import pandas as pd import torch from torch.utils.data import Dataset, DataLoader from torch.nn.utils.rnn import pad_sequence from esm_utils import get_latents, load_esm2_model import config class ProteinDataset(Dataset): def __init__(self, csv_file, tokenizer, model): self.data = pd.read_csv(csv_file).head(4) self.tokenizer = tokenizer self.model = model def __len__(self): return len(self.data) def __getitem__(self, idx): sequence = self.data.iloc[idx]['Sequence'] latents = get_latents(self.model, self.tokenizer, sequence) attention_mask = torch.ones_like(latents) attention_mask = torch.mean(attention_mask, dim=-1) return latents, attention_mask def collate_fn(batch): latents, attention_mask = zip(*batch) latents_padded = pad_sequence([torch.tensor(latent) for latent in latents], batch_first=True, padding_value=0) attention_mask_padded = pad_sequence([torch.tensor(mask) for mask in attention_mask], batch_first=True, padding_value=0) return latents_padded, attention_mask_padded def get_dataloaders(config): tokenizer, masked_model, embedding_model = load_esm2_model(config.MODEL_NAME) train_dataset = ProteinDataset(config.Loader.DATA_PATH + "/train.csv", tokenizer, embedding_model) val_dataset = ProteinDataset(config.Loader.DATA_PATH + "/val.csv", tokenizer, embedding_model) test_dataset = ProteinDataset(config.Loader.DATA_PATH + "/test.csv", tokenizer, embedding_model) train_loader = DataLoader(train_dataset, batch_size=config.Loader.BATCH_SIZE, num_workers=0, shuffle=True, collate_fn=collate_fn) val_loader = DataLoader(val_dataset, batch_size=config.Loader.BATCH_SIZE, num_workers=0, shuffle=False, collate_fn=collate_fn) test_loader = DataLoader(test_dataset, batch_size=config.Loader.BATCH_SIZE, num_workers=0, shuffle=False, collate_fn=collate_fn) return train_loader, val_loader, test_loader