tokenization_esm.py

# coding=utf-8
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#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
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"""Tokenization classes for ESM."""
import os
from typing import List, Optional, Union

from transformers.tokenization_utils import PreTrainedTokenizer
from transformers.tokenization_utils_base import AddedToken
from transformers.utils import logging


logger = logging.get_logger(__name__)

VOCAB_FILES_NAMES = {"vocab_file": "vocab.txt"}

PRETRAINED_VOCAB_FILES_MAP = {
    "vocab_file": {
        "facebook/esm2_t6_8M_UR50D": "https://huggingface.co/facebook/esm2_t6_8M_UR50D/resolve/main/vocab.txt",
        "facebook/esm2_t12_35M_UR50D": "https://huggingface.co/facebook/esm2_t12_35M_UR50D/resolve/main/vocab.txt",
    },
}

PRETRAINED_POSITIONAL_EMBEDDINGS_SIZES = {
    "facebook/esm2_t6_8M_UR50D": 1024,
    "facebook/esm2_t12_35M_UR50D": 1024,
}


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 EsmTokenizer(PreTrainedTokenizer):
    """
    Constructs an ESM tokenizer.
    """

    vocab_files_names = VOCAB_FILES_NAMES
    pretrained_vocab_files_map = PRETRAINED_VOCAB_FILES_MAP
    max_model_input_sizes = PRETRAINED_POSITIONAL_EMBEDDINGS_SIZES
    model_input_names = ["input_ids", "attention_mask"]

    def __init__(self, vocab_file, **kwargs):
        super().__init__(**kwargs)
        self.all_tokens = load_vocab_file(vocab_file)
        self._id_to_token = {ind: tok for ind, tok in enumerate(self.all_tokens)}
        self._token_to_id = {tok: ind for ind, tok in enumerate(self.all_tokens)}
        self.unk_token = "<unk>"
        self.cls_token = "<cls>"
        self.pad_token = "<pad>"
        self.mask_token = "<mask>"
        self.eos_token = "<eos>"
        self.unique_no_split_tokens = self.all_tokens
        self._create_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_size(self, with_added_tokens=False):
        return len(self._id_to_token)

    def get_vocab(self):
        return {token: i for i, token in enumerate(self.all_tokens)}

    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]:
        if token_ids_1 is None:
            return [self.cls_token_id] + token_ids_0 + [self.eos_token_id]
        cls = [self.cls_token_id]
        sep = [self.eos_token_id]  # No sep token in ESM vocabulary
        return cls + token_ids_0 + sep + token_ids_1 + sep

    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,)

    @property
    def vocab_size(self) -> int:
        return self.get_vocab_size(with_added_tokens=False)

    def _add_tokens(self, new_tokens: Union[List[str], List[AddedToken]], special_tokens: bool = False) -> int:
        return super()._add_tokens(new_tokens, special_tokens=True)