AutoAndroidController/py/venv/Lib/site-packages/transformers/models/evolla/modeling_evolla.py

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#           This file was automatically generated from src/transformers/models/evolla/modular_evolla.py.
#               Do NOT edit this file manually as any edits will be overwritten by the generation of
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#                          modular_evolla.py file directly. One of our CI enforces this.
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# coding=utf-8
# Copyright 2025 Westlake Representational Learning Lab (Fajie Yuan Lab) team and the HuggingFace Inc. team. 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
import warnings
from dataclasses import dataclass
from typing import Callable, Optional, Union

import torch
from torch import Tensor, nn

from ...activations import ACT2FN
from ...cache_utils import Cache, DynamicCache
from ...generation import GenerationMixin
from ...integrations import use_kernel_forward_from_hub
from ...masking_utils import create_causal_mask
from ...modeling_layers import GradientCheckpointingLayer
from ...modeling_outputs import (
    BaseModelOutputWithCrossAttentions,
    BaseModelOutputWithPast,
    BaseModelOutputWithPoolingAndCrossAttentions,
    CausalLMOutputWithPast,
    ModelOutput,
)
from ...modeling_rope_utils import ROPE_INIT_FUNCTIONS, dynamic_rope_update
from ...modeling_utils import ALL_ATTENTION_FUNCTIONS, ModuleUtilsMixin, PreTrainedModel, get_parameter_dtype
from ...processing_utils import Unpack
from ...pytorch_utils import find_pruneable_heads_and_indices, prune_linear_layer
from ...utils import TransformersKwargs, auto_docstring, can_return_tuple
from ...utils.deprecation import deprecate_kwarg
from ...utils.generic import OutputRecorder, check_model_inputs
from .configuration_evolla import EvollaConfig, SaProtConfig


def create_position_ids_from_input_ids(input_ids, padding_idx):
    """
    Replace non-padding symbols with their position numbers. Position numbers begin at padding_idx+1. Padding symbols
    are ignored. This is modified from fairseq's `utils.make_positions`.

    Args:
        x: torch.Tensor x:

    Returns: torch.Tensor
    """
    # The series of casts and type-conversions here are carefully balanced to both work with ONNX export and XLA.
    mask = input_ids.ne(padding_idx).int()
    incremental_indices = torch.cumsum(mask, dim=1).type_as(mask) * mask
    return incremental_indices.long() + padding_idx


class EvollaSaProtEmbeddings(nn.Module):
    """
    Same as BertEmbeddings with a tiny tweak for positional embeddings indexing.
    """

    def __init__(self, config):
        super().__init__()
        self.word_embeddings = nn.Embedding(config.vocab_size, config.hidden_size, padding_idx=config.pad_token_id)

        if config.emb_layer_norm_before:
            self.layer_norm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
        else:
            self.layer_norm = None
        self.dropout = nn.Dropout(config.hidden_dropout_prob)
        # position_ids (1, len position emb) is contiguous in memory and exported when serialized
        self.position_embedding_type = getattr(config, "position_embedding_type", "absolute")
        self.register_buffer(
            "position_ids", torch.arange(config.max_position_embeddings).expand((1, -1)), persistent=False
        )

        self.padding_idx = config.pad_token_id
        if self.position_embedding_type == "absolute":
            self.position_embeddings = nn.Embedding(
                config.max_position_embeddings, config.hidden_size, padding_idx=self.padding_idx
            )
        self.token_dropout = config.token_dropout
        self.mask_token_id = config.mask_token_id
        # remove the position_ids in EsmEmbeddings
        self.position_ids = None

    def forward(
        self,
        input_ids=None,
        attention_mask=None,
        position_ids=None,
        inputs_embeds=None,
    ):
        if position_ids is None:
            if input_ids is not None:
                # Create the position ids from the input token ids. Any padded tokens remain padded.
                position_ids = create_position_ids_from_input_ids(input_ids, self.padding_idx)
            else:
                position_ids = self.create_position_ids_from_inputs_embeds(inputs_embeds)

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

        # Note that if we want to support EVOLLA_SA_PROT-1 (not 1b!) in future then we need to support an
        # embedding_scale factor here.
        embeddings = inputs_embeds

        # Matt: EVOLLA_SA_PROT has the option to handle masking in MLM in a slightly unusual way. If the token_dropout
        # flag is False then it is handled in the same was as BERT/RoBERTa. If it is set to True, however,
        # masked tokens are treated as if they were selected for input dropout and zeroed out.
        # This "mask-dropout" is compensated for when masked tokens are not present, by scaling embeddings by
        # a factor of (fraction of unmasked tokens during training) / (fraction of unmasked tokens in sample).
        # This is analogous to the way that dropout layers scale down outputs during evaluation when not
        # actually dropping out values (or, equivalently, scale up their un-dropped outputs in training).
        if self.token_dropout and input_ids is not None:
            embeddings = embeddings.masked_fill((input_ids == self.mask_token_id).unsqueeze(-1), 0.0)
            mask_ratio_train = 0.15 * 0.8  # Hardcoded as the ratio used in all EVOLLA_SA_PROT model training runs
            src_lengths = attention_mask.sum(-1) if attention_mask is not None else input_ids.shape[1]
            mask_ratio_observed = (input_ids == self.mask_token_id).sum(-1).float() / src_lengths
            embeddings = (embeddings * (1 - mask_ratio_train) / (1 - mask_ratio_observed)[:, None, None]).to(
                embeddings.dtype
            )

        if self.position_embedding_type == "absolute":
            position_embeddings = self.position_embeddings(position_ids)
            embeddings = embeddings + position_embeddings

        if self.layer_norm is not None:
            embeddings = self.layer_norm(embeddings)
        if attention_mask is not None:
            embeddings = (embeddings * attention_mask.unsqueeze(-1)).to(embeddings.dtype)
        # Matt: I think this line was copied incorrectly from BERT, disabling it for now.
        # embeddings = self.dropout(embeddings)
        return embeddings

    def create_position_ids_from_inputs_embeds(self, inputs_embeds):
        """
        We are provided embeddings directly. We cannot infer which are padded so just generate sequential position ids.

        Args:
            inputs_embeds: torch.Tensor

        Returns: torch.Tensor
        """
        input_shape = inputs_embeds.size()[:-1]
        sequence_length = input_shape[1]

        position_ids = torch.arange(
            self.padding_idx + 1, sequence_length + self.padding_idx + 1, dtype=torch.long, device=inputs_embeds.device
        )
        return position_ids.unsqueeze(0).expand(input_shape)


def rotate_half_esm(x):
    x1, x2 = x.chunk(2, dim=-1)
    return torch.cat((-x2, x1), dim=-1)


def apply_rotary_pos_emb_esm(x, cos, sin):
    cos = cos[:, :, : x.shape[-2], :]
    sin = sin[:, :, : x.shape[-2], :]

    return (x * cos) + (rotate_half_esm(x) * sin)


class EvollaSaProtRotaryEmbedding(nn.Module):
    """
    Rotary position embeddings based on those in
    [RoFormer](https://huggingface.co/docs/transformers/model_doc/roformer). Query and keys are transformed by rotation
    matrices which depend on their relative positions.
    """

    inv_freq: torch.Tensor  # fix linting for `register_buffer`

    def __init__(self, dim: int):
        super().__init__()
        # Generate and save the inverse frequency buffer (non trainable)
        inv_freq = 1.0 / (10000 ** (torch.arange(0, dim, 2, dtype=torch.int64).float() / dim))
        self.register_buffer("inv_freq", inv_freq)

        self._seq_len_cached = None
        self._cos_cached = None
        self._sin_cached = None

    def _update_cos_sin_tables(self, x, seq_dimension=2):
        seq_len = x.shape[seq_dimension]

        # Reset the tables if the sequence length has changed,
        # or if we're on a new device (possibly due to tracing for instance)
        if seq_len != self._seq_len_cached or self._cos_cached.device != x.device:
            self._seq_len_cached = seq_len
            t = torch.arange(x.shape[seq_dimension], device=x.device).type_as(self.inv_freq)
            freqs = torch.outer(t, self.inv_freq)
            emb = torch.cat((freqs, freqs), dim=-1).to(x.device)

            self._cos_cached = emb.cos()[None, None, :, :]
            self._sin_cached = emb.sin()[None, None, :, :]

        return self._cos_cached, self._sin_cached

    def forward(self, q: torch.Tensor, k: torch.Tensor) -> tuple[torch.Tensor, torch.Tensor]:
        self._cos_cached, self._sin_cached = self._update_cos_sin_tables(k, seq_dimension=-2)

        return (
            apply_rotary_pos_emb_esm(q, self._cos_cached, self._sin_cached).to(dtype=q.dtype),
            apply_rotary_pos_emb_esm(k, self._cos_cached, self._sin_cached).to(dtype=k.dtype),
        )


def eager_attention_forward(
    module: nn.Module,
    query: torch.Tensor,
    key: torch.Tensor,
    value: torch.Tensor,
    attention_mask: Optional[torch.Tensor],
    scaling: float,
    dropout: float = 0.0,
    head_mask: Optional[torch.Tensor] = None,
    **kwargs: Unpack[TransformersKwargs],
):
    # EVOLLA_SA_PROT applies relative position embeddings and we don't copy from Llama
    attn_weights = torch.matmul(query, key.transpose(2, 3)) * scaling

    if hasattr(module, "position_embedding_type") and module.position_embedding_type in [
        "relative_key",
        "relative_key_query",
    ]:
        seq_length = query.shape[2]
        position_ids_l = torch.arange(seq_length, dtype=torch.long, device=attn_weights.device).view(-1, 1)
        position_ids_r = torch.arange(seq_length, dtype=torch.long, device=attn_weights.device).view(1, -1)
        distance = position_ids_l - position_ids_r
        positional_embedding = module.distance_embedding(distance + module.max_position_embeddings - 1)
        positional_embedding = positional_embedding.to(dtype=query.dtype)  # fp16 compatibility

        if module.position_embedding_type == "relative_key":
            relative_position_scores = torch.einsum("bhld,lrd->bhlr", query, positional_embedding)
        elif module.position_embedding_type == "relative_key_query":
            relative_position_scores_query = torch.einsum("bhld,lrd->bhlr", query, positional_embedding)
            relative_position_scores_key = torch.einsum("bhrd,lrd->bhlr", key, positional_embedding)
            relative_position_scores = relative_position_scores_query + relative_position_scores_key

        attn_weights = attn_weights + relative_position_scores

    if attention_mask is not None:
        causal_mask = attention_mask[:, :, :, : key.shape[-2]]
        attn_weights = attn_weights + causal_mask

    attn_weights = nn.functional.softmax(attn_weights, dim=-1, dtype=torch.float32).to(query.dtype)
    attn_weights = nn.functional.dropout(attn_weights, p=dropout, training=module.training)

    if head_mask is not None:
        attn_weights = attn_weights * head_mask

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

    return attn_output, attn_weights


class EvollaSaProtSelfAttention(nn.Module):
    def __init__(self, config, position_embedding_type=None, layer_idx=None, is_cross_attention=False):
        super().__init__()
        self.config = config

        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.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 = config.attention_probs_dropout_prob
        self.position_embedding_type = position_embedding_type or getattr(
            config, "position_embedding_type", "absolute"
        )
        self.rotary_embeddings = None
        if self.position_embedding_type == "relative_key" or self.position_embedding_type == "relative_key_query":
            self.max_position_embeddings = config.max_position_embeddings
            self.distance_embedding = nn.Embedding(2 * config.max_position_embeddings - 1, self.attention_head_size)
        elif self.position_embedding_type == "rotary":
            self.rotary_embeddings = EvollaSaProtRotaryEmbedding(dim=self.attention_head_size)

        self.is_decoder = config.is_decoder
        self.layer_idx = layer_idx
        self.scaling = 1.0
        self.is_causal = self.is_decoder and not is_cross_attention

    def forward(
        self,
        hidden_states: torch.Tensor,
        attention_mask: Optional[torch.FloatTensor] = None,
        head_mask: Optional[torch.FloatTensor] = None,
        encoder_hidden_states: Optional[torch.FloatTensor] = None,
        encoder_attention_mask: Optional[torch.FloatTensor] = None,
        **kwargs: Unpack[TransformersKwargs],
    ) -> tuple[torch.Tensor]:
        batch_size, seq_length = hidden_states.shape[:-1]
        hidden_shape = (batch_size, seq_length, -1, self.attention_head_size)

        query_layer = self.query(hidden_states).view(hidden_shape).transpose(1, 2)

        is_cross_attention = encoder_hidden_states is not None
        current_states = encoder_hidden_states if is_cross_attention else hidden_states
        attention_mask = encoder_attention_mask if is_cross_attention else attention_mask
        key_layer = self.key(current_states).view(hidden_shape).transpose(1, 2)
        value_layer = self.value(current_states).view(hidden_shape).transpose(1, 2)

        # Matt: Our BERT model (which this code was derived from) scales attention logits down by sqrt(head_dim).
        # EVOLLA_SA_PROT scales the query down by the same factor instead. Modulo numerical stability these are equivalent,
        # but not when rotary embeddings get involved. Therefore, we scale the query here to match the original
        # EVOLLA_SA_PROT code and fix rotary embeddings.
        query_layer = query_layer * self.attention_head_size**-0.5

        if self.position_embedding_type == "rotary":
            query_layer, key_layer = self.rotary_embeddings(query_layer, key_layer)

        attention_interface: Callable = eager_attention_forward
        if self.config._attn_implementation != "eager":
            if self.position_embedding_type in ["relative_key", "relative_key_query"]:
                raise ValueError(
                    f"ESM {self.config._attn_implementation} attention does not support {self.position_embedding_type} embeddings. "
                    "Set attention explicitly to 'eager' with `model.set_attn_implementation('eager')`"
                )
            attention_interface = ALL_ATTENTION_FUNCTIONS[self.config._attn_implementation]

        attn_output, attn_weights = attention_interface(
            self,
            query_layer,
            key_layer,
            value_layer,
            attention_mask,
            dropout=0.0 if not self.training else self.dropout,
            scaling=self.scaling,
            head_mask=head_mask,
            **kwargs,
        )

        attn_output = attn_output.reshape(batch_size, seq_length, -1).contiguous()
        return attn_output, attn_weights


class EvollaSaProtSelfOutput(nn.Module):
    def __init__(self, config):
        super().__init__()
        self.dense = nn.Linear(config.hidden_size, config.hidden_size)
        self.dropout = nn.Dropout(config.hidden_dropout_prob)

    def forward(self, hidden_states, input_tensor):
        hidden_states = self.dense(hidden_states)
        hidden_states = self.dropout(hidden_states)
        hidden_states = hidden_states + input_tensor
        return hidden_states


class EvollaSaProtAttention(nn.Module):
    def __init__(self, config, layer_idx=None, is_cross_attention=False):
        super().__init__()
        self.self = EvollaSaProtSelfAttention(config, layer_idx=layer_idx, is_cross_attention=is_cross_attention)
        self.output = EvollaSaProtSelfOutput(config)
        self.pruned_heads = set()
        self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)

    def prune_heads(self, heads):
        if len(heads) == 0:
            return
        heads, index = find_pruneable_heads_and_indices(
            heads, self.self.num_attention_heads, self.self.attention_head_size, self.pruned_heads
        )

        # Prune linear layers
        self.self.query = prune_linear_layer(self.self.query, index)
        self.self.key = prune_linear_layer(self.self.key, index)
        self.self.value = prune_linear_layer(self.self.value, index)
        self.output.dense = prune_linear_layer(self.output.dense, index, dim=1)

        # Update hyper params and store pruned heads
        self.self.num_attention_heads = self.self.num_attention_heads - len(heads)
        self.self.all_head_size = self.self.attention_head_size * self.self.num_attention_heads
        self.pruned_heads = self.pruned_heads.union(heads)

    def forward(
        self,
        hidden_states,
        attention_mask=None,
        head_mask=None,
        encoder_hidden_states=None,
        encoder_attention_mask=None,
        **kwargs: Unpack[TransformersKwargs],
    ):
        hidden_states_ln = self.LayerNorm(hidden_states)
        attn_output, _ = self.self(
            hidden_states_ln,
            attention_mask=attention_mask,
            head_mask=head_mask,
            encoder_hidden_states=encoder_hidden_states,
            encoder_attention_mask=encoder_attention_mask,
            **kwargs,
        )
        attn_output = self.output(attn_output, hidden_states)
        return attn_output


def gelu(x):
    """
    This is the gelu implementation from the original EVOLLA_SA_PROT repo. Using F.gelu yields subtly wrong results.
    """
    return x * 0.5 * (1.0 + torch.erf(x / math.sqrt(2.0)))


class EvollaSaProtIntermediate(nn.Module):
    def __init__(self, config):
        super().__init__()
        self.dense = nn.Linear(config.hidden_size, config.intermediate_size)

    def forward(self, hidden_states: torch.Tensor) -> torch.Tensor:
        hidden_states = self.dense(hidden_states)
        hidden_states = gelu(hidden_states)
        return hidden_states


class EvollaSaProtOutput(nn.Module):
    def __init__(self, config):
        super().__init__()
        self.dense = nn.Linear(config.intermediate_size, config.hidden_size)
        self.dropout = nn.Dropout(config.hidden_dropout_prob)

    def forward(self, hidden_states, input_tensor):
        hidden_states = self.dense(hidden_states)
        hidden_states = self.dropout(hidden_states)
        hidden_states = hidden_states + input_tensor
        return hidden_states


class EvollaSaProtLayer(GradientCheckpointingLayer):
    def __init__(self, config):
        super().__init__()
        self.chunk_size_feed_forward = config.chunk_size_feed_forward
        self.seq_len_dim = 1
        self.attention = EvollaSaProtAttention(config)
        self.is_decoder = config.is_decoder
        self.add_cross_attention = config.add_cross_attention
        if self.add_cross_attention:
            if not self.is_decoder:
                raise RuntimeError(f"{self} should be used as a decoder model if cross attention is added")
            self.crossattention = EvollaSaProtAttention(config, is_cross_attention=True)
        self.intermediate = EvollaSaProtIntermediate(config)
        self.output = EvollaSaProtOutput(config)
        self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)

    def forward(
        self,
        hidden_states,
        attention_mask=None,
        head_mask=None,
        encoder_hidden_states=None,
        encoder_attention_mask=None,
        **kwargs: Unpack[TransformersKwargs],
    ):
        attention_output = self.attention(
            hidden_states,
            attention_mask=attention_mask,
            head_mask=head_mask,
            **kwargs,
        )

        if self.is_decoder and encoder_hidden_states is not None:
            if not hasattr(self, "crossattention"):
                raise AttributeError(
                    f"If `encoder_hidden_states` are passed, {self} has to be instantiated"
                    " with cross-attention layers by setting `config.add_cross_attention=True`"
                )

            attention_output = self.crossattention(
                attention_output,
                attention_mask=attention_mask,
                head_mask=head_mask,
                encoder_hidden_states=encoder_hidden_states,
                encoder_attention_mask=encoder_attention_mask,
                **kwargs,
            )

        layer_output = self.feed_forward_chunk(attention_output)
        return layer_output

    def feed_forward_chunk(self, attention_output):
        attention_output_ln = self.LayerNorm(attention_output)
        intermediate_output = self.intermediate(attention_output_ln)
        layer_output = self.output(intermediate_output, attention_output)
        return layer_output


class EvollaSaProtEncoder(nn.Module):
    def __init__(self, config):
        super().__init__()
        self.config = config
        self.layer = nn.ModuleList([EvollaSaProtLayer(config) for _ in range(config.num_hidden_layers)])
        self.emb_layer_norm_after = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
        self.gradient_checkpointing = False

    @can_return_tuple
    def forward(
        self,
        hidden_states,
        attention_mask=None,
        head_mask=None,
        encoder_hidden_states=None,
        encoder_attention_mask=None,
        **kwargs: Unpack[TransformersKwargs],
    ):
        for i, layer_module in enumerate(self.layer):
            layer_head_mask = head_mask[i] if head_mask is not None else None
            hidden_states = layer_module(
                hidden_states,
                attention_mask=attention_mask,
                head_mask=layer_head_mask,
                encoder_hidden_states=encoder_hidden_states,
                encoder_attention_mask=encoder_attention_mask,
                **kwargs,
            )

        if self.emb_layer_norm_after:
            hidden_states = self.emb_layer_norm_after(hidden_states)

        return BaseModelOutputWithCrossAttentions(last_hidden_state=hidden_states)


class EvollaSaProtPooler(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) -> torch.Tensor:
        # We "pool" the model by simply taking the hidden state corresponding
        # to the first token.
        first_token_tensor = hidden_states[:, 0]
        pooled_output = self.dense(first_token_tensor)
        pooled_output = self.activation(pooled_output)
        return pooled_output


@auto_docstring
class EvollaSaProtPreTrainedModel(PreTrainedModel):
    config: SaProtConfig
    _no_split_modules = ["EvollaSaProtLayer"]
    _supports_flash_attn = True
    _supports_sdpa = True
    _supports_attention_backend = True

    _can_record_outputs = {
        "hidden_states": EvollaSaProtLayer,
        "attentions": [OutputRecorder(EvollaSaProtSelfAttention, index=1, layer_name="attention")],
        "cross_attentions": [
            OutputRecorder(EvollaSaProtSelfAttention, index=1, layer_name="crossattention"),
        ],
    }

    def _init_weights(self, module):
        """Initialize the weights"""
        std = self.config.initializer_range
        if isinstance(module, nn.Linear):
            module.weight.data.normal_(mean=0.0, std=std)
            if module.bias is not None:
                module.bias.data.zero_()
        elif isinstance(module, nn.Embedding):
            module.weight.data.normal_(mean=0.0, std=std)
            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)


class EvollaSaProtProteinEncoder(EvollaSaProtPreTrainedModel):
    def __init__(self, config: SaProtConfig):
        super().__init__(config)
        self.embeddings = EvollaSaProtEmbeddings(config)
        self.encoder = EvollaSaProtEncoder(config)

    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)

    @check_model_inputs()
    def forward(
        self,
        input_ids: Optional[torch.Tensor],
        attention_mask: Optional[torch.Tensor] = None,
    ) -> Union[tuple[torch.Tensor], BaseModelOutputWithPoolingAndCrossAttentions]:
        input_shape = input_ids.size()
        batch_size, seq_length = input_shape

        device = input_ids.device
        if attention_mask is None:
            attention_mask = torch.ones(((batch_size, seq_length)), device=device)

        inputs_embeds = self.embeddings(input_ids=input_ids, attention_mask=attention_mask)
        extended_attention_mask = self.get_extended_attention_mask(attention_mask, input_shape)
        encoder_outputs = self.encoder(inputs_embeds, attention_mask=extended_attention_mask)
        sequence_output = encoder_outputs[0]

        return BaseModelOutputWithPoolingAndCrossAttentions(
            last_hidden_state=sequence_output,
            hidden_states=encoder_outputs.hidden_states,
            attentions=encoder_outputs.attentions,
            cross_attentions=encoder_outputs.cross_attentions,
        )

    def get_extended_attention_mask(
        self,
        attention_mask: Tensor,
        input_shape: tuple[int],
        device: Optional[torch.device] = None,
        dtype: Optional[torch.dtype] = None,
    ) -> Tensor:
        """
        Makes broadcastable attention and causal masks so that future and masked tokens are ignored.

        Arguments:
            attention_mask (`torch.Tensor`):
                Mask with ones indicating tokens to attend to, zeros for tokens to ignore.
            input_shape (`Tuple[int]`):
                The shape of the input to the model.

        Returns:
            `torch.Tensor` The extended attention mask, with a the same dtype as `attention_mask.dtype`.
        """
        if dtype is None:
            dtype = get_parameter_dtype(self)

        if not (attention_mask.dim() == 2 and self.config.is_decoder):
            # show warning only if it won't be shown in `create_extended_attention_mask_for_decoder`
            if device is not None:
                warnings.warn(
                    "The `device` argument is deprecated and will be removed in v5 of Transformers.", FutureWarning
                )
        # We can provide a self-attention mask of dimensions [batch_size, from_seq_length, to_seq_length]
        # ourselves in which case we just need to make it broadcastable to all heads.
        if attention_mask.dim() == 3:
            extended_attention_mask = attention_mask[:, None, :, :]
        elif attention_mask.dim() == 2:
            # Provided a padding mask of dimensions [batch_size, seq_length]
            # - if the model is a decoder, apply a causal mask in addition to the padding mask
            # - if the model is an encoder, make the mask broadcastable to [batch_size, num_heads, seq_length, seq_length]
            if self.config.is_decoder:
                extended_attention_mask = ModuleUtilsMixin.create_extended_attention_mask_for_decoder(
                    input_shape, attention_mask, device
                )
            else:
                extended_attention_mask = attention_mask[:, None, None, :]
        else:
            raise ValueError(
                f"Wrong shape for input_ids (shape {input_shape}) or attention_mask (shape {attention_mask.shape})"
            )

        # Since attention_mask is 1.0 for positions we want to attend and 0.0 for
        # masked positions, this operation will create a tensor which is 0.0 for
        # positions we want to attend and the dtype's smallest value for masked positions.
        # Since we are adding it to the raw scores before the softmax, this is
        # effectively the same as removing these entirely.
        extended_attention_mask = extended_attention_mask.to(dtype=dtype)  # fp16 compatibility
        extended_attention_mask = (1.0 - extended_attention_mask) * torch.finfo(dtype).min
        return extended_attention_mask


class EvollaSequenceCompressorAttention(nn.Module):
    def __init__(self, dim, dim_head=64, heads=8):
        super().__init__()
        self.scale = dim_head**-0.5
        self.heads = heads
        inner_dim = dim_head * heads

        self.norm_media = nn.LayerNorm(dim)
        self.norm_latents = nn.LayerNorm(dim)

        self.to_q = nn.Linear(dim, inner_dim, bias=False)
        self.to_kv = nn.Linear(dim, inner_dim * 2, bias=False)
        self.to_out = nn.Linear(inner_dim, dim, bias=False)

    def forward(self, x, latents, mask):
        """
        Args:
            x (torch.Tensor): image features
                shape (b, n1, D)
            latent (torch.Tensor): latent features
                shape (b, n2, D);  n2: num of latent tokens
        """
        x = self.norm_media(x)
        latents = self.norm_latents(latents)

        h = self.heads

        q = self.to_q(latents)
        kv_input = torch.cat((x, latents), dim=-2)
        k, v = self.to_kv(kv_input).chunk(
            2, dim=-1
        )  # each: batch_size, max_protein_length+num_latents, dim_head*num_heads

        q = q.view(q.size(0), q.size(1), h, -1).permute(0, 2, 1, 3)
        k = k.view(k.size(0), k.size(1), h, -1).permute(0, 2, 1, 3)
        v = v.view(v.size(0), v.size(1), h, -1).permute(0, 2, 1, 3)
        q = q * self.scale  # batch_size, num_heads, num_latents, dim_head

        # attention
        sim = torch.matmul(q, k.transpose(-1, -2))
        sim = sim - sim.amax(dim=-1, keepdim=True).detach()
        bs, nh, skd, okd = sim.shape
        ones = torch.ones(nh, skd).to(mask.device)  # Create a tensor of ones with shape (nh, skd)
        mask_exp = mask[:, None, None, :]
        ones_exp = ones[None, :, :, None]
        mask = mask_exp * ones_exp

        sim = sim.masked_fill((1 - mask).bool(), -1e4)
        attn = sim.softmax(dim=-1)
        out = torch.matmul(attn, v)
        out = out.permute(0, 2, 1, 3)

        # [batch, seq, head, features] -> [batch, seq, head*features]
        out = out.reshape(out.size(0), out.size(1), -1)

        return self.to_out(out)


class EvollaFeedForward(nn.Module):
    def __init__(self, dim, mult=4):
        super().__init__()
        inner_dim = int(dim * mult)

        self.norm = nn.LayerNorm(dim)
        self.fc1 = nn.Linear(dim, inner_dim, bias=False)
        self.activation = nn.GELU()
        self.fc2 = nn.Linear(inner_dim, dim, bias=False)

    def forward(self, x):
        return self.fc2(self.activation(self.fc1(self.norm(x))))


class EvollaSequenceCompressorResampler(nn.Module):
    def __init__(self, config: EvollaConfig):
        super().__init__()
        protein_repr_dim = config.protein_encoder_config.hidden_size
        self.num_latents = config.resampler_num_latents
        self.latents = nn.Parameter(torch.randn(self.num_latents, protein_repr_dim), requires_grad=True)
        self.layers = nn.ModuleList([])
        for _ in range(config.resampler_depth):
            self.layers.append(
                nn.ModuleList(
                    [
                        EvollaSequenceCompressorAttention(
                            dim=protein_repr_dim, dim_head=config.resampler_dim_head, heads=config.resampler_heads
                        ),
                        EvollaFeedForward(dim=protein_repr_dim, mult=config.resampler_ff_mult),
                    ]
                )
            )

        self.norm = nn.LayerNorm(config.hidden_size)
        self.protein_projector = nn.Linear(protein_repr_dim, config.hidden_size)

    def forward(self, embeds, mask):
        b = embeds.shape[0]

        bs, _ = mask.shape  # bs, max_protein_length
        latent_mask = torch.ones(bs, self.num_latents).to(mask.device)
        mask = torch.cat((mask, latent_mask), dim=1)  # bs, max_protein_length + num_latents

        # blocks
        ones = torch.ones(b).to(self.latents.device)
        latents = self.latents[None] * ones.view(-1, 1, 1)  # [b,n,d]
        latents = latents.to(embeds.dtype)
        for attn, ff in self.layers:
            latents = attn(embeds, latents, mask) + latents
            latents = ff(latents) + latents

        transformed_feature = self.protein_projector(latents)

        return self.norm(transformed_feature)


@dataclass
@auto_docstring
class EvollaProteinEncoderModelOutput(ModelOutput):
    sequence_compressor_output: Optional[torch.FloatTensor] = None
    last_hidden_state: Optional[torch.FloatTensor] = None
    hidden_states: Optional[tuple[torch.FloatTensor, ...]] = None
    attentions: Optional[tuple[torch.FloatTensor, ...]] = None


class EvollaProteinEncoder(nn.Module):
    def __init__(self, config: EvollaConfig):
        super().__init__()
        self.model = EvollaSaProtProteinEncoder(config=config.protein_encoder_config)
        self.sequence_compressor_resampler = EvollaSequenceCompressorResampler(config=config)

    @can_return_tuple
    def forward(self, input_ids: torch.LongTensor, attention_mask: torch.FloatTensor, **kwargs):
        protein_output = self.model(input_ids=input_ids, attention_mask=attention_mask)
        protein_embeds = protein_output.last_hidden_state
        sequence_repr = self.sequence_compressor_resampler(protein_embeds, attention_mask)

        return EvollaProteinEncoderModelOutput(
            sequence_compressor_output=sequence_repr,
            last_hidden_state=protein_output.last_hidden_state,
        )


class EvollaSequenceAlignerCrossAttention(nn.Module):
    def __init__(
        self,
        config,
        protein_encoder_dim: Optional[int] = None,
        structure_encoder_dim: Optional[int] = None,
        msa_encoder_dim: Optional[int] = None,
    ):
        super().__init__()

        self.hidden_size = config.hidden_size
        self.num_attention_heads = config.num_attention_heads
        self.scale = self.num_attention_heads**-0.5
        self.attention_head_size = int(self.hidden_size / self.num_attention_heads)
        self.all_head_size = self.num_attention_heads * self.attention_head_size

        attention_probs_dropout_prob = config.aligner_attention_probs_dropout_prob
        enable_bias = config.aligner_enable_bias
        ffn_mult = config.aligner_ffn_mult

        self.query = nn.Linear(self.hidden_size, self.all_head_size)
        if protein_encoder_dim is not None:
            self.key_protein = nn.Linear(protein_encoder_dim, self.all_head_size)
            self.value_protein = nn.Linear(protein_encoder_dim, self.all_head_size)
        else:
            self.key_protein = None
            self.value_protein = None

        if structure_encoder_dim is not None:
            self.key_structure = nn.Linear(structure_encoder_dim, self.all_head_size)
            self.value_structure = nn.Linear(structure_encoder_dim, self.all_head_size)
        else:
            self.key_structure = None
            self.value_structure = None

        if msa_encoder_dim is not None:
            self.key_msa = nn.Linear(msa_encoder_dim, self.all_head_size)
            self.value_msa = nn.Linear(msa_encoder_dim, self.all_head_size)
        else:
            self.key_msa = None
            self.value_msa = None

        self.attention_norm = EvollaRMSNorm(self.hidden_size)

        self.dropout = nn.Dropout(attention_probs_dropout_prob)

        self.out_proj = nn.Linear(self.hidden_size, self.hidden_size, bias=enable_bias)

        self.ff = EvollaFeedForward(self.hidden_size, ffn_mult)
        self.gate_attention = nn.Parameter(torch.tensor([0.0]))
        self.gate_ffw = nn.Parameter(torch.tensor([0.0]))

    def cross_attention(
        self,
        query_states,
        protein_key_value_states,
        structure_key_value_states,
        msa_key_value_states,
        query_attn_mask,
        protein_kv_attn_mask,
        structure_kv_attn_mask,
        msa_kv_attn_mask,
    ):
        """
        query_states: text
        key_value_states: protein
        query_states: [bs, query_seq_len, dim]
        key_value_states: [bs, kv_seq_len, dim]
        query_attn_mask: [bs, query_seq_len]
        kv_attn_mask: [bs, kv_seq_len]
        """

        # Concatenate protein and structure
        kv_attn_mask = [protein_kv_attn_mask, structure_kv_attn_mask, msa_kv_attn_mask]
        kv_attn_mask = [_ for _ in kv_attn_mask if _ is not None]
        if not kv_attn_mask:
            raise ValueError("At least one modality should be provided for cross attention.")
        kv_attn_mask = torch.cat(kv_attn_mask, dim=1)

        query_layer = self.attention_norm(query_states)

        # Warning: This place might cause issues, refers to
        # https://discuss.pytorch.org/t/cuda-error-cublas-status-not-supported-when-calling-cublasltmatmul-from-torch-nn-functional-linear/170214/13
        # Solution: add `DISABLE_ADDMM_CUDA_LT=1` as environment variable
        # Apply linear transformation to input_query, input_key, and input_value
        query_layer = self.query(query_layer)  # [bs, querylength, dim]

        if self.key_protein is not None and self.value_protein is not None:
            protein_key_value_states = protein_key_value_states.to(query_states)
            key_layer_protein = self.key_protein(protein_key_value_states)  # [bs, keylength, dim]
            value_layer_protein = self.value_protein(protein_key_value_states)  # [bs, keylength, dim]
        else:
            key_layer_protein = None
            value_layer_protein = None

        if self.key_structure is not None and self.value_structure is not None:
            structure_key_value_states = structure_key_value_states.to(query_states)
            key_layer_structure = self.key_structure(structure_key_value_states)  # [bs, keylength, dim]
            value_layer_structure = self.value_structure(structure_key_value_states)  # [bs, keylength, dim]
        else:
            key_layer_structure = None
            value_layer_structure = None

        if self.key_msa is not None and self.value_msa is not None:
            msa_key_value_states = msa_key_value_states.to(query_states)
            key_layer_msa = self.key_msa(msa_key_value_states)  # [bs, keylength, dim]
            value_layer_msa = self.value_msa(msa_key_value_states)  # [bs, keylength, dim]
        else:
            key_layer_msa = None
            value_layer_msa = None

        key_layer = [key_layer_protein, key_layer_structure, key_layer_msa]
        key_layer = [_ for _ in key_layer if _ is not None]
        key_layer = torch.cat(key_layer, dim=1)

        value_layer = [value_layer_protein, value_layer_structure, value_layer_msa]
        value_layer = [_ for _ in value_layer if _ is not None]
        value_layer = torch.cat(value_layer, dim=1)

        new_query_layer_shape = query_layer.size()[:-1] + (
            self.num_attention_heads,
            self.attention_head_size,
        )
        query_layer = query_layer.view(*new_query_layer_shape).permute(0, 2, 1, 3)

        new_key_layer_shape = key_layer.size()[:-1] + (
            self.num_attention_heads,
            self.attention_head_size,
        )
        key_layer = key_layer.view(*new_key_layer_shape).permute(0, 2, 1, 3)

        new_value_layer_shape = value_layer.size()[:-1] + (
            self.num_attention_heads,
            self.attention_head_size,
        )
        value_layer = value_layer.view(*new_value_layer_shape).permute(0, 2, 1, 3)

        query_layer = query_layer * self.scale

        # attention_mask: [bs, 1, querylength, keylength]
        if query_attn_mask is None:
            query_attn_mask = torch.ones(query_states.size(0), query_states.size(1)).to(query_states.device)
        attention_mask = query_attn_mask[:, None, :, None] * kv_attn_mask[:, None, None, :]
        # Compute the scaled dot-product attention scores
        attn_weights = torch.matmul(query_layer, key_layer.transpose(-1, -2))  # [bs, numheads, querylength, keylength]
        attn_weights = attn_weights - attn_weights.amax(dim=-1, keepdim=True).detach()  # To stabilize score
        attention_scores = attn_weights.masked_fill(
            (1 - attention_mask).bool(), torch.finfo(attn_weights.dtype).min
        )  # [bs, numheads, querylength, keylength]

        attention_probs = nn.Softmax(dim=-1)(attention_scores)

        # attention_probs_dropped = self.dropout(attention_probs)

        context_layer = torch.matmul(attention_probs, value_layer)  # [bs, numheads, querylength, dim/numheads]

        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)

        context_layer = self.out_proj(context_layer)

        return context_layer

    @deprecate_kwarg("past_key_value", new_name="past_key_values", version="4.58")
    def forward(
        self,
        query_states,
        protein_kv_states,
        structure_kv_states,
        msa_kv_states,
        query_attn_mask,
        protein_kv_attn_mask=None,
        structure_kv_attn_mask=None,
        msa_kv_attn_mask=None,
        protein_batch_mask=None,
        structure_batch_mask=None,
        msa_batch_mask=None,
        past_key_values=None,
    ):
        if protein_kv_states is not None:
            bs, protein_kv_seq_len, dim = protein_kv_states.shape
            if protein_kv_attn_mask is None:
                protein_kv_attn_mask = (
                    torch.ones(bs, protein_kv_seq_len).to(protein_batch_mask.device)
                    * protein_batch_mask.expand(size=(protein_kv_seq_len, bs)).T
                ).to(protein_kv_states.device)
        else:
            protein_kv_attn_mask = None

        if structure_kv_states is not None:
            bs, structure_kv_seq_len, dim = structure_kv_states.shape
            if structure_kv_attn_mask is None:
                structure_kv_attn_mask = (
                    torch.ones(bs, structure_kv_seq_len).to(protein_batch_mask.device)
                    * structure_batch_mask.expand(size=(structure_kv_seq_len, bs)).T
                ).to(structure_kv_states.device)
        else:
            structure_kv_attn_mask = None

        if msa_kv_states is not None:
            bs, msa_kv_seq_len, dim = msa_kv_states.shape
            if msa_kv_attn_mask is None:
                msa_kv_attn_mask = (
                    torch.ones(bs, msa_kv_seq_len).to(protein_batch_mask.device)
                    * msa_batch_mask.expand(size=(msa_kv_seq_len, bs)).T
                ).to(msa_kv_states.device)
        else:
            msa_kv_attn_mask = None
        hidden_states = query_states
        # only when there's at least one valid modality, crossattention will be performed
        if (
            (protein_kv_states is not None and protein_kv_attn_mask.any())
            or (structure_kv_states is not None and structure_kv_attn_mask.any())
            or (msa_kv_states is not None and msa_kv_attn_mask.any())
        ):
            residual = hidden_states
            hidden_states = self.cross_attention(
                query_states=hidden_states,
                protein_key_value_states=protein_kv_states,
                structure_key_value_states=structure_kv_states,
                msa_key_value_states=msa_kv_states,
                query_attn_mask=query_attn_mask,
                protein_kv_attn_mask=protein_kv_attn_mask,
                structure_kv_attn_mask=structure_kv_attn_mask,
                msa_kv_attn_mask=msa_kv_attn_mask,
            )  # [bs, query_seq_len, dim]
            # tanh gate
            hidden_states = torch.tanh(self.gate_attention) * hidden_states

            hidden_states = residual + hidden_states  # input_query

            residual = hidden_states
            hidden_states = self.ff(hidden_states) * torch.tanh(self.gate_ffw)
            hidden_states = residual + hidden_states

        return hidden_states


@use_kernel_forward_from_hub("RMSNorm")
class EvollaRMSNorm(nn.Module):
    def __init__(self, hidden_size, eps=1e-6):
        """
        EvollaRMSNorm is equivalent to T5LayerNorm
        """
        super().__init__()
        self.weight = nn.Parameter(torch.ones(hidden_size))
        self.variance_epsilon = eps

    def forward(self, hidden_states):
        input_dtype = hidden_states.dtype
        hidden_states = hidden_states.to(torch.float32)
        variance = hidden_states.pow(2).mean(-1, keepdim=True)
        hidden_states = hidden_states * torch.rsqrt(variance + self.variance_epsilon)
        return self.weight * hidden_states.to(input_dtype)

    def extra_repr(self):
        return f"{tuple(self.weight.shape)}, eps={self.variance_epsilon}"


class EvollaRotaryEmbedding(nn.Module):
    inv_freq: torch.Tensor  # fix linting for `register_buffer`

    def __init__(self, config: EvollaConfig, device=None):
        super().__init__()
        # BC: "rope_type" was originally "type"
        if hasattr(config, "rope_scaling") and isinstance(config.rope_scaling, dict):
            self.rope_type = config.rope_scaling.get("rope_type", config.rope_scaling.get("type"))
        else:
            self.rope_type = "default"
        self.max_seq_len_cached = config.max_position_embeddings
        self.original_max_seq_len = config.max_position_embeddings

        self.config = config
        self.rope_init_fn = ROPE_INIT_FUNCTIONS[self.rope_type]

        inv_freq, self.attention_scaling = self.rope_init_fn(self.config, device)
        self.register_buffer("inv_freq", inv_freq, persistent=False)
        self.original_inv_freq = self.inv_freq

    @torch.no_grad()
    @dynamic_rope_update  # power user: used with advanced RoPE types (e.g. dynamic rope)
    def forward(self, x, position_ids):
        inv_freq_expanded = self.inv_freq[None, :, None].float().expand(position_ids.shape[0], -1, 1).to(x.device)
        position_ids_expanded = position_ids[:, None, :].float()

        device_type = x.device.type if isinstance(x.device.type, str) and x.device.type != "mps" else "cpu"
        with torch.autocast(device_type=device_type, enabled=False):  # Force float32
            freqs = (inv_freq_expanded.float() @ position_ids_expanded.float()).transpose(1, 2)
            emb = torch.cat((freqs, freqs), dim=-1)
            cos = emb.cos() * self.attention_scaling
            sin = emb.sin() * self.attention_scaling

        return cos.to(dtype=x.dtype), sin.to(dtype=x.dtype)


class EvollaMLP(nn.Module):
    def __init__(self, config):
        super().__init__()
        self.config = config
        self.hidden_size = config.hidden_size
        self.intermediate_size = config.intermediate_size
        self.gate_proj = nn.Linear(self.hidden_size, self.intermediate_size, bias=config.mlp_bias)
        self.up_proj = nn.Linear(self.hidden_size, self.intermediate_size, bias=config.mlp_bias)
        self.down_proj = nn.Linear(self.intermediate_size, self.hidden_size, bias=config.mlp_bias)
        self.act_fn = ACT2FN[config.hidden_act]

    def forward(self, x):
        down_proj = self.down_proj(self.act_fn(self.gate_proj(x)) * self.up_proj(x))
        return down_proj


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=None, 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`, *optional*):
            Deprecated and unused.
        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.unsqueeze(unsqueeze_dim)
    sin = sin.unsqueeze(unsqueeze_dim)
    q_embed = (q * cos) + (rotate_half(q) * sin)
    k_embed = (k * cos) + (rotate_half(k) * sin)
    return q_embed, k_embed


def repeat_kv(hidden_states: torch.Tensor, n_rep: int) -> torch.Tensor:
    """
    This is the equivalent of torch.repeat_interleave(x, dim=1, repeats=n_rep). The hidden states go from (batch,
    num_key_value_heads, seqlen, head_dim) to (batch, num_attention_heads, seqlen, head_dim)
    """
    batch, num_key_value_heads, slen, head_dim = hidden_states.shape
    if n_rep == 1:
        return hidden_states
    hidden_states = hidden_states[:, :, None, :, :].expand(batch, num_key_value_heads, n_rep, slen, head_dim)
    return hidden_states.reshape(batch, num_key_value_heads * n_rep, slen, head_dim)


class EvollaAttention(nn.Module):
    """Multi-headed attention from 'Attention Is All You Need' paper"""

    def __init__(self, config: EvollaConfig, layer_idx: int):
        super().__init__()
        self.config = config
        self.layer_idx = layer_idx
        self.head_dim = getattr(config, "head_dim", config.hidden_size // config.num_attention_heads)
        self.num_key_value_groups = config.num_attention_heads // config.num_key_value_heads
        self.scaling = self.head_dim**-0.5
        self.attention_dropout = config.attention_dropout
        self.is_causal = True

        self.q_proj = nn.Linear(
            config.hidden_size, config.num_attention_heads * self.head_dim, bias=config.attention_bias
        )
        self.k_proj = nn.Linear(
            config.hidden_size, config.num_key_value_heads * self.head_dim, bias=config.attention_bias
        )
        self.v_proj = nn.Linear(
            config.hidden_size, config.num_key_value_heads * self.head_dim, bias=config.attention_bias
        )
        self.o_proj = nn.Linear(
            config.num_attention_heads * self.head_dim, config.hidden_size, bias=config.attention_bias
        )

    @deprecate_kwarg("past_key_value", new_name="past_key_values", version="4.58")
    def forward(
        self,
        hidden_states: torch.Tensor,
        position_embeddings: tuple[torch.Tensor, torch.Tensor],
        attention_mask: Optional[torch.Tensor],
        past_key_values: Optional[Cache] = None,
        cache_position: Optional[torch.LongTensor] = None,
        **kwargs: Unpack[TransformersKwargs],
    ) -> tuple[torch.Tensor, torch.Tensor]:
        input_shape = hidden_states.shape[:-1]
        hidden_shape = (*input_shape, -1, self.head_dim)

        query_states = self.q_proj(hidden_states).view(hidden_shape).transpose(1, 2)
        key_states = self.k_proj(hidden_states).view(hidden_shape).transpose(1, 2)
        value_states = self.v_proj(hidden_states).view(hidden_shape).transpose(1, 2)

        cos, sin = position_embeddings
        query_states, key_states = apply_rotary_pos_emb(query_states, key_states, cos, sin)

        if past_key_values is not None:
            # sin and cos are specific to RoPE models; cache_position needed for the static cache
            cache_kwargs = {"sin": sin, "cos": cos, "cache_position": cache_position}
            key_states, value_states = past_key_values.update(key_states, value_states, self.layer_idx, cache_kwargs)

        attention_interface: Callable = eager_attention_forward
        if self.config._attn_implementation != "eager":
            attention_interface = ALL_ATTENTION_FUNCTIONS[self.config._attn_implementation]

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

        attn_output = attn_output.reshape(*input_shape, -1).contiguous()
        attn_output = self.o_proj(attn_output)
        return attn_output, attn_weights


class EvollaDecoderLayer(GradientCheckpointingLayer):
    def __init__(self, config: EvollaConfig, layer_idx: int):
        super().__init__()
        self.hidden_size = config.hidden_size

        self.self_attn = EvollaAttention(config=config, layer_idx=layer_idx)

        self.mlp = EvollaMLP(config)
        self.input_layernorm = EvollaRMSNorm(config.hidden_size, eps=config.rms_norm_eps)
        self.post_attention_layernorm = EvollaRMSNorm(config.hidden_size, eps=config.rms_norm_eps)
        if (layer_idx + 1) % max(config.num_hidden_layers // config.aligner_num_add_layers, 1) == 0:
            self.adapter = EvollaSequenceAlignerCrossAttention(
                config,
                protein_encoder_dim=config.hidden_size,
            )

    @deprecate_kwarg("past_key_value", new_name="past_key_values", version="4.58")
    def forward(
        self,
        hidden_states: torch.Tensor,
        position_embeddings: tuple[torch.Tensor, torch.Tensor],
        attention_mask: Optional[torch.Tensor] = None,
        position_ids: Optional[torch.LongTensor] = None,
        past_key_values: Optional[Cache] = None,
        use_cache: Optional[bool] = False,
        cache_position: Optional[torch.LongTensor] = None,
        protein_kv_states: Optional[torch.Tensor] = None,
        structure_kv_states: Optional[torch.Tensor] = None,
        msa_kv_states: Optional[torch.Tensor] = None,
        protein_batch_mask: Optional[torch.Tensor] = None,
        structure_batch_mask: Optional[torch.Tensor] = None,
        msa_batch_mask: Optional[torch.Tensor] = None,
        query_attn_mask: Optional[torch.Tensor] = None,
        **kwargs,
    ) -> torch.Tensor:
        residual = hidden_states

        hidden_states = self.input_layernorm(hidden_states)

        # Self Attention
        hidden_states, _ = self.self_attn(
            hidden_states=hidden_states,
            attention_mask=attention_mask,
            position_ids=position_ids,
            past_key_values=past_key_values,
            use_cache=use_cache,
            cache_position=cache_position,
            position_embeddings=position_embeddings,
            **kwargs,
        )
        hidden_states = residual + hidden_states

        # Fully Connected
        residual = hidden_states
        hidden_states = self.post_attention_layernorm(hidden_states)
        hidden_states = self.mlp(hidden_states)
        hidden_states = residual + hidden_states

        if hasattr(self, "adapter"):
            hidden_states = self.adapter(
                query_states=hidden_states,
                protein_kv_states=protein_kv_states,
                structure_kv_states=structure_kv_states,
                msa_kv_states=msa_kv_states,
                query_attn_mask=query_attn_mask,
                protein_batch_mask=protein_batch_mask,
                structure_batch_mask=structure_batch_mask,
                msa_batch_mask=msa_batch_mask,
            )

        return hidden_states


@auto_docstring
class EvollaPreTrainedModel(PreTrainedModel):
    config: EvollaConfig
    base_model_prefix = "model"
    supports_gradient_checkpointing = True
    _no_split_modules = [
        "EvollaDecoderLayer",
        "EvollaSequenceCompressorResampler",
        "EvollaSequenceAlignerCrossAttention",
    ]
    _skip_keys_device_placement = ["past_key_values"]
    _supports_flash_attn = False  # see dependency on `EvollaSaProtProteinEncoder`
    _supports_sdpa = True
    _supports_flex_attn = False  # see dependency on `EvollaSaProtProteinEncoder`

    _can_compile_fullgraph = True
    _supports_attention_backend = False
    _can_record_outputs = {
        "hidden_states": EvollaDecoderLayer,
        "attentions": EvollaAttention,
    }

    def _init_weights(self, module):
        std = self.config.initializer_range
        super()._init_weights(module)
        if isinstance(module, EvollaSequenceAlignerCrossAttention):
            module.gate_attention.zero_()
            module.gate_ffw.zero_()
            module.attention_norm.weight.data.fill_(1.0)
        elif isinstance(module, EvollaSequenceCompressorResampler):
            module.latents.data.normal_(mean=0.0, std=std)


class EvollaModel(EvollaPreTrainedModel):
    def __init__(self, config: EvollaConfig):
        super().__init__(config)
        self.padding_idx = config.pad_token_id
        self.vocab_size = config.vocab_size
        self.embed_tokens = nn.Embedding(self.vocab_size, config.hidden_size, self.padding_idx)
        self.protein_encoder = EvollaProteinEncoder(config=config)
        self.layers = nn.ModuleList(
            [
                EvollaDecoderLayer(
                    config=config,
                    layer_idx=layer_idx,
                )
                for layer_idx in range(config.num_hidden_layers)
            ]
        )

        self.norm = EvollaRMSNorm(config.hidden_size, eps=config.rms_norm_eps)
        self.rotary_emb = EvollaRotaryEmbedding(config=config)
        self.gradient_checkpointing = getattr(config, "gradient_checkpointing", False)
        self.post_init()

    def get_input_embeddings(self):
        return self.embed_tokens

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

    @auto_docstring
    @check_model_inputs()
    def forward(
        self,
        input_ids: Optional[torch.LongTensor] = None,
        attention_mask: Optional[torch.Tensor] = None,
        position_ids: Optional[torch.LongTensor] = None,
        past_key_values: Optional[Cache] = None,
        inputs_embeds: Optional[torch.FloatTensor] = None,
        use_cache: Optional[bool] = None,
        cache_position: Optional[torch.LongTensor] = None,
        protein_input_ids: Optional[torch.LongTensor] = None,
        protein_attention_mask: Optional[torch.Tensor] = None,
        structure_feats: Optional[torch.FloatTensor] = None,
        msa_feats: Optional[torch.FloatTensor] = None,
        structure_batch_mask: Optional[torch.Tensor] = None,
        msa_batch_mask: Optional[torch.Tensor] = None,
        **kwargs,
    ) -> Union[tuple, BaseModelOutputWithPast]:
        r"""
        protein_input_ids (torch.LongTensor):
            The input IDs for the protein sequence in structure-aware tokens. Should be of shape `(batch_size, protein_seq_length)` and type `torch.LongTensor`.
        protein_attention_mask (torch.Tensor):
            The attention mask for the protein sequence. Should be of shape `(batch_size, protein_seq_length)` and type `torch.Tensor`.
        structure_feats (torch.FloatTensor):
            The input IDs for purely structure-based features. Should be of shape `(batch_size, structure_seq_length, structure_feat_dim)` and type `torch.FloatTensor`. Dummy input for now.
        msa_feats (torch.FloatTensor):
            The input IDs for purely MSA-based features. Should be of shape `(batch_size, msa_seq_length, msa_feat_dim)` and type `torch.FloatTensor`. Dummy input for now.
        structure_batch_mask (torch.Tensor):
            The batch mask to decide which protein sequences are purely structure-based. Should be of shape `(batch_size)` and type `torch.Tensor`. Should be paired with `structure_feats`. Dummpy input for now.
        msa_batch_mask (torch.Tensor):
            The batch mask to decide which protein sequences are purely MSA-based. Should be of shape `(batch_size)` and type `torch.Tensor`. Should be paired with `msa_feats`. Dummpy input for now.
        """
        if (input_ids is None) ^ (inputs_embeds is not None):
            raise ValueError("You must specify exactly one of input_ids or inputs_embeds")

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

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

        if cache_position is None:
            past_seen_tokens = past_key_values.get_seq_length() if past_key_values is not None else 0
            cache_position = torch.arange(
                past_seen_tokens, past_seen_tokens + inputs_embeds.shape[1], device=inputs_embeds.device
            )

        if position_ids is None:
            position_ids = cache_position.unsqueeze(0)

        protein_feats = None
        protein_batch_mask = None
        # If provided, actually compute them
        if protein_input_ids is not None and protein_attention_mask is not None:
            protein_outputs = self.protein_encoder(
                input_ids=protein_input_ids,
                attention_mask=protein_attention_mask,
            )
            protein_feats = protein_outputs.sequence_compressor_output
            protein_batch_mask = torch.tensor([True] * protein_input_ids.shape[0], device=protein_input_ids.device)

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

        hidden_states = inputs_embeds

        # create position embeddings to be shared across the decoder layers
        position_embeddings = self.rotary_emb(hidden_states, position_ids)

        for decoder_layer in self.layers:
            hidden_states = decoder_layer(
                hidden_states,
                attention_mask=causal_mask,
                position_ids=position_ids,
                past_key_values=past_key_values,
                use_cache=use_cache,
                cache_position=cache_position,
                position_embeddings=position_embeddings,
                protein_kv_states=protein_feats,
                structure_kv_states=structure_feats,
                msa_kv_states=msa_feats,
                protein_batch_mask=protein_batch_mask,
                structure_batch_mask=structure_batch_mask,
                msa_batch_mask=msa_batch_mask,
                query_attn_mask=attention_mask,
                **kwargs,
            )

        hidden_states = self.norm(hidden_states)

        output = BaseModelOutputWithPast(
            last_hidden_state=hidden_states,
            past_key_values=past_key_values,
        )
        return output


class EvollaForProteinText2Text(EvollaPreTrainedModel, GenerationMixin):
    def __init__(self, config):
        super().__init__(config)
        self.model = EvollaModel(config)
        self.vocab_size = config.vocab_size
        self.lm_head = nn.Linear(config.hidden_size, self.vocab_size, bias=False)

        self.post_init()

    def get_input_embeddings(self):
        return self.model.get_input_embeddings()

    def set_input_embeddings(self, value):
        return self.model.set_input_embeddings(value)

    @can_return_tuple
    @auto_docstring
    def forward(
        self,
        input_ids: Optional[torch.LongTensor] = None,  # text input ids
        attention_mask: Optional[torch.Tensor] = None,  # text attention mask
        inputs_embeds: Optional[torch.FloatTensor] = None,  # text input embeddings
        labels: Optional[torch.LongTensor] = None,
        protein_input_ids: Optional[torch.LongTensor] = None,
        protein_attention_mask: Optional[torch.Tensor] = None,
        use_cache: Optional[bool] = None,
        **kwargs,
    ):
        r"""
        protein_input_ids (torch.LongTensor):
            The input IDs for the protein sequence. Should be of shape `(batch_size, protein_seq_length)` and type `torch.LongTensor`.
        protein_attention_mask (torch.Tensor):
            The attention mask for the protein sequence. Should be of shape `(batch_size, protein_seq_length)` and type `torch.Tensor`.

        Example:

        ```python
        >>> from transformers import EvollaProcessor, EvollaForProteinText2Text
        >>> model = EvollaForProteinText2Text.from_pretrained("westlake/Evolla-10B-hf")
        >>> processor = EvollaProcessor.from_pretrained("westlake/Evolla-10B-hf")

        >>> protein_information = {
            "aa_seq": "your amino acid sequence",
            "foldseek": "your foldseek sequence",
        }
        >>> question = "What is the function of this protein?"
        >>> message = [
            {"role": "system", "content": "You are an AI expert that can answer any questions about protein."},
            {"role": "user", "content": question},
        ]

        >>> inputs = processor(proteins=[protein_information], messages_list=[message], return_tensors="pt", padding="longest")
        >>> outputs = model.generate(**inputs)

        >>> print(processor.batch_decode(outputs, skip_special_tokens=True))
        ```"""

        outputs = self.model(
            input_ids=input_ids,
            attention_mask=attention_mask,
            inputs_embeds=inputs_embeds,
            protein_input_ids=protein_input_ids,
            protein_attention_mask=protein_attention_mask,
            use_cache=use_cache,
            **kwargs,
        )
        hidden_states = outputs[0]
        logits = self.lm_head(hidden_states)

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

        lm_outputs = CausalLMOutputWithPast(
            loss=loss,
            logits=logits,
            past_key_values=outputs.past_key_values,
            hidden_states=outputs.hidden_states,
            attentions=outputs.attentions,
        )
        return lm_outputs


__all__ = ["EvollaForProteinText2Text", "EvollaModel", "EvollaPreTrainedModel"]