Instructions to use AI4Protein/ProPrime_650M with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- Transformers
How to use AI4Protein/ProPrime_650M with Transformers:
# Use a pipeline as a high-level helper from transformers import pipeline pipe = pipeline("fill-mask", model="AI4Protein/ProPrime_650M", trust_remote_code=True)# Load model directly from transformers import AutoModelForMaskedLM model = AutoModelForMaskedLM.from_pretrained("AI4Protein/ProPrime_650M", trust_remote_code=True, dtype="auto") - Notebooks
- Google Colab
- Kaggle
| import os | |
| from typing import List, Optional | |
| from pathlib import Path | |
| from transformers.tokenization_utils import PreTrainedTokenizer | |
| from transformers.utils import logging | |
| logger = logging.get_logger(__name__) | |
| VOCAB_FILES_NAMES = {"vocab_file": "vocab.txt"} | |
| def load_vocab_file(vocab_file): | |
| with open(vocab_file, "r") as f: | |
| lines = f.read().splitlines() | |
| return [l.strip() for l in lines] | |
| class ProPrimeTokenizer(PreTrainedTokenizer): | |
| vocab_files_names = VOCAB_FILES_NAMES | |
| model_input_names = ["input_ids", "attention_mask"] | |
| def __init__( | |
| self, | |
| vocab_file=None, | |
| unk_token="<unk>", | |
| cls_token="<cls>", | |
| pad_token="<pad>", | |
| mask_token="<mask>", | |
| eos_token="<eos>", | |
| **kwargs, | |
| ): | |
| if vocab_file is None: | |
| vocab_file = Path(__file__).parent / "vocab.txt" | |
| self.all_tokens = load_vocab_file(vocab_file) | |
| self._id_to_token = dict(enumerate(self.all_tokens)) | |
| self._token_to_id = {tok: ind for ind, tok in enumerate(self.all_tokens)} | |
| super().__init__( | |
| unk_token=unk_token, | |
| cls_token=cls_token, | |
| pad_token=pad_token, | |
| mask_token=mask_token, | |
| eos_token=eos_token, | |
| **kwargs, | |
| ) | |
| # TODO, all the tokens are added? But they are also part of the vocab... bit strange. | |
| # none of them are special, but they all need special splitting. | |
| self.unique_no_split_tokens = self.all_tokens | |
| self._update_trie(self.unique_no_split_tokens) | |
| def _convert_id_to_token(self, index: int) -> str: | |
| return self._id_to_token.get(index, self.unk_token) | |
| def _convert_token_to_id(self, token: str) -> int: | |
| return self._token_to_id.get(token, self._token_to_id.get(self.unk_token)) | |
| def _tokenize(self, text, **kwargs): | |
| return text.split() | |
| def get_vocab(self): | |
| base_vocab = self._token_to_id.copy() | |
| base_vocab.update(self.added_tokens_encoder) | |
| return base_vocab | |
| def token_to_id(self, token: str) -> int: | |
| return self._token_to_id.get(token, self._token_to_id.get(self.unk_token)) | |
| def id_to_token(self, index: int) -> str: | |
| return self._id_to_token.get(index, self.unk_token) | |
| def build_inputs_with_special_tokens( | |
| self, token_ids_0: List[int], token_ids_1: Optional[List[int]] = None | |
| ) -> List[int]: | |
| cls = [self.cls_token_id] | |
| sep = [self.eos_token_id] | |
| if token_ids_1 is None: | |
| if self.eos_token_id is None: | |
| return cls + token_ids_0 | |
| else: | |
| return cls + token_ids_0 + sep | |
| elif self.eos_token_id is None: | |
| raise ValueError( | |
| "Cannot tokenize multiple sequences when EOS token is not set!" | |
| ) | |
| return ( | |
| cls + token_ids_0 + sep + token_ids_1 + sep | |
| ) # Multiple inputs always have an EOS token | |
| def get_special_tokens_mask( | |
| self, | |
| token_ids_0: List, | |
| token_ids_1: Optional[List] = None, | |
| already_has_special_tokens: bool = False, | |
| ) -> List[int]: | |
| """ | |
| Retrieves sequence ids from a token list that has no special tokens added. This method is called when adding | |
| special tokens using the tokenizer `prepare_for_model` or `encode_plus` methods. | |
| Args: | |
| token_ids_0 (`List[int]`): | |
| List of ids of the first sequence. | |
| token_ids_1 (`List[int]`, *optional*): | |
| List of ids of the second sequence. | |
| already_has_special_tokens (`bool`, *optional*, defaults to `False`): | |
| Whether or not the token list is already formatted with special tokens for the model. | |
| Returns: | |
| A list of integers in the range [0, 1]: 1 for a special token, 0 for a sequence token. | |
| """ | |
| if already_has_special_tokens: | |
| if token_ids_1 is not None: | |
| raise ValueError( | |
| "You should not supply a second sequence if the provided sequence of " | |
| "ids is already formatted with special tokens for the model." | |
| ) | |
| return [1 if token in self.all_special_ids else 0 for token in token_ids_0] | |
| mask = [1] + ([0] * len(token_ids_0)) + [1] | |
| if token_ids_1 is not None: | |
| mask += [0] * len(token_ids_1) + [1] | |
| return mask | |
| def save_vocabulary(self, save_directory, filename_prefix): | |
| vocab_file = os.path.join( | |
| save_directory, | |
| (filename_prefix + "-" if filename_prefix else "") + "vocab.txt", | |
| ) | |
| with open(vocab_file, "w") as f: | |
| f.write("\n".join(self.all_tokens)) | |
| return (vocab_file,) | |
| def vocab_size(self) -> int: | |
| return len(self.all_tokens) | |
| ProPrimeTokenizer.register_for_auto_class("AutoTokenizer") | |