modeling_helix_mrna.py

# coding=utf-8
# Copyright 2024 state-spaces/mamba2 org and HuggingFace Inc. team.
#
# 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
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"""PyTorch Helix-mRNA model."""

import math
from dataclasses import dataclass
from typing import Optional, Tuple, Union, Dict, Any, List
import torch
import torch.utils.checkpoint
from torch import nn

from transformers.cache_utils import DynamicCache
from transformers.activations import ACT2FN

from transformers.modeling_utils import PreTrainedModel
from transformers.utils import ModelOutput

from transformers.modeling_attn_mask_utils import (
    AttentionMaskConverter,
)
from .configuration_helix_mrna import HelixmRNAConfig

from transformers.utils.import_utils import (
    is_causal_conv1d_available,
    is_flash_attn_2_available,
    is_flash_attn_greater_or_equal_2_10,
    is_mamba_2_ssm_available,
)

if is_flash_attn_2_available():
    from transformers.modeling_flash_attention_utils import _flash_attention_forward

if is_mamba_2_ssm_available():
    from mamba_ssm.ops.triton.selective_state_update import selective_state_update
    from mamba_ssm.ops.triton.ssd_combined import (
        mamba_chunk_scan_combined,
        mamba_split_conv1d_scan_combined,
    )
else:
    selective_state_update = None

if is_causal_conv1d_available():
    from causal_conv1d import causal_conv1d_fn, causal_conv1d_update
else:
    causal_conv1d_update, causal_conv1d_fn = None, None

is_fast_path_available = all(
    (selective_state_update, causal_conv1d_fn, causal_conv1d_update)
)

# copied from transformers.models.mistral.modeling_mistral.pad_tensor_by_size


def pad_tensor_by_size(input_tensor: torch.Tensor, pad_size: int):
    """
    Padding x tensor with `pad_size` on the seq_len dim (dim=1)

    Assumes that we only have tensors of either size 4 or 3
    """
    pad_shape = (
        (0, 0, 0, 0, 0, pad_size, 0, 0)
        if len(input_tensor.shape) == 4
        else (0, 0, 0, pad_size, 0, 0)
    )

    return torch.nn.functional.pad(input_tensor, pad_shape, mode="constant", value=0)


def reshape_into_chunks(input_tensor, pad_size, chunk_size):
    """
    Padding input_tensor with `pad_size` on the seq_len dim (dim=1) and
    simultaneously splitting it into chunk sequences.

    Assumes that we only have tensors of either size 4 or 3
    """
    # [bsz, seq_len, ...] -> [bsz, seq_len multiple of chunk_size, ...]
    input_tensor = pad_tensor_by_size(input_tensor, pad_size)

    if len(input_tensor.shape) == 3:
        # [bsz, seq_len multiple of chunk_size, num_heads] -> [bsz, -1, chunk_size, num_heads]
        return input_tensor.reshape(
            input_tensor.shape[0], -1, chunk_size, input_tensor.shape[2]
        )
    else:
        # [bsz, seq_len multiple of chunk_size, num_heads, head_dim or state_size] -> [bsz, -1, chunk_size, num_heads, head_dim or state_size]
        return input_tensor.reshape(
            input_tensor.shape[0],
            -1,
            chunk_size,
            input_tensor.shape[2],
            input_tensor.shape[3],
        )


def segment_sum(input_tensor):
    """
    More stable segment sum calculation. Uses cumulative sums and masking instead of direct subtractions.
    """
    chunk_size = input_tensor.size(-1)
    # 1. expand input tensor to have an additional dimension and repeat along that dimension
    # [..., chunk_size] -> [..., chunk_size, chunk_size]
    input_tensor = input_tensor[..., None].expand(*input_tensor.size(), chunk_size)
    # 2. create a lower triangular mask with the diagonal set to 0 to 0 out elements above diag
    mask = torch.tril(
        torch.ones(
            chunk_size, chunk_size, device=input_tensor.device, dtype=torch.bool
        ),
        diagonal=-1,
    )
    input_tensor = input_tensor.masked_fill(~mask, 0)
    # 3. compute actual cumsum
    tensor_segsum = torch.cumsum(input_tensor, dim=-2)

    # 4. apply mask to keep only the lower triangular part of the cumulative sum result (incl diagonal this time)
    mask = torch.tril(
        torch.ones(
            chunk_size, chunk_size, device=input_tensor.device, dtype=torch.bool
        ),
        diagonal=0,
    )
    tensor_segsum = tensor_segsum.masked_fill(~mask, -torch.inf)
    return tensor_segsum


# Copied from transformers.models.llama.modeling_llama.repeat_kv
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 HybridMambaAttentionDynamicCache(DynamicCache):
    """
    A dynamic cache that can handle both the attention cache (which has a seq_len dimension) and the mamba cache
    (which has a constant shape regardless of seq_len).

    This cache has two sets of lists of tensors: `key_cache` and `value_cache` for attention cache and `conv_states`
    and `ssm_states` for mamba cache. Each of these lists has `num_layers` tensors. The expected shape for each tensor
    For attention layers, `key_cache` and `value_cache` have a shape of `(batch_size, num_heads, seq_len, head_dim)`,
    while `conv_states` and `ssm_states` have a shape of `(batch_size, 0)` (empty tensors).
    For mamba layers, `key_cache` and `value_cache` have a shape of `(batch_size, 0)` (empty tensors),
    while `conv_states` represents the convolution state and has a shape of `(batch_size, d_inner, d_conv)`,
    and `ssm_states` represents the ssm state and has a shape of `(batch_size, d_inner, d_state)`.
    """

    def __init__(self, config, batch_size, dtype=torch.float16, device=None):
        super().__init__()
        self.dtype = dtype
        self.layers_block_type = config.layers_block_type
        self.has_previous_state = False  # only used by mamba
        intermediate_size = config.expand * config.hidden_size
        ssm_state_size = config.state_size
        conv_kernel_size = config.conv_kernel
        self.seqlen_offset = 0
        self.conv_states = []
        self.ssm_states = []
        self.transformer_layers = []
        for i in range(config.num_hidden_layers):
            if self.layers_block_type[i] == "mamba":
                self.conv_states += [
                    torch.zeros(
                        batch_size,
                        intermediate_size,
                        conv_kernel_size,
                        device=device,
                        dtype=dtype,
                    )
                ]
                self.ssm_states += [
                    torch.zeros(
                        batch_size,
                        intermediate_size,
                        ssm_state_size,
                        device=device,
                        dtype=dtype,
                    )
                ]
            else:
                self.conv_states += [torch.tensor([[]] * batch_size, device=device)]
                self.ssm_states += [torch.tensor([[]] * batch_size, device=device)]
                self.transformer_layers.append(i)

        self.key_cache = [
            torch.tensor([[]] * batch_size, device=device)
            for _ in range(config.num_hidden_layers)
        ]
        self.value_cache = [
            torch.tensor([[]] * batch_size, device=device)
            for _ in range(config.num_hidden_layers)
        ]

    def update(
        self,
        key_states: torch.Tensor,
        value_states: torch.Tensor,
        layer_idx: int,
        cache_kwargs: Optional[Dict[str, Any]] = None,
    ) -> Tuple[torch.Tensor, torch.Tensor]:
        # Update the cache
        if self.key_cache[layer_idx].shape[-1] == 0:
            self.key_cache[layer_idx] = key_states
            self.value_cache[layer_idx] = value_states
        else:
            self.key_cache[layer_idx] = torch.cat(
                [self.key_cache[layer_idx], key_states], dim=2
            )
            self.value_cache[layer_idx] = torch.cat(
                [self.value_cache[layer_idx], value_states], dim=2
            )

        return self.key_cache[layer_idx], self.value_cache[layer_idx]

    def reorder_cache(self, beam_idx: torch.LongTensor):
        """Reorders the cache for beam search, given the selected beam indices."""
        for layer_idx in range(len(self.key_cache)):
            device = self.key_cache[layer_idx].device
            self.key_cache[layer_idx] = self.key_cache[layer_idx].index_select(
                0, beam_idx.to(device)
            )
            device = self.value_cache[layer_idx].device
            self.value_cache[layer_idx] = self.value_cache[layer_idx].index_select(
                0, beam_idx.to(device)
            )

            device = self.conv_states[layer_idx].device
            self.conv_states[layer_idx] = self.conv_states[layer_idx].index_select(
                0, beam_idx.to(device)
            )
            device = self.ssm_states[layer_idx].device
            self.ssm_states[layer_idx] = self.ssm_states[layer_idx].index_select(
                0, beam_idx.to(device)
            )

    def get_seq_length(self, layer_idx: Optional[int] = 0) -> int:
        """Returns the sequence length of the cached states. A layer index can be optionally passed."""
        # take any layer that contains cache and not empty tensor
        layer_idx = (
            self.transformer_layers[0]
            if layer_idx not in self.transformer_layers
            else layer_idx
        )
        if len(self.key_cache) <= layer_idx:
            return 0
        return self.key_cache[layer_idx].shape[-2]

    def to_legacy_cache(self) -> Tuple[Tuple[torch.Tensor], Tuple[torch.Tensor]]:
        raise NotImplementedError(
            "HybridMambaAttentionDynamicCache does not have a legacy cache equivalent."
        )

    @classmethod
    def from_legacy_cache(
        cls, past_key_values: Optional[Tuple[Tuple[torch.FloatTensor]]] = None
    ) -> "DynamicCache":
        raise NotImplementedError(
            "HybridMambaAttentionDynamicCache does not have a legacy cache equivalent."
        )


# Adapted from transformers.models.mistral.modeling_mistral.MistralAttention with Mistral->Jamba
class HelixmRNAAttention(nn.Module):
    """
    Multi-headed attention from 'Attention Is All You Need' paper. Modified to use sliding window attention: Longformer
    and "Generating Long Sequences with Sparse Transformers".
    """

    def __init__(
        self, config: HelixmRNAConfig, layer_idx: Optional[int] = None
    ):
        super().__init__()
        self.config = config
        self.layer_idx = layer_idx
        if layer_idx is None:
            print(
                f"Instantiating {self.__class__.__name__} without passing a `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.hidden_size = config.hidden_size
        self.num_heads = config.num_attention_heads
        self.head_dim = self.hidden_size // self.num_heads
        self.num_key_value_heads = config.num_key_value_heads
        self.num_key_value_groups = self.num_heads // self.num_key_value_heads
        self.is_causal = True
        self.attention_dropout = config.attention_dropout

        if (self.head_dim * self.num_heads) != self.hidden_size:
            raise ValueError(
                f"hidden_size must be divisible by num_heads (got `hidden_size`: {self.hidden_size}"
                f" and `num_heads`: {self.num_heads})."
            )
        self.q_proj = nn.Linear(
            self.hidden_size, self.num_heads * self.head_dim, bias=False
        )
        self.k_proj = nn.Linear(
            self.hidden_size, self.num_key_value_heads * self.head_dim, bias=False
        )
        self.v_proj = nn.Linear(
            self.hidden_size, self.num_key_value_heads * self.head_dim, bias=False
        )
        self.o_proj = nn.Linear(
            self.num_heads * self.head_dim, self.hidden_size, bias=False
        )

    def forward(
        self,
        hidden_states: torch.Tensor,
        attention_mask: Optional[torch.Tensor] = None,
        position_ids: Optional[torch.LongTensor] = None,
        past_key_value: Optional[HybridMambaAttentionDynamicCache] = None,
        output_attentions: bool = False,
        use_cache: bool = False,
        cache_position: Optional[torch.LongTensor] = None,
    ) -> Tuple[torch.Tensor, Optional[torch.Tensor], Optional[Tuple[torch.Tensor]]]:
        bsz, q_len, _ = hidden_states.size()

        query_states = self.q_proj(hidden_states)
        key_states = self.k_proj(hidden_states)
        value_states = self.v_proj(hidden_states)

        query_states = query_states.view(
            bsz, q_len, self.num_heads, self.head_dim
        ).transpose(1, 2)
        key_states = key_states.view(
            bsz, q_len, self.num_key_value_heads, self.head_dim
        ).transpose(1, 2)
        value_states = value_states.view(
            bsz, q_len, self.num_key_value_heads, self.head_dim
        ).transpose(1, 2)

        if past_key_value is not None:
            key_states, value_states = past_key_value.update(
                key_states, value_states, self.layer_idx
            )

        # repeat k/v heads if n_kv_heads < n_heads
        key_states = repeat_kv(key_states, self.num_key_value_groups)
        value_states = repeat_kv(value_states, self.num_key_value_groups)

        attn_weights = torch.matmul(
            query_states, key_states.transpose(2, 3)
        ) / math.sqrt(self.head_dim)

        if attention_mask is not None:  # no matter the length, we just slice it
            causal_mask = attention_mask[:, :, :, : key_states.shape[-2]]
            attn_weights = attn_weights + causal_mask

        # upcast attention to fp32
        attn_weights = nn.functional.softmax(
            attn_weights, dim=-1, dtype=torch.float32
        ).to(query_states.dtype)
        attn_weights = nn.functional.dropout(
            attn_weights, p=self.attention_dropout, training=self.training
        )
        attn_output = torch.matmul(attn_weights, value_states)

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

        attn_output = attn_output.transpose(1, 2).contiguous()
        attn_output = attn_output.reshape(bsz, q_len, self.hidden_size)

        attn_output = self.o_proj(attn_output)

        if not output_attentions:
            attn_weights = None

        return attn_output, attn_weights, past_key_value


# Adapted from transformers.models.mistral.modeling_mistral.MistralFlashAttention2 with Mistral->Jamba
class HelixmRNAFlashAttention2(HelixmRNAAttention):
    """
    Jamba flash attention module. This module inherits from `JambaAttention` as the weights of the module stays
    untouched. The only required change would be on the forward pass where it needs to correctly call the public API of
    flash attention and deal with padding tokens in case the input contains any of them.
    """

    # Copied from transformers.models.llama.modeling_llama.LlamaFlashAttention2.__init__
    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)

        # TODO: Should be removed once Flash Attention for RoCm is bumped to 2.1.
        # flash_attn<2.1 generates top-left aligned causal mask, while what is needed here is bottom-right alignement, that was made default for flash_attn>=2.1. This attribute is used to handle this difference. Reference: https://github.com/Dao-AILab/flash-attention/releases/tag/v2.1.0.
        # Beware that with flash_attn<2.1, using q_seqlen != k_seqlen (except for the case q_seqlen == 1) produces a wrong mask (top-left).
        self._flash_attn_uses_top_left_mask = not is_flash_attn_greater_or_equal_2_10()

    def forward(
        self,
        hidden_states: torch.Tensor,
        attention_mask: Optional[torch.Tensor] = None,
        position_ids: Optional[torch.LongTensor] = None,
        past_key_value: Optional[HybridMambaAttentionDynamicCache] = None,
        output_attentions: bool = False,
        use_cache: bool = False,
        cache_position: Optional[torch.LongTensor] = None,
        **kwargs,
    ):
        bsz, q_len, _ = hidden_states.size()

        query_states = self.q_proj(hidden_states)
        key_states = self.k_proj(hidden_states)
        value_states = self.v_proj(hidden_states)

        # Flash attention requires the input to have the shape
        # batch_size x seq_length x head_dim x hidden_dim
        # therefore we just need to keep the original shape
        query_states = query_states.view(bsz, q_len, self.num_heads, self.head_dim)
        key_states = key_states.view(
            bsz, q_len, self.num_key_value_heads, self.head_dim
        ).transpose(1, 2)
        value_states = value_states.view(
            bsz, q_len, self.num_key_value_heads, self.head_dim
        ).transpose(1, 2)

        if past_key_value is not None:
            key_states, value_states = past_key_value.update(
                key_states, value_states, self.layer_idx
            )

        # repeat k/v heads if n_kv_heads < n_heads
        key_states = repeat_kv(key_states, self.num_key_value_groups)
        value_states = repeat_kv(value_states, self.num_key_value_groups)
        dropout_rate = 0.0 if not self.training else self.attention_dropout

        # In PEFT, usually we cast the layer norms in float32 for training stability reasons
        # therefore the input hidden states gets silently casted in float32. Hence, we need
        # cast them back in float16 just to be sure everything works as expected.
        input_dtype = query_states.dtype
        if input_dtype == torch.float32:
            if torch.is_autocast_enabled():
                target_dtype = torch.get_autocast_gpu_dtype()
            # Handle the case where the model is quantized
            elif hasattr(self.config, "_pre_quantization_dtype"):
                target_dtype = self.config._pre_quantization_dtype
            else:
                target_dtype = self.q_proj.weight.dtype

            print(
                f"The input hidden states seems to be silently casted in float32, this might be related to"
                f" the fact you have upcasted embedding or layer norm layers in float32. We will cast back the input in"
                f" {target_dtype}."
            )

            query_states = query_states.to(target_dtype)
            key_states = key_states.to(target_dtype)
            value_states = value_states.to(target_dtype)

        # Reashape to the expected shape for Flash Attention
        key_states = key_states.transpose(1, 2)
        value_states = value_states.transpose(1, 2)

        attn_output = _flash_attention_forward(
            query_states,
            key_states,
            value_states,
            attention_mask,
            q_len,
            dropout=dropout_rate,
            sliding_window=getattr(self.config, "sliding_window", None),
            is_causal=self.is_causal,
            use_top_left_mask=self._flash_attn_uses_top_left_mask,
        )

        attn_output = attn_output.reshape(bsz, q_len, self.hidden_size).contiguous()
        attn_output = self.o_proj(attn_output)

        if not output_attentions:
            attn_weights = None

        return attn_output, attn_weights, past_key_value


# Adapted from transformers.models.mistral.modeling_mistral.MistralSdpaAttention with Mistral->Jamba
class HelixmRNASdpaAttention(HelixmRNAAttention):
    """
    Jamba attention module using torch.nn.functional.scaled_dot_product_attention. This module inherits from
    `JambaAttention` as the weights of the module stays untouched. The only changes are on the forward pass to adapt to
    SDPA API.
    """

    # Adapted from JambaAttention.forward
    def forward(
        self,
        hidden_states: torch.Tensor,
        attention_mask: Optional[torch.Tensor] = None,
        position_ids: Optional[torch.LongTensor] = None,
        past_key_value: Optional[HybridMambaAttentionDynamicCache] = None,
        output_attentions: bool = False,
        use_cache: bool = False,
        cache_position: Optional[torch.LongTensor] = None,
    ) -> Tuple[torch.Tensor, Optional[torch.Tensor], Optional[Tuple[torch.Tensor]]]:
        if output_attentions:
            # TODO: Improve this warning with e.g. `model.config.attn_implementation = "manual"` once this is implemented.
            print(
                "JambaModel is using JambaSdpaAttention, but `torch.nn.functional.scaled_dot_product_attention` does not support `output_attentions=True`. Falling back to the manual attention implementation, "
                'but specifying the manual implementation will be required from Transformers version v5.0.0 onwards. This warning can be removed using the argument `attn_implementation="eager"` when loading the model.'
            )
            return super().forward(
                hidden_states=hidden_states,
                attention_mask=attention_mask,
                position_ids=position_ids,
                past_key_value=past_key_value,
                output_attentions=output_attentions,
                use_cache=use_cache,
            )

        bsz, q_len, _ = hidden_states.size()

        query_states = self.q_proj(hidden_states)
        key_states = self.k_proj(hidden_states)
        value_states = self.v_proj(hidden_states)

        query_states = query_states.view(
            bsz, q_len, self.num_heads, self.head_dim
        ).transpose(1, 2)
        key_states = key_states.view(
            bsz, q_len, self.num_key_value_heads, self.head_dim
        ).transpose(1, 2)
        value_states = value_states.view(
            bsz, q_len, self.num_key_value_heads, self.head_dim
        ).transpose(1, 2)

        if past_key_value is not None:
            key_states, value_states = past_key_value.update(
                key_states, value_states, self.layer_idx
            )

        key_states = repeat_kv(key_states, self.num_key_value_groups)
        value_states = repeat_kv(value_states, self.num_key_value_groups)

        causal_mask = attention_mask
        if attention_mask is not None:
            causal_mask = causal_mask[:, :, :, : key_states.shape[-2]]

        # SDPA with memory-efficient backend is currently (torch==2.1.2) bugged with non-contiguous inputs with custom attn_mask,
        # Reference: https://github.com/pytorch/pytorch/issues/112577.
        if query_states.device.type == "cuda" and attention_mask is not None:
            query_states = query_states.contiguous()
            key_states = key_states.contiguous()
            value_states = value_states.contiguous()

        # We dispatch to SDPA's Flash Attention or Efficient kernels via this `is_causal` if statement instead of an inline conditional assignment
        # in SDPA to support both torch.compile's dynamic shapes and full graph options. An inline conditional prevents dynamic shapes from compiling.
        # The q_len > 1 is necessary to match with AttentionMaskConverter.to_causal_4d that does not create a causal mask in case q_len == 1.
        is_causal = (
            True if self.is_causal and causal_mask is None and q_len > 1 else False
        )

        attn_output = torch.nn.functional.scaled_dot_product_attention(
            query_states,
            key_states,
            value_states,
            attn_mask=causal_mask,
            dropout_p=self.attention_dropout if self.training else 0.0,
            is_causal=is_causal,
        )

        attn_output = attn_output.transpose(1, 2).contiguous()
        attn_output = attn_output.view(bsz, q_len, self.hidden_size)

        attn_output = self.o_proj(attn_output)

        return attn_output, None, past_key_value


HelixmRNA_ATTENTION_CLASSES = {
    "eager": HelixmRNAAttention,
    "flash_attention_2": HelixmRNAFlashAttention2,
    "sdpa": HelixmRNASdpaAttention,
}


class Mamba2Cache:
    """
    Arguments:
        config: Mamba2Config
        batch_size: int
        dtype: torch.dtype
        device: torch.device

    Attributes:
        seqlen_offset: int
        dtype: torch.dtype
        conv_states: Dict[int, torch.Tensor] # layer_idx -> [batch_size, intermediate_size, conv_kernel_size]
        ssm_states: Dict[int, torch.Tensor] # layer_idx -> [batch_size, intermediate_size, ssm_state_size]
    """

    def __init__(
        self,
        config: HelixmRNAConfig,
        batch_size: int,
        dtype: torch.dtype = torch.float16,
        device: Optional[str] = None,
    ):
        self.seqlen_offset = 0
        self.dtype = dtype
        self.conv_kernel_size = config.conv_kernel
        self.intermediate_size = int(config.expand * config.hidden_size)

        self.conv_states = {
            i: torch.zeros(
                batch_size,
                self.intermediate_size + 2 * config.n_groups * config.state_size,
                self.conv_kernel_size,
                device=device,
                dtype=dtype,
            )
            for i in range(config.num_hidden_layers)
        }
        self.ssm_states = {
            i: torch.zeros(
                batch_size,
                config.num_heads,
                config.head_dim,
                config.state_size,
                device=device,
                dtype=dtype,
            )
            for i in range(config.num_hidden_layers)
        }
        self.activation = config.hidden_act
        self.act = ACT2FN[config.hidden_act]

    def update_conv_state(
        self,
        layer_idx: int,
        new_conv_state: torch.Tensor,
        cache_position: torch.LongTensor,
    ) -> torch.Tensor:
        conv_state = self.conv_states[layer_idx]
        cache_position = cache_position.clamp(0, self.conv_kernel_size - 1)

        conv_state = conv_state.roll(shifts=-1, dims=-1)
        conv_state[:, :, cache_position] = new_conv_state.to(conv_state.device)
        self.conv_states[layer_idx].zero_()
        self.conv_states[layer_idx] += conv_state
        return self.conv_states[layer_idx]

    def reset(self):
        self.conv_states.zero_()
        self.ssm_states.zero_()


class MambaRMSNormGated(torch.nn.Module):
    def __init__(self, hidden_size, eps=1e-6):
        super().__init__()
        self.weight = nn.Parameter(torch.ones(hidden_size))
        self.variance_epsilon = eps

    def forward(self, hidden_states, gate=None):
        input_dtype = hidden_states.dtype
        hidden_states = hidden_states.to(torch.float32)

        if gate is not None:
            hidden_states = hidden_states * nn.functional.silu(gate.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)


class Mamba2Mixer(nn.Module):
    """
    Compute ∆, A, B, C, and D the state space parameters and compute the `contextualized_states`.
    A, D are input independent (see Mamba paper [1] Section 3.5.2 "Interpretation of A" for why A isn't selective)
    ∆, B, C are input-dependent (this is a key difference between Mamba and the linear time invariant S4,
    and is why Mamba is called **selective** state spaces)
    """

    def __init__(self, config: HelixmRNAConfig, layer_idx: int):
        super().__init__()
        self.num_heads = config.num_heads
        self.hidden_size = config.hidden_size
        self.ssm_state_size = config.state_size
        self.conv_kernel_size = config.conv_kernel
        self.intermediate_size = int(config.expand * self.hidden_size)
        self.time_step_rank = int(config.time_step_rank)
        self.layer_idx = layer_idx
        self.use_conv_bias = config.use_conv_bias
        self.activation = config.hidden_act
        self.act = ACT2FN[config.hidden_act]

        self.layer_norm_epsilon = config.layer_norm_epsilon
        self.rms_norm = config.rms_norm

        self.n_groups = config.n_groups
        self.head_dim = config.head_dim
        self.chunk_size = config.chunk_size

        self.time_step_limit = config.time_step_limit
        self.time_step_min = config.time_step_min
        self.time_step_max = config.time_step_max

        self.conv_dim = self.intermediate_size + 2 * self.n_groups * self.ssm_state_size
        self.conv1d = nn.Conv1d(
            in_channels=self.conv_dim,
            out_channels=self.conv_dim,
            bias=config.use_conv_bias,
            kernel_size=config.conv_kernel,
            groups=self.conv_dim,
            padding=config.conv_kernel - 1,
        )

        # projection of the input hidden states
        projection_size = self.intermediate_size + self.conv_dim + self.num_heads
        self.in_proj = nn.Linear(
            self.hidden_size,
            projection_size,
            bias=config.use_bias,
        )
        # selective projection used to make dt, B and C input dependant

        # time step projection (discretization)
        # instantiate once and copy inv_dt in init_weights of PretrainedModel
        self.dt_bias = nn.Parameter(torch.ones(self.num_heads))

        # S4D real initialization. These are not discretized!
        # The core is to load them, compute the discrete states, then write the updated state. Keeps the memory bounded
        A = torch.arange(1, self.num_heads + 1)
        self.A_log = nn.Parameter(torch.log(A))
        self.A_log._no_weight_decay = True
        self.norm = MambaRMSNormGated(
            self.intermediate_size, eps=self.layer_norm_epsilon
        )
        self.D = nn.Parameter(torch.ones(self.num_heads))
        self.D._no_weight_decay = True

        self.out_proj = nn.Linear(
            self.intermediate_size, self.hidden_size, bias=config.use_bias
        )
        self.use_bias = config.use_bias

        if not is_fast_path_available:
            print(
                "The fast path is not available because on of `(selective_state_update, causal_conv1d_fn, causal_conv1d_update)`"
                " is None. Falling back to the naive implementation. To install follow https://github.com/state-spaces/mamba/#installation and"
                " https://github.com/Dao-AILab/causal-conv1d"
            )

    def cuda_kernels_forward(
        self,
        hidden_states: torch.Tensor,
        cache_params: Optional[HybridMambaAttentionDynamicCache] = None,
        cache_position: Optional[torch.LongTensor] = None,
        attention_mask: Optional[torch.Tensor] = None,
    ):
        # set up dimensions for reshapes later

        batch_size, seq_len, _ = hidden_states.shape
        groups_time_state_size = self.n_groups * self.ssm_state_size
        d_to_remove = (
            2 * self.intermediate_size
            + 2 * self.n_groups * self.ssm_state_size
            + self.num_heads
        )

        # getting projected states from cache if it exists
        if cache_params is not None and cache_params.seqlen_offset > 0:
            in_projected_states = self.in_proj(hidden_states.squeeze(1))  # (B 2D)
            d_mlp = (in_projected_states.shape[-1] - d_to_remove) // 2
            split_projection_dim = [
                d_mlp,
                d_mlp,
                self.intermediate_size,
                self.conv_dim,
                self.num_heads,
            ]
            _, _, gate, hidden_states_B_C, dt = torch.split(
                in_projected_states, split_projection_dim, dim=-1
            )

            hidden_states_B_C = causal_conv1d_update(
                hidden_states_B_C,
                cache_params.conv_states[self.layer_idx],
                self.conv1d.weight.squeeze(1),
                self.conv1d.bias,
                self.activation,
            )

            hidden_states, B, C = torch.split(
                hidden_states_B_C,
                [
                    self.intermediate_size,
                    groups_time_state_size,
                    groups_time_state_size,
                ],
                dim=-1,
            )
            A = -torch.exp(self.A_log.float())  # (nheads,)

            A = (
                A[:, None, ...][:, :, None]
                .expand(-1, self.head_dim, self.ssm_state_size)
                .to(dtype=torch.float32)
            )
            dt = dt[:, :, None].expand(-1, -1, self.head_dim)
            dt_bias = self.dt_bias[:, None, ...].expand(-1, self.head_dim)
            D = self.D[:, None, ...].expand(-1, self.head_dim)
            B = B.view(batch_size, self.n_groups, B.shape[1] // self.n_groups)
            C = C.view(batch_size, self.n_groups, C.shape[1] // self.n_groups)
            hidden_states_reshaped = hidden_states.view(
                batch_size, self.num_heads, self.head_dim
            )
            hidden_states = selective_state_update(
                cache_params.ssm_states[self.layer_idx],
                hidden_states_reshaped,
                dt,
                A,
                B,
                C,
                D,
                z=None,
                dt_bias=dt_bias,
                dt_softplus=True,
            )
            hidden_states = hidden_states.view(
                batch_size, self.num_heads * self.head_dim
            )
            hidden_states = self.norm(hidden_states, gate)
            out = self.out_proj(hidden_states)[:, None, ...]
        # if no cache is found, calling the kernel
        else:
            if (
                attention_mask is not None
                and attention_mask.shape[1] > 1
                and attention_mask.shape[0] > 1
            ):
                # tune out hidden states for pad tokens, see https://github.com/state-spaces/mamba/issues/66
                dtype = hidden_states.dtype
                hidden_states = (hidden_states * attention_mask[:, :, None]).to(dtype)
            # 1. Gated MLP's linear projection
            projected_states = self.in_proj(hidden_states)
            A = -torch.exp(
                self.A_log.float()
            )  # (num_heads) or (intermediate_size, state_size)
            dt_limit_kwargs = (
                {}
                if self.time_step_limit == (0.0, float("inf"))
                else {"dt_limit": self.time_step_limit}
            )

            if self.training and cache_params is None:
                out, ssm_state = mamba_split_conv1d_scan_combined(
                    projected_states,
                    self.conv1d.weight.squeeze(1),
                    self.conv1d.bias,
                    self.dt_bias,
                    A,
                    D=self.D,
                    chunk_size=self.chunk_size,
                    seq_idx=None,  # was seq_idx
                    activation=self.activation,
                    rmsnorm_weight=self.norm.weight,
                    rmsnorm_eps=self.norm.variance_epsilon,
                    outproj_weight=self.out_proj.weight,
                    outproj_bias=self.out_proj.bias,
                    headdim=self.head_dim,
                    ngroups=self.n_groups,
                    norm_before_gate=False,
                    return_final_states=True,
                    **dt_limit_kwargs,
                )

            else:
                gate, hidden_states_B_C, time_step = torch.split(
                    projected_states,
                    [self.intermediate_size, self.conv_dim, self.num_heads],
                    dim=-1,
                )

                # 1D Convolution
                if causal_conv1d_fn is None or self.activation not in ["silu", "swish"]:
                    hidden_states_B_C = self.act(
                        self.conv1d(hidden_states_B_C.transpose(1, 2)).transpose(1, 2)[
                            :, :seq_len
                        ]
                    )  # (B, L, self.d_inner + 2 * ngroups * d_state)
                else:
                    hidden_states_B_C = causal_conv1d_fn(
                        x=hidden_states_B_C.transpose(1, 2),
                        weight=self.conv1d.weight.squeeze(1),
                        bias=self.conv1d.bias,
                        activation=self.activation,
                    ).transpose(1, 2)[:, :seq_len]
                hidden_states, B, C = torch.split(
                    hidden_states_B_C,
                    [
                        self.intermediate_size,
                        groups_time_state_size,
                        groups_time_state_size,
                    ],
                    dim=-1,
                )
                if (
                    attention_mask is not None
                    and attention_mask.shape[1] > 1
                    and attention_mask.shape[0] > 1
                ):
                    # tune out hidden states for pad tokens, see https://github.com/state-spaces/mamba/issues/66
                    dtype = hidden_states.dtype
                    hidden_states = (hidden_states * attention_mask[:, :, None]).to(
                        dtype
                    )
                scan_output, ssm_state = mamba_chunk_scan_combined(
                    hidden_states.view(batch_size, seq_len, -1, self.head_dim),
                    time_step,
                    A,
                    B.view(batch_size, seq_len, self.n_groups, -1),
                    C.view(batch_size, seq_len, self.n_groups, -1),
                    chunk_size=self.chunk_size,
                    D=self.D,
                    z=None,
                    seq_idx=None,
                    return_final_states=True,
                    dt_bias=self.dt_bias,
                    dt_softplus=True,
                    **dt_limit_kwargs,
                )
                if ssm_state is not None and cache_params is not None:
                    cache_params.ssm_states[self.layer_idx].copy_(ssm_state)
                scan_output = scan_output.view(batch_size, seq_len, -1)
                # Multiply "gate" branch and apply extra normalization layer
                scan_output = self.norm(scan_output, gate)
                out = self.out_proj(scan_output)
        return out

    # fmt: off
    def torch_forward(self, input_states, cache_params: Optional[HybridMambaAttentionDynamicCache]=None, cache_position:Optional[torch.LongTensor]=None, attention_mask: Optional[torch.Tensor]=None):
        batch_size, seq_len, _ = input_states.shape
        dtype = input_states.dtype
        # Gated MLP's linear projection
        projected_states =  self.in_proj(input_states.squeeze(1))
        d_mlp = (projected_states.shape[-1] - 2 * self.intermediate_size -  2 * self.n_groups * self.ssm_state_size- self.num_heads) // 2
        _, _, gate, hidden_states, dt = projected_states.split(
                [d_mlp, d_mlp, self.intermediate_size,  self.conv_dim, self.num_heads], dim=-1
        )

        # Convolution sequence transformation
        if cache_params is not None:
            ssm_state = cache_params.ssm_states[self.layer_idx].clone()
            ssm_state = ssm_state.to(hidden_states.device)
            if cache_params.seqlen_offset > 0:
                conv_state = cache_params.conv_states[self.layer_idx]                   # [batch, intermediate_size, conv_kernel_size]
                conv_state = torch.roll(conv_state, shifts=-1, dims=-1)
                # handle batched generation - states are copied through
                conv_state[:, :, -1] = hidden_states[:, 0, :] if hidden_states.ndim == 3 else hidden_states
                cache_params.conv_states[self.layer_idx].copy_(conv_state)
                hidden_states = torch.sum(conv_state.to(projected_states.device) * self.conv1d.weight[:, 0, :], dim=-1)
                if self.use_conv_bias:
                    hidden_states += self.conv1d.bias
                hidden_states = self.act(hidden_states).to(dtype)[:, None, ...]         # [batch, 1, intermediate_size] : decoding
            else:
                hidden_states = hidden_states.transpose(1,2)
                conv_state = nn.functional.pad(
                    hidden_states,
                    (self.conv_kernel_size - hidden_states.shape[-1], 0)
                )
                cache_params.conv_states[self.layer_idx].copy_(conv_state)
                hidden_states = self.act(self.conv1d(hidden_states).transpose(1,2))[:, :seq_len, :]     # [batch, intermediate_size, seq_len]
                if attention_mask is not None and attention_mask.shape[1] > 1 and attention_mask.shape[0] > 1:
                    dtype = hidden_states.dtype
                    # tune out hidden states for pad tokens, see https://github.com/state-spaces/mamba/issues/66
                    hidden_states = (hidden_states * attention_mask[:, :, None]).to(dtype)
        else:
            ssm_state = torch.zeros(
                (batch_size, self.num_heads, self.head_dim, self.ssm_state_size),
                device=hidden_states.device, dtype=dtype
            )
            hidden_states = self.act(self.conv1d(hidden_states.transpose(1, 2))[..., :seq_len].transpose(1, 2))
        hidden_states, B, C = torch.split(hidden_states, [self.intermediate_size, self.n_groups * self.ssm_state_size, self.n_groups * self.ssm_state_size], dim=-1)
        A = -torch.exp(self.A_log.float())                            # [num_heads]
        if cache_params is not None and cache_params.seqlen_offset > 0:
            # Note: there is no need to pad parameter matrices here, as there is just one new token
            # for batched generation
            dt = dt[:, None, ...] if dt.ndim == 2 else dt[:, 0, :][:, None, ...]
            dt = dt.transpose(1, 2).expand(batch_size, dt.shape[-1], self.head_dim)
            # [num_heads] -> [num_heads, head_dim]
            dt_bias = self.dt_bias[..., None].expand(self.dt_bias.shape[0], self.head_dim)

            dt = torch.nn.functional.softplus(dt + dt_bias.to(dt.dtype))
            dt = torch.clamp(dt, self.time_step_min) #, self.time_step_max)
            A = A[..., None, None].expand(self.num_heads, self.head_dim, self.ssm_state_size).to(dtype=torch.float32)
            # [bsz, num_heads, head_dim, state_size]
            dA = torch.exp(dt[..., None] * A)

            # Discretize B
            # [bsz, n_groups * state_size] -> [bsz, n_groups, 1, state_size] ->
            # -> [bsz, n_groups, group to head repetition factor, state_size] -> [bsz, num_heads, state_size]
            B = B.reshape(batch_size, self.n_groups, -1)[..., None, :]
            B = B.expand(batch_size, self.n_groups, self.num_heads // self.n_groups, B.shape[-1]).contiguous()
            B = B.reshape(batch_size, -1, B.shape[-1])
            # [bsz, num_heads, head_dim, state_size]
            dB = dt[..., None] * B[..., None, :]

            # Discretize x into dB
            # [bsz, intermediate_size] -> [bsz, num_heads, head_dim]
            hidden_states = hidden_states.reshape(batch_size, -1, self.head_dim)
            dBx = dB * hidden_states[..., None]

            # State calculation
            cache_params.ssm_states[self.layer_idx].copy_(
                cache_params.ssm_states[self.layer_idx] * dA + dBx
            )

            # Subsequent output
            # [bsz, n_groups * state_size] -> [bsz, num_heads, state_size]
            C = C.reshape(batch_size, self.n_groups, -1)[..., None, :]
            C = C.expand(batch_size, self.n_groups, self.num_heads // self.n_groups, C.shape[-1]).contiguous()
            C = C.reshape(batch_size, -1, C.shape[-1])
            # [bsz, num_heads, head_dim]

            ssm_states = cache_params.ssm_states[self.layer_idx].to(C.dtype)  # Shape: [b, h, d, n]
            # Reshape ssm_states to merge the first two dimensions
            ssm_states_reshaped = ssm_states.view(batch_size * self.num_heads, self.head_dim, self.ssm_state_size)  # Shape: [b*h, d, n]
            C_reshaped = C.view(batch_size * self.num_heads, self.ssm_state_size, 1)  # Shape: [b*h, n, 1]
            y = torch.bmm(ssm_states_reshaped, C_reshaped)
            y = y.view(batch_size, self.num_heads, self.head_dim)

            # D skip connection
            # [num_heads] -> [num_heads, head_dim]
            D = self.D[..., None].expand(self.D.shape[0], self.head_dim)
            y = (y + hidden_states * D).to(y.dtype)

            # [bsz, num_heads, head_dim] -> [bsz, 1, intermediate_size]
            y = y.reshape(batch_size, -1)[:, None, ...]
        else:
            # begin ssd naive implementation without einsums
            dt = nn.functional.softplus(dt + self.dt_bias)
            dt = torch.clamp(dt, self.time_step_min)
            hidden_states = hidden_states.reshape(batch_size, seq_len, -1, self.head_dim).float()
            B = B.reshape(batch_size, seq_len,  -1, self.ssm_state_size).float()
            C = C.reshape(batch_size, seq_len, -1, self.ssm_state_size).float()
            B = B.repeat(1, 1, self.num_heads // self.n_groups, 1)
            C = C.repeat(1, 1, self.num_heads // self.n_groups, 1)
            pad_size = (self.chunk_size - seq_len % self.chunk_size) % self.chunk_size

            D_residual = self.D[..., None] * pad_tensor_by_size(hidden_states, pad_size)

            # Discretize x and A
            hidden_states = hidden_states * dt[..., None]
            A = A.to(hidden_states.dtype) * dt

            # Rearrange into blocks/chunks
            hidden_states, A, B, C = [reshape_into_chunks(t, pad_size, self.chunk_size) for t in (hidden_states, A, B, C)]


            # [bsz, -1, chunk_size, num_heads] -> [bsz, num_heads, -1, chunk_size]
            A = A.permute(0, 3, 1, 2)
            A_cumsum = torch.cumsum(A, dim=-1)

            # 1. Compute the output for each intra-chunk (diagonal blocks)
            # This is the analog of a causal mask
            L = torch.exp(segment_sum(A))

            # First, contraction of C and B to get G (attention-weights like)
            G_intermediate = C[:, :, :, None, :, :] * B[:, :, None, :, : ,:]  # shape: (b, c, l, s, h, n)
            G = G_intermediate.sum(dim=-1)  # shape: (b, c, l, s, h)


            # Step 2: Compute M, equivalent to applying attention mask to weights
            M_intermediate = G[..., None] * L.permute(0, 2, 3, 4, 1)[..., None]
            M = M_intermediate.sum(dim=-1)

            # Step 3: Compute Y_diag (apply to values)
            Y_diag = (M[..., None] * hidden_states[:, :, None]).sum(3)

            # (right term of low-rank factorization of off-diagonal blocks; B terms)

            decay_states = torch.exp((A_cumsum[:, :, :, -1:] - A_cumsum))
            B_decay_contraction = B * decay_states.permute(0, 2, 3, 1)[..., None]
            # permute back B * decay states
            states = (B_decay_contraction.permute(0, 1, 3, 2, 4)[..., None]  * hidden_states.permute(0, 1, 3, 2, 4)[..., None, :]).sum(dim=3).permute(0, 1, 2, 4, 3)
            if cache_params is not None and cache_params.seqlen_offset > 0:
                previous_states = cache_params.ssm_states[self.layer_idx][:, None, ...]
            else:
                previous_states = torch.zeros_like(states[:, :1])
            states = torch.cat([previous_states, states], dim=1)
            decay_chunk = torch.exp(segment_sum(nn.functional.pad(A_cumsum[:, :, :, -1], (1, 0))))

            states_permuted = states.permute(0, 2, 1, 3, 4)
            result = (decay_chunk[..., None, None] * states_permuted[:, :, None, ...]).sum(dim=2)
            new_states = result.permute(0, 2, 1, 3, 4)
            states, ssm_state = new_states[:, :-1], new_states[:, -1]

            # Compute state -> output conversion per chunk
            # (left term of low-rank factorization of off-diagonal blocks; C terms)
            state_decay_out = torch.exp(A_cumsum)
            # compute Yoff
            C_times_states = (C[..., None, :] * states[:, :, None, ...])
            state_decay_out_permuted = state_decay_out.permute(0, 2, 3, 1)
            Y_off = (C_times_states.sum(-1) * state_decay_out_permuted[..., None])
            # Add output of intra-chunk and inter-chunk terms (diagonal and off-diagonal blocks)

            y = Y_diag + Y_off
            # [bsz, -1, self.chunk_size, num_heads, head_dim] -> [bsz, (padded) seq_len, num_heads, head_dim]
            y = y.reshape(batch_size, -1, self.num_heads, self.head_dim)

            y = y + D_residual
            # Cutting off padded chunks
            if pad_size > 0:
                y = y[:, :seq_len, :, :]
            y = y.reshape(batch_size, seq_len, -1)
            if ssm_state is not None and cache_params is not None:
                cache_params.ssm_states[self.layer_idx].copy_(ssm_state)

        scan_output = self.norm(y, gate)

        # end ssd naive

        # 4. Final linear projection
        contextualized_states = self.out_proj(scan_output.to(dtype))  # [batch, seq_len, hidden_size]
        return contextualized_states
    # fmt: on

    def forward(
        self,
        hidden_states,
        cache_params: Optional[Mamba2Cache] = None,
        cache_position: Optional[torch.LongTensor] = None,
        attention_mask: Optional[torch.Tensor] = None,
    ):
        if is_fast_path_available and "cuda" in self.in_proj.weight.device.type:
            return self.cuda_kernels_forward(
                hidden_states, cache_params, cache_position, attention_mask
            )
        dtype = hidden_states.dtype
        if (
            attention_mask is not None
            and attention_mask.shape[1] > 1
            and attention_mask.shape[0] > 1
        ):
            # tune out hidden states for pad tokens, see https://github.com/state-spaces/mamba/issues/66
            hidden_states = (hidden_states * attention_mask[:, :, None]).to(dtype)

        return self.torch_forward(
            hidden_states, cache_params, cache_position, attention_mask
        )


class Mamba2RMSNorm(nn.Module):
    def __init__(self, hidden_size, eps=1e-6):
        """
        Mamba2RMSNorm is equivalent to T5LayerNorm and LlamaRMSNorm
        """
        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)


class HelixmRNAMLP(nn.Module):
    def __init__(self, config, layer_idx=None):
        super().__init__()
        self.hidden_size = config.hidden_size
        self.intermediate_size = self.hidden_size * 4  # config.intermediate_size
        self.gate_proj = nn.Linear(self.hidden_size, self.intermediate_size, bias=False)
        self.up_proj = nn.Linear(self.hidden_size, self.intermediate_size, bias=False)
        self.down_proj = nn.Linear(self.intermediate_size, self.hidden_size, bias=False)
        self.act_fn = ACT2FN[config.hidden_act]

    def forward(self, hidden_state, **kwargs):
        hidden_states = self.down_proj(
            self.act_fn(self.gate_proj(hidden_state)) * self.up_proj(hidden_state)
        )
        return (hidden_states,)


class HelixmRNAMLPLayer(nn.Module):
    def __init__(self, config, layer_idx=None):
        super().__init__()
        ffn_layer_class = HelixmRNAMLP
        self.feed_forward = ffn_layer_class(config)
        self.input_layernorm = Mamba2RMSNorm(
            config.hidden_size, eps=config.layer_norm_epsilon
        )

    def forward(
        self,
        hidden_states,
        use_cache=True,
        past_key_value: Optional[HybridMambaAttentionDynamicCache] = None,
        **kwargs,
    ):
        residual = hidden_states

        hidden_states = self.input_layernorm(hidden_states)
        ff_outputs = self.feed_forward(hidden_states)

        hidden_states = ff_outputs[0]
        hidden_states = residual + hidden_states

        outputs = (hidden_states,)

        if use_cache:
            outputs += (past_key_value,)

        return outputs


class Mamba2Block(nn.Module):
    def __init__(self, config, layer_idx):
        super().__init__()
        self.config = config
        self.layer_idx = layer_idx
        self.residual_in_fp32 = config.residual_in_fp32
        self.norm = Mamba2RMSNorm(config.hidden_size, eps=config.layer_norm_epsilon)
        self.mixer = Mamba2Mixer(config, layer_idx=layer_idx)

    def forward(
        self,
        hidden_states,
        cache_position: Optional[torch.LongTensor] = None,
        attention_mask: Optional[torch.Tensor] = None,
        position_ids: Optional[torch.LongTensor] = None,
        output_attentions: Optional[bool] = False,
        use_cache: Optional[bool] = False,
        past_key_value: Optional[HybridMambaAttentionDynamicCache] = None,
    ):
        residual = hidden_states
        hidden_states = self.norm(hidden_states.to(dtype=self.norm.weight.dtype))
        if self.residual_in_fp32:
            residual = residual.to(torch.float32)

        hidden_states = self.mixer(
            hidden_states,
            cache_params=past_key_value,
            cache_position=cache_position,
            attention_mask=attention_mask,
        )
        hidden_states = residual + hidden_states

        hidden_states = (hidden_states,)
        if output_attentions:
            hidden_states += (None,)

        if use_cache:
            hidden_states += (past_key_value,)

        return hidden_states


class HelixmRNAAttentionDecoderLayer(nn.Module):
    def __init__(self, config: HelixmRNAConfig, layer_idx: int):
        super().__init__()
        self.self_attn = HelixmRNA_ATTENTION_CLASSES[config._attn_implementation](
            config, layer_idx
        )

        ffn_layer_class = HelixmRNAMLP
        self.feed_forward = ffn_layer_class(config)
        self.input_layernorm = Mamba2RMSNorm(
            config.hidden_size, eps=config.layer_norm_epsilon
        )
        self.pre_ff_layernorm = Mamba2RMSNorm(
            config.hidden_size, eps=config.layer_norm_epsilon
        )

    def forward(
        self,
        hidden_states: torch.Tensor,
        attention_mask: Optional[torch.Tensor] = None,
        position_ids: Optional[torch.LongTensor] = None,
        past_key_value: Optional[HybridMambaAttentionDynamicCache] = None,
        output_attentions: Optional[bool] = False,
        output_router_logits: Optional[bool] = False,
        use_cache: Optional[bool] = False,
        cache_position: Optional[torch.LongTensor] = None,
    ) -> Tuple[
        torch.FloatTensor, Optional[Tuple[torch.FloatTensor, torch.FloatTensor]]
    ]:
        """
        Args:
            hidden_states (`torch.FloatTensor`):
                Input to the layer of shape `(batch, seq_len, embed_dim)`
            attention_mask (`torch.FloatTensor`, *optional*):
                Attention mask of size `(batch, sequence_length)` where padding elements are indicated by 0.
            past_key_value (`HybridMambaAttentionDynamicCache`, *optional*): cached past key and value projection states
            output_attentions (`bool`, *optional*):
                Whether or not to return the attentions tensors of all attention layers. See `attentions` under
                returned tensors for more detail.
            output_router_logits (`bool`, *optional*):
                Whether or not to return the logits of all the routers. They are useful for computing the router loss, and
                should not be returned during inference.
            use_cache (`bool`, *optional*):
                If set to `True`, `past_key_values` key value states are returned and can be used to speed up decoding
                (see `past_key_values`).
            cache_position (`torch.LongTensor` of shape `(sequence_length)`, *optional*):
                Indices depicting the position of the input sequence tokens in the sequence.
        """

        residual = hidden_states

        hidden_states = self.input_layernorm(hidden_states)

        hidden_states, self_attn_weights, present_key_value = self.self_attn(
            hidden_states=hidden_states,
            attention_mask=attention_mask,
            position_ids=position_ids,
            past_key_value=past_key_value,
            output_attentions=output_attentions,
            use_cache=use_cache,
            cache_position=cache_position,
        )

        # residual connection after attention
        hidden_states = residual + hidden_states

        # feed-forward (experts/MLP)
        residual = hidden_states
        hidden_states = self.pre_ff_layernorm(hidden_states)
        ff_outputs = self.feed_forward(hidden_states)

        hidden_states = ff_outputs[0]
        hidden_states = residual + hidden_states

        outputs = (hidden_states,)

        if output_attentions:
            outputs += (self_attn_weights,)

        if use_cache:
            outputs += (present_key_value,)

        return outputs


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

    config_class = HelixmRNAConfig
    base_model_prefix = "backbone"
    supports_gradient_checkpointing = True
    _is_stateful = True
    _no_split_modules = ["HelixmRNAAttentionDecoderLayer", "Mamba2Block"]
    _skip_keys_device_placement = "past_key_values"
    _supports_flash_attn_2 = True
    _supports_sdpa = True
    _supports_cache_class = True  # Note: only supports HybridMambaAttentionDynamicCache

    def _init_weights(self, module):
        """Initialize the weights."""
        if isinstance(module, Mamba2Mixer):
            module.A_log._no_weight_decay = True
            module.D._no_weight_decay = True

            dt = torch.exp(
                torch.rand(self.config.num_heads)
                * (
                    math.log(self.config.time_step_max)
                    - math.log(self.config.time_step_min)
                )
                + math.log(self.config.time_step_min)
            ).clamp(min=self.config.time_step_floor)

            # # Inverse of softplus: https://github.com/pytorch/pytorch/issues/72759
            inv_dt = dt + torch.log(-torch.expm1(-dt))
            with torch.no_grad():
                module.dt_bias.copy_(inv_dt)
            module.dt_bias._no_reinit = True

        if isinstance(module, nn.Linear):
            if module.bias is not None:
                if not getattr(module.bias, "_no_reinit", False):
                    nn.init.zeros_(module.bias)
        elif isinstance(module, nn.Embedding):
            nn.init.normal_(module.weight, std=self.config.initializer_range)

        if self.config.rescale_prenorm_residual:
            # Reinitialize selected weights subject to the OpenAI GPT-2 Paper Scheme:
            #   > A modified initialization which accounts for the accumulation on the residual path with model depth. Scale
            #   > the weights of residual layers at initialization by a factor of 1/√N where N is the # of residual layers.
            #   >   -- GPT-2 :: https://openai.com/blog/better-language-models/
            #
            # Reference (Megatron-LM): https://github.com/NVIDIA/Megatron-LM/blob/main/megatron/model/gpt_model.py
            for name, p in module.named_parameters():
                if name in ["out_proj.weight"]:
                    # Special Scaled Initialization --> There are 2 Layer Norms per Transformer Block
                    # Following Pytorch init, except scale by 1/sqrt(2 * n_layer)
                    # We need to reinit p since this code could be called multiple times
                    # Having just p *= scale would repeatedly scale it down
                    nn.init.kaiming_uniform_(p, a=math.sqrt(5))
                    with torch.no_grad():
                        p /= math.sqrt(self.config.num_hidden_layers)


@dataclass
# Copied from transformers.models.mamba.modeling_mamba.MambaOutput with MAMBA->MAMBA2,Mamba->Mamba2
class HelixmRNAOutput(ModelOutput):
    """
    Class for the MAMBA2 model outputs.

    Args:
        last_hidden_state (`torch.FloatTensor` of shape `(batch_size, sequence_length, hidden_size)`):
            Sequence of hidden-states at the output of the last layer of the model.
        cache_params (`Mamba2Cache`):
            The state of the model at the last time step. Can be used in a forward method with the next `input_ids` to
            avoid providing the old `input_ids`.

            Includes both the State space model state matrices after the selective scan, and the Convolutional states
        attentions (`tuple(torch.FloatTensor)`, *optional*, returned when `output_attentions=True` is passed or when `config.output_attentions=True`):
            Attention weights of all attention layers. Each entry is a tensor of shape `(batch_size, num_heads, sequence_length, sequence_length)`.
        hidden_states (`tuple(torch.FloatTensor)`, *optional*, returned when `output_hidden_states=True` is passed or when `config.output_hidden_states=True`):
            Tuple of `torch.FloatTensor` (one for the output of the embeddings, if the model has an embedding layer, +
            one for the output of each layer) of shape `(batch_size, sequence_length, hidden_size)`.

            Hidden-states of the model at the output of each layer plus the optional initial embedding outputs.
    """

    last_hidden_state: Optional[torch.FloatTensor] = None
    cache_params: Optional[Mamba2Cache] = None
    attentions: Optional[Tuple[torch.FloatTensor]] = None
    hidden_states: Optional[Tuple[torch.FloatTensor]] = None


ALL_DECODER_LAYER_TYPES = {
    "attention": HelixmRNAAttentionDecoderLayer,
    "mamba": Mamba2Block,
    "mlp": HelixmRNAMLPLayer,
}


class HelixmRNAModel(HelixmRNAPreTrainedModel):

    @classmethod
    def from_pretrained(cls, pretrained_model_name_or_path, *model_args, **kwargs):
        wrapper_config = kwargs.pop("config", None)
        if wrapper_config is None:
            raise ValueError("Config must be provided")

        model_name = wrapper_config.model_name
        kwargs.pop("trust_remote_code", None)  # don't pass to non-Auto config class (HelixmRNAConfig)
        cfg = HelixmRNAConfig.from_pretrained(
            model_name,
            attn_implementation=wrapper_config._attn_implementation,  # manually pass attn_implementation
            **kwargs
        )
        cfg.model_name = model_name

        return super().from_pretrained(
            model_name,
            *model_args,
            config=cfg,
            **kwargs,
        )

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

        self.embeddings = nn.Embedding(config.vocab_size, config.hidden_size)
        decoder_layers = []
        for i in range(config.num_hidden_layers):
            layer_class = ALL_DECODER_LAYER_TYPES[config.layers_block_type[i]]
            decoder_layers.append(layer_class(config, layer_idx=i))
        self.layers = nn.ModuleList(decoder_layers)
        self.gradient_checkpointing = False
        self.norm_f = Mamba2RMSNorm(config.hidden_size, eps=config.layer_norm_epsilon)
        self._attn_implementation = config._attn_implementation
        # Initialize weights and apply final processing
        self._register_load_state_dict_pre_hook(self.load_hook)
        self.post_init()

    def load_hook(self, state_dict, prefix, *args):
        for k in state_dict:
            if "embedding." in k:
                state_dict[k.replace("embedding.", "embeddings.")] = state_dict.pop(k)
                break

    def get_input_embeddings(self):
        return self.embeddings

    def set_input_embeddings(self, new_embeddings):
        self.embeddings = new_embeddings

    def forward(
        self,
        input_ids: Optional[torch.LongTensor] = None,
        inputs_embeds: Optional[torch.LongTensor] = None,
        use_cache: Optional[bool] = None,
        output_hidden_states: Optional[bool] = None,
        return_dict: Optional[bool] = None,
        cache_position: Optional[torch.LongTensor] = None,
        attention_mask: Optional[torch.Tensor] = None,
        past_key_values: Optional[HybridMambaAttentionDynamicCache] = None,
        position_ids: Optional[torch.LongTensor] = None,
        output_attentions: Optional[bool] = None,
        **kwargs,
    ) -> Union[Tuple, HelixmRNAOutput]:
        output_hidden_states = (
            output_hidden_states
            if output_hidden_states is not None
            else self.config.output_hidden_states
        )
        use_cache = (
            use_cache
            if use_cache is not None
            else (self.config.use_cache if not self.training else False)
        )
        return_dict = (
            return_dict if return_dict is not None else self.config.use_return_dict
        )

        if (input_ids is None) ^ (inputs_embeds is not None):  # ^ is python for xor
            raise ValueError(
                "You must specify exactly one of input_ids or inputs_embeds"
            )

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

        if self.gradient_checkpointing and self.training and use_cache:
            use_cache = False
        cache_params = past_key_values
        if use_cache:
            if cache_params is None:
                cache_params = HybridMambaAttentionDynamicCache(
                    self.config,
                    inputs_embeds.size(0),
                    device=inputs_embeds.device,
                    dtype=inputs_embeds.dtype,
                )
                cache_position = torch.arange(
                    0, self.config.conv_kernel, device=inputs_embeds.device
                )
            elif cache_position is None:
                # cases when we do manual forward instead of using `model.generate` which will initiate
                # `cache_position` and makes sure it is not None, throw error here instead of doing some
                # hack to conjecture the current cache position
                raise ValueError(
                    "You have to specify the `cache_position` manually when `use_cache=True` and `cache_params` is passed, "
                    "you don't have to pass a `cache_params` if you are in prefilling stage because in that case it will "
                    "be initialized for you automatically"
                )
            if use_cache and past_key_values is None:
                print(
                    "HelixmRNA requires an initialized `HybridMambaAttentionDynamicCache` to return a cache. None was "
                    "provided, so no cache will be returned."
                )
        else:
            cache_params = None

        hidden_states = inputs_embeds
        if cache_position is None:
            cache_position = torch.arange(
                hidden_states.shape[1], device=hidden_states.device
            )
        if position_ids is None:
            position_ids = cache_position.unsqueeze(0)

        causal_mask = self._update_causal_mask(
            attention_mask, inputs_embeds, cache_position
        )

        all_hidden_states = () if output_hidden_states else None
        all_self_attns = () if output_attentions else None

        ####### CHANGE TO BE IN LINE WITH HF CONVENTION #######
        if output_hidden_states:
            all_hidden_states += (inputs_embeds,)  # index 0 = embedding, matching HF convention

        ####### END OF CHANGE #######

        for helix_block in self.layers:

            layer_mask = (
                attention_mask if isinstance(helix_block, Mamba2Block) else causal_mask
            )

            if self.gradient_checkpointing and self.training:
                layer_outputs = self._gradient_checkpointing_func(
                    helix_block.__call__,
                    hidden_states,
                    layer_mask,
                    position_ids,
                    past_key_values,
                    output_attentions,
                    use_cache,
                    cache_position,
                )
            else:
                layer_outputs = helix_block(
                    hidden_states,
                    attention_mask=layer_mask,
                    position_ids=position_ids,
                    past_key_value=past_key_values,
                    output_attentions=output_attentions,
                    use_cache=use_cache,
                    cache_position=cache_position,
                )

            if output_hidden_states:
                all_hidden_states += (layer_outputs[0],)

            ####### CHANGE TO BE IN LINE WITH HF CONVENTION #######
            if output_attentions:
                all_self_attns += (layer_outputs[1] if len(layer_outputs) > 1 else None,)
            ####### END OF CHANGE #######

        hidden_states = self.norm_f(layer_outputs[0])

        if output_hidden_states:
            all_hidden_states = all_hidden_states + (hidden_states,)

            ####### CHANGE TO BE IN LINE WITH HF CONVENTION #######
            # if output_attentions:
            #     if layer_outputs[1] is not None:
            #         # append attentions only of attention layers. Mamba layers return `None` as the attention weights
            #         all_self_attns += (layer_outputs[1],)
            ####### END OF CHANGE #######

        if use_cache:
            cache_params.seqlen_offset += inputs_embeds.shape[1]

        if not return_dict:
            return tuple(
                v
                for v in [hidden_states, cache_params, all_hidden_states]
                if v is not None
            )

        ####### CHANGE TO BE IN LINE WITH HF CONVENTION #######
        return HelixmRNAOutput(
            last_hidden_state=hidden_states,
            cache_params=cache_params if use_cache else None,
            attentions=all_self_attns,
            hidden_states=all_hidden_states,
        )
        ####### END OF CHANGE #######

    def _update_causal_mask(self, attention_mask, input_tensor, cache_position):
        if self.config._attn_implementation == "flash_attention_2":
            if attention_mask is not None and 0.0 in attention_mask:
                return attention_mask
            return None

        dtype, device = input_tensor.dtype, input_tensor.device
        min_dtype = torch.finfo(dtype).min
        sequence_length = input_tensor.shape[1]
        target_length = cache_position[-1] + 1

        causal_mask = torch.full(
            (sequence_length, target_length),
            fill_value=min_dtype,
            dtype=dtype,
            device=device,
        )
        if sequence_length != 1:
            causal_mask = torch.triu(causal_mask, diagonal=1)
        causal_mask *= torch.arange(
            target_length, device=device
        ) > cache_position.reshape(-1, 1)
        causal_mask = causal_mask[None, None, :, :].expand(
            input_tensor.shape[0], 1, -1, -1
        )
        if attention_mask is not None:
            causal_mask = (
                causal_mask.clone()
            )  # copy to contiguous memory for in-place edit
            if attention_mask.dim() == 2:
                mask_length = attention_mask.shape[-1]
                padding_mask = causal_mask[..., :mask_length].eq(0.0) * attention_mask[
                    :, None, None, :
                ].eq(0.0)
                causal_mask[..., :mask_length] = causal_mask[
                    ..., :mask_length
                ].masked_fill(padding_mask, min_dtype)

        if (
            self.config._attn_implementation == "sdpa"
            and attention_mask is not None
            and attention_mask.device.type == "cuda"
        ):
            # Attend to all tokens in fully masked rows in the causal_mask, for example the relevant first rows when
            # using left padding. This is required by F.scaled_dot_product_attention memory-efficient attention path.
            # Details: https://github.com/pytorch/pytorch/issues/110213
            causal_mask = AttentionMaskConverter._unmask_unattended(
                causal_mask, min_dtype
            )

        return causal_mask

    def _update_mamba_mask(self, attention_mask, cache_position):
        """
        No need for zeroing states when
            1. Cached forward
            2. Attending to all inputs
        """
        mamba_mask = attention_mask
        if cache_position[0] > 0 or (
            attention_mask is not None and torch.all(attention_mask == 1)
        ):
            mamba_mask = None
        return mamba_mask