workbench 0.8.162__py3-none-any.whl → 0.8.202__py3-none-any.whl

workbench/utils/chemprop_utils.py

@@ -0,0 +1,760 @@
+"""ChemProp utilities for Workbench models."""
+
+# flake8: noqa: E402
+import logging
+import os
+import tempfile
+from typing import Any, Tuple
+
+import numpy as np
+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
+
+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_chemprop_model_artifacts(model_dir: str) -> Tuple[Any, dict]:
+    """Load ChemProp MPNN model and artifacts from an extracted model directory.
+
+    Args:
+        model_dir: Directory containing extracted model artifacts
+
+    Returns:
+        Tuple of (MPNN model, artifacts_dict).
+        artifacts_dict contains 'label_encoder' and 'feature_metadata' if present.
+    """
+    import joblib
+    from chemprop import models
+
+    model_path = os.path.join(model_dir, "chemprop_model.pt")
+    if not os.path.exists(model_path):
+        raise FileNotFoundError(f"No chemprop_model.pt found in {model_dir}")
+
+    model = models.MPNN.load_from_file(model_path)
+    model.eval()
+
+    # 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)
+
+    feature_metadata_path = os.path.join(model_dir, "feature_metadata.joblib")
+    if os.path.exists(feature_metadata_path):
+        artifacts["feature_metadata"] = joblib.load(feature_metadata_path)
+
+    return model, artifacts
+
+
+def _find_smiles_column(columns: list) -> str:
+    """Find the SMILES column name from a list (case-insensitive match for 'smiles')."""
+    smiles_column = next((col for col in columns if col.lower() == "smiles"), None)
+    if smiles_column is None:
+        raise ValueError("Column list must contain a 'smiles' column (case-insensitive)")
+    return smiles_column
+
+
+def _create_molecule_datapoints(
+    smiles_list: list,
+    targets: list = None,
+    extra_descriptors: np.ndarray = None,
+) -> Tuple[list, list]:
+    """Create ChemProp MoleculeDatapoints from SMILES strings.
+
+    Args:
+        smiles_list: List of SMILES strings
+        targets: Optional list of target values (for training)
+        extra_descriptors: Optional array of extra features (n_samples, n_features)
+
+    Returns:
+        Tuple of (list of MoleculeDatapoint objects, list of valid indices)
+    """
+    from chemprop import data
+    from rdkit import Chem
+
+    datapoints = []
+    valid_indices = []
+    invalid_count = 0
+
+    for i, smi in enumerate(smiles_list):
+        # Validate SMILES with RDKit first
+        mol = Chem.MolFromSmiles(smi)
+        if mol is None:
+            invalid_count += 1
+            continue
+
+        # Build datapoint with optional target and extra descriptors
+        y = [targets[i]] if targets is not None else None
+        x_d = extra_descriptors[i] if extra_descriptors is not None else None
+
+        dp = data.MoleculeDatapoint.from_smi(smi, y=y, x_d=x_d)
+        datapoints.append(dp)
+        valid_indices.append(i)
+
+    if invalid_count > 0:
+        print(f"Warning: Skipped {invalid_count} invalid SMILES strings")
+
+    return datapoints, valid_indices
+
+
+def _build_mpnn_model(
+    hyperparameters: dict,
+    task: str = "regression",
+    num_classes: int = None,
+    n_extra_descriptors: int = 0,
+    x_d_transform: Any = None,
+    output_transform: Any = None,
+) -> Any:
+    """Build an MPNN model with the specified hyperparameters.
+
+    Args:
+        hyperparameters: Dictionary of model hyperparameters
+        task: Either "regression" or "classification"
+        num_classes: Number of classes for classification tasks
+        n_extra_descriptors: Number of extra descriptor features (for hybrid mode)
+        x_d_transform: Optional transform for extra descriptors (scaling)
+        output_transform: Optional transform for regression output (unscaling targets)
+
+    Returns:
+        Configured MPNN model
+    """
+    from chemprop import models, nn
+
+    # Model hyperparameters with defaults
+    hidden_dim = hyperparameters.get("hidden_dim", 300)
+    depth = hyperparameters.get("depth", 3)
+    dropout = hyperparameters.get("dropout", 0.1)
+    ffn_hidden_dim = hyperparameters.get("ffn_hidden_dim", 300)
+    ffn_num_layers = hyperparameters.get("ffn_num_layers", 1)
+
+    # Message passing component
+    mp = nn.BondMessagePassing(d_h=hidden_dim, depth=depth, dropout=dropout)
+
+    # Aggregation - NormAggregation normalizes output, recommended when using extra descriptors
+    agg = nn.NormAggregation()
+
+    # FFN input_dim = message passing output + extra descriptors
+    ffn_input_dim = hidden_dim + n_extra_descriptors
+
+    # Build FFN based on task type
+    if task == "classification" and num_classes is not None:
+        # Multi-class classification
+        ffn = nn.MulticlassClassificationFFN(
+            n_classes=num_classes,
+            input_dim=ffn_input_dim,
+            hidden_dim=ffn_hidden_dim,
+            n_layers=ffn_num_layers,
+            dropout=dropout,
+        )
+    else:
+        # Regression with optional output transform to unscale predictions
+        ffn = nn.RegressionFFN(
+            input_dim=ffn_input_dim,
+            hidden_dim=ffn_hidden_dim,
+            n_layers=ffn_num_layers,
+            dropout=dropout,
+            output_transform=output_transform,
+        )
+
+    # Create the MPNN model
+    mpnn = models.MPNN(
+        message_passing=mp,
+        agg=agg,
+        predictor=ffn,
+        batch_norm=True,
+        metrics=None,
+        X_d_transform=x_d_transform,
+    )
+
+    return mpnn
+
+
+def _extract_model_hyperparameters(loaded_model: Any) -> dict:
+    """Extract hyperparameters from a loaded ChemProp MPNN model.
+
+    Extracts architecture parameters from the model's components to replicate
+    the exact same model configuration during cross-validation.
+
+    Args:
+        loaded_model: Loaded MPNN model instance
+
+    Returns:
+        Dictionary of hyperparameters matching the training template
+    """
+    hyperparameters = {}
+
+    # Extract from message passing layer (BondMessagePassing)
+    mp = loaded_model.message_passing
+    hyperparameters["hidden_dim"] = getattr(mp, "d_h", 300)
+    hyperparameters["depth"] = getattr(mp, "depth", 3)
+
+    # Dropout is stored as a nn.Dropout module, get the p value
+    if hasattr(mp, "dropout"):
+        dropout_module = mp.dropout
+        hyperparameters["dropout"] = getattr(dropout_module, "p", 0.0)
+    else:
+        hyperparameters["dropout"] = 0.0
+
+    # Extract from predictor (FFN - either RegressionFFN or MulticlassClassificationFFN)
+    ffn = loaded_model.predictor
+
+    # FFN hidden_dim - try multiple attribute names
+    if hasattr(ffn, "hidden_dim"):
+        hyperparameters["ffn_hidden_dim"] = ffn.hidden_dim
+    elif hasattr(ffn, "d_h"):
+        hyperparameters["ffn_hidden_dim"] = ffn.d_h
+    else:
+        hyperparameters["ffn_hidden_dim"] = 300
+
+    # FFN num_layers - try multiple attribute names
+    if hasattr(ffn, "n_layers"):
+        hyperparameters["ffn_num_layers"] = ffn.n_layers
+    elif hasattr(ffn, "num_layers"):
+        hyperparameters["ffn_num_layers"] = ffn.num_layers
+    else:
+        hyperparameters["ffn_num_layers"] = 1
+
+    # Training hyperparameters (use defaults matching the template)
+    hyperparameters["max_epochs"] = 50
+    hyperparameters["patience"] = 10
+
+    return hyperparameters
+
+
+def _get_n_extra_descriptors(loaded_model: Any) -> int:
+    """Get the number of extra descriptors from the loaded model.
+
+    The model's X_d_transform contains the scaler which knows the feature dimension.
+
+    Args:
+        loaded_model: Loaded MPNN model instance
+
+    Returns:
+        Number of extra descriptors (0 if none)
+    """
+    x_d_transform = loaded_model.X_d_transform
+    if x_d_transform is None:
+        return 0
+
+    # ScaleTransform wraps a StandardScaler, check its mean_ attribute
+    if hasattr(x_d_transform, "mean"):
+        # x_d_transform.mean is a tensor
+        return len(x_d_transform.mean)
+    elif hasattr(x_d_transform, "scaler") and hasattr(x_d_transform.scaler, "mean_"):
+        return len(x_d_transform.scaler.mean_)
+
+    return 0
+
+
+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.
+
+    Args:
+        workbench_model: Workbench model object
+
+    Returns:
+        Tuple of:
+            - DataFrame with training metrics
+            - DataFrame with validation predictions
+    """
+    # Get the validation predictions from S3
+    s3_path = f"{workbench_model.model_training_path}/validation_predictions.csv"
+    predictions_df = pull_s3_data(s3_path)
+
+    if predictions_df is None:
+        raise ValueError(f"No validation predictions found at {s3_path}")
+
+    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}")
+
+    metrics_df = pd.DataFrame.from_dict(training_metrics)
+    log.info(f"Metrics summary:\n{metrics_df.to_string(index=False)}")
+
+    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 ChemProp MPNN 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
+
+    import joblib
+    import torch
+    from chemprop import data, nn
+    from lightning import pytorch as pl
+
+    from workbench.api import FeatureSet
+
+    # Create a temporary model directory
+    model_dir = tempfile.mkdtemp(prefix="chemprop_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_chemprop_model_artifacts(model_dir)
+        feature_metadata = artifacts.get("feature_metadata", {})
+
+        # Determine if classifier from predictor type
+        from chemprop.nn import MulticlassClassificationFFN
+
+        is_classifier = isinstance(loaded_model.predictor, MulticlassClassificationFFN)
+
+        # 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")
+
+        # Find SMILES column
+        smiles_column = _find_smiles_column(feature_cols)
+
+        # Determine extra feature columns:
+        # 1. First try feature_metadata (saved during training)
+        # 2. Fall back to inferring from feature_cols (exclude SMILES column)
+        # 3. Verify against model's X_d_transform dimension
+        if feature_metadata and "extra_feature_cols" in feature_metadata:
+            extra_feature_cols = feature_metadata["extra_feature_cols"]
+        else:
+            # Infer from feature list - everything except SMILES is an extra feature
+            extra_feature_cols = [f for f in feature_cols if f.lower() != "smiles"]
+
+            # Verify against model's actual extra descriptor dimension
+            n_extra_from_model = _get_n_extra_descriptors(loaded_model)
+            if n_extra_from_model > 0 and len(extra_feature_cols) != n_extra_from_model:
+                log.warning(
+                    f"Inferred {len(extra_feature_cols)} extra features but model expects "
+                    f"{n_extra_from_model}. Using inferred columns."
+                )
+
+        use_extra_features = len(extra_feature_cols) > 0
+
+        print(f"SMILES column: {smiles_column}")
+        print(f"Extra features: {extra_feature_cols if use_extra_features else 'None (SMILES only)'}")
+
+        # Drop rows with missing SMILES or target values
+        initial_count = len(df)
+        df = df.dropna(subset=[smiles_column, target_col])
+        dropped = initial_count - len(df)
+        if dropped > 0:
+            print(f"Dropped {dropped} rows with missing SMILES or target values")
+
+        # Extract hyperparameters from loaded model
+        hyperparameters = _extract_model_hyperparameters(loaded_model)
+        print(f"Extracted hyperparameters: {hyperparameters}")
+
+        # Get number of classes for classifier
+        num_classes = None
+        if is_classifier:
+            # Try to get from loaded model's FFN first (most reliable)
+            ffn = loaded_model.predictor
+            if hasattr(ffn, "n_classes"):
+                num_classes = ffn.n_classes
+            elif label_encoder is not None and hasattr(label_encoder, "classes_"):
+                num_classes = len(label_encoder.classes_)
+            else:
+                # Fit label encoder to get classes
+                if label_encoder is None:
+                    label_encoder = LabelEncoder()
+                label_encoder.fit(df[target_col])
+                num_classes = len(label_encoder.classes_)
+            print(f"Classification task with {num_classes} classes")
+
+        X = df[[smiles_column] + extra_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
+
+        # 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])
+
+            # Prepare extra features if using hybrid mode
+            train_extra_features = None
+            val_extra_features = None
+            col_means = None
+
+            if use_extra_features:
+                train_extra_features = df_train[extra_feature_cols].values.astype(np.float32)
+                val_extra_features = df_val[extra_feature_cols].values.astype(np.float32)
+
+                # Fill NaN with column means from training data
+                col_means = np.nanmean(train_extra_features, axis=0)
+                for i in range(train_extra_features.shape[1]):
+                    train_nan_mask = np.isnan(train_extra_features[:, i])
+                    val_nan_mask = np.isnan(val_extra_features[:, i])
+                    train_extra_features[train_nan_mask, i] = col_means[i]
+                    val_extra_features[val_nan_mask, i] = col_means[i]
+
+            # Create ChemProp datasets
+            train_datapoints, train_valid_idx = _create_molecule_datapoints(
+                df_train[smiles_column].tolist(),
+                df_train[target_col].tolist(),
+                train_extra_features,
+            )
+            val_datapoints, val_valid_idx = _create_molecule_datapoints(
+                df_val[smiles_column].tolist(),
+                df_val[target_col].tolist(),
+                val_extra_features,
+            )
+
+            # Update dataframes to only include valid molecules
+            df_train_valid = df_train.iloc[train_valid_idx].reset_index(drop=True)
+            df_val_valid = df_val.iloc[val_valid_idx].reset_index(drop=True)
+
+            train_dataset = data.MoleculeDataset(train_datapoints)
+            val_dataset = data.MoleculeDataset(val_datapoints)
+
+            # Save raw validation features before scaling
+            val_extra_raw = val_extra_features[val_valid_idx] if val_extra_features is not None else None
+
+            # Scale extra descriptors
+            feature_scaler = None
+            x_d_transform = None
+            if use_extra_features:
+                feature_scaler = train_dataset.normalize_inputs("X_d")
+                val_dataset.normalize_inputs("X_d", feature_scaler)
+                x_d_transform = nn.ScaleTransform.from_standard_scaler(feature_scaler)
+
+            # Scale targets for regression
+            target_scaler = None
+            output_transform = None
+            if not is_classifier:
+                target_scaler = train_dataset.normalize_targets()
+                val_dataset.normalize_targets(target_scaler)
+                output_transform = nn.UnscaleTransform.from_standard_scaler(target_scaler)
+
+            # Get batch size
+            batch_size = min(64, max(16, len(df_train_valid) // 16))
+
+            train_loader = data.build_dataloader(train_dataset, batch_size=batch_size, shuffle=True)
+            val_loader = data.build_dataloader(val_dataset, batch_size=batch_size, shuffle=False)
+
+            # Build the model
+            n_extra = len(extra_feature_cols) if use_extra_features else 0
+            mpnn = _build_mpnn_model(
+                hyperparameters,
+                task="classification" if is_classifier else "regression",
+                num_classes=num_classes,
+                n_extra_descriptors=n_extra,
+                x_d_transform=x_d_transform,
+                output_transform=output_transform,
+            )
+
+            # Training configuration
+            max_epochs = hyperparameters.get("max_epochs", 50)
+            patience = hyperparameters.get("patience", 10)
+
+            # Set up trainer
+            checkpoint_dir = os.path.join(model_dir, f"fold_{fold_idx}")
+            os.makedirs(checkpoint_dir, exist_ok=True)
+
+            callbacks = [
+                pl.callbacks.EarlyStopping(monitor="val_loss", patience=patience, mode="min"),
+                pl.callbacks.ModelCheckpoint(
+                    dirpath=checkpoint_dir,
+                    filename="best_model",
+                    monitor="val_loss",
+                    mode="min",
+                    save_top_k=1,
+                ),
+            ]
+
+            trainer = pl.Trainer(
+                accelerator="auto",
+                max_epochs=max_epochs,
+                callbacks=callbacks,
+                logger=False,
+                enable_progress_bar=True,
+            )
+
+            # Train the model
+            trainer.fit(mpnn, train_loader, val_loader)
+
+            # Load the best checkpoint
+            if trainer.checkpoint_callback and trainer.checkpoint_callback.best_model_path:
+                best_ckpt_path = trainer.checkpoint_callback.best_model_path
+                checkpoint = torch.load(best_ckpt_path, weights_only=False)
+                mpnn.load_state_dict(checkpoint["state_dict"])
+
+            mpnn.eval()
+
+            # Make predictions using raw features
+            val_datapoints_raw, _ = _create_molecule_datapoints(
+                df_val_valid[smiles_column].tolist(),
+                df_val_valid[target_col].tolist(),
+                val_extra_raw,
+            )
+            val_dataset_raw = data.MoleculeDataset(val_datapoints_raw)
+            val_loader_pred = data.build_dataloader(val_dataset_raw, batch_size=batch_size, shuffle=False)
+
+            with torch.inference_mode():
+                val_predictions = trainer.predict(mpnn, val_loader_pred)
+
+            preds = np.concatenate([p.numpy() for p in val_predictions], axis=0)
+
+            # ChemProp may return (n_samples, 1, n_classes) for multiclass - squeeze middle dim
+            if preds.ndim == 3 and preds.shape[1] == 1:
+                preds = preds.squeeze(axis=1)
+
+            # Map predictions back to original indices
+            original_val_indices = df.iloc[val_idx].index[val_valid_idx]
+
+            if is_classifier:
+                # Get class predictions
+                if preds.ndim == 2 and preds.shape[1] > 1:
+                    class_preds = np.argmax(preds, axis=1)
+                else:
+                    class_preds = (preds.flatten() > 0.5).astype(int)
+
+                preds_decoded = label_encoder.inverse_transform(class_preds)
+                predictions_df.loc[original_val_indices, "prediction"] = preds_decoded
+
+                # Store probabilities
+                if preds.ndim == 2 and preds.shape[1] > 1:
+                    for i, idx in enumerate(original_val_indices):
+                        predictions_df.at[idx, "pred_proba"] = preds[i].tolist()
+            else:
+                predictions_df.loc[original_val_indices, "prediction"] = preds.flatten()
+
+            # Calculate fold metrics
+            y_val = df_val_valid[target_col].values
+
+            if is_classifier:
+                y_val_orig = label_encoder.inverse_transform(y_val.astype(int))
+                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_
+                )
+
+                # ROC AUC
+                if preds.ndim == 2 and preds.shape[1] > 1:
+                    roc_auc_overall = roc_auc_score(y_val, preds, multi_class="ovr", average="macro")
+                    roc_auc_per_class = roc_auc_score(y_val, preds, multi_class="ovr", average=None)
+                else:
+                    roc_auc_overall = roc_auc_score(y_val, preds.flatten())
+                    roc_auc_per_class = [roc_auc_overall]
+
+                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:
+                spearman_corr, _ = spearmanr(y_val, preds.flatten())
+                rmse = np.sqrt(mean_squared_error(y_val, preds.flatten()))
+
+                fold_metrics.append(
+                    {
+                        "fold": fold_idx,
+                        "rmse": rmse,
+                        "mae": mean_absolute_error(y_val, preds.flatten()),
+                        "medae": median_absolute_error(y_val, preds.flatten()),
+                        "r2": r2_score(y_val, preds.flatten()),
+                        "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__":
+
+    # Tests for the ChemProp utilities
+    from workbench.api import Endpoint, Model
+
+    # Initialize Workbench model
+    model_name = "aqsol-chemprop-reg"
+    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()