import torch import pandas as pd import lightning.pytorch as pl from transformers import AutoModel, AutoTokenizer from torch.utils.data import Dataset, DataLoader class MembraneDataset(Dataset): def __init__(self, config, data_path): self.config = config self.data = pd.read_csv(data_path) self.tokenizer = AutoTokenizer.from_pretrained(config.lm.pretrained_evoflow) def __len__(self): return len(self.data) def __getitem__(self, idx): sequence = self.data.iloc[idx]["Sequence"] tokens = self.tokenizer( sequence.upper(), return_tensors='pt', padding='max_length', truncation=True, max_length=self.config.data.max_seq_len ) #return {"input_ids": tokens['input_ids'], "attention_mask": tokens['attention_mask']} return { "input_ids": tokens['input_ids'].squeeze(0), "attention_mask": tokens['attention_mask'].squeeze(0) } def collate_fn(batch): input_ids = torch.stack([item['input_ids'] for item in batch])#.squeeze() masks = torch.stack([item['attention_mask'] for item in batch])#.squeeze() return {'input_ids': input_ids, 'attention_mask': masks} class MembraneDataModule(pl.LightningDataModule): def __init__(self, config, train_dataset, val_dataset, test_dataset, collate_fn=collate_fn): super().__init__() self.train_dataset = train_dataset self.val_dataset = val_dataset self.test_dataset = test_dataset self.collate_fn = collate_fn self.batch_size = config.data.batch_size self.tokenizer = AutoTokenizer.from_pretrained(config.lm.pretrained_evoflow) def train_dataloader(self): return DataLoader(self.train_dataset, batch_size=self.batch_size, collate_fn=self.collate_fn, num_workers=8, pin_memory=True) def val_dataloader(self): return DataLoader(self.val_dataset, batch_size=self.batch_size, collate_fn=self.collate_fn, num_workers=8, shuffle=False, pin_memory=True) def test_dataloader(self): return DataLoader(self.test_dataset, batch_size=self.batch_size, collate_fn=self.collate_fn, num_workers=8, shuffle=False, pin_memory=True) def get_datasets(config): """Helper method to grab datasets to quickly init data module in main.py""" train_dataset = MembraneDataset(config, config.data.train) test_dataset = MembraneDataset(config, config.data.test) val_dataset = MembraneDataset(config, config.data.val) return { "train": train_dataset, "val": val_dataset, "test": test_dataset }