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README.md

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----
-license: mit
----
+---
+license: mit
+tags:
+- biology
+- transformers
+- Feature Extraction
+- bioRxiv 2025.01.23.634452
+---
+
+**This is repository for MutBERT (pretrained with mutation data in human genome)**.
+
+**You can find all MutBERT variants at [here](https://huggingface.co/JadenLong).**
+
+## Introduction
+
+This is the official pre-trained model introduced in MutBERT: Probabilistic Genome Representation Improves Genomics Foundation Models.
+
+We sincerely appreciate the Tochka-Al team for the ruRoPEBert implementation, which serves as the base of MutBERT development.
+
+MutBERT is a transformer-based genome foundation model trained only on Human genome.
+
+## Model Source
+
+- Repository: [MutBERT](https://github.com/ai4nucleome/mutBERT)
+- Paper: [MutBERT: Probabilistic Genome Representation Improves Genomics Foundation Models](https://www.biorxiv.org/content/10.1101/2025.01.23.634452v1)
+
+## Usage
+
+### Load tokenizer and model
+
+```python
+from transformers import AutoTokenizer, AutoModel
+
+model_name = "JadenLong/MutBERT"
+# Optional: JadenLong/MutBERT-Huamn-Ref, JadenLong/MutBERT-Multi
+tokenizer = AutoTokenizer.from_pretrained(model_name)
+model = AutoModel.from_pretrained(model_name, trust_remote_code=True)
+```
+
+The default attention is flash attention("sdpa"). If you want use basic attention, you can replace it with "eager". Please refer to [here](https://huggingface.co/JadenLong/MutBERT/blob/main/modeling_mutbert.py#L438).
+
+### Get embeddings
+
+```python
+import torch
+import torch.nn.functional as F
+
+from transformers import AutoTokenizer, AutoModel
+
+model_name = "JadenLong/MutBERT"
+# Optional: JadenLong/MutBERT-Huamn-Ref, JadenLong/MutBERT-Multi
+tokenizer = AutoTokenizer.from_pretrained(model_name)
+model = AutoModel.from_pretrained(model_name, trust_remote_code=True)
+
+dna = "ATCGGGGCCCATTA"
+inputs = tokenizer(dna, return_tensors='pt')["input_ids"]
+
+mut_inputs = F.one_hot(inputs, num_classes=len(tokenizer)).float().to("cpu")  # len(tokenizer) is vocab size
+last_hidden_state = model(mut_inputs).last_hidden_state   # [1, sequence_length, 768]
+# or: last_hidden_state = model(mut_inputs)[0]        # [1, sequence_length, 768]
+
+# embedding with mean pooling
+embedding_mean = torch.mean(last_hidden_state[0], dim=0)
+print(embedding_mean.shape) # expect to be 768
+
+# embedding with max pooling
+embedding_max = torch.max(last_hidden_state[0], dim=0)[0]
+print(embedding_max.shape) # expect to be 768
+```
+
+### Using as a Classifier
+
+```python
+from transformers import AutoModelForSequenceClassification
+
+model_name = "JadenLong/MutBERT"
+# Optional: JadenLong/MutBERT-Huamn-Ref, JadenLong/MutBERT-Multi
+model = AutoModelForSequenceClassification.from_pretrained(model_name, trust_remote_code=True, num_labels=2)
+```
+
+### With RoPE scaling
+
+Allowed types for RoPE scaling are: `linear` and `dynamic`. To extend the model's context window you need to add rope_scaling parameter.
+
+If you want to scale your model context by 2x:
+
+```python
+model_name = "JadenLong/MutBERT"
+# Optional: JadenLong/MutBERT-Huamn-Ref, JadenLong/MutBERT-Multi
+model = AutoModel.from_pretrained(model_name,
+                                  trust_remote_code=True,
+                                  rope_scaling={'type': 'dynamic','factor': 2.0}
+                                  ) # 2.0 for x2 scaling, 4.0 for x4, etc..
+```
+

config.json

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+{ "_name_or_path": "JadenLong/MutBERT",
+  "auto_map": {
+      "AutoConfig": "modeling_mutbert.RoPEBertConfig",
+      "AutoModel": "modeling_mutbert.RoPEBertModel",
+      "AutoModelForMaskedLM": "modeling_mutbert.RoPEBertForMaskedLM",
+      "AutoModelForSequenceClassification": "modeling_mutbert.RoPEBertForSequenceClassification"
+  },
+  "attention_probs_dropout_prob": 0.1,
+  "classifier_dropout": null,
+  "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,
+  "pooler_type": "mean",
+  "rope_scaling": null,
+  "rope_theta": 10000.0,
+  "transformers_version": "4.45.2",
+  "type_vocab_size": 2,
+  "vocab_size": 9
+}

gitattributes

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modeling_mutbert.py

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+# 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 with ROPE."""
+
+
+import math
+from dataclasses import dataclass
+from typing import Optional, Tuple, Union
+
+import torch
+import torch.utils.checkpoint
+import torch.nn.functional as F
+from torch import nn
+from torch.nn import BCEWithLogitsLoss, CrossEntropyLoss, MSELoss
+from transformers import PretrainedConfig
+from transformers.activations import ACT2FN
+from transformers.modeling_outputs import (
+    BaseModelOutputWithPooling,
+    MaskedLMOutput,
+    SequenceClassifierOutput,
+)
+from transformers.modeling_utils import PreTrainedModel
+from transformers.pytorch_utils import apply_chunking_to_forward, find_pruneable_heads_and_indices, prune_linear_layer
+from transformers.utils import (
+    ModelOutput,
+    logging,
+)
+
+logger = logging.get_logger(__name__)
+
+
+class RoPEBertConfig(PretrainedConfig):
+
+    model_type = "bert"
+
+    def __init__(
+        self,
+        vocab_size=9,
+        hidden_size=768,
+        num_hidden_layers=12,
+        num_attention_heads=12,
+        intermediate_size=3072,
+        hidden_act="gelu",
+        pooler_type="mean",  # first_token_transform
+        hidden_dropout_prob=0.1,
+        attention_probs_dropout_prob=0.1,
+        max_position_embeddings=512,
+        type_vocab_size=2,
+        initializer_range=0.02,
+        layer_norm_eps=1e-12,
+        pad_token_id=0,
+        classifier_dropout=None,
+        rope_theta=10000.0,
+        rope_scaling=None,
+        **kwargs,
+    ):
+        super().__init__(pad_token_id=pad_token_id, **kwargs)
+
+        self.vocab_size = vocab_size
+        self.hidden_size = hidden_size
+        self.num_hidden_layers = num_hidden_layers
+        self.num_attention_heads = num_attention_heads
+        self.hidden_act = hidden_act
+        self.intermediate_size = intermediate_size
+        self.hidden_dropout_prob = hidden_dropout_prob
+        self.attention_probs_dropout_prob = attention_probs_dropout_prob
+        self.max_position_embeddings = max_position_embeddings
+        self.type_vocab_size = type_vocab_size
+        self.initializer_range = initializer_range
+        self.layer_norm_eps = layer_norm_eps
+        self.classifier_dropout = classifier_dropout
+        self.rope_theta = rope_theta
+        self.rope_scaling = rope_scaling
+        self.pooler_type = pooler_type
+
+        self._pooler_type_validation()
+        self._rope_scaling_validation()
+
+    def _pooler_type_validation(self):
+        if self.pooler_type not in ['first_token_transform', 'mean']:
+            raise ValueError(
+                f"`pooler_type` must be one of `first_token_transform` or `mean`, got {self.pooler_type}"
+            )
+
+    def _rope_scaling_validation(self):
+        """
+        Validate the `rope_scaling` configuration.
+        """
+        if self.rope_scaling is None:
+            return
+
+        if not isinstance(self.rope_scaling, dict) or len(self.rope_scaling) != 2:
+            raise ValueError(
+                "`rope_scaling` must be a dictionary with with two fields, `type` and `factor`, "
+                f"got {self.rope_scaling}"
+            )
+        rope_scaling_type = self.rope_scaling.get("type", None)
+        rope_scaling_factor = self.rope_scaling.get("factor", None)
+        if rope_scaling_type is None or rope_scaling_type not in ["linear", "dynamic"]:
+            raise ValueError(
+                f"`rope_scaling`'s type field must be one of ['linear', 'dynamic'], got {rope_scaling_type}"
+            )
+        if rope_scaling_factor is None or not isinstance(rope_scaling_factor, float) or rope_scaling_factor <= 1.0:
+            raise ValueError(f"`rope_scaling`'s factor field must be a float > 1, got {rope_scaling_factor}")
+
+
+class RoPEBertEmbeddings(nn.Module):
+    """Construct the embeddings from word, 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)
+        self.token_type_embeddings = nn.Embedding(config.type_vocab_size, config.hidden_size)
+
+        self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+        self.dropout = nn.Dropout(config.hidden_dropout_prob)
+
+    def forward(
+        self,
+        input_ids: Optional[torch.FloatTensor] = None,
+        token_type_ids: Optional[torch.LongTensor] = None,
+        inputs_embeds: Optional[torch.FloatTensor] = None,
+    ) -> torch.Tensor:
+        if inputs_embeds is None:
+            # input_ids: b, l, v
+            inputs_embeds = torch.matmul(input_ids, self.word_embeddings.weight)
+            # self.word_embeddings(input_ids)
+        token_type_embeddings = self.token_type_embeddings(token_type_ids)
+
+        embeddings = inputs_embeds + token_type_embeddings
+
+        embeddings = self.LayerNorm(embeddings)
+        embeddings = self.dropout(embeddings)
+        return embeddings
+
+
+class BertRotaryEmbedding(nn.Module):
+    def __init__(self, dim, max_position_embeddings=512, base=10000, device=None):
+        super().__init__()
+
+        self.dim = dim
+        self.max_position_embeddings = max_position_embeddings
+        self.base = base
+        inv_freq = 1.0 / (self.base ** (torch.arange(0, self.dim, 2).float().to(device) / self.dim))
+        self.register_buffer("inv_freq", inv_freq, persistent=False)
+
+        # Build here to make `torch.jit.trace` work.
+        self._set_cos_sin_cache(
+            seq_len=max_position_embeddings, device=self.inv_freq.device, dtype=torch.get_default_dtype()
+        )
+
+    def _set_cos_sin_cache(self, seq_len, device, dtype):
+        self.max_seq_len_cached = seq_len
+        t = torch.arange(self.max_seq_len_cached, device=device, dtype=self.inv_freq.dtype)
+
+        freqs = torch.einsum("i,j->ij", t, self.inv_freq)  # equal to torch.outer(t, inv_freq)
+        # Different from paper, but it uses a different permutation in order to obtain the same calculation
+        emb = torch.cat((freqs, freqs), dim=-1)
+        self.register_buffer("cos_cached", emb.cos().to(dtype), persistent=False)
+        self.register_buffer("sin_cached", emb.sin().to(dtype), persistent=False)
+
+    def forward(self, x, seq_len=None):
+        # x: [bs, num_attention_heads, seq_len, head_size]
+        if seq_len > self.max_seq_len_cached:
+            self._set_cos_sin_cache(seq_len=seq_len, device=x.device, dtype=x.dtype)
+
+        return (
+            self.cos_cached[:seq_len].to(dtype=x.dtype),
+            self.sin_cached[:seq_len].to(dtype=x.dtype),
+        )
+
+
+class BertLinearScalingRotaryEmbedding(BertRotaryEmbedding):
+    """BertRotaryEmbedding extended with linear scaling. Credits to the Reddit user /u/kaiokendev"""
+
+    def __init__(self, dim, max_position_embeddings=512, base=10000, device=None, scaling_factor=1.0):
+        self.scaling_factor = scaling_factor
+        super().__init__(dim, max_position_embeddings, base, device)
+
+    def _set_cos_sin_cache(self, seq_len, device, dtype):
+        self.max_seq_len_cached = seq_len
+        t = torch.arange(self.max_seq_len_cached, device=device, dtype=self.inv_freq.dtype)
+        t = t / self.scaling_factor
+
+        freqs = torch.einsum("i,j->ij", t, self.inv_freq)
+        # Different from paper, but it uses a different permutation in order to obtain the same calculation
+        emb = torch.cat((freqs, freqs), dim=-1)
+        self.register_buffer("cos_cached", emb.cos().to(dtype), persistent=False)
+        self.register_buffer("sin_cached", emb.sin().to(dtype), persistent=False)
+
+
+class BertDynamicNTKScalingRotaryEmbedding(BertRotaryEmbedding):
+    """BertRotaryEmbedding extended with Dynamic NTK scaling. Credits to the Reddit users /u/bloc97 and /u/emozilla"""
+
+    def __init__(self, dim, max_position_embeddings=512, base=10000, device=None, scaling_factor=1.0):
+        self.scaling_factor = scaling_factor
+        super().__init__(dim, max_position_embeddings, base, device)
+
+    def _set_cos_sin_cache(self, seq_len, device, dtype):
+        self.max_seq_len_cached = seq_len
+
+        if seq_len > self.max_position_embeddings:
+            base = self.base * (
+                (self.scaling_factor * seq_len / self.max_position_embeddings) - (self.scaling_factor - 1)
+            ) ** (self.dim / (self.dim - 2))
+            inv_freq = 1.0 / (base ** (torch.arange(0, self.dim, 2).float().to(device) / self.dim))
+            self.register_buffer("inv_freq", inv_freq, persistent=False)
+
+        t = torch.arange(self.max_seq_len_cached, device=device, dtype=self.inv_freq.dtype)
+
+        freqs = torch.einsum("i,j->ij", t, self.inv_freq)
+        # Different from paper, but it uses a different permutation in order to obtain the same calculation
+        emb = torch.cat((freqs, freqs), dim=-1)
+        self.register_buffer("cos_cached", emb.cos().to(dtype), persistent=False)
+        self.register_buffer("sin_cached", emb.sin().to(dtype), persistent=False)
+
+
+def rotate_half(x):
+    """Rotates half the hidden dims of the input."""
+    x1 = x[..., : x.shape[-1] // 2]
+    x2 = x[..., x.shape[-1] // 2 :]
+    return torch.cat((-x2, x1), dim=-1)
+
+
+def apply_rotary_pos_emb(q, k, cos, sin, position_ids, unsqueeze_dim=1):
+    """Applies Rotary Position Embedding to the query and key tensors.
+    Args:
+        q (`torch.Tensor`): The query tensor.
+        k (`torch.Tensor`): The key tensor.
+        cos (`torch.Tensor`): The cosine part of the rotary embedding.
+        sin (`torch.Tensor`): The sine part of the rotary embedding.
+        position_ids (`torch.Tensor`):
+            The position indices of the tokens corresponding to the query and key tensors. For example, this can be
+            used to pass offsetted position ids when working with a KV-cache.
+        unsqueeze_dim (`int`, *optional*, defaults to 1):
+            The 'unsqueeze_dim' argument specifies the dimension along which to unsqueeze cos[position_ids] and
+            sin[position_ids] so that they can be properly broadcasted to the dimensions of q and k. For example, note
+            that cos[position_ids] and sin[position_ids] have the shape [batch_size, seq_len, head_dim]. Then, if q and
+            k have the shape [batch_size, heads, seq_len, head_dim], then setting unsqueeze_dim=1 makes
+            cos[position_ids] and sin[position_ids] broadcastable to the shapes of q and k. Similarly, if q and k have
+            the shape [batch_size, seq_len, heads, head_dim], then set unsqueeze_dim=2.
+    Returns:
+        `tuple(torch.Tensor)` comprising of the query and key tensors rotated using the Rotary Position Embedding.
+    """
+    cos = cos[position_ids].unsqueeze(unsqueeze_dim)
+    sin = sin[position_ids].unsqueeze(unsqueeze_dim)
+    q_embed = (q * cos) + (rotate_half(q) * sin)
+    k_embed = (k * cos) + (rotate_half(k) * sin)
+    return q_embed, k_embed
+
+
+class RoPEBertSelfAttention(nn.Module):
+
+    def __init__(self, config: RoPEBertConfig):
+        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.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
+
+        self.max_position_embeddings = config.max_position_embeddings
+        self.rope_theta = config.rope_theta
+
+        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.config = config
+
+        self._init_rope()
+
+    def _init_rope(self):
+        if self.config.rope_scaling is None:
+            self.rotary_emb = BertRotaryEmbedding(
+                self.attention_head_size,
+                max_position_embeddings=self.max_position_embeddings,
+                base=self.rope_theta,
+            )
+        else:
+            scaling_type = self.config.rope_scaling["type"]
+            scaling_factor = self.config.rope_scaling["factor"]
+            if scaling_type == "linear":
+                self.rotary_emb = BertLinearScalingRotaryEmbedding(
+                    self.attention_head_size,
+                    max_position_embeddings=self.max_position_embeddings,
+                    scaling_factor=scaling_factor,
+                    base=self.rope_theta,
+                )
+            elif scaling_type == "dynamic":
+                self.rotary_emb = BertDynamicNTKScalingRotaryEmbedding(
+                    self.attention_head_size,
+                    max_position_embeddings=self.max_position_embeddings,
+                    scaling_factor=scaling_factor,
+                    base=self.rope_theta,
+                )
+            else:
+                raise ValueError(f"Unknown RoPE scaling type {scaling_type}")
+
+    def transpose_for_scores(self, x: torch.Tensor) -> torch.Tensor:
+        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 forward(
+        self,
+        hidden_states: torch.Tensor,
+        attention_mask: Optional[torch.FloatTensor] = None,
+        head_mask: Optional[torch.FloatTensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        output_attentions: Optional[bool] = False,
+    ) -> Tuple[torch.Tensor]:
+        query_layer = self.transpose_for_scores(self.query(hidden_states))
+        key_layer = self.transpose_for_scores(self.key(hidden_states))
+        value_layer = self.transpose_for_scores(self.value(hidden_states))
+
+        kv_seq_len = key_layer.shape[-2]
+        cos, sin = self.rotary_emb(value_layer, seq_len=kv_seq_len)
+        query_layer, key_layer = apply_rotary_pos_emb(query_layer, key_layer, cos, sin, position_ids)
+
+        # Take the dot product between "query" and "key" to get the raw attention scores.
+        attention_scores = torch.matmul(query_layer, key_layer.transpose(-1, -2))
+
+        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 = nn.functional.softmax(attention_scores, dim=-1)
+
+        # 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)
+
+        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)
+
+        outputs = (context_layer, attention_probs) if output_attentions else (context_layer,)
+
+        return outputs
+
+
+class RoPEBertSdpaAttention(RoPEBertSelfAttention):
+
+    def forward(
+        self,
+        hidden_states: torch.Tensor,
+        attention_mask: Optional[torch.FloatTensor] = None,
+        head_mask: Optional[torch.FloatTensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        output_attentions: Optional[bool] = False,
+    ) -> Tuple[torch.Tensor]:
+
+        bsz, q_len, _ = hidden_states.size()
+
+        query_layer = self.transpose_for_scores(self.query(hidden_states))
+        key_layer = self.transpose_for_scores(self.key(hidden_states))
+        value_layer = self.transpose_for_scores(self.value(hidden_states))
+
+        kv_seq_len = key_layer.shape[-2]
+        cos, sin = self.rotary_emb(value_layer, seq_len=kv_seq_len)
+        query_layer, key_layer = apply_rotary_pos_emb(query_layer, key_layer, cos, sin, position_ids)
+
+        # SDPA with memory-efficient backend is currently (torch==2.1.2) bugged with non-contiguous inputs with custom attn_mask,
+        # Reference: https://github.com/pytorch/pytorch/issues/112577.
+        if query_layer.device.type == "cuda" and attention_mask is not None:
+            query_layer = query_layer.contiguous()
+            key_layer = key_layer.contiguous()
+            value_layer = value_layer.contiguous()
+
+        context_layer = torch.nn.functional.scaled_dot_product_attention(
+            query_layer,
+            key_layer,
+            value_layer,
+            attn_mask=attention_mask,
+            dropout_p=self.config.attention_probs_dropout_prob if self.training else 0.0,
+            is_causal=False
+        )
+
+        context_layer = context_layer.transpose(1, 2).contiguous()
+        context_layer = context_layer.reshape(bsz, q_len, self.all_head_size)
+
+        outputs = (context_layer,)
+
+        return outputs
+
+
+ROPEBERT_ATTENTION_CLASSES = {
+    "eager": RoPEBertSelfAttention,
+    "sdpa": RoPEBertSdpaAttention,
+}
+
+
+class RoPEBertSelfOutput(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.dense = nn.Linear(config.hidden_size, config.hidden_size)
+        self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+        self.dropout = nn.Dropout(config.hidden_dropout_prob)
+
+    def forward(self, hidden_states: torch.Tensor, input_tensor: torch.Tensor) -> torch.Tensor:
+        hidden_states = self.dense(hidden_states)
+        hidden_states = self.dropout(hidden_states)
+        hidden_states = self.LayerNorm(hidden_states + input_tensor)
+        return hidden_states
+
+
+class RoPEBertAttention(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.self = ROPEBERT_ATTENTION_CLASSES["sdpa"](config=config)
+        self.output = RoPEBertSelfOutput(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: torch.Tensor,
+        attention_mask: Optional[torch.FloatTensor] = None,
+        head_mask: Optional[torch.FloatTensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        output_attentions: Optional[bool] = False,
+    ) -> Tuple[torch.Tensor]:
+        self_outputs = self.self(
+            hidden_states,
+            attention_mask,
+            head_mask,
+            position_ids,
+            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 RoPEBertIntermediate(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: torch.Tensor) -> torch.Tensor:
+        hidden_states = self.dense(hidden_states)
+        hidden_states = self.intermediate_act_fn(hidden_states)
+        return hidden_states
+
+
+class RoPEBertOutput(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.dense = nn.Linear(config.intermediate_size, config.hidden_size)
+        self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+        self.dropout = nn.Dropout(config.hidden_dropout_prob)
+
+    def forward(self, hidden_states: torch.Tensor, input_tensor: torch.Tensor) -> torch.Tensor:
+        hidden_states = self.dense(hidden_states)
+        hidden_states = self.dropout(hidden_states)
+        hidden_states = self.LayerNorm(hidden_states + input_tensor)
+        return hidden_states
+
+
+class RoPEBertLayer(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.chunk_size_feed_forward = config.chunk_size_feed_forward
+        self.seq_len_dim = 1
+        self.attention = RoPEBertAttention(config)
+        self.intermediate = RoPEBertIntermediate(config)
+        self.output = RoPEBertOutput(config)
+
+    def forward(
+        self,
+        hidden_states: torch.Tensor,
+        attention_mask: Optional[torch.FloatTensor] = None,
+        head_mask: Optional[torch.FloatTensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        output_attentions: Optional[bool] = False,
+    ) -> Tuple[torch.Tensor]:
+        self_attention_outputs = self.attention(
+            hidden_states,
+            attention_mask,
+            head_mask,
+            position_ids,
+            output_attentions=output_attentions
+        )
+        attention_output = self_attention_outputs[0]
+        outputs = self_attention_outputs[1:]  # add self attentions if we output attention weights
+
+        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
+
+        return outputs
+
+    def feed_forward_chunk(self, attention_output):
+        intermediate_output = self.intermediate(attention_output)
+        layer_output = self.output(intermediate_output, attention_output)
+        return layer_output
+
+
+class RoPEBertEncoder(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.config = config
+        self.layer = nn.ModuleList([RoPEBertLayer(config) for _ in range(config.num_hidden_layers)])
+        self.gradient_checkpointing = False
+
+    def forward(
+        self,
+        hidden_states: torch.Tensor,
+        attention_mask: Optional[torch.FloatTensor] = None,
+        head_mask: Optional[torch.FloatTensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        output_attentions: Optional[bool] = False,
+        output_hidden_states: Optional[bool] = False,
+        return_dict: Optional[bool] = True,
+    ) -> Union[Tuple[torch.Tensor], BaseModelOutputWithPooling]:
+        all_hidden_states = () if output_hidden_states else None
+        all_self_attentions = () if output_attentions 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
+
+            if self.gradient_checkpointing and self.training:
+                layer_outputs = self._gradient_checkpointing_func(
+                    layer_module.__call__,
+                    hidden_states,
+                    attention_mask,
+                    layer_head_mask,
+                    position_ids,
+                    output_attentions
+                )
+            else:
+                layer_outputs = layer_module(
+                    hidden_states,
+                    attention_mask,
+                    layer_head_mask,
+                    position_ids,
+                    output_attentions
+                )
+
+            hidden_states = layer_outputs[0]
+            if output_attentions:
+                all_self_attentions = all_self_attentions + (layer_outputs[1],)
+
+        if output_hidden_states:
+            all_hidden_states = all_hidden_states + (hidden_states,)
+
+        if not return_dict:
+            return tuple(
+                v
+                for v in [
+                    hidden_states,
+                    all_hidden_states,
+                    all_self_attentions,
+                ]
+                if v is not None
+            )
+        return BaseModelOutputWithPooling(
+            last_hidden_state=hidden_states,
+            hidden_states=all_hidden_states,
+            attentions=all_self_attentions,
+        )
+
+
+class RoPEBertMeanTokensPooler(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+
+    def forward(self, hidden_states: torch.Tensor, attention_mask: torch.LongTensor) -> torch.Tensor:
+        input_mask_expanded = attention_mask.unsqueeze(-1).expand(hidden_states.size()).float()
+        pooled_output = torch.sum(hidden_states * input_mask_expanded, 1) / torch.clamp(input_mask_expanded.sum(1),  min=1e-9)
+
+        return pooled_output
+
+
+class RoPEBertCLSTokenTransformPooler(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: torch.Tensor, attention_mask: torch.LongTensor) -> torch.Tensor:
+
+        first_token_tensor = hidden_states[:, 0]
+        pooled_output = self.dense(first_token_tensor)
+        pooled_output = self.activation(pooled_output)
+
+        return pooled_output
+
+
+ROPEBERT_POOLER_CLASSES = {
+    "mean": RoPEBertMeanTokensPooler,
+    "first_token_transform": RoPEBertCLSTokenTransformPooler,
+}
+
+
+class RoPEBertPredictionHeadTransform(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: torch.Tensor) -> torch.Tensor:
+        hidden_states = self.dense(hidden_states)
+        hidden_states = self.transform_act_fn(hidden_states)
+        hidden_states = self.LayerNorm(hidden_states)
+        return hidden_states
+
+
+class RoPEBertLMPredictionHead(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.transform = RoPEBertPredictionHeadTransform(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 RoPEBertOnlyMLMHead(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.predictions = RoPEBertLMPredictionHead(config)
+
+    def forward(self, sequence_output: torch.Tensor) -> torch.Tensor:
+        prediction_scores = self.predictions(sequence_output)
+        return prediction_scores
+
+
+class RoPEBertOnlyNSPHead(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 RoPEBertPreTrainingHeads(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.predictions = RoPEBertLMPredictionHead(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 RoPEBertPreTrainedModel(PreTrainedModel):
+    """
+    An abstract class to handle weights initialization and a simple interface for downloading and loading pretrained
+    models.
+    """
+
+    config_class = RoPEBertConfig
+    base_model_prefix = "bert"
+    supports_gradient_checkpointing = True
+    _supports_sdpa = True
+
+    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
+            module.weight.data.normal_(mean=0.0, std=self.config.initializer_range)
+            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)
+
+
+@dataclass
+class RoPEBertForPreTrainingOutput(ModelOutput):
+
+    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
+
+
+class RoPEBertModel(RoPEBertPreTrainedModel):
+
+    def __init__(self, config, add_pooling_layer=True):
+        super().__init__(config)
+        self.config = config
+
+        self.embeddings = RoPEBertEmbeddings(config)
+        self.encoder = RoPEBertEncoder(config)
+
+        self.pooler = ROPEBERT_POOLER_CLASSES[config.pooler_type](config=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)
+
+    def forward(
+        self,
+        input_ids: Optional[torch.Tensor] = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        token_type_ids: Optional[torch.Tensor] = None,
+        position_ids: Optional[torch.Tensor] = None,
+        head_mask: Optional[torch.Tensor] = None,
+        inputs_embeds: Optional[torch.Tensor] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[Tuple[torch.Tensor], BaseModelOutputWithPooling]:
+
+        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 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:
+            self.warn_if_padding_and_no_attention_mask(input_ids, attention_mask)
+            input_shape = input_ids.size()[:-1]  # modified
+        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")
+
+        if output_attentions and self.config.attn_implementation == 'sdpa':
+            logger.warning("Cant use output_attentions with sdpa attention, turning off")
+            output_attentions = False
+
+        batch_size, seq_length = input_shape
+        device = input_ids.device if input_ids is not None else inputs_embeds.device
+
+        if attention_mask is None:
+            attention_mask = torch.ones((batch_size, seq_length), device=device)
+
+        if position_ids is None:
+            position_ids = torch.arange(
+                0, seq_length, dtype=torch.long, device=device
+            )
+            position_ids = position_ids.unsqueeze(0)
+
+        if token_type_ids is None:
+            token_type_ids = torch.zeros(input_shape, dtype=torch.long, device=device)
+
+        # We can provide a self-attention mask of dimensions [batch_size, 1, 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)
+
+        # 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,
+            token_type_ids=token_type_ids,
+            inputs_embeds=inputs_embeds
+        )
+        encoder_outputs = self.encoder(
+            embedding_output,
+            attention_mask=extended_attention_mask,
+            head_mask=head_mask,
+            position_ids=position_ids,
+            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, attention_mask) if self.pooler is not None else None
+
+        if not return_dict:
+            return (sequence_output, pooled_output) + encoder_outputs[1:]
+
+        return BaseModelOutputWithPooling(
+            last_hidden_state=sequence_output,
+            pooler_output=pooled_output,
+            hidden_states=encoder_outputs.hidden_states,
+            attentions=encoder_outputs.attentions,
+        )
+
+
+class RoPEBertForPreTraining(RoPEBertPreTrainedModel):
+    _tied_weights_keys = ["predictions.decoder.bias", "cls.predictions.decoder.weight"]
+
+    def __init__(self, config):
+        super().__init__(config)
+
+        self.bert = RoPEBertModel(config)
+        self.cls = RoPEBertPreTrainingHeads(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
+
+    def forward(
+        self,
+        input_ids: Optional[torch.Tensor] = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        token_type_ids: Optional[torch.Tensor] = None,
+        position_ids: Optional[torch.Tensor] = None,
+        head_mask: Optional[torch.Tensor] = None,
+        inputs_embeds: Optional[torch.Tensor] = None,
+        labels: Optional[torch.Tensor] = None,
+        next_sentence_label: Optional[torch.Tensor] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[Tuple[torch.Tensor], RoPEBertForPreTrainingOutput]:
+
+        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
+        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 RoPEBertForPreTrainingOutput(
+            loss=total_loss,
+            prediction_logits=prediction_scores,
+            seq_relationship_logits=seq_relationship_score,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )
+
+
+class DNACrossEntropy(nn.Module):
+    def __init__(self, *args, **kwargs) -> None:
+        super().__init__(*args, **kwargs)
+
+    def forward(self, predictions, labels):
+        # labels: (n_mask, vocab_size)
+        # predicts: (n_mask, vocab_size)
+        log_probs = F.log_softmax(predictions, dim=-1)
+        loss = -(labels * log_probs).sum(dim=-1).mean()
+
+        return loss
+
+
+class RoPEBertForMaskedLM(RoPEBertPreTrainedModel):
+    _tied_weights_keys = ["predictions.decoder.bias", "cls.predictions.decoder.weight"]
+
+    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 = RoPEBertModel(config, add_pooling_layer=False)
+        self.cls = RoPEBertOnlyMLMHead(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
+
+    def forward(
+        self,
+        input_ids: Optional[torch.Tensor] = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        token_type_ids: Optional[torch.Tensor] = None,
+        position_ids: Optional[torch.Tensor] = None,
+        head_mask: Optional[torch.Tensor] = None,
+        inputs_embeds: Optional[torch.Tensor] = None,
+        labels: Optional[torch.Tensor] = None,
+        masked_indices: Optional[torch.Tensor] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[Tuple[torch.Tensor], MaskedLMOutput]:
+        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=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]
+        prediction_scores = self.cls(sequence_output)
+
+        masked_lm_loss = None
+        if labels is not None:
+            # CrossEntropyLoss()  # -100 index = padding token
+            loss_fct = DNACrossEntropy()
+            masked_lm_loss = loss_fct(prediction_scores[masked_indices].view(-1, self.config.vocab_size),
+                                      labels[masked_indices].view(-1, self.config.vocab_size))
+
+        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}
+
+
+class RoPEBertForSequenceClassification(RoPEBertPreTrainedModel):
+    def __init__(self, config):
+        super().__init__(config)
+        self.num_labels = config.num_labels
+        self.config = config
+
+        self.bert = RoPEBertModel(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()
+
+    def forward(
+        self,
+        input_ids: Optional[torch.Tensor] = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        token_type_ids: Optional[torch.Tensor] = None,
+        position_ids: Optional[torch.Tensor] = None,
+        head_mask: Optional[torch.Tensor] = None,
+        inputs_embeds: Optional[torch.Tensor] = None,
+        labels: Optional[torch.Tensor] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[Tuple[torch.Tensor], SequenceClassifierOutput]:
+        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()
+                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,
+        )

pytorch_model.bin

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:73a10975b93bed0f259698985f8420b86c7c5dedcf8b992053643085dd9d1140
+size 342710382

tokenizer.json

@@ -0,0 +1,153 @@
+{
+  "version": "1.0",
+  "truncation": null,
+  "padding": null,
+  "added_tokens": [
+    {
+      "id": 0,
+      "special": true,
+      "content": "[UNK]",
+      "single_word": false,
+      "lstrip": false,
+      "rstrip": false,
+      "normalized": false
+    },
+    {
+      "id": 1,
+      "special": true,
+      "content": "[CLS]",
+      "single_word": false,
+      "lstrip": false,
+      "rstrip": false,
+      "normalized": false
+    },
+    {
+      "id": 2,
+      "special": true,
+      "content": "[SEP]",
+      "single_word": false,
+      "lstrip": false,
+      "rstrip": false,
+      "normalized": false
+    },
+    {
+      "id": 3,
+      "special": true,
+      "content": "[PAD]",
+      "single_word": false,
+      "lstrip": false,
+      "rstrip": false,
+      "normalized": false
+    },
+    {
+      "id": 4,
+      "special": true,
+      "content": "[MASK]",
+      "single_word": false,
+      "lstrip": false,
+      "rstrip": false,
+      "normalized": false
+    }
+  ],
+  "normalizer": null,
+  "pre_tokenizer": {
+    "type": "Whitespace"
+  },
+  "post_processor": {
+    "type": "TemplateProcessing",
+    "single": [
+      {
+        "SpecialToken": {
+          "id": "[CLS]",
+          "type_id": 0
+        }
+      },
+      {
+        "Sequence": {
+          "id": "A",
+          "type_id": 0
+        }
+      },
+      {
+        "SpecialToken": {
+          "id": "[SEP]",
+          "type_id": 0
+        }
+      }
+    ],
+    "pair": [
+      {
+        "SpecialToken": {
+          "id": "[CLS]",
+          "type_id": 0
+        }
+      },
+      {
+        "Sequence": {
+          "id": "A",
+          "type_id": 0
+        }
+      },
+      {
+        "SpecialToken": {
+          "id": "[SEP]",
+          "type_id": 0
+        }
+      },
+      {
+        "Sequence": {
+          "id": "B",
+          "type_id": 1
+        }
+      },
+      {
+        "SpecialToken": {
+          "id": "[SEP]",
+          "type_id": 1
+        }
+      }
+    ],
+    "special_tokens": {
+      "[CLS]": {
+        "id": "[CLS]",
+        "ids": [
+          1
+        ],
+        "tokens": [
+          "[CLS]"
+        ]
+      },
+      "[SEP]": {
+        "id": "[SEP]",
+        "ids": [
+          2
+        ],
+        "tokens": [
+          "[SEP]"
+        ]
+      }
+    }
+  },
+  "decoder": null,
+  "model": {
+    "type": "BPE",
+    "dropout": null,
+    "unk_token": "[UNK]",
+    "continuing_subword_prefix": null,
+    "end_of_word_suffix": null,
+    "fuse_unk": false,
+    "vocab": {
+      "[UNK]": 0,
+      "[CLS]": 1,
+      "[SEP]": 2,
+      "[PAD]": 3,
+      "[MASK]": 4,
+      "A": 5,
+      "C": 6,
+      "G": 7,
+      "T": 8
+    },
+    "merges": [
+    ]
+  }
+}

tokenizer_config.json

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

vocab.txt

@@ -0,0 +1,9 @@
+[PAD]
+[UNK]
+[CLS]
+[SEP]
+[MASK]
+A
+T
+C
+G