workbench 0.8.212__py3-none-any.whl → 0.8.217__py3-none-any.whl

workbench/model_scripts/custom_models/proximity/proximity.py

@@ -1,410 +0,0 @@
-import pandas as pd
-import numpy as np
-from sklearn.preprocessing import StandardScaler
-from sklearn.neighbors import NearestNeighbors
-from typing import List, Dict, Optional, Union
-import logging
-
-# Set up logging
-log = logging.getLogger("workbench")
-
-
-class Proximity:
-    def __init__(
-        self,
-        df: pd.DataFrame,
-        id_column: str,
-        features: List[str],
-        target: Optional[str] = None,
-        track_columns: Optional[List[str]] = None,
-    ):
-        """
-        Initialize the Proximity class.
-
-        Args:
-            df: DataFrame containing data for neighbor computations.
-            id_column: Name of the column used as the identifier.
-            features: List of feature column names to be used for neighbor computations.
-            target: Name of the target column. Defaults to None.
-            track_columns: Additional columns to track in results. Defaults to None.
-        """
-        self.id_column = id_column
-        self.target = target
-        self.track_columns = track_columns or []
-
-        # Filter out non-numeric features
-        self.features = self._validate_features(df, features)
-
-        # Drop NaN rows and set up DataFrame
-        self.df = df.dropna(subset=self.features).copy()
-
-        # Compute target range if target is provided
-        self.target_range = None
-        if self.target and self.target in self.df.columns:
-            self.target_range = self.df[self.target].max() - self.df[self.target].min()
-
-        # Build the proximity model
-        self._build_model()
-
-        # Precompute landscape metrics
-        self._precompute_metrics()
-
-    def isolated(self, top_percent: float = 1.0) -> pd.DataFrame:
-        """
-        Find isolated data points based on distance to nearest neighbor.
-
-        Args:
-            top_percent: Percentage of most isolated data points to return (e.g., 1.0 returns top 1%)
-
-        Returns:
-            DataFrame of observations above the percentile threshold, sorted by distance (descending)
-        """
-        percentile = 100 - top_percent
-        threshold = np.percentile(self.df["nn_distance"], percentile)
-        isolated = self.df[self.df["nn_distance"] >= threshold].copy()
-        return isolated.sort_values("nn_distance", ascending=False).reset_index(drop=True)
-
-    def target_gradients(
-        self,
-        top_percent: float = 1.0,
-        min_delta: Optional[float] = None,
-        k_neighbors: int = 4,
-        only_coincident: bool = False,
-    ) -> pd.DataFrame:
-        """
-        Find compounds with steep target gradients (data quality issues and activity cliffs).
-
-        Uses a two-phase approach:
-        1. Quick filter using nearest neighbor gradient
-        2. Verify using k-neighbor median to handle cases where the nearest neighbor is the outlier
-
-        Args:
-            top_percent: Percentage of compounds with steepest gradients to return (e.g., 1.0 = top 1%)
-            min_delta: Minimum absolute target difference to consider. If None, defaults to target_range/100
-            k_neighbors: Number of neighbors to use for median calculation (default: 4)
-            only_coincident: If True, only consider compounds that are coincident (default: False)
-
-        Returns:
-            DataFrame of compounds with steepest gradients, sorted by gradient (descending)
-        """
-        if self.target is None:
-            raise ValueError("Target column must be specified")
-
-        epsilon = 1e-5
-
-        # Phase 1: Quick filter using precomputed nearest neighbor
-        candidates = self.df.copy()
-        candidates["gradient"] = candidates["nn_target_diff"] / (candidates["nn_distance"] + epsilon)
-
-        # Apply min_delta
-        if min_delta is None:
-            min_delta = self.target_range / 100.0 if self.target_range > 0 else 0.0
-        candidates = candidates[candidates["nn_target_diff"] >= min_delta]
-
-        # Filter based on mode
-        if only_coincident:
-            # Only keep coincident points (nn_distance ~= 0)
-            candidates = candidates[candidates["nn_distance"] < epsilon].copy()
-        else:
-            # Get top X% by initial gradient
-            percentile = 100 - top_percent
-            threshold = np.percentile(candidates["gradient"], percentile)
-            candidates = candidates[candidates["gradient"] >= threshold].copy()
-
-        # Phase 2: Verify with k-neighbor median to filter out cases where nearest neighbor is the outlier
-        results = []
-        for _, row in candidates.iterrows():
-            cmpd_id = row[self.id_column]
-            cmpd_target = row[self.target]
-
-            # Get k nearest neighbors (excluding self)
-            nbrs = self.neighbors(cmpd_id, n_neighbors=k_neighbors, include_self=False)
-
-            # Calculate median target of k neighbors, excluding the nearest neighbor (index 0)
-            neighbor_median = nbrs.iloc[1:k_neighbors][self.target].median()
-            median_diff = abs(cmpd_target - neighbor_median)
-
-            # Only keep if compound differs from neighborhood median
-            # This filters out cases where the nearest neighbor is the outlier
-            if median_diff >= min_delta:
-                results.append(
-                    {
-                        self.id_column: cmpd_id,
-                        self.target: cmpd_target,
-                        "nn_target": row["nn_target"],
-                        "nn_target_diff": row["nn_target_diff"],
-                        "nn_distance": row["nn_distance"],
-                        "gradient": row["gradient"],  # Keep Phase 1 gradient
-                        "neighbor_median": neighbor_median,
-                        "neighbor_median_diff": median_diff,
-                    }
-                )
-
-        # Handle empty results
-        if not results:
-            return pd.DataFrame(
-                columns=[
-                    self.id_column,
-                    self.target,
-                    "neighbor_median",
-                    "neighbor_median_diff",
-                    "mean_distance",
-                    "gradient",
-                ]
-            )
-
-        results_df = pd.DataFrame(results)
-        results_df = results_df.sort_values("gradient", ascending=False).reset_index(drop=True)
-        return results_df
-
-    def neighbors(
-        self,
-        id_or_ids: Union[str, int, List[Union[str, int]]],
-        n_neighbors: Optional[int] = 5,
-        radius: Optional[float] = None,
-        include_self: bool = True,
-    ) -> pd.DataFrame:
-        """
-        Return neighbors for ID(s) from the existing dataset.
-
-        Args:
-            id_or_ids: Single ID or list of IDs to look up
-            n_neighbors: Number of neighbors to return (default: 5, ignored if radius is set)
-            radius: If provided, find all neighbors within this radius
-            include_self: Whether to include self in results (default: True)
-
-        Returns:
-            DataFrame containing neighbors and distances
-        """
-        # Normalize to list
-        ids = [id_or_ids] if not isinstance(id_or_ids, list) else id_or_ids
-
-        # Validate IDs exist
-        missing_ids = set(ids) - set(self.df[self.id_column])
-        if missing_ids:
-            raise ValueError(f"IDs not found in dataset: {missing_ids}")
-
-        # Filter to requested IDs and preserve order
-        query_df = self.df[self.df[self.id_column].isin(ids)]
-        query_df = query_df.set_index(self.id_column).loc[ids].reset_index()
-
-        # Transform query features
-        X_query = self.scaler.transform(query_df[self.features])
-
-        # Get neighbors
-        if radius is not None:
-            distances, indices = self.nn.radius_neighbors(X_query, radius=radius)
-        else:
-            distances, indices = self.nn.kneighbors(X_query, n_neighbors=n_neighbors)
-
-        # Build results
-        results = []
-        for i, (dists, nbrs) in enumerate(zip(distances, indices)):
-            query_id = query_df.iloc[i][self.id_column]
-
-            for neighbor_idx, dist in zip(nbrs, dists):
-                neighbor_id = self.df.iloc[neighbor_idx][self.id_column]
-
-                # Skip self if requested
-                if not include_self and neighbor_id == query_id:
-                    continue
-
-                results.append(self._build_neighbor_result(query_id=query_id, neighbor_idx=neighbor_idx, distance=dist))
-
-        df_results = pd.DataFrame(results)
-        df_results["is_self"] = df_results["neighbor_id"] == df_results[self.id_column]
-        df_results = df_results.sort_values([self.id_column, "is_self", "distance"], ascending=[True, False, True])
-        return df_results.drop("is_self", axis=1).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_model(self) -> None:
-        """Standardize features and fit Nearest Neighbors model."""
-        self.scaler = StandardScaler()
-        X = self.scaler.fit_transform(self.df[self.features])
-        self.nn = NearestNeighbors().fit(X)
-
-    def _precompute_metrics(self, n_neighbors: int = 10) -> None:
-        """
-        Precompute landscape metrics for all compounds.
-
-        Adds columns to self.df:
-        - nn_distance: Distance to nearest neighbor
-        - nn_id: ID of nearest neighbor
-
-        If target is specified, also adds:
-        - nn_target: Target value of nearest neighbor
-        - nn_target_diff: Absolute difference from nearest neighbor target
-        """
-        log.info("Precomputing proximity metrics...")
-
-        # Make sure n_neighbors isn't greater than dataset size
-        n_neighbors = min(n_neighbors, len(self.df) - 1)
-
-        # Get nearest neighbors for all points (including self)
-        X = self.scaler.transform(self.df[self.features])
-        distances, indices = self.nn.kneighbors(X, n_neighbors=2)  # Just need nearest neighbor
-
-        # Extract nearest neighbor (index 1, since index 0 is self)
-        self.df["nn_distance"] = distances[:, 1]
-        self.df["nn_id"] = self.df.iloc[indices[:, 1]][self.id_column].values
-
-        # If target exists, compute target-based metrics
-        if self.target and self.target in self.df.columns:
-            # Get target values for nearest neighbor
-            nn_target_values = self.df.iloc[indices[:, 1]][self.target].values
-            self.df["nn_target"] = nn_target_values
-            self.df["nn_target_diff"] = np.abs(self.df[self.target].values - nn_target_values)
-
-            # Precompute target range for min_delta default
-            self.target_range = self.df[self.target].max() - self.df[self.target].min()
-
-        log.info("Proximity metrics precomputed successfully")
-
-    def _build_neighbor_result(self, query_id, neighbor_idx: int, distance: float) -> Dict:
-        """
-        Build a result dictionary for a single neighbor.
-
-        Args:
-            query_id: ID of the query point
-            neighbor_idx: Index of the neighbor in the original DataFrame
-            distance: Distance between query and neighbor
-
-        Returns:
-            Dictionary containing neighbor information
-        """
-        neighbor_row = self.df.iloc[neighbor_idx]
-        neighbor_id = neighbor_row[self.id_column]
-
-        # Start with basic info
-        result = {
-            self.id_column: query_id,
-            "neighbor_id": neighbor_id,
-            "distance": 0.0 if distance < 1e-5 else distance,
-        }
-
-        # Add target if present
-        if self.target and self.target in self.df.columns:
-            result[self.target] = neighbor_row[self.target]
-
-        # Add tracked columns
-        for col in self.track_columns:
-            if col in self.df.columns:
-                result[col] = neighbor_row[col]
-
-        # Add prediction/probability columns if they exist
-        for col in self.df.columns:
-            if col == "prediction" or "_proba" in col or "residual" in col or col == "in_model":
-                result[col] = neighbor_row[col]
-
-        return result
-
-
-# Testing the Proximity class
-if __name__ == "__main__":
-
-    pd.set_option("display.max_columns", None)
-    pd.set_option("display.width", 1000)
-
-    # Create a sample DataFrame
-    data = {
-        "ID": [1, 2, 3, 4, 5],
-        "Feature1": [0.1, 0.2, 0.3, 0.4, 0.5],
-        "Feature2": [0.5, 0.4, 0.3, 0.2, 0.1],
-        "Feature3": [2.5, 2.4, 2.3, 2.3, np.nan],
-    }
-    df = pd.DataFrame(data)
-
-    # Test the Proximity class
-    features = ["Feature1", "Feature2", "Feature3"]
-    prox = Proximity(df, id_column="ID", features=features)
-    print(prox.neighbors(1, n_neighbors=2))
-
-    # Test the neighbors method with radius
-    print(prox.neighbors(1, radius=2.0))
-
-    # Test with Features list
-    prox = Proximity(df, id_column="ID", features=["Feature1"])
-    print(prox.neighbors(1))
-
-    # Create a sample DataFrame
-    data = {
-        "foo_id": ["a", "b", "c", "d", "e"],  # Testing string IDs
-        "Feature1": [0.1, 0.2, 0.3, 0.4, 0.5],
-        "Feature2": [0.5, 0.4, 0.3, 0.2, 0.1],
-        "target": [1, 0, 1, 0, 5],
-    }
-    df = pd.DataFrame(data)
-
-    # Test with String Ids
-    prox = Proximity(
-        df,
-        id_column="foo_id",
-        features=["Feature1", "Feature2"],
-        target="target",
-        track_columns=["Feature1", "Feature2"],
-    )
-    print(prox.neighbors(["a", "b"]))
-
-    # Test duplicate IDs
-    data = {
-        "foo_id": ["a", "b", "c", "d", "d"],  # Duplicate ID (d)
-        "Feature1": [0.1, 0.2, 0.3, 0.4, 0.5],
-        "Feature2": [0.5, 0.4, 0.3, 0.2, 0.1],
-        "target": [1, 0, 1, 0, 5],
-    }
-    df = pd.DataFrame(data)
-    prox = Proximity(df, id_column="foo_id", features=["Feature1", "Feature2"], target="target")
-    print(df.equals(prox.df))
-
-    # Test with a categorical feature
-    from workbench.api import FeatureSet, Model
-
-    fs = FeatureSet("aqsol_features")
-    model = Model("aqsol-regression")
-    features = model.features()
-    df = fs.pull_dataframe()
-    prox = Proximity(
-        df, id_column=fs.id_column, features=model.features(), target=model.target(), track_columns=features
-    )
-    print(prox.neighbors(df[fs.id_column].tolist()[:3]))
-
-    print("\n" + "=" * 80)
-    print("Testing isolated_compounds...")
-    print("=" * 80)
-
-    # Test isolated data in the top 1%
-    isolated_1pct = prox.isolated(top_percent=1.0)
-    print(f"\nTop 1% most isolated compounds (n={len(isolated_1pct)}):")
-    print(isolated_1pct[[fs.id_column, "nn_distance", "nn_id"]].head(10))
-
-    # Test isolated data in the top 5%
-    isolated_5pct = prox.isolated(top_percent=5.0)
-    print(f"\nTop 5% most isolated compounds (n={len(isolated_5pct)}):")
-    print(isolated_5pct[[fs.id_column, "nn_distance", "nn_id"]].head(10))
-
-    print("\n" + "=" * 80)
-    print("Testing target_gradients...")
-    print("=" * 80)
-
-    # Test with different parameters
-    gradients_1pct = prox.target_gradients(top_percent=1.0, min_delta=1.0)
-    print(f"\nTop 1% target gradients (min_delta=5.0) (n={len(gradients_1pct)}):")
-    print(
-        gradients_1pct[
-            [fs.id_column, model.target(), "neighbor_median", "neighbor_median_diff", "mean_distance", "gradient"]
-        ].head(10)
-    )
-
-    gradients_5pct = prox.target_gradients(top_percent=5.0, min_delta=5.0)
-    print(f"\nTop 5% target gradients (min_delta=5.0) (n={len(gradients_5pct)}):")
-    print(
-        gradients_5pct[
-            [fs.id_column, model.target(), "neighbor_median", "neighbor_median_diff", "mean_distance", "gradient"]
-        ].head(10)
-    )