Add APE SELFIES tokenizer

special_tokens_map.json

@@ -0,0 +1,7 @@
+{
+  "bos_token": "<s>",
+  "eos_token": "</s>",
+  "unk_token": "<unk>",
+  "pad_token": "<pad>",
+  "mask_token": "<mask>"
+}

tokenization_ape.py

@@ -0,0 +1,524 @@
+"""Hugging Face-compatible tokenizer for APE molecular vocabularies.
+
+This file is intentionally self-contained so it can be copied into a model repo
+and loaded by ``AutoTokenizer.from_pretrained(..., trust_remote_code=True)``.
+"""
+
+import json
+import os
+import re
+from collections import defaultdict
+from pathlib import Path
+from typing import Any, Literal
+
+from transformers import PreTrainedTokenizer
+
+
+Representation = Literal["SELFIES", "SMILES"]
+
+VOCAB_FILES_NAMES = {"vocab_file": "vocab.json"}
+SELFIES_RE = re.compile(r"\[[^\]]+\]")
+SMILES_RE = re.compile(
+    r"(\[[^\]]+\]|Br?|Cl?|Si?|Se?|Li?|Na?|Mg?|Al?|Ca?|Fe?|Zn?|"
+    r"N|O|S|P|F|I|K|B|C|H|"
+    r"b|c|n|o|s|p|"
+    r"\%\d{2}|\d|"
+    r"\(|\)|\.|=|#|-|\+|\\|/|:|~|@|\?|\*|\$)"
+)
+
+
+def _normalize_representation(representation: str) -> Representation:
+    normalized = representation.upper()
+    if normalized not in {"SELFIES", "SMILES"}:
+        raise ValueError(f"representation must be 'SELFIES' or 'SMILES', got {representation!r}")
+    return normalized  # type: ignore[return-value]
+
+
+def pre_tokenize_molecule(molecule: str, representation: str) -> list[str]:
+    active_representation = _normalize_representation(representation)
+    if active_representation == "SELFIES":
+        return SELFIES_RE.findall(molecule)
+
+    tokens: list[str] = []
+    cursor = 0
+    for match in SMILES_RE.finditer(molecule):
+        if match.start() > cursor:
+            tokens.extend(molecule[cursor : match.start()])
+        tokens.append(match.group(0))
+        cursor = match.end()
+    if cursor < len(molecule):
+        tokens.extend(molecule[cursor:])
+    return [token for token in tokens if token and not token.isspace()]
+
+
+def ape_tokenize(
+    text: str,
+    vocab: dict[str, int],
+    representation: str,
+    unk_token: str = "<unk>",
+) -> list[str]:
+    pieces = pre_tokenize_molecule(text, representation)
+    if not pieces:
+        return [unk_token]
+
+    tokens: list[str] = []
+    i = 0
+    while i < len(pieces):
+        for j in range(len(pieces), i, -1):
+            possible_match = "".join(pieces[i:j])
+            if possible_match in vocab:
+                tokens.append(possible_match)
+                i = j
+                break
+        else:
+            tokens.append(unk_token)
+            i += 1
+    return tokens
+
+
+class APEPreTrainedTokenizer(PreTrainedTokenizer):
+    """Hugging Face tokenizer backend for APE molecular tokenization. (Not fast)"""
+
+    vocab_files_names = VOCAB_FILES_NAMES
+    model_input_names = ["input_ids", "attention_mask"]
+
+    def __init__(
+        self,
+        vocab_file: str | os.PathLike[str] | None = None,
+        vocab: dict[str, int] | None = None,
+        representation: str = "SELFIES",
+        bos_token: str = "<s>",
+        eos_token: str = "</s>",
+        unk_token: str = "<unk>",
+        pad_token: str = "<pad>",
+        mask_token: str = "<mask>",
+        model_max_length: int = 512,
+        **kwargs,
+    ) -> None:
+        if vocab is None:
+            if vocab_file is None:
+                vocab = {
+                    bos_token: 0,
+                    pad_token: 1,
+                    eos_token: 2,
+                    unk_token: 3,
+                    mask_token: 4,
+                }
+            else:
+                with open(vocab_file, encoding="utf-8") as f:
+                    vocab = json.load(f)
+
+        if vocab is None:
+            raise ValueError("Loaded vocabulary is None.")
+
+        self.vocab_file = str(vocab_file) if vocab_file is not None else None
+        self.vocab = {str(token): int(idx) for token, idx in vocab.items()}
+        self.ids_to_tokens = {idx: token for token, idx in self.vocab.items()}
+        self.representation = _normalize_representation(representation)
+        self.vocabulary_frequency: dict[str, int] = {}
+        self.pair_counts: dict[tuple[str, str] | str, int] = {}
+
+        super().__init__(
+            bos_token=bos_token,
+            eos_token=eos_token,
+            unk_token=unk_token,
+            pad_token=pad_token,
+            mask_token=mask_token,
+            model_max_length=model_max_length,
+            representation=self.representation,
+            **kwargs,
+        )
+
+    @property
+    def vocab_size(self) -> int:
+        return len(self.vocab)
+
+    @property
+    def vocabulary(self) -> dict[str, int]:
+        """Legacy alias for callers that previously used APETokenizer."""
+        return self.vocab
+
+    @vocabulary.setter
+    def vocabulary(self, value: dict[str, int]) -> None:
+        self.vocab = {str(token): int(idx) for token, idx in value.items()}
+        self.update_reverse_vocabulary()
+
+    @property
+    def special_tokens(self) -> dict[str, int]:
+        bos_token = str(self.bos_token)
+        pad_token = str(self.pad_token)
+        eos_token = str(self.eos_token)
+        unk_token = str(self.unk_token)
+        mask_token = str(self.mask_token)
+        return {
+            bos_token: self._convert_token_to_id(bos_token),
+            pad_token: self._convert_token_to_id(pad_token),
+            eos_token: self._convert_token_to_id(eos_token),
+            unk_token: self._convert_token_to_id(unk_token),
+            mask_token: self._convert_token_to_id(mask_token),
+        }
+
+    @special_tokens.setter
+    def special_tokens(self, value: dict[str, int]) -> None:
+        for token, token_id in value.items():
+            self.vocab.setdefault(str(token), int(token_id))
+        self.update_reverse_vocabulary()
+
+    def get_vocab(self) -> dict[str, int]:
+        return dict(self.vocab)
+
+    def update_reverse_vocabulary(self) -> None:
+        self.ids_to_tokens = {idx: token for token, idx in self.vocab.items()}
+
+    def pre_tokenize(self, molecule: str, representation: str | None = None) -> list[str]:
+        return pre_tokenize_molecule(molecule, representation or self.representation)
+
+    def _tokenize(self, text: str, **kwargs) -> list[str]:
+        return ape_tokenize(
+            text,
+            vocab=self.vocab,
+            representation=self.representation,
+            unk_token=str(self.unk_token),
+        )
+
+    def _convert_token_to_id(self, token: str) -> int:
+        return self.vocab.get(token, self.vocab[str(self.unk_token)])
+
+    def _convert_id_to_token(self, index: int) -> str:
+        return self.ids_to_tokens.get(int(index), str(self.unk_token))
+
+    def convert_tokens_to_string(self, tokens: list[str]) -> str:
+        return "".join(tokens)
+
+    def _required_special_token_id(
+        self,
+        token_value: int | list[int] | str | list[str] | None,
+        token_name: str,
+    ) -> int:
+        if token_value is None:
+            raise ValueError(f"{token_name} must be set.")
+        if isinstance(token_value, int):
+            return token_value
+        if isinstance(token_value, str):
+            return self._convert_token_to_id(token_value)
+        if len(token_value) == 1:
+            only_value = token_value[0]
+            if isinstance(only_value, int):
+                return only_value
+            if isinstance(only_value, str):
+                return self._convert_token_to_id(only_value)
+        raise ValueError(f"{token_name} must resolve to a single token id.")
+
+    def build_inputs_with_special_tokens(
+        self,
+        token_ids_0: list[int],
+        token_ids_1: list[int] | None = None,
+    ) -> list[int]:
+        bos_id = self._required_special_token_id(self.bos_token, "bos_token")
+        eos_id = self._required_special_token_id(self.eos_token, "eos_token")
+        if token_ids_1 is None:
+            return [bos_id, *token_ids_0, eos_id]
+        return [bos_id, *token_ids_0, eos_id, *token_ids_1, eos_id]
+
+    def create_token_type_ids_from_sequences(
+        self,
+        token_ids_0: list[int],
+        token_ids_1: list[int] | None = None,
+    ) -> list[int]:
+        return [0] * len(self.build_inputs_with_special_tokens(token_ids_0, token_ids_1))
+
+    def pad(
+        self,
+        encoded_inputs: Any,
+        padding: Any = True,
+        max_length: int | None = None,
+        pad_to_multiple_of: int | None = None,
+        padding_side: str | None = None,
+        return_attention_mask: bool | None = None,
+        return_tensors: Any = None,
+        verbose: bool = True,
+    ):
+        padding_enabled = padding not in (False, "do_not_pad")
+        if (
+            padding_enabled
+            and isinstance(encoded_inputs, list)
+            and any("labels" in item for item in encoded_inputs)
+        ):
+            target_length = max(
+                len(item.get("input_ids", item.get("labels", []))) for item in encoded_inputs
+            )
+            if padding == "max_length" and max_length is not None:
+                target_length = max_length
+
+            if pad_to_multiple_of and target_length % pad_to_multiple_of:
+                target_length = ((target_length // pad_to_multiple_of) + 1) * pad_to_multiple_of
+
+            padded_inputs = []
+            for item in encoded_inputs:
+                item = dict(item)
+                labels = list(item.get("labels", []))
+                pad_len = max(0, target_length - len(labels))
+                if pad_len:
+                    label_padding = [-100] * pad_len
+                    if self.padding_side == "left":
+                        labels = label_padding + labels
+                    else:
+                        labels = labels + label_padding
+                    item["labels"] = labels
+                padded_inputs.append(item)
+            encoded_inputs = padded_inputs
+
+        return super().pad(
+            encoded_inputs,
+            padding=padding,
+            max_length=max_length,
+            pad_to_multiple_of=pad_to_multiple_of,
+            padding_side=padding_side,
+            return_attention_mask=return_attention_mask,
+            return_tensors=return_tensors,
+            verbose=verbose,
+        )
+
+    def save_vocabulary(
+        self,
+        save_directory: str,
+        filename_prefix: str | None = None,
+    ) -> tuple[str, ...]:
+        if not os.path.isdir(save_directory):
+            raise ValueError(f"Vocabulary path ({save_directory}) should be a directory.")
+
+        vocab_file = Path(save_directory) / (
+            f"{filename_prefix}-vocab.json" if filename_prefix else "vocab.json"
+        )
+        with vocab_file.open("w", encoding="utf-8") as f:
+            json.dump(self.vocab, f, ensure_ascii=False, indent=4)
+        return (str(vocab_file),)
+
+    def add_tokens_to_vocabulary(self, tokens: list[str]) -> int:
+        """Add tokens to the tokenizer vocabulary if they are not already present.
+
+        This is intended for forcing coverage of rare valid molecular primitive
+        symbols, especially SELFIES bracket tokens, after APE merge training.
+        """
+
+        if not tokens:
+            return 0
+
+        next_id = max(self.vocab.values(), default=-1) + 1
+        added = 0
+
+        for token in tokens:
+            token = str(token).strip()
+            if not token:
+                continue
+            if token in self.vocab:
+                continue
+
+            self.vocab[token] = next_id
+            next_id += 1
+            added += 1
+
+        if added:
+            self.update_reverse_vocabulary()
+
+        return added
+
+    def save_pretrained(self, save_directory: str | os.PathLike[str], *args, **kwargs):
+        saved_files = super().save_pretrained(save_directory, *args, **kwargs)
+        save_path = Path(save_directory)
+
+        special_tokens_map = {
+            "bos_token": str(self.bos_token),
+            "eos_token": str(self.eos_token),
+            "unk_token": str(self.unk_token),
+            "pad_token": str(self.pad_token),
+            "mask_token": str(self.mask_token),
+        }
+        with (save_path / "special_tokens_map.json").open("w", encoding="utf-8") as f:
+            json.dump(special_tokens_map, f, ensure_ascii=False, indent=2)
+
+        tokenizer_config_path = save_path / "tokenizer_config.json"
+        if tokenizer_config_path.exists():
+            with tokenizer_config_path.open(encoding="utf-8") as f:
+                tokenizer_config = json.load(f)
+        else:
+            tokenizer_config = {}
+        tokenizer_config.update(
+            {
+                "tokenizer_class": self.__class__.__name__,
+                "representation": self.representation,
+                "model_max_length": self.model_max_length,
+                "auto_map": {
+                    "AutoTokenizer": [
+                        "tokenization_ape.APEPreTrainedTokenizer",
+                        None,
+                    ],
+                },
+            }
+        )
+        with tokenizer_config_path.open("w", encoding="utf-8") as f:
+            json.dump(tokenizer_config, f, ensure_ascii=False, indent=2)
+
+        return saved_files
+
+    def save_vocabulary_file(self, file_path: str | os.PathLike[str]) -> None:
+        path = Path(file_path)
+        path.parent.mkdir(parents=True, exist_ok=True)
+        freq_path = path.with_name(f"{path.stem}_freq.json")
+
+        with path.open("w", encoding="utf-8") as f:
+            json.dump(self.vocab, f, ensure_ascii=False, indent=4)
+        with freq_path.open("w", encoding="utf-8") as f:
+            json.dump(self.vocabulary_frequency, f, ensure_ascii=False, indent=4)
+
+    def load_vocabulary_file(
+        self,
+        file_path: str | os.PathLike[str],
+        representation: str | None = None,
+    ) -> None:
+        if representation is not None:
+            self.representation = _normalize_representation(representation)
+        with open(file_path, encoding="utf-8") as f:
+            vocab = json.load(f)
+        self.vocab = {str(token): int(idx) for token, idx in vocab.items()}
+        self.ids_to_tokens = {idx: token for token, idx in self.vocab.items()}
+
+    def train(
+        self,
+        corpus,
+        type: str = "selfies",
+        representation: str | None = None,
+        max_vocab_size: int = 5000,
+        min_freq_for_merge: int = 2000,
+        save_checkpoint: bool = False,
+        checkpoint_path: str = "checkpoint",
+        checkpoint_interval: int = 500,
+    ) -> None:
+        self.representation = _normalize_representation(representation or type)
+        text_padding = " " * 80
+
+        print(f"Pretokenizing {self.representation}", end="\r")
+        tokenized_corpus = [
+            tokens for sentence in corpus if (tokens := self.pre_tokenize(str(sentence)))
+        ]
+        vocabulary_frequency: defaultdict[str, int] = defaultdict(int)
+        for tokens in tokenized_corpus:
+            for token in tokens:
+                vocabulary_frequency[token] += 1
+        print(
+            f"Pretokenization complete, found {len(vocabulary_frequency)} tokens",
+            end="\r",
+        )
+
+        pre_tokens_counts = len(vocabulary_frequency)
+        merged_counter = len(vocabulary_frequency) + 1
+        checkpoint_increment = checkpoint_interval
+        batch = checkpoint_interval + pre_tokens_counts
+
+        def get_most_common_pair(tokenized):
+            pair_counts: defaultdict[tuple[str, str], int] = defaultdict(int)
+            for tokens in tokenized:
+                for i in range(len(tokens) - 1):
+                    pair_counts[(tokens[i], tokens[i + 1])] += 1
+
+            merged_pair_counts: dict[tuple[str, str] | str, int] = {
+                pair: count for pair, count in pair_counts.items()
+            }
+            self.pair_counts = merged_pair_counts
+            if not pair_counts:
+                return ("", ""), 0
+            return max(pair_counts.items(), key=lambda x: x[1], default=(("", ""), 0))
+
+        while True:
+            if save_checkpoint and len(vocabulary_frequency) == batch:
+                self.vocabulary_frequency = dict(vocabulary_frequency)
+                self.vocab = {
+                    **{
+                        str(self.bos_token): 0,
+                        str(self.pad_token): 1,
+                        str(self.eos_token): 2,
+                        str(self.unk_token): 3,
+                        str(self.mask_token): 4,
+                    },
+                    **{
+                        word: idx
+                        for idx, word in enumerate(
+                            vocabulary_frequency.keys(),
+                            start=5,
+                        )
+                    },
+                }
+                self.ids_to_tokens = {idx: token for token, idx in self.vocab.items()}
+                checkpoint_dir = Path(checkpoint_path)
+                checkpoint_dir.mkdir(parents=True, exist_ok=True)
+                self.save_vocabulary_file(checkpoint_dir / f"checkpoint_{batch}.json")
+                self.save_pretrained(str(checkpoint_dir / f"checkpoint_{batch}"))
+                print(f"Checkpoint saved at {checkpoint_dir}/checkpoint_{batch}.json")
+                batch += checkpoint_increment
+
+            if len(vocabulary_frequency) >= max_vocab_size:
+                print("\rMax vocabulary achieved", text_padding)
+                break
+
+            if all(len(tokens) < 2 for tokens in tokenized_corpus):
+                print("\rNo more mergeable pairs", text_padding)
+                break
+
+            most_common_pair, freq = get_most_common_pair(tokenized_corpus)
+            if freq < min_freq_for_merge:
+                print("\rNot enough frequency found", text_padding)
+                break
+
+            if not most_common_pair[0] or not most_common_pair[1]:
+                print("\rNo valid merge pair found", text_padding)
+                break
+
+            merged_word = "".join(most_common_pair)
+            if merged_word not in vocabulary_frequency:
+                print(
+                    f"New merge found: {merged_word} {merged_counter}/{max_vocab_size} "
+                    f"{round(merged_counter / max_vocab_size * 100, 2)}%"
+                )
+                merged_counter += 1
+            vocabulary_frequency[merged_word] = vocabulary_frequency.get(merged_word, 0) + freq
+
+            new_tokenized_corpus = []
+            for tokens in tokenized_corpus:
+                new_tokens = []
+                skip_next = False
+                for i in range(len(tokens)):
+                    if skip_next:
+                        skip_next = False
+                        continue
+
+                    if (
+                        i < len(tokens) - 1
+                        and tokens[i] == most_common_pair[0]
+                        and tokens[i + 1] == most_common_pair[1]
+                    ):
+                        new_tokens.append(merged_word)
+                        skip_next = True
+                    else:
+                        new_tokens.append(tokens[i])
+
+                new_tokenized_corpus.append(new_tokens)
+
+            tokenized_corpus = new_tokenized_corpus
+
+        self.vocabulary_frequency = dict(vocabulary_frequency)
+        self.vocab = {
+            str(self.bos_token): 0,
+            str(self.pad_token): 1,
+            str(self.eos_token): 2,
+            str(self.unk_token): 3,
+            str(self.mask_token): 4,
+            **{word: idx for idx, word in enumerate(vocabulary_frequency.keys(), start=5)},
+        }
+        self.ids_to_tokens = {idx: token for token, idx in self.vocab.items()}
+        print("\nTraining complete.")
+
+    def train_from_iterator(self, iterator, *args, **kwargs) -> None:
+        raise NotImplementedError("train_from_iterator is not implemented for APE")
+
+
+APEPreTrainedTokenizer.register_for_auto_class("AutoTokenizer")

tokenizer_config.json

@@ -0,0 +1,59 @@
+{
+  "added_tokens_decoder": {
+    "0": {
+      "content": "<s>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "1": {
+      "content": "<pad>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "2": {
+      "content": "</s>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "3": {
+      "content": "<unk>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "4": {
+      "content": "<mask>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    }
+  },
+  "auto_map": {
+    "AutoTokenizer": [
+      "tokenization_ape.APEPreTrainedTokenizer",
+      null
+    ]
+  },
+  "backend": "custom",
+  "bos_token": "<s>",
+  "eos_token": "</s>",
+  "mask_token": "<mask>",
+  "model_max_length": 512,
+  "pad_token": "<pad>",
+  "representation": "SELFIES",
+  "tokenizer_class": "APEPreTrainedTokenizer",
+  "unk_token": "<unk>"
+}

vocab.json

@@ -0,0 +1,2441 @@
+{
+    "</s>": 2,
+    "<mask>": 4,
+    "<pad>": 1,
+    "<s>": 0,
+    "<unk>": 3,
+    "[#11C]": 168,
+    "[#14C]": 275,
+    "[#Branch1]": 26,
+    "[#Branch1][C][=Branch1][C][=O]": 1233,
+    "[#Branch1][C][=Branch1][C][=O][N]": 1304,
+    "[#Branch1][C][=C][Ring1][=Branch1]": 1118,
+    "[#Branch1][C][C]": 1231,
+    "[#Branch1][C][C][=Branch1][C][=O]": 1043,
+    "[#Branch1][C][C][=Branch1][C][=O][O]": 1238,
+    "[#Branch1][C][C][Branch1][C][C]": 815,
+    "[#Branch1][C][C][Branch1][C][C][C][N][C][=Branch1][C][=O]": 1575,
+    "[#Branch1][C][C][Branch1][C][N][=O]": 1918,
+    "[#Branch1][C][C][C][C]": 844,
+    "[#Branch1][C][C][C][C][Ring1][Ring1]": 1433,
+    "[#Branch1][C][C][C][C][Ring1][Ring2]": 2264,
+    "[#Branch1][N][C]": 934,
+    "[#Branch1][N][C][=Branch1][C][=O]": 1490,
+    "[#Branch1][N][C][Branch1][C][C][=O]": 1242,
+    "[#Branch1][O][C]": 578,
+    "[#Branch1][O][C][Branch1][C][C][=O]": 698,
+    "[#Branch1][O][C][Branch1][C][F][F]": 1985,
+    "[#Branch2]": 25,
+    "[#Branch2][C]": 420,
+    "[#Branch2][C][=Branch1][C][=O]": 1410,
+    "[#Branch2][C][=C][C][=C][C][=C][Ring1][=Branch1]": 709,
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