pretraining_graph_only.py

#!/usr/bin/env python
# coding=utf-8
# Copyright 2020 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.
"""
Fine-tuning the library models for masked language modeling (BERT, ALBERT, RoBERTa...) on a text file or a dataset.
Here is the full list of checkpoints on the hub that can be fine-tuned by this script:
https://huggingface.co/models?filter=fill-mask
"""
# You can also adapt this script on your own masked language modeling task. Pointers for this are left as comments.

import logging
import math
import os
import sys
from dataclasses import dataclass, field
from itertools import chain
from typing import Optional

import datasets
from datasets import load_dataset

import evaluate
import transformers
from transformers import (
    CONFIG_MAPPING,
    MODEL_FOR_MASKED_LM_MAPPING,
    AutoConfig,
    AutoModelForMaskedLM,
    AutoTokenizer,
    DataCollatorForLanguageModeling,
    HfArgumentParser,
    Trainer,
    TrainingArguments,
    is_torch_tpu_available,
    set_seed,
)
from transformers.trainer_utils import get_last_checkpoint
from transformers.utils import check_min_version, send_example_telemetry
from transformers.utils.versions import require_version
from transformers import AutoTokenizer, T5ForConditionalGeneration
from transformers.data.data_collator import _torch_collate_batch
from transformers.tokenization_utils_base import BatchEncoding

from model import GraphT5TransformerForConditionalGeneration,GraphormerModel,GraphTransformer_dict,GraphormerConfig,GinConfig,Graphormer_version_dict,GraphormerModelMultiTask
from dataloaders import graph_text_tokenizer_dict,graph_text_collator_dict,tokenize_function_graphormer_multitask,CollaterForGraphormerMultiTask

from ogb.utils import smiles2graph

from collections.abc import Mapping, Sequence

import torch.utils.data
from torch.utils.data.dataloader import default_collate

from torch_geometric.data import Data, Batch

import numpy as np
from sklearn.metrics import (roc_auc_score,f1_score,confusion_matrix)
from tqdm import tqdm
import argparse
# Will error if the minimal version of Transformers is not installed. Remove at your own risks.
import faulthandler
faulthandler.enable()

check_min_version("4.24.0.dev0")

require_version("datasets>=1.8.0", "To fix: pip install -r examples/pytorch/language-modeling/requirements.txt")

logger = logging.getLogger(__name__)
MODEL_CONFIG_CLASSES = list(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_overrides: Optional[str] = field(
        default=None,
        metadata={
            "help": (
                "Override some existing default config settings when a model is trained from scratch. Example: "
                "n_embd=10,resid_pdrop=0.2,scale_attn_weights=false,summary_type=cls_index"
            )
        },
    )
    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 huggingface.co"},
    )
    use_fast_tokenizer: bool = field(
        default=True,
        metadata={"help": "Whether to use one of the fast tokenizer (backed by the tokenizers library) or not."},
    )
    model_revision: str = field(
        default="main",
        metadata={"help": "The specific model version to use (can be a branch name, tag name or commit id)."},
    )
    use_auth_token: bool = field(
        default=False,
        metadata={
            "help": (
                "Will use the token generated when running `huggingface-cli login` (necessary to use this script "
                "with private models)."
            )
        },
    )

    # all_data_to_lower_case: Optional[bool] = field(default=False)

    use_graph_transformer: bool = field(default=False)
    transformer_backbone: str = field(default='gin')
    # graph_transformer_text_backbone: str = field(default='t5')
    # attention_fasion: str= field(default='sequential')




    def __post_init__(self):
        if self.config_overrides is not None and (self.config_name is not None or self.model_name_or_path is not None):
            raise ValueError(
                "--config_overrides can't be used in combination with --config_name or --model_name_or_path"
            )


@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)."},
    )
    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. Sequences longer "
                "than this will be truncated."
            )
        },
    )
    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 masked language modeling loss"}
    )
    line_by_line: bool = field(
        default=False,
        metadata={"help": "Whether distinct lines of text in the dataset are to be handled as distinct sequences."},
    )
    pad_to_max_length: bool = field(
        default=False,
        metadata={
            "help": (
                "Whether to pad all samples to `max_seq_length`. "
                "If False, will pad the samples dynamically when batching to the maximum length in the batch."
            )
        },
    )
    max_train_samples: Optional[int] = field(
        default=None,
        metadata={
            "help": (
                "For debugging purposes or quicker training, truncate the number of training examples to this "
                "value if set."
            )
        },
    )
    max_eval_samples: Optional[int] = field(
        default=None,
        metadata={
            "help": (
                "For debugging purposes or quicker training, truncate the number of evaluation examples to this "
                "value if set."
            )
        },
    )

    rich_features: Optional[bool] = field(default=False)

    transform_in_collator: Optional[bool] = field(default=False)



    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]
                if extension not in ["csv", "json", "txt"]:
                    raise ValueError("`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]
                if extension not in ["csv", "json", "txt"]:
                    raise ValueError("`validation_file` should be a csv, a json or a txt file.")



def evaluate_performance(trainer,device):
    dataloader = trainer.get_eval_dataloader()
    model = trainer._wrap_model(trainer.model, training=False, dataloader=dataloader)
    model.eval()

    id_y=4273
    id_n=150


    # labels_all = []
    # for step, inputs in tqdm(enumerate(dataloader)):
    #     labels_all+=inputs['labels'][:,0].cpu().numpy().tolist()
    #     # if len(labels_all)>=80020:
    #     #     break
    # rate=(np.asarray(labels_all) == id_y).mean()
    # print('rate ',rate)
    #
    # # rate=0.7510904956840987
    # sudo_pred=np.random.choice([1.0, 0.0], size=(len(labels_all),), p=[rate, 1-rate])
    # sudo_pred+=np.random.rand(len(labels_all))
    #
    # sudo_auc=roc_auc_score(((torch.tensor(labels_all)==id_y)*2-1).numpy(), sudo_pred)
    # print('sudo_auc ',sudo_auc)

    preds_cla_all=[]
    scores_cla_all=[]
    preds_reg_all=[]
    labels_cla_all = []
    labels_reg_all=[]

    for step, inputs in tqdm(enumerate(dataloader)):
        # Prediction step
        for key in inputs.keys():
            inputs[key] = inputs[key].to(device)
        output=model(**inputs)
        preds_cla_all+=output['output_cla'].argmax(2).tolist()
        scores_cla_all+=(output['output_cla'][:,:,1]-output['output_cla'][:,:,0]).tolist()
        preds_reg_all += output['output_reg'].tolist()
        labels_cla_all+=inputs['label_cla'].tolist()
        labels_reg_all+=inputs['label_reg'].tolist()
        # loss, logits, labels = trainer.prediction_step(model, inputs,prediction_loss_only=False)
        # labels_all+=labels[:,0].cpu().numpy().tolist()
        # preds_all+=logits[0].argmax(2)[:,0].cpu().numpy().tolist()
        # scores_all+=(logits[0][:,0,id_y]-logits[0][:,0,id_n]).cpu().numpy().tolist()
        # if len(labels_all)>=80000:
        #     break
    preds_cla_all = np.array(preds_cla_all)
    scores_cla_all =np.array(scores_cla_all)
    preds_reg_all = np.array(preds_reg_all)
    labels_cla_all = np.array(labels_cla_all)
    labels_reg_all = np.array(labels_reg_all)
    try:
        roc_list = []
        for i in range(labels_cla_all.shape[1]):
            # AUC is only defined when there is at least one positive data.
            if np.sum(labels_cla_all[:, i] == 1) > 0 and np.sum(labels_cla_all[:, i] == 0) > 0:
                is_valid = labels_cla_all[:, i] != -100
                roc_list.append(roc_auc_score(labels_cla_all[is_valid, i], scores_cla_all[is_valid, i]))
            else:
                print('{} is invalid'.format(i))

        if len(roc_list) < labels_cla_all.shape[1]:
            print(len(roc_list))
            print('Some target is missing!')
            print('Missing ratio: %f' %(1 - float(len(roc_list)) / labels_cla_all.shape[1]))

        final_roc=sum(roc_list) / len(roc_list)
    except:
        final_roc=0

    is_valid=labels_cla_all != -100
    acc=(preds_cla_all[is_valid]==labels_cla_all[is_valid]).sum()/is_valid.sum() if is_valid.sum()>0 else 0

    is_valid=labels_reg_all != -100
    mae=np.abs(preds_reg_all[is_valid]-labels_reg_all[is_valid]).sum()/is_valid.sum() if is_valid.sum()>0 else 0

    return {'acc':acc,'auc':final_roc,'mae':mae}

def 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))
    # args_tem,left=parser.parse_known_args()



        #


    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, extra_paras = parser.parse_json_file(json_file=os.path.abspath(sys.argv[1]))
    else:
        model_args, data_args, training_args,left = parser.parse_args_into_dataclasses(return_remaining_strings=True)
    assert model_args.transformer_backbone in ['graphormer', 'gin']
    if model_args.transformer_backbone == 'graphormer':
        parsernew = HfArgumentParser(GraphormerConfig)
        # parsernew = argparse.ArgumentParser()
        parsernew=GraphormerModelMultiTask.add_args(parsernew)
        graph_args=parsernew.parse_args(left)
        graph_args=Graphormer_version_dict[graph_args.arch](graph_args)
        # print('graphormer_args',graphormer_args)
    elif model_args.transformer_backbone == 'gin':
        parsernew = HfArgumentParser(GinConfig)
        graph_args = parsernew.parse_args(left)

    # Sending telemetry. Tracking the example usage helps us better allocate resources to maintain them. The
    # information sent is the one passed as arguments along with your Python/PyTorch versions.
    send_example_telemetry("run_mlm", model_args, data_args)

    # Setup logging
    logging.basicConfig(
        format="%(asctime)s - %(levelname)s - %(name)s - %(message)s",
        datefmt="%m/%d/%Y %H:%M:%S",
        handlers=[logging.StreamHandler(sys.stdout)],
    )

    log_level = training_args.get_process_log_level()
    logger.setLevel(log_level)
    datasets.utils.logging.set_verbosity(log_level)
    transformers.utils.logging.set_verbosity(log_level)
    transformers.utils.logging.enable_default_handler()
    transformers.utils.logging.enable_explicit_format()

    # Log on each process the small summary:
    logger.warning(
        f"Process rank: {training_args.local_rank}, device: {training_args.device}, n_gpu: {training_args.n_gpu}"
        + f"distributed training: {bool(training_args.local_rank != -1)}, 16-bits training: {training_args.fp16}"
    )
    # Set the verbosity to info of the Transformers logger (on main process only):
    logger.info(f"Training/evaluation parameters {training_args}")

    # Detecting last checkpoint.
    last_checkpoint = None
    if os.path.isdir(training_args.output_dir) and training_args.do_train and not training_args.overwrite_output_dir:
        last_checkpoint = get_last_checkpoint(training_args.output_dir)
        if last_checkpoint is None and len(os.listdir(training_args.output_dir)) > 0:
            raise ValueError(
                f"Output directory ({training_args.output_dir}) already exists and is not empty. "
                "Use --overwrite_output_dir to overcome."
            )
        elif last_checkpoint is not None and training_args.resume_from_checkpoint is None:
            logger.info(
                f"Checkpoint detected, resuming training at {last_checkpoint}. To avoid this behavior, change "
                "the `--output_dir` or add `--overwrite_output_dir` to train from scratch."
            )

    # Set seed before initializing model.
    set_seed(training_args.seed)

    # 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. You can easily tweak this
    # behavior (see below)
    #
    # In distributed training, the load_dataset function guarantee that only one local process can concurrently
    # download the dataset.
    if data_args.dataset_name is not None:
        # Downloading and loading a dataset from the hub.
        raw_datasets = load_dataset(
            data_args.dataset_name,
            data_args.dataset_config_name,
            cache_dir=model_args.cache_dir,
            use_auth_token=True if model_args.use_auth_token else None,
        )
        if "validation" not in raw_datasets.keys():
            raw_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,
                use_auth_token=True if model_args.use_auth_token else None,
            )
            raw_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,
                use_auth_token=True if model_args.use_auth_token else None,
            )
    else:
        data_files = {}
        if data_args.train_file is not None:
            data_files["train"] = data_args.train_file
            extension = data_args.train_file.split(".")[-1]
        if data_args.validation_file is not None:
            data_files["validation"] = data_args.validation_file
            extension = data_args.validation_file.split(".")[-1]
        if extension == "txt":
            extension = "text"
        raw_datasets = load_dataset(
            extension,
            data_files=data_files,
            cache_dir=model_args.cache_dir,
            use_auth_token=True if model_args.use_auth_token else None,
        )

        # # If no validation data is there, validation_split_percentage will be used to divide the dataset.
        # if "validation" not in raw_datasets.keys():
        #     raw_datasets["validation"] = load_dataset(
        #         extension,
        #         data_files=data_files,
        #         split=f"train[:{data_args.validation_split_percentage}%]",
        #         cache_dir=model_args.cache_dir,
        #         use_auth_token=True if model_args.use_auth_token else None,
        #     )
        #     raw_datasets["train"] = load_dataset(
        #         extension,
        #         data_files=data_files,
        #         split=f"train[{data_args.validation_split_percentage}%:]",
        #         cache_dir=model_args.cache_dir,
        #         use_auth_token=True if model_args.use_auth_token else None,
        #     )

    # 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
    #
    # Distributed training:
    # The .from_pretrained methods guarantee that only one local process can concurrently
    # download model & vocab.
    # config_kwargs = {
    #     "cache_dir": model_args.cache_dir,
    #     "revision": model_args.model_revision,
    #     "use_auth_token": True if model_args.use_auth_token else None,
    # }
    # if model_args.config_name:
    #     config = AutoConfig.from_pretrained(model_args.config_name, **config_kwargs)
    # elif model_args.model_name_or_path:
    #     config = AutoConfig.from_pretrained(model_args.model_name_or_path, **config_kwargs)
    # else:
    #     config = CONFIG_MAPPING[model_args.model_type]()
    #     logger.warning("You are instantiating a new config instance from scratch.")
    #     if model_args.config_overrides is not None:
    #         logger.info(f"Overriding config: {model_args.config_overrides}")
    #         config.update_from_string(model_args.config_overrides)
    #         logger.info(f"New config: {config}")
    #
    # tokenizer_kwargs = {
    #     "cache_dir": model_args.cache_dir,
    #     "use_fast": model_args.use_fast_tokenizer,
    #     "revision": model_args.model_revision,
    #     "use_auth_token": True if model_args.use_auth_token else None,
    #     # "do_lower_case": model_args.all_data_to_lower_case,
    # }
    # if model_args.tokenizer_name:
    #     tokenizer = AutoTokenizer.from_pretrained(model_args.tokenizer_name, **tokenizer_kwargs)
    # elif model_args.model_name_or_path:
    #     tokenizer = AutoTokenizer.from_pretrained(model_args.model_name_or_path, **tokenizer_kwargs)
    # 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."
    #     )


    # special_tokens_dict = {'mask_token':'<MASK>','additional_special_tokens': ['<BOA>', '<EOA>']}

    # num_added_toks = tokenizer.add_special_tokens(special_tokens_dict)
    # print('We have added', num_added_toks, 'tokens')
    # tokenizer.model_input_names.append('answer_mask')




    # if model_args.model_name_or_path:
    #     if model_args.use_graph_transformer:
    #         graph_args.transformer_backbone=model_args.transformer_backbone
    #         graph_args.attention_fasion=model_args.attention_fasion
    #         model = GraphTransformer_dict[model_args.graph_transformer_text_backbone].from_pretrained(
    #             model_args.model_name_or_path,
    #             from_tf=bool(".ckpt" in model_args.model_name_or_path),
    #             config=config,
    #             graph_args=graph_args,
    #             cache_dir=model_args.cache_dir,
    #             revision=model_args.model_revision,
    #             use_auth_token=True if model_args.use_auth_token else None,
    #             ignore_mismatched_sizes=True
    #         )
    #     else:
    #         model = AutoModelForMaskedLM.from_pretrained(
    #             model_args.model_name_or_path,
    #             from_tf=bool(".ckpt" in model_args.model_name_or_path),
    #             config=config,
    #             cache_dir=model_args.cache_dir,
    #             revision=model_args.model_revision,
    #             use_auth_token=True if model_args.use_auth_token else None,
    #         )
    model = GraphormerModelMultiTask.build_model(graph_args)
    #
    # else:
    #     logger.info("Training new model from scratch")
    #     model = AutoModelForMaskedLM.from_config(config)
    #
    # model.resize_token_embeddings(len(tokenizer))



    # tokenizer = AutoTokenizer.from_pretrained("laituan245/molt5-small", model_max_length=512)
    # model = T5ForConditionalGeneration.from_pretrained('laituan245/molt5-small')
    # Preprocessing the datasets.
    # First we tokenize all the texts.
    if training_args.do_train:
        column_names = raw_datasets["train"].column_names
    else:
        column_names = raw_datasets["validation"].column_names
    text_column_name = "text" if "text" in column_names else column_names[0]

    # if data_args.max_seq_length is None:
    #     max_seq_length = tokenizer.model_max_length
    #     if max_seq_length > 1024:
    #         logger.warning(
    #             f"The tokenizer picked seems to have a very large `model_max_length` ({tokenizer.model_max_length}). "
    #             "Picking 1024 instead. You can change that default value by passing --max_seq_length xxx."
    #         )
    #         max_seq_length = 1024
    # else:
    #     if data_args.max_seq_length > tokenizer.model_max_length:
    #         logger.warning(
    #             f"The max_seq_length passed ({data_args.max_seq_length}) is larger than the maximum length for the"
    #             f"model ({tokenizer.model_max_length}). Using max_seq_length={tokenizer.model_max_length}."
    #         )
    #     max_seq_length = min(data_args.max_seq_length, tokenizer.model_max_length)

    if data_args.line_by_line:
        # When using line_by_line, we just tokenize each nonempty line.
        padding = "max_length" if data_args.pad_to_max_length else False

        # if model_args.use_graph_transformer:
        tokenize_function=lambda x: tokenize_function_graphormer_multitask(x,data_args.rich_features,data_args.transform_in_collator)
            # def tokenize_function(examples):
            #     # Remove empty lines
            #     # examples[text_column_name] = [line for line in examples[text_column_name] if len(line) > 0 and not line.isspace()]
            #     text=tokenizer(
            #         examples[text_column_name],
            #         padding=padding,
            #         truncation=True,
            #         max_length=max_seq_length,
            #         # We use this option because DataCollatorForLanguageModeling (see below) is more efficient when it
            #         # receives the `special_tokens_mask`.
            #         return_special_tokens_mask=True,
            #     )
            #     labels = tokenizer(
            #         examples['label'],
            #         padding=padding,
            #         truncation=True,
            #         max_length=max_seq_length,
            #         # We use this option because DataCollatorForLanguageModeling (see below) is more efficient when it
            #         # receives the `special_tokens_mask`.
            #         return_special_tokens_mask=True,
            #     )
            #
            #
            #     #在这里转换tensor是没有意义的，需要在collater里面转换，因为dataset会被缓存后再加载，缓存会把tensor变成list
            #     graph_data=smiles2graph(examples['graph'])
            #     # graph_data={'x':torch.tensor(graph_data['node_feat']).long(),
            #     #             'edge_index':torch.tensor(graph_data['edge_index']).long(),
            #     #             'edge_attr':torch.tensor(graph_data['edge_feat']).long()}
            #     return {'graph':graph_data,
            #             'input_ids':text.data['input_ids'],
            #             'attention_mask':text.data['attention_mask'],
            #             'special_tokens_mask':text.data['special_tokens_mask'],
            #             'labels':labels.data['input_ids']}
        # else:
        #     def tokenize_function(examples):
        #         # Remove empty lines
        #         examples[text_column_name] = [
        #             line for line in examples[text_column_name] if len(line) > 0 and not line.isspace()
        #         ]
        #         return tokenizer(
        #             examples[text_column_name],
        #             padding=padding,
        #             truncation=True,
        #             max_length=max_seq_length,
        #             # We use this option because DataCollatorForLanguageModeling (see below) is more efficient when it
        #             # receives the `special_tokens_mask`.
        #             return_special_tokens_mask=True,
        #         )
        # tokenize_function(raw_datasets['train'][0])
        if data_args.max_train_samples is not None:
            max_train_samples = min(len(raw_datasets['train']), data_args.max_train_samples)
            raw_datasets['train'] = raw_datasets['train'].shuffle().select(range(max_train_samples))
        if data_args.max_eval_samples is not None:
            max_eval_samples = min(len(raw_datasets['validation']), data_args.max_eval_samples)
            raw_datasets['validation'] = raw_datasets['validation'].shuffle().select(range(max_eval_samples))


        with training_args.main_process_first(desc="dataset map tokenization"):
            # for item in tqdm(raw_datasets['train']):
            #     tokenize_function(item)

            tokenized_datasets = raw_datasets.map(
                tokenize_function,
                batched=False,
                num_proc=data_args.preprocessing_num_workers,
                # remove_columns=[text_column_name],
                load_from_cache_file=not data_args.overwrite_cache,
                desc="Running tokenizer on dataset line_by_line",
            )
    # else:
    #     # Otherwise, we tokenize every text, then concatenate them together before splitting them in smaller parts.
    #     # We use `return_special_tokens_mask=True` because DataCollatorForLanguageModeling (see below) is more
    #     # efficient when it receives the `special_tokens_mask`.
    #     def tokenize_function(examples):
    #         return tokenizer(examples[text_column_name], return_special_tokens_mask=True)
    #
    #     with training_args.main_process_first(desc="dataset map tokenization"):
    #         tokenized_datasets = raw_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,
    #             desc="Running tokenizer on every text in dataset",
    #         )

        # Main data processing function that will concatenate all texts from our dataset and generate chunks of
        # max_seq_length.
        # def group_texts(examples):
        #     # Concatenate all texts.
        #     concatenated_examples = {k: list(chain(*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 >= max_seq_length:
        #         total_length = (total_length // max_seq_length) * max_seq_length
        #     # Split by chunks of max_len.
        #     result = {
        #         k: [t[i : i + max_seq_length] for i in range(0, total_length, max_seq_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

        # with training_args.main_process_first(desc="grouping texts together"):
        #     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,
        #         desc=f"Grouping texts in chunks of {max_seq_length}",
        #     )

    if training_args.do_train:
        if "train" not in tokenized_datasets:
            raise ValueError("--do_train requires a train dataset")
        train_dataset = tokenized_datasets["train"]
        # if data_args.max_train_samples is not None:
        #     max_train_samples = min(len(train_dataset), data_args.max_train_samples)
        #     train_dataset = train_dataset.select(range(max_train_samples))

    if training_args.do_eval:
        if "validation" not in tokenized_datasets:
            raise ValueError("--do_eval requires a validation dataset")
        eval_dataset = tokenized_datasets["validation"]
        # if data_args.max_eval_samples is not None:
        #     max_eval_samples = min(len(eval_dataset), data_args.max_eval_samples)
        #     eval_dataset = eval_dataset.shuffle().select(range(max_eval_samples))

        def preprocess_logits_for_metrics(logits, labels):
            if isinstance(logits, tuple):
                # Depending on the model and config, logits may contain extra tensors,
                # like past_key_values, but logits always come first
                logits = logits[0]
            return logits.argmax(dim=-1)

        metric = evaluate.load("accuracy")

        def compute_metrics(eval_preds):
            preds, labels = eval_preds
            # preds have the same shape as the labels, after the argmax(-1) has been calculated
            # by preprocess_logits_for_metrics
            labels = labels.reshape(-1)
            preds = preds.reshape(-1)
            mask = labels != -100
            labels = labels[mask]
            preds = preds[mask]
            return metric.compute(predictions=preds, references=labels)

    # Data collator
    # This one will take care of randomly masking the tokens.
    # pad_to_multiple_of_8 = data_args.line_by_line and training_args.fp16 and not data_args.pad_to_max_length
    # if model_args.use_graph_transformer:
    # data_collator = GraphTransformer_collator_dict[model_args.transformer_backbone][model_args.graph_transformer_text_backbone](
    #     tokenizer=tokenizer,
    #     mlm_probability=data_args.mlm_probability,
    #     pad_to_multiple_of=8 if pad_to_multiple_of_8 else None,
    #     transform_in_collator=data_args.transform_in_collator,
    #     rich_features=data_args.rich_features
    # )
    data_collator = CollaterForGraphormerMultiTask(transform_in_collator=data_args.transform_in_collator,include_y=False,rich_features=data_args.rich_features)
    # else:
    #     data_collator = DataCollatorForLanguageModeling(
    #         tokenizer=tokenizer,
    #         mlm_probability=data_args.mlm_probability,
    #         pad_to_multiple_of=8 if pad_to_multiple_of_8 else None,
    #     )

    # Initialize our Trainer
    training_args.remove_unused_columns=False
    trainer = Trainer(
        model=model,
        args=training_args,
        train_dataset=train_dataset if training_args.do_train else None,
        eval_dataset=eval_dataset if training_args.do_eval else None,
        # tokenizer=tokenizer,
        data_collator=data_collator,
        compute_metrics=compute_metrics if training_args.do_eval and not is_torch_tpu_available() else None,
        preprocess_logits_for_metrics=preprocess_logits_for_metrics
        if training_args.do_eval and not is_torch_tpu_available()
        else None,
    )

    # Training
    if training_args.do_train:
        checkpoint = None
        if training_args.resume_from_checkpoint is not None:
            checkpoint = training_args.resume_from_checkpoint
        elif last_checkpoint is not None:
            checkpoint = last_checkpoint
        train_result = trainer.train(resume_from_checkpoint=checkpoint)
        trainer.save_model()  # Saves the tokenizer too for easy upload
        metrics = train_result.metrics

        max_train_samples = (
            data_args.max_train_samples if data_args.max_train_samples is not None else len(train_dataset)
        )
        metrics["train_samples"] = min(max_train_samples, len(train_dataset))

        trainer.log_metrics("train", metrics)
        trainer.save_metrics("train", metrics)
        trainer.save_state()

    # Evaluation
    if training_args.do_eval:
        logger.info("*** Evaluate ***")

        # metrics = trainer.evaluate()
        metrics = evaluate_performance(trainer,training_args.device)

        max_eval_samples = data_args.max_eval_samples if data_args.max_eval_samples is not None else len(eval_dataset)
        metrics["eval_samples"] = min(max_eval_samples, len(eval_dataset))
        # try:
        #     perplexity = math.exp(metrics["eval_loss"])
        # except OverflowError:
        #     perplexity = float("inf")
        # metrics["perplexity"] = perplexity

        trainer.log_metrics("eval", metrics)
        trainer.save_metrics("eval", metrics)

    kwargs = {"finetuned_from": model_args.model_name_or_path, "tasks": "fill-mask"}
    if data_args.dataset_name is not None:
        kwargs["dataset_tags"] = data_args.dataset_name
        if data_args.dataset_config_name is not None:
            kwargs["dataset_args"] = data_args.dataset_config_name
            kwargs["dataset"] = f"{data_args.dataset_name} {data_args.dataset_config_name}"
        else:
            kwargs["dataset"] = data_args.dataset_name

    if training_args.push_to_hub:
        trainer.push_to_hub(**kwargs)
    else:
        trainer.create_model_card(**kwargs)


def _mp_fn(index):
    # For xla_spawn (TPUs)
    main()


if __name__ == "__main__":
    main()