ssbc 0.1.0__py3-none-any.whl → 1.1.0__py3-none-any.whl

ssbc/__init__.py

@@ -1,12 +1,21 @@
 """Top-level package for SSBC (Small-Sample Beta Correction)."""
 
+from importlib.metadata import version
+
 __author__ = """Petrus H Zwart"""
 __email__ = "phzwart@lbl.gov"
-__version__ = "0.1.0"
+__version__ = version("ssbc")  # Read from package metadata (pyproject.toml)
 
 # Core SSBC algorithm
 # Conformal prediction
+# Bootstrap uncertainty analysis
+from .bootstrap import (
+    bootstrap_calibration_uncertainty,
+    plot_bootstrap_distributions,
+)
 from .conformal import (
+    alpha_scan,
+    compute_pac_operational_metrics,
     mondrian_conformal_calibrate,
     split_by_class,
 )
@@ -15,12 +24,23 @@ from .core import (
     ssbc_correct,
 )
 
+# Cross-conformal validation
+from .cross_conformal import (
+    cross_conformal_validation,
+    print_cross_conformal_results,
+)
+
 # Hyperparameter tuning
 from .hyperparameter import (
     sweep_and_plot_parallel_plotly,
     sweep_hyperparams_and_collect,
 )
 
+# Visualization and reporting
+from .rigorous_report import (
+    generate_rigorous_pac_report,
+)
+
 # Simulation (for testing and examples)
 from .simulation import (
     BinaryClassifierSimulator,
@@ -29,10 +49,21 @@ from .simulation import (
 # Statistics utilities
 from .statistics import (
     clopper_pearson_intervals,
+    clopper_pearson_lower,
+    clopper_pearson_upper,
     cp_interval,
 )
 
-# Visualization and reporting
+# Utility functions
+from .utils import (
+    compute_operational_rate,
+)
+
+# Validation utilities
+from .validation import (
+    print_validation_results,
+    validate_pac_bounds,
+)
 from .visualization import (
     plot_parallel_coordinates_plotly,
     report_prediction_stats,
@@ -43,16 +74,33 @@ __all__ = [
     "SSBCResult",
     "ssbc_correct",
     # Conformal
+    "alpha_scan",
+    "compute_pac_operational_metrics",
     "mondrian_conformal_calibrate",
     "split_by_class",
     # Statistics
     "clopper_pearson_intervals",
+    "clopper_pearson_lower",
+    "clopper_pearson_upper",
     "cp_interval",
+    # Utilities
+    "compute_operational_rate",
     # Simulation
     "BinaryClassifierSimulator",
     # Visualization
     "report_prediction_stats",
     "plot_parallel_coordinates_plotly",
+    # Bootstrap uncertainty
+    "bootstrap_calibration_uncertainty",
+    "plot_bootstrap_distributions",
+    # Cross-conformal validation
+    "cross_conformal_validation",
+    "print_cross_conformal_results",
+    # Validation utilities
+    "validate_pac_bounds",
+    "print_validation_results",
+    # Rigorous reporting
+    "generate_rigorous_pac_report",
     # Hyperparameter
     "sweep_hyperparams_and_collect",
     "sweep_and_plot_parallel_plotly",

ssbc/bootstrap.py

@@ -0,0 +1,411 @@
+"""Bootstrap analysis of calibration uncertainty for operational rates.
+
+This models: "If I recalibrate many times on similar datasets, how do rates vary?"
+Different from LOO-CV which models: "Given ONE fixed calibration, how do test sets vary?"
+"""
+
+from typing import Protocol
+
+import numpy as np
+from joblib import Parallel, delayed
+
+from ssbc.conformal import split_by_class
+from ssbc.core import ssbc_correct
+
+# Optional plotting dependencies
+try:
+    import matplotlib.pyplot as plt
+
+    HAS_MATPLOTLIB = True
+except ImportError:
+    HAS_MATPLOTLIB = False
+
+
+class DataGenerator(Protocol):
+    """Protocol for data generators (e.g., BinaryClassifierSimulator)."""
+
+    def generate(self, n_samples: int) -> tuple[np.ndarray, np.ndarray]:
+        """Generate samples.
+
+        Returns
+        -------
+        tuple
+            (labels, probabilities)
+        """
+        ...
+
+
+def _bootstrap_single_trial(
+    labels: np.ndarray,
+    probs: np.ndarray,
+    alpha_target: float,
+    delta: float,
+    test_size: int,
+    bootstrap_seed: int,
+    simulator: DataGenerator,
+) -> dict[str, float]:
+    """Single bootstrap trial: resample calibration → calibrate → evaluate on fresh test set.
+
+    Parameters
+    ----------
+    labels : np.ndarray
+        Calibration labels
+    probs : np.ndarray
+        Calibration probabilities
+    alpha_target : float
+        Target miscoverage
+    delta : float
+        PAC risk
+    test_size : int
+        Test set size
+    bootstrap_seed : int
+        Random seed for this trial
+    simulator : DataGenerator
+        Simulator to generate fresh test sets
+
+    Returns
+    -------
+    dict
+        Operational rates for this bootstrap sample
+    """
+    np.random.seed(bootstrap_seed)
+
+    n = len(labels)
+
+    # Bootstrap resample calibration data (with replacement)
+    bootstrap_idx = np.random.choice(n, size=n, replace=True)
+    labels_boot = labels[bootstrap_idx]
+    probs_boot = probs[bootstrap_idx]
+
+    # Split by class
+    class_data_boot = split_by_class(labels_boot, probs_boot)
+
+    # Calibrate on bootstrap sample
+    try:
+        ssbc_0 = ssbc_correct(alpha_target=alpha_target, n=class_data_boot[0]["n"], delta=delta)
+        ssbc_1 = ssbc_correct(alpha_target=alpha_target, n=class_data_boot[1]["n"], delta=delta)
+    except Exception:
+        # Handle edge cases (e.g., all samples from one class)
+        return {
+            "singleton": np.nan,
+            "doublet": np.nan,
+            "abstention": np.nan,
+            "singleton_error": np.nan,
+            "singleton_0": np.nan,
+            "doublet_0": np.nan,
+            "abstention_0": np.nan,
+            "singleton_error_0": np.nan,
+            "singleton_1": np.nan,
+            "doublet_1": np.nan,
+            "abstention_1": np.nan,
+            "singleton_error_1": np.nan,
+        }
+
+    # Compute thresholds
+    n_0 = class_data_boot[0]["n"]
+    n_1 = class_data_boot[1]["n"]
+
+    k_0 = int(np.ceil((n_0 + 1) * (1 - ssbc_0.alpha_corrected)))
+    k_1 = int(np.ceil((n_1 + 1) * (1 - ssbc_1.alpha_corrected)))
+
+    mask_0 = labels_boot == 0
+    mask_1 = labels_boot == 1
+
+    scores_0 = 1.0 - probs_boot[mask_0, 0]
+    scores_1 = 1.0 - probs_boot[mask_1, 1]
+
+    sorted_0 = np.sort(scores_0)
+    sorted_1 = np.sort(scores_1)
+
+    threshold_0 = sorted_0[min(k_0 - 1, len(sorted_0) - 1)]
+    threshold_1 = sorted_1[min(k_1 - 1, len(sorted_1) - 1)]
+
+    # Generate FRESH test set
+    labels_test, probs_test = simulator.generate(test_size)
+
+    # Evaluate on test set
+    n_test = len(labels_test)
+    n_singletons = 0
+    n_doublets = 0
+    n_abstentions = 0
+    n_singletons_correct = 0
+
+    # Per-class counters
+    n_singletons_0 = 0
+    n_doublets_0 = 0
+    n_abstentions_0 = 0
+    n_singletons_correct_0 = 0
+    n_class_0 = 0
+
+    n_singletons_1 = 0
+    n_doublets_1 = 0
+    n_abstentions_1 = 0
+    n_singletons_correct_1 = 0
+    n_class_1 = 0
+
+    for i in range(n_test):
+        true_label = labels_test[i]
+        score_0 = 1.0 - probs_test[i, 0]
+        score_1 = 1.0 - probs_test[i, 1]
+
+        in_0 = score_0 <= threshold_0
+        in_1 = score_1 <= threshold_1
+
+        # Marginal
+        if in_0 and in_1:
+            n_doublets += 1
+        elif in_0 or in_1:
+            n_singletons += 1
+            if (in_0 and true_label == 0) or (in_1 and true_label == 1):
+                n_singletons_correct += 1
+        else:
+            n_abstentions += 1
+
+        # Per-class
+        if true_label == 0:
+            n_class_0 += 1
+            if in_0 and in_1:
+                n_doublets_0 += 1
+            elif in_0 or in_1:
+                n_singletons_0 += 1
+                if in_0:
+                    n_singletons_correct_0 += 1
+            else:
+                n_abstentions_0 += 1
+        else:
+            n_class_1 += 1
+            if in_0 and in_1:
+                n_doublets_1 += 1
+            elif in_0 or in_1:
+                n_singletons_1 += 1
+                if in_1:
+                    n_singletons_correct_1 += 1
+            else:
+                n_abstentions_1 += 1
+
+    # Compute rates
+    singleton_rate = n_singletons / n_test
+    doublet_rate = n_doublets / n_test
+    abstention_rate = n_abstentions / n_test
+    singleton_error_rate = (n_singletons - n_singletons_correct) / n_singletons if n_singletons > 0 else np.nan
+
+    # Per-class rates
+    singleton_0 = n_singletons_0 / n_class_0 if n_class_0 > 0 else np.nan
+    doublet_0 = n_doublets_0 / n_class_0 if n_class_0 > 0 else np.nan
+    abstention_0 = n_abstentions_0 / n_class_0 if n_class_0 > 0 else np.nan
+    singleton_error_0 = (n_singletons_0 - n_singletons_correct_0) / n_singletons_0 if n_singletons_0 > 0 else np.nan
+
+    singleton_1 = n_singletons_1 / n_class_1 if n_class_1 > 0 else np.nan
+    doublet_1 = n_doublets_1 / n_class_1 if n_class_1 > 0 else np.nan
+    abstention_1 = n_abstentions_1 / n_class_1 if n_class_1 > 0 else np.nan
+    singleton_error_1 = (n_singletons_1 - n_singletons_correct_1) / n_singletons_1 if n_singletons_1 > 0 else np.nan
+
+    return {
+        "singleton": singleton_rate,
+        "doublet": doublet_rate,
+        "abstention": abstention_rate,
+        "singleton_error": singleton_error_rate,
+        "singleton_0": singleton_0,
+        "doublet_0": doublet_0,
+        "abstention_0": abstention_0,
+        "singleton_error_0": singleton_error_0,
+        "singleton_1": singleton_1,
+        "doublet_1": doublet_1,
+        "abstention_1": abstention_1,
+        "singleton_error_1": singleton_error_1,
+    }
+
+
+def bootstrap_calibration_uncertainty(
+    labels: np.ndarray,
+    probs: np.ndarray,
+    simulator: DataGenerator,
+    alpha_target: float = 0.10,
+    delta: float = 0.10,
+    test_size: int = 1000,
+    n_bootstrap: int = 1000,
+    n_jobs: int = -1,
+    seed: int | None = None,
+) -> dict:
+    """Bootstrap analysis of calibration uncertainty.
+
+    For each bootstrap iteration:
+    1. Resample calibration data with replacement
+    2. Calibrate (compute SSBC thresholds)
+    3. Evaluate on fresh independent test set
+    4. Record operational rates
+
+    This models: "If I recalibrate on similar datasets, how do rates vary?"
+
+    Parameters
+    ----------
+    labels : np.ndarray
+        Calibration labels
+    probs : np.ndarray
+        Calibration probabilities
+    simulator : DataGenerator
+        Simulator to generate independent test sets
+    alpha_target : float, default=0.10
+        Target miscoverage
+    delta : float, default=0.10
+        PAC risk
+    test_size : int, default=1000
+        Size of test sets for evaluation
+    n_bootstrap : int, default=1000
+        Number of bootstrap iterations
+    n_jobs : int, default=-1
+        Parallel jobs (-1 for all cores)
+    seed : int, optional
+        Random seed
+
+    Returns
+    -------
+    dict
+        Bootstrap distributions with keys:
+        - 'marginal': dict with 'singleton', 'doublet', 'abstention', 'singleton_error'
+        - 'class_0': dict with same metrics
+        - 'class_1': dict with same metrics
+        Each metric contains:
+        - 'samples': array of rates across bootstrap trials
+        - 'mean': mean rate
+        - 'std': standard deviation
+        - 'quantiles': dict with q05, q25, q50, q75, q95
+
+    Examples
+    --------
+    >>> from ssbc import BinaryClassifierSimulator, bootstrap_calibration_uncertainty
+    >>> sim = BinaryClassifierSimulator(p_class1=0.2, beta_params_class0=(1,7), beta_params_class1=(5,2))
+    >>> labels, probs = sim.generate(100)
+    >>> results = bootstrap_calibration_uncertainty(labels, probs, sim, n_bootstrap=100)
+    >>> print(results['marginal']['singleton']['mean'])
+    """
+    if seed is not None:
+        np.random.seed(seed)
+
+    # Generate bootstrap seeds
+    bootstrap_seeds = np.random.randint(0, 2**31, size=n_bootstrap)
+
+    # Parallel bootstrap
+    results = Parallel(n_jobs=n_jobs)(
+        delayed(_bootstrap_single_trial)(labels, probs, alpha_target, delta, test_size, bs_seed, simulator)
+        for bs_seed in bootstrap_seeds
+    )
+
+    # Extract metrics
+    metrics = ["singleton", "doublet", "abstention", "singleton_error"]
+
+    def compute_stats(values):
+        """Compute statistics for a metric."""
+        arr = np.array(values)
+        valid = arr[~np.isnan(arr)]
+        if len(valid) == 0:
+            return {
+                "samples": arr,
+                "mean": np.nan,
+                "std": np.nan,
+                "quantiles": {"q05": np.nan, "q25": np.nan, "q50": np.nan, "q75": np.nan, "q95": np.nan},
+            }
+        return {
+            "samples": arr,
+            "mean": np.mean(valid),
+            "std": np.std(valid),
+            "quantiles": {
+                "q05": np.percentile(valid, 5),
+                "q25": np.percentile(valid, 25),
+                "q50": np.percentile(valid, 50),
+                "q75": np.percentile(valid, 75),
+                "q95": np.percentile(valid, 95),
+            },
+        }
+
+    # Organize results
+    return {
+        "n_bootstrap": n_bootstrap,
+        "n_calibration": len(labels),
+        "test_size": test_size,
+        "marginal": {metric: compute_stats([r[metric] for r in results]) for metric in metrics},
+        "class_0": {metric: compute_stats([r[f"{metric}_0"] for r in results]) for metric in metrics},
+        "class_1": {metric: compute_stats([r[f"{metric}_1"] for r in results]) for metric in metrics},
+    }
+
+
+def plot_bootstrap_distributions(
+    bootstrap_results: dict,
+    figsize: tuple[int, int] = (16, 12),
+    save_path: str | None = None,
+) -> None:
+    """Plot bootstrap distributions.
+
+    Parameters
+    ----------
+    bootstrap_results : dict
+        Results from bootstrap_calibration_uncertainty()
+    figsize : tuple, default=(16, 12)
+        Figure size
+    save_path : str, optional
+        Path to save figure. If None, displays interactively.
+
+    Raises
+    ------
+    ImportError
+        If matplotlib is not installed
+
+    Examples
+    --------
+    >>> from ssbc import bootstrap_calibration_uncertainty, plot_bootstrap_distributions
+    >>> results = bootstrap_calibration_uncertainty(...)
+    >>> plot_bootstrap_distributions(results, save_path='bootstrap_results.png')
+    """
+    if not HAS_MATPLOTLIB:
+        raise ImportError("matplotlib is required for plotting. Install with: pip install matplotlib")
+
+    fig, axes = plt.subplots(3, 4, figsize=figsize)
+    fig.suptitle(
+        f"Bootstrap Calibration Uncertainty ({bootstrap_results['n_bootstrap']} trials)\n"
+        f"Calibration n={bootstrap_results['n_calibration']}, Test size={bootstrap_results['test_size']}",
+        fontsize=14,
+        fontweight="bold",
+    )
+
+    metrics = ["singleton", "doublet", "abstention", "singleton_error"]
+    metric_names = ["Singleton Rate", "Doublet Rate", "Abstention Rate", "Singleton Error Rate"]
+    colors = ["steelblue", "coral", "mediumpurple"]
+    row_names = ["MARGINAL", "CLASS 0", "CLASS 1"]
+    data_keys = ["marginal", "class_0", "class_1"]
+
+    for row, (row_name, data_key, color) in enumerate(zip(row_names, data_keys, colors, strict=False)):
+        for col, (metric, name) in enumerate(zip(metrics, metric_names, strict=False)):
+            ax = axes[row, col]
+            m = bootstrap_results[data_key][metric]
+
+            # Filter NaNs
+            samples = m["samples"]
+            samples = samples[~np.isnan(samples)]
+
+            if len(samples) == 0:
+                ax.text(0.5, 0.5, "No data", ha="center", va="center")
+                continue
+
+            # Histogram
+            ax.hist(samples, bins=50, alpha=0.7, color=color, edgecolor="black")
+
+            # Quantiles
+            q = m["quantiles"]
+            ax.axvline(q["q50"], color="green", linestyle="-", linewidth=2, label=f"Median: {q['q50']:.3f}")
+            ax.axvline(q["q05"], color="red", linestyle="--", linewidth=2, label=f"5%: {q['q05']:.3f}")
+            ax.axvline(q["q95"], color="red", linestyle="--", linewidth=2, label=f"95%: {q['q95']:.3f}")
+            ax.axvline(m["mean"], color="orange", linestyle=":", linewidth=2, label=f"Mean: {m['mean']:.3f}")
+
+            ax.set_title(f"{row_name}: {name}", fontweight="bold")
+            ax.set_xlabel("Rate")
+            ax.set_ylabel("Count")
+            ax.legend(loc="best", fontsize=8)
+            ax.grid(True, alpha=0.3)
+
+    plt.tight_layout()
+
+    if save_path:
+        plt.savefig(save_path, dpi=300, bbox_inches="tight")
+        print(f"✅ Saved bootstrap visualization to: {save_path}")
+    else:
+        plt.show()

ssbc/cli.py

@@ -3,8 +3,6 @@
 import typer
 from rich.console import Console
 
-from ssbc import utils
-
 app = typer.Typer()
 console = Console()
 
@@ -14,7 +12,6 @@ def main():
     """Console script for ssbc."""
     console.print("Replace this message by putting your code into ssbc.cli.main")
     console.print("See Typer documentation at https://typer.tiangolo.com/")
-    utils.do_something_useful()
 
 
 if __name__ == "__main__":