claude-flow-novice 1.2.1 → 1.3.1

package/examples/ml_foundation/foundation_agent_enhanced.py

@@ -0,0 +1,1002 @@
+"""
+MLE-STAR Foundation Agent - Enhanced Implementation
+Advanced Foundation Model Builder with Multi-Dataset Support
+
+This enhanced version includes:
+- Automated dataset detection and handling
+- Advanced preprocessing pipelines
+- Multi-model baseline creation
+- Hyperparameter optimization
+- Model interpretability
+- Performance tracking and coordination
+"""
+
+import numpy as np
+import pandas as pd
+from typing import Dict, List, Tuple, Any, Optional, Union
+from pathlib import Path
+import json
+import logging
+import joblib
+from datetime import datetime
+import subprocess
+import sys
+
+# Core ML libraries
+from sklearn.model_selection import (
+    train_test_split, cross_val_score, StratifiedKFold, KFold,
+    GridSearchCV, RandomizedSearchCV
+)
+from sklearn.preprocessing import (
+    StandardScaler, MinMaxScaler, RobustScaler,
+    LabelEncoder, OneHotEncoder, OrdinalEncoder
+)
+from sklearn.compose import ColumnTransformer
+from sklearn.pipeline import Pipeline
+from sklearn.impute import SimpleImputer, KNNImputer
+from sklearn.feature_selection import (
+    SelectKBest, f_classif, f_regression,
+    RFE, SelectFromModel, mutual_info_classif, mutual_info_regression
+)
+from sklearn.metrics import (
+    accuracy_score, precision_recall_fscore_support, 
+    mean_squared_error, r2_score, roc_auc_score,
+    confusion_matrix, classification_report
+)
+
+# Models
+from sklearn.linear_model import LogisticRegression, LinearRegression, Ridge, Lasso
+from sklearn.ensemble import (
+    RandomForestClassifier, RandomForestRegressor,
+    GradientBoostingClassifier, GradientBoostingRegressor,
+    ExtraTreesClassifier, ExtraTreesRegressor
+)
+from sklearn.svm import SVC, SVR
+from sklearn.neural_network import MLPClassifier, MLPRegressor
+from sklearn.naive_bayes import GaussianNB
+from sklearn.neighbors import KNeighborsClassifier, KNeighborsRegressor
+
+# Advanced features
+from sklearn.decomposition import PCA, TruncatedSVD
+from sklearn.manifold import TSNE
+from sklearn.cluster import KMeans
+import warnings
+warnings.filterwarnings('ignore')
+
+# Configure logging
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
+
+class EnhancedFoundationAgent:
+    """
+    Enhanced MLE-STAR Foundation Agent
+    
+    Advanced features:
+    - Multi-dataset support (CSV, Parquet, JSON, etc.)
+    - Automated feature engineering
+    - Advanced model selection
+    - Hyperparameter optimization
+    - Model interpretability
+    - Claude Flow coordination
+    """
+    
+    def __init__(self, 
+                 task_type: str = 'auto',
+                 session_id: Optional[str] = None,
+                 agent_id: str = 'foundation_agent',
+                 config: Optional[Dict] = None):
+        """
+        Initialize Enhanced Foundation Agent
+        
+        Args:
+            task_type: 'classification', 'regression', or 'auto' for automatic detection
+            session_id: Session ID for coordination
+            agent_id: Agent identifier
+            config: Advanced configuration
+        """
+        self.task_type = task_type
+        self.session_id = session_id or f"foundation-{datetime.now().strftime('%Y%m%d-%H%M%S')}"
+        self.agent_id = agent_id
+        self.config = config or self._get_advanced_config()
+        
+        # Components
+        self.data_handler = DataHandler()
+        self.feature_engineer = FeatureEngineer()
+        self.model_builder = ModelBuilder(task_type)
+        self.performance_tracker = PerformanceTracker()
+        
+        # Results storage
+        self.data_insights = {}
+        self.preprocessing_pipeline = None
+        self.baseline_models = {}
+        self.best_model = None
+        self.performance_metrics = {}
+        
+        # Claude Flow coordination
+        self._setup_coordination()
+        
+        logger.info(f"Initialized Enhanced Foundation Agent: {agent_id}")
+        
+    def _get_advanced_config(self) -> Dict:
+        """Get advanced configuration with sensible defaults"""
+        return {
+            'data': {
+                'auto_detect_task': True,
+                'handle_imbalanced': True,
+                'outlier_detection': True,
+                'feature_scaling': 'auto'  # auto, standard, minmax, robust
+            },
+            'preprocessing': {
+                'numeric_imputation': 'knn',  # mean, median, knn
+                'categorical_imputation': 'mode',
+                'encoding_strategy': 'auto',  # auto, onehot, ordinal, target
+                'handle_high_cardinality': True,
+                'feature_generation': True,
+                'dimensionality_reduction': 'auto'
+            },
+            'feature_selection': {
+                'enabled': True,
+                'method': 'auto',  # auto, univariate, rfe, model_based
+                'n_features': 'auto',
+                'importance_threshold': 0.01
+            },
+            'modeling': {
+                'algorithms': 'auto',  # auto, basic, advanced, all
+                'hyperparameter_tuning': True,
+                'tuning_method': 'random',  # grid, random, bayesian
+                'cv_folds': 5,
+                'scoring': 'auto',
+                'ensemble_creation': True
+            },
+            'validation': {
+                'test_size': 0.2,
+                'stratify': True,
+                'random_state': 42
+            },
+            'output': {
+                'save_models': True,
+                'save_reports': True,
+                'save_visualizations': True,
+                'output_dir': './foundation_output',
+                'coordinate_with_agents': True
+            }
+        }
+    
+    def _setup_coordination(self):
+        """Setup Claude Flow coordination"""
+        try:
+            # Notify coordination start
+            cmd = f"npx claude-flow@alpha hooks notify --message 'Foundation Agent initialized: {self.agent_id}'"
+            subprocess.run(cmd, shell=True, capture_output=True)
+            
+            # Store agent status
+            status = {
+                'agent': self.agent_id,
+                'status': 'initialized',
+                'session': self.session_id,
+                'capabilities': ['data_preprocessing', 'feature_engineering', 'baseline_models', 'hyperparameter_tuning']
+            }
+            
+            cmd = f"npx claude-flow@alpha memory store 'agent/{self.agent_id}/status' '{json.dumps(status)}'"
+            subprocess.run(cmd, shell=True, capture_output=True)
+            
+        except Exception as e:
+            logger.warning(f"Coordination setup warning: {e}")
+    
+    def run(self, 
+            data_path: Optional[str] = None,
+            X: Optional[pd.DataFrame] = None,
+            y: Optional[pd.Series] = None) -> Dict:
+        """
+        Main execution method for Foundation Agent
+        
+        Args:
+            data_path: Path to dataset file
+            X: Feature dataframe (if data already loaded)
+            y: Target variable (if data already loaded)
+            
+        Returns:
+            Dictionary with comprehensive results
+        """
+        logger.info("Starting Enhanced Foundation Pipeline...")
+        start_time = datetime.now()
+        
+        try:
+            # Step 1: Load and analyze data
+            if data_path:
+                X, y = self.data_handler.load_data(data_path)
+            elif X is None or y is None:
+                # Create demo dataset
+                logger.info("No data provided, creating demonstration dataset...")
+                X, y = self._create_demo_dataset()
+            
+            # Auto-detect task type if needed
+            if self.task_type == 'auto':
+                self.task_type = self._detect_task_type(y)
+                self.model_builder.task_type = self.task_type
+            
+            # Step 2: Comprehensive data analysis
+            self.data_insights = self._analyze_data_comprehensively(X, y)
+            self._store_insights('data_analysis', self.data_insights)
+            
+            # Step 3: Advanced preprocessing
+            X_processed, preprocessing_pipeline = self._create_advanced_preprocessing(X, y)
+            self.preprocessing_pipeline = preprocessing_pipeline
+            
+            # Step 4: Feature engineering
+            X_engineered = self.feature_engineer.engineer_features(
+                X_processed, y, self.task_type
+            )
+            
+            # Step 5: Feature selection
+            X_selected, feature_selector = self._select_features(X_engineered, y)
+            
+            # Step 6: Train-test split
+            X_train, X_test, y_train, y_test = train_test_split(
+                X_selected, y,
+                test_size=self.config['validation']['test_size'],
+                random_state=self.config['validation']['random_state'],
+                stratify=y if self.task_type == 'classification' and self.config['validation']['stratify'] else None
+            )
+            
+            # Step 7: Build baseline models
+            baseline_results = self._build_baseline_models(X_train, y_train, X_test, y_test)
+            self.baseline_models = baseline_results['models']
+            self.performance_metrics = baseline_results['metrics']
+            
+            # Step 8: Hyperparameter optimization (if enabled)
+            if self.config['modeling']['hyperparameter_tuning']:
+                best_model_info = self._optimize_hyperparameters(X_train, y_train, X_test, y_test)
+                self.best_model = best_model_info['model']
+            else:
+                # Select best baseline
+                self.best_model = self._select_best_baseline()
+            
+            # Step 9: Create final pipeline
+            final_pipeline = self._create_final_pipeline(
+                preprocessing_pipeline, feature_selector, self.best_model
+            )
+            
+            # Step 10: Generate comprehensive report
+            results = self._generate_comprehensive_report(
+                X, y, X_test, y_test, final_pipeline, start_time
+            )
+            
+            # Step 11: Save outputs and coordinate
+            if self.config['output']['save_models']:
+                self._save_all_outputs(results, final_pipeline)
+            
+            # Step 12: Coordinate with other agents
+            if self.config['output']['coordinate_with_agents']:
+                self._coordinate_handoff(results)
+            
+            logger.info("Foundation Pipeline completed successfully!")
+            return results
+            
+        except Exception as e:
+            logger.error(f"Error in Foundation Pipeline: {e}")
+            self._handle_error(e)
+            raise
+    
+    def _detect_task_type(self, y: pd.Series) -> str:
+        """Automatically detect if task is classification or regression"""
+        unique_values = y.nunique()
+        
+        # Simple heuristic: if less than 20 unique values and no floats, likely classification
+        if unique_values < 20 and y.dtype in ['int64', 'object', 'category']:
+            return 'classification'
+        else:
+            return 'regression'
+    
+    def _analyze_data_comprehensively(self, X: pd.DataFrame, y: pd.Series) -> Dict:
+        """Perform comprehensive data analysis"""
+        logger.info("Performing comprehensive data analysis...")
+        
+        insights = {
+            'basic_stats': {
+                'n_samples': len(X),
+                'n_features': X.shape[1],
+                'memory_usage': f"{X.memory_usage().sum() / 1024**2:.2f} MB"
+            },
+            'feature_types': {},
+            'missing_analysis': {},
+            'outlier_analysis': {},
+            'correlation_analysis': {},
+            'target_analysis': {},
+            'recommendations': []
+        }
+        
+        # Analyze feature types
+        numeric_cols = X.select_dtypes(include=['number']).columns.tolist()
+        categorical_cols = X.select_dtypes(include=['object', 'category']).columns.tolist()
+        
+        insights['feature_types'] = {
+            'numeric': numeric_cols,
+            'categorical': categorical_cols,
+            'datetime': X.select_dtypes(include=['datetime']).columns.tolist()
+        }
+        
+        # Missing value analysis
+        missing_data = X.isnull().sum()
+        insights['missing_analysis'] = {
+            'total_missing': int(missing_data.sum()),
+            'columns_with_missing': missing_data[missing_data > 0].to_dict(),
+            'missing_patterns': self._analyze_missing_patterns(X)
+        }
+        
+        # Outlier detection for numeric features
+        if numeric_cols:
+            outlier_info = {}
+            for col in numeric_cols:
+                Q1 = X[col].quantile(0.25)
+                Q3 = X[col].quantile(0.75)
+                IQR = Q3 - Q1
+                outliers = X[(X[col] < Q1 - 1.5 * IQR) | (X[col] > Q3 + 1.5 * IQR)]
+                if len(outliers) > 0:
+                    outlier_info[col] = {
+                        'count': len(outliers),
+                        'percentage': len(outliers) / len(X) * 100
+                    }
+            insights['outlier_analysis'] = outlier_info
+        
+        # Correlation analysis
+        if len(numeric_cols) > 1:
+            corr_matrix = X[numeric_cols].corr()
+            high_corr = []
+            for i in range(len(corr_matrix.columns)):
+                for j in range(i+1, len(corr_matrix.columns)):
+                    if abs(corr_matrix.iloc[i, j]) > 0.8:
+                        high_corr.append({
+                            'feature1': corr_matrix.columns[i],
+                            'feature2': corr_matrix.columns[j],
+                            'correlation': corr_matrix.iloc[i, j]
+                        })
+            insights['correlation_analysis']['high_correlations'] = high_corr
+        
+        # Target variable analysis
+        if self.task_type == 'classification':
+            value_counts = y.value_counts()
+            insights['target_analysis'] = {
+                'unique_classes': len(value_counts),
+                'class_distribution': value_counts.to_dict(),
+                'imbalance_ratio': value_counts.max() / value_counts.min()
+            }
+            
+            if insights['target_analysis']['imbalance_ratio'] > 3:
+                insights['recommendations'].append(
+                    "High class imbalance detected. Consider SMOTE or class weights."
+                )
+        else:
+            insights['target_analysis'] = {
+                'mean': y.mean(),
+                'std': y.std(),
+                'skewness': y.skew(),
+                'kurtosis': y.kurtosis()
+            }
+            
+            if abs(y.skew()) > 1:
+                insights['recommendations'].append(
+                    "Target variable is skewed. Consider log transformation."
+                )
+        
+        return insights
+    
+    def _analyze_missing_patterns(self, X: pd.DataFrame) -> Dict:
+        """Analyze patterns in missing data"""
+        missing_mask = X.isnull()
+        
+        # Check if missingness is completely random or has patterns
+        patterns = {
+            'random': True,
+            'columns_always_missing_together': []
+        }
+        
+        # Simple check for columns that are always missing together
+        for i, col1 in enumerate(missing_mask.columns):
+            for col2 in missing_mask.columns[i+1:]:
+                if (missing_mask[col1] == missing_mask[col2]).all():
+                    patterns['columns_always_missing_together'].append([col1, col2])
+                    patterns['random'] = False
+        
+        return patterns
+    
+    def _create_advanced_preprocessing(self, X: pd.DataFrame, y: pd.Series) -> Tuple[np.ndarray, Pipeline]:
+        """Create advanced preprocessing pipeline"""
+        logger.info("Creating advanced preprocessing pipeline...")
+        
+        numeric_features = X.select_dtypes(include=['number']).columns.tolist()
+        categorical_features = X.select_dtypes(include=['object', 'category']).columns.tolist()
+        
+        # Numeric pipeline
+        numeric_transformer = self._get_numeric_transformer()
+        
+        # Categorical pipeline
+        categorical_transformer = self._get_categorical_transformer(X[categorical_features] if categorical_features else pd.DataFrame())
+        
+        # Combine transformers
+        preprocessor = ColumnTransformer(
+            transformers=[
+                ('num', numeric_transformer, numeric_features),
+                ('cat', categorical_transformer, categorical_features)
+            ]
+        )
+        
+        # Fit and transform
+        X_processed = preprocessor.fit_transform(X)
+        
+        return X_processed, preprocessor
+    
+    def _get_numeric_transformer(self) -> Pipeline:
+        """Get numeric preprocessing pipeline"""
+        steps = []
+        
+        # Imputation
+        if self.config['preprocessing']['numeric_imputation'] == 'knn':
+            steps.append(('imputer', KNNImputer(n_neighbors=5)))
+        else:
+            steps.append(('imputer', SimpleImputer(strategy=self.config['preprocessing']['numeric_imputation'])))
+        
+        # Scaling
+        if self.config['data']['feature_scaling'] == 'standard':
+            steps.append(('scaler', StandardScaler()))
+        elif self.config['data']['feature_scaling'] == 'minmax':
+            steps.append(('scaler', MinMaxScaler()))
+        elif self.config['data']['feature_scaling'] == 'robust':
+            steps.append(('scaler', RobustScaler()))
+        
+        return Pipeline(steps)
+    
+    def _get_categorical_transformer(self, cat_data: pd.DataFrame) -> Pipeline:
+        """Get categorical preprocessing pipeline"""
+        steps = []
+        
+        # Imputation
+        steps.append(('imputer', SimpleImputer(strategy='constant', fill_value='missing')))
+        
+        # Encoding
+        if self.config['preprocessing']['encoding_strategy'] == 'auto':
+            # Use ordinal for high cardinality, onehot for low
+            high_card_threshold = 10
+            if cat_data.shape[1] > 0:
+                avg_cardinality = cat_data.nunique().mean()
+                if avg_cardinality > high_card_threshold:
+                    steps.append(('encoder', OrdinalEncoder(handle_unknown='use_encoded_value', unknown_value=-1)))
+                else:
+                    steps.append(('encoder', OneHotEncoder(handle_unknown='ignore', sparse_output=False)))
+            else:
+                steps.append(('encoder', OneHotEncoder(handle_unknown='ignore', sparse_output=False)))
+        
+        return Pipeline(steps)
+    
+    def _select_features(self, X: np.ndarray, y: pd.Series) -> Tuple[np.ndarray, Any]:
+        """Advanced feature selection"""
+        if not self.config['feature_selection']['enabled']:
+            return X, None
+        
+        logger.info("Performing feature selection...")
+        
+        if self.config['feature_selection']['method'] == 'auto':
+            # Use mutual information
+            if self.task_type == 'classification':
+                selector = SelectKBest(mutual_info_classif, k='all')
+            else:
+                selector = SelectKBest(mutual_info_regression, k='all')
+            
+            selector.fit(X, y)
+            
+            # Determine optimal number of features
+            scores = selector.scores_
+            if self.config['feature_selection']['n_features'] == 'auto':
+                # Keep features with score above threshold
+                threshold = np.percentile(scores, 25)  # Keep top 75% features
+                n_features = sum(scores > threshold)
+            else:
+                n_features = min(self.config['feature_selection']['n_features'], X.shape[1])
+            
+            selector.set_params(k=n_features)
+            X_selected = selector.fit_transform(X, y)
+            
+            logger.info(f"Selected {n_features} out of {X.shape[1]} features")
+            
+            return X_selected, selector
+        
+        return X, None
+    
+    def _build_baseline_models(self, X_train, y_train, X_test, y_test) -> Dict:
+        """Build and evaluate baseline models"""
+        logger.info("Building baseline models...")
+        
+        models = self.model_builder.get_baseline_models(self.config['modeling']['algorithms'])
+        results = {'models': {}, 'metrics': {}}
+        
+        for name, model in models.items():
+            logger.info(f"Training {name}...")
+            
+            # Train model
+            model.fit(X_train, y_train)
+            
+            # Make predictions
+            y_pred = model.predict(X_test)
+            
+            # Evaluate
+            metrics = self.performance_tracker.evaluate_model(
+                model, X_test, y_test, y_pred, self.task_type
+            )
+            
+            results['models'][name] = model
+            results['metrics'][name] = metrics
+            
+            # Store intermediate results
+            self._store_model_performance(name, metrics)
+        
+        return results
+    
+    def _optimize_hyperparameters(self, X_train, y_train, X_test, y_test) -> Dict:
+        """Optimize hyperparameters for best models"""
+        logger.info("Optimizing hyperparameters...")
+        
+        # Select top 3 models for optimization
+        sorted_models = sorted(
+            self.performance_metrics.items(),
+            key=lambda x: x[1].get('cv_score', 0),
+            reverse=True
+        )[:3]
+        
+        best_score = -np.inf
+        best_model_info = None
+        
+        for model_name, _ in sorted_models:
+            model = self.baseline_models[model_name]
+            param_grid = self.model_builder.get_param_grid(model_name)
+            
+            if param_grid:
+                logger.info(f"Tuning {model_name}...")
+                
+                if self.config['modeling']['tuning_method'] == 'grid':
+                    search = GridSearchCV(
+                        model, param_grid,
+                        cv=self.config['modeling']['cv_folds'],
+                        scoring=self._get_scoring_metric(),
+                        n_jobs=-1
+                    )
+                else:
+                    search = RandomizedSearchCV(
+                        model, param_grid,
+                        n_iter=20,
+                        cv=self.config['modeling']['cv_folds'],
+                        scoring=self._get_scoring_metric(),
+                        n_jobs=-1,
+                        random_state=42
+                    )
+                
+                search.fit(X_train, y_train)
+                
+                if search.best_score_ > best_score:
+                    best_score = search.best_score_
+                    best_model_info = {
+                        'name': model_name,
+                        'model': search.best_estimator_,
+                        'params': search.best_params_,
+                        'score': search.best_score_
+                    }
+        
+        logger.info(f"Best optimized model: {best_model_info['name']} with score: {best_score:.4f}")
+        return best_model_info
+    
+    def _get_scoring_metric(self) -> str:
+        """Get appropriate scoring metric"""
+        if self.config['modeling']['scoring'] != 'auto':
+            return self.config['modeling']['scoring']
+        
+        if self.task_type == 'classification':
+            return 'f1_weighted'
+        else:
+            return 'r2'
+    
+    def _select_best_baseline(self) -> Any:
+        """Select best baseline model without hyperparameter tuning"""
+        if self.task_type == 'classification':
+            best_model_name = max(
+                self.performance_metrics.items(),
+                key=lambda x: x[1].get('f1_score', 0)
+            )[0]
+        else:
+            best_model_name = max(
+                self.performance_metrics.items(),
+                key=lambda x: x[1].get('r2_score', 0)
+            )[0]
+        
+        return self.baseline_models[best_model_name]
+    
+    def _create_final_pipeline(self, preprocessor, feature_selector, model) -> Pipeline:
+        """Create final end-to-end pipeline"""
+        steps = [('preprocessor', preprocessor)]
+        
+        if feature_selector is not None:
+            steps.append(('feature_selector', feature_selector))
+        
+        steps.append(('model', model))
+        
+        return Pipeline(steps)
+    
+    def _generate_comprehensive_report(self, X, y, X_test, y_test, pipeline, start_time) -> Dict:
+        """Generate comprehensive results report"""
+        logger.info("Generating comprehensive report...")
+        
+        report = {
+            'execution_info': {
+                'agent_id': self.agent_id,
+                'session_id': self.session_id,
+                'task_type': self.task_type,
+                'execution_time': str(datetime.now() - start_time),
+                'timestamp': datetime.now().isoformat()
+            },
+            'data_insights': self.data_insights,
+            'preprocessing_steps': self._get_preprocessing_summary(),
+            'baseline_performance': self.performance_metrics,
+            'best_model': {
+                'name': type(self.best_model).__name__,
+                'parameters': self.best_model.get_params() if hasattr(self.best_model, 'get_params') else {}
+            },
+            'feature_importance': self._get_feature_importance(),
+            'recommendations': self._generate_recommendations()
+        }
+        
+        return report
+    
+    def _get_preprocessing_summary(self) -> List[str]:
+        """Get summary of preprocessing steps"""
+        steps = []
+        if self.preprocessing_pipeline:
+            for name, transformer in self.preprocessing_pipeline.named_transformers_.items():
+                if hasattr(transformer, 'steps'):
+                    for step_name, step in transformer.steps:
+                        steps.append(f"{name}_{step_name}: {type(step).__name__}")
+        return steps
+    
+    def _get_feature_importance(self) -> Dict:
+        """Extract feature importance if available"""
+        importance = {}
+        
+        if hasattr(self.best_model, 'feature_importances_'):
+            importance['values'] = self.best_model.feature_importances_.tolist()
+            importance['type'] = 'tree_based'
+        elif hasattr(self.best_model, 'coef_'):
+            importance['values'] = np.abs(self.best_model.coef_).flatten().tolist()
+            importance['type'] = 'linear'
+        
+        return importance
+    
+    def _generate_recommendations(self) -> List[str]:
+        """Generate actionable recommendations"""
+        recommendations = []
+        
+        # Based on data insights
+        if self.data_insights.get('missing_analysis', {}).get('total_missing', 0) > 0:
+            recommendations.append("Consider advanced imputation methods for missing data")
+        
+        if self.data_insights.get('outlier_analysis'):
+            recommendations.append("Outliers detected - consider robust scaling or outlier removal")
+        
+        # Based on model performance
+        best_score = max(
+            m.get('cv_score', 0) for m in self.performance_metrics.values()
+        )
+        
+        if best_score < 0.8:
+            recommendations.append("Model performance is moderate - consider feature engineering or ensemble methods")
+        
+        # Based on task type
+        if self.task_type == 'classification' and self.data_insights.get('target_analysis', {}).get('imbalance_ratio', 1) > 3:
+            recommendations.append("Use SMOTE or adjust class weights for imbalanced data")
+        
+        return recommendations
+    
+    def _save_all_outputs(self, results: Dict, pipeline: Pipeline):
+        """Save all outputs to disk"""
+        output_dir = Path(self.config['output']['output_dir'])
+        output_dir.mkdir(parents=True, exist_ok=True)
+        
+        # Save models
+        joblib.dump(pipeline, output_dir / 'final_pipeline.pkl')
+        
+        for name, model in self.baseline_models.items():
+            joblib.dump(model, output_dir / f'baseline_{name}.pkl')
+        
+        # Save results
+        with open(output_dir / 'foundation_results.json', 'w') as f:
+            json.dump(results, f, indent=2, default=str)
+        
+        # Save performance metrics
+        pd.DataFrame(self.performance_metrics).T.to_csv(
+            output_dir / 'performance_metrics.csv'
+        )
+        
+        logger.info(f"All outputs saved to {output_dir}")
+    
+    def _coordinate_handoff(self, results: Dict):
+        """Coordinate handoff to next agent"""
+        try:
+            # Store results for next agent
+            handoff_data = {
+                'from': self.agent_id,
+                'to': 'refinement_agent',
+                'session': self.session_id,
+                'timestamp': datetime.now().isoformat(),
+                'best_baseline_score': max(
+                    m.get('cv_score', 0) for m in self.performance_metrics.values()
+                ),
+                'pipeline_path': str(Path(self.config['output']['output_dir']) / 'final_pipeline.pkl'),
+                'recommendations': results['recommendations']
+            }
+            
+            cmd = f"npx claude-flow@alpha memory store 'agent/{self.agent_id}/handoff' '{json.dumps(handoff_data)}'"
+            subprocess.run(cmd, shell=True, capture_output=True)
+            
+            # Notify completion
+            cmd = f"npx claude-flow@alpha hooks post-task --task-id '{self.agent_id}' --analyze-performance true"
+            subprocess.run(cmd, shell=True, capture_output=True)
+            
+            logger.info("Handoff to next agent completed")
+            
+        except Exception as e:
+            logger.warning(f"Handoff coordination warning: {e}")
+    
+    def _store_insights(self, key: str, data: Dict):
+        """Store insights in memory"""
+        try:
+            cmd = f"npx claude-flow@alpha memory store 'agent/{self.agent_id}/{key}' '{json.dumps(data, default=str)}'"
+            subprocess.run(cmd, shell=True, capture_output=True)
+        except Exception as e:
+            logger.warning(f"Memory storage warning: {e}")
+    
+    def _store_model_performance(self, model_name: str, metrics: Dict):
+        """Store individual model performance"""
+        try:
+            key = f'agent/{self.agent_id}/model_{model_name}'
+            cmd = f"npx claude-flow@alpha memory store '{key}' '{json.dumps(metrics, default=str)}'"
+            subprocess.run(cmd, shell=True, capture_output=True)
+        except Exception as e:
+            logger.warning(f"Performance storage warning: {e}")
+    
+    def _handle_error(self, error: Exception):
+        """Handle errors and notify coordination system"""
+        try:
+            error_data = {
+                'agent': self.agent_id,
+                'error': str(error),
+                'timestamp': datetime.now().isoformat(),
+                'session': self.session_id
+            }
+            
+            cmd = f"npx claude-flow@alpha memory store 'agent/{self.agent_id}/error' '{json.dumps(error_data)}'"
+            subprocess.run(cmd, shell=True, capture_output=True)
+            
+            cmd = f"npx claude-flow@alpha hooks notify --message 'Foundation Agent error: {str(error)}'"
+            subprocess.run(cmd, shell=True, capture_output=True)
+            
+        except Exception as e:
+            logger.warning(f"Error handling warning: {e}")
+    
+    def _create_demo_dataset(self) -> Tuple[pd.DataFrame, pd.Series]:
+        """Create a demonstration dataset"""
+        from sklearn.datasets import make_classification
+        
+        X, y = make_classification(
+            n_samples=2000,
+            n_features=30,
+            n_informative=20,
+            n_redundant=5,
+            n_repeated=2,
+            n_classes=3,
+            n_clusters_per_class=2,
+            weights=[0.5, 0.3, 0.2],  # Imbalanced
+            flip_y=0.05,  # Add noise
+            random_state=42
+        )
+        
+        # Convert to DataFrame
+        feature_names = [f'feature_{i}' for i in range(30)]
+        X_df = pd.DataFrame(X, columns=feature_names)
+        
+        # Add categorical features
+        X_df['category_A'] = np.random.choice(['low', 'medium', 'high'], size=2000, p=[0.5, 0.3, 0.2])
+        X_df['category_B'] = np.random.choice(['alpha', 'beta', 'gamma', 'delta'], size=2000)
+        X_df['category_C'] = np.random.choice(['X', 'Y', 'Z'], size=2000)
+        
+        # Add some missing values
+        for col in np.random.choice(X_df.columns, 5):
+            missing_idx = np.random.choice(X_df.index, size=int(0.1 * len(X_df)))
+            X_df.loc[missing_idx, col] = np.nan
+        
+        # Add some outliers
+        for col in ['feature_0', 'feature_1', 'feature_2']:
+            outlier_idx = np.random.choice(X_df.index, size=20)
+            X_df.loc[outlier_idx, col] = X_df[col].mean() + 5 * X_df[col].std()
+        
+        return X_df, pd.Series(y, name='target')
+
+
+class DataHandler:
+    """Handle various data formats and sources"""
+    
+    def load_data(self, path: str) -> Tuple[pd.DataFrame, pd.Series]:
+        """Load data from various formats"""
+        path = Path(path)
+        
+        if path.suffix == '.csv':
+            df = pd.read_csv(path)
+        elif path.suffix == '.parquet':
+            df = pd.read_parquet(path)
+        elif path.suffix == '.json':
+            df = pd.read_json(path)
+        else:
+            raise ValueError(f"Unsupported file format: {path.suffix}")
+        
+        # Assume last column is target (can be made more sophisticated)
+        X = df.iloc[:, :-1]
+        y = df.iloc[:, -1]
+        
+        return X, y
+
+
+class FeatureEngineer:
+    """Advanced feature engineering"""
+    
+    def engineer_features(self, X: np.ndarray, y: pd.Series, task_type: str) -> np.ndarray:
+        """Create engineered features"""
+        # For now, return as-is
+        # Can be extended with polynomial features, interactions, etc.
+        return X
+
+
+class ModelBuilder:
+    """Build and manage models"""
+    
+    def __init__(self, task_type: str):
+        self.task_type = task_type
+    
+    def get_baseline_models(self, algorithm_set: str = 'auto') -> Dict:
+        """Get baseline models based on configuration"""
+        if self.task_type == 'classification':
+            if algorithm_set in ['auto', 'basic']:
+                return {
+                    'logistic_regression': LogisticRegression(max_iter=1000, random_state=42),
+                    'random_forest': RandomForestClassifier(n_estimators=100, random_state=42),
+                    'gradient_boosting': GradientBoostingClassifier(n_estimators=100, random_state=42)
+                }
+            elif algorithm_set == 'advanced':
+                return {
+                    'logistic_regression': LogisticRegression(max_iter=1000, random_state=42),
+                    'random_forest': RandomForestClassifier(n_estimators=200, random_state=42),
+                    'gradient_boosting': GradientBoostingClassifier(n_estimators=200, random_state=42),
+                    'extra_trees': ExtraTreesClassifier(n_estimators=200, random_state=42),
+                    'mlp': MLPClassifier(hidden_layers=(100, 50), max_iter=1000, random_state=42),
+                    'svm': SVC(probability=True, random_state=42)
+                }
+        else:  # regression
+            if algorithm_set in ['auto', 'basic']:
+                return {
+                    'linear_regression': LinearRegression(),
+                    'ridge': Ridge(random_state=42),
+                    'random_forest': RandomForestRegressor(n_estimators=100, random_state=42),
+                    'gradient_boosting': GradientBoostingRegressor(n_estimators=100, random_state=42)
+                }
+            elif algorithm_set == 'advanced':
+                return {
+                    'linear_regression': LinearRegression(),
+                    'ridge': Ridge(random_state=42),
+                    'lasso': Lasso(random_state=42),
+                    'random_forest': RandomForestRegressor(n_estimators=200, random_state=42),
+                    'gradient_boosting': GradientBoostingRegressor(n_estimators=200, random_state=42),
+                    'extra_trees': ExtraTreesRegressor(n_estimators=200, random_state=42),
+                    'mlp': MLPRegressor(hidden_layers=(100, 50), max_iter=1000, random_state=42),
+                    'svr': SVR()
+                }
+        
+        return {}
+    
+    def get_param_grid(self, model_name: str) -> Dict:
+        """Get hyperparameter grid for model"""
+        param_grids = {
+            'random_forest': {
+                'n_estimators': [100, 200, 300],
+                'max_depth': [10, 20, None],
+                'min_samples_split': [2, 5, 10]
+            },
+            'gradient_boosting': {
+                'n_estimators': [100, 200],
+                'learning_rate': [0.01, 0.1, 0.3],
+                'max_depth': [3, 5, 7]
+            },
+            'logistic_regression': {
+                'C': [0.1, 1.0, 10.0],
+                'penalty': ['l1', 'l2'],
+                'solver': ['liblinear', 'saga']
+            },
+            'svm': {
+                'C': [0.1, 1, 10],
+                'kernel': ['rbf', 'poly'],
+                'gamma': ['scale', 'auto']
+            }
+        }
+        
+        return param_grids.get(model_name, {})
+
+
+class PerformanceTracker:
+    """Track and evaluate model performance"""
+    
+    def evaluate_model(self, model, X_test, y_test, y_pred, task_type: str) -> Dict:
+        """Comprehensive model evaluation"""
+        metrics = {}
+        
+        if task_type == 'classification':
+            metrics['accuracy'] = accuracy_score(y_test, y_pred)
+            
+            # Handle multi-class
+            precision, recall, f1, _ = precision_recall_fscore_support(
+                y_test, y_pred, average='weighted', zero_division=0
+            )
+            metrics['precision'] = precision
+            metrics['recall'] = recall
+            metrics['f1_score'] = f1
+            
+            # ROC-AUC for binary
+            if len(np.unique(y_test)) == 2 and hasattr(model, 'predict_proba'):
+                y_proba = model.predict_proba(X_test)[:, 1]
+                metrics['roc_auc'] = roc_auc_score(y_test, y_proba)
+            
+            # Confusion matrix
+            metrics['confusion_matrix'] = confusion_matrix(y_test, y_pred).tolist()
+            
+        else:  # regression
+            metrics['mse'] = mean_squared_error(y_test, y_pred)
+            metrics['rmse'] = np.sqrt(metrics['mse'])
+            metrics['mae'] = np.mean(np.abs(y_test - y_pred))
+            metrics['r2_score'] = r2_score(y_test, y_pred)
+            
+            # Additional regression metrics
+            metrics['explained_variance'] = 1 - np.var(y_test - y_pred) / np.var(y_test)
+        
+        # Cross-validation score (simplified - in practice would use training data)
+        metrics['cv_score'] = metrics.get('f1_score', metrics.get('r2_score', 0))
+        
+        return metrics
+
+
+def main():
+    """Main execution function for standalone testing"""
+    # Create enhanced foundation agent
+    agent = EnhancedFoundationAgent(
+        task_type='auto',
+        session_id='test-session-' + datetime.now().strftime('%Y%m%d-%H%M%S'),
+        agent_id='foundation_agent'
+    )
+    
+    # Run with demo data
+    results = agent.run()
+    
+    # Print summary
+    print("\n" + "="*60)
+    print("ENHANCED FOUNDATION AGENT - EXECUTION COMPLETE")
+    print("="*60)
+    print(f"Task Type: {agent.task_type}")
+    print(f"Execution Time: {results['execution_info']['execution_time']}")
+    print(f"\nBaseline Models Performance:")
+    
+    for model, metrics in results['baseline_performance'].items():
+        print(f"\n{model}:")
+        for metric, value in metrics.items():
+            if metric != 'confusion_matrix':
+                print(f"  {metric}: {value:.4f}" if isinstance(value, (int, float)) else f"  {metric}: {value}")
+    
+    print(f"\nBest Model: {results['best_model']['name']}")
+    print(f"\nRecommendations:")
+    for rec in results['recommendations']:
+        print(f"  - {rec}")
+
+
+if __name__ == "__main__":
+    main()