Rocketknight1 HF staff commited on
Commit
4a3f199
1 Parent(s): 16a090d

Upload tokenizer

Browse files
special_tokens_map.json ADDED
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+ {
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+ "bos_token": {
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+ "content": "[BOS]",
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+ "lstrip": false,
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+ "normalized": false,
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+ "rstrip": false,
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+ "single_word": false
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+ },
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+ "cls_token": {
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+ "content": "[CLS]",
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+ "lstrip": false,
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+ "normalized": false,
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+ "rstrip": false,
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+ "single_word": false
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+ },
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+ "eos_token": {
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+ "content": "[SEP]",
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+ "lstrip": false,
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+ "normalized": false,
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+ "rstrip": false,
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+ "single_word": false
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+ },
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+ "mask_token": {
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+ "content": "[MASK]",
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+ "lstrip": false,
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+ "normalized": false,
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+ "rstrip": false,
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+ "single_word": false
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+ },
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+ "pad_token": {
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+ "content": "[PAD]",
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+ "lstrip": false,
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+ "normalized": false,
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+ "rstrip": false,
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+ "single_word": false
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+ },
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+ "sep_token": {
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+ "content": "[SEP]",
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+ "lstrip": false,
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+ "normalized": false,
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+ "rstrip": false,
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+ "single_word": false
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+ },
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+ "unk_token": {
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+ "content": "[UNK]",
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+ "lstrip": false,
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+ "normalized": false,
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+ "rstrip": false,
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+ "single_word": false
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+ }
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+ }
tokenization_hyena.py ADDED
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+ from transformers import PreTrainedTokenizer, AddedToken
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+ from typing import List, Optional, Union, Dict, Sequence, Tuple
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+ from pathlib import Path
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+ import json
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+ import os
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+
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+
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+ class HyenaDNATokenizer(PreTrainedTokenizer):
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+ model_input_names = ["input_ids", "attention_mask"]
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+
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+ def __init__(self,
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+ model_max_length: int,
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+ bos_token="[BOS]",
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+ eos_token="[SEP]",
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+ sep_token="[SEP]",
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+ cls_token="[CLS]",
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+ pad_token="[PAD]",
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+ mask_token="[MASK]",
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+ unk_token="[UNK]",
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+ **kwargs):
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+ """Character tokenizer for Hugging Face transformers.
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+ Args:
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+ characters (Sequence[str]): List of desired characters. Any character which
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+ is not included in this list will be replaced by a special token called
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+ [UNK] with id=6. Following are list of all of the special tokens with
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+ their corresponding ids:
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+ "[CLS]": 0
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+ "[SEP]": 1
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+ "[BOS]": 2
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+ "[MASK]": 3
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+ "[PAD]": 4
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+ "[RESERVED]": 5
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+ "[UNK]": 6
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+ an id (starting at 7) will be assigned to each character.
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+ model_max_length (int): Model maximum sequence length.
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+ """
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+ self.characters = ('A', 'C', 'G', 'T', 'N')
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+ self.model_max_length = model_max_length
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+
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+ self._vocab_str_to_int = {
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+ "[CLS]": 0,
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+ "[SEP]": 1,
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+ "[BOS]": 2,
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+ "[MASK]": 3,
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+ "[PAD]": 4,
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+ "[RESERVED]": 5,
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+ "[UNK]": 6,
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+ **{ch: i + 7 for i, ch in enumerate(self.characters)},
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+ }
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+ self._vocab_int_to_str = {v: k for k, v in self._vocab_str_to_int.items()}
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+ add_prefix_space = kwargs.pop("add_prefix_space", False)
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+ padding_side = kwargs.pop("padding_side", "left")
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+
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+ super().__init__(
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+ bos_token=bos_token,
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+ eos_token=eos_token,
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+ sep_token=sep_token,
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+ cls_token=cls_token,
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+ pad_token=pad_token,
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+ mask_token=mask_token,
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+ unk_token=unk_token,
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+ add_prefix_space=add_prefix_space,
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+ model_max_length=model_max_length,
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+ padding_side=padding_side,
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+ **kwargs,
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+ )
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+
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+ @property
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+ def vocab_size(self) -> int:
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+ return len(self._vocab_str_to_int)
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+
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+ def _tokenize(self, text: str) -> List[str]:
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+ return list(text)
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+
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+ def _convert_token_to_id(self, token: str) -> int:
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+ return self._vocab_str_to_int.get(token, self._vocab_str_to_int["[UNK]"])
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+
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+ def _convert_id_to_token(self, index: int) -> str:
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+ return self._vocab_int_to_str[index]
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+
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+ def convert_tokens_to_string(self, tokens):
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+ return "".join(tokens)
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+
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+ def get_special_tokens_mask(
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+ self,
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+ token_ids_0: List[int],
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+ token_ids_1: Optional[List[int]] = None,
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+ already_has_special_tokens: bool = False,
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+ ) -> List[int]:
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+ if already_has_special_tokens:
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+ return super().get_special_tokens_mask(
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+ token_ids_0=token_ids_0,
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+ token_ids_1=token_ids_1,
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+ already_has_special_tokens=True,
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+ )
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+
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+ result = [1] + ([0] * len(token_ids_0)) + [1]
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+ if token_ids_1 is not None:
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+ result += ([0] * len(token_ids_1)) + [1]
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+ return result
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+
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+ def build_inputs_with_special_tokens(
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+ self, token_ids_0: List[int], token_ids_1: Optional[List[int]] = None
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+ ) -> List[int]:
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+ sep = [self.sep_token_id]
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+ # cls = [self.cls_token_id]
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+ result = token_ids_0 + sep
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+ if token_ids_1 is not None:
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+ result += token_ids_1 + sep
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+ return result
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+
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+ def get_vocab(self) -> Dict[str, int]:
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+ return self._vocab_str_to_int
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+
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+ # HyenaDNA has a fixed vocabulary with no vocab file
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+ def save_vocabulary(self, save_directory: str, filename_prefix: Optional[str] = None) -> Tuple:
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+ return ()
tokenizer_config.json ADDED
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+ {
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+ "add_prefix_space": false,
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+ "added_tokens_decoder": {
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+ "0": {
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+ "content": "[CLS]",
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+ "lstrip": false,
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+ "normalized": false,
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+ "rstrip": false,
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+ "single_word": false,
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+ "special": true
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+ },
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+ "1": {
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+ "content": "[SEP]",
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+ "lstrip": false,
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+ "normalized": false,
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+ "rstrip": false,
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+ "single_word": false,
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+ "special": true
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+ },
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+ "2": {
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+ "content": "[BOS]",
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+ "lstrip": false,
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+ "normalized": false,
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+ "rstrip": false,
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+ "single_word": false,
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+ "special": true
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+ },
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+ "3": {
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+ "content": "[MASK]",
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+ "lstrip": false,
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+ "normalized": false,
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+ "rstrip": false,
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+ "single_word": false,
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+ "special": true
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+ },
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+ "4": {
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+ "content": "[PAD]",
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+ "lstrip": false,
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+ "normalized": false,
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+ "rstrip": false,
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+ "single_word": false,
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+ "special": true
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+ },
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+ "6": {
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+ "content": "[UNK]",
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+ "lstrip": false,
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+ "normalized": false,
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+ "rstrip": false,
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+ "single_word": false,
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+ "special": true
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+ }
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+ },
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+ "auto_map": {
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+ "AutoTokenizer": [
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+ "tokenization_hyena.HyenaDNATokenizer",
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+ null
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+ ]
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+ },
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+ "bos_token": "[BOS]",
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+ "clean_up_tokenization_spaces": true,
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+ "cls_token": "[CLS]",
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+ "eos_token": "[SEP]",
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+ "mask_token": "[MASK]",
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+ "model_max_length": 1026,
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+ "pad_token": "[PAD]",
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+ "padding_side": "left",
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+ "sep_token": "[SEP]",
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+ "tokenizer_class": "HyenaDNATokenizer",
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+ "unk_token": "[UNK]"
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+ }