workbench 0.8.168__py3-none-any.whl → 0.8.192__py3-none-any.whl

workbench/model_scripts/xgb_model/generated_model_script.py

@@ -1,477 +0,0 @@
-# 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,
-    precision_recall_fscore_support,
-    confusion_matrix,
-)
-
-# Classification Encoder
-from sklearn.preprocessing import LabelEncoder
-
-# Scikit Learn Imports
-from sklearn.model_selection import train_test_split
-
-from io import StringIO
-import json
-import argparse
-import joblib
-import os
-import pandas as pd
-from typing import List, Tuple
-
-# Template Parameters
-TEMPLATE_PARAMS = {
-    "model_type": "classifier",
-    "target_column": "class",
-    "features": ['bcut2d_logplow', 'numradicalelectrons', 'smr_vsa5', 'fr_lactam', 'fr_morpholine', 'fr_aldehyde', 'slogp_vsa1', 'fr_amidine', 'bpol', 'fr_ester', 'fr_azo', 'kappa3', 'peoe_vsa5', 'fr_ketone_topliss', 'vsa_estate9', 'estate_vsa9', 'bcut2d_mrhi', 'fr_ndealkylation1', 'numrotatablebonds', 'minestateindex', 'fr_quatn', 'peoe_vsa3', 'fr_epoxide', 'fr_aniline', 'minpartialcharge', 'fr_nitroso', 'fpdensitymorgan2', 'fr_oxime', 'fr_sulfone', 'smr_vsa1', 'kappa1', 'fr_pyridine', 'numaromaticrings', 'vsa_estate6', 'molmr', 'estate_vsa1', 'fr_dihydropyridine', 'vsa_estate10', 'fr_alkyl_halide', 'chi2n', 'fr_thiocyan', 'fpdensitymorgan1', 'fr_unbrch_alkane', 'slogp_vsa9', 'chi4n', 'fr_nitro_arom', 'fr_al_oh', 'fr_furan', 'fr_c_s', 'peoe_vsa8', 'peoe_vsa14', 'numheteroatoms', 'fr_ndealkylation2', 'maxabspartialcharge', 'vsa_estate2', 'peoe_vsa7', 'apol', 'numhacceptors', 'fr_tetrazole', 'vsa_estate1', 'peoe_vsa9', 'naromatom', 'bcut2d_chghi', 'fr_sh', 'fr_halogen', 'slogp_vsa4', 'fr_benzodiazepine', 'molwt', 'fr_isocyan', 'fr_prisulfonamd', 'maxabsestateindex', 'minabsestateindex', 'peoe_vsa11', 'slogp_vsa12', 'estate_vsa5', 'numaliphaticcarbocycles', 'bcut2d_mwlow', 'slogp_vsa7', 'fr_allylic_oxid', 'fr_methoxy', 'fr_nh0', 'fr_coo2', 'fr_phenol', 'nacid', 'nbase', 'chi3v', 'fr_ar_nh', 'fr_nitrile', 'fr_imidazole', 'fr_urea', 'bcut2d_mrlow', 'chi1', 'smr_vsa6', 'fr_aryl_methyl', 'narombond', 'fr_alkyl_carbamate', 'fr_piperzine', 'exactmolwt', 'qed', 'chi0n', 'fr_sulfonamd', 'fr_thiazole', 'numvalenceelectrons', 'fr_phos_acid', 'peoe_vsa12', 'fr_nh1', 'fr_hdrzine', 'fr_c_o_nocoo', 'fr_lactone', 'estate_vsa6', 'bcut2d_logphi', 'vsa_estate7', 'peoe_vsa13', 'numsaturatedcarbocycles', 'fr_nitro', 'fr_phenol_noorthohbond', 'rotratio', 'fr_barbitur', 'fr_isothiocyan', 'balabanj', 'fr_arn', 'fr_imine', 'maxpartialcharge', 'fr_sulfide', 'slogp_vsa11', 'fr_hoccn', 'fr_n_o', 'peoe_vsa1', 'slogp_vsa6', 'heavyatommolwt', 'fractioncsp3', 'estate_vsa8', 'peoe_vsa10', 'numaliphaticrings', 'fr_thiophene', 'maxestateindex', 'smr_vsa10', 'labuteasa', 'smr_vsa2', 'fpdensitymorgan3', 'smr_vsa9', 'slogp_vsa10', 'numaromaticheterocycles', 'fr_nh2', 'fr_diazo', 'chi3n', 'fr_ar_coo', 'slogp_vsa5', 'fr_bicyclic', 'fr_amide', 'estate_vsa10', 'fr_guanido', 'chi1n', 'numsaturatedrings', 'fr_piperdine', 'fr_term_acetylene', 'estate_vsa4', 'slogp_vsa3', 'fr_coo', 'fr_ether', 'estate_vsa7', 'bcut2d_chglo', 'fr_oxazole', 'peoe_vsa6', 'hallkieralpha', 'peoe_vsa2', 'chi2v', 'nocount', 'vsa_estate5', 'fr_nhpyrrole', 'fr_al_coo', 'bertzct', 'estate_vsa11', 'minabspartialcharge', 'slogp_vsa8', 'fr_imide', 'kappa2', 'numaliphaticheterocycles', 'numsaturatedheterocycles', 'fr_hdrzone', 'smr_vsa4', 'fr_ar_n', 'nrot', 'smr_vsa8', 'slogp_vsa2', 'chi4v', 'fr_phos_ester', 'fr_para_hydroxylation', 'smr_vsa3', 'nhohcount', 'estate_vsa2', 'mollogp', 'tpsa', 'fr_azide', 'peoe_vsa4', 'numhdonors', 'fr_al_oh_notert', 'fr_c_o', 'chi0', 'fr_nitro_arom_nonortho', 'vsa_estate3', 'fr_benzene', 'fr_ketone', 'vsa_estate8', 'smr_vsa7', 'fr_ar_oh', 'fr_priamide', 'ringcount', 'estate_vsa3', 'numaromaticcarbocycles', 'bcut2d_mwhi', 'chi1v', 'heavyatomcount', 'vsa_estate4', 'chi0v', 'pred_pka_reg'],
-    "compressed_features": [],
-    "model_metrics_s3_path": "s3://ideaya-sageworks-bucket/models/sol-with-pka-class-100-test/training",
-    "train_all_data": True
-}
-
-# 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 expand_proba_column(df: pd.DataFrame, class_labels: List[str]) -> pd.DataFrame:
-    """
-    Expands a column in a DataFrame containing a list of probabilities into separate columns.
-
-    Args:
-        df (pd.DataFrame): DataFrame containing a "pred_proba" column
-        class_labels (List[str]): List of class labels
-
-    Returns:
-        pd.DataFrame: DataFrame with the "pred_proba" expanded into separate columns
-    """
-
-    # Sanity check
-    proba_column = "pred_proba"
-    if proba_column not in df.columns:
-        raise ValueError('DataFrame does not contain a "pred_proba" column')
-
-    # Construct new column names with '_proba' suffix
-    proba_splits = [f"{label}_proba" for label in class_labels]
-
-    # Expand the proba_column into separate columns for each probability
-    proba_df = pd.DataFrame(df[proba_column].tolist(), columns=proba_splits)
-
-    # Drop any proba columns and reset the index in prep for the concat
-    df = df.drop(columns=[proba_column]+proba_splits, errors="ignore")
-    df = df.reset_index(drop=True)
-
-    # Concatenate the new columns with the original DataFrame
-    df = pd.concat([df, proba_df], axis=1)
-    print(df)
-    return df
-
-
-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}")
-    
-    return df.rename(columns=rename_dict)
-
-
-def convert_categorical_types(df: pd.DataFrame, features: list, category_mappings={}) -> tuple:
-    """
-    Converts appropriate columns to categorical type with consistent mappings.
-
-    Args:
-        df (pd.DataFrame): The DataFrame to process.
-        features (list): List of feature names to consider for conversion.
-        category_mappings (dict, optional): Existing category mappings. If empty dict, we're in
-                                            training mode. If populated, we're in inference mode.
-
-    Returns:
-        tuple: (processed DataFrame, category mappings dictionary)
-    """
-    # Training mode
-    if category_mappings == {}:
-        for col in df.select_dtypes(include=["object", "string"]):
-            if col in features and df[col].nunique() < 20:
-                print(f"Training mode: Converting {col} to category")
-                df[col] = df[col].astype("category")
-                category_mappings[col] = df[col].cat.categories.tolist()  # Store category mappings
-
-    # Inference mode
-    else:
-        for col, categories in category_mappings.items():
-            if col in df.columns:
-                print(f"Inference mode: Applying categorical mapping for {col}")
-                df[col] = pd.Categorical(df[col], categories=categories)  # Apply consistent categorical mapping
-
-    return df, category_mappings
-
-
-def decompress_features(df: pd.DataFrame, features: List[str], compressed_features: List[str]) -> Tuple[pd.DataFrame, List[str]]:
-    """Prepare features for the XGBoost model
-
-    Args:
-        df (pd.DataFrame): The features DataFrame
-        features (List[str]): Full list of feature names
-        compressed_features (List[str]): List of feature names to decompress (bitstrings)
-
-    Returns:
-        pd.DataFrame: DataFrame with the decompressed features
-        List[str]: Updated list of feature names after decompression
-
-    Raises:
-        ValueError: If any missing values are found in the specified features
-    """
-
-    # Check for any missing values in the required features
-    missing_counts = df[features].isna().sum()
-    if missing_counts.any():
-        missing_features = missing_counts[missing_counts > 0]
-        print(
-            f"WARNING: Found missing values in features: {missing_features.to_dict()}. "
-            "WARNING: You might want to remove/replace all NaN values before processing."
-        )
-
-    # Decompress the specified compressed features
-    decompressed_features = features
-    for feature in compressed_features:
-        if (feature not in df.columns) or (feature not in features):
-            print(f"Feature '{feature}' not in the features list, skipping decompression.")
-            continue
-
-        # Remove the feature from the list of features to avoid duplication
-        decompressed_features.remove(feature)
-
-        # Handle all compressed features as bitstrings
-        bit_matrix = np.array([list(bitstring) for bitstring in df[feature]], dtype=np.uint8)
-        prefix = feature[:3]
-
-        # Create all new columns at once - avoids fragmentation
-        new_col_names = [f"{prefix}_{i}" for i in range(bit_matrix.shape[1])]
-        new_df = pd.DataFrame(bit_matrix, columns=new_col_names, index=df.index)
-
-        # Add to features list
-        decompressed_features.extend(new_col_names)
-
-        # Drop original column and concatenate new ones
-        df = df.drop(columns=[feature])
-        df = pd.concat([df, new_df], axis=1)
-
-    return df, decompressed_features
-
-
-if __name__ == "__main__":
-    """The main function is for training the XGBoost model"""
-
-    # Harness Template Parameters
-    target = TEMPLATE_PARAMS["target_column"]
-    features = TEMPLATE_PARAMS["features"]
-    orig_features = features.copy()
-    compressed_features = TEMPLATE_PARAMS["compressed_features"]
-    model_type = TEMPLATE_PARAMS["model_type"]
-    model_metrics_s3_path = TEMPLATE_PARAMS["model_metrics_s3_path"]
-    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()
-
-    # 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
-    all_df = pd.concat([pd.read_csv(file, engine="python") for file in training_files])
-
-    # Check if the dataframe is empty
-    check_dataframe(all_df, "training_df")
-
-    # Features/Target output
-    print(f"Target: {target}")
-    print(f"Features: {str(features)}")
-
-    # Convert any features that might be categorical to 'category' type
-    all_df, category_mappings = convert_categorical_types(all_df, features)
-
-    # If we have compressed features, decompress them
-    if compressed_features:
-        print(f"Decompressing features {compressed_features}...")
-        all_df, features = decompress_features(all_df, features, compressed_features)
-
-    # Do we want to train on all the data?
-    if train_all_data:
-        print("Training on ALL of the data")
-        df_train = all_df.copy()
-        df_val = all_df.copy()
-
-    # Does the dataframe have a training column?
-    elif "training" in all_df.columns:
-        print("Found training column, splitting data based on training column")
-        df_train = all_df[all_df["training"]]
-        df_val = all_df[~all_df["training"]]
-    else:
-        # Just do a random training Split
-        print("WARNING: No training column found, splitting data with random state=42")
-        df_train, df_val = train_test_split(
-            all_df, test_size=validation_split, random_state=42
-        )
-    print(f"FIT/TRAIN: {df_train.shape}")
-    print(f"VALIDATION: {df_val.shape}")
-
-    # Now spin up our XGB Model
-    if model_type == "classifier":
-        xgb_model = xgb.XGBClassifier(enable_categorical=True)
-
-        # Encode the target column
-        label_encoder = LabelEncoder()
-        df_train[target] = label_encoder.fit_transform(df_train[target])
-        df_val[target] = label_encoder.transform(df_val[target])
-
-    else:
-        xgb_model = xgb.XGBRegressor(enable_categorical=True)
-        label_encoder = None  # We don't need this for regression
-
-    # Grab our Features, Target and Train the Model
-    y_train = df_train[target]
-    X_train= df_train[features]
-    xgb_model.fit(X_train, y_train)
-
-    # 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)
-    if model_type == "classifier":
-        # Also get the probabilities for each class
-        print("Processing Probabilities...")
-        probs = xgb_model.predict_proba(X_validate)
-        df_val["pred_proba"] = [p.tolist() for p in probs]
-
-        # Expand the pred_proba column into separate columns for each class
-        print(df_val.columns)
-        df_val = expand_proba_column(df_val, label_encoder.classes_)
-        print(df_val.columns)
-
-        # Decode the target and prediction labels
-        y_validate = label_encoder.inverse_transform(y_validate)
-        preds = label_encoder.inverse_transform(preds)
-
-    # Save predictions to S3 (just the target, prediction, and '_proba' columns)
-    df_val["prediction"] = preds
-    output_columns = [target, "prediction"]
-    output_columns += [col for col in df_val.columns if col.endswith("_proba")]
-    wr.s3.to_csv(
-        df_val[output_columns],
-        path=f"{model_metrics_s3_path}/validation_predictions.csv",
-        index=False,
-    )
-
-    # Report Performance Metrics
-    if model_type == "classifier":
-        # Get the label names and their integer mapping
-        label_names = label_encoder.classes_
-
-        # Calculate various model performance metrics
-        scores = precision_recall_fscore_support(
-            y_validate, preds, average=None, labels=label_names
-        )
-
-        # Put the scores into a dataframe
-        score_df = pd.DataFrame(
-            {
-                target: label_names,
-                "precision": scores[0],
-                "recall": scores[1],
-                "fscore": scores[2],
-                "support": scores[3],
-            }
-        )
-
-        # We need to get creative with the Classification Metrics
-        metrics = ["precision", "recall", "fscore", "support"]
-        for t in label_names:
-            for m in metrics:
-                value = score_df.loc[score_df[target] == t, m].iloc[0]
-                print(f"Metrics:{t}:{m} {value}")
-
-        # Compute and output the confusion matrix
-        conf_mtx = confusion_matrix(y_validate, preds, labels=label_names)
-        for i, row_name in enumerate(label_names):
-            for j, col_name in enumerate(label_names):
-                value = conf_mtx[i, j]
-                print(f"ConfusionMatrix:{row_name}:{col_name} {value}")
-
-    else:
-        # 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)}")
-
-    # Now save the model to the standard place/name
-    xgb_model.save_model(os.path.join(args.model_dir, "xgb_model.json"))
-    if label_encoder:
-        joblib.dump(label_encoder, os.path.join(args.model_dir, "label_encoder.joblib"))
-
-    # 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(orig_features, fp)  # We save the original features, not the decompressed ones
-
-    # Save the category mappings
-    with open(os.path.join(args.model_dir, "category_mappings.json"), "w") as fp:
-        json.dump(category_mappings, fp)
-
-
-def model_fn(model_dir):
-    """Deserialize and return fitted XGBoost model"""
-
-    model_path = os.path.join(model_dir, "xgb_model.json")
-
-    with open(model_path, "r") as f:
-        model_json = json.load(f)
-
-    sklearn_data = model_json['learner']['attributes']['scikit_learn']
-    model_type = json.loads(sklearn_data)['_estimator_type']
-
-    model_class = xgb.XGBClassifier if model_type == "classifier" else xgb.XGBRegressor
-    model = model_class(enable_categorical=True)
-    model.load_model(model_path)
-
-    return 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, model) -> pd.DataFrame:
-    """Make Predictions with our XGB Model
-
-    Args:
-        df (pd.DataFrame): The input DataFrame
-        model: The model use for predictions
-
-    Returns:
-        pd.DataFrame: The DataFrame with the predictions added
-    """
-    compressed_features = TEMPLATE_PARAMS["compressed_features"]
-
-    # 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:
-        features = json.load(fp)
-    print(f"Model Features: {features}")
-
-    # Load the category mappings (from training)
-    with open(os.path.join(model_dir, "category_mappings.json")) as fp:
-        category_mappings = json.load(fp)
-
-    # Load our Label Encoder if we have one
-    label_encoder = None
-    if os.path.exists(os.path.join(model_dir, "label_encoder.joblib")):
-        label_encoder = joblib.load(os.path.join(model_dir, "label_encoder.joblib"))
-
-    # 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, features)
-
-    # Detect categorical types in the incoming DataFrame
-    matched_df, _ = convert_categorical_types(matched_df, features, category_mappings)
-
-    # If we have compressed features, decompress them
-    if compressed_features:
-        print("Decompressing features for prediction...")
-        matched_df, features = decompress_features(matched_df, features, compressed_features)
-
-    # Predict the features against our XGB Model
-    X = matched_df[features]
-    predictions = model.predict(X)
-
-    # If we have a label encoder, decode the predictions
-    if label_encoder:
-        predictions = label_encoder.inverse_transform(predictions)
-
-    # Set the predictions on the DataFrame
-    df["prediction"] = predictions
-
-    # Does our model have a 'predict_proba' method? If so we will call it and add the results to the DataFrame
-    if getattr(model, "predict_proba", None):
-        probs = model.predict_proba(matched_df[features])
-        df["pred_proba"] = [p.tolist() for p in probs]
-
-        # Expand the pred_proba column into separate columns for each class
-        df = expand_proba_column(df, label_encoder.classes_)
-
-    # All done, return the DataFrame with new columns for the predictions
-    return df