""" We use the FastPLM implementation of DPLM. """ import sys import os import torch import torch.nn as nn from typing import List, Optional, Union, Dict _FASTPLMS = os.path.join(os.path.dirname(os.path.dirname(os.path.abspath(__file__))), 'FastPLMs') if _FASTPLMS not in sys.path: sys.path.insert(0, _FASTPLMS) from dplm_fastplms.modeling_dplm import ( DPLMForMaskedLM, DPLMForSequenceClassification, DPLMForTokenClassification, ) from transformers import EsmTokenizer from .base_tokenizer import BaseSequenceTokenizer presets = { 'DPLM-150': 'airkingbd/dplm_150m', 'DPLM-650': 'airkingbd/dplm_650m', 'DPLM-3B': 'airkingbd/dplm_3b', } class DPLMTokenizerWrapper(BaseSequenceTokenizer): def __init__(self, tokenizer: EsmTokenizer): super().__init__(tokenizer) def __call__(self, sequences: Union[str, List[str]], **kwargs) -> Dict[str, torch.Tensor]: if isinstance(sequences, str): sequences = [sequences] kwargs.setdefault('return_tensors', 'pt') kwargs.setdefault('padding', 'longest') kwargs.setdefault('add_special_tokens', True) tokenized = self.tokenizer(sequences, **kwargs) return tokenized class DPLMForEmbedding(nn.Module): def __init__(self, model_path: str, return_logits: bool = False, dtype: torch.dtype = None): super().__init__() self.dplm = DPLMForMaskedLM.from_pretrained(model_path, dtype=dtype) self.return_logits = return_logits def forward( self, input_ids: torch.Tensor, attention_mask: Optional[torch.Tensor] = None, output_attentions: Optional[bool] = None, output_hidden_states: Optional[bool] = False, **kwargs, ) -> torch.Tensor: if output_attentions: out = self.dplm(input_ids, attention_mask=attention_mask, output_attentions=output_attentions) return out.last_hidden_state, out.attentions out = self.dplm(input_ids, attention_mask=attention_mask) if self.return_logits: return out.last_hidden_state, out.logits return out.last_hidden_state def get_dplm_tokenizer(preset: str, model_path: str = None): return DPLMTokenizerWrapper(EsmTokenizer.from_pretrained('facebook/esm2_t6_8M_UR50D')) def build_dplm_model(preset: str, masked_lm: bool = False, dtype: torch.dtype = None, model_path: str = None, **kwargs): model = DPLMForEmbedding(model_path or presets[preset], return_logits=masked_lm, dtype=dtype).eval() tokenizer = get_dplm_tokenizer(preset) return model, tokenizer def get_dplm_for_training(preset: str, tokenwise: bool = False, num_labels: int = None, hybrid: bool = False, dtype: torch.dtype = None, model_path: str = None): model_path = model_path or presets[preset] if hybrid: model = DPLMForMaskedLM.from_pretrained(model_path, dtype=dtype).eval() else: if tokenwise: model = DPLMForTokenClassification.from_pretrained(model_path, num_labels=num_labels, dtype=dtype).eval() else: model = DPLMForSequenceClassification.from_pretrained(model_path, num_labels=num_labels, dtype=dtype).eval() tokenizer = get_dplm_tokenizer(preset) return model, tokenizer if __name__ == '__main__': # py -m src.protify.base_models.dplm model, tokenizer = build_dplm_model('DPLM-150') print(model) print(tokenizer) print(tokenizer('MEKVQYLTRSAIRRASTIEMPQQARQKLQNLFINFCLILICBBOLLICIIVMLL'))