workbench 0.8.162__py3-none-any.whl → 0.8.220__py3-none-any.whl

workbench/model_scripts/custom_models/uq_models/generated_model_script.py

@@ -1,393 +0,0 @@
-# Model: NGBoost Regressor with Distribution output
-from ngboost import NGBRegressor
-from xgboost import XGBRegressor  # Base Estimator
-from sklearn.model_selection import train_test_split
-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 joblib
-import os
-import pandas as pd
-
-# Local Imports
-from proximity import Proximity
-
-
-
-# Template Placeholders
-TEMPLATE_PARAMS = {
-    "id_column": "id",
-    "features": ['molwt', 'mollogp', 'molmr', 'heavyatomcount', 'numhacceptors', 'numhdonors', 'numheteroatoms', 'numrotatablebonds', 'numvalenceelectrons', 'numaromaticrings', 'numsaturatedrings', 'numaliphaticrings', 'ringcount', 'tpsa', 'labuteasa', 'balabanj', 'bertzct'],
-    "target": "solubility",
-    "train_all_data": True,
-    "track_columns": ['solubility']
-}
-
-
-# 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 DataFrame columns to match model feature names (case-insensitive).
-    Prioritizes exact matches, then case-insensitive matches.
-
-    Raises ValueError if any model features cannot be matched.
-    """
-    df_columns_lower = {col.lower(): col for col in df.columns}
-    rename_dict = {}
-    missing = []
-    for feature in model_features:
-        if feature in df.columns:
-            continue  # Exact match
-        elif feature.lower() in df_columns_lower:
-            rename_dict[df_columns_lower[feature.lower()]] = feature
-        else:
-            missing.append(feature)
-
-    if missing:
-        raise ValueError(f"Features not found: {missing}")
-
-    # Rename the DataFrame columns to match the model features
-    return df.rename(columns=rename_dict)
-
-
-def distance_weighted_calibrated_intervals(
-        df_pred: pd.DataFrame,
-        prox_df: pd.DataFrame,
-        calibration_strength: float = 0.7,
-        distance_decay: float = 3.0,
-) -> pd.DataFrame:
-    """
-    Calibrate intervals using distance-weighted neighbor quantiles.
-    Uses all 10 neighbors with distance-based weighting.
-    """
-    id_column = TEMPLATE_PARAMS["id_column"]
-    target_column = TEMPLATE_PARAMS["target"]
-
-    # Distance-weighted neighbor statistics
-    def weighted_quantile(values, weights, q):
-        """Calculate weighted quantile"""
-        if len(values) == 0:
-            return np.nan
-        sorted_indices = np.argsort(values)
-        sorted_values = values[sorted_indices]
-        sorted_weights = weights[sorted_indices]
-        cumsum = np.cumsum(sorted_weights)
-        cutoff = q * cumsum[-1]
-        return np.interp(cutoff, cumsum, sorted_values)
-
-    # Calculate distance weights (closer neighbors get more weight)
-    prox_df = prox_df.copy()
-    prox_df['weight'] = 1 / (1 + prox_df['distance'] ** distance_decay)
-
-    # Get weighted quantiles and statistics for each ID
-    neighbor_stats = []
-    for id_val, group in prox_df.groupby(id_column):
-        values = group[target_column].values
-        weights = group['weight'].values
-
-        # Normalize weights
-        weights = weights / weights.sum()
-
-        stats = {
-            id_column: id_val,
-            'local_q025': weighted_quantile(values, weights, 0.025),
-            'local_q25': weighted_quantile(values, weights, 0.25),
-            'local_q75': weighted_quantile(values, weights, 0.75),
-            'local_q975': weighted_quantile(values, weights, 0.975),
-            'local_median': weighted_quantile(values, weights, 0.5),
-            'local_std': np.sqrt(np.average((values - np.average(values, weights=weights)) ** 2, weights=weights)),
-            'avg_distance': group['distance'].mean(),
-            'min_distance': group['distance'].min(),
-            'max_distance': group['distance'].max(),
-        }
-        neighbor_stats.append(stats)
-
-    neighbor_df = pd.DataFrame(neighbor_stats)
-    out = df_pred.merge(neighbor_df, on=id_column, how='left')
-
-    # Model disagreement score (normalized by prediction std)
-    model_disagreement = (out["prediction"] - out["prediction_uq"]).abs()
-    disagreement_score = (model_disagreement / out["prediction_std"]).clip(0, 2)
-
-    # Local confidence based on:
-    # 1. How close the neighbors are (closer = more confident)
-    # 2. How much local variance there is (less variance = more confident)
-    max_reasonable_distance = out['max_distance'].quantile(0.8)  # 80th percentile as reference
-    distance_confidence = (1 - (out['avg_distance'] / max_reasonable_distance)).clip(0.1, 1.0)
-
-    variance_confidence = (out["prediction_std"] / out["local_std"]).clip(0.5, 2.0)
-    local_confidence = distance_confidence * variance_confidence.clip(0.5, 1.5)
-
-    # Calibration weight: higher when models disagree and we have good local data
-    calibration_weight = (
-            calibration_strength *
-            local_confidence *  # Weight by local data quality
-            disagreement_score.clip(0.3, 1.0)  # More calibration when models disagree
-    )
-
-    # Consensus prediction (slight preference for NGBoost since it provides intervals)
-    consensus_pred = 0.65 * out["prediction_uq"] + 0.35 * out["prediction"]
-
-    # Re-center local intervals around consensus prediction
-    local_center_offset = consensus_pred - out["local_median"]
-
-    # Apply calibration to each quantile
-    quantile_pairs = [
-        ("q_025", "local_q025"),
-        ("q_25", "local_q25"),
-        ("q_75", "local_q75"),
-        ("q_975", "local_q975")
-    ]
-
-    for model_q, local_q in quantile_pairs:
-        # Adjust local quantiles to be centered around consensus
-        adjusted_local_q = out[local_q] + local_center_offset
-
-        # Blend model and local intervals
-        out[model_q] = (
-                (1 - calibration_weight) * out[model_q] +
-                calibration_weight * adjusted_local_q
-        )
-
-    # Ensure proper interval ordering and bounds using pandas
-    out["q_025"] = pd.concat([out["q_025"], consensus_pred], axis=1).min(axis=1)
-    out["q_975"] = pd.concat([out["q_975"], consensus_pred], axis=1).max(axis=1)
-    out["q_25"] = pd.concat([out["q_25"], out["q_75"]], axis=1).min(axis=1)
-
-    # Optional: Add some interval expansion when neighbors are very far
-    # (indicates we're in a sparse region of feature space)
-    sparse_region_mask = out['min_distance'] > out['min_distance'].quantile(0.9)
-    expansion_factor = 1 + 0.2 * sparse_region_mask  # 20% expansion in sparse regions
-
-    for q in ["q_025", "q_25", "q_75", "q_975"]:
-        interval_width = out[q] - consensus_pred
-        out[q] = consensus_pred + interval_width * expansion_factor
-
-    # Clean up temporary columns
-    cleanup_cols = [col for col in out.columns if col.startswith("local_")] + \
-                   ['avg_distance', 'min_distance', 'max_distance']
-
-    return out.drop(columns=cleanup_cols)
-
-
-# TRAINING SECTION
-#
-# This section (__main__) is where SageMaker will execute the training job
-# and save the model artifacts to the model directory.
-#
-if __name__ == "__main__":
-    # Template Parameters
-    id_column = TEMPLATE_PARAMS["id_column"]
-    features = TEMPLATE_PARAMS["features"]
-    target = TEMPLATE_PARAMS["target"]
-    train_all_data = TEMPLATE_PARAMS["train_all_data"]
-    track_columns = TEMPLATE_PARAMS["track_columns"]  # Can be None
-    validation_split = 0.2
-
-    # 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()
-
-    # Load training data from the specified directory
-    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")
-
-    # Training data split logic
-    if train_all_data:
-        # Use all data for both training and validation
-        print("Training on all data...")
-        df_train = df.copy()
-        df_val = df.copy()
-    elif "training" in df.columns:
-        # Split data based on a 'training' column if it exists
-        print("Splitting data based on 'training' column...")
-        df_train = df[df["training"]].copy()
-        df_val = df[~df["training"]].copy()
-    else:
-        # Perform a random split if no 'training' column is found
-        print("Splitting data randomly...")
-        df_train, df_val = train_test_split(df, test_size=validation_split, random_state=42)
-
-    # We're using XGBoost for point predictions and NGBoost for uncertainty quantification
-    xgb_model = XGBRegressor()
-    ngb_model = NGBRegressor()
-
-    # Prepare features and targets for training
-    X_train = df_train[features]
-    X_val = df_val[features]
-    y_train = df_train[target]
-    y_val = df_val[target]
-
-    # Train both models using the training data
-    xgb_model.fit(X_train, y_train)
-    ngb_model.fit(X_train, y_train, X_val=X_val, Y_val=y_val)
-
-    # Make Predictions on the Validation Set
-    print(f"Making Predictions on Validation Set...")
-    y_validate = df_val[target]
-    X_validate = df_val[features]
-    preds = xgb_model.predict(X_validate)
-
-    # Calculate various model performance metrics (regression)
-    rmse = root_mean_squared_error(y_validate, preds)
-    mae = mean_absolute_error(y_validate, preds)
-    r2 = r2_score(y_validate, preds)
-    print(f"RMSE: {rmse:.3f}")
-    print(f"MAE: {mae:.3f}")
-    print(f"R2: {r2:.3f}")
-    print(f"NumRows: {len(df_val)}")
-
-    # Save the trained XGBoost model
-    xgb_model.save_model(os.path.join(args.model_dir, "xgb_model.json"))
-
-    # Save the trained NGBoost model
-    joblib.dump(ngb_model, os.path.join(args.model_dir, "ngb_model.joblib"))
-
-    # Save the feature list to validate input during predictions
-    with open(os.path.join(args.model_dir, "feature_columns.json"), "w") as fp:
-        json.dump(features, fp)
-
-    # Now the Proximity model
-    model = Proximity(df_train, id_column, features, target, track_columns=track_columns)
-
-    # Now serialize the model
-    model.serialize(args.model_dir)
-
-
-#
-# Inference Section
-#
-def model_fn(model_dir) -> dict:
-    """Load and return XGBoost and NGBoost regressors from model directory."""
-
-    # Load XGBoost regressor
-    xgb_path = os.path.join(model_dir, "xgb_model.json")
-    xgb_model = XGBRegressor(enable_categorical=True)
-    xgb_model.load_model(xgb_path)
-
-    # Load NGBoost regressor
-    ngb_model = joblib.load(os.path.join(model_dir, "ngb_model.joblib"))
-
-    # Deserialize the proximity model
-    prox_model = Proximity.deserialize(model_dir)
-
-    return {
-        "xgboost": xgb_model,
-        "ngboost": ngb_model,
-        "proximity": prox_model
-    }
-
-
-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)
-
-    # Match features in a case-insensitive manner
-    matched_df = match_features_case_insensitive(df, model_features)
-
-    # Use XGBoost for point predictions
-    df["prediction"] = models["xgboost"].predict(matched_df[model_features])
-
-    # NGBoost predict returns distribution objects
-    y_dists = models["ngboost"].pred_dist(matched_df[model_features])
-
-    # Extract parameters from distribution
-    dist_params = y_dists.params
-
-    # Extract mean and std from distribution parameters
-    df["prediction_uq"] = dist_params['loc']  # mean
-    df["prediction_std"] = dist_params['scale']  # standard deviation
-
-    # Add 95% prediction intervals using ppf (percent point function)
-    df["q_025"] = y_dists.ppf(0.025)  # 2.5th percentile
-    df["q_975"] = y_dists.ppf(0.975)  # 97.5th percentile
-
-    # Add 50% prediction intervals
-    df["q_25"] = y_dists.ppf(0.25)   # 25th percentile
-    df["q_75"] = y_dists.ppf(0.75)   # 75th percentile
-
-    # Compute Nearest neighbors with Proximity model
-    prox_df = models["proximity"].neighbors(df)
-
-    # Shrink prediction intervals based on KNN variance
-    df = distance_weighted_calibrated_intervals(df, prox_df)
-
-    # Return the modified DataFrame
-    return df

workbench/model_scripts/custom_models/uq_models/mapie_xgb.template

@@ -1,203 +0,0 @@
-# Model: HistGradientBoosting with MAPIE Conformalized Quantile Regression
-from mapie.regression import MapieQuantileRegressor
-from sklearn.ensemble import HistGradientBoostingRegressor
-from sklearn.model_selection import train_test_split
-import numpy as np
-
-# Template Placeholders
-TEMPLATE_PARAMS = {
-    "features": "{{feature_list}}",
-    "target": "{{target_column}}",
-    "train_all_data": "{{train_all_data}}"
-}
-
-from io import StringIO
-import json
-import argparse
-import joblib
-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 DataFrame is empty and raise an error if so."""
-    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 DataFrame columns to match model feature names (case-insensitive).
-    Prioritizes exact matches, then case-insensitive matches.
-    
-    Raises ValueError if any model features cannot be matched.
-    """
-    df_columns_lower = {col.lower(): col for col in df.columns}
-    rename_dict = {}
-    missing = []
-    for feature in model_features:
-        if feature in df.columns:
-            continue  # Exact match
-        elif feature.lower() in df_columns_lower:
-            rename_dict[df_columns_lower[feature.lower()]] = feature
-        else:
-            missing.append(feature)
-    
-    if missing:
-        raise ValueError(f"Features not found: {missing}")
-
-    # Rename the DataFrame columns to match the model features
-    return df.rename(columns=rename_dict)
-
-
-# TRAINING SECTION
-#
-# This section (__main__) is where SageMaker will execute the training job
-# and save the model artifacts to the model directory.
-#
-if __name__ == "__main__":
-    # Template Parameters
-    features = TEMPLATE_PARAMS["features"]
-    target = TEMPLATE_PARAMS["target"]
-    train_all_data = TEMPLATE_PARAMS["train_all_data"]
-    validation_split = 0.2
-
-    # 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()
-
-    # Load training data from the specified directory
-    training_files = [
-        os.path.join(args.train, file)
-        for file in os.listdir(args.train) if file.endswith(".csv")
-    ]
-    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")
-
-    # Training data split logic
-    if train_all_data:
-        # Use all data for both training and validation
-        print("Training on all data...")
-        df_train = df.copy()
-        df_val = df.copy()
-    elif "training" in df.columns:
-        # Split data based on a 'training' column if it exists
-        print("Splitting data based on 'training' column...")
-        df_train = df[df["training"]].copy()
-        df_val = df[~df["training"]].copy()
-    else:
-        # Perform a random split if no 'training' column is found
-        print("Splitting data randomly...")
-        df_train, df_val = train_test_split(df, test_size=validation_split, random_state=42)
-
-    # Create HistGradientBoosting base model configured for quantile regression
-    base_estimator = HistGradientBoostingRegressor(
-        loss='quantile',  # Required for MAPIE CQR
-        quantile=0.5,  # Will be overridden by MAPIE for different quantiles
-        max_iter=1000,
-        max_depth=6,
-        learning_rate=0.01,
-        random_state=42
-    )
-
-    # Create MAPIE CQR predictor - it will create quantile versions internally
-    model = MapieQuantileRegressor(
-        estimator=base_estimator,
-        method="quantile",
-        cv="split",
-        alpha=0.05  # For 95% coverage
-    )
-
-    # Prepare features and targets for training
-    X_train = df_train[features]
-    X_val = df_val[features]
-    y_train = df_train[target]
-    y_val = df_val[target]
-
-    # Fit the MAPIE CQR model (train/calibration is handled internally)
-    model.fit(X_train, y_train)
-
-    # Save the trained model and any necessary assets
-    joblib.dump(model, os.path.join(args.model_dir, "model.joblib"))
-
-    # Save the feature list to validate input during predictions
-    with open(os.path.join(args.model_dir, "feature_columns.json"), "w") as fp:
-        json.dump(features, fp)
-
-
-#
-# Inference Section
-#
-def model_fn(model_dir):
-    """Load and return the model from the specified directory."""
-    return joblib.load(os.path.join(model_dir, "model.joblib"))
-
-
-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, model):
-    """Make predictions using MAPIE CQR and return the DataFrame with results."""
-    model_dir = os.environ.get("SM_MODEL_DIR", "/opt/ml/model")
-
-    # Load feature columns from the saved file
-    with open(os.path.join(model_dir, "feature_columns.json")) as fp:
-        model_features = json.load(fp)
-
-    # Match features in a case-insensitive manner
-    matched_df = match_features_case_insensitive(df, model_features)
-
-    # Get CQR predictions - returns point prediction and intervals
-    X_pred = matched_df[model_features]
-    y_pred, y_pis = model.predict(X_pred)
-
-    # Add predictions to dataframe with 95% intervals
-    df["prediction"] = y_pred
-    df["q_025"] = y_pis[:, 0, 0]  # Lower bound (2.5th percentile)
-    df["q_975"] = y_pis[:, 1, 0]  # Upper bound (97.5th percentile)
-
-    # Calculate std estimate from 95% interval
-    interval_width_95 = df["q_975"] - df["q_025"]
-    df["prediction_std"] = interval_width_95 / 3.92  # 95% CI = ±1.96σ, so width = 3.92σ
-
-    # Calculate 50% intervals using normal approximation
-    df["q_25"] = df["prediction"] - 0.674 * df["prediction_std"]
-    df["q_75"] = df["prediction"] + 0.674 * df["prediction_std"]
-
-    # Return the modified DataFrame
-    return df