image-match/python/py/Lib/site-packages/transformers/models/biogpt/modeling_biogpt.py

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# 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.

import math
from collections.abc import Callable

import torch
import torch.nn as nn
from torch.nn import BCEWithLogitsLoss, CrossEntropyLoss, MSELoss

from ...activations import ACT2FN
from ...cache_utils import Cache, DynamicCache, EncoderDecoderCache
from ...generation import GenerationMixin
from ...masking_utils import create_causal_mask
from ...modeling_flash_attention_utils import FlashAttentionKwargs
from ...modeling_layers import GradientCheckpointingLayer
from ...modeling_outputs import (
    BaseModelOutputWithPastAndCrossAttentions,
    CausalLMOutputWithCrossAttentions,
    SequenceClassifierOutputWithPast,
    TokenClassifierOutput,
)
from ...modeling_utils import ALL_ATTENTION_FUNCTIONS, PreTrainedModel
from ...processing_utils import Unpack
from ...utils import TransformersKwargs, auto_docstring, can_return_tuple, logging
from ...utils.generic import merge_with_config_defaults
from ...utils.output_capturing import capture_outputs
from .configuration_biogpt import BioGptConfig


logger = logging.get_logger(__name__)


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,
        position_ids: torch.LongTensor | None = None,
    ):
        """`input_ids_shape` is expected to be [bsz x seqlen]."""

        if position_ids is None:
            position_ids = torch.cumsum(attention_mask, dim=1)
            position_ids = (position_ids * attention_mask - 1).long()
            # cut positions if `past_key_values_length` is > 0
            position_ids = position_ids[:, past_key_values_length:]

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


class BioGptScaledWordEmbedding(nn.Embedding):
    """
    This module overrides nn.Embeddings' forward by multiplying with embeddings scale.
    """

    def __init__(self, num_embeddings: int, embedding_dim: int, padding_idx: int, embed_scale: float | None = 1.0):
        super().__init__(num_embeddings, embedding_dim, padding_idx)
        self.embed_scale = embed_scale

    def forward(self, input_ids: torch.Tensor):
        return super().forward(input_ids) * self.embed_scale


def eager_attention_forward(
    module: nn.Module,
    query: torch.Tensor,
    key: torch.Tensor,
    value: torch.Tensor,
    attention_mask: torch.Tensor | None,
    scaling: float | None = None,
    dropout: float = 0.0,
    **kwargs: Unpack[TransformersKwargs],
):
    if scaling is None:
        scaling = query.size(-1) ** -0.5

    # Take the dot product between "query" and "key" to get the raw attention scores.
    attn_weights = torch.matmul(query, key.transpose(2, 3)) * scaling

    if attention_mask is not None:
        attn_weights = attn_weights + attention_mask

    attn_weights = nn.functional.softmax(attn_weights, dim=-1)
    attn_weights = nn.functional.dropout(attn_weights, p=dropout, training=module.training)

    attn_output = torch.matmul(attn_weights, value)
    attn_output = attn_output.transpose(1, 2).contiguous()

    return attn_output, attn_weights


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,
        is_causal: bool = False,
        config: BioGptConfig | None = None,
        layer_idx: int | None = None,
    ):
        super().__init__()
        self.embed_dim = embed_dim
        self.num_heads = num_heads
        self.dropout = dropout
        self.head_dim = embed_dim // num_heads
        self.config = config

        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.is_causal = is_causal
        self.layer_idx = layer_idx
        if layer_idx is None and self.is_decoder:
            logger.warning_once(
                f"Instantiating a decoder {self.__class__.__name__} without passing `layer_idx` is not recommended and "
                "will lead to errors during the forward call, if caching is used. Please make sure to provide a `layer_idx` "
                "when creating this class."
            )

        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 forward(
        self,
        hidden_states: torch.Tensor,
        key_value_states: torch.Tensor | None = None,
        past_key_values: Cache | None = None,
        attention_mask: torch.Tensor | None = None,
        # TODO: we need a refactor so that the different attention modules can get their specific kwargs
        # ATM, we have mixed things encoder, decoder, and encoder-decoder attn
        **kwargs: Unpack[FlashAttentionKwargs],
    ) -> tuple[torch.Tensor, torch.Tensor | None]:
        """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

        # determine input shapes
        input_shape = hidden_states.shape[:-1]

        hidden_shape = (*input_shape, -1, self.head_dim)

        # get query proj
        query_states = self.q_proj(hidden_states).view(hidden_shape).transpose(1, 2)

        is_updated = False
        if past_key_values is not None:
            if isinstance(past_key_values, EncoderDecoderCache):
                is_updated = past_key_values.is_updated.get(self.layer_idx)
                if is_cross_attention:
                    # after the first generated id, we can subsequently re-use all key/value_states from cache
                    curr_past_key_values = past_key_values.cross_attention_cache
                else:
                    curr_past_key_values = past_key_values.self_attention_cache
            else:
                curr_past_key_values = past_key_values

        current_states = key_value_states if is_cross_attention else hidden_states
        if is_cross_attention and past_key_values is not None and is_updated:
            # reuse k,v, cross_attentions
            key_states = curr_past_key_values.layers[self.layer_idx].keys
            value_states = curr_past_key_values.layers[self.layer_idx].values
        else:
            key_states = self.k_proj(current_states)
            value_states = self.v_proj(current_states)
            kv_shape = (*current_states.shape[:-1], -1, self.head_dim)
            key_states = key_states.view(kv_shape).transpose(1, 2)
            value_states = value_states.view(kv_shape).transpose(1, 2)

            if past_key_values is not None:
                key_states, value_states = curr_past_key_values.update(key_states, value_states, self.layer_idx)
                # set flag that curr layer for cross-attn is already updated so we can re-use in subsequent calls
                if is_cross_attention and isinstance(past_key_values, EncoderDecoderCache):
                    past_key_values.is_updated[self.layer_idx] = True

        attention_interface: Callable = ALL_ATTENTION_FUNCTIONS.get_interface(
            self.config._attn_implementation, eager_attention_forward
        )

        attn_output, attn_weights = attention_interface(
            self,
            query_states,
            key_states,
            value_states,
            attention_mask,
            dropout=0.0 if not self.training else self.dropout,
            scaling=self.scaling,
            **kwargs,
        )

        attn_output = attn_output.reshape(*input_shape, -1).contiguous()
        attn_output = self.out_proj(attn_output)

        return attn_output, attn_weights


class BioGptDecoderLayer(GradientCheckpointingLayer):
    def __init__(self, config: BioGptConfig, layer_idx: int | None = None):
        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,
            is_causal=True,
            config=config,
            layer_idx=layer_idx,
        )
        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: torch.Tensor | None = None,
        past_key_values: Cache | None = None,
        use_cache: bool | None = True,
        position_ids: torch.LongTensor | None = None,
        **kwargs: Unpack[TransformersKwargs],
    ) -> torch.Tensor:
        """
        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.
            past_key_values (`Cache`): cached past key and value projection states
        """
        residual = hidden_states

        hidden_states = self.self_attn_layer_norm(hidden_states)

        # Self Attention
        hidden_states, _ = self.self_attn(
            hidden_states=hidden_states,
            past_key_values=past_key_values,
            attention_mask=attention_mask,
            position_ids=position_ids,
            **kwargs,
        )
        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

        return hidden_states


@auto_docstring
class BioGptPreTrainedModel(PreTrainedModel):
    config: BioGptConfig
    base_model_prefix = "biogpt"
    supports_gradient_checkpointing = True
    _supports_flash_attn = True
    _supports_sdpa = True
    _supports_flex_attn = True
    _can_compile_fullgraph = True
    _can_record_outputs = {
        "hidden_states": BioGptDecoderLayer,
        "attentions": BioGptAttention,
    }


@auto_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
        embed_scale = math.sqrt(config.hidden_size) if config.scale_embedding else 1.0

        self.embed_tokens = BioGptScaledWordEmbedding(
            config.vocab_size, self.embed_dim, self.padding_idx, embed_scale=embed_scale
        )
        self.embed_positions = BioGptLearnedPositionalEmbedding(config.max_position_embeddings, self.embed_dim)

        self.layers = nn.ModuleList([BioGptDecoderLayer(config, layer_idx=i) for i 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()

    @merge_with_config_defaults
    @capture_outputs
    @auto_docstring
    def forward(
        self,
        input_ids: torch.LongTensor | None = None,
        attention_mask: torch.FloatTensor | None = None,
        inputs_embeds: torch.FloatTensor | None = None,
        past_key_values: Cache | None = None,
        use_cache: bool | None = None,
        position_ids: torch.LongTensor | None = None,
        **kwargs: Unpack[TransformersKwargs],
    ) -> tuple | BaseModelOutputWithPastAndCrossAttentions:
        if (input_ids is None) ^ (inputs_embeds is not None):
            raise ValueError("You cannot specify both decoder_input_ids and decoder_inputs_embeds at the same time")

        if inputs_embeds is None:
            inputs_embeds = self.embed_tokens(input_ids)

        # initialize past_key_values
        if use_cache and past_key_values is None:
            past_key_values = DynamicCache(config=self.config)

        batch_size, seq_length = inputs_embeds.size()[:-1]
        past_key_values_length = past_key_values.get_seq_length() if past_key_values is not None else 0

        if attention_mask is None:
            # required mask seq length can be calculated via length of past cache
            mask_seq_length = past_key_values_length + seq_length
            attention_mask = torch.ones(batch_size, mask_seq_length, device=inputs_embeds.device)

        self_attn_cache = past_key_values

        causal_mask = create_causal_mask(
            config=self.config,
            input_embeds=inputs_embeds,
            attention_mask=attention_mask,
            past_key_values=self_attn_cache,
        )

        # embed positions
        if position_ids is None:
            position_ids = torch.arange(seq_length, device=inputs_embeds.device) + past_key_values_length
            position_ids = position_ids.unsqueeze(0)

        positions = self.embed_positions(attention_mask, past_key_values_length, position_ids=position_ids)
        hidden_states = inputs_embeds + positions
        hidden_states = nn.functional.dropout(hidden_states, p=self.dropout, training=self.training)

        for idx, decoder_layer in enumerate(self.layers):
            if self.training:
                dropout_probability = torch.rand([])
                if dropout_probability < self.layerdrop:
                    continue

            hidden_states = decoder_layer(
                hidden_states,
                attention_mask=causal_mask,
                past_key_values=past_key_values,
                use_cache=use_cache,
                position_ids=position_ids,
                **kwargs,
            )

        hidden_states = self.layer_norm(hidden_states)

        return BaseModelOutputWithPastAndCrossAttentions(
            last_hidden_state=hidden_states,
            past_key_values=past_key_values,
        )


@auto_docstring(
    custom_intro="""
    BioGPT Model with a `language modeling` head on top for CLM fine-tuning.
    """
)
class BioGptForCausalLM(BioGptPreTrainedModel, GenerationMixin):
    _tied_weights_keys = {"output_projection.weight": "biogpt.embed_tokens.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

    @can_return_tuple
    @auto_docstring
    def forward(
        self,
        input_ids: torch.LongTensor | None = None,
        attention_mask: torch.FloatTensor | None = None,
        inputs_embeds: torch.FloatTensor | None = None,
        past_key_values: Cache | None = None,
        labels: torch.LongTensor | None = None,
        use_cache: bool | None = None,
        position_ids: torch.LongTensor | None = None,
        logits_to_keep: int | torch.Tensor = 0,
        **kwargs: Unpack[TransformersKwargs],
    ) -> 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]`
        """
        outputs = self.biogpt(
            input_ids,
            attention_mask=attention_mask,
            inputs_embeds=inputs_embeds,
            past_key_values=past_key_values,
            use_cache=use_cache,
            position_ids=position_ids,
            **kwargs,
        )

        hidden_states = outputs[0]
        slice_indices = slice(-logits_to_keep, None) if isinstance(logits_to_keep, int) else logits_to_keep
        logits = self.output_projection(hidden_states[:, slice_indices, :])

        loss = None
        if labels is not None:
            loss = self.loss_function(logits=logits, labels=labels, vocab_size=self.config.vocab_size, **kwargs)

        return CausalLMOutputWithCrossAttentions(
            loss=loss,
            logits=logits,
            past_key_values=outputs.past_key_values,
            hidden_states=outputs.hidden_states,
            attentions=outputs.attentions,
            cross_attentions=outputs.cross_attentions,
        )


@auto_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()

    @can_return_tuple
    @auto_docstring
    def forward(
        self,
        input_ids: torch.LongTensor | None = None,
        token_type_ids: torch.LongTensor | None = None,
        attention_mask: torch.FloatTensor | None = None,
        past_key_values: Cache | None = None,
        inputs_embeds: torch.FloatTensor | None = None,
        labels: torch.LongTensor | None = None,
        use_cache: bool | None = None,
        position_ids: torch.LongTensor | None = None,
        **kwargs,
    ) -> 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).
        """
        transformer_outputs = self.biogpt(
            input_ids,
            past_key_values=past_key_values,
            attention_mask=attention_mask,
            inputs_embeds=inputs_embeds,
            use_cache=use_cache,
            position_ids=position_ids,
            **kwargs,
        )

        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()
            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))

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


@auto_docstring(
    custom_intro="""
    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).
    """
)
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()

    @can_return_tuple
    @auto_docstring
    def forward(
        self,
        input_ids: torch.LongTensor | None = None,
        attention_mask: torch.FloatTensor | None = None,
        past_key_values: Cache | None = None,
        inputs_embeds: torch.FloatTensor | None = None,
        labels: torch.LongTensor | None = None,
        use_cache: bool | None = None,
        position_ids: torch.LongTensor | None = None,
        logits_to_keep: int | torch.Tensor = 0,
        **kwargs,
    ) -> 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).
        """
        transformer_outputs = self.biogpt(
            input_ids,
            past_key_values=past_key_values,
            attention_mask=attention_mask,
            inputs_embeds=inputs_embeds,
            use_cache=use_cache,
            position_ids=position_ids,
            **kwargs,
        )
        hidden_states = transformer_outputs[0]
        slice_indices = slice(-logits_to_keep, None) if isinstance(logits_to_keep, int) else logits_to_keep
        logits = self.score(hidden_states[:, slice_indices, :])

        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_once(
                    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)

        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


__all__ = [
    "BioGptForCausalLM",
    "BioGptForTokenClassification",
    "BioGptForSequenceClassification",
    "BioGptModel",
    "BioGptPreTrainedModel",
]