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models/dmodel_256_run_decoding.py

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+#!/usr/bin/env python3
+# coding: utf-8
+
+"""
+ProtT5 Encoder-Decoder decoding
+Support beam search and top-k/top-p sampling decoding methods
+"""
+
+import subprocess
+import sys
+import os
+
+def run_decoding():
+    """Run the decoding script"""
+    
+    # Configuration parameters - Please modify these paths according to your actual situation
+    config = {
+        'data_pkl_path': 'data.pkl',  # data.pkl file path
+        'model_path': 'best_model.pt',  # The path to the trained model weight file
+        'test_data_path': 'test_data.csv',  # Test data CSV file path
+        'output_path': './dmodel_256_decoding',  # Output result file path
+        'test_genome_pkl_path':'test_genome_dict.pkl',
+        
+        # Model parameters - need to be consistent with training
+        'heads': 8,
+        'd_model': 256,
+        'src_input_dim': 1024,
+        'first_linear_dim': 512,
+        'num_encoder_layer': 3,
+        'num_decoder_layer': 3,
+        'dropout': 0.1,
+        'compound_max_len': 113,
+        
+        # Decoder parameters
+        'top_k': [8, 9, 10],  # Top-K鍊?
+        'top_p': [0.9],  # Top-P鍊?
+        'beam_size': [1, 2, 3, 4, 5, 6, 7, 8, 9, 10],  # Beam size鍊?
+        'decode_methods': ['beam_search'],  # 瑙ｇ爜鏂规硶
+        
+        # Other parameters
+        'device': 'cuda:1',  # 璁惧
+        'batch_size': 1  # 鎵规澶у皬
+    }
+    
+    # Build Commands
+    cmd = [
+        'python', 'dmodel_256_decode_model.py',
+        '--data_pkl_path', config['data_pkl_path'],
+        '--model_path', config['model_path'],
+        '--test_data_path', config['test_data_path'],
+        '--test_genome_pkl_path', config['test_genome_pkl_path'],
+        '--output_path', config['output_path'],
+        '--heads', str(config['heads']),
+        '--d_model', str(config['d_model']),
+        '--src_input_dim', str(config['src_input_dim']),
+        '--first_linear_dim', str(config['first_linear_dim']),
+        '--num_encoder_layer', str(config['num_encoder_layer']),
+        '--num_decoder_layer', str(config['num_decoder_layer']),
+        '--dropout', str(config['dropout']),
+        '--compound_max_len', str(config['compound_max_len']),
+        '--top_k'] + [str(k) for k in config['top_k']] + [
+        '--top_p'] + [str(p) for p in config['top_p']] + [
+        '--beam_size'] + [str(b) for b in config['beam_size']] + [
+        '--decode_methods'] + config['decode_methods'] + [
+        '--device', config['device'],
+        '--batch_size', str(config['batch_size'])
+    ]
+    
+    print("=== Start decoding ===")
+    print(f"Data files: {config['data_pkl_path']}")
+    print(f"Model file: {config['model_path']}")
+    print(f"Test data: {config['test_data_path']}")
+    print(f"Output File: {config['output_path']}")
+    print(f"device: {config['device']}")
+    print(f"Decoding method: {config['decode_methods']}")
+    print(f"Top-K value: {config['top_k']}")
+    print(f"Top-P value: {config['top_p']}")
+    print(f"Beam size value: {config['beam_size']}")
+    
+    try:
+        # Run the decoding script
+        result = subprocess.run(cmd, check=True, capture_output=True, text=True)
+        print("Decoding completed successfully!")
+        print(f"Results saved to: {config['output_path']}")
+        
+    except subprocess.CalledProcessError as e:
+        print(f"Decoding failed: {e}")
+        print(f"Error Output: {e.stderr}")
+        return False
+    except FileNotFoundError:
+        print("The decode_model.py file cannot be found. Please make sure the file is in the current directory.")
+        return False
+    
+    return True
+
+def check_files():
+    """Check if necessary files exist"""
+    required_files = [
+        'dmodel_256_decode_model.py',
+        'data.pkl',
+        'test_data.csv'
+    ]
+    
+    missing_files = []
+    for file in required_files:
+        if not os.path.exists(file):
+            missing_files.append(file)
+    
+    if missing_files:
+        print("Missing necessary documents:")
+        for file in missing_files:
+            print(f"  - {file}")
+        return False
+    
+    return True
+
+def main():
+    print("ProtT5 Encoder-Decoder Model decoding tool")
+    print("=" * 50)
+    
+    # 妫€鏌ユ枃浠?
+    if not check_files():
+        print("\nPlease make sure all necessary files are present before running the decoder.")
+        return
+    
+    # 杩愯瑙ｇ爜
+    success = run_decoding()
+    
+    if success:
+        print("\nDecoding task completed!")
+        print("You can view the decoded results in the output file.")
+    else:
+        print("\nDecoding task failed, please check the error message.")
+
+if __name__ == "__main__":
+    main()