workbench 0.8.202__py3-none-any.whl → 0.8.220__py3-none-any.whl

workbench/utils/pytorch_utils.py

@@ -1,169 +1,53 @@
 """PyTorch Tabular utilities for Workbench models."""
 
-# flake8: noqa: E402
 import logging
 import os
+import tarfile
 import tempfile
-from pprint import pformat
 from typing import Any, Tuple
 
-# Disable OpenMP parallelism to avoid segfaults on macOS with conflicting OpenMP runtimes
-# (libomp from LLVM vs libiomp from Intel). Must be set before importing numpy/sklearn/torch.
-# See: https://github.com/scikit-learn/scikit-learn/issues/21302
-os.environ.setdefault("OMP_NUM_THREADS", "1")
-os.environ.setdefault("MKL_NUM_THREADS", "1")
-
-import numpy as np
+import awswrangler as wr
 import pandas as pd
-from scipy.stats import spearmanr
-from sklearn.metrics import (
-    mean_absolute_error,
-    mean_squared_error,
-    median_absolute_error,
-    precision_recall_fscore_support,
-    r2_score,
-    roc_auc_score,
-)
-from sklearn.model_selection import KFold, StratifiedKFold
-from sklearn.preprocessing import LabelEncoder
 
-from workbench.utils.model_utils import safe_extract_tarfile
-from workbench.utils.pandas_utils import expand_proba_column
 from workbench.utils.aws_utils import pull_s3_data
+from workbench.utils.metrics_utils import compute_metrics_from_predictions
 
 log = logging.getLogger("workbench")
 
 
 def download_and_extract_model(s3_uri: str, model_dir: str) -> None:
-    """Download model artifact from S3 and extract it.
-
-    Args:
-        s3_uri: S3 URI to the model artifact (model.tar.gz)
-        model_dir: Directory to extract model artifacts to
-    """
-    import awswrangler as wr
-
-    log.info(f"Downloading model from {s3_uri}...")
-
-    # Download to temp file
-    local_tar_path = os.path.join(model_dir, "model.tar.gz")
-    wr.s3.download(path=s3_uri, local_file=local_tar_path)
-
-    # Extract using safe extraction
-    log.info(f"Extracting to {model_dir}...")
-    safe_extract_tarfile(local_tar_path, model_dir)
-
-    # Cleanup tar file
-    os.unlink(local_tar_path)
-
-
-def load_pytorch_model_artifacts(model_dir: str) -> Tuple[Any, dict]:
-    """Load PyTorch Tabular model and artifacts from an extracted model directory.
+    """Download and extract a PyTorch model artifact from S3.
 
     Args:
-        model_dir: Directory containing extracted model artifacts
-
-    Returns:
-        Tuple of (TabularModel, artifacts_dict).
-        artifacts_dict contains 'label_encoder' and 'category_mappings' if present.
+        s3_uri: S3 URI of the model.tar.gz artifact
+        model_dir: Local directory to extract the model to
     """
-    import json
+    with tempfile.NamedTemporaryFile(suffix=".tar.gz", delete=False) as tmp:
+        tmp_path = tmp.name
 
-    import joblib
-
-    # pytorch-tabular saves complex objects, use legacy loading behavior
-    os.environ["TORCH_FORCE_NO_WEIGHTS_ONLY_LOAD"] = "1"
-    from pytorch_tabular import TabularModel
-
-    model_path = os.path.join(model_dir, "tabular_model")
-    if not os.path.exists(model_path):
-        raise FileNotFoundError(f"No tabular_model directory found in {model_dir}")
-
-    # PyTorch Tabular needs write access, so chdir to /tmp
-    original_cwd = os.getcwd()
     try:
-        os.chdir("/tmp")
-        model = TabularModel.load_model(model_path)
+        wr.s3.download(path=s3_uri, local_file=tmp_path)
+        with tarfile.open(tmp_path, "r:gz") as tar:
+            tar.extractall(model_dir)
+        log.info(f"Extracted model to {model_dir}")
     finally:
-        os.chdir(original_cwd)
-
-    # Load additional artifacts
-    artifacts = {}
-
-    label_encoder_path = os.path.join(model_dir, "label_encoder.joblib")
-    if os.path.exists(label_encoder_path):
-        artifacts["label_encoder"] = joblib.load(label_encoder_path)
-
-    category_mappings_path = os.path.join(model_dir, "category_mappings.json")
-    if os.path.exists(category_mappings_path):
-        with open(category_mappings_path) as f:
-            artifacts["category_mappings"] = json.load(f)
-
-    return model, artifacts
-
-
-def _extract_model_configs(loaded_model: Any, n_train: int) -> dict:
-    """Extract trainer and model configs from a loaded PyTorch Tabular model.
-
-    Args:
-        loaded_model: Loaded TabularModel instance
-        n_train: Number of training samples (used for batch_size calculation)
-
-    Returns:
-        Dictionary with 'trainer' and 'model' config dictionaries
-    """
-    config = loaded_model.config
-
-    # Trainer config - extract from loaded model, matching template defaults
-    trainer_defaults = {
-        "auto_lr_find": False,
-        "batch_size": min(128, max(32, n_train // 16)),
-        "max_epochs": 100,
-        "min_epochs": 10,
-        "early_stopping": "valid_loss",
-        "early_stopping_patience": 10,
-        "gradient_clip_val": 1.0,
-    }
-
-    trainer_config = {}
-    for key, default in trainer_defaults.items():
-        value = getattr(config, key, default)
-        if value == default and not hasattr(config, key):
-            log.warning(f"Trainer config '{key}' not found in loaded model, using default: {default}")
-        trainer_config[key] = value
-
-    # Model config - extract from loaded model, matching template defaults
-    model_defaults = {
-        "layers": "256-128-64",
-        "activation": "LeakyReLU",
-        "learning_rate": 1e-3,
-        "dropout": 0.3,
-        "use_batch_norm": True,
-        "initialization": "kaiming",
-    }
-
-    model_config = {}
-    for key, default in model_defaults.items():
-        value = getattr(config, key, default)
-        if value == default and not hasattr(config, key):
-            log.warning(f"Model config '{key}' not found in loaded model, using default: {default}")
-        model_config[key] = value
-
-    return {"trainer": trainer_config, "model": model_config}
+        if os.path.exists(tmp_path):
+            os.remove(tmp_path)
 
 
 def pull_cv_results(workbench_model: Any) -> Tuple[pd.DataFrame, pd.DataFrame]:
     """Pull cross-validation results from AWS training artifacts.
 
-    This retrieves the validation predictions and training metrics that were
-    saved during model training.
+    This retrieves the validation predictions saved during model training and
+    computes metrics directly from them. For PyTorch models trained with
+    n_folds > 1, these are out-of-fold predictions from k-fold cross-validation.
 
     Args:
         workbench_model: Workbench model object
 
     Returns:
         Tuple of:
-            - DataFrame with training metrics
+            - DataFrame with computed metrics
             - DataFrame with validation predictions
     """
     # Get the validation predictions from S3
@@ -175,352 +59,29 @@ def pull_cv_results(workbench_model: Any) -> Tuple[pd.DataFrame, pd.DataFrame]:
 
     log.info(f"Pulled {len(predictions_df)} validation predictions from {s3_path}")
 
-    # Get training metrics from model metadata
-    training_metrics = workbench_model.workbench_meta().get("workbench_training_metrics")
-
-    if training_metrics is None:
-        raise ValueError(f"No training metrics found in model metadata for {workbench_model.model_name}")
+    # Compute metrics from predictions
+    target = workbench_model.target()
+    class_labels = workbench_model.class_labels()
 
-    metrics_df = pd.DataFrame.from_dict(training_metrics)
-    log.info(f"Metrics summary:\n{metrics_df.to_string(index=False)}")
+    if target in predictions_df.columns and "prediction" in predictions_df.columns:
+        metrics_df = compute_metrics_from_predictions(predictions_df, target, class_labels)
+    else:
+        metrics_df = pd.DataFrame()
 
     return metrics_df, predictions_df
 
 
-def cross_fold_inference(
-    workbench_model: Any,
-    nfolds: int = 5,
-) -> Tuple[pd.DataFrame, pd.DataFrame]:
-    """Performs K-fold cross-validation for PyTorch Tabular models.
-
-    Replicates the training setup from the original model to ensure
-    cross-validation results are comparable to the deployed model.
-
-    Args:
-        workbench_model: Workbench model object
-        nfolds: Number of folds for cross-validation (default is 5)
-
-    Returns:
-        Tuple of:
-            - DataFrame with per-class metrics (and 'all' row for overall metrics)
-            - DataFrame with columns: id, target, prediction, and *_proba columns (for classifiers)
-    """
-    import shutil
-
-    from pytorch_tabular import TabularModel
-    from pytorch_tabular.config import DataConfig, OptimizerConfig, TrainerConfig
-    from pytorch_tabular.models import CategoryEmbeddingModelConfig
-
-    from workbench.api import FeatureSet
-
-    # Create a temporary model directory
-    model_dir = tempfile.mkdtemp(prefix="pytorch_cv_")
-    log.info(f"Using model directory: {model_dir}")
-
-    try:
-        # Download and extract model artifacts to get config and artifacts
-        model_artifact_uri = workbench_model.model_data_url()
-        download_and_extract_model(model_artifact_uri, model_dir)
-
-        # Load model and artifacts
-        loaded_model, artifacts = load_pytorch_model_artifacts(model_dir)
-        category_mappings = artifacts.get("category_mappings", {})
-
-        # Determine if classifier from the loaded model's config
-        is_classifier = loaded_model.config.task == "classification"
-
-        # Use saved label encoder if available, otherwise create fresh one
-        if is_classifier:
-            label_encoder = artifacts.get("label_encoder")
-            if label_encoder is None:
-                log.warning("No saved label encoder found, creating fresh one")
-                label_encoder = LabelEncoder()
-        else:
-            label_encoder = None
-
-        # Prepare data
-        fs = FeatureSet(workbench_model.get_input())
-        df = workbench_model.training_view().pull_dataframe()
-
-        # Get columns
-        id_col = fs.id_column
-        target_col = workbench_model.target()
-        feature_cols = workbench_model.features()
-        print(f"Target column: {target_col}")
-        print(f"Feature columns: {len(feature_cols)} features")
-
-        # Convert string columns to category for PyTorch Tabular compatibility
-        for col in feature_cols:
-            if pd.api.types.is_string_dtype(df[col]):
-                if col in category_mappings:
-                    df[col] = pd.Categorical(df[col], categories=category_mappings[col])
-                else:
-                    df[col] = df[col].astype("category")
-
-        # Determine categorical and continuous columns
-        categorical_cols = [col for col in feature_cols if df[col].dtype.name == "category"]
-        continuous_cols = [col for col in feature_cols if col not in categorical_cols]
-
-        # Cast continuous columns to float
-        if continuous_cols:
-            df[continuous_cols] = df[continuous_cols].astype("float64")
-
-        # Drop rows with NaN features or target (PyTorch Tabular cannot handle NaN values)
-        nan_mask = df[feature_cols].isna().any(axis=1) | df[target_col].isna()
-        if nan_mask.any():
-            n_nan_rows = nan_mask.sum()
-            log.warning(
-                f"Dropping {n_nan_rows} rows ({100*n_nan_rows/len(df):.1f}%) with NaN values for cross-validation"
-            )
-            df = df[~nan_mask].reset_index(drop=True)
-
-        X = df[feature_cols]
-        y = df[target_col]
-        ids = df[id_col]
-
-        # Encode target if classifier
-        if label_encoder is not None:
-            if not hasattr(label_encoder, "classes_"):
-                label_encoder.fit(y)
-            y_encoded = label_encoder.transform(y)
-            y_for_cv = pd.Series(y_encoded, index=y.index, name=target_col)
-        else:
-            y_for_cv = y
-
-        # Extract configs from loaded model (pass approx train size for batch_size calculation)
-        n_train_approx = int(len(df) * (1 - 1 / nfolds))
-        configs = _extract_model_configs(loaded_model, n_train_approx)
-        trainer_params = configs["trainer"]
-        model_params = configs["model"]
-
-        log.info(f"Trainer config:\n{pformat(trainer_params)}")
-        log.info(f"Model config:\n{pformat(model_params)}")
-
-        # Prepare KFold
-        kfold = (StratifiedKFold if is_classifier else KFold)(n_splits=nfolds, shuffle=True, random_state=42)
-
-        # Initialize results collection
-        fold_metrics = []
-        predictions_df = pd.DataFrame({id_col: ids, target_col: y})
-        if is_classifier:
-            predictions_df["pred_proba"] = [None] * len(predictions_df)
-
-        # Perform cross-validation
-        for fold_idx, (train_idx, val_idx) in enumerate(kfold.split(X, y_for_cv), 1):
-            print(f"\n{'='*50}")
-            print(f"Fold {fold_idx}/{nfolds}")
-            print(f"{'='*50}")
-
-            # Split data
-            df_train = df.iloc[train_idx].copy()
-            df_val = df.iloc[val_idx].copy()
-
-            # Encode target for this fold
-            if is_classifier:
-                df_train[target_col] = label_encoder.transform(df_train[target_col])
-                df_val[target_col] = label_encoder.transform(df_val[target_col])
-
-            # Create configs for this fold - matching the training template exactly
-            data_config = DataConfig(
-                target=[target_col],
-                continuous_cols=continuous_cols,
-                categorical_cols=categorical_cols,
-            )
-
-            trainer_config = TrainerConfig(
-                auto_lr_find=trainer_params["auto_lr_find"],
-                batch_size=trainer_params["batch_size"],
-                max_epochs=trainer_params["max_epochs"],
-                min_epochs=trainer_params["min_epochs"],
-                early_stopping=trainer_params["early_stopping"],
-                early_stopping_patience=trainer_params["early_stopping_patience"],
-                gradient_clip_val=trainer_params["gradient_clip_val"],
-                checkpoints="valid_loss",  # Save best model based on validation loss
-                accelerator="cpu",
-            )
-
-            optimizer_config = OptimizerConfig()
-
-            model_config = CategoryEmbeddingModelConfig(
-                task="classification" if is_classifier else "regression",
-                layers=model_params["layers"],
-                activation=model_params["activation"],
-                learning_rate=model_params["learning_rate"],
-                dropout=model_params["dropout"],
-                use_batch_norm=model_params["use_batch_norm"],
-                initialization=model_params["initialization"],
-            )
-
-            # Create and train fresh model
-            tabular_model = TabularModel(
-                data_config=data_config,
-                model_config=model_config,
-                optimizer_config=optimizer_config,
-                trainer_config=trainer_config,
-            )
-
-            # Change to /tmp for training (PyTorch Tabular needs write access)
-            original_cwd = os.getcwd()
-            try:
-                os.chdir("/tmp")
-                # Clean up checkpoint directory from previous fold
-                checkpoint_dir = "/tmp/saved_models"
-                if os.path.exists(checkpoint_dir):
-                    shutil.rmtree(checkpoint_dir)
-                tabular_model.fit(train=df_train, validation=df_val)
-            finally:
-                os.chdir(original_cwd)
-
-            # Make predictions
-            result = tabular_model.predict(df_val[feature_cols])
-
-            # Extract predictions
-            prediction_col = f"{target_col}_prediction"
-            preds = result[prediction_col].values
-
-            # Store predictions at the correct indices
-            val_indices = df.iloc[val_idx].index
-            if is_classifier:
-                preds_decoded = label_encoder.inverse_transform(preds.astype(int))
-                predictions_df.loc[val_indices, "prediction"] = preds_decoded
-
-                # Get probabilities and store at validation indices only
-                prob_cols = sorted([col for col in result.columns if col.endswith("_probability")])
-                if prob_cols:
-                    probs = result[prob_cols].values
-                    for i, idx in enumerate(val_indices):
-                        predictions_df.at[idx, "pred_proba"] = probs[i].tolist()
-            else:
-                predictions_df.loc[val_indices, "prediction"] = preds
-
-            # Calculate fold metrics
-            if is_classifier:
-                y_val_orig = label_encoder.inverse_transform(df_val[target_col])
-                preds_orig = preds_decoded
-
-                prec, rec, f1, _ = precision_recall_fscore_support(
-                    y_val_orig, preds_orig, average="weighted", zero_division=0
-                )
-
-                prec_per_class, rec_per_class, f1_per_class, _ = precision_recall_fscore_support(
-                    y_val_orig, preds_orig, average=None, zero_division=0, labels=label_encoder.classes_
-                )
-
-                y_val_encoded = df_val[target_col].values
-                roc_auc_overall = roc_auc_score(y_val_encoded, probs, multi_class="ovr", average="macro")
-                roc_auc_per_class = roc_auc_score(y_val_encoded, probs, multi_class="ovr", average=None)
-
-                fold_metrics.append(
-                    {
-                        "fold": fold_idx,
-                        "precision": prec,
-                        "recall": rec,
-                        "f1": f1,
-                        "roc_auc": roc_auc_overall,
-                        "precision_per_class": prec_per_class,
-                        "recall_per_class": rec_per_class,
-                        "f1_per_class": f1_per_class,
-                        "roc_auc_per_class": roc_auc_per_class,
-                    }
-                )
-
-                print(f"Fold {fold_idx} - F1: {f1:.4f}, ROC-AUC: {roc_auc_overall:.4f}")
-            else:
-                y_val = df_val[target_col].values
-                spearman_corr, _ = spearmanr(y_val, preds)
-                rmse = np.sqrt(mean_squared_error(y_val, preds))
-
-                fold_metrics.append(
-                    {
-                        "fold": fold_idx,
-                        "rmse": rmse,
-                        "mae": mean_absolute_error(y_val, preds),
-                        "medae": median_absolute_error(y_val, preds),
-                        "r2": r2_score(y_val, preds),
-                        "spearmanr": spearman_corr,
-                    }
-                )
-
-                print(f"Fold {fold_idx} - RMSE: {rmse:.4f}, R2: {fold_metrics[-1]['r2']:.4f}")
-
-        # Calculate summary metrics
-        fold_df = pd.DataFrame(fold_metrics)
-
-        if is_classifier:
-            if "pred_proba" in predictions_df.columns:
-                predictions_df = expand_proba_column(predictions_df, label_encoder.classes_)
-
-            metric_rows = []
-            for idx, class_name in enumerate(label_encoder.classes_):
-                prec_scores = np.array([fold["precision_per_class"][idx] for fold in fold_metrics])
-                rec_scores = np.array([fold["recall_per_class"][idx] for fold in fold_metrics])
-                f1_scores = np.array([fold["f1_per_class"][idx] for fold in fold_metrics])
-                roc_auc_scores = np.array([fold["roc_auc_per_class"][idx] for fold in fold_metrics])
-
-                y_orig = label_encoder.inverse_transform(y_for_cv)
-                support = int((y_orig == class_name).sum())
-
-                metric_rows.append(
-                    {
-                        "class": class_name,
-                        "precision": prec_scores.mean(),
-                        "recall": rec_scores.mean(),
-                        "f1": f1_scores.mean(),
-                        "roc_auc": roc_auc_scores.mean(),
-                        "support": support,
-                    }
-                )
-
-            metric_rows.append(
-                {
-                    "class": "all",
-                    "precision": fold_df["precision"].mean(),
-                    "recall": fold_df["recall"].mean(),
-                    "f1": fold_df["f1"].mean(),
-                    "roc_auc": fold_df["roc_auc"].mean(),
-                    "support": len(y_for_cv),
-                }
-            )
-
-            metrics_df = pd.DataFrame(metric_rows)
-        else:
-            metrics_df = pd.DataFrame(
-                [
-                    {
-                        "rmse": fold_df["rmse"].mean(),
-                        "mae": fold_df["mae"].mean(),
-                        "medae": fold_df["medae"].mean(),
-                        "r2": fold_df["r2"].mean(),
-                        "spearmanr": fold_df["spearmanr"].mean(),
-                        "support": len(y_for_cv),
-                    }
-                ]
-            )
-
-        print(f"\n{'='*50}")
-        print("Cross-Validation Summary")
-        print(f"{'='*50}")
-        print(metrics_df.to_string(index=False))
-
-        return metrics_df, predictions_df
-
-    finally:
-        log.info(f"Cleaning up model directory: {model_dir}")
-        shutil.rmtree(model_dir, ignore_errors=True)
-
-
 if __name__ == "__main__":
+    from workbench.api import Model
 
-    # Tests for the PyTorch utilities
-    from workbench.api import Model, Endpoint
-
-    # Initialize Workbench model
-    model_name = "caco2-er-reg-pytorch-test"
-    # model_name = "aqsol-pytorch-reg"
+    # Test pulling CV results
+    model_name = "aqsol-reg-pytorch"
     print(f"Loading Workbench model: {model_name}")
     model = Model(model_name)
     print(f"Model Framework: {model.model_framework}")
 
-    # Perform cross-fold inference
-    end = Endpoint(model.endpoints()[0])
-    end.cross_fold_inference()
+    # Pull CV results from training artifacts
+    metrics_df, predictions_df = pull_cv_results(model)
+    print(f"\nMetrics:\n{metrics_df}")
+    print(f"\nPredictions shape: {predictions_df.shape}")
+    print(f"Predictions columns: {predictions_df.columns.tolist()}")

workbench/utils/shap_utils.py

@@ -9,6 +9,7 @@ from typing import Optional, List, Tuple, Dict, Union
 from workbench.utils.xgboost_model_utils import xgboost_model_from_s3
 from workbench.utils.model_utils import load_category_mappings_from_s3
 from workbench.utils.pandas_utils import convert_categorical_types
+from workbench.model_script_utils.model_script_utils import decompress_features
 
 # Set up the log
 log = logging.getLogger("workbench")
@@ -111,61 +112,6 @@ def shap_values_data(
         return result_df, feature_df
 
 
-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
-
-
 def _calculate_shap_values(workbench_model, sample_df: pd.DataFrame = None):
     """
     Internal function to calculate SHAP values for Workbench Models.