workbench 0.8.205__py3-none-any.whl → 0.8.213__py3-none-any.whl

workbench/algorithms/models/noise_model.py

@@ -0,0 +1,388 @@
+import pandas as pd
+import numpy as np
+from xgboost import XGBRegressor
+from typing import List
+import logging
+
+from workbench.algorithms.dataframe.proximity import Proximity
+
+# Set up logging
+log = logging.getLogger("workbench")
+
+
+class NoiseModel:
+    """Composite noise detection for regression data using multiple complementary signals.
+
+    The NoiseModel identifies potentially noisy or problematic samples in regression datasets
+    by combining three independent signals:
+
+    1. **Underfit Model Residuals**: A deliberately simple XGBoost model (low depth, few trees)
+       that captures only the main trends. High residuals indicate samples in complex regions
+       or unusual areas of the feature space.
+
+    2. **Overfit Model Residuals**: A deliberately complex XGBoost model (deep trees, many
+       iterations, no regularization) that attempts to memorize the training data. High residuals
+       here indicate samples the model *cannot* fit even when trying to memorize - a strong
+       signal of label noise. This is the "training error" approach validated in:
+       "Denoising Drug Discovery Data for Improved ADMET Property Prediction" (Merck, JCIM 2024)
+
+    3. **High Target Gradient (HTG)**: Using the Proximity class, measures disagreement between
+       a sample's target value and its neighbors in feature space. High gradients indicate
+       activity cliffs or potential measurement errors where similar compounds have very
+       different target values.
+
+    The combined noise score weights the overfit residual signal more heavily (2x) based on
+    the paper's finding that training error is the most reliable noise detector for regression.
+
+    Example:
+        ```python
+        from workbench.algorithms.models.noise_model import NoiseModel
+
+        # Create noise model
+        noise_model = NoiseModel(df, id_column="id", features=feature_list, target="target")
+
+        # Get noise scores for all samples
+        scores_df = noise_model.get_scores()
+
+        # Get sample weights for training (lower weight for noisy samples)
+        weights = noise_model.get_sample_weights(strategy="inverse")
+
+        # Get clean subset (bottom 90% by noise score)
+        clean_df = noise_model.get_clean_subset(percentile=90)
+
+        # Find samples with same features but different targets (definite noise)
+        conflicts = noise_model.coincident_conflicts()
+        ```
+
+    References:
+        Adrian, M., Chung, Y., & Cheng, A. C. (2024). Denoising Drug Discovery Data for
+        Improved ADMET Property Prediction. J. Chem. Inf. Model., 64(16), 6324-6337.
+    """
+
+    def __init__(
+        self,
+        df: pd.DataFrame,
+        id_column: str,
+        features: List[str],
+        target: str,
+    ):
+        """
+        Initialize the NoiseModel class.
+
+        Args:
+            df: DataFrame containing data for noise detection.
+            id_column: Name of the column used as the identifier.
+            features: List of feature column names.
+            target: Name of the target column.
+        """
+        self.id_column = id_column
+        self.target = target
+
+        # Filter out non-numeric features
+        self.features = self._validate_features(df, features)
+
+        # Drop NaN rows in features and target
+        self.df = df.dropna(subset=self.features + [self.target]).copy()
+
+        # Compute target stats for normalization
+        self.target_std = self.df[self.target].std()
+        self.target_range = self.df[self.target].max() - self.df[self.target].min()
+
+        # Build all component models
+        self._build_models()
+
+        # Precompute all noise signals
+        self._precompute_signals()
+
+    def get_scores(self) -> pd.DataFrame:
+        """
+        Get noise scores for all samples.
+
+        Returns:
+            DataFrame with id, individual signal columns, and combined noise_score
+        """
+        result = self.df[[self.id_column, self.target]].copy()
+        result["underfit_residual"] = self.df["underfit_residual"]
+        result["overfit_residual"] = self.df["overfit_residual"]
+        result["htg_score"] = self.df["htg_score"]
+        result["noise_score"] = self.df["noise_score"]
+        return result.sort_values("noise_score", ascending=False).reset_index(drop=True)
+
+    def get_sample_weights(self, strategy: str = "inverse") -> pd.Series:
+        """
+        Get sample weights for training, indexed by id_column.
+
+        Args:
+            strategy: Weighting strategy
+                - "inverse": 1 / (1 + noise_score)
+                - "soft": 1 - noise_score (clipped to [0.1, 1.0])
+                - "threshold": 1.0 if noise_score < median, else 0.5
+
+        Returns:
+            Series of weights indexed by id_column
+        """
+        scores = self.df.set_index(self.id_column)["noise_score"]
+
+        if strategy == "inverse":
+            weights = 1.0 / (1.0 + scores)
+        elif strategy == "soft":
+            weights = (1.0 - scores).clip(lower=0.1, upper=1.0)
+        elif strategy == "threshold":
+            median_score = scores.median()
+            weights = (scores < median_score).apply(lambda x: 1.0 if x else 0.5)
+        else:
+            raise ValueError(f"Unknown strategy: {strategy}")
+
+        return weights
+
+    def get_clean_subset(self, percentile: float = 90.0) -> pd.DataFrame:
+        """
+        Get a subset of data with lowest noise scores.
+
+        Args:
+            percentile: Keep samples below this percentile of noise score (default: 90 = bottom 90%)
+
+        Returns:
+            DataFrame of "clean" samples
+        """
+        threshold = np.percentile(self.df["noise_score"], percentile)
+        return self.df[self.df["noise_score"] <= threshold].copy()
+
+    def get_noisy_samples(self, top_percent: float = 10.0) -> pd.DataFrame:
+        """
+        Get samples with highest noise scores.
+
+        Args:
+            top_percent: Percentage of noisiest samples to return (default: 10%)
+
+        Returns:
+            DataFrame of noisy samples, sorted by noise_score descending
+        """
+        percentile = 100 - top_percent
+        threshold = np.percentile(self.df["noise_score"], percentile)
+        noisy = self.df[self.df["noise_score"] >= threshold].copy()
+        return noisy.sort_values("noise_score", ascending=False).reset_index(drop=True)
+
+    def coincident_conflicts(self, distance_threshold: float = 1e-5) -> pd.DataFrame:
+        """
+        Find samples that map to the same point in feature space but have different targets.
+
+        These are definitive noise - same features, different target values.
+
+        Args:
+            distance_threshold: Maximum distance to consider "coincident" (default: 1e-5)
+
+        Returns:
+            DataFrame of coincident conflicts with their target differences
+        """
+        # Use proximity to find coincident points
+        coincident = self.df[self.df["nn_distance"] < distance_threshold].copy()
+
+        if len(coincident) == 0:
+            return pd.DataFrame(columns=[self.id_column, self.target, "nn_id", "nn_target", "nn_target_diff"])
+
+        return (
+            coincident[[self.id_column, self.target, "nn_id", "nn_target", "nn_target_diff", "noise_score"]]
+            .sort_values("nn_target_diff", ascending=False)
+            .reset_index(drop=True)
+        )
+
+    def _validate_features(self, df: pd.DataFrame, features: List[str]) -> List[str]:
+        """Remove non-numeric features and log warnings."""
+        non_numeric = [f for f in features if f not in df.select_dtypes(include=["number"]).columns]
+        if non_numeric:
+            log.warning(f"Non-numeric features {non_numeric} aren't currently supported, excluding them")
+        return [f for f in features if f not in non_numeric]
+
+    def _build_models(self) -> None:
+        """Build the underfit, overfit, and proximity models."""
+        log.info("Building noise detection models...")
+
+        X = self.df[self.features]
+        y = self.df[self.target]
+
+        # Underfit model: intentionally simple (high bias)
+        log.info("  Fitting underfit model...")
+        self.underfit_model = XGBRegressor(
+            max_depth=2,
+            n_estimators=20,
+            learning_rate=0.1,
+            random_state=42,
+            verbosity=0,
+        )
+        self.underfit_model.fit(X, y)
+
+        # Overfit model: intentionally complex (high variance, low regularization)
+        log.info("  Fitting overfit model...")
+        self.overfit_model = XGBRegressor(
+            max_depth=12,
+            n_estimators=500,
+            learning_rate=0.1,
+            reg_lambda=0.0,
+            reg_alpha=0.0,
+            min_child_weight=1,
+            random_state=42,
+            verbosity=0,
+        )
+        self.overfit_model.fit(X, y)
+
+        # Proximity model for feature space analysis
+        log.info("  Building proximity model...")
+        self.proximity = Proximity(
+            self.df,
+            id_column=self.id_column,
+            features=self.features,
+            target=self.target,
+        )
+
+        # Copy proximity metrics to our df
+        self.df["nn_distance"] = self.proximity.df["nn_distance"].values
+        self.df["nn_id"] = self.proximity.df["nn_id"].values
+        self.df["nn_target"] = self.proximity.df["nn_target"].values
+        self.df["nn_target_diff"] = self.proximity.df["nn_target_diff"].values
+
+        log.info("Noise detection models built successfully")
+
+    def _precompute_signals(self) -> None:
+        """Precompute all noise signals for every sample."""
+        log.info("Precomputing noise signals...")
+
+        X = self.df[self.features]
+        y = self.df[self.target].values
+
+        # Underfit residuals (normalized by target std)
+        underfit_pred = self.underfit_model.predict(X)
+        self.df["underfit_residual"] = np.abs(y - underfit_pred) / self.target_std
+
+        # Overfit residuals (normalized by target std)
+        # This is the key "training error" signal from the paper
+        overfit_pred = self.overfit_model.predict(X)
+        self.df["overfit_residual"] = np.abs(y - overfit_pred) / self.target_std
+
+        # HTG score: neighbor disagreement (normalized by target std)
+        # Using nn_target_diff directly, normalized
+        self.df["htg_score"] = self.df["nn_target_diff"] / self.target_std
+
+        # Combine into overall noise score
+        # Scale each component to [0, 1] using percentile ranks, then average
+        self.df["noise_score"] = self._compute_combined_score()
+
+        log.info("Noise signals precomputed successfully")
+
+    def _compute_combined_score(self) -> np.ndarray:
+        """
+        Combine individual signals into a single noise score.
+
+        Uses percentile ranks to normalize each signal to [0, 1], then averages.
+        Overfit residual gets higher weight as it's the most validated signal (per the paper).
+        """
+        # Convert to percentile ranks (0-1 scale)
+        overfit_rank = self.df["overfit_residual"].rank(pct=True)
+        htg_rank = self.df["htg_score"].rank(pct=True)
+
+        # Weighted average: overfit gets 2x weight based on paper's findings
+        # that training error is the best noise detector
+        combined = (2.0 * overfit_rank + 1.0 * htg_rank) / 3.0
+
+        return combined.values
+
+
+# Testing the NoiseModel class
+if __name__ == "__main__":
+
+    from workbench.api import FeatureSet, Model
+
+    pd.set_option("display.max_columns", None)
+    pd.set_option("display.width", 1000)
+
+    # Create a sample DataFrame with some noisy points
+    np.random.seed(42)
+    n_samples = 100
+
+    # Generate clean data: y = 2*x1 + 3*x2 + noise
+    x1 = np.random.randn(n_samples)
+    x2 = np.random.randn(n_samples)
+    y_clean = 2 * x1 + 3 * x2 + np.random.randn(n_samples) * 0.1
+
+    # Add some noisy points (last 10 samples)
+    y_noisy = y_clean.copy()
+    y_noisy[-10:] += np.random.randn(10) * 5  # Large noise
+
+    data = {
+        "ID": [f"sample_{i}" for i in range(n_samples)],
+        "Feature1": x1,
+        "Feature2": x2,
+        "target": y_noisy,
+    }
+    df = pd.DataFrame(data)
+
+    print("=" * 80)
+    print("Testing NoiseModel...")
+    print("=" * 80)
+
+    # Create noise model
+    noise_model = NoiseModel(
+        df,
+        id_column="ID",
+        features=["Feature1", "Feature2"],
+        target="target",
+    )
+
+    # Get noise scores
+    print("\nTop 10 noisiest samples:")
+    scores = noise_model.get_scores()
+    print(scores.head(10))
+
+    # Check if our artificially noisy samples are detected
+    noisy_ids = [f"sample_{i}" for i in range(90, 100)]
+    detected = scores[scores["ID"].isin(noisy_ids)]
+    median_score = scores["noise_score"].median()
+    print(f"\nOf 10 noisy samples, {len(detected[detected['noise_score'] > median_score])} above median noise score")
+
+    # Get sample weights
+    print("\nSample weights (inverse strategy):")
+    weights = noise_model.get_sample_weights(strategy="inverse")
+    print(f"  Min weight: {weights.min():.3f}")
+    print(f"  Max weight: {weights.max():.3f}")
+    print(f"  Mean weight: {weights.mean():.3f}")
+
+    # Get clean subset
+    clean = noise_model.get_clean_subset(percentile=90)
+    print(f"\nClean subset (bottom 90%): {len(clean)} samples")
+
+    # Get noisy samples
+    noisy = noise_model.get_noisy_samples(top_percent=10)
+    print(f"\nNoisy samples (top 10%): {len(noisy)} samples")
+    print(noisy[["ID", "target", "overfit_residual", "htg_score", "noise_score"]].head())
+
+    # Test with real data
+    print("\n" + "=" * 80)
+    print("Testing with AQSol data...")
+    print("=" * 80)
+    fs = FeatureSet("aqsol_features")
+    model = Model("aqsol-regression")
+
+    if fs.exists():
+        features = model.features()
+        target = model.target()
+        df = fs.pull_dataframe()
+
+        noise_model = NoiseModel(
+            df,
+            id_column=fs.id_column,
+            features=features,
+            target=target,
+        )
+
+        print("\nTop 10 noisiest compounds:")
+        scores = noise_model.get_scores()
+        print(scores.head(10))
+
+        print("\nCoincident conflicts:")
+        conflicts = noise_model.coincident_conflicts()
+        print(f"Found {len(conflicts)} coincident conflicts")
+        if len(conflicts) > 0:
+            print(conflicts.head())
+
+        print("\nNoise score distribution:")
+        print(scores["noise_score"].describe())

workbench/api/endpoint.py

@@ -70,16 +70,13 @@ class Endpoint(EndpointCore):
         """
         return super().fast_inference(eval_df, threads=threads)
 
-    def cross_fold_inference(self, nfolds: int = 5) -> pd.DataFrame:
-        """Run cross-fold inference (only works for XGBoost models)
-
-        Args:
-            nfolds (int): The number of folds to use for cross-validation (default: 5)
+    def cross_fold_inference(self) -> pd.DataFrame:
+        """Pull cross-fold inference from model associated with this Endpoint
 
         Returns:
             pd.DataFrame: A DataFrame with cross fold predictions
         """
-        return super().cross_fold_inference(nfolds)
+        return super().cross_fold_inference()
 
 
 if __name__ == "__main__":

workbench/api/feature_set.py

@@ -128,7 +128,7 @@ class FeatureSet(FeatureSetCore):
         tags = [name] if tags is None else tags
 
         # If the model framework is PyTorch or ChemProp, ensure we set the training and inference images
-        if model_framework in (ModelFramework.PYTORCH_TABULAR, ModelFramework.CHEMPROP):
+        if model_framework in (ModelFramework.PYTORCH, ModelFramework.CHEMPROP):
             training_image = "pytorch_training"
             inference_image = "pytorch_inference"
 

workbench/api/model.py

@@ -10,7 +10,7 @@ from workbench.core.artifacts.artifact import Artifact
 from workbench.core.artifacts.model_core import ModelCore, ModelType, ModelFramework  # noqa: F401
 from workbench.core.transforms.model_to_endpoint.model_to_endpoint import ModelToEndpoint
 from workbench.api.endpoint import Endpoint
-from workbench.utils.model_utils import proximity_model_local, uq_model
+from workbench.utils.model_utils import proximity_model_local, noise_model_local
 
 
 class Model(ModelCore):
@@ -91,19 +91,13 @@ class Model(ModelCore):
         """
         return proximity_model_local(self)
 
-    def uq_model(self, uq_model_name: str = None, train_all_data: bool = False) -> "Model":
-        """Create a Uncertainty Quantification Model for this Model
-
-        Args:
-            uq_model_name (str, optional): Name of the UQ Model (if not specified, a name will be generated)
-            train_all_data (bool, optional): Whether to train the UQ Model on all data (default: False)
+    def noise_model(self):
+        """Create a local Noise Model for this Model
 
         Returns:
-            Model: The UQ Model
+           NoiseModel: A local Noise Model
         """
-        if uq_model_name is None:
-            uq_model_name = self.model_name + "-uq"
-        return uq_model(self, uq_model_name, train_all_data=train_all_data)
+        return noise_model_local(self)
 
 
 if __name__ == "__main__":

workbench/cached/cached_model.py

@@ -72,11 +72,11 @@ class CachedModel(CachedArtifactMixin, ModelCore):
         return super().list_inference_runs()
 
     @CachedArtifactMixin.cache_result
-    def get_inference_metrics(self, capture_name: str = "latest") -> Union[pd.DataFrame, None]:
+    def get_inference_metrics(self, capture_name: str = "auto") -> Union[pd.DataFrame, None]:
         """Retrieve the captured prediction results for this model
 
         Args:
-            capture_name (str, optional): Specific capture_name (default: latest)
+            capture_name (str, optional): Specific capture_name (default: auto)
 
         Returns:
             pd.DataFrame: DataFrame of the Captured Metrics (might be None)
@@ -101,11 +101,11 @@ class CachedModel(CachedArtifactMixin, ModelCore):
         return df
 
     @CachedArtifactMixin.cache_result
-    def confusion_matrix(self, capture_name: str = "latest") -> Union[pd.DataFrame, None]:
+    def confusion_matrix(self, capture_name: str = "auto") -> Union[pd.DataFrame, None]:
         """Retrieve the confusion matrix for the model
 
         Args:
-            capture_name (str, optional): Specific capture_name (default: latest)
+            capture_name (str, optional): Specific capture_name (default: auto)
 
         Returns:
             pd.DataFrame: DataFrame of the Confusion Matrix (might be None)