workbench 0.8.224__py3-none-any.whl → 0.8.231__py3-none-any.whl

workbench/model_scripts/pytorch_model/generated_model_script.py

@@ -59,12 +59,12 @@ DEFAULT_HYPERPARAMETERS = {
 
 # Template parameters (filled in by Workbench)
 TEMPLATE_PARAMS = {
-    "model_type": "uq_regressor",
-    "target": "udm_asy_res_efflux_ratio",
+    "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'],
     "id_column": "udm_mol_bat_id",
     "compressed_features": [],
-    "model_metrics_s3_path": "s3://ideaya-sageworks-bucket/models/caco2-er-pytorch-260113/training",
+    "model_metrics_s3_path": "s3://ideaya-sageworks-bucket/models/caco2-er-class-pytorch-1-fr/training",
     "hyperparameters": {},
 }
 
@@ -152,24 +152,30 @@ def predict_fn(df: pd.DataFrame, model_dict: dict) -> pd.DataFrame:
         print("Decompressing features for prediction...")
         matched_df, features = decompress_features(matched_df, features, compressed_features)
 
-    # Track missing features
-    missing_mask = matched_df[features].isna().any(axis=1)
-    if missing_mask.any():
-        print(f"Warning: {missing_mask.sum()} rows have missing features")
+    # Impute missing values (categorical with mode, continuous handled by scaler)
+    missing_counts = matched_df[features].isna().sum()
+    if missing_counts.any():
+        missing_features = missing_counts[missing_counts > 0]
+        print(f"Imputing missing values: {missing_features.to_dict()}")
+
+        # Load categorical imputation values if available
+        impute_path = os.path.join(model_dir, "categorical_impute.json")
+        if os.path.exists(impute_path):
+            with open(impute_path) as f:
+                cat_impute_values = json.load(f)
+            for col in categorical_cols:
+                if col in cat_impute_values and matched_df[col].isna().any():
+                    matched_df[col] = matched_df[col].fillna(cat_impute_values[col])
+        # Continuous features are imputed by FeatureScaler.transform() using column means
 
     # Initialize output columns
     df["prediction"] = np.nan
     if model_type in ["regressor", "uq_regressor"]:
         df["prediction_std"] = np.nan
 
-    complete_df = matched_df[~missing_mask].copy()
-    if len(complete_df) == 0:
-        print("Warning: No complete rows to predict on")
-        return df
-
-    # Prepare data for inference (with standardization)
+    # Prepare data for inference (with standardization and continuous imputation)
     x_cont, x_cat, _, _, _ = prepare_data(
-        complete_df, continuous_cols, categorical_cols, category_mappings=category_mappings, scaler=scaler
+        matched_df, continuous_cols, categorical_cols, category_mappings=category_mappings, scaler=scaler
     )
 
     # Collect ensemble predictions
@@ -191,28 +197,20 @@ def predict_fn(df: pd.DataFrame, model_dict: dict) -> pd.DataFrame:
         class_preds = np.argmax(avg_probs, axis=1)
         predictions = label_encoder.inverse_transform(class_preds)
 
-        all_proba = pd.Series([None] * len(df), index=df.index, dtype=object)
-        all_proba.loc[~missing_mask] = [p.tolist() for p in avg_probs]
-        df["pred_proba"] = all_proba
+        df["pred_proba"] = [p.tolist() for p in avg_probs]
         df = expand_proba_column(df, label_encoder.classes_)
     else:
         # Regression
         predictions = preds.flatten()
-        df.loc[~missing_mask, "prediction_std"] = preds_std.flatten()
+        df["prediction_std"] = preds_std.flatten()
 
         # Add UQ intervals if available
         if uq_models and uq_metadata:
-            X_complete = complete_df[features]
-            df_complete = df.loc[~missing_mask].copy()
-            df_complete["prediction"] = predictions  # Set prediction before compute_confidence
-            df_complete = predict_intervals(df_complete, X_complete, uq_models, uq_metadata)
-            df_complete = compute_confidence(df_complete, uq_metadata["median_interval_width"], "q_10", "q_90")
-            # Copy UQ columns back to main dataframe
-            for col in df_complete.columns:
-                if col.startswith("q_") or col == "confidence":
-                    df.loc[~missing_mask, col] = df_complete[col].values
-
-    df.loc[~missing_mask, "prediction"] = predictions
+            df["prediction"] = predictions  # Set prediction before compute_confidence
+            df = predict_intervals(df, matched_df[features], uq_models, uq_metadata)
+            df = compute_confidence(df, uq_metadata["median_interval_width"], "q_10", "q_90")
+
+    df["prediction"] = predictions
     return df
 
 
@@ -275,11 +273,11 @@ if __name__ == "__main__":
     all_df = pd.concat([pd.read_csv(f, engine="python") for f in training_files])
     check_dataframe(all_df, "training_df")
 
-    # Drop rows with missing features
+    # Drop rows with missing target (required for training)
     initial_count = len(all_df)
-    all_df = all_df.dropna(subset=features)
+    all_df = all_df.dropna(subset=[target])
     if len(all_df) < initial_count:
-        print(f"Dropped {initial_count - len(all_df)} rows with missing features")
+        print(f"Dropped {initial_count - len(all_df)} rows with missing target")
 
     print(f"Target: {target}")
     print(f"Features: {features}")
@@ -301,6 +299,23 @@ if __name__ == "__main__":
     print(f"Categorical: {categorical_cols}")
     print(f"Continuous: {len(continuous_cols)} columns")
 
+    # Report and handle missing values in features
+    # Compute categorical imputation values (mode) for use at inference time
+    cat_impute_values = {}
+    for col in categorical_cols:
+        mode_val = all_df[col].mode().iloc[0] if not all_df[col].mode().empty else all_df[col].cat.categories[0]
+        cat_impute_values[col] = str(mode_val)  # Convert to string for JSON serialization
+
+    missing_counts = all_df[features].isna().sum()
+    if missing_counts.any():
+        missing_features = missing_counts[missing_counts > 0]
+        print(f"Missing values in features (will be imputed): {missing_features.to_dict()}")
+        # Impute categorical features with mode (most frequent value)
+        for col in categorical_cols:
+            if all_df[col].isna().any():
+                all_df[col] = all_df[col].fillna(cat_impute_values[col])
+        # Continuous features are imputed by FeatureScaler.transform() using column means
+
     # -------------------------------------------------------------------------
     # Classification setup
     # -------------------------------------------------------------------------
@@ -506,6 +521,9 @@ if __name__ == "__main__":
     with open(os.path.join(args.model_dir, "feature_metadata.json"), "w") as f:
         json.dump({"continuous_cols": continuous_cols, "categorical_cols": categorical_cols}, f)
 
+    with open(os.path.join(args.model_dir, "categorical_impute.json"), "w") as f:
+        json.dump(cat_impute_values, f)
+
     with open(os.path.join(args.model_dir, "hyperparameters.json"), "w") as f:
         json.dump(hyperparameters, f, indent=2)
 

workbench/model_scripts/pytorch_model/model_script_utils.py

@@ -249,6 +249,36 @@ def output_fn(output_df: pd.DataFrame, accept_type: str) -> tuple[str, str]:
         raise RuntimeError(f"{accept_type} accept type is not supported by this script.")
 
 
+def cap_std_outliers(std_array: np.ndarray) -> np.ndarray:
+    """Cap extreme outliers in prediction_std using IQR method.
+
+    Uses the standard IQR fence (Q3 + 1.5*IQR) to cap extreme values.
+    This prevents unreasonably large std values while preserving the
+    relative ordering and keeping meaningful high-uncertainty signals.
+
+    Args:
+        std_array: Array of standard deviations (n_samples,) or (n_samples, n_targets)
+
+    Returns:
+        Array with outliers capped at the upper fence
+    """
+    if std_array.ndim == 1:
+        std_array = std_array.reshape(-1, 1)
+        squeeze = True
+    else:
+        squeeze = False
+
+    capped = std_array.copy()
+    for col in range(capped.shape[1]):
+        col_data = capped[:, col]
+        q1, q3 = np.percentile(col_data, [25, 75])
+        iqr = q3 - q1
+        upper_bound = q3 + 1.5 * iqr
+        capped[:, col] = np.minimum(col_data, upper_bound)
+
+    return capped.squeeze() if squeeze else capped
+
+
 def compute_regression_metrics(y_true: np.ndarray, y_pred: np.ndarray) -> dict[str, float]:
     """Compute standard regression metrics.
 

workbench/model_scripts/pytorch_model/pytorch.template

@@ -152,24 +152,30 @@ def predict_fn(df: pd.DataFrame, model_dict: dict) -> pd.DataFrame:
         print("Decompressing features for prediction...")
         matched_df, features = decompress_features(matched_df, features, compressed_features)
 
-    # Track missing features
-    missing_mask = matched_df[features].isna().any(axis=1)
-    if missing_mask.any():
-        print(f"Warning: {missing_mask.sum()} rows have missing features")
+    # Impute missing values (categorical with mode, continuous handled by scaler)
+    missing_counts = matched_df[features].isna().sum()
+    if missing_counts.any():
+        missing_features = missing_counts[missing_counts > 0]
+        print(f"Imputing missing values: {missing_features.to_dict()}")
+
+        # Load categorical imputation values if available
+        impute_path = os.path.join(model_dir, "categorical_impute.json")
+        if os.path.exists(impute_path):
+            with open(impute_path) as f:
+                cat_impute_values = json.load(f)
+            for col in categorical_cols:
+                if col in cat_impute_values and matched_df[col].isna().any():
+                    matched_df[col] = matched_df[col].fillna(cat_impute_values[col])
+        # Continuous features are imputed by FeatureScaler.transform() using column means
 
     # Initialize output columns
     df["prediction"] = np.nan
     if model_type in ["regressor", "uq_regressor"]:
         df["prediction_std"] = np.nan
 
-    complete_df = matched_df[~missing_mask].copy()
-    if len(complete_df) == 0:
-        print("Warning: No complete rows to predict on")
-        return df
-
-    # Prepare data for inference (with standardization)
+    # Prepare data for inference (with standardization and continuous imputation)
     x_cont, x_cat, _, _, _ = prepare_data(
-        complete_df, continuous_cols, categorical_cols, category_mappings=category_mappings, scaler=scaler
+        matched_df, continuous_cols, categorical_cols, category_mappings=category_mappings, scaler=scaler
     )
 
     # Collect ensemble predictions
@@ -191,28 +197,20 @@ def predict_fn(df: pd.DataFrame, model_dict: dict) -> pd.DataFrame:
         class_preds = np.argmax(avg_probs, axis=1)
         predictions = label_encoder.inverse_transform(class_preds)
 
-        all_proba = pd.Series([None] * len(df), index=df.index, dtype=object)
-        all_proba.loc[~missing_mask] = [p.tolist() for p in avg_probs]
-        df["pred_proba"] = all_proba
+        df["pred_proba"] = [p.tolist() for p in avg_probs]
         df = expand_proba_column(df, label_encoder.classes_)
     else:
         # Regression
         predictions = preds.flatten()
-        df.loc[~missing_mask, "prediction_std"] = preds_std.flatten()
+        df["prediction_std"] = preds_std.flatten()
 
         # Add UQ intervals if available
         if uq_models and uq_metadata:
-            X_complete = complete_df[features]
-            df_complete = df.loc[~missing_mask].copy()
-            df_complete["prediction"] = predictions  # Set prediction before compute_confidence
-            df_complete = predict_intervals(df_complete, X_complete, uq_models, uq_metadata)
-            df_complete = compute_confidence(df_complete, uq_metadata["median_interval_width"], "q_10", "q_90")
-            # Copy UQ columns back to main dataframe
-            for col in df_complete.columns:
-                if col.startswith("q_") or col == "confidence":
-                    df.loc[~missing_mask, col] = df_complete[col].values
-
-    df.loc[~missing_mask, "prediction"] = predictions
+            df["prediction"] = predictions  # Set prediction before compute_confidence
+            df = predict_intervals(df, matched_df[features], uq_models, uq_metadata)
+            df = compute_confidence(df, uq_metadata["median_interval_width"], "q_10", "q_90")
+
+    df["prediction"] = predictions
     return df
 
 
@@ -275,11 +273,11 @@ if __name__ == "__main__":
     all_df = pd.concat([pd.read_csv(f, engine="python") for f in training_files])
     check_dataframe(all_df, "training_df")
 
-    # Drop rows with missing features
+    # Drop rows with missing target (required for training)
     initial_count = len(all_df)
-    all_df = all_df.dropna(subset=features)
+    all_df = all_df.dropna(subset=[target])
     if len(all_df) < initial_count:
-        print(f"Dropped {initial_count - len(all_df)} rows with missing features")
+        print(f"Dropped {initial_count - len(all_df)} rows with missing target")
 
     print(f"Target: {target}")
     print(f"Features: {features}")
@@ -301,6 +299,23 @@ if __name__ == "__main__":
     print(f"Categorical: {categorical_cols}")
     print(f"Continuous: {len(continuous_cols)} columns")
 
+    # Report and handle missing values in features
+    # Compute categorical imputation values (mode) for use at inference time
+    cat_impute_values = {}
+    for col in categorical_cols:
+        mode_val = all_df[col].mode().iloc[0] if not all_df[col].mode().empty else all_df[col].cat.categories[0]
+        cat_impute_values[col] = str(mode_val)  # Convert to string for JSON serialization
+
+    missing_counts = all_df[features].isna().sum()
+    if missing_counts.any():
+        missing_features = missing_counts[missing_counts > 0]
+        print(f"Missing values in features (will be imputed): {missing_features.to_dict()}")
+        # Impute categorical features with mode (most frequent value)
+        for col in categorical_cols:
+            if all_df[col].isna().any():
+                all_df[col] = all_df[col].fillna(cat_impute_values[col])
+        # Continuous features are imputed by FeatureScaler.transform() using column means
+
     # -------------------------------------------------------------------------
     # Classification setup
     # -------------------------------------------------------------------------
@@ -506,6 +521,9 @@ if __name__ == "__main__":
     with open(os.path.join(args.model_dir, "feature_metadata.json"), "w") as f:
         json.dump({"continuous_cols": continuous_cols, "categorical_cols": categorical_cols}, f)
 
+    with open(os.path.join(args.model_dir, "categorical_impute.json"), "w") as f:
+        json.dump(cat_impute_values, f)
+
     with open(os.path.join(args.model_dir, "hyperparameters.json"), "w") as f:
         json.dump(hyperparameters, f, indent=2)
 

workbench/model_scripts/pytorch_model/uq_harness.py

@@ -22,7 +22,6 @@ import joblib
 from lightgbm import LGBMRegressor
 from mapie.regression import ConformalizedQuantileRegressor
 
-
 # Default confidence levels for prediction intervals
 DEFAULT_CONFIDENCE_LEVELS = [0.50, 0.68, 0.80, 0.90, 0.95]
 

workbench/model_scripts/script_generation.py

@@ -6,7 +6,6 @@ import logging
 from pathlib import Path
 import importlib.util
 
-
 # Setup the logger
 log = logging.getLogger("workbench")
 

workbench/model_scripts/xgb_model/model_script_utils.py

@@ -249,6 +249,36 @@ def output_fn(output_df: pd.DataFrame, accept_type: str) -> tuple[str, str]:
         raise RuntimeError(f"{accept_type} accept type is not supported by this script.")
 
 
+def cap_std_outliers(std_array: np.ndarray) -> np.ndarray:
+    """Cap extreme outliers in prediction_std using IQR method.
+
+    Uses the standard IQR fence (Q3 + 1.5*IQR) to cap extreme values.
+    This prevents unreasonably large std values while preserving the
+    relative ordering and keeping meaningful high-uncertainty signals.
+
+    Args:
+        std_array: Array of standard deviations (n_samples,) or (n_samples, n_targets)
+
+    Returns:
+        Array with outliers capped at the upper fence
+    """
+    if std_array.ndim == 1:
+        std_array = std_array.reshape(-1, 1)
+        squeeze = True
+    else:
+        squeeze = False
+
+    capped = std_array.copy()
+    for col in range(capped.shape[1]):
+        col_data = capped[:, col]
+        q1, q3 = np.percentile(col_data, [25, 75])
+        iqr = q3 - q1
+        upper_bound = q3 + 1.5 * iqr
+        capped[:, col] = np.minimum(col_data, upper_bound)
+
+    return capped.squeeze() if squeeze else capped
+
+
 def compute_regression_metrics(y_true: np.ndarray, y_pred: np.ndarray) -> dict[str, float]:
     """Compute standard regression metrics.
 

workbench/model_scripts/xgb_model/uq_harness.py

@@ -22,7 +22,6 @@ import joblib
 from lightgbm import LGBMRegressor
 from mapie.regression import ConformalizedQuantileRegressor
 
-
 # Default confidence levels for prediction intervals
 DEFAULT_CONFIDENCE_LEVELS = [0.50, 0.68, 0.80, 0.90, 0.95]
 

workbench/themes/dark/custom.css

@@ -3,6 +3,7 @@ h1, h2, h3, h4 {
 }
 body {
     color: rgb(180, 180, 180); /* We want the text dim white */
+    background: linear-gradient(90deg, rgb(45, 45, 45) 0%, rgb(35, 35, 35) 100%);
 }
 
 /* Custom CSS to style bold text */
@@ -36,21 +37,38 @@ a:hover {
 
 /* AgGrid custom CSS */
 
-/* There's a one pixel border around the grid that we want to remove */
-.ag-root-wrapper {
-    border: none !important; /* Force removal with !important */
-}
-
-
-/* Box shadow and rounded corners for all AgGrid themes */
+/* AG Grid 33+ uses CSS variables for theming - set them at the theme level */
 [class*="ag-theme-"] {
+    --ag-background-color: rgb(40, 40, 40);
+    --ag-odd-row-background-color: rgb(40, 40, 40);
+    --ag-row-background-color: rgb(50, 50, 50);
+    --ag-selected-row-background-color: rgb(60, 70, 90);
+    --ag-row-hover-color: rgb(55, 55, 65);
+    --ag-header-background-color: rgb(35, 35, 35);
+    --ag-border-color: rgba(80, 80, 80, 0.5);
+    --ag-foreground-color: rgb(180, 180, 180);
+    --ag-header-foreground-color: rgb(220, 220, 220);
+    --ag-wrapper-border-radius: 12px;
+
+    /* Box shadow and rounded corners */
     box-shadow: 2px 2px 6px 5px rgba(0, 0, 0, 0.25);
-    border-radius: 12px; /* Rounded corners */
+    border-radius: 12px;
     border: 0.5px solid rgba(0, 0, 0, 0.5);
     margin: 0;
     padding: 0;
 }
 
+/* Remove border from the grid wrapper */
+.ag-root-wrapper {
+    border: none !important;
+}
+
+/* AG Grid container - remove padding but allow shadow overflow */
+div:has(> [class*="ag-theme-"]) {
+    padding: 0 !important;
+    overflow: visible !important;
+}
+
 /* Apply styling to Workbench containers */
 .workbench-container {
     box-shadow: 2px 2px 6px 5px rgba(0, 0, 0, 0.25);
@@ -110,6 +128,40 @@ a:hover {
     color: rgb(100, 255, 100);
 }
 
+/* Dropdown styling (dcc.Dropdown) - override Bootstrap's variables */
+.dash-dropdown {
+    --bs-body-bg: rgb(35, 35, 35);
+    --bs-body-color: rgb(210, 210, 210);
+    --bs-border-color: rgb(60, 60, 60);
+}
+
+/* Bootstrap form controls (dbc components) */
+.form-select, .form-control {
+    background-color: rgb(35, 35, 35) !important;
+    border: 1px solid rgb(60, 60, 60) !important;
+    color: rgb(210, 210, 210) !important;
+}
+
+.form-select:focus, .form-control:focus {
+    background-color: rgb(45, 45, 45) !important;
+    border-color: rgb(80, 80, 80) !important;
+    box-shadow: 0 0 0 0.2rem rgba(80, 80, 80, 0.25) !important;
+}
+
+.dropdown-menu {
+    background-color: rgb(35, 35, 35) !important;
+    border: 1px solid rgb(60, 60, 60) !important;
+}
+
+.dropdown-item {
+    color: rgb(210, 210, 210) !important;
+}
+
+.dropdown-item:hover, .dropdown-item:focus {
+    background-color: rgb(50, 50, 50) !important;
+    color: rgb(230, 230, 230) !important;
+}
+
 /* Table styling */
 table {
     width: 100%;
@@ -128,4 +180,29 @@ td {
     padding: 5px;
     border: 0.5px solid #444;
     text-align: center !important;
+}
+
+/* AG Grid table header colors - gradient theme */
+/* Data Sources tables - red gradient */
+#main_data_sources .ag-header,
+#data_sources_table .ag-header {
+    background: linear-gradient(180deg, rgb(140, 60, 60) 0%, rgb(80, 35, 35) 100%) !important;
+}
+
+/* Feature Sets tables - yellow/olive gradient */
+#main_feature_sets .ag-header,
+#feature_sets_table .ag-header {
+    background: linear-gradient(180deg, rgb(120, 115, 55) 0%, rgb(70, 65, 30) 100%) !important;
+}
+
+/* Models tables - green gradient */
+#main_models .ag-header,
+#models_table .ag-header {
+    background: linear-gradient(180deg, rgb(55, 110, 55) 0%, rgb(30, 60, 30) 100%) !important;
+}
+
+/* Endpoints tables - purple gradient */
+#main_endpoints .ag-header,
+#endpoints_table .ag-header {
+    background: linear-gradient(180deg, rgb(100, 60, 120) 0%, rgb(55, 30, 70) 100%) !important;
 }

workbench/themes/dark/plotly.json

@@ -483,11 +483,11 @@
                 [1.0, "rgb(200, 100, 100)"]
             ],
             "sequential": [
-                [0.0, "rgb(100, 100, 200)"],
-                [0.4, "rgb(100, 200, 100)"],
-                [0.65, "rgb(180, 180, 50)"],
-                [0.85, "rgb(200, 100, 100)"],
-                [1.0, "rgb(200, 100, 100)"]
+                [0.0, "rgba(80, 100, 255, 1.0)"],
+                [0.25, "rgba(70, 145, 220, 1.0)"],
+                [0.5, "rgba(70, 220, 100, 1.0)"],
+                [0.75, "rgba(255, 181, 80, 1.0)"],
+                [1.0, "rgba(232, 50, 131, 1.0)"]
             ],
             "sequentialminus": [
                 [0.0, "rgb(255, 100, 100)"],
@@ -527,7 +527,7 @@
             "style": "dark"
         },
         "paper_bgcolor": "rgba(0, 0, 0, 0.0)",
-        "plot_bgcolor": "rgba(0, 0, 0, 0.0)",
+        "plot_bgcolor": "rgb(40, 40, 40)",
         "polar": {
             "angularaxis": {
                 "gridcolor": "#506784",