before_train

config.json

@@ -0,0 +1,27 @@
+{
+  "_name_or_path": "/home/zoez/chemT5",
+  "architectures": [
+    "T5ForConditionalGeneration"
+  ],
+  "d_ff": 2048,
+  "d_kv": 64,
+  "d_model": 768,
+  "decoder_start_token_id": 0,
+  "dropout_rate": 0.1,
+  "eos_token_id": 1,
+  "feed_forward_proj": "gated-gelu",
+  "initializer_factor": 1.0,
+  "is_encoder_decoder": true,
+  "layer_norm_epsilon": 1e-06,
+  "model_type": "t5",
+  "num_decoder_layers": 12,
+  "num_heads": 12,
+  "num_layers": 12,
+  "output_past": true,
+  "pad_token_id": 0,
+  "relative_attention_num_buckets": 32,
+  "tie_word_embeddings": false,
+  "transformers_version": "4.11.3",
+  "use_cache": true,
+  "vocab_size": 32003
+}

pretokenizer.py

@@ -0,0 +1,24 @@
+#https://github.com/XinhaoLi74/SmilesPE/blob/master/SmilesPE/pretokenizer.py
+
+def atomwise_tokenizer(smi, exclusive_tokens = None):
+    """
+    Tokenize a SMILES molecule at atom-level:
+        (1) 'Br' and 'Cl' are two-character tokens
+        (2) Symbols with bracket are considered as tokens
+    exclusive_tokens: A list of specifical symbols with bracket you want to keep. e.g., ['[C@@H]', '[nH]'].
+    Other symbols with bracket will be replaced by '[UNK]'. default is `None`.
+    """
+    import re
+    pattern = r"(\[[^\]]+]|Br?|Cl?|N|O|S|P|F|I|b|c|n|o|s|p|\(|\)|\.|=|#|-|\+|\\|\/|:|~|@|\?|>>?|\*|\$|\%[0-9]{2}|[0-9])"
+
+    #pattern =  r"(\[[^\]]]|Br|Cl|B|C|N|O|P|S|F|c+\%[0-9]{2}|c+\%[0-9]|.+)"
+    regex = re.compile(pattern)
+    tokens = [token for token in regex.findall(smi)]
+
+    if exclusive_tokens:
+        for i, tok in enumerate(tokens):
+            if tok.startswith('['):
+                if tok not in exclusive_tokens:
+                    tokens[i] = '[UNK]'
+    return ' '.join(tokens)
+    #return tokens

run_t5_mlm_flax.py

@@ -0,0 +1,802 @@
+#!/usr/bin/env python
+# coding=utf-8
+# Copyright 2021 The HuggingFace Team All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     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,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""
+Pretraining the library models for T5-like span-masked language modeling on a text file or a dataset.
+Here is the full list of checkpoints on the hub that can be pretrained by this script:
+https://huggingface.co/models?filter=t5
+"""
+# You can also adapt this script on your own masked language modeling task. Pointers for this are left as comments.
+import logging
+import os
+import sys
+import time
+from dataclasses import dataclass, field
+from pathlib import Path
+from typing import Dict, List, Optional
+
+import numpy as np
+from datasets import load_dataset
+from tqdm import tqdm
+
+import flax
+import jax
+import jax.numpy as jnp
+import optax
+from flax import jax_utils, traverse_util
+from flax.training import train_state
+from flax.training.common_utils import get_metrics, onehot, shard
+from huggingface_hub import Repository
+from transformers import (
+    CONFIG_MAPPING,
+    FLAX_MODEL_FOR_MASKED_LM_MAPPING,
+    AutoTokenizer,
+    BatchEncoding,
+    FlaxT5ForConditionalGeneration,
+    HfArgumentParser,
+    PreTrainedTokenizerBase,
+    T5Config,
+    TrainingArguments,
+    is_tensorboard_available,
+    set_seed,
+)
+from transformers.file_utils import get_full_repo_name
+from transformers.models.t5.modeling_flax_t5 import shift_tokens_right
+
+
+MODEL_CONFIG_CLASSES = list(FLAX_MODEL_FOR_MASKED_LM_MAPPING.keys())
+MODEL_TYPES = tuple(conf.model_type for conf in MODEL_CONFIG_CLASSES)
+
+
+@dataclass
+class ModelArguments:
+    """
+    Arguments pertaining to which model/config/tokenizer we are going to fine-tune, or train from scratch.
+    """
+
+    model_name_or_path: Optional[str] = field(
+        default=None,
+        metadata={
+            "help": "The model checkpoint for weights initialization."
+            "Don't set if you want to train a model from scratch."
+        },
+    )
+    model_type: Optional[str] = field(
+        default=None,
+        metadata={"help": "If training from scratch, pass a model type from the list: " + ", ".join(MODEL_TYPES)},
+    )
+    config_name: Optional[str] = field(
+        default=None, metadata={"help": "Pretrained config name or path if not the same as model_name"}
+    )
+    tokenizer_name: Optional[str] = field(
+        default=None, metadata={"help": "Pretrained tokenizer name or path if not the same as model_name"}
+    )
+    cache_dir: Optional[str] = field(
+        default=None, metadata={"help": "Where do you want to store the pretrained models downloaded from s3"}
+    )
+    use_fast_tokenizer: bool = field(
+        default=True,
+        metadata={"help": "Whether to use one of the fast tokenizer (backed by the tokenizers library) or not."},
+    )
+    dtype: Optional[str] = field(
+        default="float32",
+        metadata={
+            "help": "Floating-point format in which the model weights should be initialized and trained. Choose one of `[float32, float16, bfloat16]`."
+        },
+    )
+
+
+@dataclass
+class DataTrainingArguments:
+    """
+    Arguments pertaining to what data we are going to input our model for training and eval.
+    """
+
+    dataset_name: Optional[str] = field(
+        default=None, metadata={"help": "The name of the dataset to use (via the datasets library)."}
+    )
+    dataset_config_name: Optional[str] = field(
+        default=None, metadata={"help": "The configuration name of the dataset to use (via the datasets library)."}
+    )
+    train_file: Optional[str] = field(default=None, metadata={"help": "The input training data file (a text file)."})
+    validation_file: Optional[str] = field(
+        default=None,
+        metadata={"help": "An optional input evaluation data file to evaluate the perplexity on (a text file)."},
+    )
+    train_ref_file: Optional[str] = field(
+        default=None,
+        metadata={"help": "An optional input train ref data file for whole word masking in Chinese."},
+    )
+    validation_ref_file: Optional[str] = field(
+        default=None,
+        metadata={"help": "An optional input validation ref data file for whole word masking in Chinese."},
+    )
+    overwrite_cache: bool = field(
+        default=False, metadata={"help": "Overwrite the cached training and evaluation sets"}
+    )
+    validation_split_percentage: Optional[int] = field(
+        default=5,
+        metadata={
+            "help": "The percentage of the train set used as validation set in case there's no validation split"
+        },
+    )
+    max_seq_length: Optional[int] = field(
+        default=None,
+        metadata={
+            "help": "The maximum total input sequence length after tokenization and masking. Sequences longer than this will be truncated. Default to the max input length of the model."
+        },
+    )
+    preprocessing_num_workers: Optional[int] = field(
+        default=None,
+        metadata={"help": "The number of processes to use for the preprocessing."},
+    )
+    mlm_probability: float = field(
+        default=0.15, metadata={"help": "Ratio of tokens to mask for span masked language modeling loss"}
+    )
+    mean_noise_span_length: float = field(
+        default=3.0,
+        metadata={"help": "Mean span length of masked tokens"},
+    )
+
+    def __post_init__(self):
+        if self.dataset_name is None and self.train_file is None and self.validation_file is None:
+            raise ValueError("Need either a dataset name or a training/validation file.")
+        else:
+            if self.train_file is not None:
+                extension = self.train_file.split(".")[-1]
+                assert extension in ["csv", "json", "txt"], "`train_file` should be a csv, a json or a txt file."
+            if self.validation_file is not None:
+                extension = self.validation_file.split(".")[-1]
+                assert extension in ["csv", "json", "txt"], "`validation_file` should be a csv, a json or a txt file."
+
+
+def compute_input_and_target_lengths(inputs_length, noise_density, mean_noise_span_length):
+    """This function is copy of `random_spans_helper <https://github.com/google-research/text-to-text-transfer-transformer/blob/84f8bcc14b5f2c03de51bd3587609ba8f6bbd1cd/t5/data/preprocessors.py#L2466>`__ .
+    Training parameters to avoid padding with random_spans_noise_mask.
+    When training a model with random_spans_noise_mask, we would like to set the other
+    training hyperparmeters in a way that avoids padding.
+    This function helps us compute these hyperparameters.
+    We assume that each noise span in the input is replaced by extra_tokens_per_span_inputs sentinel tokens,
+    and each non-noise span in the targets is replaced by extra_tokens_per_span_targets sentinel tokens.
+    This function tells us the required number of tokens in the raw example (for split_tokens())
+    as well as the length of the encoded targets. Note that this function assumes
+    the inputs and targets will have EOS appended and includes that in the reported length.
+    Args:
+        inputs_length: an integer - desired length of the tokenized inputs sequence
+        noise_density: a float
+        mean_noise_span_length: a float
+    Returns:
+        tokens_length: length of original text in tokens
+        targets_length: an integer - length in tokens of encoded targets sequence
+    """
+
+    def _tokens_length_to_inputs_length_targets_length(tokens_length):
+        num_noise_tokens = int(round(tokens_length * noise_density))
+        num_nonnoise_tokens = tokens_length - num_noise_tokens
+        num_noise_spans = int(round(num_noise_tokens / mean_noise_span_length))
+        # inputs contain all nonnoise tokens, sentinels for all noise spans
+        # and one EOS token.
+        _input_length = num_nonnoise_tokens + num_noise_spans + 1
+        _output_length = num_noise_tokens + num_noise_spans + 1
+        return _input_length, _output_length
+
+    tokens_length = inputs_length
+
+    while _tokens_length_to_inputs_length_targets_length(tokens_length + 1)[0] <= inputs_length:
+        tokens_length += 1
+
+    inputs_length, targets_length = _tokens_length_to_inputs_length_targets_length(tokens_length)
+
+    # minor hack to get the targets length to be equal to inputs length
+    # which is more likely to have been set to a nice round number.
+    if noise_density == 0.5 and targets_length > inputs_length:
+        tokens_length -= 1
+        targets_length -= 1
+    return tokens_length, targets_length
+
+
+@flax.struct.dataclass
+class FlaxDataCollatorForT5MLM:
+    """
+    Data collator used for T5 span-masked language modeling.
+    It is made sure that after masking the inputs are of length `data_args.max_seq_length` and targets are also of fixed length.
+    For more information on how T5 span-masked language modeling works, one can take a look
+    at the `official paper <https://arxiv.org/pdf/1910.10683.pdf>`__
+    or the `official code for preprocessing <https://github.com/google-research/text-to-text-transfer-transformer/blob/master/t5/data/preprocessors.py>`__ .
+    Args:
+        tokenizer (:class:`~transformers.PreTrainedTokenizer` or :class:`~transformers.PreTrainedTokenizerFast`):
+            The tokenizer used for encoding the data.
+        noise_density (:obj:`float`):
+            The probability with which to (randomly) mask tokens in the input.
+        mean_noise_span_length (:obj:`float`):
+            The average span length of the masked tokens.
+        input_length (:obj:`int`):
+            The expected input length after masking.
+        target_length (:obj:`int`):
+            The expected target length after masking.
+        pad_token_id: (:obj:`int`):
+            The pad token id of the model
+        decoder_start_token_id: (:obj:`int):
+            The decoder start token id of the model
+    """
+
+    tokenizer: PreTrainedTokenizerBase
+    noise_density: float
+    mean_noise_span_length: float
+    input_length: int
+    target_length: int
+    pad_token_id: int
+    decoder_start_token_id: int
+
+    def __call__(self, examples: List[Dict[str, np.ndarray]]) -> Dict[str, np.ndarray]:
+
+        # convert list to dict and tensorize input
+        batch = BatchEncoding(
+            {k: np.array([examples[i][k] for i in range(len(examples))]) for k, v in examples[0].items()}
+        )
+
+        input_ids = batch["input_ids"]
+        batch_size, expandend_input_length = input_ids.shape
+
+        mask_indices = np.asarray([self.random_spans_noise_mask(expandend_input_length) for i in range(batch_size)])
+        labels_mask = ~mask_indices
+
+        input_ids_sentinel = self.create_sentinel_ids(mask_indices.astype(np.int8))
+        labels_sentinel = self.create_sentinel_ids(labels_mask.astype(np.int8))
+
+        batch["input_ids"] = self.filter_input_ids(input_ids, input_ids_sentinel)
+        batch["labels"] = self.filter_input_ids(input_ids, labels_sentinel)
+
+        if batch["input_ids"].shape[-1] != self.input_length:
+            raise ValueError(
+                f"`input_ids` are incorrectly preprocessed. `input_ids` length is {batch['input_ids'].shape[-1]}, but should be {self.target_length}."
+            )
+
+        if batch["labels"].shape[-1] != self.target_length:
+            raise ValueError(
+                f"`labels` are incorrectly preprocessed. `labels` length is {batch['labels'].shape[-1]}, but should be {self.target_length}."
+            )
+
+        # to check that tokens are correctly proprocessed, one can run `self.tokenizer.batch_decode(input_ids)` and `self.tokenizer.batch_decode(labels)` here...
+        batch["decoder_input_ids"] = shift_tokens_right(
+            batch["labels"], self.pad_token_id, self.decoder_start_token_id
+        )
+
+        return batch
+
+    def create_sentinel_ids(self, mask_indices):
+        """
+        Sentinel ids creation given the indices that should be masked.
+        The start indices of each mask are replaced by the sentinel ids in increasing
+        order. Consecutive mask indices to be deleted are replaced with `-1`.
+        """
+        start_indices = mask_indices - np.roll(mask_indices, 1, axis=-1) * mask_indices
+        start_indices[:, 0] = mask_indices[:, 0]
+
+        sentinel_ids = np.where(start_indices != 0, np.cumsum(start_indices, axis=-1), start_indices)
+        sentinel_ids = np.where(sentinel_ids != 0, (sentinel_ids + self.tokenizer.vocab_size - 1), 0)
+        sentinel_ids -= mask_indices - start_indices
+
+        return sentinel_ids
+
+    def filter_input_ids(self, input_ids, sentinel_ids):
+        """
+        Puts sentinel mask on `input_ids` and fuse consecutive mask tokens into a single mask token by deleting.
+        This will reduce the sequence length from `expanded_inputs_length` to `input_length`.
+        """
+        batch_size = input_ids.shape[0]
+
+        input_ids_full = np.where(sentinel_ids != 0, sentinel_ids, input_ids)
+        input_ids = input_ids_full[input_ids_full > 0].reshape((batch_size, -1))
+        input_ids = np.concatenate(
+            [input_ids, np.full((batch_size, 1), self.tokenizer.eos_token_id, dtype=np.int32)], axis=-1
+        )
+        return input_ids
+
+    def random_spans_noise_mask(self, length):
+
+        """This function is copy of `random_spans_helper <https://github.com/google-research/text-to-text-transfer-transformer/blob/84f8bcc14b5f2c03de51bd3587609ba8f6bbd1cd/t5/data/preprocessors.py#L2682>`__ .
+        Noise mask consisting of random spans of noise tokens.
+        The number of noise tokens and the number of noise spans and non-noise spans
+        are determined deterministically as follows:
+        num_noise_tokens = round(length * noise_density)
+        num_nonnoise_spans = num_noise_spans = round(num_noise_tokens / mean_noise_span_length)
+        Spans alternate between non-noise and noise, beginning with non-noise.
+        Subject to the above restrictions, all masks are equally likely.
+        Args:
+            length: an int32 scalar (length of the incoming token sequence)
+            noise_density: a float - approximate density of output mask
+            mean_noise_span_length: a number
+        Returns:
+            a boolean tensor with shape [length]
+        """
+
+        orig_length = length
+
+        num_noise_tokens = int(np.round(length * self.noise_density))
+        # avoid degeneracy by ensuring positive numbers of noise and nonnoise tokens.
+        num_noise_tokens = min(max(num_noise_tokens, 1), length - 1)
+        num_noise_spans = int(np.round(num_noise_tokens / self.mean_noise_span_length))
+
+        # avoid degeneracy by ensuring positive number of noise spans
+        num_noise_spans = max(num_noise_spans, 1)
+        num_nonnoise_tokens = length - num_noise_tokens
+
+        # pick the lengths of the noise spans and the non-noise spans
+        def _random_segmentation(num_items, num_segments):
+            """Partition a sequence of items randomly into non-empty segments.
+            Args:
+                num_items: an integer scalar > 0
+                num_segments: an integer scalar in [1, num_items]
+            Returns:
+                a Tensor with shape [num_segments] containing positive integers that add
+                up to num_items
+            """
+            mask_indices = np.arange(num_items - 1) < (num_segments - 1)
+            np.random.shuffle(mask_indices)
+            first_in_segment = np.pad(mask_indices, [[1, 0]])
+            segment_id = np.cumsum(first_in_segment)
+            # count length of sub segments assuming that list is sorted
+            _, segment_length = np.unique(segment_id, return_counts=True)
+            return segment_length
+
+        noise_span_lengths = _random_segmentation(num_noise_tokens, num_noise_spans)
+        nonnoise_span_lengths = _random_segmentation(num_nonnoise_tokens, num_noise_spans)
+
+        interleaved_span_lengths = np.reshape(
+            np.stack([nonnoise_span_lengths, noise_span_lengths], axis=1), [num_noise_spans * 2]
+        )
+        span_starts = np.cumsum(interleaved_span_lengths)[:-1]
+        span_start_indicator = np.zeros((length,), dtype=np.int8)
+        span_start_indicator[span_starts] = True
+        span_num = np.cumsum(span_start_indicator)
+        is_noise = np.equal(span_num % 2, 1)
+
+        return is_noise[:orig_length]
+
+
+def generate_batch_splits(samples_idx: jnp.ndarray, batch_size: int) -> jnp.ndarray:
+    num_samples = len(samples_idx)
+    samples_to_remove = num_samples % batch_size
+
+    if samples_to_remove != 0:
+        samples_idx = samples_idx[:-samples_to_remove]
+    sections_split = num_samples // batch_size
+    batch_idx = np.split(samples_idx, sections_split)
+    return batch_idx
+
+
+def write_train_metric(summary_writer, train_metrics, train_time, step):
+    summary_writer.scalar("train_time", train_time, step)
+
+    train_metrics = get_metrics(train_metrics)
+    for key, vals in train_metrics.items():
+        tag = f"train_{key}"
+        for i, val in enumerate(vals):
+            summary_writer.scalar(tag, val, step - len(vals) + i + 1)
+
+
+def write_eval_metric(summary_writer, eval_metrics, step):
+    for metric_name, value in eval_metrics.items():
+        summary_writer.scalar(f"eval_{metric_name}", value, step)
+
+
+if __name__ == "__main__":
+    # See all possible arguments in src/transformers/training_args.py
+    # or by passing the --help flag to this script.
+    # We now keep distinct sets of args, for a cleaner separation of concerns.
+
+    parser = HfArgumentParser((ModelArguments, DataTrainingArguments, TrainingArguments))
+    if len(sys.argv) == 2 and sys.argv[1].endswith(".json"):
+        # If we pass only one argument to the script and it's the path to a json file,
+        # let's parse it to get our arguments.
+        model_args, data_args, training_args = parser.parse_json_file(json_file=os.path.abspath(sys.argv[1]))
+    else:
+        model_args, data_args, training_args = parser.parse_args_into_dataclasses()
+
+    if (
+        os.path.exists(training_args.output_dir)
+        and os.listdir(training_args.output_dir)
+        and training_args.do_train
+        and not training_args.overwrite_output_dir
+    ):
+        raise ValueError(
+            f"Output directory ({training_args.output_dir}) already exists and is not empty."
+            "Use --overwrite_output_dir to overcome."
+        )
+
+    # Setup logging
+    logging.basicConfig(
+        format="%(asctime)s - %(levelname)s - %(name)s -   %(message)s",
+        level="NOTSET",
+        datefmt="[%X]",
+    )
+
+    # Log on each process the small summary:
+    logger = logging.getLogger(__name__)
+
+    # Set the verbosity to info of the Transformers logger (on main process only):
+    logger.info(f"Training/evaluation parameters {training_args}")
+
+    # Set seed before initializing model.
+    set_seed(training_args.seed)
+
+    # Handle the repository creation
+    if training_args.push_to_hub:
+        if training_args.hub_model_id is None:
+            repo_name = get_full_repo_name(
+                Path(training_args.output_dir).absolute().name, token=training_args.hub_token
+            )
+        else:
+            repo_name = training_args.hub_model_id
+        repo = Repository(training_args.output_dir, clone_from=repo_name)
+
+    # Get the datasets: you can either provide your own CSV/JSON/TXT training and evaluation files (see below)
+    # or just provide the name of one of the public datasets available on the hub at https://huggingface.co/datasets/
+    # (the dataset will be downloaded automatically from the datasets Hub).
+    #
+    # For CSV/JSON files, this script will use the column called 'text' or the first column if no column called
+    # 'text' is found. You can easily tweak this behavior (see below).
+    if data_args.dataset_name is not None:
+        # Downloading and loading a dataset from the hub.
+        datasets = load_dataset(data_args.dataset_name, data_args.dataset_config_name, cache_dir=model_args.cache_dir)
+
+        if "validation" not in datasets.keys():
+            datasets["validation"] = load_dataset(
+                data_args.dataset_name,
+                data_args.dataset_config_name,
+                split=f"train[:{data_args.validation_split_percentage}%]",
+                cache_dir=model_args.cache_dir,
+            )
+            datasets["train"] = load_dataset(
+                data_args.dataset_name,
+                data_args.dataset_config_name,
+                split=f"train[{data_args.validation_split_percentage}%:]",
+                cache_dir=model_args.cache_dir,
+            )
+    else:
+        data_files = {}
+        if data_args.train_file is not None:
+            data_files["train"] = data_args.train_file
+        if data_args.validation_file is not None:
+            data_files["validation"] = data_args.validation_file
+        extension = data_args.train_file.split(".")[-1]
+        if extension == "txt":
+            extension = "text"
+        datasets = load_dataset(extension, data_files=data_files, cache_dir=model_args.cache_dir)
+
+        if "validation" not in datasets.keys():
+            datasets["validation"] = load_dataset(
+                extension,
+                data_files=data_files,
+                split=f"train[:{data_args.validation_split_percentage}%]",
+                cache_dir=model_args.cache_dir,
+            )
+            datasets["train"] = load_dataset(
+                extension,
+                data_files=data_files,
+                split=f"train[{data_args.validation_split_percentage}%:]",
+                cache_dir=model_args.cache_dir,
+            )
+    # See more about loading any type of standard or custom dataset (from files, python dict, pandas DataFrame, etc) at
+    # https://huggingface.co/docs/datasets/loading_datasets.html.
+
+    # Load pretrained model and tokenizer
+
+    if model_args.tokenizer_name:
+        tokenizer = AutoTokenizer.from_pretrained(
+            model_args.tokenizer_name, cache_dir=model_args.cache_dir, use_fast=model_args.use_fast_tokenizer
+        )
+    elif model_args.model_name_or_path:
+        tokenizer = AutoTokenizer.from_pretrained(
+            model_args.model_name_or_path, cache_dir=model_args.cache_dir, use_fast=model_args.use_fast_tokenizer
+        )
+    else:
+        raise ValueError(
+            "You are instantiating a new tokenizer from scratch. This is not supported by this script."
+            "You can do it from another script, save it, and load it from here, using --tokenizer_name."
+        )
+
+    if model_args.config_name:
+        config = T5Config.from_pretrained(
+            model_args.config_name, cache_dir=model_args.cache_dir, vocab_size=len(tokenizer)
+        )
+    elif model_args.model_name_or_path:
+        config = T5Config.from_pretrained(
+            model_args.model_name_or_path, cache_dir=model_args.cache_dir, vocab_size=len(tokenizer)
+        )
+    else:
+        config = CONFIG_MAPPING[model_args.model_type]()
+        logger.warning("You are instantiating a new config instance from scratch.")
+
+    # Preprocessing the datasets.
+    # First we tokenize all the texts.
+    if training_args.do_train:
+        column_names = datasets["train"].column_names
+    else:
+        column_names = datasets["validation"].column_names
+    text_column_name = "text" if "text" in column_names else column_names[0]
+
+    max_seq_length = min(data_args.max_seq_length, tokenizer.model_max_length)
+
+    # Otherwise, we tokenize every text, then concatenate them together before splitting them in smaller parts.
+    # Since we make sure that all sequences are of the same length, no attention_mask is needed.
+    def tokenize_function(examples):
+        return tokenizer(examples[text_column_name], return_attention_mask=False)
+
+    tokenized_datasets = datasets.map(
+        tokenize_function,
+        batched=True,
+        num_proc=data_args.preprocessing_num_workers,
+        remove_columns=column_names,
+        load_from_cache_file=not data_args.overwrite_cache,
+    )
+
+    # T5-like span masked language modeling will fuse consecutively masked tokens to a single sentinel token.
+    # To ensure that the input length is `max_seq_length`, we need to increase the maximum length
+    # according to `mlm_probability` and `mean_noise_span_length`. We can also define the label length accordingly.
+    expanded_inputs_length, targets_length = compute_input_and_target_lengths(
+        inputs_length=max_seq_length,
+        noise_density=data_args.mlm_probability,
+        mean_noise_span_length=data_args.mean_noise_span_length,
+    )
+
+    # Main data processing function that will concatenate all texts from our dataset and generate chunks of expanded_inputs_length.
+    def group_texts(examples):
+        # Concatenate all texts.
+        concatenated_examples = {k: sum(examples[k], []) for k in examples.keys()}
+        total_length = len(concatenated_examples[list(examples.keys())[0]])
+        # We drop the small remainder, we could add padding if the model supported it instead of this drop, you can
+        # customize this part to your needs.
+        if total_length >= expanded_inputs_length:
+            total_length = (total_length // expanded_inputs_length) * expanded_inputs_length
+        # Split by chunks of max_len.
+        result = {
+            k: [t[i : i + expanded_inputs_length] for i in range(0, total_length, expanded_inputs_length)]
+            for k, t in concatenated_examples.items()
+        }
+        return result
+
+    # Note that with `batched=True`, this map processes 1,000 texts together, so group_texts throws away a
+    # remainder for each of those groups of 1,000 texts. You can adjust that batch_size here but a higher value
+    # might be slower to preprocess.
+    #
+    # To speed up this part, we use multiprocessing. See the documentation of the map method for more information:
+    # https://huggingface.co/docs/datasets/package_reference/main_classes.html#datasets.Dataset.map
+    tokenized_datasets = tokenized_datasets.map(
+        group_texts,
+        batched=True,
+        num_proc=data_args.preprocessing_num_workers,
+        load_from_cache_file=not data_args.overwrite_cache,
+    )
+
+    # Enable tensorboard only on the master node
+    has_tensorboard = is_tensorboard_available()
+    if has_tensorboard and jax.process_index() == 0:
+        try:
+            from flax.metrics.tensorboard import SummaryWriter
+
+            summary_writer = SummaryWriter(log_dir=Path(training_args.output_dir))
+        except ImportError as ie:
+            has_tensorboard = False
+            logger.warning(
+                f"Unable to display metrics through TensorBoard because some package are not installed: {ie}"
+            )
+    else:
+        logger.warning(
+            "Unable to display metrics through TensorBoard because the package is not installed: "
+            "Please run pip install tensorboard to enable."
+        )
+
+    # Initialize our training
+    rng = jax.random.PRNGKey(training_args.seed)
+    dropout_rngs = jax.random.split(rng, jax.local_device_count())
+
+    if model_args.model_name_or_path:
+        model = FlaxT5ForConditionalGeneration.from_pretrained(
+            model_args.model_name_or_path, config=config, seed=training_args.seed, dtype=getattr(jnp, model_args.dtype)
+        )
+    else:
+        model = FlaxT5ForConditionalGeneration(config, seed=training_args.seed, dtype=getattr(jnp, model_args.dtype))
+
+    # Data collator
+    # This one will take care of randomly masking the tokens.
+    data_collator = FlaxDataCollatorForT5MLM(
+        tokenizer=tokenizer,
+        noise_density=data_args.mlm_probability,
+        mean_noise_span_length=data_args.mean_noise_span_length,
+        input_length=max_seq_length,
+        target_length=targets_length,
+        pad_token_id=model.config.pad_token_id,
+        decoder_start_token_id=model.config.decoder_start_token_id,
+    )
+
+    # Store some constant
+    num_epochs = int(training_args.num_train_epochs)
+    train_batch_size = int(training_args.per_device_train_batch_size) * jax.device_count()
+    eval_batch_size = int(training_args.per_device_eval_batch_size) * jax.device_count()
+
+    num_train_steps = len(tokenized_datasets["train"]) // train_batch_size * num_epochs
+
+    # Create learning rate schedule
+    warmup_fn = optax.linear_schedule(
+        init_value=0.0, end_value=training_args.learning_rate, transition_steps=training_args.warmup_steps
+    )
+    decay_fn = optax.linear_schedule(
+        init_value=training_args.learning_rate,
+        end_value=0,
+        transition_steps=num_train_steps - training_args.warmup_steps,
+    )
+    linear_decay_lr_schedule_fn = optax.join_schedules(
+        schedules=[warmup_fn, decay_fn], boundaries=[training_args.warmup_steps]
+    )
+
+    # We use Optax's "masking" functionality to not apply weight decay
+    # to bias and LayerNorm scale parameters. decay_mask_fn returns a
+    # mask boolean with the same structure as the parameters.
+    # The mask is True for parameters that should be decayed.
+    def decay_mask_fn(params):
+        flat_params = traverse_util.flatten_dict(params)
+        flat_mask = {
+            path: (path[-1] != "bias" and path[-2:] not in [("layer_norm", "scale"), ("final_layer_norm", "scale")])
+            for path in flat_params
+        }
+        return traverse_util.unflatten_dict(flat_mask)
+
+    # create adam optimizer
+    if training_args.adafactor:
+        # We use the default parameters here to initialize adafactor,
+        # For more details about the parameters please check https://github.com/deepmind/optax/blob/ed02befef9bf81cbbf236be3d2b0e032e9ed4a40/optax/_src/alias.py#L74
+        optimizer = optax.adafactor(
+            learning_rate=linear_decay_lr_schedule_fn,
+        )
+    else:
+        optimizer = optax.adamw(
+            learning_rate=linear_decay_lr_schedule_fn,
+            b1=training_args.adam_beta1,
+            b2=training_args.adam_beta2,
+            weight_decay=training_args.weight_decay,
+            mask=decay_mask_fn,
+        )
+
+    # Setup train state
+    state = train_state.TrainState.create(apply_fn=model.__call__, params=model.params, tx=optimizer)
+
+    # Define gradient update step fn
+    def train_step(state, batch, dropout_rng):
+        dropout_rng, new_dropout_rng = jax.random.split(dropout_rng)
+
+        def loss_fn(params):
+            labels = batch.pop("labels")
+
+            logits = state.apply_fn(**batch, params=params, dropout_rng=dropout_rng, train=True)[0]
+
+            # compute loss
+            loss = optax.softmax_cross_entropy(logits, onehot(labels, logits.shape[-1])).mean()
+
+            return loss
+
+        grad_fn = jax.value_and_grad(loss_fn)
+        loss, grad = grad_fn(state.params)
+        grad = jax.lax.pmean(grad, "batch")
+        new_state = state.apply_gradients(grads=grad)
+
+        metrics = jax.lax.pmean(
+            {"loss": loss, "learning_rate": linear_decay_lr_schedule_fn(state.step)}, axis_name="batch"
+        )
+
+        return new_state, metrics, new_dropout_rng
+
+    # Create parallel version of the train step
+    p_train_step = jax.pmap(train_step, "batch", donate_argnums=(0,))
+
+    # Define eval fn
+    def eval_step(params, batch):
+        labels = batch.pop("labels")
+
+        logits = model(**batch, params=params, train=False)[0]
+
+        # compute loss
+        loss = optax.softmax_cross_entropy(logits, onehot(labels, logits.shape[-1]))
+
+        # compute accuracy
+        accuracy = jnp.equal(jnp.argmax(logits, axis=-1), labels)
+
+        # summarize metrics
+        metrics = {"loss": loss.mean(), "accuracy": accuracy.mean()}
+        metrics = jax.lax.pmean(metrics, axis_name="batch")
+
+        return metrics
+
+    p_eval_step = jax.pmap(eval_step, "batch", donate_argnums=(0,))
+
+    # Replicate the train state on each device
+    state = jax_utils.replicate(state)
+
+    train_time = 0
+    epochs = tqdm(range(num_epochs), desc="Epoch ... ", position=0)
+    for epoch in epochs:
+        # ======================== Training ================================
+        train_start = time.time()
+        train_metrics = []
+
+        # Create sampling rng
+        rng, input_rng = jax.random.split(rng)
+
+        # Generate an epoch by shuffling sampling indices from the train dataset
+        num_train_samples = len(tokenized_datasets["train"])
+        train_samples_idx = jax.random.permutation(input_rng, jnp.arange(num_train_samples))
+        train_batch_idx = generate_batch_splits(train_samples_idx, train_batch_size)
+
+        # Gather the indexes for creating the batch and do a training step
+        for step, batch_idx in enumerate(tqdm(train_batch_idx, desc="Training...", position=1)):
+            samples = [tokenized_datasets["train"][int(idx)] for idx in batch_idx]
+            model_inputs = data_collator(samples)
+
+            # Model forward
+            model_inputs = shard(model_inputs.data)
+            state, train_metric, dropout_rngs = p_train_step(state, model_inputs, dropout_rngs)
+            train_metrics.append(train_metric)
+
+            cur_step = epoch * (num_train_samples // train_batch_size) + step
+
+            if cur_step % training_args.logging_steps == 0 and cur_step > 0:
+                # Save metrics
+                train_metric = jax_utils.unreplicate(train_metric)
+                train_time += time.time() - train_start
+                if has_tensorboard and jax.process_index() == 0:
+                    write_train_metric(summary_writer, train_metrics, train_time, cur_step)
+
+                epochs.write(
+                    f"Step... ({cur_step} | Loss: {train_metric['loss'].mean()}, Learning Rate: {train_metric['learning_rate'].mean()})"
+                )
+
+                train_metrics = []
+
+            if cur_step % training_args.eval_steps == 0 and cur_step > 0:
+                # ======================== Evaluating ==============================
+                num_eval_samples = len(tokenized_datasets["validation"])
+                eval_samples_idx = jnp.arange(num_eval_samples)
+                eval_batch_idx = generate_batch_splits(eval_samples_idx, eval_batch_size)
+
+                eval_metrics = []
+                for i, batch_idx in enumerate(tqdm(eval_batch_idx, desc="Evaluating ...", position=2)):
+                    samples = [tokenized_datasets["validation"][int(idx)] for idx in batch_idx]
+                    model_inputs = data_collator(samples)
+
+                    # Model forward
+                    model_inputs = shard(model_inputs.data)
+                    metrics = p_eval_step(state.params, model_inputs)
+                    eval_metrics.append(metrics)
+
+                # get eval metrics
+                eval_metrics = get_metrics(eval_metrics)
+                eval_metrics = jax.tree_map(jnp.mean, eval_metrics)
+
+                # Update progress bar
+                epochs.write(f"Step... ({cur_step} | Loss: {eval_metrics['loss']}, Acc: {eval_metrics['accuracy']})")
+
+                # Save metrics
+                if has_tensorboard and jax.process_index() == 0:
+                    write_eval_metric(summary_writer, eval_metrics, cur_step)
+
+            if cur_step % training_args.save_steps == 0 and cur_step > 0:
+                # save checkpoint after each epoch and push checkpoint to the hub
+                if jax.process_index() == 0:
+                    params = jax.device_get(jax.tree_map(lambda x: x[0], state.params))
+                    model.save_pretrained(training_args.output_dir, params=params)
+                    tokenizer.save_pretrained(training_args.output_dir)
+                    if training_args.push_to_hub:
+                        repo.push_to_hub(commit_message=f"Saving weights and logs of step {cur_step}", blocking=False)

t5_tokenizer_model.py

@@ -0,0 +1,217 @@
+#!/usr/bin/env python3
+import json
+from typing import Iterator, List, Union
+
+from tokenizers import AddedToken, Regex, Tokenizer, decoders, normalizers, pre_tokenizers, trainers
+from tokenizers.implementations.base_tokenizer import BaseTokenizer
+from tokenizers.models import BPE, Unigram
+from tokenizers.processors import TemplateProcessing
+
+
+class SentencePieceUnigramTokenizer(BaseTokenizer):
+    """
+    This class is a copy of `DeDLOC's tokenizer implementation <https://github.com/yandex-research/DeDLOC/blob/main/sahajbert/tokenizer/tokenizer_model.py>`__ .
+    Custom SentencePiece Unigram Tokenizer with NMT, NKFC, spaces and lower-casing characters normalization
+    Represents the Unigram algorithm, with the pretokenization used by SentencePiece
+    """
+
+    def __init__(
+        self,
+        replacement: str = "▁",
+        add_prefix_space: bool = True,
+        unk_token: Union[str, AddedToken] = "<unk>",
+        eos_token: Union[str, AddedToken] = "</s>",
+        pad_token: Union[str, AddedToken] = "<pad>",
+    ):
+        self.special_tokens = {
+            "pad": {"id": 0, "token": pad_token},
+            "eos": {"id": 1, "token": eos_token},
+            "unk": {"id": 2, "token": unk_token},
+        }
+
+        self.special_tokens_list = [None] * len(self.special_tokens)
+        for token_dict in self.special_tokens.values():
+            self.special_tokens_list[token_dict["id"]] = token_dict["token"]
+
+        tokenizer = Tokenizer(Unigram())
+
+        tokenizer.normalizer = normalizers.Sequence(
+            [
+                normalizers.Nmt(),
+                normalizers.NFKC(),
+                normalizers.Replace(Regex(" {2,}"), " "),
+                #commented to be cased
+                #normalizers.Lowercase(),
+            ]
+        )
+        tokenizer.pre_tokenizer = pre_tokenizers.Sequence(
+            [
+                #pre_tokenizers.Metaspace(replacement=replacement, add_prefix_space=add_prefix_space),
+                #pre_tokenizers.Split(pattern='&',behavior='removed',invert=False),
+                #pre_tokenizers.Digits(),#individual_digits=True
+                pre_tokenizers.Metaspace(replacement=replacement, add_prefix_space=add_prefix_space),
+                #pre_tokenizers.Punctuation(),
+            ]
+        )
+        tokenizer.decoder = decoders.Metaspace(replacement=replacement, add_prefix_space=add_prefix_space)
+
+        tokenizer.post_processor = TemplateProcessing(
+            single=f"$A {self.special_tokens['eos']['token']}",
+            special_tokens=[(self.special_tokens["eos"]["token"], self.special_tokens["eos"]["id"])],
+        )
+
+        parameters = {
+            "model": "SentencePieceUnigram",
+            "replacement": replacement,
+            "add_prefix_space": add_prefix_space,
+        }
+
+        super().__init__(tokenizer, parameters)
+
+    def train(
+        self,
+        files: Union[str, List[str]],
+        vocab_size: int = 8000,
+        show_progress: bool = True,
+    ):
+        """Train the model using the given files"""
+
+        trainer = trainers.UnigramTrainer(
+            vocab_size=vocab_size,
+            special_tokens=self.special_tokens_list,
+            show_progress=show_progress,
+        )
+
+        if isinstance(files, str):
+            files = [files]
+        self._tokenizer.train(files, trainer=trainer)
+
+        self.add_unk_id()
+
+    def train_from_iterator(
+        self,
+        iterator: Union[Iterator[str], Iterator[Iterator[str]]],
+        vocab_size: int = 8000,
+        show_progress: bool = True,
+    ):
+        """Train the model using the given iterator"""
+
+        trainer = trainers.UnigramTrainer(
+            vocab_size=vocab_size,
+            special_tokens=self.special_tokens_list,
+            show_progress=show_progress,
+        )
+
+        self._tokenizer.train_from_iterator(iterator, trainer=trainer)
+
+        self.add_unk_id()
+
+    def add_unk_id(self):
+        tokenizer_json = json.loads(self._tokenizer.to_str())
+
+        tokenizer_json["model"]["unk_id"] = self.special_tokens["unk"]["id"]
+
+        self._tokenizer = Tokenizer.from_str(json.dumps(tokenizer_json))
+
+class SentencePieceBPETokenizer(BaseTokenizer):
+    """
+    This class is a copy of `DeDLOC's tokenizer implementation <https://github.com/yandex-research/DeDLOC/blob/main/sahajbert/tokenizer/tokenizer_model.py>`__ .
+    Custom SentencePiece Unigram Tokenizer with NMT, NKFC, spaces and lower-casing characters normalization
+    Represents the Unigram algorithm, with the pretokenization used by SentencePiece
+    """
+
+    def __init__(
+        self,
+        replacement: str = "▁",
+        add_prefix_space: bool = True,
+        unk_token: Union[str, AddedToken] = "<unk>",
+        eos_token: Union[str, AddedToken] = "</s>",
+        pad_token: Union[str, AddedToken] = "<pad>",
+    ):
+        self.special_tokens = {
+            "pad": {"id": 0, "token": pad_token},
+            "eos": {"id": 1, "token": eos_token},
+            "unk": {"id": 2, "token": unk_token},
+        }
+
+        self.special_tokens_list = [None] * len(self.special_tokens)
+        for token_dict in self.special_tokens.values():
+            self.special_tokens_list[token_dict["id"]] = token_dict["token"]
+
+        tokenizer = Tokenizer(BPE())
+
+        tokenizer.normalizer = normalizers.Sequence(
+            [
+                normalizers.Nmt(),
+                normalizers.NFKC(),
+                normalizers.Replace(Regex(" {2,}"), " "),
+                #commented to be cased
+                #normalizers.Lowercase(),
+            ]
+        )
+        tokenizer.pre_tokenizer = pre_tokenizers.Sequence(
+            [
+                #pre_tokenizers.Metaspace(replacement=replacement, add_prefix_space=add_prefix_space),
+                pre_tokenizers.Digits(individual_digits=True),
+                pre_tokenizers.Punctuation(),
+            ]
+        )
+        #tokenizer.decoder = decoders.Metaspace(replacement=replacement, add_prefix_space=add_prefix_space)
+
+        tokenizer.post_processor = TemplateProcessing(
+            single=f"$A {self.special_tokens['eos']['token']}",
+            special_tokens=[(self.special_tokens["eos"]["token"], self.special_tokens["eos"]["id"])],
+        )
+
+        parameters = {
+            "model": "SentencePieceBPE",
+            "replacement": replacement,
+            "add_prefix_space": add_prefix_space,
+        }
+
+        super().__init__(tokenizer, parameters)
+
+    def train(
+        self,
+        files: Union[str, List[str]],
+        vocab_size: int = 8000,
+        show_progress: bool = True,
+    ):
+        """Train the model using the given files"""
+
+        trainer = trainers.BpeTrainer(
+            vocab_size=vocab_size,
+            special_tokens=self.special_tokens_list,
+            show_progress=show_progress,
+        )
+
+        if isinstance(files, str):
+            files = [files]
+        self._tokenizer.train(files, trainer=trainer)
+
+        self.add_unk_id()
+
+    def train_from_iterator(
+        self,
+        iterator: Union[Iterator[str], Iterator[Iterator[str]]],
+        vocab_size: int = 8000,
+        show_progress: bool = True,
+    ):
+        """Train the model using the given iterator"""
+
+        trainer = trainers.BpeTrainer(
+            vocab_size=vocab_size,
+            special_tokens=self.special_tokens_list,
+            show_progress=show_progress,
+        )
+
+        self._tokenizer.train_from_iterator(iterator, trainer=trainer)
+
+        self.add_unk_id()
+
+    def add_unk_id(self):
+        tokenizer_json = json.loads(self._tokenizer.to_str())
+
+        tokenizer_json["model"]["unk_id"] = self.special_tokens["unk"]["id"]
+
+        self._tokenizer = Tokenizer.from_str(json.dumps(tokenizer_json))

tokenizer-trainer_atom.py

@@ -0,0 +1,65 @@
+import numpy as np
+import pandas as pd
+import re
+from t5_tokenizer_model import SentencePieceAtomwiseTokenizer
+from pretokenizer import atomwise_tokenizer
+from tqdm import tqdm
+
+
+
+vocab_size = 32_000
+input_sentence_size = None
+
+# Initialize a dataset
+#dataset = load_dataset('csv', data_files='/home/zoez/Chem-T5/train-file.csv',split="train")
+dataset = pd.read_csv('/home/zoez/Chem-T5/train-file.csv')
+
+tokenizer = SentencePieceAtomwiseTokenizer(unk_token="<unk>", eos_token="</s>", pad_token="<pad>")
+dataset.columns=['SMILES']
+#print(dataset.columns)
+dataset=pd.DataFrame(columns=['SMILES','SMILESs'],data=dataset)
+dataset.fillna('', inplace=True)
+#print(dataset.iloc[0])
+#trainset=pd.DataFrame(columns=['SMILESs'])
+
+for i, line in tqdm(enumerate(dataset['SMILES'])):
+    line = re.sub('\d+\t', '',line)
+    #print(line)
+    newLine=atomwise_tokenizer(line)
+    #print(newLine)
+    #print(int(i/10))
+    dataset.iloc[int(i/50)]['SMILESs']+="&"+newLine
+    #print(dataset.loc[int(i/10)]['SMILESs'])
+    #dataset.iloc[i]['SMILES']=newLine
+#dataset = dataset.iloc
+    
+#print(dataset.iloc[5]['SMILESs'])
+# Build an iterator over this dataset
+def batch_iterator(input_sentence_size=None):
+    if input_sentence_size is None:
+        input_sentence_size = len(dataset)
+    batch_length = 100
+    for i in range(0, input_sentence_size, batch_length):
+        #print(dataset[i: i + batch_length]['SMILES'])
+        yield dataset[i: i + batch_length]['SMILESs']
+
+
+# Train tokenizer
+tokenizer.train_from_iterator(
+    iterator=batch_iterator(input_sentence_size=input_sentence_size),
+    vocab_size=vocab_size,
+    show_progress=True,
+)
+
+
+# Save files to disk
+tokenizer.save("/home/zoez/chemT5/tokenizer.json")
+
+
+print(tokenizer.encode(atomwise_tokenizer("O=[N+]([O-])c1ccc(Cl)cc1O=[N+]([O-])c1ccc(Cl)cc1")).tokens)
+
+#from transformers import T5Config
+
+
+#config = T5Config.from_pretrained("google/t5-v1_1-base", vocab_size=tokenizer.get_vocab_size())
+#config.save_pretrained("/home/zoez/chem-T5")

tokenizer-trainer_uni.py

@@ -0,0 +1,69 @@
+import numpy as np
+import pandas as pd
+import re
+from t5_tokenizer_model import SentencePieceUnigramTokenizer
+#from pretokenizer import atomwise_tokenizer
+from tqdm import tqdm
+
+
+
+vocab_size = 32_000
+input_sentence_size = None
+
+# Initialize a dataset
+#dataset = load_dataset('csv', data_files='/home/zoez/Chem-T5/train-file.csv',split="train")
+dataset = pd.read_csv('./chemT5_data.csv')#('/home/zoez/Chem-T5/train-file.csv')
+#print(dataset.iloc[0])
+tokenizer = SentencePieceUnigramTokenizer(unk_token="<unk>", eos_token="</s>", pad_token="<pad>")
+dataset=pd.DataFrame(columns=['SMILES'],data=dataset)
+#dataset.drop('Unnamed: 0',1)
+#print(dataset.columns)
+dataset.columns=['SMILES']
+
+
+dataset.fillna('', inplace=True)
+#print(dataset.iloc[0])
+#trainset=pd.DataFrame(columns=['SMILESs'])
+
+#dataset = dataset.iloc[:10000]
+for i, line in tqdm(enumerate(dataset['SMILES'])):
+    #line = re.sub('\d+\t', '',line)
+    #print(line) 
+    newLine=line#atomwise_tokenizer(line)
+    #print(newLine)
+    #print(int(i/10))
+    dataset.iloc[i]['SMILES']=newLine
+    #print(dataset.loc[int(i/10)]['SMILESs'])
+    #dataset.iloc[i]['SMILES']=newLine
+#dataset = dataset.iloc
+    
+#print(dataset.iloc[5]['SMILESs'])
+# Build an iterator over this dataset
+def batch_iterator(input_sentence_size=None):
+    if input_sentence_size is None:
+        input_sentence_size = len(dataset)
+    batch_length = 100
+    for i in range(0, input_sentence_size, batch_length):
+        #print(dataset[i: i + batch_length]['SMILES'])
+        yield dataset[i: i + batch_length]['SMILES']
+
+
+# Train tokenizer
+tokenizer.train_from_iterator(
+    iterator=batch_iterator(input_sentence_size=input_sentence_size),
+    vocab_size=vocab_size,
+    show_progress=True,
+)
+
+
+# Save files to disk
+tokenizer.save("/home/zoez/chemT5/uni-tokenizer.json")
+
+
+print(tokenizer.encode("O=[N+]([O-])c1ccc(Cl)cc1").tokens)
+
+from transformers import T5Config
+
+
+config = T5Config.from_pretrained("google/t5-v1_1-base", vocab_size=tokenizer.get_vocab_size())
+config.save_pretrained("./")

train_scprit.sh

@@ -0,0 +1,22 @@
+#!/usr/bin/env bash
+python run_t5_mlm_flax.py \
+	--output_dir="./" \
+	--model_type="t5" \
+	--config_name="./" \
+	--tokenizer_name="./" \
+	--train_file="chemT5_data.csv" \
+	--max_seq_length="256" \
+	--per_device_train_batch_size="16" \
+	--per_device_eval_batch_size="16" \
+	--adafactor \
+	--learning_rate="0.005" \
+	--weight_decay="0.001" \
+	--warmup_steps="2000" \
+	--overwrite_output_dir \
+	--logging_steps="500" \
+	--save_steps="10000" \
+	--eval_steps="2500"  \
+	--push_to_hub
+	
+
+	

try.py

@@ -0,0 +1,79 @@
+#from rdkit import Chem
+import tensorflow as tf
+import torch as pt
+#from t5_tokenizer_model import SentencePieceUnigramTokenizer
+from pretokenizer import atomwise_tokenizer
+from transformers import AutoTokenizer, T5Tokenizer, T5ForConditionalGeneration, T5Config
+from tokenizers import Tokenizer
+import numpy as np 
+
+
+#device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
+
+
+
+
+#model = T5ForConditionalGeneration.from_pretrained(pretrained_model_name_or_path="/home/zoez/Chem-T5", from_flax=True)
+tokenizer = AutoTokenizer.from_pretrained("/home/zoez/chemT5")
+#tokenizer = Tokenizer.from_file("/home/zoez/Chem-T5/tokenizer.json")
+#model = model.to(device)
+
+print(tokenizer.encode(atomwise_tokenizer("O=[N+]([O-])c1ccc(Cl)cc1O=[N+]([O-])c1ccc(Cl)cc1")).tokens)
+
+
+# # encode context the generation is conditioned on
+# input_ids1 = tokenizer.encode(": O[N+]([O-])c1ccc(Cl)cc1",return_tensors='pt')
+
+# # activate beam search and early_stopping
+# beam_output1 = model.generate(
+#     input_ids1, 
+#     max_length=50, 
+#     num_beams=5, 
+#     early_stopping=True
+# )
+# #print(tokenizer.encode("O=[N+]([O-])c1ccc(Cl)cc1").tokens)
+# print("Output: 1\n" + 100 * '-')
+# print(tokenizer.decode(beam_output1[0], skip_special_tokens=True))
+
+# # encode context the generation is conditioned on
+# input_ids2 = tokenizer.encode("SMILES: ",return_tensors='pt')
+
+# # activate beam search and early_stopping
+# beam_output2 = model.generate(
+#     input_ids2, 
+#     max_length=50, 
+#     num_beams=9, 
+#     no_repeat_ngram_size=2, 
+#     num_return_sequences=9, 
+#     early_stopping=True
+# )
+# #print(tokenizer.encode("O=[N+]([O-])c1ccc(Cl)cc1").tokens)
+# print("Output: 2\n" + 100 * '-')
+# #print(tokenizer.decode(beam_output2[0], skip_special_tokens=True))
+
+# #start = latent_to_string(latent0)
+# #destination = latent_to_string(latent1)
+# mols1 = []
+# step = np.linspace(0,1,100)
+# invalid = 0
+# steps = []
+# step_invalid = []
+# # Generate molcules using interpolation
+# for i, beam in enumerate(beam_output2):
+#     #target_latent = (1.0-step[i])*latent0 + step[i]*latent1
+#     #string  = latent_to_string(target_latent)
+#     smiles = tokenizer.decode(beam, skip_special_tokens=True)    # when using smies
+#     print(tokenizer.decode(beam, skip_special_tokens=True))
+#     #smiles = sel.decoder(string)  # when using SELFIES
+#     mol = Chem.MolFromSmiles(smiles)
+#     if mol:
+#         if smiles not in mols1:
+#             mols1.append(smiles)
+#             steps.append(i)
+#     else:
+#         invalid = invalid + 1
+#         step_invalid.append(i)
+# #print("starting mol:", start)
+# #print('destination mol:', destination)
+# print("generated mols:", mols1)
+