workbench 0.8.171__py3-none-any.whl → 0.8.173__py3-none-any.whl

workbench/model_scripts/custom_models/chem_info/tautomerize.py

@@ -1,83 +0,0 @@
-# Model: tautomerization_processor
-#
-# Description: The tautomerization_processor model uses RDKit to perform tautomer enumeration
-#     and canonicalization of chemical compounds. Tautomerization is the chemical process where
-#     compounds can interconvert between structurally distinct forms, often affecting their
-#     chemical properties and reactivity. This model provides a robust approach to identifying
-#     and processing tautomers, crucial for improving molecular modeling and cheminformatics tasks
-#     like virtual screening, QSAR modeling, and property prediction.
-#
-import argparse
-import os
-import joblib
-from io import StringIO
-import pandas as pd
-import json
-
-# Local imports
-from local_utils import tautomerize_smiles
-
-
-# TRAINING SECTION
-#
-# This section (__main__) is where SageMaker will execute the job and save the model artifacts.
-#
-if __name__ == "__main__":
-    # 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()
-
-    # This model doesn't get trained; it's a feature processing 'model'
-
-    # Sagemaker expects a model artifact, so we'll save a placeholder
-    placeholder_model = {}
-    joblib.dump(placeholder_model, os.path.join(args.model_dir, "model.joblib"))
-
-
-# Model loading and prediction functions
-def model_fn(model_dir):
-    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."""
-    use_explicit_na = False
-    if "text/csv" in accept_type:
-        if use_explicit_na:
-            csv_output = output_df.fillna("N/A").to_csv(index=False)  # CSV with N/A for missing values
-        else:
-            csv_output = output_df.to_csv(index=False)
-        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.")
-
-
-# Prediction function
-def predict_fn(df, model):
-    # Perform Tautomerization
-    df = tautomerize_smiles(df)
-    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