upload GENA-LM Athaliana

README.md

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+---
+tags:
+- dna
+---
+
+# GENA-LM Athaliana 🌱 (gena-lm-bert-base-athaliana)
+
+GENA-LM is a Family of Open-Source Foundational Models for Long DNA Sequences.
+
+`gena-lm-bert-base-athaliana` is trained on Arabidopsis thaliana genome.
+
+## Model description
+GENA-LM (`gena-lm-bert-base-athaliana`) model is trained with a masked language model (MLM) objective, following data preprocessing methods pipeline in the BigBird paper and by masking 15% of tokens. Model config for `gena-lm-bert-base-athaliana` is similar to the bert-base:
+
+- 512 Maximum sequence length
+- 12 Layers, 12 Attention heads
+- 768 Hidden size
+- 32k Vocabulary size
+
+We pre-trained `gena-lm-bert-base-athaliana` on data obtained from [Kang et al.](https://doi.org/10.1038/s41467-023-42029-4), using this download [link](https://figshare.com/ndownloader/files/41661786) and contains chromosome-level genomes of 32 A. thaliana ecotypes.
+Pre-training was performed for 1,700,000 iterations with batch size 256 and sequence length was equal to 512 tokens. We modified Transformer to use [Pre-Layer normalization](https://arxiv.org/abs/2002.04745). We upload the checkpoint with the best loss on validation set (iteration 425000) to `main` branch and the latest checkpoint to `step_1700000` branch.
+
+Source code and data: https://github.com/AIRI-Institute/GENA_LM
+
+Paper: https://www.biorxiv.org/content/10.1101/2023.06.12.544594
+
+## Examples
+
+### How to load pre-trained model for Masked Language Modeling
+```python
+from transformers import AutoTokenizer, AutoModel
+
+tokenizer = AutoTokenizer.from_pretrained('AIRI-Institute/gena-lm-bert-base-athaliana')
+model = AutoModel.from_pretrained('AIRI-Institute/gena-lm-bert-base-athaliana', trust_remote_code=True)
+
+```
+
+### How to load pre-trained model to fine-tune it on classification task
+Get model class from GENA-LM repository:
+```bash
+git clone https://github.com/AIRI-Institute/GENA_LM.git
+```
+
+```python
+from GENA_LM.src.gena_lm.modeling_bert import BertForSequenceClassification
+from transformers import AutoTokenizer
+
+tokenizer = AutoTokenizer.from_pretrained('AIRI-Institute/gena-lm-bert-base-athaliana')
+model = BertForSequenceClassification.from_pretrained('AIRI-Institute/gena-lm-bert-base-athaliana')
+```
+or you can just download [modeling_bert.py](https://github.com/AIRI-Institute/GENA_LM/tree/main/src/gena_lm) and put it close to your code.
+
+OR you can get model class from HuggingFace AutoModel:
+```python
+from transformers import AutoTokenizer, AutoModel
+model = AutoModel.from_pretrained('AIRI-Institute/gena-lm-bert-base-athaliana', trust_remote_code=True)
+gena_module_name = model.__class__.__module__
+print(gena_module_name)
+import importlib
+# available class names:
+# - BertModel, BertForPreTraining, BertForMaskedLM, BertForNextSentencePrediction,
+# - BertForSequenceClassification, BertForMultipleChoice, BertForTokenClassification,
+# - BertForQuestionAnswering
+# check https://huggingface.co/docs/transformers/model_doc/bert
+cls = getattr(importlib.import_module(gena_module_name), 'BertForSequenceClassification')
+print(cls)
+model = cls.from_pretrained('AIRI-Institute/gena-lm-bert-base-athaliana', num_labels=2)
+```
+
+## Evaluation
+For evaluation results, see our paper: https://www.biorxiv.org/content/10.1101/2023.06.12.544594
+
+
+## Citation
+```bibtex
+@article{GENA_LM,
+	author = {Veniamin Fishman and Yuri Kuratov and Maxim Petrov and Aleksei Shmelev and Denis Shepelin and Nikolay Chekanov and Olga Kardymon and Mikhail Burtsev},
+	title = {GENA-LM: A Family of Open-Source Foundational DNA Language Models for Long Sequences},
+	elocation-id = {2023.06.12.544594},
+	year = {2023},
+	doi = {10.1101/2023.06.12.544594},
+	publisher = {Cold Spring Harbor Laboratory},
+	URL = {https://www.biorxiv.org/content/early/2023/11/01/2023.06.12.544594},
+	eprint = {https://www.biorxiv.org/content/early/2023/11/01/2023.06.12.544594.full.pdf},
+	journal = {bioRxiv}
+}
+
+```

config.json

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+{
+  "architectures": [
+    "BertForMaskedLM"
+  ],
+  "auto_map": {
+    "AutoModel": "modeling_bert.BertForMaskedLM"
+  },
+  "attention_probs_dropout_prob": 0.1,
+  "gradient_checkpointing": false,
+  "hidden_act": "gelu",
+  "hidden_dropout_prob": 0.1,
+  "hidden_size": 768,
+  "initializer_range": 0.02,
+  "intermediate_size": 3072,
+  "layer_norm_eps": 1e-12,
+  "max_position_embeddings": 512,
+  "model_type": "bert",
+  "num_attention_heads": 12,
+  "num_hidden_layers": 12,
+  "pad_token_id": 3,
+  "pre_layer_norm": true,
+  "position_embedding_type": "absolute",
+  "transformers_version": "4.6.0.dev0",
+  "type_vocab_size": 2,
+  "use_cache": true,
+  "vocab_size": 32000
+}

events.out.tfevents

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+version https://git-lfs.github.com/spec/v1
+oid sha256:a60902d19f54dbf550b321b08423c08dd5681077c1c9eda61dc64f8a90b355ea
+size 2393729

modeling_bert.py

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+# code from huggingface transformers 4.17.0
+# coding=utf-8
+# Copyright 2018 The Google AI Language Team Authors and The HuggingFace Inc. team.
+# Copyright (c) 2018, NVIDIA CORPORATION.  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.
+"""PyTorch BERT model."""
+
+import importlib
+import math
+import os
+import warnings
+from dataclasses import dataclass
+from typing import Optional, Tuple
+
+import torch
+import torch.utils.checkpoint
+from packaging import version
+from torch import nn
+from torch.nn import BCEWithLogitsLoss, CrossEntropyLoss, MSELoss
+
+from transformers.activations import ACT2FN
+from transformers.file_utils import (
+    ModelOutput,
+    add_code_sample_docstrings,
+    add_start_docstrings,
+    add_start_docstrings_to_model_forward,
+    replace_return_docstrings,
+)
+from transformers.modeling_outputs import (
+    BaseModelOutputWithPastAndCrossAttentions,
+    BaseModelOutputWithPoolingAndCrossAttentions,
+    CausalLMOutputWithCrossAttentions,
+    MaskedLMOutput,
+    MultipleChoiceModelOutput,
+    NextSentencePredictorOutput,
+    QuestionAnsweringModelOutput,
+    SequenceClassifierOutput,
+    TokenClassifierOutput,
+)
+from transformers.modeling_utils import (
+    PreTrainedModel,
+    apply_chunking_to_forward,
+    find_pruneable_heads_and_indices,
+    prune_linear_layer,
+)
+from transformers.utils import logging
+from transformers.models.bert.configuration_bert import BertConfig
+
+
+logger = logging.get_logger(__name__)
+
+_CHECKPOINT_FOR_DOC = "bert-base-uncased"
+_CONFIG_FOR_DOC = "BertConfig"
+_TOKENIZER_FOR_DOC = "BertTokenizer"
+
+BERT_PRETRAINED_MODEL_ARCHIVE_LIST = [
+    "bert-base-uncased",
+    "bert-large-uncased",
+    "bert-base-cased",
+    "bert-large-cased",
+    "bert-base-multilingual-uncased",
+    "bert-base-multilingual-cased",
+    "bert-base-chinese",
+    "bert-base-german-cased",
+    "bert-large-uncased-whole-word-masking",
+    "bert-large-cased-whole-word-masking",
+    "bert-large-uncased-whole-word-masking-finetuned-squad",
+    "bert-large-cased-whole-word-masking-finetuned-squad",
+    "bert-base-cased-finetuned-mrpc",
+    "bert-base-german-dbmdz-cased",
+    "bert-base-german-dbmdz-uncased",
+    "cl-tohoku/bert-base-japanese",
+    "cl-tohoku/bert-base-japanese-whole-word-masking",
+    "cl-tohoku/bert-base-japanese-char",
+    "cl-tohoku/bert-base-japanese-char-whole-word-masking",
+    "TurkuNLP/bert-base-finnish-cased-v1",
+    "TurkuNLP/bert-base-finnish-uncased-v1",
+    "wietsedv/bert-base-dutch-cased",
+    # See all BERT models at https://huggingface.co/models?filter=bert
+]
+
+
+def get_cls_by_name(name: str) -> type:
+    """Get class by its name and module path.
+
+    Args:
+        name (str): e.g., transfomers:T5ForConditionalGeneration, modeling_t5:my_class
+
+    Returns:
+        type: found class for `name`
+    """
+    module_name, cls_name = name.split(':')
+    return getattr(importlib.import_module(module_name), cls_name)
+
+
+def load_tf_weights_in_bert(model, config, tf_checkpoint_path):
+    """Load tf checkpoints in a pytorch model."""
+    try:
+        import re
+
+        import numpy as np
+        import tensorflow as tf
+    except ImportError:
+        logger.error(
+            "Loading a TensorFlow model in PyTorch, requires TensorFlow to be installed. Please see "
+            "https://www.tensorflow.org/install/ for installation instructions."
+        )
+        raise
+    tf_path = os.path.abspath(tf_checkpoint_path)
+    logger.info(f"Converting TensorFlow checkpoint from {tf_path}")
+    # Load weights from TF model
+    init_vars = tf.train.list_variables(tf_path)
+    names = []
+    arrays = []
+    for name, shape in init_vars:
+        logger.info(f"Loading TF weight {name} with shape {shape}")
+        array = tf.train.load_variable(tf_path, name)
+        names.append(name)
+        arrays.append(array)
+
+    for name, array in zip(names, arrays):
+        name = name.split("/")
+        # adam_v and adam_m are variables used in AdamWeightDecayOptimizer to calculated m and v
+        # which are not required for using pretrained model
+        if any(
+            n in ["adam_v", "adam_m", "AdamWeightDecayOptimizer", "AdamWeightDecayOptimizer_1", "global_step"]
+            for n in name
+        ):
+            logger.info(f"Skipping {'/'.join(name)}")
+            continue
+        pointer = model
+        for m_name in name:
+            if re.fullmatch(r"[A-Za-z]+_\d+", m_name):
+                scope_names = re.split(r"_(\d+)", m_name)
+            else:
+                scope_names = [m_name]
+            if scope_names[0] == "kernel" or scope_names[0] == "gamma":
+                pointer = getattr(pointer, "weight")
+            elif scope_names[0] == "output_bias" or scope_names[0] == "beta":
+                pointer = getattr(pointer, "bias")
+            elif scope_names[0] == "output_weights":
+                pointer = getattr(pointer, "weight")
+            elif scope_names[0] == "squad":
+                pointer = getattr(pointer, "classifier")
+            else:
+                try:
+                    pointer = getattr(pointer, scope_names[0])
+                except AttributeError:
+                    logger.info(f"Skipping {'/'.join(name)}")
+                    continue
+            if len(scope_names) >= 2:
+                num = int(scope_names[1])
+                pointer = pointer[num]
+        if m_name[-11:] == "_embeddings":
+            pointer = getattr(pointer, "weight")
+        elif m_name == "kernel":
+            array = np.transpose(array)
+        try:
+            if pointer.shape != array.shape:
+                raise ValueError(f"Pointer shape {pointer.shape} and array shape {array.shape} mismatched")
+        except AssertionError as e:
+            e.args += (pointer.shape, array.shape)
+            raise
+        logger.info(f"Initialize PyTorch weight {name}")
+        pointer.data = torch.from_numpy(array)
+    return model
+
+
+class BertEmbeddings(nn.Module):
+    """Construct the embeddings from word, position and token_type embeddings."""
+
+    def __init__(self, config):
+        super().__init__()
+        self.word_embeddings = nn.Embedding(config.vocab_size, config.hidden_size, padding_idx=config.pad_token_id)
+        if config.position_embedding_type == 'absolute':
+            self.position_embeddings = nn.Embedding(config.max_position_embeddings, config.hidden_size)
+        self.token_type_embeddings = nn.Embedding(config.type_vocab_size, config.hidden_size)
+
+        # self.LayerNorm is not snake-cased to stick with TensorFlow model variable name and be able to load
+        # any TensorFlow checkpoint file
+        self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+        self.dropout = nn.Dropout(config.hidden_dropout_prob)
+        # position_ids (1, len position emb) is contiguous in memory and exported when serialized
+        self.position_embedding_type = getattr(config, "position_embedding_type", "absolute")
+        self.register_buffer("position_ids", torch.arange(config.max_position_embeddings).expand((1, -1)))
+        if version.parse(torch.__version__) > version.parse("1.6.0"):
+            self.register_buffer(
+                "token_type_ids",
+                torch.zeros(self.position_ids.size(), dtype=torch.long),
+                persistent=False,
+            )
+
+    def forward(
+        self, input_ids=None, token_type_ids=None, position_ids=None, inputs_embeds=None, past_key_values_length=0
+    ):
+        if input_ids is not None:
+            input_shape = input_ids.size()
+        else:
+            input_shape = inputs_embeds.size()[:-1]
+
+        seq_length = input_shape[1]
+
+        if position_ids is None:
+            position_ids = self.position_ids[:, past_key_values_length: seq_length + past_key_values_length]
+
+        # Setting the token_type_ids to the registered buffer in constructor where it is all zeros, which usually occurs
+        # when its auto-generated, registered buffer helps users when tracing the model without passing token_type_ids, solves
+        # issue #5664
+        if token_type_ids is None:
+            if hasattr(self, "token_type_ids"):
+                buffered_token_type_ids = self.token_type_ids[:, :seq_length]
+                buffered_token_type_ids_expanded = buffered_token_type_ids.expand(input_shape[0], seq_length)
+                token_type_ids = buffered_token_type_ids_expanded
+            else:
+                token_type_ids = torch.zeros(input_shape, dtype=torch.long, device=self.position_ids.device)
+        if inputs_embeds is None:
+            inputs_embeds = self.word_embeddings(input_ids)
+        token_type_embeddings = self.token_type_embeddings(token_type_ids)
+        embeddings = inputs_embeds + token_type_embeddings
+        if self.position_embedding_type == "absolute":
+            position_embeddings = self.position_embeddings(position_ids)
+            embeddings += position_embeddings
+        embeddings = self.LayerNorm(embeddings)
+        embeddings = self.dropout(embeddings)
+        return embeddings
+
+
+class BertSelfAttention(nn.Module):
+    def __init__(self, config, position_embedding_type=None, has_relative_attention_bias=False):
+        """Bert self-attention with abs/relative position encodings and sparsity.
+
+        Args:
+            config: HF model configuration loaded from json
+            position_embedding_type (str, optional): absolute, relative_key, relative_key_query or
+                relative_attention_bias . Defaults to None.
+            has_relative_attention_bias (bool, optional): Use it's own relative embeddings matrix. Defaults to False.
+        """
+        super().__init__()
+        if config.hidden_size % config.num_attention_heads != 0 and not hasattr(config, "embedding_size"):
+            raise ValueError(
+                f"The hidden size ({config.hidden_size}) is not a multiple of the number of attention "
+                f"heads ({config.num_attention_heads})"
+            )
+
+        self.config = config
+        self.is_decoder = config.is_decoder
+        # max_seq_len is used in absolute, relative_key & relative_key_query and to pre-define sparsity layout
+        self.max_seq_len = config.max_position_embeddings
+
+        self.num_attention_heads = config.num_attention_heads
+        self.attention_head_size = int(config.hidden_size / config.num_attention_heads)
+        self.all_head_size = self.num_attention_heads * self.attention_head_size
+
+        # sparse attention configuration
+        self.is_sparse = False
+        sparse_config_cls_name = getattr(config, 'sparse_config_cls', None)
+        if sparse_config_cls_name:
+            self.is_sparse = True
+            sparse_config_cls = get_cls_by_name(sparse_config_cls_name)
+            self.sparse_config = sparse_config_cls(**self.config.sparse_attention)
+
+        if self.is_decoder and self.is_sparse:
+            raise RuntimeError('SparseAttention with BertModel decoder is not currently supported!')
+
+        self.query = nn.Linear(config.hidden_size, self.all_head_size)
+        self.key = nn.Linear(config.hidden_size, self.all_head_size)
+        self.value = nn.Linear(config.hidden_size, self.all_head_size)
+
+        self.dropout = nn.Dropout(config.attention_probs_dropout_prob)
+        self.softmax = nn.Softmax(dim=-1)
+        self.position_embedding_type = position_embedding_type or getattr(config, "position_embedding_type", "absolute")
+        self.has_relative_attention_bias = has_relative_attention_bias
+
+        if self.is_sparse and self.position_embedding_type not in ['absolute', 'relative_attention_bias', 'rotary']:
+            raise RuntimeError(f'SparseAttention supports `absolute`, `relative_attention_bias` and `rotary` position '
+                               f'embeddings, but: position_embeddings_type = {self.position_embedding_type}')
+
+        if self.is_decoder and self.position_embedding_type == 'relative_attention_bias':
+            raise RuntimeError(f'BertSelfAttention does not support `relative_attention_bias` with `is_decoder` '
+                               f' = {self.is_decoder}')
+
+        if self.position_embedding_type == "relative_key" or self.position_embedding_type == "relative_key_query":
+            self.max_position_embeddings = config.max_position_embeddings
+            self.max_seq_len = 2 * config.max_position_embeddings
+            self.distance_embedding = nn.Embedding(self.max_distance - 1, self.attention_head_size)
+        elif self.position_embedding_type == 'relative_attention_bias' and self.has_relative_attention_bias:
+            self.relative_attention_num_buckets = self.config.relative_attention_num_buckets
+            self.relative_last_bucket_distance = self.config.relative_last_bucket_distance
+            self.relative_attention_bias = nn.Embedding(self.relative_attention_num_buckets, self.num_attention_heads)
+        elif self.position_embedding_type == 'rotary':
+            self.rotary_base = getattr(config, 'rotary_base', None)
+            self.rotary_dim = getattr(config, 'rotary_dim', self.attention_head_size)
+            self.rotary_emb = RotaryEmbedding(self.rotary_dim, base=self.rotary_base)
+
+        if self.is_sparse:
+            try:
+                from deepspeed.ops.sparse_attention import SparseSelfAttention
+            except ImportError as e:
+                logger.error(f'DeepSpeed is required for Sparse Ops: {e}')
+                raise
+            self.sparse_self_attention = SparseSelfAttention(self.sparse_config, max_seq_length=self.max_seq_len)
+
+    def transpose_for_scores(self, x):
+        new_x_shape = x.size()[:-1] + (self.num_attention_heads, self.attention_head_size)
+        x = x.view(new_x_shape)
+        return x.permute(0, 2, 1, 3)
+
+    def transpose_key_for_scores(self, x):
+        # to remove redundant transpose in attention_scores matmul operation
+        new_x_shape = x.size()[:-1] + (self.num_attention_heads, self.attention_head_size)
+        x = x.view(*new_x_shape)
+        return x.permute(0, 2, 3, 1)
+
+    @staticmethod
+    def _relative_position_bucket(relative_position, bidirectional=True, num_buckets=32, max_distance=128):
+        """
+        Adapted from Mesh Tensorflow:
+        https://github.com/tensorflow/mesh/blob/0cb87fe07da627bf0b7e60475d59f95ed6b5be3d/mesh_tensorflow/transformer/transformer_layers.py#L593
+
+        #todo: refactor, the same code is used in modeling_t5
+
+        Translate relative position to a bucket number for relative attention. The relative position is defined as
+        memory_position - query_position, i.e. the distance in tokens from the attending position to the attended-to
+        position. If bidirectional=False, then positive relative positions are invalid. We use smaller buckets for
+        small absolute relative_position and larger buckets for larger absolute relative_positions. All relative
+        positions >=max_distance map to the same bucket. All relative positions <=-max_distance map to the same bucket.
+        This should allow for more graceful generalization to longer sequences than the model has been trained on
+
+        Args:
+            relative_position: an int32 Tensor
+            bidirectional: a boolean - whether the attention is bidirectional
+            num_buckets: an integer
+            max_distance: an integer
+
+        Returns:
+            a Tensor with the same shape as relative_position, containing int32 values in the range [0, num_buckets)
+        """
+        relative_buckets = 0
+        if bidirectional:
+            num_buckets //= 2
+            relative_buckets += (relative_position > 0).to(torch.long) * num_buckets
+            relative_position = torch.abs(relative_position)
+        else:
+            relative_position = -torch.min(relative_position, torch.zeros_like(relative_position))
+        # now relative_position is in the range [0, inf)
+
+        # half of the buckets are for exact increments in positions
+        max_exact = num_buckets // 2
+        is_small = relative_position < max_exact
+
+        # The other half of the buckets are for logarithmically bigger bins in positions up to max_distance
+        relative_postion_if_large = max_exact + (
+            torch.log(relative_position.float() / max_exact)
+            / math.log(max_distance / max_exact)
+            * (num_buckets - max_exact)
+        ).to(torch.long)
+        relative_postion_if_large = torch.min(
+            relative_postion_if_large, torch.full_like(relative_postion_if_large, num_buckets - 1)
+        )
+
+        relative_buckets += torch.where(is_small, relative_position, relative_postion_if_large)
+        return relative_buckets
+
+    def compute_bias(self, query_length, key_length):
+        """ Compute binned relative position bias """
+        context_position = torch.arange(query_length, dtype=torch.long)[:, None]
+        memory_position = torch.arange(key_length, dtype=torch.long)[None, :]
+        relative_position = memory_position - context_position  # shape (query_length, key_length)
+        relative_position_bucket = self._relative_position_bucket(
+            relative_position,  # shape (query_length, key_length)
+            bidirectional=(not self.is_decoder),
+            num_buckets=self.relative_attention_num_buckets,
+            max_distance=self.relative_last_bucket_distance,
+        )
+        relative_position_bucket = relative_position_bucket.to(self.relative_attention_bias.weight.device)
+        values = self.relative_attention_bias(relative_position_bucket)  # shape (query_length, key_length, num_heads)
+        values = values.permute([2, 0, 1]).unsqueeze(0)  # shape (1, num_heads, query_length, key_length)
+        return values
+
+    def get_relative_attention_bias(self, position_bias, batch_size, query_length, key_length):
+        if position_bias is None and self.has_relative_attention_bias:
+            position_bias = self.compute_bias(query_length, key_length)
+            position_bias = position_bias.repeat(batch_size, 1, 1, 1)
+        return position_bias
+
+    def forward(
+        self,
+        hidden_states,
+        attention_mask=None,
+        head_mask=None,
+        encoder_hidden_states=None,
+        encoder_attention_mask=None,
+        past_key_value=None,
+        position_bias=None,
+        output_attentions=False,
+    ):
+        mixed_query_layer = self.query(hidden_states)
+
+        # If this is instantiated as a cross-attention module, the keys
+        # and values come from an encoder; the attention mask needs to be
+        # such that the encoder's padding tokens are not attended to.
+        is_cross_attention = encoder_hidden_states is not None
+
+        if is_cross_attention and past_key_value is not None:
+            # reuse k,v, cross_attentions
+            key_layer = past_key_value[0]
+            value_layer = past_key_value[1]
+            attention_mask = encoder_attention_mask
+        elif is_cross_attention:
+            key_layer = self.transpose_key_for_scores(self.key(encoder_hidden_states))
+            value_layer = self.transpose_for_scores(self.value(encoder_hidden_states))
+            attention_mask = encoder_attention_mask
+        elif past_key_value is not None:
+            key_layer = self.transpose_key_for_scores(self.key(hidden_states))
+            value_layer = self.transpose_for_scores(self.value(hidden_states))
+            key_layer = torch.cat([past_key_value[0], key_layer], dim=2)
+            value_layer = torch.cat([past_key_value[1], value_layer], dim=2)
+        else:
+            key_layer = self.transpose_key_for_scores(self.key(hidden_states))
+            value_layer = self.transpose_for_scores(self.value(hidden_states))
+
+        query_layer = self.transpose_for_scores(mixed_query_layer)
+
+        if self.is_decoder:
+            # if cross_attention save Tuple(torch.Tensor, torch.Tensor) of all cross attention key/value_states.
+            # Further calls to cross_attention layer can then reuse all cross-attention
+            # key/value_states (first "if" case)
+            # if uni-directional self-attention (decoder) save Tuple(torch.Tensor, torch.Tensor) of
+            # all previous decoder key/value_states. Further calls to uni-directional self-attention
+            # can concat previous decoder key/value_states to current projected key/value_states (third "elif" case)
+            # if encoder bi-directional self-attention `past_key_value` is always `None`
+            past_key_value = (key_layer, value_layer)
+
+        bs, seq_len, _ = hidden_states.shape
+        # query shape: bs x n_heads x seq_len x head_dim
+        # key shape:   bs x n_heads x head_dim x seq_len
+
+        if self.position_embedding_type == 'rotary':
+            # todo: in key_layer and value_layer past states already concatenated
+            # but rotary embeddings should not be applied to past states
+            if past_key_value is not None:
+                raise RuntimeError(f'past_key_values is not None are not supported in BertSelfAttention.forward with '
+                                   f'position_embedding_type = {self.position_embedding_type}.')
+            # traspose to bs x n_heads x seq_len x head_dim
+            key_layer = key_layer.transpose(-1, -2)
+            if self.rotary_dim < self.attention_head_size:
+                query_rot = query_layer[..., :self.rotary_dim]
+                query_pass = query_layer[..., self.rotary_dim:]
+
+                key_rot = key_layer[..., :self.rotary_dim]
+                key_pass = key_layer[..., self.rotary_dim:]
+            else:  # full rotary
+                query_rot = query_layer
+                key_rot = key_layer
+
+            cos, sin = self.rotary_emb(key_rot, seq_len=seq_len)
+            query_layer, key_layer = apply_rotary_pos_emb(query_rot, key_rot, cos, sin, offset=0)
+            if self.rotary_dim < self.attention_head_size:
+                query_layer = torch.cat((query_layer, query_pass), dim=-1)
+                key_layer = torch.cat((key_layer, key_pass), dim=-1)
+            # transpose to bs x n_heads x head_dim x seq_len
+            key_layer = key_layer.transpose(-1, -2)
+
+        if not self.is_sparse:
+            # Take the dot product between "query" and "key" to get the raw attention scores.
+            attention_scores = torch.matmul(query_layer, key_layer)
+
+            if self.position_embedding_type in ["relative_key", "relative_key_query"]:
+                position_ids_l = torch.arange(seq_len, dtype=torch.long, device=hidden_states.device).view(-1, 1)
+                position_ids_r = torch.arange(seq_len, dtype=torch.long, device=hidden_states.device).view(1, -1)
+                distance = position_ids_l - position_ids_r
+                positional_embedding = self.distance_embedding(distance + self.max_position_embeddings - 1)
+                positional_embedding = positional_embedding.to(dtype=query_layer.dtype)  # fp16 compatibility
+
+                # https://arxiv.org/abs/2009.13658
+                if self.position_embedding_type == "relative_key":
+                    relative_position_scores = torch.einsum("bhld,lrd->bhlr", query_layer, positional_embedding)
+                    attention_scores = attention_scores + relative_position_scores
+                elif self.position_embedding_type == "relative_key_query":
+                    relative_position_scores_query = torch.einsum("bhld,lrd->bhlr", query_layer, positional_embedding)
+                    relative_position_scores_key = torch.einsum("bhdr,lrd->bhlr", key_layer, positional_embedding)
+                    attention_scores = attention_scores + relative_position_scores_query + relative_position_scores_key
+                elif self.position_embedding_type == 'relative_attention_bias':
+                    position_bias = self.get_relative_attention_bias(position_bias, bs, seq_len, seq_len)
+                    attention_scores = attention_scores + position_bias
+
+            attention_scores = attention_scores / math.sqrt(self.attention_head_size)
+            if attention_mask is not None:
+                # Apply the attention mask is (precomputed for all layers in BertModel forward() function)
+                attention_scores = attention_scores + attention_mask
+
+            # Normalize the attention scores to probabilities.
+            attention_probs = self.softmax(attention_scores)
+
+            # This is actually dropping out entire tokens to attend to, which might
+            # seem a bit unusual, but is taken from the original Transformer paper.
+            attention_probs = self.dropout(attention_probs)
+
+            # Mask heads if we want to
+            if head_mask is not None:
+                attention_probs = attention_probs * head_mask
+
+            context_layer = torch.matmul(attention_probs, value_layer)
+        else:
+            # sparse attention
+            # todo: return attention_probs
+            # todo: support relative_key -> need to change einsum with sparse operators..
+            # sparse attention supports masks with following shapes:
+            # key_padding_mask: (bs x seq_len) or (bs x 1 x 1 x seq_len)
+            # attention_mask: seq_len x seq_len or (1 x 1 x seq_len x seq_len)
+            if self.position_embedding_type == 'relative_attention_bias':
+                position_bias = self.get_relative_attention_bias(position_bias, bs, seq_len, seq_len)
+
+            query_dtype = query_layer.dtype
+            if query_dtype != torch.half:
+                # deepspeed sparse_self_attention supports only fp16 inputs
+                # manually cast to half in case if running in fp32 or O1 modes
+                query_layer, key_layer, value_layer = query_layer.half(), key_layer.half(), value_layer.half()
+                # attention_mask = attention_mask.half()
+                if position_bias is not None:
+                    position_bias = position_bias.half()
+            context_layer = self.sparse_self_attention(query_layer, key_layer, value_layer, rpe=position_bias,
+                                                       key_padding_mask=attention_mask)
+            if query_dtype == torch.float:
+                context_layer = context_layer.float()
+
+        context_layer = context_layer.permute(0, 2, 1, 3).contiguous()
+        new_context_layer_shape = context_layer.size()[:-2] + (self.all_head_size,)
+        context_layer = context_layer.view(new_context_layer_shape)
+
+        if self.is_sparse and output_attentions:
+            # todo: return sparse attention_scores or None, to not break the run
+            raise RuntimeError(f'SparseAttention does not support output_attention = {output_attentions}')
+
+        outputs = (context_layer, attention_probs) if output_attentions else (context_layer,)
+
+        if self.position_embedding_type == 'relative_attention_bias':
+            outputs = outputs + (position_bias,)
+
+        if self.is_decoder:
+            outputs = outputs + (past_key_value,)
+        return outputs
+
+
+class BertSelfOutput(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.pre_layer_norm = getattr(config, 'pre_layer_norm', False)
+        self.bert_output_layer = True
+        self.dense = nn.Linear(config.hidden_size, config.hidden_size)
+        self.dropout = nn.Dropout(config.hidden_dropout_prob)
+        if not self.pre_layer_norm:
+            self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+
+    def forward(self, hidden_states, input_tensor):
+        hidden_states = self.dense(hidden_states)
+        hidden_states = self.dropout(hidden_states)
+        if not self.pre_layer_norm:
+            hidden_states = self.LayerNorm(hidden_states + input_tensor)
+        return hidden_states
+
+
+class BertAttention(nn.Module):
+    def __init__(self, config, position_embedding_type=None, has_relative_attention_bias=False):
+        super().__init__()
+        self.self = BertSelfAttention(config, position_embedding_type=position_embedding_type,
+                                      has_relative_attention_bias=has_relative_attention_bias)
+        self.output = BertSelfOutput(config)
+        self.pruned_heads = set()
+
+    def prune_heads(self, heads):
+        if len(heads) == 0:
+            return
+        heads, index = find_pruneable_heads_and_indices(
+            heads, self.self.num_attention_heads, self.self.attention_head_size, self.pruned_heads
+        )
+
+        # Prune linear layers
+        self.self.query = prune_linear_layer(self.self.query, index)
+        self.self.key = prune_linear_layer(self.self.key, index)
+        self.self.value = prune_linear_layer(self.self.value, index)
+        self.output.dense = prune_linear_layer(self.output.dense, index, dim=1)
+
+        # Update hyper params and store pruned heads
+        self.self.num_attention_heads = self.self.num_attention_heads - len(heads)
+        self.self.all_head_size = self.self.attention_head_size * self.self.num_attention_heads
+        self.pruned_heads = self.pruned_heads.union(heads)
+
+    def forward(
+        self,
+        hidden_states,
+        attention_mask=None,
+        head_mask=None,
+        encoder_hidden_states=None,
+        encoder_attention_mask=None,
+        past_key_value=None,
+        position_bias=None,
+        output_attentions=False,
+    ):
+        self_outputs = self.self(
+            hidden_states,
+            attention_mask,
+            head_mask,
+            encoder_hidden_states,
+            encoder_attention_mask,
+            past_key_value,
+            position_bias,
+            output_attentions,
+        )
+        attention_output = self.output(self_outputs[0], hidden_states)
+        outputs = (attention_output,) + self_outputs[1:]  # add attentions if we output them
+        return outputs
+
+
+class BertIntermediate(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.dense = nn.Linear(config.hidden_size, config.intermediate_size)
+        if isinstance(config.hidden_act, str):
+            self.intermediate_act_fn = ACT2FN[config.hidden_act]
+        else:
+            self.intermediate_act_fn = config.hidden_act
+
+    def forward(self, hidden_states):
+        hidden_states = self.dense(hidden_states)
+        hidden_states = self.intermediate_act_fn(hidden_states)
+        return hidden_states
+
+
+class BertOutput(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.pre_layer_norm = getattr(config, 'pre_layer_norm', False)
+        self.bert_output_layer = True
+        self.dense = nn.Linear(config.intermediate_size, config.hidden_size)
+        self.dropout = nn.Dropout(config.hidden_dropout_prob)
+        if not self.pre_layer_norm:
+            self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+
+    def forward(self, hidden_states, input_tensor):
+        hidden_states = self.dense(hidden_states)
+        hidden_states = self.dropout(hidden_states)
+        if not self.pre_layer_norm:
+            hidden_states = self.LayerNorm(hidden_states + input_tensor)
+        return hidden_states
+
+
+class BertLayer(nn.Module):
+    def __init__(self, config, has_relative_attention_bias=False):
+        super().__init__()
+        self.chunk_size_feed_forward = config.chunk_size_feed_forward
+        self.seq_len_dim = 1
+        self.pre_layer_norm = getattr(config, 'pre_layer_norm', False)
+        if self.pre_layer_norm:
+            self.pre_attention_ln = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+            self.post_attention_ln = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+        self.attention = BertAttention(config, has_relative_attention_bias=has_relative_attention_bias)
+        self.is_decoder = config.is_decoder
+        self.add_cross_attention = config.add_cross_attention
+        if self.add_cross_attention:
+            if not self.is_decoder:
+                raise ValueError(f"{self} should be used as a decoder model if cross attention is added")
+            self.crossattention = BertAttention(config, position_embedding_type="absolute")
+        self.intermediate = BertIntermediate(config)
+        self.output = BertOutput(config)
+
+    def forward(
+        self,
+        hidden_states,
+        attention_mask=None,
+        head_mask=None,
+        encoder_hidden_states=None,
+        encoder_attention_mask=None,
+        past_key_value=None,
+        position_bias=None,
+        output_attentions=False,
+    ):
+        # decoder uni-directional self-attention cached key/values tuple is at positions 1,2
+        self_attn_past_key_value = past_key_value[:2] if past_key_value is not None else None
+        self_attention_outputs = self.attention(
+            hidden_states if not self.pre_layer_norm else self.pre_attention_ln(hidden_states),
+            attention_mask,
+            head_mask,
+            position_bias=position_bias,
+            output_attentions=output_attentions,
+            past_key_value=self_attn_past_key_value,
+        )
+        attention_output = self_attention_outputs[0]
+
+        # if decoder, the last output is tuple of self-attn cache
+        if self.is_decoder:
+            outputs = self_attention_outputs[1:-1]
+            present_key_value = self_attention_outputs[-1]
+        else:
+            outputs = self_attention_outputs[1:]  # add self attentions if we output attention weights
+
+        cross_attn_present_key_value = None
+        if self.is_decoder and encoder_hidden_states is not None:
+            if not hasattr(self, "crossattention"):
+                raise ValueError(
+                    f"If `encoder_hidden_states` are passed, {self} has to be instantiated with cross-attention layers by setting `config.add_cross_attention=True`"
+                )
+
+            # cross_attn cached key/values tuple is at positions 3,4 of past_key_value tuple
+            cross_attn_past_key_value = past_key_value[-2:] if past_key_value is not None else None
+            cross_attention_outputs = self.crossattention(
+                attention_output,
+                attention_mask,
+                head_mask,
+                encoder_hidden_states,
+                encoder_attention_mask,
+                cross_attn_past_key_value,
+                position_bias,
+                output_attentions,
+            )
+            attention_output = cross_attention_outputs[0]
+            outputs = outputs + cross_attention_outputs[1:-1]  # add cross attentions if we output attention weights
+
+            # add cross-attn cache to positions 3,4 of present_key_value tuple
+            cross_attn_present_key_value = cross_attention_outputs[-1]
+            present_key_value = present_key_value + cross_attn_present_key_value
+
+        if self.pre_layer_norm:
+            attention_output = hidden_states + attention_output
+
+        layer_output = apply_chunking_to_forward(
+            self.feed_forward_chunk, self.chunk_size_feed_forward, self.seq_len_dim, attention_output
+        )
+
+        outputs = (layer_output,) + outputs
+
+        # if decoder, return the attn key/values as the last output
+        if self.is_decoder:
+            outputs = outputs + (present_key_value,)
+
+        return outputs
+
+    def feed_forward_chunk(self, attention_output):
+        intermediate_inp = attention_output if not self.pre_layer_norm else self.post_attention_ln(attention_output)
+        intermediate_output = self.intermediate(intermediate_inp)
+        layer_output = self.output(intermediate_output, attention_output)
+        if self.pre_layer_norm:
+            layer_output = layer_output + attention_output
+        return layer_output
+
+
+class BertEncoder(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.config = config
+        self.pre_layer_norm = getattr(config, 'pre_layer_norm', False)
+        # last_layer_ln is used with pre_layer_norm:
+        # pre_layer_norm: https://arxiv.org/abs/2002.04745
+        #   x = x + mha(ln(x))
+        #   x = x + ffn(mha)
+        #   if last_layer:
+        #       x = ln(x)
+        # post_layer_norm (standart bert):
+        #  x = ln(x + mha(x))
+        #  x = ln(x + ffn(x))
+        self.last_layer_norm = getattr(config, 'last_layer_norm', self.pre_layer_norm)
+        if not self.pre_layer_norm and self.last_layer_norm:
+            raise RuntimeError('last_layer_norm could be used only with pre_layer_norm=True')
+        self.layer = nn.ModuleList(
+                [BertLayer(config, has_relative_attention_bias=bool(i == 0)) for i in range(config.num_hidden_layers)]
+            )
+        self.gradient_checkpointing = False
+        if self.pre_layer_norm and self.last_layer_norm:
+            self.last_layer_ln = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+
+    def forward(
+        self,
+        hidden_states,
+        attention_mask=None,
+        head_mask=None,
+        encoder_hidden_states=None,
+        encoder_attention_mask=None,
+        past_key_values=None,
+        use_cache=None,
+        output_attentions=False,
+        output_hidden_states=False,
+        return_dict=True,
+    ):
+        all_hidden_states = () if output_hidden_states else None
+        all_self_attentions = () if output_attentions else None
+        all_cross_attentions = () if output_attentions and self.config.add_cross_attention else None
+        position_bias = None
+
+        next_decoder_cache = () if use_cache else None
+        for i, layer_module in enumerate(self.layer):
+            if output_hidden_states:
+                all_hidden_states = all_hidden_states + (hidden_states,)
+
+            layer_head_mask = head_mask[i] if head_mask is not None else None
+            past_key_value = past_key_values[i] if past_key_values is not None else None
+
+            if self.gradient_checkpointing and self.training:
+
+                if use_cache:
+                    logger.warning(
+                        "`use_cache=True` is incompatible with gradient checkpointing. Setting `use_cache=False`..."
+                    )
+                    use_cache = False
+
+                def create_custom_forward(module):
+                    def custom_forward(*inputs):
+                        return module(*inputs, past_key_value, position_bias, output_attentions)
+
+                    return custom_forward
+
+                layer_outputs = torch.utils.checkpoint.checkpoint(
+                    create_custom_forward(layer_module),
+                    hidden_states,
+                    attention_mask,
+                    layer_head_mask,
+                    encoder_hidden_states,
+                    encoder_attention_mask,
+                )
+            else:
+                layer_outputs = layer_module(
+                    hidden_states,
+                    attention_mask,
+                    layer_head_mask,
+                    encoder_hidden_states,
+                    encoder_attention_mask,
+                    past_key_value,
+                    position_bias,
+                    output_attentions,
+                )
+
+            hidden_states = layer_outputs[0]
+            if use_cache:
+                next_decoder_cache += (layer_outputs[-1],)
+            if output_attentions:
+                all_self_attentions = all_self_attentions + (layer_outputs[1],)
+                if self.config.add_cross_attention:
+                    all_cross_attentions = all_cross_attentions + (layer_outputs[2],)
+
+            if self.config.position_embedding_type == 'relative_attention_bias':
+                if not output_attentions:
+                    position_bias = layer_outputs[1]
+                else:
+                    position_bias = layer_outputs[2]
+
+        if self.pre_layer_norm and self.last_layer_norm:
+            hidden_states = self.last_layer_ln(hidden_states)
+
+        if output_hidden_states:
+            all_hidden_states = all_hidden_states + (hidden_states,)
+
+        if not return_dict:
+            return tuple(
+                v
+                for v in [
+                    hidden_states,
+                    next_decoder_cache,
+                    all_hidden_states,
+                    all_self_attentions,
+                    all_cross_attentions,
+                ]
+                if v is not None
+            )
+        return BaseModelOutputWithPastAndCrossAttentions(
+            last_hidden_state=hidden_states,
+            past_key_values=next_decoder_cache,
+            hidden_states=all_hidden_states,
+            attentions=all_self_attentions,
+            cross_attentions=all_cross_attentions,
+        )
+
+
+class BertPooler(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.dense = nn.Linear(config.hidden_size, config.hidden_size)
+        self.activation = nn.Tanh()
+
+    def forward(self, hidden_states):
+        # We "pool" the model by simply taking the hidden state corresponding
+        # to the first token.
+        first_token_tensor = hidden_states[:, 0]
+        pooled_output = self.dense(first_token_tensor)
+        pooled_output = self.activation(pooled_output)
+        return pooled_output
+
+
+class BertPredictionHeadTransform(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.dense = nn.Linear(config.hidden_size, config.hidden_size)
+        if isinstance(config.hidden_act, str):
+            self.transform_act_fn = ACT2FN[config.hidden_act]
+        else:
+            self.transform_act_fn = config.hidden_act
+        self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+
+    def forward(self, hidden_states):
+        hidden_states = self.dense(hidden_states)
+        hidden_states = self.transform_act_fn(hidden_states)
+        hidden_states = self.LayerNorm(hidden_states)
+        return hidden_states
+
+
+class BertLMPredictionHead(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.transform = BertPredictionHeadTransform(config)
+
+        # The output weights are the same as the input embeddings, but there is
+        # an output-only bias for each token.
+        self.decoder = nn.Linear(config.hidden_size, config.vocab_size, bias=False)
+
+        self.bias = nn.Parameter(torch.zeros(config.vocab_size))
+
+        # Need a link between the two variables so that the bias is correctly resized with `resize_token_embeddings`
+        self.decoder.bias = self.bias
+
+    def forward(self, hidden_states):
+        hidden_states = self.transform(hidden_states)
+        hidden_states = self.decoder(hidden_states)
+        return hidden_states
+
+
+class BertOnlyMLMHead(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.predictions = BertLMPredictionHead(config)
+
+    def forward(self, sequence_output):
+        prediction_scores = self.predictions(sequence_output)
+        return prediction_scores
+
+
+class BertOnlyNSPHead(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.seq_relationship = nn.Linear(config.hidden_size, 2)
+
+    def forward(self, pooled_output):
+        seq_relationship_score = self.seq_relationship(pooled_output)
+        return seq_relationship_score
+
+
+class BertPreTrainingHeads(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.predictions = BertLMPredictionHead(config)
+        self.seq_relationship = nn.Linear(config.hidden_size, 2)
+
+    def forward(self, sequence_output, pooled_output):
+        prediction_scores = self.predictions(sequence_output)
+        seq_relationship_score = self.seq_relationship(pooled_output)
+        return prediction_scores, seq_relationship_score
+
+
+class BertPreTrainedModel(PreTrainedModel):
+    """
+    An abstract class to handle weights initialization and a simple interface for downloading and loading pretrained
+    models.
+    """
+
+    config_class = BertConfig
+    load_tf_weights = load_tf_weights_in_bert
+    base_model_prefix = "bert"
+    supports_gradient_checkpointing = True
+    _keys_to_ignore_on_load_missing = [r"position_ids"]
+
+    def _init_weights(self, module):
+        """Initialize the weights"""
+        if isinstance(module, nn.Linear):
+            # Slightly different from the TF version which uses truncated_normal for initialization
+            # cf https://github.com/pytorch/pytorch/pull/5617
+            std = self.config.initializer_range
+            if hasattr(module, 'bert_output_layer') and self.config.pre_layer_norm:
+                std /= math.sqrt(2.0 * self.config.num_hidden_layers)
+            module.weight.data.normal_(mean=0.0, std=std)
+            if module.bias is not None:
+                module.bias.data.zero_()
+        elif isinstance(module, nn.Embedding):
+            module.weight.data.normal_(mean=0.0, std=self.config.initializer_range)
+            if module.padding_idx is not None:
+                module.weight.data[module.padding_idx].zero_()
+        elif isinstance(module, nn.LayerNorm):
+            module.bias.data.zero_()
+            module.weight.data.fill_(1.0)
+
+    def _set_gradient_checkpointing(self, module, value=False):
+        if isinstance(module, BertEncoder):
+            module.gradient_checkpointing = value
+
+
+@dataclass
+class BertForPreTrainingOutput(ModelOutput):
+    """
+    Output type of [`BertForPreTraining`].
+
+    Args:
+        loss (*optional*, returned when `labels` is provided, `torch.FloatTensor` of shape `(1,)`):
+            Total loss as the sum of the masked language modeling loss and the next sequence prediction
+            (classification) loss.
+        mlm_loss: masked language modeling loss
+        nsp_loss: next sequence prediction loss
+        prediction_logits (`torch.FloatTensor` of shape `(batch_size, sequence_length, config.vocab_size)`):
+            Prediction scores of the language modeling head (scores for each vocabulary token before SoftMax).
+        seq_relationship_logits (`torch.FloatTensor` of shape `(batch_size, 2)`):
+            Prediction scores of the next sequence prediction (classification) head (scores of True/False continuation
+            before SoftMax).
+        hidden_states (`tuple(torch.FloatTensor)`, *optional*, returned when `output_hidden_states=True` is passed or when `config.output_hidden_states=True`):
+            Tuple of `torch.FloatTensor` (one for the output of the embeddings + one for the output of each layer) of
+            shape `(batch_size, sequence_length, hidden_size)`.
+
+            Hidden-states of the model at the output of each layer plus the initial embedding outputs.
+        attentions (`tuple(torch.FloatTensor)`, *optional*, returned when `output_attentions=True` is passed or when `config.output_attentions=True`):
+            Tuple of `torch.FloatTensor` (one for each layer) of shape `(batch_size, num_heads, sequence_length,
+            sequence_length)`.
+
+            Attentions weights after the attention softmax, used to compute the weighted average in the self-attention
+            heads.
+    """
+
+    loss: Optional[torch.FloatTensor] = None
+    mlm_loss: Optional[torch.FloatTensor] = None
+    nsp_loss: Optional[torch.FloatTensor] = None
+    prediction_logits: torch.FloatTensor = None
+    seq_relationship_logits: torch.FloatTensor = None
+    hidden_states: Optional[Tuple[torch.FloatTensor]] = None
+    attentions: Optional[Tuple[torch.FloatTensor]] = None
+
+
+BERT_START_DOCSTRING = r"""
+
+    This model inherits from [`PreTrainedModel`]. Check the superclass documentation for the generic methods the
+    library implements for all its model (such as downloading or saving, resizing the input embeddings, pruning heads
+    etc.)
+
+    This model is also a PyTorch [torch.nn.Module](https://pytorch.org/docs/stable/nn.html#torch.nn.Module) subclass.
+    Use it as a regular PyTorch Module and refer to the PyTorch documentation for all matter related to general usage
+    and behavior.
+
+    Parameters:
+        config ([`BertConfig`]): Model configuration class with all the parameters of the model.
+            Initializing with a config file does not load the weights associated with the model, only the
+            configuration. Check out the [`~PreTrainedModel.from_pretrained`] method to load the model weights.
+"""
+
+BERT_INPUTS_DOCSTRING = r"""
+    Args:
+        input_ids (`torch.LongTensor` of shape `({0})`):
+            Indices of input sequence tokens in the vocabulary.
+
+            Indices can be obtained using [`BertTokenizer`]. See [`PreTrainedTokenizer.encode`] and
+            [`PreTrainedTokenizer.__call__`] for details.
+
+            [What are input IDs?](../glossary#input-ids)
+        attention_mask (`torch.FloatTensor` of shape `({0})`, *optional*):
+            Mask to avoid performing attention on padding token indices. Mask values selected in `[0, 1]`:
+
+            - 1 for tokens that are **not masked**,
+            - 0 for tokens that are **masked**.
+
+            [What are attention masks?](../glossary#attention-mask)
+        token_type_ids (`torch.LongTensor` of shape `({0})`, *optional*):
+            Segment token indices to indicate first and second portions of the inputs. Indices are selected in `[0,
+            1]`:
+
+            - 0 corresponds to a *sentence A* token,
+            - 1 corresponds to a *sentence B* token.
+
+            [What are token type IDs?](../glossary#token-type-ids)
+        position_ids (`torch.LongTensor` of shape `({0})`, *optional*):
+            Indices of positions of each input sequence tokens in the position embeddings. Selected in the range `[0,
+            config.max_position_embeddings - 1]`.
+
+            [What are position IDs?](../glossary#position-ids)
+        head_mask (`torch.FloatTensor` of shape `(num_heads,)` or `(num_layers, num_heads)`, *optional*):
+            Mask to nullify selected heads of the self-attention modules. Mask values selected in `[0, 1]`:
+
+            - 1 indicates the head is **not masked**,
+            - 0 indicates the head is **masked**.
+
+        inputs_embeds (`torch.FloatTensor` of shape `({0}, hidden_size)`, *optional*):
+            Optionally, instead of passing `input_ids` you can choose to directly pass an embedded representation. This
+            is useful if you want more control over how to convert `input_ids` indices into associated vectors than the
+            model's internal embedding lookup matrix.
+        output_attentions (`bool`, *optional*):
+            Whether or not to return the attentions tensors of all attention layers. See `attentions` under returned
+            tensors for more detail.
+        output_hidden_states (`bool`, *optional*):
+            Whether or not to return the hidden states of all layers. See `hidden_states` under returned tensors for
+            more detail.
+        return_dict (`bool`, *optional*):
+            Whether or not to return a [`~file_utils.ModelOutput`] instead of a plain tuple.
+"""
+
+
+@add_start_docstrings(
+    "The bare Bert Model transformer outputting raw hidden-states without any specific head on top.",
+    BERT_START_DOCSTRING,
+)
+class BertModel(BertPreTrainedModel):
+    """
+
+    The model can behave as an encoder (with only self-attention) as well as a decoder, in which case a layer of
+    cross-attention is added between the self-attention layers, following the architecture described in [Attention is
+    all you need](https://arxiv.org/abs/1706.03762) by Ashish Vaswani, Noam Shazeer, Niki Parmar, Jakob Uszkoreit,
+    Llion Jones, Aidan N. Gomez, Lukasz Kaiser and Illia Polosukhin.
+
+    To behave as an decoder the model needs to be initialized with the `is_decoder` argument of the configuration set
+    to `True`. To be used in a Seq2Seq model, the model needs to initialized with both `is_decoder` argument and
+    `add_cross_attention` set to `True`; an `encoder_hidden_states` is then expected as an input to the forward pass.
+    """
+
+    def __init__(self, config, add_pooling_layer=True):
+        super().__init__(config)
+        self.config = config
+
+        if hasattr(config, 'sparse_attention'):
+            self.is_sparse = True
+            self.sparse_block_size = self.config.sparse_attention['block']
+        else:
+            self.is_sparse = False
+
+        if self.is_sparse and self.config.is_decoder:
+            raise RuntimeError('SparseAttention with BertModel decoder is not currently supported!')
+
+        self.embeddings = BertEmbeddings(config)
+        self.encoder = BertEncoder(config)
+
+        self.pooler = BertPooler(config) if add_pooling_layer else None
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    def get_input_embeddings(self):
+        return self.embeddings.word_embeddings
+
+    def set_input_embeddings(self, value):
+        self.embeddings.word_embeddings = value
+
+    def _prune_heads(self, heads_to_prune):
+        """
+        Prunes heads of the model. heads_to_prune: dict of {layer_num: list of heads to prune in this layer} See base
+        class PreTrainedModel
+        """
+        for layer, heads in heads_to_prune.items():
+            self.encoder.layer[layer].attention.prune_heads(heads)
+
+    @add_start_docstrings_to_model_forward(BERT_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
+    @add_code_sample_docstrings(
+        processor_class=_TOKENIZER_FOR_DOC,
+        checkpoint=_CHECKPOINT_FOR_DOC,
+        output_type=BaseModelOutputWithPoolingAndCrossAttentions,
+        config_class=_CONFIG_FOR_DOC,
+    )
+    def forward(
+        self,
+        input_ids=None,
+        attention_mask=None,
+        token_type_ids=None,
+        position_ids=None,
+        head_mask=None,
+        inputs_embeds=None,
+        encoder_hidden_states=None,
+        encoder_attention_mask=None,
+        past_key_values=None,
+        use_cache=None,
+        output_attentions=None,
+        output_hidden_states=None,
+        return_dict=None,
+    ):
+        r"""
+        encoder_hidden_states  (`torch.FloatTensor` of shape `(batch_size, sequence_length, hidden_size)`, *optional*):
+            Sequence of hidden-states at the output of the last layer of the encoder. Used in the cross-attention if
+            the model is configured as a decoder.
+        encoder_attention_mask (`torch.FloatTensor` of shape `(batch_size, sequence_length)`, *optional*):
+            Mask to avoid performing attention on the padding token indices of the encoder input. This mask is used in
+            the cross-attention if the model is configured as a decoder. Mask values selected in `[0, 1]`:
+
+            - 1 for tokens that are **not masked**,
+            - 0 for tokens that are **masked**.
+        past_key_values (`tuple(tuple(torch.FloatTensor))` of length `config.n_layers` with each tuple having 4 tensors of shape `(batch_size, num_heads, sequence_length - 1, embed_size_per_head)`):
+            Contains precomputed key and value hidden states of the attention blocks. Can be used to speed up decoding.
+
+            If `past_key_values` are used, the user can optionally input only the last `decoder_input_ids` (those that
+            don't have their past key value states given to this model) of shape `(batch_size, 1)` instead of all
+            `decoder_input_ids` of shape `(batch_size, sequence_length)`.
+        use_cache (`bool`, *optional*):
+            If set to `True`, `past_key_values` key value states are returned and can be used to speed up decoding (see
+            `past_key_values`).
+        """
+        output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
+        output_hidden_states = (
+            output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
+        )
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        if self.config.is_decoder:
+            use_cache = use_cache if use_cache is not None else self.config.use_cache
+        else:
+            use_cache = False
+
+        if input_ids is not None and inputs_embeds is not None:
+            raise ValueError("You cannot specify both input_ids and inputs_embeds at the same time")
+        elif input_ids is not None:
+            input_shape = input_ids.size()
+        elif inputs_embeds is not None:
+            input_shape = inputs_embeds.size()[:-1]
+        else:
+            raise ValueError("You have to specify either input_ids or inputs_embeds")
+
+        batch_size, seq_length = input_shape
+        device = input_ids.device if input_ids is not None else inputs_embeds.device
+
+        # if sparse attention is used, input sequence length should be divisible by block size
+        if self.is_sparse and seq_length % self.sparse_block_size != 0:
+            raise RuntimeError(f'BertModel with sparse attention is used, but seq_len = {seq_length} '
+                               f'is not divisible by block_size = {self.sparse_block_size}')
+
+        # past_key_values_length
+        past_key_values_length = past_key_values[0][0].shape[2] if past_key_values is not None else 0
+
+        if attention_mask is None:
+            attention_mask = torch.ones(((batch_size, seq_length + past_key_values_length)), device=device)
+
+        if token_type_ids is None:
+            if hasattr(self.embeddings, "token_type_ids"):
+                buffered_token_type_ids = self.embeddings.token_type_ids[:, :seq_length]
+                buffered_token_type_ids_expanded = buffered_token_type_ids.expand(batch_size, seq_length)
+                token_type_ids = buffered_token_type_ids_expanded
+            else:
+                token_type_ids = torch.zeros(input_shape, dtype=torch.long, device=device)
+
+        # We can provide a self-attention mask of dimensions [batch_size, from_seq_length, to_seq_length]
+        # ourselves in which case we just need to make it broadcastable to all heads.
+        extended_attention_mask: torch.Tensor = self.get_extended_attention_mask(attention_mask, input_shape, device)
+
+        # If a 2D or 3D attention mask is provided for the cross-attention
+        # we need to make broadcastable to [batch_size, num_heads, seq_length, seq_length]
+        if self.config.is_decoder and encoder_hidden_states is not None:
+            encoder_batch_size, encoder_sequence_length, _ = encoder_hidden_states.size()
+            encoder_hidden_shape = (encoder_batch_size, encoder_sequence_length)
+            if encoder_attention_mask is None:
+                encoder_attention_mask = torch.ones(encoder_hidden_shape, device=device)
+            encoder_extended_attention_mask = self.invert_attention_mask(encoder_attention_mask)
+        else:
+            encoder_extended_attention_mask = None
+
+        # Prepare head mask if needed
+        # 1.0 in head_mask indicate we keep the head
+        # attention_probs has shape bsz x n_heads x N x N
+        # input head_mask has shape [num_heads] or [num_hidden_layers x num_heads]
+        # and head_mask is converted to shape [num_hidden_layers x batch x num_heads x seq_length x seq_length]
+        head_mask = self.get_head_mask(head_mask, self.config.num_hidden_layers)
+
+        embedding_output = self.embeddings(
+            input_ids=input_ids,
+            position_ids=position_ids,
+            token_type_ids=token_type_ids,
+            inputs_embeds=inputs_embeds,
+            past_key_values_length=past_key_values_length,
+        )
+        encoder_outputs = self.encoder(
+            embedding_output,
+            attention_mask=extended_attention_mask,
+            head_mask=head_mask,
+            encoder_hidden_states=encoder_hidden_states,
+            encoder_attention_mask=encoder_extended_attention_mask,
+            past_key_values=past_key_values,
+            use_cache=use_cache,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+        sequence_output = encoder_outputs[0]
+        pooled_output = self.pooler(sequence_output) if self.pooler is not None else None
+
+        if not return_dict:
+            return (sequence_output, pooled_output) + encoder_outputs[1:]
+
+        return BaseModelOutputWithPoolingAndCrossAttentions(
+            last_hidden_state=sequence_output,
+            pooler_output=pooled_output,
+            past_key_values=encoder_outputs.past_key_values,
+            hidden_states=encoder_outputs.hidden_states,
+            attentions=encoder_outputs.attentions,
+            cross_attentions=encoder_outputs.cross_attentions,
+        )
+
+
+@add_start_docstrings(
+    """
+    Bert Model with two heads on top as done during the pretraining: a `masked language modeling` head and a `next
+    sentence prediction (classification)` head.
+    """,
+    BERT_START_DOCSTRING,
+)
+class BertForPreTraining(BertPreTrainedModel):
+    def __init__(self, config):
+        super().__init__(config)
+
+        self.bert = BertModel(config)
+        self.cls = BertPreTrainingHeads(config)
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    def get_output_embeddings(self):
+        return self.cls.predictions.decoder
+
+    def set_output_embeddings(self, new_embeddings):
+        self.cls.predictions.decoder = new_embeddings
+
+    @add_start_docstrings_to_model_forward(BERT_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
+    @replace_return_docstrings(output_type=BertForPreTrainingOutput, config_class=_CONFIG_FOR_DOC)
+    def forward(
+        self,
+        input_ids=None,
+        attention_mask=None,
+        token_type_ids=None,
+        position_ids=None,
+        head_mask=None,
+        inputs_embeds=None,
+        labels=None,
+        next_sentence_label=None,
+        output_attentions=None,
+        output_hidden_states=None,
+        return_dict=None,
+    ):
+        r"""
+            labels (`torch.LongTensor` of shape `(batch_size, sequence_length)`, *optional*):
+                Labels for computing the masked language modeling loss. Indices should be in `[-100, 0, ...,
+                config.vocab_size]` (see `input_ids` docstring) Tokens with indices set to `-100` are ignored (masked),
+                the loss is only computed for the tokens with labels in `[0, ..., config.vocab_size]`
+            next_sentence_label (`torch.LongTensor` of shape `(batch_size,)`, *optional*):
+                Labels for computing the next sequence prediction (classification) loss. Input should be a sequence
+                pair (see `input_ids` docstring) Indices should be in `[0, 1]`:
+
+                - 0 indicates sequence B is a continuation of sequence A,
+                - 1 indicates sequence B is a random sequence.
+            kwargs (`Dict[str, any]`, optional, defaults to *{}*):
+                Used to hide legacy arguments that have been deprecated.
+
+        Returns:
+
+        Example:
+
+        ```python
+        >>> from transformers import BertTokenizer, BertForPreTraining
+        >>> import torch
+
+        >>> tokenizer = BertTokenizer.from_pretrained("bert-base-uncased")
+        >>> model = BertForPreTraining.from_pretrained("bert-base-uncased")
+
+        >>> inputs = tokenizer("Hello, my dog is cute", return_tensors="pt")
+        >>> outputs = model(**inputs)
+
+        >>> prediction_logits = outputs.prediction_logits
+        >>> seq_relationship_logits = outputs.seq_relationship_logits
+        ```
+        """
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        outputs = self.bert(
+            input_ids,
+            attention_mask=attention_mask,
+            token_type_ids=token_type_ids,
+            position_ids=position_ids,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        sequence_output, pooled_output = outputs[:2]
+        prediction_scores, seq_relationship_score = self.cls(sequence_output, pooled_output)
+
+        total_loss = None
+        masked_lm_loss = None
+        next_sentence_loss = None
+        if labels is not None and next_sentence_label is not None:
+            loss_fct = CrossEntropyLoss()
+            masked_lm_loss = loss_fct(prediction_scores.view(-1, self.config.vocab_size), labels.view(-1))
+            next_sentence_loss = loss_fct(seq_relationship_score.view(-1, 2), next_sentence_label.view(-1))
+            total_loss = masked_lm_loss + next_sentence_loss
+
+        if not return_dict:
+            output = (prediction_scores, seq_relationship_score) + outputs[2:]
+            return ((total_loss,) + output) if total_loss is not None else output
+
+        return BertForPreTrainingOutput(
+            loss=total_loss,
+            mlm_loss=masked_lm_loss,
+            nsp_loss=next_sentence_loss,
+            prediction_logits=prediction_scores,
+            seq_relationship_logits=seq_relationship_score,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )
+
+
+@add_start_docstrings(
+    """Bert Model with a `language modeling` head on top for CLM fine-tuning.""", BERT_START_DOCSTRING
+)
+class BertLMHeadModel(BertPreTrainedModel):
+
+    _keys_to_ignore_on_load_unexpected = [r"pooler"]
+    _keys_to_ignore_on_load_missing = [r"position_ids", r"predictions.decoder.bias"]
+
+    def __init__(self, config):
+        super().__init__(config)
+
+        if not config.is_decoder:
+            logger.warning("If you want to use `BertLMHeadModel` as a standalone, add `is_decoder=True.`")
+
+        self.bert = BertModel(config, add_pooling_layer=False)
+        self.cls = BertOnlyMLMHead(config)
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    def get_output_embeddings(self):
+        return self.cls.predictions.decoder
+
+    def set_output_embeddings(self, new_embeddings):
+        self.cls.predictions.decoder = new_embeddings
+
+    @add_start_docstrings_to_model_forward(BERT_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
+    @replace_return_docstrings(output_type=CausalLMOutputWithCrossAttentions, config_class=_CONFIG_FOR_DOC)
+    def forward(
+        self,
+        input_ids=None,
+        attention_mask=None,
+        token_type_ids=None,
+        position_ids=None,
+        head_mask=None,
+        inputs_embeds=None,
+        encoder_hidden_states=None,
+        encoder_attention_mask=None,
+        labels=None,
+        past_key_values=None,
+        use_cache=None,
+        output_attentions=None,
+        output_hidden_states=None,
+        return_dict=None,
+    ):
+        r"""
+            encoder_hidden_states  (`torch.FloatTensor` of shape `(batch_size, sequence_length, hidden_size)`, *optional*):
+                Sequence of hidden-states at the output of the last layer of the encoder. Used in the cross-attention
+                if the model is configured as a decoder.
+            encoder_attention_mask (`torch.FloatTensor` of shape `(batch_size, sequence_length)`, *optional*):
+                Mask to avoid performing attention on the padding token indices of the encoder input. This mask is used
+                in the cross-attention if the model is configured as a decoder. Mask values selected in `[0, 1]`:
+
+                - 1 for tokens that are **not masked**,
+                - 0 for tokens that are **masked**.
+            labels (`torch.LongTensor` of shape `(batch_size, sequence_length)`, *optional*):
+                Labels for computing the left-to-right language modeling loss (next word prediction). Indices should be
+                in `[-100, 0, ..., config.vocab_size]` (see `input_ids` docstring) Tokens with indices set to `-100`
+                are ignored (masked), the loss is only computed for the tokens with labels n `[0, ...,
+                config.vocab_size]`
+            past_key_values (`tuple(tuple(torch.FloatTensor))` of length `config.n_layers` with each tuple having 4 tensors of shape `(batch_size, num_heads, sequence_length - 1, embed_size_per_head)`):
+                Contains precomputed key and value hidden states of the attention blocks. Can be used to speed up
+                decoding.
+
+                If `past_key_values` are used, the user can optionally input only the last `decoder_input_ids` (those
+                that don't have their past key value states given to this model) of shape `(batch_size, 1)` instead of
+                all `decoder_input_ids` of shape `(batch_size, sequence_length)`.
+            use_cache (`bool`, *optional*):
+                If set to `True`, `past_key_values` key value states are returned and can be used to speed up decoding
+                (see `past_key_values`).
+
+        Returns:
+
+        Example:
+
+        ```python
+        >>> from transformers import BertTokenizer, BertLMHeadModel, BertConfig
+        >>> import torch
+
+        >>> tokenizer = BertTokenizer.from_pretrained("bert-base-cased")
+        >>> config = BertConfig.from_pretrained("bert-base-cased")
+        >>> config.is_decoder = True
+        >>> model = BertLMHeadModel.from_pretrained("bert-base-cased", config=config)
+
+        >>> inputs = tokenizer("Hello, my dog is cute", return_tensors="pt")
+        >>> outputs = model(**inputs)
+
+        >>> prediction_logits = outputs.logits
+        ```
+        """
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+        if labels is not None:
+            use_cache = False
+
+        outputs = self.bert(
+            input_ids,
+            attention_mask=attention_mask,
+            token_type_ids=token_type_ids,
+            position_ids=position_ids,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            encoder_hidden_states=encoder_hidden_states,
+            encoder_attention_mask=encoder_attention_mask,
+            past_key_values=past_key_values,
+            use_cache=use_cache,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        sequence_output = outputs[0]
+        prediction_scores = self.cls(sequence_output)
+
+        lm_loss = None
+        if labels is not None:
+            # we are doing next-token prediction; shift prediction scores and input ids by one
+            shifted_prediction_scores = prediction_scores[:, :-1, :].contiguous()
+            labels = labels[:, 1:].contiguous()
+            loss_fct = CrossEntropyLoss()
+            lm_loss = loss_fct(shifted_prediction_scores.view(-1, self.config.vocab_size), labels.view(-1))
+
+        if not return_dict:
+            output = (prediction_scores,) + outputs[2:]
+            return ((lm_loss,) + output) if lm_loss is not None else output
+
+        return CausalLMOutputWithCrossAttentions(
+            loss=lm_loss,
+            logits=prediction_scores,
+            past_key_values=outputs.past_key_values,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+            cross_attentions=outputs.cross_attentions,
+        )
+
+    def prepare_inputs_for_generation(self, input_ids, past=None, attention_mask=None, **model_kwargs):
+        input_shape = input_ids.shape
+        # if model is used as a decoder in encoder-decoder model, the decoder attention mask is created on the fly
+        if attention_mask is None:
+            attention_mask = input_ids.new_ones(input_shape)
+
+        # cut decoder_input_ids if past is used
+        if past is not None:
+            input_ids = input_ids[:, -1:]
+
+        return {"input_ids": input_ids, "attention_mask": attention_mask, "past_key_values": past}
+
+    def _reorder_cache(self, past, beam_idx):
+        reordered_past = ()
+        for layer_past in past:
+            reordered_past += (tuple(past_state.index_select(0, beam_idx) for past_state in layer_past),)
+        return reordered_past
+
+
+@add_start_docstrings("""Bert Model with a `language modeling` head on top.""", BERT_START_DOCSTRING)
+class BertForMaskedLM(BertPreTrainedModel):
+
+    _keys_to_ignore_on_load_unexpected = [r"pooler"]
+    _keys_to_ignore_on_load_missing = [r"position_ids", r"predictions.decoder.bias"]
+
+    def __init__(self, config):
+        super().__init__(config)
+
+        if config.is_decoder:
+            logger.warning(
+                "If you want to use `BertForMaskedLM` make sure `config.is_decoder=False` for "
+                "bi-directional self-attention."
+            )
+
+        self.bert = BertModel(config, add_pooling_layer=False)
+        self.cls = BertOnlyMLMHead(config)
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    def get_output_embeddings(self):
+        return self.cls.predictions.decoder
+
+    def set_output_embeddings(self, new_embeddings):
+        self.cls.predictions.decoder = new_embeddings
+
+    @add_start_docstrings_to_model_forward(BERT_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
+    @add_code_sample_docstrings(
+        processor_class=_TOKENIZER_FOR_DOC,
+        checkpoint=_CHECKPOINT_FOR_DOC,
+        output_type=MaskedLMOutput,
+        config_class=_CONFIG_FOR_DOC,
+    )
+    def forward(
+        self,
+        input_ids=None,
+        attention_mask=None,
+        token_type_ids=None,
+        position_ids=None,
+        head_mask=None,
+        inputs_embeds=None,
+        encoder_hidden_states=None,
+        encoder_attention_mask=None,
+        labels=None,
+        output_attentions=None,
+        output_hidden_states=None,
+        return_dict=None,
+    ):
+        r"""
+        labels (`torch.LongTensor` of shape `(batch_size, sequence_length)`, *optional*):
+            Labels for computing the masked language modeling loss. Indices should be in `[-100, 0, ...,
+            config.vocab_size]` (see `input_ids` docstring) Tokens with indices set to `-100` are ignored (masked), the
+            loss is only computed for the tokens with labels in `[0, ..., config.vocab_size]`
+        """
+
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        outputs = self.bert(
+            input_ids,
+            attention_mask=attention_mask,
+            token_type_ids=token_type_ids,
+            position_ids=position_ids,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            encoder_hidden_states=encoder_hidden_states,
+            encoder_attention_mask=encoder_attention_mask,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        sequence_output = outputs[0]
+        prediction_scores = self.cls(sequence_output)
+
+        masked_lm_loss = None
+        if labels is not None:
+            loss_fct = CrossEntropyLoss()  # -100 index = padding token
+            masked_lm_loss = loss_fct(prediction_scores.view(-1, self.config.vocab_size), labels.view(-1))
+
+        if not return_dict:
+            output = (prediction_scores,) + outputs[2:]
+            return ((masked_lm_loss,) + output) if masked_lm_loss is not None else output
+
+        return MaskedLMOutput(
+            loss=masked_lm_loss,
+            logits=prediction_scores,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )
+
+    def prepare_inputs_for_generation(self, input_ids, attention_mask=None, **model_kwargs):
+        input_shape = input_ids.shape
+        effective_batch_size = input_shape[0]
+
+        #  add a dummy token
+        if self.config.pad_token_id is None:
+            raise ValueError("The PAD token should be defined for generation")
+
+        attention_mask = torch.cat([attention_mask, attention_mask.new_zeros((attention_mask.shape[0], 1))], dim=-1)
+        dummy_token = torch.full(
+            (effective_batch_size, 1), self.config.pad_token_id, dtype=torch.long, device=input_ids.device
+        )
+        input_ids = torch.cat([input_ids, dummy_token], dim=1)
+
+        return {"input_ids": input_ids, "attention_mask": attention_mask}
+
+
+@add_start_docstrings(
+    """Bert Model with a `next sentence prediction (classification)` head on top.""",
+    BERT_START_DOCSTRING,
+)
+class BertForNextSentencePrediction(BertPreTrainedModel):
+    def __init__(self, config):
+        super().__init__(config)
+
+        self.bert = BertModel(config)
+        self.cls = BertOnlyNSPHead(config)
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    @add_start_docstrings_to_model_forward(BERT_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
+    @replace_return_docstrings(output_type=NextSentencePredictorOutput, config_class=_CONFIG_FOR_DOC)
+    def forward(
+        self,
+        input_ids=None,
+        attention_mask=None,
+        token_type_ids=None,
+        position_ids=None,
+        head_mask=None,
+        inputs_embeds=None,
+        labels=None,
+        output_attentions=None,
+        output_hidden_states=None,
+        return_dict=None,
+        **kwargs,
+    ):
+        r"""
+        labels (`torch.LongTensor` of shape `(batch_size,)`, *optional*):
+            Labels for computing the next sequence prediction (classification) loss. Input should be a sequence pair
+            (see `input_ids` docstring). Indices should be in `[0, 1]`:
+
+            - 0 indicates sequence B is a continuation of sequence A,
+            - 1 indicates sequence B is a random sequence.
+
+        Returns:
+
+        Example:
+
+        ```python
+        >>> from transformers import BertTokenizer, BertForNextSentencePrediction
+        >>> import torch
+
+        >>> tokenizer = BertTokenizer.from_pretrained("bert-base-uncased")
+        >>> model = BertForNextSentencePrediction.from_pretrained("bert-base-uncased")
+
+        >>> prompt = "In Italy, pizza served in formal settings, such as at a restaurant, is presented unsliced."
+        >>> next_sentence = "The sky is blue due to the shorter wavelength of blue light."
+        >>> encoding = tokenizer(prompt, next_sentence, return_tensors="pt")
+
+        >>> outputs = model(**encoding, labels=torch.LongTensor([1]))
+        >>> logits = outputs.logits
+        >>> assert logits[0, 0] < logits[0, 1]  # next sentence was random
+        ```
+        """
+
+        if "next_sentence_label" in kwargs:
+            warnings.warn(
+                "The `next_sentence_label` argument is deprecated and will be removed in a future version, use `labels` instead.",
+                FutureWarning,
+            )
+            labels = kwargs.pop("next_sentence_label")
+
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        outputs = self.bert(
+            input_ids,
+            attention_mask=attention_mask,
+            token_type_ids=token_type_ids,
+            position_ids=position_ids,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        pooled_output = outputs[1]
+
+        seq_relationship_scores = self.cls(pooled_output)
+
+        next_sentence_loss = None
+        if labels is not None:
+            loss_fct = CrossEntropyLoss()
+            next_sentence_loss = loss_fct(seq_relationship_scores.view(-1, 2), labels.view(-1))
+
+        if not return_dict:
+            output = (seq_relationship_scores,) + outputs[2:]
+            return ((next_sentence_loss,) + output) if next_sentence_loss is not None else output
+
+        return NextSentencePredictorOutput(
+            loss=next_sentence_loss,
+            logits=seq_relationship_scores,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )
+
+
+@add_start_docstrings(
+    """
+    Bert Model transformer with a sequence classification/regression head on top (a linear layer on top of the pooled
+    output) e.g. for GLUE tasks.
+    """,
+    BERT_START_DOCSTRING,
+)
+class BertForSequenceClassification(BertPreTrainedModel):
+    def __init__(self, config):
+        super().__init__(config)
+        self.num_labels = config.num_labels
+        self.config = config
+
+        self.bert = BertModel(config)
+        classifier_dropout = (
+            config.classifier_dropout if config.classifier_dropout is not None else config.hidden_dropout_prob
+        )
+        self.dropout = nn.Dropout(classifier_dropout)
+        self.classifier = nn.Linear(config.hidden_size, config.num_labels)
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    @add_start_docstrings_to_model_forward(BERT_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
+    @add_code_sample_docstrings(
+        processor_class=_TOKENIZER_FOR_DOC,
+        checkpoint=_CHECKPOINT_FOR_DOC,
+        output_type=SequenceClassifierOutput,
+        config_class=_CONFIG_FOR_DOC,
+    )
+    def forward(
+        self,
+        input_ids=None,
+        attention_mask=None,
+        token_type_ids=None,
+        position_ids=None,
+        head_mask=None,
+        inputs_embeds=None,
+        labels=None,
+        pos_weight=None,
+        output_attentions=None,
+        output_hidden_states=None,
+        return_dict=None,
+    ):
+        r"""
+        labels (`torch.LongTensor` of shape `(batch_size,)`, *optional*):
+            Labels for computing the sequence classification/regression loss. Indices should be in `[0, ...,
+            config.num_labels - 1]`. If `config.num_labels == 1` a regression loss is computed (Mean-Square loss), If
+            `config.num_labels > 1` a classification loss is computed (Cross-Entropy).
+        """
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        outputs = self.bert(
+            input_ids,
+            attention_mask=attention_mask,
+            token_type_ids=token_type_ids,
+            position_ids=position_ids,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        pooled_output = outputs[1]
+
+        pooled_output = self.dropout(pooled_output)
+        logits = self.classifier(pooled_output)
+
+        loss = None
+        if labels is not None:
+            if self.config.problem_type is None:
+                if self.num_labels == 1:
+                    self.config.problem_type = "regression"
+                elif self.num_labels > 1 and (labels.dtype == torch.long or labels.dtype == torch.int):
+                    self.config.problem_type = "single_label_classification"
+                else:
+                    self.config.problem_type = "multi_label_classification"
+
+            if self.config.problem_type == "regression":
+                loss_fct = MSELoss()
+                if self.num_labels == 1:
+                    loss = loss_fct(logits.squeeze(), labels.squeeze())
+                else:
+                    loss = loss_fct(logits, labels)
+            elif self.config.problem_type == "single_label_classification":
+                loss_fct = CrossEntropyLoss()
+                loss = loss_fct(logits.view(-1, self.num_labels), labels.view(-1))
+            elif self.config.problem_type == "multi_label_classification":
+                loss_fct = BCEWithLogitsLoss(pos_weight=pos_weight)
+                loss = loss_fct(logits, labels)
+        if not return_dict:
+            output = (logits,) + outputs[2:]
+            return ((loss,) + output) if loss is not None else output
+
+        return SequenceClassifierOutput(
+            loss=loss,
+            logits=logits,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )
+
+
+@add_start_docstrings(
+    """
+    Bert Model with a multiple choice classification head on top (a linear layer on top of the pooled output and a
+    softmax) e.g. for RocStories/SWAG tasks.
+    """,
+    BERT_START_DOCSTRING,
+)
+class BertForMultipleChoice(BertPreTrainedModel):
+    def __init__(self, config):
+        super().__init__(config)
+
+        self.bert = BertModel(config)
+        classifier_dropout = (
+            config.classifier_dropout if config.classifier_dropout is not None else config.hidden_dropout_prob
+        )
+        self.dropout = nn.Dropout(classifier_dropout)
+        self.classifier = nn.Linear(config.hidden_size, 1)
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    @add_start_docstrings_to_model_forward(BERT_INPUTS_DOCSTRING.format("batch_size, num_choices, sequence_length"))
+    @add_code_sample_docstrings(
+        processor_class=_TOKENIZER_FOR_DOC,
+        checkpoint=_CHECKPOINT_FOR_DOC,
+        output_type=MultipleChoiceModelOutput,
+        config_class=_CONFIG_FOR_DOC,
+    )
+    def forward(
+        self,
+        input_ids=None,
+        attention_mask=None,
+        token_type_ids=None,
+        position_ids=None,
+        head_mask=None,
+        inputs_embeds=None,
+        labels=None,
+        output_attentions=None,
+        output_hidden_states=None,
+        return_dict=None,
+    ):
+        r"""
+        labels (`torch.LongTensor` of shape `(batch_size,)`, *optional*):
+            Labels for computing the multiple choice classification loss. Indices should be in `[0, ...,
+            num_choices-1]` where `num_choices` is the size of the second dimension of the input tensors. (See
+            `input_ids` above)
+        """
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+        num_choices = input_ids.shape[1] if input_ids is not None else inputs_embeds.shape[1]
+
+        input_ids = input_ids.view(-1, input_ids.size(-1)) if input_ids is not None else None
+        attention_mask = attention_mask.view(-1, attention_mask.size(-1)) if attention_mask is not None else None
+        token_type_ids = token_type_ids.view(-1, token_type_ids.size(-1)) if token_type_ids is not None else None
+        position_ids = position_ids.view(-1, position_ids.size(-1)) if position_ids is not None else None
+        inputs_embeds = (
+            inputs_embeds.view(-1, inputs_embeds.size(-2), inputs_embeds.size(-1))
+            if inputs_embeds is not None
+            else None
+        )
+
+        outputs = self.bert(
+            input_ids,
+            attention_mask=attention_mask,
+            token_type_ids=token_type_ids,
+            position_ids=position_ids,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        pooled_output = outputs[1]
+
+        pooled_output = self.dropout(pooled_output)
+        logits = self.classifier(pooled_output)
+        reshaped_logits = logits.view(-1, num_choices)
+
+        loss = None
+        if labels is not None:
+            loss_fct = CrossEntropyLoss()
+            loss = loss_fct(reshaped_logits, labels)
+
+        if not return_dict:
+            output = (reshaped_logits,) + outputs[2:]
+            return ((loss,) + output) if loss is not None else output
+
+        return MultipleChoiceModelOutput(
+            loss=loss,
+            logits=reshaped_logits,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )
+
+
+@add_start_docstrings(
+    """
+    Bert Model with a token classification head on top (a linear layer on top of the hidden-states output) e.g. for
+    Named-Entity-Recognition (NER) tasks.
+    """,
+    BERT_START_DOCSTRING,
+)
+class BertForTokenClassification(BertPreTrainedModel):
+
+    _keys_to_ignore_on_load_unexpected = [r"pooler"]
+
+    def __init__(self, config):
+        super().__init__(config)
+        self.num_labels = config.num_labels
+        self.config = config
+        if getattr(self.config, 'problem_type', None) is None:
+            self.config.problem_type = 'single_label_classification'
+
+        self.bert = BertModel(config, add_pooling_layer=False)
+        classifier_dropout = (
+            config.classifier_dropout if config.classifier_dropout is not None else config.hidden_dropout_prob
+        )
+        self.dropout = nn.Dropout(classifier_dropout)
+        self.classifier = nn.Linear(config.hidden_size, config.num_labels)
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    @add_start_docstrings_to_model_forward(BERT_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
+    @add_code_sample_docstrings(
+        processor_class=_TOKENIZER_FOR_DOC,
+        checkpoint=_CHECKPOINT_FOR_DOC,
+        output_type=TokenClassifierOutput,
+        config_class=_CONFIG_FOR_DOC,
+    )
+    def forward(
+        self,
+        input_ids=None,
+        attention_mask=None,
+        token_type_ids=None,
+        position_ids=None,
+        head_mask=None,
+        inputs_embeds=None,
+        labels=None,
+        labels_mask=None,
+        pos_weight=None,
+        output_attentions=None,
+        output_hidden_states=None,
+        return_dict=None,
+    ):
+        r"""
+        labels (`torch.LongTensor` of shape `(batch_size, sequence_length)`, *optional*):
+            Labels for computing the token classification loss. Indices should be in `[0, ..., config.num_labels - 1]`.
+        """
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        outputs = self.bert(
+            input_ids,
+            attention_mask=attention_mask,
+            token_type_ids=token_type_ids,
+            position_ids=position_ids,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        sequence_output = outputs[0]
+
+        sequence_output = self.dropout(sequence_output)
+        logits = self.classifier(sequence_output)
+
+        loss = None
+        if labels is not None:
+            if self.config.problem_type == 'single_label_classification':
+                loss_fct = CrossEntropyLoss()
+                loss = loss_fct(logits.view(-1, self.num_labels), labels.view(-1))
+            elif self.config.problem_type == 'multi_label_classification':
+                if labels_mask is None:
+                    loss_fct = BCEWithLogitsLoss(pos_weight=pos_weight)
+                    loss = loss_fct(logits, labels)
+                else:
+                    loss_fct = BCEWithLogitsLoss(reduction='none', pos_weight=pos_weight)
+                    loss = loss_fct(logits, labels)
+                    loss = loss * labels_mask.unsqueeze(-1)
+                    loss = loss.sum() / labels_mask.sum() if labels_mask.sum() != 0.0 else torch.tensor(0.0, device=logits.device)
+
+        if not return_dict:
+            output = (logits,) + outputs[2:]
+            return ((loss,) + output) if loss is not None else output
+
+        return TokenClassifierOutput(
+            loss=loss,
+            logits=logits,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )
+
+
+@add_start_docstrings(
+    """
+    Bert Model with a span classification head on top for extractive question-answering tasks like SQuAD (a linear
+    layers on top of the hidden-states output to compute `span start logits` and `span end logits`).
+    """,
+    BERT_START_DOCSTRING,
+)
+class BertForQuestionAnswering(BertPreTrainedModel):
+
+    _keys_to_ignore_on_load_unexpected = [r"pooler"]
+
+    def __init__(self, config):
+        super().__init__(config)
+        self.num_labels = config.num_labels
+
+        self.bert = BertModel(config, add_pooling_layer=False)
+        self.qa_outputs = nn.Linear(config.hidden_size, config.num_labels)
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    @add_start_docstrings_to_model_forward(BERT_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
+    @add_code_sample_docstrings(
+        processor_class=_TOKENIZER_FOR_DOC,
+        checkpoint=_CHECKPOINT_FOR_DOC,
+        output_type=QuestionAnsweringModelOutput,
+        config_class=_CONFIG_FOR_DOC,
+    )
+    def forward(
+        self,
+        input_ids=None,
+        attention_mask=None,
+        token_type_ids=None,
+        position_ids=None,
+        head_mask=None,
+        inputs_embeds=None,
+        start_positions=None,
+        end_positions=None,
+        output_attentions=None,
+        output_hidden_states=None,
+        return_dict=None,
+    ):
+        r"""
+        start_positions (`torch.LongTensor` of shape `(batch_size,)`, *optional*):
+            Labels for position (index) of the start of the labelled span for computing the token classification loss.
+            Positions are clamped to the length of the sequence (`sequence_length`). Position outside of the sequence
+            are not taken into account for computing the loss.
+        end_positions (`torch.LongTensor` of shape `(batch_size,)`, *optional*):
+            Labels for position (index) of the end of the labelled span for computing the token classification loss.
+            Positions are clamped to the length of the sequence (`sequence_length`). Position outside of the sequence
+            are not taken into account for computing the loss.
+        """
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        outputs = self.bert(
+            input_ids,
+            attention_mask=attention_mask,
+            token_type_ids=token_type_ids,
+            position_ids=position_ids,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        sequence_output = outputs[0]
+
+        logits = self.qa_outputs(sequence_output)
+        start_logits, end_logits = logits.split(1, dim=-1)
+        start_logits = start_logits.squeeze(-1).contiguous()
+        end_logits = end_logits.squeeze(-1).contiguous()
+
+        total_loss = None
+        if start_positions is not None and end_positions is not None:
+            # If we are on multi-GPU, split add a dimension
+            if len(start_positions.size()) > 1:
+                start_positions = start_positions.squeeze(-1)
+            if len(end_positions.size()) > 1:
+                end_positions = end_positions.squeeze(-1)
+            # sometimes the start/end positions are outside our model inputs, we ignore these terms
+            ignored_index = start_logits.size(1)
+            start_positions = start_positions.clamp(0, ignored_index)
+            end_positions = end_positions.clamp(0, ignored_index)
+
+            loss_fct = CrossEntropyLoss(ignore_index=ignored_index)
+            start_loss = loss_fct(start_logits, start_positions)
+            end_loss = loss_fct(end_logits, end_positions)
+            total_loss = (start_loss + end_loss) / 2
+
+        if not return_dict:
+            output = (start_logits, end_logits) + outputs[2:]
+            return ((total_loss,) + output) if total_loss is not None else output
+
+        return QuestionAnsweringModelOutput(
+            loss=total_loss,
+            start_logits=start_logits,
+            end_logits=end_logits,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )
+
+
+# todo: move to separate file with other position embeddings?
+# https://github.com/EleutherAI/gpt-neox/blob/8229d921d329266323706c01dd6778fa71649ac7/megatron/model/positional_embeddings.py#L24
+# https://blog.eleuther.ai/rotary-embeddings/
+class RotaryEmbedding(torch.nn.Module):
+    def __init__(self, dim, base=10000):
+        super().__init__()
+        inv_freq = 1.0 / (base ** (torch.arange(0, dim, 2).float() / dim))
+        self.register_buffer("inv_freq", inv_freq)
+        self.seq_len_cached = None
+        self.cos_cached = None
+        self.sin_cached = None
+
+    def forward(self, x, seq_dim=1, seq_len=None):
+        if seq_len is None:
+            seq_len = x.shape[seq_dim]
+        if seq_len != self.seq_len_cached:
+            self.seq_len_cached = seq_len
+            t = torch.arange(seq_len, device=x.device).type_as(self.inv_freq)
+            freqs = torch.einsum("i,j->ij", t, self.inv_freq)
+            emb = torch.cat((freqs, freqs), dim=-1).to(x.device)
+            self.cos_cached = emb.cos()[None, None, :, :]
+            self.sin_cached = emb.sin()[None, None, :, :]
+        return self.cos_cached, self.sin_cached
+
+
+def rotate_half(x):
+    x1, x2 = x[..., : x.shape[-1] // 2], x[..., x.shape[-1] // 2:]
+    return torch.cat((-x2, x1), dim=x1.ndim - 1)  # dim=-1 triggers a bug in earlier torch versions
+
+
+def apply_rotary_pos_emb(q, k, cos, sin, offset: int = 0):
+    cos, sin = cos[:, :, offset: q.shape[2] + offset, :], sin[:, :, offset: q.shape[2] + offset, :]
+    return (q * cos) + (rotate_half(q) * sin), (k * cos) + (rotate_half(k) * sin)

pytorch_model.bin

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:5effd8cb1c74689c397221cb81a5c2026dd3a9ac6d2037fcab0774812cc8af66
+size 541130889

special_tokens_map.json

@@ -0,0 +1 @@
+{"unk_token": "[UNK]", "sep_token": "[SEP]", "pad_token": "[PAD]", "cls_token": "[CLS]", "mask_token": "[MASK]"}

tokenizer_config.json

@@ -0,0 +1 @@
+{"tokenizer_class": "PreTrainedTokenizerFast"}