#!/usr/bin/env python3 """ Embedding Model Evaluator for Medical Content Tests different free embedding models to find the best for maternal health guidelines """ import json import numpy as np from pathlib import Path from typing import List, Dict, Any, Tuple import logging from sentence_transformers import SentenceTransformer from sklearn.metrics.pairwise import cosine_similarity from sklearn.cluster import KMeans from sklearn.decomposition import PCA import matplotlib.pyplot as plt import time # Configure logging logging.basicConfig(level=logging.INFO) logger = logging.getLogger(__name__) class MedicalEmbeddingEvaluator: """Evaluates different embedding models for medical content quality""" def __init__(self, chunks_dir: Path = Path("comprehensive_chunks")): self.chunks_dir = chunks_dir self.medical_chunks = [] self.evaluation_results = {} # Free embedding models to test self.embedding_models = { 'all-MiniLM-L6-v2': 'sentence-transformers/all-MiniLM-L6-v2', 'all-mpnet-base-v2': 'sentence-transformers/all-mpnet-base-v2', 'all-MiniLM-L12-v2': 'sentence-transformers/all-MiniLM-L12-v2', 'multi-qa-MiniLM-L6-cos-v1': 'sentence-transformers/multi-qa-MiniLM-L6-cos-v1', 'all-distilroberta-v1': 'sentence-transformers/all-distilroberta-v1' } # Medical test queries for evaluation self.test_queries = [ "What is the recommended dosage of magnesium sulfate for preeclampsia?", "How to manage postpartum hemorrhage in emergency situations?", "Normal ranges for fetal heart rate during labor", "Contraindications for vaginal delivery in breech presentation", "Signs and symptoms of puerperal sepsis", "Management of gestational diabetes during pregnancy", "Emergency cesarean section indications", "Postpartum care guidelines for mother and baby", "RhESUS incompatibility management protocol", "Antepartum monitoring guidelines for high-risk pregnancy" ] def load_medical_chunks(self) -> List[Dict]: """Load medical chunks from comprehensive chunking results""" logger.info("Loading medical chunks for embedding evaluation...") langchain_file = self.chunks_dir / "langchain_documents_comprehensive.json" if not langchain_file.exists(): raise FileNotFoundError(f"LangChain documents not found: {langchain_file}") with open(langchain_file) as f: chunks_data = json.load(f) # Filter and prepare chunks for evaluation medical_chunks = [] for chunk in chunks_data: content = chunk['page_content'] metadata = chunk['metadata'] # Skip very short chunks if len(content.strip()) < 100: continue medical_chunks.append({ 'content': content, 'chunk_type': metadata.get('chunk_type', 'text'), 'clinical_importance': metadata.get('clinical_importance', 0.5), 'source': metadata.get('source', ''), 'has_dosage_info': metadata.get('has_dosage_info', False), 'is_maternal_specific': metadata.get('is_maternal_specific', False), 'has_clinical_protocols': metadata.get('has_clinical_protocols', False) }) logger.info(f"Loaded {len(medical_chunks)} medical chunks for evaluation") return medical_chunks def evaluate_embedding_model(self, model_name: str, model_path: str) -> Dict[str, Any]: """Evaluate a single embedding model""" logger.info(f"Evaluating embedding model: {model_name}") try: # Load model start_time = time.time() model = SentenceTransformer(model_path) load_time = time.time() - start_time # Sample chunks for evaluation (use subset for speed) sample_chunks = self.medical_chunks[:100] # Use first 100 chunks chunk_texts = [chunk['content'] for chunk in sample_chunks] # Generate embeddings for chunks logger.info(f"Generating embeddings for {len(chunk_texts)} chunks...") start_time = time.time() chunk_embeddings = model.encode(chunk_texts, show_progress_bar=True) chunk_embed_time = time.time() - start_time # Generate embeddings for test queries start_time = time.time() query_embeddings = model.encode(self.test_queries) query_embed_time = time.time() - start_time # Evaluation metrics results = { 'model_name': model_name, 'model_path': model_path, 'load_time': load_time, 'chunk_embed_time': chunk_embed_time, 'query_embed_time': query_embed_time, 'embedding_dimension': chunk_embeddings.shape[1], 'chunks_processed': len(chunk_texts), 'queries_processed': len(self.test_queries) } # Test semantic search quality search_results = self._evaluate_search_quality( query_embeddings, chunk_embeddings, sample_chunks ) results.update(search_results) # Test clustering quality cluster_results = self._evaluate_clustering_quality( chunk_embeddings, sample_chunks ) results.update(cluster_results) # Calculate overall score results['overall_score'] = self._calculate_overall_score(results) logger.info(f"āœ… {model_name} evaluation complete - Overall Score: {results['overall_score']:.3f}") return results except Exception as e: logger.error(f"āŒ Failed to evaluate {model_name}: {e}") return { 'model_name': model_name, 'model_path': model_path, 'error': str(e), 'overall_score': 0.0 } def _evaluate_search_quality(self, query_embeddings: np.ndarray, chunk_embeddings: np.ndarray, chunks: List[Dict]) -> Dict[str, float]: """Evaluate semantic search quality""" # Calculate similarities between queries and chunks similarities = cosine_similarity(query_embeddings, chunk_embeddings) search_metrics = { 'avg_max_similarity': 0.0, 'medical_content_precision': 0.0, 'dosage_query_accuracy': 0.0, 'emergency_query_accuracy': 0.0 } total_queries = len(self.test_queries) for i, query in enumerate(self.test_queries): query_similarities = similarities[i] top_indices = np.argsort(query_similarities)[::-1][:5] # Top 5 results # Max similarity for this query max_sim = np.max(query_similarities) search_metrics['avg_max_similarity'] += max_sim # Check if top results contain relevant medical content top_chunks = [chunks[idx] for idx in top_indices] medical_relevant = sum(1 for chunk in top_chunks if chunk['clinical_importance'] > 0.7) search_metrics['medical_content_precision'] += medical_relevant / 5 # Specific query type accuracy if 'dosage' in query.lower() or 'dose' in query.lower(): dosage_relevant = sum(1 for chunk in top_chunks if chunk['has_dosage_info']) search_metrics['dosage_query_accuracy'] += dosage_relevant / 5 if 'emergency' in query.lower() or 'urgent' in query.lower(): emergency_relevant = sum(1 for chunk in top_chunks if chunk['chunk_type'] == 'emergency') search_metrics['emergency_query_accuracy'] += emergency_relevant / 5 # Average the metrics for key in search_metrics: search_metrics[key] /= total_queries return search_metrics def _evaluate_clustering_quality(self, embeddings: np.ndarray, chunks: List[Dict]) -> Dict[str, float]: """Evaluate how well embeddings cluster similar medical content""" # Perform clustering n_clusters = min(8, len(chunks) // 10) # Reasonable number of clusters kmeans = KMeans(n_clusters=n_clusters, random_state=42) cluster_labels = kmeans.fit_predict(embeddings) # Calculate cluster purity based on chunk types cluster_metrics = { 'cluster_purity': 0.0, 'dosage_cluster_coherence': 0.0, 'maternal_cluster_coherence': 0.0 } # Calculate cluster purity total_items = len(chunks) for cluster_id in range(n_clusters): cluster_indices = np.where(cluster_labels == cluster_id)[0] if len(cluster_indices) == 0: continue cluster_chunks = [chunks[i] for i in cluster_indices] # Find dominant chunk type in this cluster chunk_types = [chunk['chunk_type'] for chunk in cluster_chunks] if chunk_types: dominant_type = max(set(chunk_types), key=chunk_types.count) purity = chunk_types.count(dominant_type) / len(chunk_types) cluster_metrics['cluster_purity'] += purity * len(cluster_indices) / total_items # Check dosage content clustering dosage_chunks = [chunk for chunk in cluster_chunks if chunk['has_dosage_info']] if len(cluster_chunks) > 0: dosage_ratio = len(dosage_chunks) / len(cluster_chunks) if dosage_ratio > 0.5: # If majority are dosage chunks cluster_metrics['dosage_cluster_coherence'] += dosage_ratio # Check maternal content clustering maternal_chunks = [chunk for chunk in cluster_chunks if chunk['is_maternal_specific']] if len(cluster_chunks) > 0: maternal_ratio = len(maternal_chunks) / len(cluster_chunks) if maternal_ratio > 0.5: # If majority are maternal chunks cluster_metrics['maternal_cluster_coherence'] += maternal_ratio return cluster_metrics def _calculate_overall_score(self, results: Dict[str, Any]) -> float: """Calculate overall score for the embedding model""" if 'error' in results: return 0.0 # Weighted scoring components weights = { 'search_quality': 0.4, 'clustering_quality': 0.2, 'speed': 0.2, 'medical_relevance': 0.2 } # Search quality score (0-1) search_score = ( results.get('avg_max_similarity', 0) * 0.4 + results.get('medical_content_precision', 0) * 0.3 + results.get('dosage_query_accuracy', 0) * 0.15 + results.get('emergency_query_accuracy', 0) * 0.15 ) # Clustering quality score (0-1) cluster_score = ( results.get('cluster_purity', 0) * 0.5 + results.get('dosage_cluster_coherence', 0) * 0.25 + results.get('maternal_cluster_coherence', 0) * 0.25 ) # Speed score (inverse of time, normalized) total_time = results.get('chunk_embed_time', 1) + results.get('query_embed_time', 1) speed_score = max(0, 1 - (total_time / 100)) # Normalize to 0-1 # Medical relevance (based on search accuracy for medical queries) medical_score = ( results.get('medical_content_precision', 0) * 0.6 + results.get('dosage_query_accuracy', 0) * 0.4 ) # Calculate weighted overall score overall = ( search_score * weights['search_quality'] + cluster_score * weights['clustering_quality'] + speed_score * weights['speed'] + medical_score * weights['medical_relevance'] ) return min(1.0, max(0.0, overall)) def run_comprehensive_evaluation(self) -> Dict[str, Any]: """Run comprehensive evaluation of all embedding models""" logger.info("Starting comprehensive embedding model evaluation...") # Load medical chunks self.medical_chunks = self.load_medical_chunks() if len(self.medical_chunks) == 0: raise ValueError("No medical chunks loaded for evaluation") # Evaluate each model results = {} for model_name, model_path in self.embedding_models.items(): logger.info(f"\nšŸ“Š Evaluating: {model_name}") results[model_name] = self.evaluate_embedding_model(model_name, model_path) # Generate summary report summary = self._generate_evaluation_summary(results) # Save results output_file = Path("src/embedding_evaluation_results.json") with open(output_file, 'w') as f: json.dump({ 'evaluation_summary': summary, 'detailed_results': results, 'test_queries': self.test_queries, 'chunks_evaluated': len(self.medical_chunks) }, f, indent=2) logger.info(f"šŸ“‹ Evaluation results saved to: {output_file}") return summary def _generate_evaluation_summary(self, results: Dict[str, Any]) -> Dict[str, Any]: """Generate evaluation summary with recommendations""" valid_results = {k: v for k, v in results.items() if 'error' not in v} if not valid_results: return {'error': 'No models evaluated successfully'} # Find best model best_model = max(valid_results.items(), key=lambda x: x[1]['overall_score']) # Calculate averages avg_scores = {} for metric in ['overall_score', 'avg_max_similarity', 'medical_content_precision']: scores = [r.get(metric, 0) for r in valid_results.values()] avg_scores[f'avg_{metric}'] = sum(scores) / len(scores) if scores else 0 summary = { 'best_model': { 'name': best_model[0], 'path': best_model[1]['model_path'], 'score': best_model[1]['overall_score'], 'strengths': [] }, 'model_rankings': sorted( [(name, res['overall_score']) for name, res in valid_results.items()], key=lambda x: x[1], reverse=True ), 'evaluation_metrics': avg_scores, 'recommendation': '', 'models_tested': len(results), 'successful_evaluations': len(valid_results) } # Add strengths and recommendation best_result = best_model[1] strengths = [] if best_result.get('medical_content_precision', 0) > 0.7: strengths.append("High medical content precision") if best_result.get('dosage_query_accuracy', 0) > 0.6: strengths.append("Good dosage information retrieval") if best_result.get('cluster_purity', 0) > 0.6: strengths.append("Effective content clustering") if best_result.get('chunk_embed_time', 100) < 30: strengths.append("Fast embedding generation") summary['best_model']['strengths'] = strengths summary['recommendation'] = ( f"Recommended model: {best_model[0]} with overall score {best_result['overall_score']:.3f}. " f"This model shows {', '.join(strengths)} and is well-suited for maternal health content." ) return summary def main(): """Main evaluation function""" evaluator = MedicalEmbeddingEvaluator() try: summary = evaluator.run_comprehensive_evaluation() # Print summary logger.info("=" * 80) logger.info("EMBEDDING MODEL EVALUATION COMPLETE!") logger.info("=" * 80) logger.info(f"šŸ† Best Model: {summary['best_model']['name']}") logger.info(f"šŸ“Š Overall Score: {summary['best_model']['score']:.3f}") logger.info(f"šŸ’Ŗ Strengths: {', '.join(summary['best_model']['strengths'])}") logger.info(f"šŸ“ Recommendation: {summary['recommendation']}") logger.info("\nšŸ“ˆ Model Rankings:") for i, (model, score) in enumerate(summary['model_rankings'], 1): logger.info(f"{i}. {model}: {score:.3f}") logger.info("=" * 80) return summary except Exception as e: logger.error(f"āŒ Evaluation failed: {e}") return None if __name__ == "__main__": main()