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

# 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

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

from ...activations import ACT2FN
from ...cache_utils import Cache, DynamicCache
from ...generation import GenerationMixin
from ...masking_utils import create_causal_mask
from ...modeling_outputs import (
    BaseModelOutputWithPastAndCrossAttentions,
    CausalLMOutputWithCrossAttentions,
    SequenceClassifierOutputWithPast,
    TokenClassifierOutput,
)
from ...modeling_utils import PreTrainedModel
from ...processing_utils import Unpack
from ...utils import (
    TransformersKwargs,
    auto_docstring,
    can_return_tuple,
    logger,
)
from ...utils.generic import merge_with_config_defaults
from ...utils.output_capturing import capture_outputs
from ..bart.modeling_bart import (
    BartAttention,
    BartDecoderLayer,
    BartScaledWordEmbedding,
)
from ..opt.modeling_opt import OPTLearnedPositionalEmbedding
from .configuration_biogpt import BioGptConfig


class BioGptLearnedPositionalEmbedding(OPTLearnedPositionalEmbedding):
    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]."""
        return super().forward(attention_mask, past_key_values_length, position_ids)


class BioGptScaledWordEmbedding(BartScaledWordEmbedding):
    pass


class BioGptAttention(BartAttention):
    pass


class BioGptDecoderLayer(BartDecoderLayer):
    def __init__(self, config: BioGptConfig, layer_idx: int | None = None):
        super().__init__(config)
        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.fc1 = nn.Linear(self.embed_dim, config.intermediate_size)
        self.fc2 = nn.Linear(config.intermediate_size, self.embed_dim)

        del self.encoder_attn
        del self.encoder_attn_layer_norm

    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",
]