#!/usr/bin/env python3 """ Train OHCA Classifier from Pre-labeled Data This script trains a v3.0 OHCA classifier using your manually labeled data. Your data should have columns: hadm_id, clean_text, ohca_label (and optionally subject_id, confidence) """ import sys import os sys.path.append(os.path.join(os.path.dirname(__file__), '..', 'src')) import pandas as pd from sklearn.model_selection import train_test_split from ohca_training_pipeline import prepare_training_data, train_ohca_model, find_optimal_threshold, save_model_with_metadata def validate_labeled_data(df): """Validate that the labeled data has required columns and format""" required_cols = ['hadm_id', 'clean_text', 'ohca_label'] missing_cols = [col for col in required_cols if col not in df.columns] if missing_cols: raise ValueError(f"Missing required columns: {missing_cols}") # Check ohca_label values unique_labels = df['ohca_label'].unique() if not set(unique_labels).issubset({0, 1}): raise ValueError(f"ohca_label must be 0 or 1, found: {unique_labels}") print(f"Data validation passed:") print(f" Total cases: {len(df)}") print(f" OHCA cases (label=1): {(df['ohca_label']==1).sum()}") print(f" Non-OHCA cases (label=0): {(df['ohca_label']==0).sum()}") print(f" OHCA prevalence: {(df['ohca_label']==1).mean():.1%}") def train_from_labeled_data(data_path, model_save_path="./trained_ohca_model", test_size=0.2, num_epochs=3): """ Train OHCA model from pre-labeled data Args: data_path: Path to CSV with labeled data model_save_path: Where to save the trained model test_size: Fraction to use for validation (default 0.2 = 20%) num_epochs: Number of training epochs """ print("OHCA Classifier Training from Pre-labeled Data") print("="*50) # Load and validate data print(f"Loading labeled data from: {data_path}") df = pd.read_csv(data_path) # Add missing columns if needed if 'subject_id' not in df.columns: print("Adding subject_id column (using hadm_id as patient ID)") df['subject_id'] = df['hadm_id'] if 'confidence' not in df.columns: print("Adding default confidence scores") df['confidence'] = 4 # Default confidence validate_labeled_data(df) # Split into train/validation print(f"\nSplitting data (train: {1-test_size:.0%}, validation: {test_size:.0%})") train_df, val_df = train_test_split( df, test_size=test_size, stratify=df['ohca_label'], random_state=42 ) print(f"Training data: {len(train_df)} cases ({(train_df['ohca_label']==1).sum()} OHCA)") print(f"Validation data: {len(val_df)} cases ({(val_df['ohca_label']==1).sum()} OHCA)") # Save as temporary Excel files temp_train = 'temp_train_data.xlsx' temp_val = 'temp_val_data.xlsx' train_df.to_excel(temp_train, index=False) val_df.to_excel(temp_val, index=False) try: # Prepare training datasets print("\nPreparing training datasets...") train_dataset, val_dataset, train_df_balanced, val_df_clean, tokenizer = prepare_training_data( temp_train, temp_val ) # Train the model print(f"\nTraining model for {num_epochs} epochs...") model, trained_tokenizer = train_ohca_model( train_dataset, val_dataset, train_df_balanced, tokenizer, num_epochs=num_epochs, save_path=model_save_path ) # Find optimal threshold print("\nFinding optimal threshold...") optimal_threshold, val_metrics = find_optimal_threshold( model, trained_tokenizer, val_df_clean ) # Save model with metadata print("\nSaving model with metadata...") test_metrics = {'message': 'Trained on user-provided labeled data', 'test_set_size': 0} save_model_with_metadata( model, trained_tokenizer, optimal_threshold, val_metrics, test_metrics, model_save_path ) print(f"\nTraining completed successfully!") print(f"Model saved to: {model_save_path}") print(f"Optimal threshold: {optimal_threshold:.3f}") print(f"Validation F1-score: {val_metrics['f1_score']:.3f}") return { 'model_path': model_save_path, 'optimal_threshold': optimal_threshold, 'metrics': val_metrics } finally: # Clean up temporary files for temp_file in [temp_train, temp_val]: if os.path.exists(temp_file): os.remove(temp_file) if __name__ == "__main__": import argparse parser = argparse.ArgumentParser(description='Train OHCA classifier from labeled data') parser.add_argument('data_path', help='Path to CSV file with labeled data') parser.add_argument('--model_path', default='./trained_ohca_model', help='Where to save trained model (default: ./trained_ohca_model)') parser.add_argument('--epochs', type=int, default=3, help='Number of training epochs (default: 3)') parser.add_argument('--test_size', type=float, default=0.2, help='Validation split fraction (default: 0.2)') args = parser.parse_args() if not os.path.exists(args.data_path): print(f"Error: Data file not found: {args.data_path}") print("\nYour CSV file should have columns:") print(" hadm_id: Unique admission identifier") print(" clean_text: Discharge note text") print(" ohca_label: 1 for OHCA, 0 for non-OHCA") print(" subject_id: Patient ID (optional - will use hadm_id if missing)") sys.exit(1) try: train_from_labeled_data(args.data_path, args.model_path, args.test_size, args.epochs) except Exception as e: print(f"Training failed: {e}") sys.exit(1)