workbench 0.8.184__py3-none-any.whl → 0.8.185__py3-none-any.whl

workbench/core/artifacts/endpoint_core.py

@@ -475,17 +475,20 @@ class EndpointCore(Artifact):
             training_df = fs.view("training").pull_dataframe()
 
             # Run inference on the endpoint to get UQ outputs
-            full_inference_df = self.inference(training_df)
+            uq_df = self.inference(training_df)
 
             # Identify UQ-specific columns (quantiles and prediction_std)
-            uq_columns = [col for col in full_inference_df.columns if col.startswith("q_") or col == "prediction_std"]
+            uq_columns = [col for col in uq_df.columns if col.startswith("q_") or col == "prediction_std"]
 
             # Merge UQ columns with out-of-fold predictions
             if uq_columns:
-                # Keep id_column and UQ columns, drop 'prediction' to avoid conflict
-                merge_columns = [id_column] + uq_columns
-                uq_df = full_inference_df[merge_columns]
+                # Keep id_column and UQ columns, drop 'prediction' to avoid conflict when merging
+                uq_df = uq_df[[id_column] + uq_columns]
 
+                # Drop duplicates in uq_df based on id_column
+                uq_df = uq_df.drop_duplicates(subset=[id_column])
+
+                # Merge UQ columns into out_of_fold_df
                 out_of_fold_df = pd.merge(out_of_fold_df, uq_df, on=id_column, how="left")
                 additional_columns = uq_columns
                 self.log.info(f"Added UQ columns: {', '.join(additional_columns)}")

workbench/core/transforms/pandas_transforms/pandas_to_features.py

@@ -327,9 +327,36 @@ class PandasToFeatures(Transform):
         self.delete_existing()
         self.output_feature_group = self.create_feature_group()
 
+    def mac_spawn_hack(self):
+        """Workaround for macOS Tahoe fork/spawn issue with SageMaker FeatureStore ingest.
+
+        See: https://github.com/aws/sagemaker-python-sdk/issues/5312
+        macOS Tahoe 26+ has issues with forked processes creating boto3 sessions.
+        This forces spawn mode on macOS to avoid the hang.
+        """
+        import platform
+
+        if platform.system() == "Darwin":  # macOS
+            self.log.warning("macOS detected, forcing 'spawn' mode for multiprocessing (Tahoe hang workaround)")
+            import multiprocessing
+
+            try:
+                import multiprocess
+
+                multiprocess.set_start_method("spawn", force=True)
+            except (RuntimeError, ImportError):
+                pass  # Already set or multiprocess not available
+            try:
+                multiprocessing.set_start_method("spawn", force=True)
+            except RuntimeError:
+                pass  # Already set
+
     def transform_impl(self):
         """Transform Implementation: Ingest the data into the Feature Group"""
 
+        # Workaround for macOS Tahoe hang issue
+        self.mac_spawn_hack()
+
         # Now we actually push the data into the Feature Group (called ingestion)
         self.log.important(f"Ingesting rows into Feature Group {self.output_name}...")
         ingest_manager = self.output_feature_group.ingest(self.output_df, max_workers=8, max_processes=4, wait=False)

workbench/model_scripts/uq_models/generated_model_script.py

@@ -19,7 +19,7 @@ from typing import List, Tuple
 # Template Placeholders
 TEMPLATE_PARAMS = {
     "target": "udm_asy_res_free_percent",
-    "features": ['naromatom', 'fr_nh2', 'mollogp', 'numheterocycles', 'bcut2d_mrhi', 'numaromaticrings', 'smr_vsa7', 'peoe_vsa4', 'slogp_vsa6', 'peoe_vsa8', 'vsa_estate3', 'maxabspartialcharge', 'fr_arn', 'bcut2d_logplow', 'chi1v', 'axp_6d', 'bcut2d_chglo', 'balabanj', 'slogp_vsa10', 'hallkieralpha', 'vsa_estate6', 'fpdensitymorgan1', 'sps', 'qed', 'peoe_vsa7', 'maxestateindex', 'estate_vsa8', 'vsa_estate9', 'fr_nhpyrrole', 'mz', 'mp', 'bcut2d_mwhi', 'peoe_vsa13', 'c2sp2', 'numrotatablebonds', 'kappa3', 'peoe_vsa1', 'slogp_vsa2', 'xc_5dv', 'bertzct', 'estate_vsa10', 'axp_0d', 'estate_vsa2', 'xc_4d', 'smr_vsa1', 'phi', 'estate_vsa3', 'vsa_estate2', 'mv', 'estate_vsa4', 'mm', 'fr_nh1', 'slogp_vsa7', 'chi4n', 'estate_vsa6', 'fpdensitymorgan2', 'molmr', 'mse', 'bcut2d_mwlow', 'bcut2d_mrlow', 'chi2v', 'minestateindex', 'xpc_4dv', 'fr_nh0', 'axp_2d', 'vsa_estate8', 'nhohcount', 'smr_vsa6', 'peoe_vsa9', 'smr_vsa5', 'num_r_centers', 'xpc_6dv', 'xc_3d', 'slogp_vsa5', 'axp_7dv', 'minabsestateindex', 'xc_5d', 'vsa_estate10', 'fr_hoccn', 'smr_vsa3', 'vsa_estate1', 'axp_5d', 'num_s_centers', 'axp_1d', 'estate_vsa1', 'fpdensitymorgan3', 'axp_5dv', 'chi3n', 'peoe_vsa6', 'labuteasa', 'chi2n', 'xc_6d', 'xp_7d', 'tpsa', 'xpc_4d', 'avgipc', 'xp_5d', 'vsa_estate5', 'xch_7d', 'xch_5d', 'axp_4dv', 'nbase', 'xc_3dv', 'kappa2', 'axp_3d', 'c1sp3', 'numhacceptors', 'bcut2d_logphi', 'smr_vsa10', 'fr_piperzine', 'peoe_vsa11', 'axp_6dv', 'peoe_vsa10', 'estate_vsa9', 'bcut2d_chghi', 'xp_6d', 'xch_6dv', 'chi0', 'vsa_estate7', 'mi', 'xpc_5d', 'fractioncsp3', 'xp_0dv', 'kappa1', 'minpartialcharge', 'xp_6dv', 'peoe_vsa2', 'chi3v', 'axp_0dv', 'mare', 'xch_5dv', 'vsa_estate4', 'xp_4dv', 'estate_vsa7', 'xp_3d', 'numaliphaticheterocycles', 'chi1', 'xp_3dv', 'fr_ether', 'xch_6d', 'peoe_vsa12', 'xch_7dv', 'axp_1dv', 'axp_7d', 'fr_ndealkylation2', 'smr_vsa9', 'axp_2dv', 'estate_vsa5', 'mpe', 'molwt', 'xch_4d', 'axp_3dv', 'xp_5dv', 'chi4v', 'heavyatommolwt', 'fr_al_oh', 'xpc_5dv', 'xpc_6d', 'maxpartialcharge', 'numatomstereocenters', 'peoe_vsa3', 'fr_aniline', 'minabspartialcharge', 'c3sp3', 'slogp_vsa1', 'exactmolwt', 'chi1n', 'xp_7dv', 'chi0n', 'xp_2d', 'xch_4dv', 'fr_bicyclic', 'xc_4dv', 'axp_4d', 'slogp_vsa4', 'fr_benzene', 'numaromaticheterocycles', 'fr_aryl_methyl', 'fr_pyridine', 'fr_imine', 'chi0v', 'slogp_vsa12'],
+    "features": ['naromatom', 'minabspartialcharge', 'bcut2d_mrhi', 'smr_vsa10', 'vsa_estate2', 'minpartialcharge', 'xpc_5d', 'sps', 'xc_3dv', 'smr_vsa7', 'bcut2d_logplow', 'mollogp', 'vsa_estate1', 'num_s_centers', 'vsa_estate4', 'peoe_vsa13', 'fr_nh2', 'bertzct', 'estate_vsa4', 'vsa_estate9', 'smr_vsa3', 'fr_nh1', 'molwt', 'estate_vsa5', 'slogp_vsa5', 'maxpartialcharge', 'estate_vsa1', 'fr_hoccn', 'xc_5d', 'nbase', 'chi1v', 'peoe_vsa10', 'tpsa', 'vsa_estate3', 'chi2v', 'estate_vsa8', 'numheteroatoms', 'estate_vsa2', 'peoe_vsa1', 'labuteasa', 'axp_4d', 'xch_7dv', 'chi0n', 'num_r_centers', 'vsa_estate8', 'minabsestateindex', 'bcut2d_chglo', 'bcut2d_mwhi', 'fr_nh0', 'chi4n', 'estate_vsa9', 'smr_vsa5', 'peoe_vsa2', 'peoe_vsa7', 'peoe_vsa9', 'kappa3', 'slogp_vsa3', 'fr_arn', 'estate_vsa3', 'avgipc', 'axp_5d', 'xpc_6d', 'c2sp2', 'peoe_vsa5', 'vsa_estate5', 'balabanj', 'maxabspartialcharge', 'fr_aniline', 'fr_piperdine', 'vsa_estate6', 'bcut2d_mwlow', 'numsaturatedheterocycles', 'vsa_estate10', 'smr_vsa1', 'estate_vsa6', 'smr_vsa6', 'fpdensitymorgan1', 'peoe_vsa3', 'peoe_vsa8', 'smr_vsa9', 'slogp_vsa2', 'nocount', 'fpdensitymorgan3', 'axp_6d', 'bcut2d_mrlow', 'bcut2d_logphi', 'axp_4dv', 'fpdensitymorgan2', 'mp', 'xp_5d', 'fr_nhpyrrole', 'mz', 'mv', 'vsa_estate7', 'axp_7dv', 'mi', 'c1sp2', 'xpc_6dv', 'slogp_vsa10', 'xp_7d', 'axp_3dv', 'peoe_vsa4', 'peoe_vsa6', 'axp_2dv', 'xch_5dv', 'qed', 'estate_vsa7', 'numaromaticrings', 'chi1n', 'axp_0d', 'axp_6dv', 'numrotatablebonds', 'hallkieralpha', 'c1sp3', 'xc_4dv', 'kappa2', 'bcut2d_chghi', 'xch_7d', 'axp_0dv', 'slogp_vsa7', 'axp_7d', 'minestateindex', 'axp_2d', 'axp_1d', 'chi0', 'fractioncsp3', 'slogp_vsa6', 'axp_1dv', 'chi2n', 'xp_6dv', 'maxestateindex', 'xpc_4d', 'numaliphaticheterocycles', 'chi1', 'phi', 'chi3n', 'xc_4d', 'xc_3d', 'peoe_vsa12', 'xp_6d', 'chi3v', 'axp_3d', 'axp_5dv', 'fr_benzene', 'slogp_vsa4', 'fr_pyridine', 'fr_aryl_methyl', 'xp_5dv', 'c3sp3', 'xp_7dv', 'slogp_vsa1', 'peoe_vsa11', 'mse', 'xc_5dv', 'xpc_5dv', 'xc_6dv', 'xp_0dv', 'xch_5d', 'c3sp2', 'numatomstereocenters', 'numhacceptors', 'fr_imidazole', 'numsaturatedrings', 'xpc_4dv', 'chi0v', 'numheterocycles', 'xch_6dv', 'estate_vsa10', 'chi4v', 'mare', 'numhdonors', 'xch_6d', 'xp_4d', 'fr_ar_n', 'numunspecifiedatomstereocenters', 'numspiroatoms', 'xch_4dv', 'fr_morpholine', 'fr_methoxy', 'mm', 'fr_piperzine'],
     "compressed_features": [],
     "train_all_data": True,
     "hyperparameters": {},

workbench/utils/xgboost_model_utils.py

@@ -386,6 +386,106 @@ def cross_fold_inference(workbench_model: Any, nfolds: int = 5) -> Tuple[Dict[st
     return metrics_dict, predictions_df
 
 
+def leave_one_out_inference(workbench_model: Any) -> pd.DataFrame:
+    """
+    Performs leave-one-out cross-validation (parallelized).
+    For datasets > 1000 rows, first identifies top 100 worst predictions via 10-fold CV,
+    then performs true leave-one-out on those 100 samples.
+    Each model trains on ALL data except one sample.
+    """
+    from workbench.api import FeatureSet
+    from joblib import Parallel, delayed
+    from tqdm import tqdm
+
+    def train_and_predict_one(model_params, is_classifier, X, y, train_idx, val_idx):
+        """Train on train_idx, predict on val_idx."""
+        model = xgb.XGBClassifier(**model_params) if is_classifier else xgb.XGBRegressor(**model_params)
+        model.fit(X[train_idx], y[train_idx])
+        return model.predict(X[val_idx])[0]
+
+    # Load model and get params
+    model_artifact_uri = workbench_model.model_data_url()
+    loaded_model = xgboost_model_from_s3(model_artifact_uri)
+    if loaded_model is None:
+        log.error("No XGBoost model found in the artifact.")
+        return pd.DataFrame()
+
+    if isinstance(loaded_model, (xgb.XGBClassifier, xgb.XGBRegressor)):
+        is_classifier = isinstance(loaded_model, xgb.XGBClassifier)
+        model_params = loaded_model.get_params()
+    elif isinstance(loaded_model, xgb.Booster):
+        log.warning("Deprecated: Loaded model is a Booster, wrapping in sklearn model.")
+        is_classifier = workbench_model.model_type.value == "classifier"
+        model_params = {"enable_categorical": True}
+    else:
+        log.error(f"Unexpected model type: {type(loaded_model)}")
+        return pd.DataFrame()
+
+    # Load and prepare data
+    fs = FeatureSet(workbench_model.get_input())
+    df = fs.view("training").pull_dataframe()
+    id_col = fs.id_column
+    target_col = workbench_model.target()
+    feature_cols = workbench_model.features()
+
+    # Convert string features to categorical
+    for col in feature_cols:
+        if df[col].dtype in ["object", "string"]:
+            df[col] = df[col].astype("category")
+
+    # Determine which samples to run LOO on
+    if len(df) > 1000:
+        log.important(f"Dataset has {len(df)} rows. Running 10-fold CV to identify top 1000 worst predictions...")
+        _, predictions_df = cross_fold_inference(workbench_model, nfolds=10)
+        predictions_df["residual_abs"] = np.abs(predictions_df[target_col] - predictions_df["prediction"])
+        worst_samples = predictions_df.nlargest(1000, "residual_abs")
+        worst_ids = worst_samples[id_col].values
+        loo_indices = df[df[id_col].isin(worst_ids)].index.values
+        log.important(f"Running leave-one-out CV on 1000 worst samples. Each model trains on {len(df)-1} rows...")
+    else:
+        log.important(f"Running leave-one-out CV on all {len(df)} samples...")
+        loo_indices = df.index.values
+
+    # Prepare full dataset for training
+    X_full = df[feature_cols].values
+    y_full = df[target_col].values
+
+    # Encode target if classifier
+    label_encoder = LabelEncoder() if is_classifier else None
+    if label_encoder:
+        y_full = label_encoder.fit_transform(y_full)
+
+    # Generate LOO splits
+    splits = []
+    for loo_idx in loo_indices:
+        train_idx = np.delete(np.arange(len(X_full)), loo_idx)
+        val_idx = np.array([loo_idx])
+        splits.append((train_idx, val_idx))
+
+    # Parallel execution
+    predictions = Parallel(n_jobs=4)(
+        delayed(train_and_predict_one)(model_params, is_classifier, X_full, y_full, train_idx, val_idx)
+        for train_idx, val_idx in tqdm(splits, desc="LOO CV")
+    )
+
+    # Build results dataframe
+    predictions_array = np.array(predictions)
+    if label_encoder:
+        predictions_array = label_encoder.inverse_transform(predictions_array.astype(int))
+
+    predictions_df = pd.DataFrame(
+        {
+            id_col: df.loc[loo_indices, id_col].values,
+            target_col: df.loc[loo_indices, target_col].values,
+            "prediction": predictions_array,
+        }
+    )
+
+    predictions_df["residual_abs"] = np.abs(predictions_df[target_col] - predictions_df["prediction"])
+
+    return predictions_df
+
+
 if __name__ == "__main__":
     """Exercise the Model Utilities"""
     from workbench.api import Model, FeatureSet

{workbench-0.8.184.dist-info → workbench-0.8.185.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: workbench
-Version: 0.8.184
+Version: 0.8.185
 Summary: Workbench: A Dashboard and Python API for creating and deploying AWS SageMaker Model Pipelines
 Author-email: SuperCowPowers LLC <support@supercowpowers.com>
 License-Expression: MIT

{workbench-0.8.184.dist-info → workbench-0.8.185.dist-info}/RECORD

@@ -54,7 +54,7 @@ workbench/core/artifacts/cached_artifact_mixin.py,sha256=ngqFLZ4cQx_TFouXZgXZQsv
 workbench/core/artifacts/data_capture_core.py,sha256=q8f79rRTYiZ7T4IQRWXl8ZvPpcvZyNxYERwvo8o0OQc,14858
 workbench/core/artifacts/data_source_abstract.py,sha256=5IRCzFVK-17cd4NXPMRfx99vQAmQ0WHE5jcm5RfsVTg,10619
 workbench/core/artifacts/data_source_factory.py,sha256=YL_tA5fsgubbB3dPF6T4tO0rGgz-6oo3ge4i_YXVC-M,2380
-workbench/core/artifacts/endpoint_core.py,sha256=b3cNj1UnlHmQdG1C8bmD2jWpD4h-O6F-75fWSm01uGU,51850
+workbench/core/artifacts/endpoint_core.py,sha256=gQdOHtjEeC1WCHbKZNaDQ0eeOka1sCO-zcABDO4_Egk,51965
 workbench/core/artifacts/feature_set_core.py,sha256=7b1o_PzxtwaYC-W2zxlkltiO0fYULA8CVGWwHNmqgtI,31457
 workbench/core/artifacts/model_core.py,sha256=wjoa2GQnzrrTM-E2VgYZHT9Ixebl3LaKbJL0YvEdrJY,51546
 workbench/core/artifacts/monitor_core.py,sha256=M307yz7tEzOEHgv-LmtVy9jKjSbM98fHW3ckmNYrwlU,27897
@@ -109,7 +109,7 @@ workbench/core/transforms/pandas_transforms/__init__.py,sha256=xL4MT8-fZ1SFqDbTL
 workbench/core/transforms/pandas_transforms/data_to_pandas.py,sha256=sJHPeuNF8Q8aQqgRnkdWkyvur5cbggdUVIwR-xF3Dlo,3621
 workbench/core/transforms/pandas_transforms/features_to_pandas.py,sha256=af6xdPt2V4zhh-SzQa_UYxdmNMzMLXbrbsznV5QoIJg,3441
 workbench/core/transforms/pandas_transforms/pandas_to_data.py,sha256=cqo6hQmzUGUFACvNuVLZQdgrlXrQIu4NjqK-ujPmoIc,9181
-workbench/core/transforms/pandas_transforms/pandas_to_features.py,sha256=XiUz2BqOX4N34g6hvFvcLswhkEouyU0AjyIy9EGv2zg,20440
+workbench/core/transforms/pandas_transforms/pandas_to_features.py,sha256=mj00L40PXhw-JHG2SZe53yJAzicgn4xuM2VbmOY-wsM,21480
 workbench/core/transforms/pandas_transforms/pandas_to_features_chunked.py,sha256=0R8mQlWfbIlTVmYUmrtu2gsw0AE815k6kqPgpd0bmyQ,4422
 workbench/core/views/__init__.py,sha256=UZJMAJBCMVM3uSYmnFg8c2LWtdu9-479WNAdVMIohAc,962
 workbench/core/views/column_subset_view.py,sha256=vGDKTTGrPIY-IFOeWvudJrhKiq0OjWDp5rTuuj-X40U,4261
@@ -156,7 +156,7 @@ workbench/model_scripts/pytorch_model/requirements.txt,sha256=ICS5nW0wix44EJO2tJ
 workbench/model_scripts/scikit_learn/generated_model_script.py,sha256=c73ZpJBlU5k13Nx-ZDkLXu7da40CYyhwjwwmuPq6uLg,12870
 workbench/model_scripts/scikit_learn/requirements.txt,sha256=aVvwiJ3LgBUhM_PyFlb2gHXu_kpGPho3ANBzlOkfcvs,107
 workbench/model_scripts/scikit_learn/scikit_learn.template,sha256=QQvqx-eX9ZTbYmyupq6R6vIQwosmsmY_MRBPaHyfjdk,12586
-workbench/model_scripts/uq_models/generated_model_script.py,sha256=OS_ufhyLR9IQcyRV2ukO_CfDnjp60UE9kwcAN4RY0Is,21191
+workbench/model_scripts/uq_models/generated_model_script.py,sha256=gJb_5jBb4mcf41jb6578H9uYYH6Y-uFtPp1MNKXNFQQ,21231
 workbench/model_scripts/uq_models/mapie.template,sha256=8VzoP-Wp3ECVIDqXVkiTS6bwmn3cd3dDZ2WjYPzXTi8,18955
 workbench/model_scripts/uq_models/requirements.txt,sha256=fw7T7t_YJAXK3T6Ysbesxh_Agx_tv0oYx72cEBTqRDY,98
 workbench/model_scripts/xgb_model/generated_model_script.py,sha256=Tbn7EMXxZZO8rDdKQ5fYCbpltACsMXNvuusLL9p-U5c,22319
@@ -242,7 +242,7 @@ workbench/utils/workbench_cache.py,sha256=IQchxB81iR4eVggHBxUJdXxUCRkqWz1jKe5gxN
 workbench/utils/workbench_event_bridge.py,sha256=z1GmXOB-Qs7VOgC6Hjnp2DI9nSEWepaSXejACxTIR7o,4150
 workbench/utils/workbench_logging.py,sha256=WCuMWhQwibrvcGAyj96h2wowh6dH7zNlDJ7sWUzdCeI,10263
 workbench/utils/workbench_sqs.py,sha256=RwM80z7YWwdtMaCKh7KWF8v38f7eBRU7kyC7ZhTRuI0,2072
-workbench/utils/xgboost_model_utils.py,sha256=wSUrs9VlftaTZ-cWZMEeHY6TmcLvxwrKk4S4lr7kWWw,17482
+workbench/utils/xgboost_model_utils.py,sha256=rPfbl5sCZOttkilAHSmYU_u9JIDeYsGi2JrEs-zzcwI,21597
 workbench/utils/chem_utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 workbench/utils/chem_utils/fingerprints.py,sha256=Qvs8jaUwguWUq3Q3j695MY0t0Wk3BvroW-oWBwalMUo,5255
 workbench/utils/chem_utils/misc.py,sha256=Nevf8_opu-uIPrv_1_0ubuFVVo2_fGUkMoLAHB3XAeo,7372
@@ -287,9 +287,9 @@ workbench/web_interface/page_views/main_page.py,sha256=X4-KyGTKLAdxR-Zk2niuLJB2Y
 workbench/web_interface/page_views/models_page_view.py,sha256=M0bdC7bAzLyIaE2jviY12FF4abdMFZmg6sFuOY_LaGI,2650
 workbench/web_interface/page_views/page_view.py,sha256=Gh6YnpOGlUejx-bHZAf5pzqoQ1H1R0OSwOpGhOBO06w,455
 workbench/web_interface/page_views/pipelines_page_view.py,sha256=v2pxrIbsHBcYiblfius3JK766NZ7ciD2yPx0t3E5IJo,2656
-workbench-0.8.184.dist-info/licenses/LICENSE,sha256=z4QMMPlLJkZjU8VOKqJkZiQZCEZ--saIU2Z8-p3aVc0,1080
-workbench-0.8.184.dist-info/METADATA,sha256=3B5uP_y9cOctNaxDK6Z9Fwfcwzf7p9f3HyjJ35B-nqY,9210
-workbench-0.8.184.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-workbench-0.8.184.dist-info/entry_points.txt,sha256=zPFPruY9uayk8-wsKrhfnIyIB6jvZOW_ibyllEIsLWo,356
-workbench-0.8.184.dist-info/top_level.txt,sha256=Dhy72zTxaA_o_yRkPZx5zw-fwumnjGaeGf0hBN3jc_w,10
-workbench-0.8.184.dist-info/RECORD,,
+workbench-0.8.185.dist-info/licenses/LICENSE,sha256=z4QMMPlLJkZjU8VOKqJkZiQZCEZ--saIU2Z8-p3aVc0,1080
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