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MolAS-Active-Learning / code /downstream /upstream_molas /embedding_generation /data /protein_dataset.py
Download code/downstream/upstream_molas/embedding_generation/data/protein_dataset.py from SeanWan05/MolAS-Active-Learning: direct link, hf CLI and curl.
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https://huggingface.co/datasets/SeanWan05/MolAS-Active-Learning/resolve/main/code/downstream/upstream_molas/embedding_generation/data/protein_dataset.py
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hf download hf://datasets/SeanWan05/MolAS-Active-Learning/code/downstream/upstream_molas/embedding_generation/data/protein_dataset.py
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curl -L -o protein_dataset.py https://huggingface.co/datasets/SeanWan05/MolAS-Active-Learning/resolve/main/code/downstream/upstream_molas/embedding_generation/data/protein_dataset.py
30.5 kB
| import torch | |
| from torch.utils.data import Dataset | |
| import os | |
| import glob | |
| from pathlib import Path | |
| from sklearn.model_selection import train_test_split | |
| from tools.subgraph_sampler import ProteinSubgraphSampler | |
| from .pdb_processor import PDBProcessor | |
| from .cache_manager import CacheManager | |
| import random | |
| import threading | |
| from collections import OrderedDict | |
| class ProteinDataset(Dataset): | |
| def __init__(self, train=True, data_path=None, pdb_path=None, cache_path=None, transform=None, **kwargs): | |
| self.train = train | |
| self.data_path = data_path | |
| self.pdb_path = pdb_path or "dataset/rcsb/human" # Default PDB path | |
| self.cache_path = cache_path or "dataset/protein_cache" # Default cache path | |
| self.transform = transform | |
| # New parameters for on-the-fly processing | |
| self.enable_pdb_processing = kwargs.get('enable_pdb_processing', True) | |
| self.force_pdb_processing = kwargs.get('force_pdb_processing', False) # Force PDB processing even if .pt files exist | |
| # Subgraph sampling parameters | |
| self.min_nodes = kwargs.get('min_nodes', 10) | |
| self.max_nodes = kwargs.get('max_nodes', 100) | |
| # Initialize components | |
| self.subgraph_sampler = ProteinSubgraphSampler( | |
| min_nodes=self.min_nodes, | |
| max_nodes=self.max_nodes | |
| ) | |
| # Initialize PDB processor and cache manager | |
| self.pdb_processor = None # Lazy initialization | |
| self.cache_manager = CacheManager(self.cache_path) | |
| # Determine data source and index files | |
| self._determine_data_source() | |
| self.file_paths = self._get_file_paths() | |
| self.protein_ids = self._generate_protein_ids() | |
| # Split the dataset | |
| self.seed = kwargs.get('seed', 42) | |
| self._create_data_splits() | |
| # Improved memory management for multiprocessing | |
| self.cache_size = kwargs.get('cache_size', 512) # Reduced default for multiprocessing | |
| self.enable_cache = kwargs.get('enable_cache', True) | |
| self.preload_cache = kwargs.get('preload_cache', False) | |
| # Thread-safe cache using OrderedDict (LRU) | |
| self._cache_lock = threading.Lock() | |
| self._cache = OrderedDict() | |
| # Worker-specific settings | |
| self._worker_id = None | |
| self._is_main_process = True | |
| # Statistics | |
| self._pdb_processed_count = 0 | |
| self._cache_hit_count = 0 | |
| self._pt_file_count = 0 | |
| self._failed_files = set() # Track files that failed to process | |
| self._valid_files = None # Cache of validated files | |
| # Error handling options | |
| self.skip_invalid_files = kwargs.get('skip_invalid_files', True) | |
| self.validate_on_init = kwargs.get('validate_on_init', False) # Pre-validate files during init | |
| self.max_retry_attempts = kwargs.get('max_retry_attempts', 1) | |
| # ESM-C configuration | |
| self.esm_use_cpu = kwargs.get('esm_use_cpu', False) | |
| if self.esm_use_cpu: | |
| os.environ['ESM_USE_CPU'] = 'true' | |
| print("Dataset: Configured ESM-C to use CPU only") | |
| # Pre-validate files if requested | |
| if self.validate_on_init and self.use_pdb_files: | |
| self._validate_pdb_files() | |
| def __getstate__(self): | |
| """Custom pickling - exclude locks and worker-specific state.""" | |
| state = self.__dict__.copy() | |
| # Remove unpickleable entries | |
| del state['_cache_lock'] | |
| # Reset worker-specific state for new process | |
| state['_worker_id'] = None | |
| state['_is_main_process'] = False # Workers are not main process | |
| return state | |
| def __setstate__(self, state): | |
| """Custom unpickling - restore state and create new lock.""" | |
| self.__dict__.update(state) | |
| # Create new lock in worker process | |
| self._cache_lock = threading.Lock() | |
| # Worker will determine its own ID later | |
| def _determine_data_source(self): | |
| """Determine whether to use preprocessed .pt files or PDB files.""" | |
| self.use_pdb_files = False | |
| self.data_source_type = "unknown" | |
| # Check if we should force PDB processing | |
| if self.force_pdb_processing: | |
| if os.path.exists(self.pdb_path): | |
| self.use_pdb_files = True | |
| self.data_source_type = "pdb_forced" | |
| print(f"Dataset: Forced PDB processing from {self.pdb_path}") | |
| else: | |
| raise ValueError(f"PDB path not found: {self.pdb_path}") | |
| # Check for preprocessed .pt files first (backward compatibility) | |
| elif self.data_path and os.path.exists(self.data_path): | |
| pt_files = glob.glob(os.path.join(self.data_path, "*.pt")) | |
| if pt_files: | |
| self.use_pdb_files = False | |
| self.data_source_type = "preprocessed" | |
| print(f"Dataset: Using preprocessed .pt files from {self.data_path}") | |
| return | |
| # Fall back to PDB files if enabled | |
| if self.enable_pdb_processing and os.path.exists(self.pdb_path): | |
| pdb_files = glob.glob(os.path.join(self.pdb_path, "*.pdb")) | |
| if pdb_files: | |
| self.use_pdb_files = True | |
| self.data_source_type = "pdb_fallback" | |
| print(f"Dataset: Using PDB files from {self.pdb_path} (no preprocessed files found)") | |
| else: | |
| raise ValueError(f"No PDB files found in {self.pdb_path}") | |
| else: | |
| if not self.enable_pdb_processing: | |
| raise ValueError(f"No preprocessed files found in {self.data_path} and PDB processing is disabled") | |
| else: | |
| raise ValueError(f"No data files found in {self.data_path} or {self.pdb_path}") | |
| def _get_file_paths(self): | |
| """Get all protein file paths based on determined data source.""" | |
| file_paths = [] | |
| if self.use_pdb_files: | |
| # Use PDB files | |
| if os.path.exists(self.pdb_path): | |
| pattern = '*.pdb' | |
| file_paths.extend(glob.glob(os.path.join(self.pdb_path, pattern))) | |
| else: | |
| # Use preprocessed .pt files | |
| if self.data_path and os.path.exists(self.data_path): | |
| pattern = '*.pt' | |
| file_paths.extend(glob.glob(os.path.join(self.data_path, pattern))) | |
| # Sort for consistent ordering | |
| file_paths.sort() | |
| print(f"Dataset: Found {len(file_paths)} files ({self.data_source_type})") | |
| return file_paths | |
| def _generate_protein_ids(self): | |
| """Generate protein IDs from file names""" | |
| protein_ids = [] | |
| for file_path in self.file_paths: | |
| filename = Path(file_path).stem # Get filename without extension | |
| # Handle different filename patterns | |
| if self.use_pdb_files: | |
| # For PDB files, use the filename directly | |
| protein_ids.append(filename) | |
| else: | |
| # For .pt files, remove 'pytorch_graph_' prefix if present | |
| if filename.startswith('pytorch_graph_'): | |
| protein_id = filename[len('pytorch_graph_'):] | |
| else: | |
| protein_id = filename | |
| protein_ids.append(protein_id) | |
| return protein_ids | |
| def _create_data_splits(self): | |
| """Create train/test splits and select files based on self.train""" | |
| if not hasattr(self, 'file_paths') or not self.file_paths: | |
| raise ValueError("File paths are not initialized. Please check data_path.") | |
| # Split the dataset into train and test sets | |
| train_files, test_files = train_test_split( | |
| self.file_paths, test_size=0.1, random_state=self.seed) | |
| # if self.train: | |
| # self.file_paths = train_files | |
| # else: | |
| # self.file_paths = test_files | |
| # Regenerate protein IDs after split | |
| self.protein_ids = self._generate_protein_ids() | |
| def _validate_pdb_files(self): | |
| """Pre-validate PDB files to identify problematic ones.""" | |
| if not self.use_pdb_files: | |
| return | |
| print(f"Dataset: Pre-validating {len(self.file_paths)} PDB files...") | |
| valid_files = [] | |
| failed_files = [] | |
| for i, file_path in enumerate(self.file_paths): | |
| if i % 50 == 0: | |
| print(f"Dataset: Validation progress: {i}/{len(self.file_paths)}") | |
| try: | |
| if self._is_pdb_file_valid(file_path): | |
| valid_files.append(file_path) | |
| else: | |
| failed_files.append(file_path) | |
| self._failed_files.add(file_path) | |
| except Exception as e: | |
| print(f"Dataset: Validation failed for {file_path}: {e}") | |
| failed_files.append(file_path) | |
| self._failed_files.add(file_path) | |
| print(f"Dataset: Validation complete - Valid: {len(valid_files)}, Failed: {len(failed_files)}") | |
| if failed_files: | |
| print(f"Dataset: Failed files: {[Path(f).name for f in failed_files[:10]]}" + | |
| (f" (and {len(failed_files)-10} more)" if len(failed_files) > 10 else "")) | |
| # Update file paths to only include valid files | |
| if self.skip_invalid_files: | |
| self.file_paths = valid_files | |
| self.protein_ids = self._generate_protein_ids() | |
| print(f"Dataset: Using {len(self.file_paths)} valid files after filtering") | |
| def _is_pdb_file_valid(self, pdb_file_path): | |
| """Quick validation check for PDB file without full processing.""" | |
| try: | |
| from Bio.PDB import PDBParser | |
| import numpy as np | |
| parser = PDBParser(QUIET=True) | |
| structure = parser.get_structure("test", pdb_file_path) | |
| # Check if we have any valid chains with coordinates | |
| valid_residues = 0 | |
| for model in structure: | |
| for chain in model: | |
| for residue in chain: | |
| if residue.has_id("CA"): | |
| ca_atom = residue["CA"] | |
| coords = ca_atom.get_coord() | |
| # Check for NaN or infinite coordinates | |
| if np.any(np.isnan(coords)) or np.any(np.isinf(coords)): | |
| print(f"Dataset: Invalid coordinates in {pdb_file_path}: {coords}") | |
| return False | |
| valid_residues += 1 | |
| # Early exit if we have enough valid residues | |
| if valid_residues >= self.min_nodes: | |
| return True | |
| if valid_residues < self.min_nodes: | |
| print(f"Dataset: Too few valid residues in {pdb_file_path}: {valid_residues} < {self.min_nodes}") | |
| return False | |
| return True | |
| except Exception as e: | |
| print(f"Dataset: Validation error for {pdb_file_path}: {e}") | |
| return False | |
| def _get_worker_info(self): | |
| """Get current worker information for multiprocessing awareness""" | |
| try: | |
| import torch.utils.data as data | |
| worker_info = data.get_worker_info() | |
| if worker_info is not None: | |
| self._worker_id = worker_info.id | |
| self._is_main_process = False | |
| # Adjust cache size per worker | |
| self.cache_size = max(32, self.cache_size // worker_info.num_workers) | |
| return worker_info | |
| except: | |
| return None | |
| def _get_pdb_processor(self): | |
| """Get PDB processor with lazy initialization.""" | |
| if self.pdb_processor is None: | |
| self.pdb_processor = PDBProcessor() | |
| return self.pdb_processor | |
| def _load_single_graph(self, file_path): | |
| """Load a single protein graph with improved thread-safe caching""" | |
| if not self.enable_cache: | |
| return self._load_from_disk(file_path) | |
| # Get worker info on first access | |
| if self._worker_id is None: | |
| self._get_worker_info() | |
| # Thread-safe cache access | |
| with self._cache_lock: | |
| # Check cache first | |
| if file_path in self._cache: | |
| # Move to end (most recently used) | |
| graph_data = self._cache.pop(file_path) | |
| self._cache[file_path] = graph_data | |
| return graph_data | |
| # Load from disk if not in cache | |
| graph_data = self._load_from_disk(file_path) | |
| if graph_data is not None and self.enable_cache: | |
| self._add_to_cache(file_path, graph_data) | |
| return graph_data | |
| def _load_from_disk(self, file_path): | |
| """Load graph data from disk or process PDB file on-demand.""" | |
| try: | |
| if self.use_pdb_files: | |
| return self._load_from_pdb(file_path) | |
| else: | |
| return self._load_from_pt_file(file_path) | |
| except Exception as e: | |
| print(f"Error loading {file_path}: {e}") | |
| return None | |
| def _load_from_pt_file(self, file_path): | |
| """Load graph data from preprocessed .pt file.""" | |
| try: | |
| graph_data = torch.load(file_path, map_location='cpu') | |
| self._pt_file_count += 1 | |
| return graph_data | |
| except Exception as e: | |
| print(f"Error loading .pt file {file_path}: {e}") | |
| return None | |
| def _load_from_pdb(self, pdb_file_path): | |
| """Load graph data from PDB file with persistent caching.""" | |
| try: | |
| # Check persistent cache first | |
| if self.cache_manager.exists(pdb_file_path): | |
| graph_data = self.cache_manager.load(pdb_file_path) | |
| if graph_data is not None: | |
| self._cache_hit_count += 1 | |
| return graph_data | |
| # Process PDB file on-the-fly | |
| print(f"Processing PDB file on-the-fly: {pdb_file_path}") | |
| processor = self._get_pdb_processor() | |
| graph_data = processor.process_pdb_file(pdb_file_path) | |
| if graph_data is not None: | |
| # Save to persistent cache | |
| self.cache_manager.save(pdb_file_path, graph_data) | |
| self._pdb_processed_count += 1 | |
| return graph_data | |
| else: | |
| print(f"Failed to process PDB file: {pdb_file_path}") | |
| return None | |
| except Exception as e: | |
| print(f"Error processing PDB file {pdb_file_path}: {e}") | |
| return None | |
| def _add_to_cache(self, file_path, graph_data): | |
| """Add graph to cache with thread-safe LRU eviction""" | |
| if self.cache_size <= 0: | |
| # Cache is disabled | |
| return | |
| with self._cache_lock: | |
| # Remove oldest items if cache is full | |
| while len(self._cache) >= self.cache_size: | |
| if self._cache: # Check if cache is not empty before popitem | |
| self._cache.popitem(last=False) # Remove oldest (FIFO) | |
| else: | |
| break # Exit if cache becomes empty | |
| # Add new item (will be most recent) | |
| self._cache[file_path] = graph_data | |
| def clear_cache(self): | |
| """Clear the cache to free memory""" | |
| with self._cache_lock: | |
| self._cache.clear() | |
| def get_cache_info(self): | |
| """Get cache statistics""" | |
| with self._cache_lock: | |
| basic_info = { | |
| 'cache_size': len(self._cache), | |
| 'max_cache_size': self.cache_size, | |
| 'worker_id': self._worker_id, | |
| 'is_main_process': self._is_main_process, | |
| 'cache_enabled': self.enable_cache, | |
| 'data_source_type': self.data_source_type, | |
| 'use_pdb_files': self.use_pdb_files, | |
| 'pdb_processed_count': self._pdb_processed_count, | |
| 'cache_hit_count': self._cache_hit_count, | |
| 'pt_file_count': self._pt_file_count | |
| } | |
| # Add persistent cache info if using PDB files | |
| if self.use_pdb_files: | |
| persistent_cache_info = self.cache_manager.get_cache_stats() | |
| basic_info.update({ | |
| 'persistent_cache': persistent_cache_info | |
| }) | |
| return basic_info | |
| def get_processing_stats(self): | |
| """Get detailed processing statistics.""" | |
| return { | |
| 'data_source': self.data_source_type, | |
| 'total_files': len(self.file_paths), | |
| 'failed_files_count': len(self._failed_files), | |
| 'failed_files': [Path(f).name for f in list(self._failed_files)[:10]], # Show first 10 | |
| 'pdb_processed_on_fly': self._pdb_processed_count, | |
| 'persistent_cache_hits': self._cache_hit_count, | |
| 'pt_files_loaded': self._pt_file_count, | |
| 'success_rate': (len(self.file_paths) - len(self._failed_files)) / len(self.file_paths) if len(self.file_paths) > 0 else 0, | |
| 'cache_manager_stats': self.cache_manager.get_cache_stats() if self.use_pdb_files else None | |
| } | |
| def get_failed_files(self): | |
| """Get list of files that failed to process.""" | |
| return list(self._failed_files) | |
| def clear_failed_files(self): | |
| """Clear the list of failed files (useful for retrying).""" | |
| self._failed_files.clear() | |
| print("Dataset: Cleared failed files list") | |
| def warm_cache(self, num_samples=None): | |
| """Pre-load a subset of the dataset into cache""" | |
| if not self.enable_cache or not self._is_main_process: | |
| return | |
| num_samples = num_samples or min(self.cache_size, len(self.file_paths)) | |
| print(f"Warming cache with {num_samples} samples...") | |
| # Load a random subset for better distribution | |
| indices = random.sample(range(len(self.file_paths)), num_samples) | |
| for i, idx in enumerate(indices): | |
| file_path = self.file_paths[idx] | |
| self._load_single_graph(file_path) | |
| if (i + 1) % 50 == 0: | |
| print(f"Cache warming progress: {i + 1}/{num_samples}") | |
| print(f"Cache warmed. Current cache info: {self.get_cache_info()}") | |
| def __len__(self): | |
| # Return dataset size | |
| return len(self.file_paths) | |
| def _data_to_dict(self, data_obj): | |
| """Convert PyTorch Geometric Data object to dictionary format for subgraph sampler.""" | |
| from torch_geometric.data import Data | |
| if isinstance(data_obj, Data): | |
| return { | |
| 'node_features': data_obj.x, | |
| 'edge_index': data_obj.edge_index, | |
| 'edge_attr': data_obj.edge_attr, | |
| 'node_pos': data_obj.pos, | |
| 'num_nodes': data_obj.x.shape[0] if data_obj.x is not None else 0 | |
| } | |
| else: | |
| # Already dictionary format | |
| return data_obj | |
| def _dict_to_data(self, dict_obj): | |
| """Convert dictionary format back to PyTorch Geometric Data object.""" | |
| from torch_geometric.data import Data | |
| if isinstance(dict_obj, dict): | |
| return Data( | |
| x=dict_obj['node_features'], | |
| edge_index=dict_obj['edge_index'], | |
| edge_attr=dict_obj['edge_attr'], | |
| pos=dict_obj['node_pos'] | |
| ) | |
| else: | |
| # Already Data object | |
| return dict_obj | |
| def _get_num_nodes(self, graph_obj): | |
| """Get number of nodes from either Data object or dictionary.""" | |
| from torch_geometric.data import Data | |
| if isinstance(graph_obj, Data): | |
| return graph_obj.x.shape[0] if graph_obj.x is not None else 0 | |
| else: | |
| return graph_obj.get('num_nodes', graph_obj['node_features'].shape[0]) | |
| def __getitem__(self, idx): | |
| """Load protein graph on-demand and generate two contrastive views with robust error handling.""" | |
| max_attempts = len(self.file_paths) # Maximum attempts to find a valid sample | |
| attempt = 0 | |
| while attempt < max_attempts: | |
| try: | |
| # Get current file (with wraparound if we've tried many times) | |
| current_idx = (idx + attempt) % len(self.file_paths) | |
| file_path = self.file_paths[current_idx] | |
| protein_id = self.protein_ids[current_idx] | |
| # Skip files that we know have failed before | |
| if self.skip_invalid_files and file_path in self._failed_files: | |
| attempt += 1 | |
| continue | |
| # Check graph file existence, skip to debug | |
| pt_file_path = '/'.join(file_path.split('/')[:-2]) + '/graph_cache/protein_pdb_files/' + 'pytorch_graph_' + protein_id + '.pt' | |
| if os.path.exists(pt_file_path) and not self.force_pdb_processing: | |
| return { | |
| 'load_error': False | |
| } | |
| # Load graph data | |
| protein_graph = self._load_single_graph(file_path) | |
| if protein_graph is None: | |
| # Mark this file as failed and try next | |
| self._failed_files.add(file_path) | |
| print(f"Dataset: Marking {Path(file_path).name} as failed, trying next file...") | |
| attempt += 1 | |
| continue | |
| # Validate graph data | |
| if not self._validate_graph_data(protein_graph): | |
| self._failed_files.add(file_path) | |
| print(f"Dataset: Graph validation failed for {Path(file_path).name}, trying next file...") | |
| attempt += 1 | |
| continue | |
| # Check if graph is large enough for subgraph sampling | |
| num_nodes = self._get_num_nodes(protein_graph) | |
| if num_nodes < self.min_nodes: | |
| self._failed_files.add(file_path) | |
| print(f"Dataset: Graph too small for {Path(file_path).name} ({num_nodes} < {self.min_nodes}), trying next file...") | |
| attempt += 1 | |
| continue | |
| # Generate two contrastive views | |
| view1, view2, sampling_strategy, noise_applied = self._generate_contrastive_views(protein_graph) | |
| # Validate views | |
| if view1 is None or view2 is None: | |
| print(f"Dataset: Failed to generate views for {Path(file_path).name}, trying next file...") | |
| attempt += 1 | |
| continue | |
| # Successfully created a valid sample | |
| return { | |
| 'protein_graph': protein_graph, | |
| 'protein_id': protein_id, | |
| 'idx': current_idx, | |
| 'file_path': file_path, | |
| 'load_error': False, | |
| 'view1': view1, | |
| 'view2': view2, | |
| 'sampling_strategy': sampling_strategy, | |
| 'noise_applied': noise_applied, | |
| 'attempts_needed': attempt + 1 | |
| } | |
| except Exception as e: | |
| print(f"Dataset: Unexpected error processing {self.file_paths[(idx + attempt) % len(self.file_paths)]}: {e}") | |
| attempt += 1 | |
| continue | |
| # If we get here, we couldn't find any valid sample after many attempts | |
| print(f"Dataset: Could not find valid sample after {max_attempts} attempts starting from idx {idx}") | |
| # Return a dummy sample to prevent DataLoader from crashing | |
| return self._create_dummy_sample(idx) | |
| def _validate_graph_data(self, graph_data): | |
| """Validate that graph data is complete and has no NaN/infinite values.""" | |
| try: | |
| if graph_data is None: | |
| return False | |
| # Check for NaN or infinite values | |
| import torch | |
| # Check node features | |
| if torch.any(torch.isnan(graph_data.x)) or torch.any(torch.isinf(graph_data.x)): | |
| print("Dataset: NaN/Inf found in node_features") | |
| return False | |
| # Check node positions | |
| if torch.any(torch.isnan(graph_data.pos)) or torch.any(torch.isinf(graph_data.pos)): | |
| print("Dataset: NaN/Inf found in node_pos") | |
| return False | |
| # Check edge attributes if present | |
| if graph_data.edge_attr is not None: | |
| if torch.any(torch.isnan(graph_data.edge_attr)) or torch.any(torch.isinf(graph_data.edge_attr)): | |
| print("Dataset: NaN/Inf found in edge_attr") | |
| return False | |
| # Check tensor shapes are consistent | |
| num_nodes = graph_data.x.shape[0] | |
| if graph_data.pos.shape[0] != num_nodes: | |
| print(f"Dataset: Inconsistent shapes - features: {graph_data.x.shape}, pos: {graph_data.pos.shape}") | |
| return False | |
| return True | |
| except Exception as e: | |
| print(f"Dataset: Error validating graph data: {e}") | |
| return False | |
| def _generate_contrastive_views(self, protein_graph): | |
| """Generate two contrastive views with error handling.""" | |
| try: | |
| num_nodes = protein_graph.x.shape[0] | |
| can_sample_subgraph = num_nodes >= self.min_nodes | |
| # Generate two contrastive views with sampling probabilities | |
| a = getattr(self, 'complete_graph_percent', 0) | |
| complete_prob = a / 100.0 | |
| seq_prob = (50 - 0.5 * a) / 100.0 | |
| dist_prob = seq_prob | |
| rand_val = random.random() | |
| # Convert Data object to dictionary for subgraph sampler compatibility | |
| protein_graph_dict = self._data_to_dict(protein_graph) | |
| if not can_sample_subgraph or rand_val < complete_prob: | |
| # Use complete graph for both views | |
| view1_dict = self.subgraph_sampler.apply_noise(protein_graph_dict, "identity") | |
| view2_dict = self.subgraph_sampler.apply_noise(protein_graph_dict, "identity") | |
| sampling_strategy = 'complete' if can_sample_subgraph else 'complete_forced' | |
| elif rand_val < complete_prob + seq_prob: | |
| # Sequential sampling for both views | |
| view1_dict = self.subgraph_sampler.sample_sequential_subgraph(protein_graph_dict) | |
| view2_dict = self.subgraph_sampler.sample_sequential_subgraph(protein_graph_dict) | |
| sampling_strategy = 'sequential' | |
| else: | |
| # Distance-based sampling for both views | |
| view1_dict = self.subgraph_sampler.sample_distance_subgraph(protein_graph_dict) | |
| view2_dict = self.subgraph_sampler.sample_distance_subgraph(protein_graph_dict) | |
| sampling_strategy = 'distance' | |
| # Convert back to Data objects | |
| view1 = self._dict_to_data(view1_dict) | |
| view2 = self._dict_to_data(view2_dict) # Validate views before applying noise | |
| if not self._validate_graph_data(view1) or not self._validate_graph_data(view2): | |
| print("Dataset: Invalid views generated during subgraph sampling") | |
| return None, None, sampling_strategy, 'none' | |
| # Apply noise transformations | |
| apply_masking = random.random() < 0.5 | |
| if apply_masking: | |
| view1_dict = self._data_to_dict(view1) | |
| view2_dict = self._data_to_dict(view2) | |
| view1_dict = self.subgraph_sampler.apply_noise(view1_dict, "random_edge_masking", edge_mask_prob=0.15) | |
| view2_dict = self.subgraph_sampler.apply_noise(view2_dict, "random_edge_masking", edge_mask_prob=0.15) | |
| view1 = self._dict_to_data(view1_dict) | |
| view2 = self._dict_to_data(view2_dict) | |
| noise_applied = 'masking' | |
| else: | |
| view1_dict = self._data_to_dict(view1) | |
| view2_dict = self._data_to_dict(view2) | |
| view1_dict = self.subgraph_sampler.apply_noise(view1_dict, "identity") | |
| view2_dict = self.subgraph_sampler.apply_noise(view2_dict, "identity") | |
| view1 = self._dict_to_data(view1_dict) | |
| view2 = self._dict_to_data(view2_dict) | |
| noise_applied = 'identity' | |
| # Final validation of views | |
| if not self._validate_graph_data(view1) or not self._validate_graph_data(view2): | |
| print("Dataset: Invalid views after noise application") | |
| return None, None, sampling_strategy, noise_applied | |
| return view1, view2, sampling_strategy, noise_applied | |
| except Exception as e: | |
| print(f"Dataset: Error generating contrastive views: {e}") | |
| return None, None, 'error', 'none' | |
| def _create_dummy_sample(self, idx): | |
| """Create a dummy sample when all else fails to prevent DataLoader crashes.""" | |
| return { | |
| 'protein_graph': None, | |
| 'protein_id': f'dummy_{idx}', | |
| 'idx': idx, | |
| 'file_path': 'dummy', | |
| 'load_error': True, | |
| 'view1': None, | |
| 'view2': None, | |
| 'sampling_strategy': 'dummy', | |
| 'noise_applied': 'none', | |
| 'attempts_needed': -1 | |
| } |