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

workbench/model_scripts/custom_models/uq_models/mapie.template

@@ -0,0 +1,502 @@
+# Model: XGBoost for point predictions + LightGBM with MAPIE for conformalized intervals
+from mapie.regression import ConformalizedQuantileRegressor
+from lightgbm import LGBMRegressor
+from xgboost import XGBRegressor
+from sklearn.model_selection import train_test_split
+
+# 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 numpy as np
+import pandas as pd
+from typing import List, Tuple
+
+# Template Placeholders
+TEMPLATE_PARAMS = {
+    "target": "{{target_column}}",
+    "features": "{{feature_list}}",
+    "compressed_features": "{{compressed_features}}",
+    "train_all_data": "{{train_all_data}}"
+}
+
+
+# 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 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 model by decompressing bitstring features
+
+    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.copy()
+    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__":
+    # Template Parameters
+    target = TEMPLATE_PARAMS["target"]
+    features = TEMPLATE_PARAMS["features"]
+    orig_features = features.copy()
+    compressed_features = TEMPLATE_PARAMS["compressed_features"]
+    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}")
+
+    # Prepare features and targets for training
+    X_train = df_train[features]
+    X_validate = df_val[features]
+    y_train = df_train[target]
+    y_validate = df_val[target]
+
+    # Train XGBoost for point predictions
+    print("\nTraining XGBoost for point predictions...")
+    xgb_model = XGBRegressor(
+        n_estimators=1000,
+        max_depth=6,
+        learning_rate=0.01,
+        subsample=0.8,
+        colsample_bytree=0.8,
+        random_state=42,
+        verbosity=0
+    )
+    xgb_model.fit(X_train, y_train)
+
+    # Evaluate XGBoost performance
+    y_pred_xgb = xgb_model.predict(X_validate)
+    xgb_rmse = root_mean_squared_error(y_validate, y_pred_xgb)
+    xgb_mae = mean_absolute_error(y_validate, y_pred_xgb)
+    xgb_r2 = r2_score(y_validate, y_pred_xgb)
+
+    print(f"\nXGBoost Point Prediction Performance:")
+    print(f"RMSE: {xgb_rmse:.3f}")
+    print(f"MAE: {xgb_mae:.3f}")
+    print(f"R2: {xgb_r2:.3f}")
+
+    # Define confidence levels we want to model
+    confidence_levels = [0.50, 0.80, 0.90, 0.95]  # 50%, 80%, 90%, 95% confidence intervals
+
+    # Store MAPIE models for each confidence level
+    mapie_models = {}
+
+    # Train models for each confidence level
+    for confidence_level in confidence_levels:
+        alpha = 1 - confidence_level
+        lower_q = alpha / 2
+        upper_q = 1 - alpha / 2
+
+        print(f"\nTraining quantile models for {confidence_level * 100:.0f}% confidence interval...")
+        print(f"  Quantiles: {lower_q:.3f}, {upper_q:.3f}, 0.500")
+
+        # Train three models for this confidence level
+        quantile_estimators = []
+        for q in [lower_q, upper_q, 0.5]:
+            print(f"    Training model for quantile {q:.3f}...")
+            est = LGBMRegressor(
+                objective="quantile",
+                alpha=q,
+                n_estimators=1000,
+                max_depth=6,
+                learning_rate=0.01,
+                num_leaves=31,
+                min_child_samples=20,
+                subsample=0.8,
+                colsample_bytree=0.8,
+                random_state=42,
+                verbose=-1,
+                force_col_wise=True
+            )
+            est.fit(X_train, y_train)
+            quantile_estimators.append(est)
+
+        # Create MAPIE CQR model for this confidence level
+        print(f"  Setting up MAPIE CQR for {confidence_level * 100:.0f}% confidence...")
+        mapie_model = ConformalizedQuantileRegressor(
+            quantile_estimators,
+            confidence_level=confidence_level,
+            prefit=True
+        )
+
+        # Conformalize the model
+        print(f"  Conformalizing with validation data...")
+        mapie_model.conformalize(X_validate, y_validate)
+
+        # Store the model
+        mapie_models[f"mapie_{confidence_level:.2f}"] = mapie_model
+
+        # Validate coverage for this confidence level
+        y_pred, y_pis = mapie_model.predict_interval(X_validate)
+        coverage = np.mean((y_validate >= y_pis[:, 0, 0]) & (y_validate <= y_pis[:, 1, 0]))
+        print(f"  Coverage: Target={confidence_level * 100:.0f}%, Empirical={coverage * 100:.1f}%")
+
+    print(f"\nOverall Model Performance Summary:")
+    print(f"XGBoost RMSE: {xgb_rmse:.3f}")
+    print(f"XGBoost MAE: {xgb_mae:.3f}")
+    print(f"XGBoost R2: {xgb_r2:.3f}")
+    print(f"NumRows: {len(df_val)}")
+
+    # Analyze interval widths across confidence levels
+    print(f"\nInterval Width Analysis:")
+    for conf_level in confidence_levels:
+        model = mapie_models[f"mapie_{conf_level:.2f}"]
+        _, y_pis = model.predict_interval(X_validate)
+        widths = y_pis[:, 1, 0] - y_pis[:, 0, 0]
+        print(f"  {conf_level * 100:.0f}% CI: Mean width={np.mean(widths):.3f}, Std={np.std(widths):.3f}")
+
+    # Save the trained XGBoost model
+    xgb_model.save_model(os.path.join(args.model_dir, "xgb_model.json"))
+
+    # Save all MAPIE models
+    for model_name, model in mapie_models.items():
+        joblib.dump(model, os.path.join(args.model_dir, f"{model_name}.joblib"))
+
+    # Save the feature list
+    with open(os.path.join(args.model_dir, "feature_columns.json"), "w") as fp:
+        json.dump(features, fp)
+
+    # Save category mappings if any
+    if category_mappings:
+        with open(os.path.join(args.model_dir, "category_mappings.json"), "w") as fp:
+            json.dump(category_mappings, fp)
+
+    # Save model configuration
+    model_config = {
+        "model_type": "XGBoost_MAPIE_CQR_LightGBM",
+        "confidence_levels": confidence_levels,
+        "n_features": len(features),
+        "target": target,
+        "validation_metrics": {
+            "xgb_rmse": float(xgb_rmse),
+            "xgb_mae": float(xgb_mae),
+            "xgb_r2": float(xgb_r2),
+            "n_validation": len(df_val)
+        }
+    }
+    with open(os.path.join(args.model_dir, "model_config.json"), "w") as fp:
+        json.dump(model_config, fp, indent=2)
+
+    print(f"\nModel training complete!")
+    print(f"Saved 1 XGBoost model and {len(mapie_models)} MAPIE models to {args.model_dir}")
+
+
+#
+# Inference Section
+#
+def model_fn(model_dir) -> dict:
+    """Load XGBoost and all MAPIE models from the specified directory."""
+
+    # Load model configuration to know which models to load
+    with open(os.path.join(model_dir, "model_config.json")) as fp:
+        config = json.load(fp)
+
+    # 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 all MAPIE models
+    mapie_models = {}
+    for conf_level in config["confidence_levels"]:
+        model_name = f"mapie_{conf_level:.2f}"
+        mapie_models[model_name] = joblib.load(os.path.join(model_dir, f"{model_name}.joblib"))
+
+    # Load category mappings if they exist
+    category_mappings = {}
+    category_path = os.path.join(model_dir, "category_mappings.json")
+    if os.path.exists(category_path):
+        with open(category_path) as fp:
+            category_mappings = json.load(fp)
+
+    return {
+        "xgb_model": xgb_model,
+        "mapie_models": mapie_models,
+        "confidence_levels": config["confidence_levels"],
+        "category_mappings": category_mappings
+    }
+
+
+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))
+    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:
+        # Convert categorical columns to string to avoid fillna issues
+        for col in output_df.select_dtypes(include=['category']).columns:
+            output_df[col] = output_df[col].astype(str)
+        csv_output = output_df.fillna("N/A").to_csv(index=False)
+        return csv_output, "text/csv"
+    elif "application/json" in accept_type:
+        return output_df.to_json(orient="records"), "application/json"
+    else:
+        raise RuntimeError(f"{accept_type} accept type is not supported by this script.")
+
+
+def predict_fn(df, models) -> pd.DataFrame:
+    """Make predictions using XGBoost for point estimates and MAPIE for conformalized intervals
+
+    Args:
+        df (pd.DataFrame): The input DataFrame
+        models (dict): Dictionary containing XGBoost and MAPIE models
+
+    Returns:
+        pd.DataFrame: DataFrame with XGBoost predictions and conformalized intervals
+    """
+
+    # 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)
+
+    # Apply categorical mappings if they exist
+    if models.get("category_mappings"):
+        matched_df, _ = convert_categorical_types(
+            matched_df,
+            model_features,
+            models["category_mappings"]
+        )
+
+    # Get features for prediction
+    X = matched_df[model_features]
+
+    # Get XGBoost point predictions
+    df["prediction"] = models["xgb_model"].predict(X)
+
+    # Get predictions from each MAPIE model for conformalized intervals
+    for conf_level in models["confidence_levels"]:
+        model_name = f"mapie_{conf_level:.2f}"
+        model = models["mapie_models"][model_name]
+
+        # Get conformalized predictions
+        y_pred, y_pis = model.predict_interval(X)
+
+        # Map confidence levels to quantile names
+        if conf_level == 0.50:  # 50% CI
+            df["q_25"] = y_pis[:, 0, 0]
+            df["q_75"] = y_pis[:, 1, 0]
+        elif conf_level == 0.80:  # 80% CI
+            df["q_10"] = y_pis[:, 0, 0]
+            df["q_90"] = y_pis[:, 1, 0]
+        elif conf_level == 0.90:  # 90% CI
+            df["q_05"] = y_pis[:, 0, 0]
+            df["q_95"] = y_pis[:, 1, 0]
+        elif conf_level == 0.95:  # 95% CI
+            df["q_025"] = y_pis[:, 0, 0]
+            df["q_975"] = y_pis[:, 1, 0]
+
+    # Add median (q_50) from XGBoost prediction
+    df["q_50"] = df["prediction"]
+
+    # Calculate uncertainty metrics based on 95% interval
+    interval_width = df["q_975"] - df["q_025"]
+    df["prediction_std"] = interval_width / 3.92
+
+    # Reorder the quantile columns for easier reading
+    quantile_cols = ["q_025", "q_05", "q_10", "q_25", "q_75", "q_90", "q_95", "q_975"]
+    other_cols = [col for col in df.columns if col not in quantile_cols]
+    df = df[other_cols + quantile_cols]
+
+    # Uncertainty score
+    df["uncertainty_score"] = interval_width / (np.abs(df["prediction"]) + 1e-6)
+
+    # Confidence bands
+    df["confidence_band"] = pd.cut(
+        df["uncertainty_score"],
+        bins=[0, 0.5, 1.0, 2.0, np.inf],
+        labels=["high", "medium", "low", "very_low"]
+    )
+
+    return df

workbench/model_scripts/custom_models/uq_models/meta_uq.template

@@ -1,6 +1,7 @@
 # Model: NGBoost Regressor with Distribution output
 from ngboost import NGBRegressor
-from xgboost import XGBRegressor  # Base Estimator
+from ngboost.distns import Cauchy
+from xgboost import XGBRegressor  # Point Estimator
 from sklearn.model_selection import train_test_split
 
 # Model Performance Scores
@@ -106,8 +107,10 @@ def convert_categorical_types(df: pd.DataFrame, features: list, category_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
+def decompress_features(
+    df: pd.DataFrame, features: List[str], compressed_features: List[str]
+) -> Tuple[pd.DataFrame, List[str]]:
+    """Prepare features for the model by decompressing bitstring features
 
     Args:
         df (pd.DataFrame): The features DataFrame
@@ -132,7 +135,7 @@ def decompress_features(df: pd.DataFrame, features: List[str], compressed_featur
         )
 
     # Decompress the specified compressed features
-    decompressed_features = features
+    decompressed_features = features.copy()
     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.")
@@ -227,7 +230,7 @@ if __name__ == "__main__":
 
     # We're using XGBoost for point predictions and NGBoost for uncertainty quantification
     xgb_model = XGBRegressor()
-    ngb_model = NGBRegressor()
+    ngb_model = NGBRegressor()  # Dist=Cauchy) Seems to give HUGE prediction intervals
 
     # Prepare features and targets for training
     X_train = df_train[features]

workbench/model_scripts/custom_models/uq_models/requirements.txt

@@ -1,3 +1 @@
-# Note: NGBoost is not included in the default inference image, so it must be specified here.
-ngboost
-mapie
+# Note: Most libs are already in the training/inference images, ONLY specify additional libs here

workbench/model_scripts/script_generation.py

@@ -70,6 +70,11 @@ def fill_template(template_path: str, params: dict, output_script: str) -> str:
     # Sanity check to ensure all placeholders were replaced
     if "{{" in template and "}}" in template:
         msg = "Not all template placeholders were replaced. Please check your params."
+
+        # Show which placeholders are still present
+        start = template.index("{{")
+        end = template.index("}}", start) + 2
+        msg += f" Unreplaced placeholder: {template[start:end]}"
         log.critical(msg)
         raise ValueError(msg)
 

workbench/model_scripts/xgb_model/generated_model_script.py

@@ -28,12 +28,12 @@ from typing import List, Tuple
 
 # Template Parameters
 TEMPLATE_PARAMS = {
-    "model_type": "regressor",
-    "target": "udm_asy_res_intrinsic_clearance_ul_per_min_per_mg_protein",
-    "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'],
+    "model_type": "classifier",
+    "target": "class",
+    "features": ['chi2v', 'fr_sulfone', 'chi1v', 'bcut2d_logplow', 'fr_piperzine', 'kappa3', 'smr_vsa1', 'slogp_vsa5', 'fr_ketone_topliss', 'fr_sulfonamd', 'fr_imine', 'fr_benzene', 'fr_ester', 'chi2n', 'labuteasa', 'peoe_vsa2', 'smr_vsa6', 'bcut2d_chglo', 'fr_sh', 'peoe_vsa1', 'fr_allylic_oxid', 'chi4n', 'fr_ar_oh', 'fr_nh0', 'fr_term_acetylene', 'slogp_vsa7', 'slogp_vsa4', 'estate_vsa1', 'vsa_estate4', 'numbridgeheadatoms', 'numheterocycles', 'fr_ketone', 'fr_morpholine', 'fr_guanido', 'estate_vsa2', 'numheteroatoms', 'fr_nitro_arom_nonortho', 'fr_piperdine', 'nocount', 'numspiroatoms', 'fr_aniline', 'fr_thiophene', 'slogp_vsa10', 'fr_amide', 'slogp_vsa2', 'fr_epoxide', 'vsa_estate7', 'fr_ar_coo', 'fr_imidazole', 'fr_nitrile', 'fr_oxazole', 'numsaturatedrings', 'fr_pyridine', 'fr_hoccn', 'fr_ndealkylation1', 'numaliphaticheterocycles', 'fr_phenol', 'maxpartialcharge', 'vsa_estate5', 'peoe_vsa13', 'minpartialcharge', 'qed', 'fr_al_oh', 'slogp_vsa11', 'chi0n', 'fr_bicyclic', 'peoe_vsa12', 'fpdensitymorgan1', 'fr_oxime', 'molwt', 'fr_dihydropyridine', 'smr_vsa5', 'peoe_vsa5', 'fr_nitro', 'hallkieralpha', 'heavyatommolwt', 'fr_alkyl_halide', 'peoe_vsa8', 'fr_nhpyrrole', 'fr_isocyan', 'bcut2d_chghi', 'fr_lactam', 'peoe_vsa11', 'smr_vsa9', 'tpsa', 'chi4v', 'slogp_vsa1', 'phi', 'bcut2d_logphi', 'avgipc', 'estate_vsa11', 'fr_coo', 'bcut2d_mwhi', 'numunspecifiedatomstereocenters', 'vsa_estate10', 'estate_vsa8', 'numvalenceelectrons', 'fr_nh2', 'fr_lactone', 'vsa_estate1', 'estate_vsa4', 'numatomstereocenters', 'vsa_estate8', 'fr_para_hydroxylation', 'peoe_vsa3', 'fr_thiazole', 'peoe_vsa10', 'fr_ndealkylation2', 'slogp_vsa12', 'peoe_vsa9', 'maxestateindex', 'fr_quatn', 'smr_vsa7', 'minestateindex', 'numaromaticheterocycles', 'numrotatablebonds', 'fr_ar_nh', 'fr_ether', 'exactmolwt', 'fr_phenol_noorthohbond', 'slogp_vsa3', 'fr_ar_n', 'sps', 'fr_c_o_nocoo', 'bertzct', 'peoe_vsa7', 'slogp_vsa8', 'numradicalelectrons', 'molmr', 'fr_tetrazole', 'numsaturatedcarbocycles', 'bcut2d_mrhi', 'kappa1', 'numamidebonds', 'fpdensitymorgan2', 'smr_vsa8', 'chi1n', 'estate_vsa6', 'fr_barbitur', 'fr_diazo', 'kappa2', 'chi0', 'bcut2d_mrlow', 'balabanj', 'peoe_vsa4', 'numhacceptors', 'fr_sulfide', 'chi3n', 'smr_vsa2', 'fr_al_oh_notert', 'fr_benzodiazepine', 'fr_phos_ester', 'fr_aldehyde', 'fr_coo2', 'estate_vsa5', 'fr_prisulfonamd', 'numaromaticcarbocycles', 'fr_unbrch_alkane', 'fr_urea', 'fr_nitroso', 'smr_vsa10', 'fr_c_s', 'smr_vsa3', 'fr_methoxy', 'maxabspartialcharge', 'slogp_vsa9', 'heavyatomcount', 'fr_azide', 'chi3v', 'smr_vsa4', 'mollogp', 'chi0v', 'fr_aryl_methyl', 'fr_nh1', 'fpdensitymorgan3', 'fr_furan', 'fr_hdrzine', 'fr_arn', 'numaromaticrings', 'vsa_estate3', 'fr_azo', 'fr_halogen', 'estate_vsa9', 'fr_hdrzone', 'numhdonors', 'fr_alkyl_carbamate', 'fr_isothiocyan', 'minabspartialcharge', 'fr_al_coo', 'ringcount', 'chi1', 'estate_vsa7', 'fr_nitro_arom', 'vsa_estate9', 'minabsestateindex', 'maxabsestateindex', 'vsa_estate6', 'estate_vsa10', 'estate_vsa3', 'fr_n_o', 'fr_amidine', 'fr_thiocyan', 'fr_phos_acid', 'fr_c_o', 'fr_imide', 'numaliphaticrings', 'peoe_vsa6', 'vsa_estate2', 'nhohcount', 'numsaturatedheterocycles', 'slogp_vsa6', 'peoe_vsa14', 'fractioncsp3', 'bcut2d_mwlow', 'numaliphaticcarbocycles', 'fr_priamide', 'nacid', 'nbase', 'naromatom', 'narombond', 'sz', 'sm', 'sv', 'sse', 'spe', 'sare', 'sp', 'si', 'mz', 'mm', 'mv', 'mse', 'mpe', 'mare', 'mp', 'mi', 'xch_3d', 'xch_4d', 'xch_5d', 'xch_6d', 'xch_7d', 'xch_3dv', 'xch_4dv', 'xch_5dv', 'xch_6dv', 'xch_7dv', 'xc_3d', 'xc_4d', 'xc_5d', 'xc_6d', 'xc_3dv', 'xc_4dv', 'xc_5dv', 'xc_6dv', 'xpc_4d', 'xpc_5d', 'xpc_6d', 'xpc_4dv', 'xpc_5dv', 'xpc_6dv', 'xp_0d', 'xp_1d', 'xp_2d', 'xp_3d', 'xp_4d', 'xp_5d', 'xp_6d', 'xp_7d', 'axp_0d', 'axp_1d', 'axp_2d', 'axp_3d', 'axp_4d', 'axp_5d', 'axp_6d', 'axp_7d', 'xp_0dv', 'xp_1dv', 'xp_2dv', 'xp_3dv', 'xp_4dv', 'xp_5dv', 'xp_6dv', 'xp_7dv', 'axp_0dv', 'axp_1dv', 'axp_2dv', 'axp_3dv', 'axp_4dv', 'axp_5dv', 'axp_6dv', 'axp_7dv', 'c1sp1', 'c2sp1', 'c1sp2', 'c2sp2', 'c3sp2', 'c1sp3', 'c2sp3', 'c3sp3', 'c4sp3', 'hybratio', 'fcsp3', 'num_stereocenters', 'num_unspecified_stereocenters', 'num_defined_stereocenters', 'num_r_centers', 'num_s_centers', 'num_stereobonds', 'num_e_bonds', 'num_z_bonds', 'stereo_complexity', 'frac_defined_stereo'],
     "compressed_features": [],
-    "model_metrics_s3_path": "s3://ideaya-sageworks-bucket/models/temp-hlm-phase1-reg-0-80/training",
-    "train_all_data": False
+    "model_metrics_s3_path": "s3://ideaya-sageworks-bucket/models/sol-class-f1-100/training",
+    "train_all_data": True
 }
 
 # Function to check if dataframe is empty

workbench/repl/workbench_shell.py

@@ -41,7 +41,7 @@ from workbench.cached.cached_meta import CachedMeta
 try:
     import rdkit  # noqa
     import mordred  # noqa
-    from workbench.utils import chem_utils
+    from workbench.utils.chem_utils import vis
 
     HAVE_CHEM_UTILS = True
 except ImportError:
@@ -178,12 +178,12 @@ class WorkbenchShell:
 
         # Add cheminformatics utils if available
         if HAVE_CHEM_UTILS:
-            self.commands["show"] = chem_utils.show
+            self.commands["show"] = vis.show
 
     def start(self):
         """Start the Workbench IPython shell"""
         cprint("magenta", "\nWelcome to Workbench!")
-        if self.aws_status is False:
+        if not self.aws_status:
             cprint("red", "AWS Account Connection Failed...Review/Fix the Workbench Config:")
             cprint("red", f"Path: {self.cm.site_config_path}")
             self.show_config()