modeling_hyena.py

# -*- coding: utf-8 -*-
"""HyenaDNA custom code port to Hugging Face Hub"""

import math
import torch
import torch.nn as nn
from torch.nn import functional as F
from .configuration_hyena import HyenaConfig
from transformers import PreTrainedModel
from typing import Optional, Tuple, Union
from transformers.modeling_outputs import CausalLMOutput, SequenceClassifierOutput, BaseModelOutputWithNoAttention


def fftconv(u, k, D):
    """
    We apply a convolution through the fourier domain (from the Convolution Theorem)

    """
    seqlen = u.shape[-1]
    fft_size = 2 * seqlen

    k_f = torch.fft.rfft(k.to(torch.float32), n=fft_size) / fft_size
    u_f = torch.fft.rfft(u.to(dtype=torch.float32), n=fft_size)

    if len(u.shape) > 3: k_f = k_f.unsqueeze(1)
    y = torch.fft.irfft(u_f * k_f, n=fft_size, norm='forward')[..., :seqlen]

    out = y + u * D.unsqueeze(-1)
    return out.to(dtype=u.dtype)


@torch.jit.script
def mul_sum(q, y):
    return (q * y).sum(dim=1)


class HyenaSin(nn.Module):
    """The Sin activation function for the Hyena Filter function."""
    def __init__(self, config):
        super().__init__()
        self.freq = nn.Parameter(config.activation_freq * torch.ones(1, config.filter_order)) if config.train_freq else config.activation_freq * torch.ones(1, config.filter_order)

    def forward(self, x):
        return torch.sin(self.freq * x)


class HyenaPositionalEmbedding(nn.Module):
    def __init__(self, config):
        """Complex exponential positional embeddings for Hyena filters."""
        super().__init__()

        self.seq_len = config.max_seq_len
        # The time embedding fed to the filteres is normalized so that t_f = 1
        t = torch.linspace(0, 1, self.seq_len)[None, :, None] # 1, L, 1

        if config.emb_dim > 1:
            bands = (config.emb_dim - 1) // 2
        # To compute the right embeddings we use the "proper" linspace
        t_rescaled = torch.linspace(0, self.seq_len - 1, self.seq_len)[None, :, None]
        w = 2 * math.pi * t_rescaled / self.seq_len # 1, L, 1

        f = torch.linspace(1e-4, bands - 1, bands)[None, None]

        z = torch.cat([t, torch.cos(-f * w), torch.sin(-f * w)], dim=-1)

        self.register_buffer("z", z)
        self.register_buffer("t", t)

    def forward(self, L):
        return self.z[:, :L], self.t[:, :L]


class HyenaExponentialModulation(nn.Module):
    """The window function applied to the output of the (MLP) filter function."""
    def __init__(
        self,
        d_model,
        fast_decay_pct=0.3,
        slow_decay_pct=1.5,
        target=1e-2,
        modulate: bool=True,
        shift: float = 0.05,
        **kwargs
    ):
        super().__init__()
        self.modulate = modulate
        self.shift = shift
        max_decay = math.log(target) / fast_decay_pct
        min_decay = math.log(target) / slow_decay_pct
        deltas = torch.linspace(min_decay, max_decay, d_model)[None, None]
        self.register_buffer("deltas", deltas)

    def forward(self, t, x):
        if self.modulate:
            decay = torch.exp(-t * self.deltas.abs())
            x = x * (decay + self.shift)
        return x


class HyenaFilter(nn.Module):
    def __init__(
            self,
            config,
            **kwargs
        ):
        """
        Implicit long filter with modulation.

        Args:
            d_model: number of channels in the input
            emb_dim: dimension of the positional encoding (`emb_dim` - 1) // 2 is the number of bands
            order: width of the FFN
            num_inner_mlps: number of inner linear layers inside filter MLP

        Note:
            filter_dropout is not implemented
        """
        super().__init__()

        self.d_model = config.d_model * (config.hyena_order - 1)
        self.use_bias = config.use_bias
        self.bias = nn.Parameter(torch.randn(self.d_model))
        self.dropout = nn.Dropout(config.hyena_filter_dropout)

        act = HyenaSin(config)
        self.emb_dim = config.emb_dim
        assert self.emb_dim % 2 != 0 and self.emb_dim >= 3, "emb_dim must be odd and greater or equal to 3 (time, sine and cosine)"
        self.seq_len = config.max_seq_len

        self.pos_emb = HyenaPositionalEmbedding(config)

        self.implicit_filter = nn.Sequential(
            nn.Linear(self.emb_dim, config.filter_order),
            act,
        )
        for i in range(config.num_inner_mlps):
            self.implicit_filter.append(nn.Linear(config.filter_order, config.filter_order))
            self.implicit_filter.append(act)

        self.implicit_filter.append(nn.Linear(config.filter_order, config.d_model, bias=False))

        self.modulation = HyenaExponentialModulation(config.d_model)

        self.normalized = False

    def filter(self, L, *args, **kwargs):
        z, t = self.pos_emb(L)
        h = self.implicit_filter(z.to(dtype=self.implicit_filter[0].weight.dtype))
        h = self.modulation(t, h)
        return h

    def forward(self, x, L, k=None, bias=None, *args, **kwargs):
        if k is None: k = self.filter(L)

        # Ensure compatibility with filters that return a tuple
        k = k[0] if type(k) is tuple else k

        y = fftconv(x, k, bias)
        return y


class HyenaOperator(nn.Module):
    def __init__(
            self,
            config,
            **filter_args,
        ):
        r"""
        Hyena operator described in the paper https://arxiv.org/pdf/2302.10866.pdf

        Args:
            d_model (int): Dimension of the input and output embeddings (width of the layer)
            l_max: (int): Maximum input sequence length. Defaults to None
            order: (int): Depth of the Hyena recurrence. Defaults to 2
            dropout: (float): Dropout probability. Defaults to 0.0
            filter_dropout: (float): Dropout probability for the filter. Defaults to 0.0
        """
        super().__init__()

        self.d_model = config.d_model
        self.l_max = config.max_seq_len
        self.order = config.hyena_order
        inner_width = config.d_model * (self.order + 1)
        self.dropout = nn.Dropout(config.hyena_dropout)
        self.in_proj = nn.Linear(self.d_model, inner_width)
        self.out_proj = nn.Linear(self.d_model, self.d_model)

        self.short_filter = nn.Conv1d(
            inner_width,
            inner_width,
            config.short_filter_order,
            padding=2,
            groups=inner_width
        )
        self.filter_fn = HyenaFilter(config)

    def forward(self, u):
        l = u.size(-2)
        l_filter = min(l, self.l_max)
        u = self.in_proj(u).transpose(1, 2)

        uc = self.short_filter(u)[...,:l_filter]
        *x, v = uc.split(self.d_model, dim=1)

        k = self.filter_fn.filter(l_filter)[0]
        k = k.transpose(0, 1).reshape(self.order - 1, self.d_model, l_filter)
        bias = self.filter_fn.bias.reshape(self.order - 1, self.d_model)

        for o, x_i in enumerate(reversed(x[1:])):
            v = self.dropout(v * x_i)
            v = self.filter_fn(v, l_filter, k=k[o], bias=bias[o])

        y = (v * x[0]).transpose(1, 2)

        y = self.out_proj(y)
        return y

class HyenaMlp(nn.Module):

    def __init__(self, config):
        """
        From https://github.com/HazyResearch/flash-attention/blob/main/flash_attn/modules/mlp.py
        """
        super().__init__()
        in_features = config.d_model
        hidden_features = config.d_inner
        self.fc1 = nn.Linear(in_features, hidden_features)
        self.fc2 = nn.Linear(hidden_features, config.d_model)

    def forward(self, x):
        y = self.fc1(x)
        y = F.gelu(y, approximate="tanh")
        y = self.fc2(y)
        return y

class HyenaBlock(nn.Module):

    def __init__(self, config):
        """
        From https://github.com/HazyResearch/flash-attention/blob/main/flash_attn/modules/block.py
        For prenorm=True, this Block has a slightly different structure compared to a regular
        prenorm Transformer block.
        The standard block is: LN -> MHA -> Dropout -> Add -> LN -> MLP -> Dropout -> Add.
        [Ref: https://arxiv.org/abs/2002.04745]
        Here we have: Dropout -> Add -> LN -> MHA -> Dropout -> Add -> LN -> MLP, returning both
        the hidden_states (output of the MLP) and the residual.
        This is for performance reasons, as we can fuse the dropout, add and LayerNorm.
        The residual needs to be provided (except for the very first block).
        For prenorm=False, this Block has the same structure as a regular postnorm Transformer
        block: MHA -> Dropout -> Add -> LN -> MLP -> Dropout -> Add -> LN.
        return_residual: whether each of the sub-layers (mixer and mlp) will return the residual.
        This is for performance reason: for post-norm architecture, returning the input allows us
        to fuse the backward of nn.Linear with the residual connection.
        """
        super().__init__()
        self.mixer = HyenaOperator(config)
        self.norm1 = nn.LayerNorm(config.d_model)
        self.mlp = HyenaMlp(config)
        self.norm2 = nn.LayerNorm(config.d_model)

    def forward(self, hidden_states):
        r"""Pass the input through the encoder layer.
        Args:
            hidden_states: the sequence to the encoder layer (required).
            residual: if postnorm, residual=None, If prenorm, hidden_states = Attn/MLP(LN(residual))
            mixer_subset: for cross-attention only. If not None, will take a subset of x
                before applying the query projection. Useful for e.g., ViT where we only care
                about the CLS token in the last layer.
        """
        residual = hidden_states
        residual = residual.to(torch.float32)
        hyena_normed = self.norm1(residual.to(dtype=self.norm1.weight.dtype))
        hidden_states = self.mixer(hyena_normed)
        # Tested above here and all is equivalent. That means the mixer is fine!!!
        residual = hidden_states + residual
        hidden_states = self.norm2(residual.to(dtype=self.norm2.weight.dtype))
        residual = residual.to(torch.float32)

        hidden_states = self.mlp(hidden_states)
        return hidden_states + residual


# https://github.com/huggingface/transformers/blob/c28d04e9e252a1a099944e325685f14d242ecdcd/src/transformers/models/gpt2/modeling_gpt2.py#L454


class HyenaEmbeddings(nn.Module):

    def __init__(self, config, padding_idx=None):
        """
            If max_position_embeddings <= 0, there's no position embeddings
            If word_embe_proj_dim is not None (e.g., OPT-350m), we embed to that dimension
                the project up to embed_dim
        """
        super().__init__()
        vocab_size = config.vocab_size
        if vocab_size % config.pad_vocab_size_multiple != 0:
            vocab_size += config.pad_vocab_size_multiple - (vocab_size % config.pad_vocab_size_multiple)
        self.word_embeddings = nn.Embedding(vocab_size, config.d_model, padding_idx=padding_idx)

    def forward(self, input_ids):
        """
            input_ids: (batch, seqlen)
        """
        embeddings = self.word_embeddings(input_ids)
        return embeddings

class HyenaLMBackbone(nn.Module):

    def __init__(self, config) -> None:
        super().__init__()
        # note max_position_embeddings is 0 for Hyena, and therefore isn't used
        self.embeddings = HyenaEmbeddings(config)
        self.dropout = nn.Dropout(config.embed_dropout)

        self.layers = nn.ModuleList([HyenaBlock(config) for i in range(config.n_layer)])

        self.ln_f = nn.LayerNorm(config.d_model, eps=config.layer_norm_epsilon)
        self.gradient_checkpointing = False

    def forward(self, input_ids, inputs_embeds=None, output_hidden_states=False):
        all_hidden_states = []
        if inputs_embeds is not None:
            hidden_states = inputs_embeds
        else:
            hidden_states = self.embeddings(input_ids)
        if output_hidden_states:
            all_hidden_states.append(hidden_states)

        for layer in self.layers:
            if self.gradient_checkpointing and self.training:
                hidden_states = self._gradient_checkpointing_func(layer.__call__, hidden_states)
            else:
                hidden_states = layer(hidden_states)
            if output_hidden_states:
                all_hidden_states.append(hidden_states)

        hidden_states = self.ln_f(hidden_states.to(dtype=self.ln_f.weight.dtype))
        if output_hidden_states:
            all_hidden_states.append(hidden_states)

        return hidden_states, all_hidden_states


class HyenaDNAPreTrainedModel(PreTrainedModel):
    config_class = HyenaConfig
    base_model_prefix = "hyena"
    supports_gradient_checkpointing = True
    _no_split_modules = ["HyenaBlock"]
    _skip_keys_device_placement = "past_key_values"
    _keys_to_ignore_on_load_missing = [r"freq"]  # Shared tensors that safetensors merges

    def _init_weights(self, module, initializer_range=0.02):
        if isinstance(module, nn.Linear):
            nn.init.normal_(module.weight, std=initializer_range)
            if module.bias is not None:
                nn.init.zeros_(module.bias)
        elif isinstance(module, nn.Embedding):
            nn.init.normal_(module.weight, std=initializer_range)
        # 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 self.named_parameters():
            if name in ["out_proj.weight", "fc2.weight"]:
                # Special Scaled Initialization --> There are 2 Layer Norms per Transformer Block
                nn.init.normal_(p, mean=0.0, std=initializer_range / math.sqrt(2 * self.config.num_layers))
            # If using GLU activation for now, we scale the std by 2
            elif name in ["output_linear.0.weight"]:
                # Special Scaled Initialization --> There are 2 Layer Norms per Transformer Block
                nn.init.normal_(p, mean=0.0, std=initializer_range / math.sqrt(2 * self.config.num_layers))


class HyenaDNAModel(HyenaDNAPreTrainedModel):
    def __init__(self, config, **kwargs) -> None:
        super().__init__(config, **kwargs)

        self.backbone = HyenaLMBackbone(config)
        self.config = config

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

    def forward(self, input_ids, inputs_embeds=None, output_hidden_states=None, return_dict=None):
        output_hidden_states = (
            output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
        )
        return_dict = return_dict if return_dict is not None else self.config.use_return_dict

        hidden_states, all_hidden_states = self.backbone(input_ids, inputs_embeds=inputs_embeds, output_hidden_states=output_hidden_states)
        if return_dict:
            return BaseModelOutputWithNoAttention(last_hidden_state=hidden_states,
                                                  hidden_states=all_hidden_states if output_hidden_states else None)
        elif output_hidden_states:
            return hidden_states, all_hidden_states
        else:
            return hidden_states


class HyenaDNAForCausalLM(HyenaDNAPreTrainedModel):

    def __init__(self, config, **kwargs):
        super().__init__(config, **kwargs)
        self.hyena = HyenaDNAModel(config)
        vocab_size = config.vocab_size
        if vocab_size % config.pad_vocab_size_multiple != 0:
            vocab_size += config.pad_vocab_size_multiple - (vocab_size % config.pad_vocab_size_multiple)
        self.vocab_size = vocab_size
        self.lm_head = nn.Linear(config.d_model, vocab_size, bias=False)

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

    def get_input_embeddings(self):
        return self.hyena.backbone.embeddings.word_embeddings

    def set_input_embeddings(self, value):
        self.hyena.backbone.embeddings.word_embeddings = value

    def get_output_embeddings(self):
        return self.lm_head

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

    def set_decoder(self, decoder):
        self.hyena = decoder

    def get_decoder(self):
        return self.hyena

    def forward(
        self,
        input_ids: torch.LongTensor = None,
        inputs_embeds: Optional[torch.FloatTensor] = None,
        labels: Optional[torch.LongTensor] = None,
        output_hidden_states: Optional[bool] = None,
        return_dict: Optional[bool] = None,
    ) -> Union[Tuple, CausalLMOutput]:

        output_hidden_states = (
            output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
        )
        return_dict = return_dict if return_dict is not None else self.config.use_return_dict

        # decoder outputs consists of (dec_features, layer_state, dec_hidden, dec_attn)
        outputs = self.hyena(
            input_ids=input_ids,
            inputs_embeds=inputs_embeds,
            output_hidden_states=output_hidden_states,
            return_dict=return_dict,
        )

        hidden_states = outputs[0]
        logits = self.lm_head(hidden_states)
        logits = logits.float()

        loss = None
        if labels is not None:
            # Shift so that tokens < n predict n
            shift_logits = logits[..., :-1, :].contiguous()
            shift_labels = labels[..., 1:].contiguous()
            # Flatten the tokens
            loss_fct = nn.CrossEntropyLoss()
            shift_logits = shift_logits.view(-1, self.vocab_size)
            shift_labels = shift_labels.view(-1)
            # Enable model parallelism
            shift_labels = shift_labels.to(shift_logits.device)
            loss = loss_fct(shift_logits, shift_labels)

        if not return_dict:
            output = (logits,) + outputs[1:]
            return (loss,) + output if loss is not None else output

        return CausalLMOutput(
            loss=loss,
            logits=logits,
            hidden_states=outputs.hidden_states,
        )


class HyenaDNAForSequenceClassification(HyenaDNAPreTrainedModel):
    def __init__(self, config, **kwargs):
        super().__init__(config, **kwargs)
        self.num_labels = kwargs.get("num_labels", config.num_labels)
        self.hyena = HyenaDNAModel(config)
        self.score = nn.Linear(config.d_model, self.num_labels, bias=False)

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

    def get_input_embeddings(self):
        return self.hyena.backbone.embeddings.word_embeddings

    def set_input_embeddings(self, value):
        self.hyena.backbone.embeddings.word_embeddings = value

    def forward(
        self,
        input_ids: torch.LongTensor = None,
        inputs_embeds: Optional[torch.FloatTensor] = None,
        labels: Optional[torch.LongTensor] = None,
        output_hidden_states: Optional[bool] = None,
        return_dict: Optional[bool] = None,
    ) -> Union[Tuple, SequenceClassifierOutput]:
        r"""
        labels (`torch.LongTensor` of shape `(batch_size,)`, *optional*):
            Labels for computing the sequence classification/regression loss. Indices should be in `[0, ...,
            config.num_labels - 1]`. If `config.num_labels == 1` a regression loss is computed (Mean-Square loss), If
            `config.num_labels > 1` a classification loss is computed (Cross-Entropy).
        """
        return_dict = return_dict if return_dict is not None else self.config.use_return_dict

        transformer_outputs = self.hyena(
            input_ids,
            inputs_embeds=inputs_embeds,
            output_hidden_states=output_hidden_states,
            return_dict=return_dict,
        )
        hidden_states = transformer_outputs[0]
        logits = self.score(hidden_states)

        if input_ids is not None:
            batch_size = input_ids.shape[0]
        else:
            batch_size = inputs_embeds.shape[0]

        if self.config.pad_token_id is None and batch_size != 1:
            raise ValueError("Cannot handle batch sizes > 1 if no padding token is defined.")
        if self.config.pad_token_id is None:
            sequence_lengths = -1
        else:
            if input_ids is not None:
                sequence_lengths = (torch.eq(input_ids, self.config.pad_token_id).long().argmax(-1) - 1).to(
                    logits.device
                )
            else:
                sequence_lengths = -1

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

        loss = None
        if labels is not None:
            labels = labels.to(logits.device)
            if self.config.problem_type is None:
                if self.num_labels == 1:
                    self.config.problem_type = "regression"
                elif self.num_labels > 1 and (labels.dtype == torch.long or labels.dtype == torch.int):
                    self.config.problem_type = "single_label_classification"
                else:
                    self.config.problem_type = "multi_label_classification"

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

        return SequenceClassifierOutput(
            loss=loss,
            logits=pooled_logits,
            hidden_states=transformer_outputs.hidden_states,
        )