workbench 0.8.174__py3-none-any.whl → 0.8.227__py3-none-any.whl

workbench/model_scripts/custom_models/uq_models/proximity.py

@@ -1,384 +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
-import logging
-import pickle
-import os
-import json
-from pathlib import Path
-from enum import Enum
-
-# Set up logging
-log = logging.getLogger("workbench")
-
-
-# ^Enumerated^ Proximity Types (distance or similarity)
-class ProximityType(Enum):
-    DISTANCE = "distance"
-    SIMILARITY = "similarity"
-
-
-class Proximity:
-    def __init__(
-        self,
-        df: pd.DataFrame,
-        id_column: str,
-        features: List[str],
-        target: str = None,
-        track_columns: List[str] = None,
-        n_neighbors: int = 10,
-    ):
-        """
-        Initialize the Proximity class.
-
-        Args:
-            df (pd.DataFrame): DataFrame containing data for neighbor computations.
-            id_column (str): Name of the column used as the identifier.
-            features (List[str]): List of feature column names to be used for neighbor computations.
-            target (str, optional): Name of the target column. Defaults to None.
-            track_columns (List[str], optional): Additional columns to track in results. Defaults to None.
-            n_neighbors (int): Number of neighbors to compute. Defaults to 10.
-        """
-        self.df = df.dropna(subset=features).copy()
-        self.id_column = id_column
-        self.n_neighbors = min(n_neighbors, len(self.df) - 1)
-        self.target = target
-        self.features = features
-        self.scaler = None
-        self.X = None
-        self.nn = None
-        self.proximity_type = None
-        self.track_columns = track_columns or []
-
-        # Right now we only support numeric features, so remove any columns that are not numeric
-        non_numeric_features = self.df[self.features].select_dtypes(exclude=["number"]).columns.tolist()
-        if non_numeric_features:
-            log.warning(f"Non-numeric features {non_numeric_features} aren't currently supported...")
-            self.features = [f for f in self.features if f not in non_numeric_features]
-
-        # Build the proximity model
-        self.build_proximity_model()
-
-    def build_proximity_model(self) -> None:
-        """Standardize features and fit Nearest Neighbors model.
-        Note: This method can be overridden in subclasses for custom behavior."""
-        self.proximity_type = ProximityType.DISTANCE
-        self.scaler = StandardScaler()
-        self.X = self.scaler.fit_transform(self.df[self.features])
-        self.nn = NearestNeighbors(n_neighbors=self.n_neighbors + 1).fit(self.X)
-
-    def all_neighbors(self) -> pd.DataFrame:
-        """
-        Compute nearest neighbors for all rows in the dataset.
-
-        Returns:
-            pd.DataFrame: A DataFrame of neighbors and their distances.
-        """
-        distances, indices = self.nn.kneighbors(self.X)
-        results = []
-
-        for i, (dists, nbrs) in enumerate(zip(distances, indices)):
-            query_id = self.df.iloc[i][self.id_column]
-
-            # Process neighbors
-            for neighbor_idx, dist in zip(nbrs, dists):
-                # Skip self (neighbor index == current row index)
-                if neighbor_idx == i:
-                    continue
-                results.append(self._build_neighbor_result(query_id=query_id, neighbor_idx=neighbor_idx, distance=dist))
-
-        return pd.DataFrame(results)
-
-    def neighbors(
-        self,
-        query_df: pd.DataFrame,
-        radius: float = None,
-        include_self: bool = True,
-    ) -> pd.DataFrame:
-        """
-        Return neighbors for rows in a query DataFrame.
-
-        Args:
-            query_df: DataFrame containing query points
-            radius: If provided, find all neighbors within this radius
-            include_self: Whether to include self in results (if present)
-
-        Returns:
-            DataFrame containing neighbors and distances
-
-        Note: The query DataFrame must include the feature columns. The id_column is optional.
-        """
-        # Check if all required features are present
-        missing = set(self.features) - set(query_df.columns)
-        if missing:
-            raise ValueError(f"Query DataFrame is missing required feature columns: {missing}")
-
-        # Check if id_column is present
-        id_column_present = self.id_column in query_df.columns
-
-        # None of the features can be NaNs, so report rows with NaNs and then drop them
-        rows_with_nan = query_df[self.features].isna().any(axis=1)
-
-        # Print the ID column for rows with NaNs
-        if rows_with_nan.any():
-            log.warning(f"Found {rows_with_nan.sum()} rows with NaNs in feature columns:")
-            log.warning(query_df.loc[rows_with_nan, self.id_column])
-
-        # Drop rows with NaNs in feature columns and reassign to query_df
-        query_df = query_df.dropna(subset=self.features)
-
-        # Transform the query features using the model's scaler
-        X_query = self.scaler.transform(query_df[self.features])
-
-        # Get neighbors using either radius or k-nearest neighbors
-        if radius is not None:
-            distances, indices = self.nn.radius_neighbors(X_query, radius=radius)
-        else:
-            distances, indices = self.nn.kneighbors(X_query)
-
-        # Build results
-        all_results = []
-        for i, (dists, nbrs) in enumerate(zip(distances, indices)):
-            # Use the ID from the query DataFrame if available, otherwise use the row index
-            query_id = query_df.iloc[i][self.id_column] if id_column_present else f"query_{i}"
-
-            for neighbor_idx, dist in zip(nbrs, dists):
-                # Skip if the neighbor is the query itself and include_self is False
-                neighbor_id = self.df.iloc[neighbor_idx][self.id_column]
-                if not include_self and neighbor_id == query_id:
-                    continue
-
-                all_results.append(
-                    self._build_neighbor_result(query_id=query_id, neighbor_idx=neighbor_idx, distance=dist)
-                )
-
-        return pd.DataFrame(all_results)
-
-    def _build_neighbor_result(self, query_id, neighbor_idx: int, distance: float) -> Dict:
-        """
-        Internal: 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_id = self.df.iloc[neighbor_idx][self.id_column]
-
-        # Basic neighbor info
-        neighbor_info = {
-            self.id_column: query_id,
-            "neighbor_id": neighbor_id,
-            "distance": distance,
-        }
-
-        # Determine which additional columns to include
-        relevant_cols = [self.target, "prediction"] if self.target else []
-        relevant_cols += [c for c in self.df.columns if "_proba" in c or "residual" in c]
-        relevant_cols += ["outlier"]
-
-        # Add user-specified columns
-        relevant_cols += self.track_columns
-
-        # Add values for each relevant column that exists in the dataframe
-        for col in filter(lambda c: c in self.df.columns, relevant_cols):
-            neighbor_info[col] = self.df.iloc[neighbor_idx][col]
-
-        return neighbor_info
-
-    def serialize(self, directory: str) -> None:
-        """
-        Serialize the Proximity model to a directory.
-
-        Args:
-            directory: Directory path to save the model components
-        """
-        # Create directory if it doesn't exist
-        os.makedirs(directory, exist_ok=True)
-
-        # Save metadata
-        metadata = {
-            "id_column": self.id_column,
-            "features": self.features,
-            "target": self.target,
-            "track_columns": self.track_columns,
-            "n_neighbors": self.n_neighbors,
-        }
-
-        with open(os.path.join(directory, "metadata.json"), "w") as f:
-            json.dump(metadata, f)
-
-        # Save the DataFrame
-        self.df.to_pickle(os.path.join(directory, "df.pkl"))
-
-        # Save the scaler and nearest neighbors model
-        with open(os.path.join(directory, "scaler.pkl"), "wb") as f:
-            pickle.dump(self.scaler, f)
-
-        with open(os.path.join(directory, "nn_model.pkl"), "wb") as f:
-            pickle.dump(self.nn, f)
-
-        log.info(f"Proximity model serialized to {directory}")
-
-    @classmethod
-    def deserialize(cls, directory: str) -> "Proximity":
-        """
-        Deserialize a Proximity model from a directory.
-
-        Args:
-            directory: Directory path containing the serialized model components
-
-        Returns:
-            Proximity: A new Proximity instance
-        """
-        directory_path = Path(directory)
-        if not directory_path.exists() or not directory_path.is_dir():
-            raise ValueError(f"Directory {directory} does not exist or is not a directory")
-
-        # Load metadata
-        with open(os.path.join(directory, "metadata.json"), "r") as f:
-            metadata = json.load(f)
-
-        # Load DataFrame
-        df_path = os.path.join(directory, "df.pkl")
-        if not os.path.exists(df_path):
-            raise FileNotFoundError(f"DataFrame file not found at {df_path}")
-        df = pd.read_pickle(df_path)
-
-        # Create instance but skip _prepare_data
-        instance = cls.__new__(cls)
-        instance.df = df
-        instance.id_column = metadata["id_column"]
-        instance.features = metadata["features"]
-        instance.target = metadata["target"]
-        instance.track_columns = metadata["track_columns"]
-        instance.n_neighbors = metadata["n_neighbors"]
-
-        # Load scaler and nn model
-        with open(os.path.join(directory, "scaler.pkl"), "rb") as f:
-            instance.scaler = pickle.load(f)
-
-        with open(os.path.join(directory, "nn_model.pkl"), "rb") as f:
-            instance.nn = pickle.load(f)
-
-        # Load X from scaler transform
-        instance.X = instance.scaler.transform(instance.df[instance.features])
-
-        log.info(f"Proximity model deserialized from {directory}")
-        return instance
-
-
-# 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, n_neighbors=3)
-    print(prox.all_neighbors())
-
-    # Test the neighbors method
-    print(prox.neighbors(query_df=df.iloc[[0]]))
-
-    # Test the neighbors method with radius
-    print(prox.neighbors(query_df=df.iloc[0:2], radius=2.0))
-
-    # Test with data that isn't in the 'train' dataframe
-    query_data = {
-        "ID": [6],
-        "Feature1": [0.31],
-        "Feature2": [0.31],
-        "Feature3": [2.31],
-    }
-    query_df = pd.DataFrame(query_data)
-    print(prox.neighbors(query_df=query_df))
-
-    # Test with Features list
-    prox = Proximity(df, id_column="ID", features=["Feature1"], n_neighbors=2)
-    print(prox.all_neighbors())
-
-    # 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"],
-        n_neighbors=3,
-    )
-    print(prox.all_neighbors())
-
-    # Test the neighbors method
-    print(prox.neighbors(query_df=df.iloc[0:2]))
-
-    # Time neighbors with all IDs versus calling all_neighbors
-    import time
-
-    start_time = time.time()
-    prox_df = prox.neighbors(query_df=df, include_self=False)
-    end_time = time.time()
-    print(f"Time taken for neighbors: {end_time - start_time:.4f} seconds")
-    start_time = time.time()
-    prox_df_all = prox.all_neighbors()
-    end_time = time.time()
-    print(f"Time taken for all_neighbors: {end_time - start_time:.4f} seconds")
-
-    # Now compare the two dataframes
-    print("Neighbors DataFrame:")
-    print(prox_df)
-    print("\nAll Neighbors DataFrame:")
-    print(prox_df_all)
-    # Check for any discrepancies
-    if prox_df.equals(prox_df_all):
-        print("The two DataFrames are equal :)")
-    else:
-        print("ERROR: The two DataFrames are not equal!")
-
-    # Test querying without the id_column
-    df_no_id = df.drop(columns=["foo_id"])
-    print(prox.neighbors(query_df=df_no_id, include_self=False))
-
-    # 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", n_neighbors=3)
-    print(df.equals(prox.df))
-
-    # Test with a categorical feature
-    from workbench.api import FeatureSet, Model
-
-    fs = FeatureSet("abalone_features")
-    model = Model("abalone-regression")
-    df = fs.pull_dataframe()
-    prox = Proximity(df, id_column=fs.id_column, features=model.features(), target=model.target())
-    print(prox.neighbors(query_df=df[0:2]))

workbench/model_scripts/ensemble_xgb/generated_model_script.py

@@ -1,279 +0,0 @@
-# Template Placeholders
-TEMPLATE_PARAMS = {
-    "model_type": "ensemble_regressor",
-    "target_column": "solubility",
-    "feature_list": ['molwt', 'mollogp', 'molmr', 'heavyatomcount', 'numhacceptors', 'numhdonors', 'numheteroatoms', 'numrotatablebonds', 'numvalenceelectrons', 'numaromaticrings', 'numsaturatedrings', 'numaliphaticrings', 'ringcount', 'tpsa', 'labuteasa', 'balabanj', 'bertzct'],
-    "model_metrics_s3_path": "s3://sandbox-sageworks-artifacts/models/aqsol-ensemble/training"
-}
-
-# Imports for XGB Model
-import xgboost as xgb
-import awswrangler as wr
-import numpy as np
-
-# Model Performance Scores
-from sklearn.metrics import (
-    mean_absolute_error,
-    r2_score,
-    root_mean_squared_error
-)
-
-from io import StringIO
-import json
-import argparse
-import os
-import pandas as pd
-
-
-# Function to check if dataframe is empty
-def check_dataframe(df: pd.DataFrame, df_name: str) -> None:
-    """
-    Check if the provided dataframe is empty and raise an exception if it is.
-
-    Args:
-        df (pd.DataFrame): DataFrame to check
-        df_name (str): Name of the DataFrame
-    """
-    if df.empty:
-        msg = f"*** The training data {df_name} has 0 rows! ***STOPPING***"
-        print(msg)
-        raise ValueError(msg)
-
-def match_features_case_insensitive(df: pd.DataFrame, model_features: list) -> pd.DataFrame:
-    """
-    Matches and renames the DataFrame's column names to match the model's feature names (case-insensitive).
-    Prioritizes exact case matches first, then falls back to case-insensitive matching if no exact match exists.
-
-    Args:
-        df (pd.DataFrame): The DataFrame with the original columns.
-        model_features (list): The desired list of feature names (mixed case allowed).
-
-    Returns:
-        pd.DataFrame: The DataFrame with renamed columns to match the model's feature names.
-    """
-    # Create a mapping for exact and case-insensitive matching
-    exact_match_set = set(df.columns)
-    column_map = {}
-
-    # Build the case-insensitive map (if we have any duplicate columns, the first one wins)
-    for col in df.columns:
-        lower_col = col.lower()
-        if lower_col not in column_map:
-            column_map[lower_col] = col
-
-    # Create a dictionary for renaming
-    rename_dict = {}
-    for feature in model_features:
-        # Check for an exact match first
-        if feature in exact_match_set:
-            rename_dict[feature] = feature
-
-        # If not an exact match, fall back to case-insensitive matching
-        elif feature.lower() in column_map:
-            rename_dict[column_map[feature.lower()]] = feature
-
-    # Rename the columns in the DataFrame to match the model's feature names
-    return df.rename(columns=rename_dict)
-
-
-if __name__ == "__main__":
-    """The main function is for training the XGBoost Quantile Regression models"""
-
-    # Harness Template Parameters
-    target = TEMPLATE_PARAMS["target_column"]
-    feature_list = TEMPLATE_PARAMS["feature_list"]
-    model_metrics_s3_path = TEMPLATE_PARAMS["model_metrics_s3_path"]
-    models = {}
-
-    # Script arguments for input/output directories
-    parser = argparse.ArgumentParser()
-    parser.add_argument("--model-dir", type=str, default=os.environ.get("SM_MODEL_DIR", "/opt/ml/model"))
-    parser.add_argument("--train", type=str, default=os.environ.get("SM_CHANNEL_TRAIN", "/opt/ml/input/data/train"))
-    parser.add_argument(
-        "--output-data-dir", type=str, default=os.environ.get("SM_OUTPUT_DATA_DIR", "/opt/ml/output/data")
-    )
-    args = parser.parse_args()
-
-    # Read the training data into DataFrames
-    training_files = [
-        os.path.join(args.train, file)
-        for file in os.listdir(args.train)
-        if file.endswith(".csv")
-    ]
-    print(f"Training Files: {training_files}")
-
-    # Combine files and read them all into a single pandas dataframe
-    df = pd.concat([pd.read_csv(file, engine="python") for file in training_files])
-
-    # Check if the dataframe is empty
-    check_dataframe(df, "training_df")
-
-    # Features/Target output
-    print(f"Target: {target}")
-    print(f"Features: {str(feature_list)}")
-    print(f"Data Shape: {df.shape}")
-
-    # Grab our Features and Target with traditional X, y handles
-    y = df[target]
-    X = df[feature_list]
-
-    # Train 50 models with random 70/30 splits of the data
-    for model_id in range(50):
-        # Model Name
-        model_name = f"m_{model_id:02}"
-
-        # Bootstrap sample (50% with replacement)
-        sample_size = int(0.5 * len(X))
-        bootstrap_indices = np.random.choice(len(X), size=sample_size, replace=True)
-        X_train, y_train = X.iloc[bootstrap_indices], y.iloc[bootstrap_indices]
-        print(f"Training Model {model_name} with {len(X_train)} rows")
-        model = xgb.XGBRegressor(reg_alpha=0.1, reg_lambda=1.0)
-        model.fit(X_train, y_train)
-
-        # Store the model
-        models[model_name] = model
-
-    # Run predictions for each model
-    all_predictions = {model_name: model.predict(X) for model_name, model in models.items()}
-
-    # Create a copy of the provided DataFrame and add the new columns
-    result_df = df[[target]].copy()
-
-    # Add the model predictions to the DataFrame
-    for name, preds in all_predictions.items():
-        result_df[name] = preds
-
-    # Add the main prediction to the DataFrame (mean of all models)
-    result_df["prediction"] = result_df[[name for name in result_df.columns if name.startswith("m_")]].mean(axis=1)
-
-    # Now compute residuals on the rmse prediction
-    result_df["residual"] = result_df[target] - result_df["prediction"]
-    result_df["residual_abs"] = result_df["residual"].abs()
-
-
-    # Save the results dataframe to S3
-    wr.s3.to_csv(
-        result_df,
-        path=f"{model_metrics_s3_path}/validation_predictions.csv",
-        index=False,
-    )
-
-    # Report Performance Metrics
-    rmse = root_mean_squared_error(result_df[target], result_df["prediction"])
-    mae = mean_absolute_error(result_df[target], result_df["prediction"])
-    r2 = r2_score(result_df[target], result_df["prediction"])
-    print(f"RMSE: {rmse:.3f}")
-    print(f"MAE: {mae:.3f}")
-    print(f"R2: {r2:.3f}")
-    print(f"NumRows: {len(result_df)}")
-
-    # Now save the models
-    for name, model in models.items():
-        model_path = os.path.join(args.model_dir, f"{name}.json")
-        print(f"Saving model:  {model_path}")
-        model.save_model(model_path)
-
-    # Also save the features (this will validate input during predictions)
-    with open(os.path.join(args.model_dir, "feature_columns.json"), "w") as fp:
-        json.dump(feature_list, fp)
-
-
-def model_fn(model_dir) -> dict:
-    """Deserialized and return all the fitted models from the model directory.
-
-    Args:
-        model_dir (str): The directory where the models are stored.
-
-    Returns:
-        dict: A dictionary of the models.
-    """
-
-    # Load ALL the models from the model directory
-    models = {}
-    for file in os.listdir(model_dir):
-        if file.startswith("m_") and file.endswith(".json"):  # The Quantile models
-            # Load the model
-            model_path = os.path.join(model_dir, file)
-            print(f"Loading model: {model_path}")
-            model = xgb.XGBRegressor()
-            model.load_model(model_path)
-
-            # Store the model
-            m_name = os.path.splitext(file)[0]
-            models[m_name] = model
-
-    # Return all the models
-    return models
-
-
-def input_fn(input_data, content_type):
-    """Parse input data and return a DataFrame."""
-    if not input_data:
-        raise ValueError("Empty input data is not supported!")
-    
-    # Decode bytes to string if necessary
-    if isinstance(input_data, bytes):
-        input_data = input_data.decode("utf-8")
-
-    if "text/csv" in content_type:
-        return pd.read_csv(StringIO(input_data))
-    elif "application/json" in content_type:
-        return pd.DataFrame(json.loads(input_data))  # Assumes JSON array of records
-    else:
-        raise ValueError(f"{content_type} not supported!")
-
-
-def output_fn(output_df, accept_type):
-    """Supports both CSV and JSON output formats."""
-    if "text/csv" in accept_type:
-        csv_output = output_df.fillna("N/A").to_csv(index=False)  # CSV with N/A for missing values
-        return csv_output, "text/csv"
-    elif "application/json" in accept_type:
-        return output_df.to_json(orient="records"), "application/json"  # JSON array of records (NaNs -> null)
-    else:
-        raise RuntimeError(f"{accept_type} accept type is not supported by this script.")
-
-
-def predict_fn(df, models) -> pd.DataFrame:
-    """Make Predictions with our XGB Quantile Regression Model
-
-    Args:
-        df (pd.DataFrame): The input DataFrame
-        models (dict): The dictionary of models to use for predictions
-
-    Returns:
-        pd.DataFrame: The DataFrame with the predictions added
-    """
-
-    # Grab our feature columns (from training)
-    model_dir = os.environ.get("SM_MODEL_DIR", "/opt/ml/model")
-    with open(os.path.join(model_dir, "feature_columns.json")) as fp:
-        model_features = json.load(fp)
-    print(f"Model Features: {model_features}")
-
-    # We're going match features in a case-insensitive manner, accounting for all the permutations
-    # - Model has a feature list that's any case ("Id", "taCos", "cOunT", "likes_tacos")
-    # - Incoming data has columns that are mixed case ("ID", "Tacos", "Count", "Likes_Tacos")
-    matched_df = match_features_case_insensitive(df, model_features)
-
-    # Predict the features against all the models
-    for name, model in models.items():
-        df[name] = model.predict(matched_df[model_features])
-
-    # Add quantiles for consistency with other UQ models
-    df["q_025"] = df[[name for name in df.columns if name.startswith("m_")]].quantile(0.025, axis=1)
-    df["q_975"] = df[[name for name in df.columns if name.startswith("m_")]].quantile(0.975, axis=1)
-    df["q_25"] = df[[name for name in df.columns if name.startswith("m_")]].quantile(0.25, axis=1)
-    df["q_75"] = df[[name for name in df.columns if name.startswith("m_")]].quantile(0.75, axis=1)
-
-    # Compute the mean, min, max and stddev of the predictions
-    df["prediction"] = df[[name for name in df.columns if name.startswith("m_")]].mean(axis=1)
-    df["p_min"] = df[[name for name in df.columns if name.startswith("m_")]].min(axis=1)
-    df["p_max"] = df[[name for name in df.columns if name.startswith("m_")]].max(axis=1)
-    df["prediction_std"] = df[[name for name in df.columns if name.startswith("m_")]].std(axis=1)
-
-    # Reorganize the columns so they are in alphabetical order
-    df = df.reindex(sorted(df.columns), axis=1)
-
-    # All done, return the DataFrame
-    return df