator(base_estimator=LGBMRegressor(), task_type="regression")
+anchor.fit(X_harmonized, y_train, anchors=train_centers)
+print(f"Best gamma: {anchor.best_gamma_}")
+print(f"Cross-center stability: {anchor.stability_score_:.3f}")
+
+# Tier 3: calibrate with conformal prediction
+cal = ConformalCalibrator(method="weighted", alpha=0.10)
+cal.calibrate(anchor, X_cal, y_cal, X_test=X_test)
+result = cal.predict(X_test)
+print(f"Interval widths: {(result.upper - result.lower).mean():.2f}")
+```
+
+### Save and load
+
+```python
+pipe.save("model.mosaic")
+pipe = MOSAICPipeline.load("model.mosaic")
+```
+
+### Register a new center at inference time
+
+```python
+pipe.register_center("hospital_B", X_new_center)
+result = pipe.predict(X_query, center_id="hospital_B")
+```
+
+## API reference
+
+### OTHarmonizer
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `n_quantiles` | int | 1000 | Number of quantile points for the OT map |
+| `features` | list[str] or None | None | Columns to harmonize (None = all numeric) |
+| `reference` | str | "global" | Reference distribution: "global" or a center name |
+| `min_samples` | int | 50 | Minimum non-null samples to build a map |
+
+Methods: `fit(X, center_ids)`, `transform(X, center_id=..., center_ids=...)`, `fit_transform(X, center_ids)`, `wasserstein_distances()`, `feature_shift_report()`.
+
+### AnchorEstimator
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `base_estimator` | sklearn estimator or None | None | Base learner (None = Ridge/LogisticRegression) |
+| `gammas` | list[float] or None | [1.5, 3.0, 7.0] | Anchor penalty strengths to search |
+| `task_type` | str | "auto" | "auto", "regression", "binary", or "multiclass" |
+| `n_vrex_rounds` | int | 5 | V-REx reweighting iterations (fallback mode) |
+
+Methods: `fit(X, y, anchors, X_val=None, y_val=None)`, `predict(X)`, `predict_proba(X)`. Properties: `best_gamma_`, `stability_score_`.
+
+### ConformalCalibrator
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `method` | str | "weighted" | "weighted", "standard", or "lac" |
+| `alpha` | float | 0.10 | Miscoverage level (0.10 = 90% target coverage) |
+
+Methods: `calibrate(model, X_cal, y_cal, X_test=None)`, `predict(X_test)` returning `ConformalResult`.
+
+### MOSAICPipeline
+
+| Parameter | Type | Default | Description |
+|-----------|------|---------|-------------|
+| `harmonizer` | str or None | "ot" | "ot" or None |
+| `robust_learner` | str or None | "anchor" | "anchor" or None |
+| `uncertainty` | str or None | "weighted_conformal" | "weighted_conformal", "standard", "lac", or None |
+| `base_estimator` | sklearn estimator | None | Base learner passed to AnchorEstimator |
+
+Methods: `fit(X_train, y_train, center_ids, X_cal=None, y_cal=None)`, `predict(X, center_id=..., center_ids=...)`, `register_center(name, X_new)`, `diagnose(X, center_id)`, `save(path)`, `load(path)`.
+
+## Benchmarks
+
+Evaluated on a multi-center IVF dataset (334K rows, 5 centers, 15 prediction targets). Full results in `benchmarks/results/`.
+
+### Ablation (Exp 1): each tier adds value
+
+| Target | Baseline R² | +OT | +OT+Anchor | Full MOSAIC |
+|--------|------------|-----|------------|-------------|
+| HCG_Day_E2 | -0.665 | 0.127 | 0.229 | 0.229 |
+| egg_num | 0.210 | 0.205 | 0.352 | 0.352 |
+| HCG_Day_Endo | -0.775 | -0.177 | 0.120 | 0.120 |
+
+OT corrects distribution shift (E2: R² from -0.67 to 0.13). Anchor regression adds further gains for regression targets (egg_num: 0.21 to 0.35).
+
+### Cross-center generalization gap (Exp 2)
+
+On an external test center unseen during training, MOSAIC reduces the validation-to-test performance gap by 42-76% for high-shift features (HCG_Day_E2: 75%, HCG_Day_P: 52%, HCG_Day_Endo: 72%).
+
+### Conformal coverage (Exp 3)
+
+All 11 regression targets achieve 81-93% empirical coverage at the 90% nominal level. Weighted conformal consistently produces narrower intervals than standard split conformal at comparable coverage.
+
+### Comparison with existing methods (Exp 5)
+
+| Feature | No harmonization | Z-score | ComBat | MOSAIC (OT) |
+|---------|-----------------|---------|--------|-------------|
+| HCG_Day_E2 (R²) | -0.665 | 0.069 | -0.383 | 0.127 |
+| Clinical_pregnancy (AUC) | 0.838 | 0.837 | 0.837 | 0.839 |
+| total_Gn (R²) | -0.121 | -0.327 | -0.034 | -0.022 |
+
+MOSAIC outperforms Z-score and ComBat on high-shift features while maintaining comparable performance on low-shift targets.
+
+## Citation
+
+If you use MOSAIC in your research, please cite:
+
+```
+@article{chen2026mosaic,
+  title={MOSAIC: Multi-site Optimal-transport Shift Alignment with Interval
+         Calibration for Clinical Data Harmonization},
+  author={Chen, Peigen},
+  journal={npj Digital Medicine},
+  year={2026},
+  note={Manuscript in preparation}
+}
+```
+
+## License
+
+Apache-2.0. See [LICENSE](LICENSE) for details.