modeling_biogpt.py

# coding=utf-8
# Copyright 2022 The HuggingFace Team and Microsoft Research AI4Science 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 BioGPT model."""


import math
from typing import Optional, Tuple, Union

import torch
import torch.utils.checkpoint
from torch import nn
from torch.nn import BCEWithLogitsLoss, CrossEntropyLoss, MSELoss

from ...activations import ACT2FN
from ...modeling_outputs import (
    BaseModelOutputWithPastAndCrossAttentions,
    CausalLMOutputWithCrossAttentions,
    SequenceClassifierOutputWithPast,
    TokenClassifierOutput,
)
from ...modeling_utils import PreTrainedModel
from ...utils import (
    add_code_sample_docstrings,
    add_start_docstrings,
    add_start_docstrings_to_model_forward,
    logging,
)
from .configuration_biogpt import BioGptConfig


logger = logging.get_logger(__name__)

_CHECKPOINT_FOR_DOC = "microsoft/biogpt"
_CONFIG_FOR_DOC = "BioGptConfig"


BIOGPT_PRETRAINED_MODEL_ARCHIVE_LIST = [
    "microsoft/biogpt",
    "microsoft/BioGPT-Large",
    # See all BioGPT models at https://huggingface.co/models?filter=biogpt
]


# Copied from transformers.models.bart.modeling_bart._make_causal_mask
def _make_causal_mask(
    input_ids_shape: torch.Size, dtype: torch.dtype, device: torch.device, past_key_values_length: int = 0
):
    """
    Make causal mask used for bi-directional self-attention.
    """
    bsz, tgt_len = input_ids_shape
    mask = torch.full((tgt_len, tgt_len), torch.finfo(dtype).min, device=device)
    mask_cond = torch.arange(mask.size(-1), device=device)
    mask.masked_fill_(mask_cond < (mask_cond + 1).view(mask.size(-1), 1), 0)
    mask = mask.to(dtype)

    if past_key_values_length > 0:
        mask = torch.cat([torch.zeros(tgt_len, past_key_values_length, dtype=dtype, device=device), mask], dim=-1)
    return mask[None, None, :, :].expand(bsz, 1, tgt_len, tgt_len + past_key_values_length)


# Copied from transformers.models.bart.modeling_bart._expand_mask
def _expand_mask(mask: torch.Tensor, dtype: torch.dtype, tgt_len: Optional[int] = None):
    """
    Expands attention_mask from `[bsz, seq_len]` to `[bsz, 1, tgt_seq_len, src_seq_len]`.
    """
    bsz, src_len = mask.size()
    tgt_len = tgt_len if tgt_len is not None else src_len

    expanded_mask = mask[:, None, None, :].expand(bsz, 1, tgt_len, src_len).to(dtype)

    inverted_mask = 1.0 - expanded_mask

    return inverted_mask.masked_fill(inverted_mask.to(torch.bool), torch.finfo(dtype).min)


# Copied from transformers.models.opt.modeling_opt.OPTLearnedPositionalEmbedding with OPT->BioGpt
class BioGptLearnedPositionalEmbedding(nn.Embedding):
    """
    This module learns positional embeddings up to a fixed maximum size.
    """

    def __init__(self, num_embeddings: int, embedding_dim: int):
        # BioGpt is set up so that if padding_idx is specified then offset the embedding ids by 2
        # and adjust num_embeddings appropriately. Other models don't have this hack
        self.offset = 2
        super().__init__(num_embeddings + self.offset, embedding_dim)

    def forward(self, attention_mask: torch.LongTensor, past_key_values_length: int = 0):
        """`input_ids_shape` is expected to be [bsz x seqlen]."""
        attention_mask = attention_mask.long()

        # create positions depending on attention_mask
        positions = (torch.cumsum(attention_mask, dim=1).type_as(attention_mask) * attention_mask).long() - 1

        # cut positions if `past_key_values_length` is > 0
        positions = positions[:, past_key_values_length:]

        return super().forward(positions + self.offset)


# Copied from transformers.models.bart.modeling_bart.BartAttention with Bart->BioGpt
class BioGptAttention(nn.Module):
    """Multi-headed attention from 'Attention Is All You Need' paper"""

    def __init__(
        self,
        embed_dim: int,
        num_heads: int,
        dropout: float = 0.0,
        is_decoder: bool = False,
        bias: bool = True,
    ):
        super().__init__()
        self.embed_dim = embed_dim
        self.num_heads = num_heads
        self.dropout = dropout
        self.head_dim = embed_dim // num_heads

        if (self.head_dim * num_heads) != self.embed_dim:
            raise ValueError(
                f"embed_dim must be divisible by num_heads (got `embed_dim`: {self.embed_dim}"
                f" and `num_heads`: {num_heads})."
            )
        self.scaling = self.head_dim**-0.5
        self.is_decoder = is_decoder

        self.k_proj = nn.Linear(embed_dim, embed_dim, bias=bias)
        self.v_proj = nn.Linear(embed_dim, embed_dim, bias=bias)
        self.q_proj = nn.Linear(embed_dim, embed_dim, bias=bias)
        self.out_proj = nn.Linear(embed_dim, embed_dim, bias=bias)

    def _shape(self, tensor: torch.Tensor, seq_len: int, bsz: int):
        return tensor.view(bsz, seq_len, self.num_heads, self.head_dim).transpose(1, 2).contiguous()

    def forward(
        self,
        hidden_states: torch.Tensor,
        key_value_states: Optional[torch.Tensor] = None,
        past_key_value: Optional[Tuple[torch.Tensor]] = None,
        attention_mask: Optional[torch.Tensor] = None,
        layer_head_mask: Optional[torch.Tensor] = None,
        output_attentions: bool = False,
    ) -> Tuple[torch.Tensor, Optional[torch.Tensor], Optional[Tuple[torch.Tensor]]]:
        """Input shape: Batch x Time x Channel"""

        # if key_value_states are provided this layer is used as a cross-attention layer
        # for the decoder
        is_cross_attention = key_value_states is not None

        bsz, tgt_len, _ = hidden_states.size()

        # get query proj
        query_states = self.q_proj(hidden_states) * self.scaling
        # get key, value proj
        # `past_key_value[0].shape[2] == key_value_states.shape[1]`
        # is checking that the `sequence_length` of the `past_key_value` is the same as
        # the provided `key_value_states` to support prefix tuning
        if (
            is_cross_attention
            and past_key_value is not None
            and past_key_value[0].shape[2] == key_value_states.shape[1]
        ):
            # reuse k,v, cross_attentions
            key_states = past_key_value[0]
            value_states = past_key_value[1]
        elif is_cross_attention:
            # cross_attentions
            key_states = self._shape(self.k_proj(key_value_states), -1, bsz)
            value_states = self._shape(self.v_proj(key_value_states), -1, bsz)
        elif past_key_value is not None:
            # reuse k, v, self_attention
            key_states = self._shape(self.k_proj(hidden_states), -1, bsz)
            value_states = self._shape(self.v_proj(hidden_states), -1, bsz)
            key_states = torch.cat([past_key_value[0], key_states], dim=2)
            value_states = torch.cat([past_key_value[1], value_states], dim=2)
        else:
            # self_attention
            key_states = self._shape(self.k_proj(hidden_states), -1, bsz)
            value_states = self._shape(self.v_proj(hidden_states), -1, bsz)

        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_states, value_states)

        proj_shape = (bsz * self.num_heads, -1, self.head_dim)
        query_states = self._shape(query_states, tgt_len, bsz).view(*proj_shape)
        key_states = key_states.reshape(*proj_shape)
        value_states = value_states.reshape(*proj_shape)

        src_len = key_states.size(1)
        attn_weights = torch.bmm(query_states, key_states.transpose(1, 2))

        if attn_weights.size() != (bsz * self.num_heads, tgt_len, src_len):
            raise ValueError(
                f"Attention weights should be of size {(bsz * self.num_heads, tgt_len, src_len)}, but is"
                f" {attn_weights.size()}"
            )

        if attention_mask is not None:
            if attention_mask.size() != (bsz, 1, tgt_len, src_len):
                raise ValueError(
                    f"Attention mask should be of size {(bsz, 1, tgt_len, src_len)}, but is {attention_mask.size()}"
                )
            attn_weights = attn_weights.view(bsz, self.num_heads, tgt_len, src_len) + attention_mask
            attn_weights = attn_weights.view(bsz * self.num_heads, tgt_len, src_len)

        attn_weights = nn.functional.softmax(attn_weights, dim=-1)

        if layer_head_mask is not None:
            if layer_head_mask.size() != (self.num_heads,):
                raise ValueError(
                    f"Head mask for a single layer should be of size {(self.num_heads,)}, but is"
                    f" {layer_head_mask.size()}"
                )
            attn_weights = layer_head_mask.view(1, -1, 1, 1) * attn_weights.view(bsz, self.num_heads, tgt_len, src_len)
            attn_weights = attn_weights.view(bsz * self.num_heads, tgt_len, src_len)

        if output_attentions:
            # this operation is a bit awkward, but it's required to
            # make sure that attn_weights keeps its gradient.
            # In order to do so, attn_weights have to be reshaped
            # twice and have to be reused in the following
            attn_weights_reshaped = attn_weights.view(bsz, self.num_heads, tgt_len, src_len)
            attn_weights = attn_weights_reshaped.view(bsz * self.num_heads, tgt_len, src_len)
        else:
            attn_weights_reshaped = None

        attn_probs = nn.functional.dropout(attn_weights, p=self.dropout, training=self.training)

        attn_output = torch.bmm(attn_probs, value_states)

        if attn_output.size() != (bsz * self.num_heads, tgt_len, self.head_dim):
            raise ValueError(
                f"`attn_output` should be of size {(bsz * self.num_heads, tgt_len, self.head_dim)}, but is"
                f" {attn_output.size()}"
            )

        attn_output = attn_output.view(bsz, self.num_heads, tgt_len, self.head_dim)
        attn_output = attn_output.transpose(1, 2)

        # Use the `embed_dim` from the config (stored in the class) rather than `hidden_state` because `attn_output` can be
        # partitioned across GPUs when using tensor-parallelism.
        attn_output = attn_output.reshape(bsz, tgt_len, self.embed_dim)

        attn_output = self.out_proj(attn_output)

        return attn_output, attn_weights_reshaped, past_key_value


class BioGptDecoderLayer(nn.Module):
    def __init__(self, config: BioGptConfig):
        super().__init__()
        self.embed_dim = config.hidden_size

        self.self_attn = BioGptAttention(
            embed_dim=self.embed_dim,
            num_heads=config.num_attention_heads,
            dropout=config.attention_probs_dropout_prob,
            is_decoder=True,
        )
        self.dropout = config.hidden_dropout_prob
        self.activation_fn = ACT2FN[config.hidden_act]
        self.activation_dropout = config.activation_dropout

        self.self_attn_layer_norm = nn.LayerNorm(self.embed_dim)

        self.fc1 = nn.Linear(self.embed_dim, config.intermediate_size)
        self.fc2 = nn.Linear(config.intermediate_size, self.embed_dim)
        self.final_layer_norm = nn.LayerNorm(self.embed_dim)

    def forward(
        self,
        hidden_states: torch.Tensor,
        attention_mask: Optional[torch.Tensor] = None,
        layer_head_mask: Optional[torch.Tensor] = None,
        past_key_value: Optional[Tuple[torch.Tensor]] = None,
        output_attentions: Optional[bool] = False,
        use_cache: Optional[bool] = True,
    ) -> Tuple[torch.FloatTensor, Optional[Tuple[torch.FloatTensor, torch.FloatTensor]]]:
        """
        Args:
            hidden_states (`torch.FloatTensor`): input to the layer of shape `(batch, seq_len, embed_dim)`
            attention_mask (`torch.FloatTensor`): attention mask of size
                `(batch, 1, tgt_len, src_len)` where padding elements are indicated by very large negative values.
            layer_head_mask (`torch.FloatTensor`): mask for attention heads in a given layer of size
                `(encoder_attention_heads,)`.
            past_key_value (`Tuple(torch.FloatTensor)`): cached past key and value projection states
            output_attentions (`bool`, *optional*):
                Whether or not to return the attentions tensors of all attention layers. See `attentions` under
                returned tensors for more detail.
            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`).
        """
        residual = hidden_states

        hidden_states = self.self_attn_layer_norm(hidden_states)

        # Self Attention
        # 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
        # add present self-attn cache to positions 1,2 of present_key_value tuple
        hidden_states, self_attn_weights, present_key_value = self.self_attn(
            hidden_states=hidden_states,
            past_key_value=self_attn_past_key_value,
            attention_mask=attention_mask,
            layer_head_mask=layer_head_mask,
            output_attentions=output_attentions,
        )
        hidden_states = nn.functional.dropout(hidden_states, p=self.dropout, training=self.training)
        hidden_states = residual + hidden_states

        # Fully Connected
        residual = hidden_states
        hidden_states = self.final_layer_norm(hidden_states)
        hidden_states = self.fc1(hidden_states)
        hidden_states = self.activation_fn(hidden_states)
        hidden_states = nn.functional.dropout(hidden_states, p=self.activation_dropout, training=self.training)
        hidden_states = self.fc2(hidden_states)
        hidden_states = nn.functional.dropout(hidden_states, p=self.dropout, training=self.training)
        hidden_states = residual + hidden_states

        outputs = (hidden_states,)

        if output_attentions:
            outputs += (self_attn_weights,)

        if use_cache:
            outputs += (present_key_value,)

        return outputs


class BioGptPreTrainedModel(PreTrainedModel):
    """
    An abstract class to handle weights initialization and a simple interface for downloading and loading pretrained
    models.
    """

    config_class = BioGptConfig
    base_model_prefix = "biogpt"
    supports_gradient_checkpointing = 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)

    def _set_gradient_checkpointing(self, module, value=False):
        if isinstance(module, BioGptModel):
            module.gradient_checkpointing = value


BIOGPT_START_DOCSTRING = r"""
    This model is a PyTorch [torch.nn.Module](https://pytorch.org/docs/stable/nn.html#torch.nn.Module) sub-class. Use
    it as a regular PyTorch Module and refer to the PyTorch documentation for all matter related to general usage and
    behavior.

    Parameters:
        config ([`~BioGptConfig`]): 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.
"""

BIOGPT_INPUTS_DOCSTRING = r"""
    Args:
        input_ids (`torch.LongTensor` of shape `({0})`):
            Indices of input sequence tokens in the vocabulary.

            Indices can be obtained using [`AutoTokenizer`]. 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)
        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.
        past_key_values (`tuple(tuple(torch.FloatTensor))`, *optional*, returned when `use_cache=True` is passed or when `config.use_cache=True`):
            Tuple of `tuple(torch.FloatTensor)` of length `config.n_layers`, with each tuple having 2 tensors of shape
            `(batch_size, num_heads, sequence_length, embed_size_per_head)`) and 2 additional tensors of shape
            `(batch_size, num_heads, encoder_sequence_length, embed_size_per_head)`.

            Contains pre-computed hidden-states (key and values in the self-attention blocks and in the cross-attention
            blocks) that can be used (see `past_key_values` input) to speed up sequential 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)`. inputs_embeds (`torch.FloatTensor` of shape
            `(batch_size, sequence_length, 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.
        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 (`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 [`~utils.ModelOutput`] instead of a plain tuple.
"""


@add_start_docstrings(
    "The bare BioGPT Model transformer outputting raw hidden-states without any specific head on top.",
    BIOGPT_START_DOCSTRING,
)
class BioGptModel(BioGptPreTrainedModel):
    def __init__(self, config: BioGptConfig):
        super().__init__(config)
        self.config = config
        self.layerdrop = config.layerdrop
        self.dropout = config.hidden_dropout_prob
        self.embed_dim = config.hidden_size
        self.padding_idx = config.pad_token_id
        self.embed_scale = math.sqrt(config.hidden_size) if config.scale_embedding else 1.0

        self.embed_tokens = nn.Embedding(config.vocab_size, self.embed_dim, self.padding_idx)
        self.embed_positions = BioGptLearnedPositionalEmbedding(config.max_position_embeddings, self.embed_dim)

        self.layers = nn.ModuleList([BioGptDecoderLayer(config) for _ in range(config.num_hidden_layers)])
        self.layer_norm = nn.LayerNorm(self.embed_dim)

        self.gradient_checkpointing = False
        # Initialize weights and apply final processing
        self.post_init()

    def get_input_embeddings(self):
        return self.embed_tokens

    def set_input_embeddings(self, value):
        self.embed_tokens = value

    # Copied from transformers.models.bart.modeling_bart.BartDecoder._prepare_decoder_attention_mask
    def _prepare_decoder_attention_mask(self, attention_mask, input_shape, inputs_embeds, past_key_values_length):
        # create causal mask
        # [bsz, seq_len] -> [bsz, 1, tgt_seq_len, src_seq_len]
        combined_attention_mask = None
        if input_shape[-1] > 1:
            combined_attention_mask = _make_causal_mask(
                input_shape,
                inputs_embeds.dtype,
                device=inputs_embeds.device,
                past_key_values_length=past_key_values_length,
            )

        if attention_mask is not None:
            # [bsz, seq_len] -> [bsz, 1, tgt_seq_len, src_seq_len]
            expanded_attn_mask = _expand_mask(attention_mask, inputs_embeds.dtype, tgt_len=input_shape[-1]).to(
                inputs_embeds.device
            )
            combined_attention_mask = (
                expanded_attn_mask if combined_attention_mask is None else expanded_attn_mask + combined_attention_mask
            )

        return combined_attention_mask

    @add_start_docstrings_to_model_forward(BIOGPT_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
    @add_code_sample_docstrings(
        checkpoint=_CHECKPOINT_FOR_DOC,
        output_type=BaseModelOutputWithPastAndCrossAttentions,
        config_class=_CONFIG_FOR_DOC,
    )
    def forward(
        self,
        input_ids: Optional[torch.LongTensor] = None,
        attention_mask: Optional[torch.FloatTensor] = None,
        head_mask: Optional[torch.FloatTensor] = None,
        inputs_embeds: Optional[torch.FloatTensor] = None,
        past_key_values: Optional[Tuple[Tuple[torch.Tensor]]] = None,
        use_cache: Optional[bool] = None,
        output_attentions: Optional[bool] = None,
        output_hidden_states: Optional[bool] = None,
        return_dict: Optional[bool] = None,
    ) -> Union[Tuple, BaseModelOutputWithPastAndCrossAttentions]:
        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
        )
        use_cache = use_cache if use_cache is not None else self.config.use_cache
        return_dict = return_dict if return_dict is not None else self.config.use_return_dict

        # retrieve input_ids and inputs_embeds
        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 = input_ids
            input_shape = input.size()
        elif inputs_embeds is not None:
            input_shape = inputs_embeds.size()[:-1]
            input = inputs_embeds[:, :, -1]
        else:
            raise ValueError("You have to specify either input_ids or inputs_embeds")

        # 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 inputs_embeds is None:
            inputs_embeds = self.embed_tokens(input) * self.embed_scale

        if attention_mask is None:
            attention_mask = torch.ones(inputs_embeds.shape[:2], dtype=torch.bool, device=inputs_embeds.device)
        elif attention_mask.shape[1] != past_key_values_length + input_shape[1]:
            raise ValueError(
                f"The provided attention mask has length {attention_mask.shape[1]}, but its length should be "
                f"{past_key_values_length + input_shape[1]} (sum of the lengths of current and past inputs)"
            )

        # embed positions
        positions = self.embed_positions(attention_mask, past_key_values_length)

        attention_mask = self._prepare_decoder_attention_mask(
            attention_mask, input_shape, inputs_embeds, past_key_values_length
        )

        hidden_states = inputs_embeds + positions

        hidden_states = nn.functional.dropout(hidden_states, p=self.dropout, training=self.training)

        if self.gradient_checkpointing and self.training:
            if use_cache:
                logger.warning_once(
                    "`use_cache=True` is incompatible with gradient checkpointing. Setting `use_cache=False`..."
                )
                use_cache = False

        all_hidden_states = () if output_hidden_states else None
        all_self_attns = () if output_attentions else None
        all_cross_attentions = None
        next_decoder_cache = () if use_cache else None

        for idx, decoder_layer in enumerate(self.layers):
            # add LayerDrop (see https://arxiv.org/abs/1909.11556 for description)
            if output_hidden_states:
                all_hidden_states += (hidden_states,)
            if self.training:
                dropout_probability = torch.rand([])
                if dropout_probability < self.layerdrop:
                    continue

            past_key_value = past_key_values[idx] if past_key_values is not None else None

            if self.gradient_checkpointing and self.training:

                def create_custom_forward(module):
                    def custom_forward(*inputs):
                        # None for past_key_value
                        return module(*inputs, output_attentions, use_cache)

                    return custom_forward

                layer_outputs = torch.utils.checkpoint.checkpoint(
                    create_custom_forward(decoder_layer),
                    hidden_states,
                    attention_mask,
                    head_mask[idx] if head_mask is not None else None,
                    None,
                )
            else:
                layer_outputs = decoder_layer(
                    hidden_states,
                    attention_mask=attention_mask,
                    layer_head_mask=(head_mask[idx] if head_mask is not None else None),
                    past_key_value=past_key_value,
                    output_attentions=output_attentions,
                    use_cache=use_cache,
                )

            hidden_states = layer_outputs[0]

            if use_cache:
                next_decoder_cache += (layer_outputs[2 if output_attentions else 1],)

            if output_attentions:
                all_self_attns += (layer_outputs[1],)

        # add hidden states from the last decoder layer
        if output_hidden_states:
            all_hidden_states += (hidden_states,)

        hidden_states = self.layer_norm(hidden_states)

        next_cache = next_decoder_cache if use_cache else None

        if not return_dict:
            return tuple(
                v
                for v in [hidden_states, next_cache, all_hidden_states, all_self_attns, all_cross_attentions]
                if v is not None
            )
        return BaseModelOutputWithPastAndCrossAttentions(
            last_hidden_state=hidden_states,
            past_key_values=next_cache,
            hidden_states=all_hidden_states,
            attentions=all_self_attns,
            cross_attentions=all_cross_attentions,
        )


@add_start_docstrings(
    """BioGPT Model with a `language modeling` head on top for CLM fine-tuning.""", BIOGPT_START_DOCSTRING
)
class BioGptForCausalLM(BioGptPreTrainedModel):
    _tied_weights_keys = ["output_projection.weight"]

    def __init__(self, config):
        super().__init__(config)

        self.biogpt = BioGptModel(config)
        self.output_projection = nn.Linear(config.hidden_size, config.vocab_size, bias=False)

        # Initialize weights and apply final processing
        self.post_init()

    def get_output_embeddings(self):
        return self.output_projection

    def set_output_embeddings(self, new_embeddings):
        self.output_projection = new_embeddings

    @add_start_docstrings_to_model_forward(BIOGPT_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
    @add_code_sample_docstrings(
        checkpoint=_CHECKPOINT_FOR_DOC,
        output_type=CausalLMOutputWithCrossAttentions,
        config_class=_CONFIG_FOR_DOC,
    )
    def forward(
        self,
        input_ids: Optional[torch.LongTensor] = None,
        attention_mask: Optional[torch.FloatTensor] = None,
        head_mask: Optional[torch.FloatTensor] = None,
        inputs_embeds: Optional[torch.FloatTensor] = None,
        past_key_values: Optional[Tuple[Tuple[torch.Tensor]]] = None,
        labels: Optional[torch.LongTensor] = None,
        use_cache: Optional[bool] = None,
        output_attentions: Optional[bool] = None,
        output_hidden_states: Optional[bool] = None,
        return_dict: Optional[bool] = None,
    ) -> Union[Tuple, CausalLMOutputWithCrossAttentions]:
        r"""
        labels (`torch.LongTensor` of shape `(batch_size, sequence_length)`, *optional*):
            Labels for language modeling. Note that the labels **are shifted** inside the model, i.e. you can set
            `labels = input_ids` Indices are selected in `[-100, 0, ..., config.vocab_size]` All labels set to `-100`
            are ignored (masked), the loss is only computed for labels in `[0, ..., config.vocab_size]`
        """
        return_dict = return_dict if return_dict is not None else self.config.use_return_dict

        outputs = self.biogpt(
            input_ids,
            attention_mask=attention_mask,
            head_mask=head_mask,
            inputs_embeds=inputs_embeds,
            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.output_projection(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[1:]
            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, attention_mask, inputs_embeds=None, past_key_values=None, **kwargs
    ):
        # only last token for inputs_ids if past is defined in kwargs
        if past_key_values:
            input_ids = input_ids[:, -1].unsqueeze(-1)

        if inputs_embeds is not None and past_key_values is None:
            model_inputs = {"inputs_embeds": inputs_embeds}
        else:
            model_inputs = {"input_ids": input_ids}

        model_inputs.update(
            {
                "attention_mask": attention_mask,
                "past_key_values": past_key_values,
                "use_cache": kwargs.get("use_cache"),
            }
        )

        return model_inputs

    @staticmethod
    def _reorder_cache(past_key_values, beam_idx):
        reordered_past = ()
        for layer_past in past_key_values:
            reordered_past += (tuple(past_state.index_select(0, beam_idx) for past_state in layer_past),)
        return reordered_past


@add_start_docstrings(
    """
    BioGPT 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.
    """,
    BIOGPT_START_DOCSTRING,
)
class BioGptForTokenClassification(BioGptPreTrainedModel):
    def __init__(self, config):
        super().__init__(config)
        self.num_labels = config.num_labels

        self.biogpt = BioGptModel(config)
        if hasattr(config, "classifier_dropout") and config.classifier_dropout is not None:
            classifier_dropout = config.classifier_dropout
        else:
            classifier_dropout = config.hidden_dropout_prob
        self.dropout = nn.Dropout(classifier_dropout)
        self.classifier = nn.Linear(config.hidden_size, config.num_labels)

        self.post_init()

    @add_start_docstrings_to_model_forward(BIOGPT_INPUTS_DOCSTRING)
    @add_code_sample_docstrings(
        checkpoint=_CHECKPOINT_FOR_DOC,
        output_type=TokenClassifierOutput,
        config_class=_CONFIG_FOR_DOC,
    )
    def forward(
        self,
        input_ids: Optional[torch.LongTensor] = None,
        token_type_ids: Optional[torch.LongTensor] = None,
        attention_mask: Optional[torch.FloatTensor] = None,
        head_mask: Optional[torch.FloatTensor] = None,
        past_key_values: Optional[Tuple[Tuple[torch.Tensor]]] = None,
        inputs_embeds: Optional[torch.FloatTensor] = None,
        labels: Optional[torch.LongTensor] = None,
        use_cache: Optional[bool] = None,
        output_attentions: Optional[bool] = None,
        output_hidden_states: Optional[bool] = None,
        return_dict: Optional[bool] = None,
    ) -> Union[Tuple, TokenClassifierOutput]:
        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

        transformer_outputs = self.biogpt(
            input_ids,
            past_key_values=past_key_values,
            attention_mask=attention_mask,
            head_mask=head_mask,
            inputs_embeds=inputs_embeds,
            use_cache=use_cache,
            output_attentions=output_attentions,
            output_hidden_states=output_hidden_states,
            return_dict=return_dict,
        )

        hidden_states = transformer_outputs[0]
        hidden_states = self.dropout(hidden_states)
        logits = self.classifier(hidden_states)

        loss = None
        if labels is not None:
            loss_fct = CrossEntropyLoss()
            # Only keep active parts of the loss
            if attention_mask is not None:
                active_loss = attention_mask.view(-1) == 1
                active_logits = logits.view(-1, self.num_labels)
                active_labels = torch.where(
                    active_loss, labels.view(-1), torch.tensor(loss_fct.ignore_index).type_as(labels)
                )
                loss = loss_fct(active_logits, active_labels)
            else:
                loss = loss_fct(logits.view(-1, self.num_labels), labels.view(-1))

        if not return_dict:
            output = (logits,) + transformer_outputs[2:]
            return ((loss,) + output) if loss is not None else output

        return TokenClassifierOutput(
            loss=loss,
            logits=logits,
            hidden_states=transformer_outputs.hidden_states,
            attentions=transformer_outputs.attentions,
        )


@add_start_docstrings(
    """
    The BioGpt Model transformer with a sequence classification head on top (linear layer).

    [`BioGptForSequenceClassification`] uses the last token in order to do the classification, as other causal models
    (e.g. GPT-2) do.

    Since it does classification on the last token, it is required to know the position of the last token. If a
    `pad_token_id` is defined in the configuration, it finds the last token that is not a padding token in each row. If
    no `pad_token_id` is defined, it simply takes the last value in each row of the batch. Since it cannot guess the
    padding tokens when `inputs_embeds` are passed instead of `input_ids`, it does the same (take the last value in
    each row of the batch).
    """,
    BIOGPT_START_DOCSTRING,
)
class BioGptForSequenceClassification(BioGptPreTrainedModel):
    def __init__(self, config: BioGptConfig):
        super().__init__(config)
        self.num_labels = config.num_labels
        self.biogpt = BioGptModel(config)
        self.score = nn.Linear(config.hidden_size, self.num_labels, bias=False)

        # Initialize weights and apply final processing
        self.post_init()

    @add_start_docstrings_to_model_forward(BIOGPT_INPUTS_DOCSTRING)
    @add_code_sample_docstrings(
        checkpoint=_CHECKPOINT_FOR_DOC,
        output_type=SequenceClassifierOutputWithPast,
        config_class=_CONFIG_FOR_DOC,
    )
    def forward(
        self,
        input_ids: Optional[torch.LongTensor] = None,
        attention_mask: Optional[torch.FloatTensor] = None,
        head_mask: Optional[torch.FloatTensor] = None,
        past_key_values: Optional[Tuple[Tuple[torch.Tensor]]] = None,
        inputs_embeds: Optional[torch.FloatTensor] = None,
        labels: Optional[torch.LongTensor] = None,
        use_cache: Optional[bool] = None,
        output_attentions: Optional[bool] = None,
        output_hidden_states: Optional[bool] = None,
        return_dict: Optional[bool] = None,
    ) -> Union[Tuple, SequenceClassifierOutputWithPast]:
        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

        transformer_outputs = self.biogpt(
            input_ids,
            past_key_values=past_key_values,
            attention_mask=attention_mask,
            head_mask=head_mask,
            inputs_embeds=inputs_embeds,
            use_cache=use_cache,
            output_attentions=output_attentions,
            output_hidden_states=output_hidden_states,
            return_dict=return_dict,
        )
        hidden_states = transformer_outputs[0]
        logits = self.score(hidden_states)

        if input_ids is not None:
            batch_size, sequence_length = input_ids.shape[:2]
        else:
            batch_size, sequence_length = inputs_embeds.shape[:2]

        if self.config.pad_token_id is None:
            sequence_length = -1
        else:
            if input_ids is not None:
                sequence_length = (torch.ne(input_ids, self.config.pad_token_id).sum(-1) - 1).to(logits.device)
            else:
                sequence_length = -1
                logger.warning(
                    f"{self.__class__.__name__} will not detect padding tokens in `inputs_embeds`. Results may be "
                    "unexpected if using padding tokens in conjunction with `inputs_embeds.`"
                )

        pooled_logits = logits[torch.arange(batch_size, device=logits.device), sequence_length]

        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(pooled_logits.squeeze(), labels.squeeze())
                else:
                    loss = loss_fct(pooled_logits, labels)
            elif self.config.problem_type == "single_label_classification":
                loss_fct = CrossEntropyLoss()
                loss = loss_fct(pooled_logits.view(-1, self.num_labels), labels.view(-1))
            elif self.config.problem_type == "multi_label_classification":
                loss_fct = BCEWithLogitsLoss()
                loss = loss_fct(pooled_logits, labels)
        if not return_dict:
            output = (pooled_logits,) + transformer_outputs[1:]
            return ((loss,) + output) if loss is not None else output

        return SequenceClassifierOutputWithPast(
            loss=loss,
            logits=pooled_logits,
            past_key_values=transformer_outputs.past_key_values,
            hidden_states=transformer_outputs.hidden_states,
            attentions=transformer_outputs.attentions,
        )

    def get_input_embeddings(self):
        return self.biogpt.embed_tokens

    def set_input_embeddings(self, value):
        self.biogpt.embed_tokens = value