modeling_esm_plusplus.py

"""
ESM++ model implementation.

ESM++ is a faithful implementation of ESMC that allows for batching and standard Huggingface compatibility
The ESM Python package is not required

Modified from https://github.com/evolutionaryscale/esm
License: https://www.evolutionaryscale.ai/policies/cambrian-non-commercial-license-agreement
"""

import entrypoint_setup
import math
import os
import warnings
import torch
import torch.nn as nn
import torch.nn.functional as F
from dataclasses import dataclass
from functools import cache, partial
from pathlib import Path
from typing import Optional, Tuple, Union, List
from einops import rearrange, repeat
from huggingface_hub import snapshot_download
from tokenizers import Tokenizer
from tokenizers.models import BPE
from tokenizers.processors import TemplateProcessing
from torch.nn.attention.flex_attention import create_block_mask
from torch.nn.attention.flex_attention import flex_attention
from transformers import PreTrainedModel, PreTrainedTokenizerFast, PretrainedConfig
from transformers.modeling_outputs import ModelOutput

try:
    # when used from AutoModel, these are in the same directory
    from .embedding_mixin import EmbeddingMixin, Pooler
except:
    # when running from our repo, these are in the base directory
    from embedding_mixin import EmbeddingMixin, Pooler


def _create_pad_block_mask(attention_mask_2d: torch.Tensor):
    token_valid = attention_mask_2d.bool()
    batch_size, seq_len = token_valid.shape

    def mask_mod(batch_idx, head_idx, q_idx, kv_idx):
        return token_valid[batch_idx, q_idx] & token_valid[batch_idx, kv_idx]

    return create_block_mask(
        mask_mod,
        batch_size,
        1,
        seq_len,
        seq_len,
        device=attention_mask_2d.device,
    )


class ESMplusplusConfig(PretrainedConfig):
    """Configuration class for ESM++ model.
    
    Args:
        vocab_size: Size of the vocabulary
        hidden_size: Dimension of hidden layers
        num_attention_heads: Number of attention heads
        num_hidden_layers: Number of transformer layers
        num_labels: Number of output labels for classification
        problem_type: Type of problem - regression, single/multi label classification
    """
    model_type = "ESMplusplus"
    def __init__(
        self,
        vocab_size: int = 64,
        hidden_size: int = 960,
        num_attention_heads: int = 15,
        num_hidden_layers: int = 30,
        num_labels: int = 2,
        problem_type: str | None = None,
        dropout: float = 0.0,
        initializer_range: float = 0.02,
        attn_backend: str = "sdpa",
        **kwargs,
    ):
        super().__init__(**kwargs)
        self.vocab_size = vocab_size
        self.hidden_size = hidden_size
        self.num_attention_heads = num_attention_heads
        self.num_hidden_layers = num_hidden_layers
        self.num_labels = num_labels
        self.problem_type = problem_type
        self.dropout = dropout
        self.initializer_range = initializer_range
        self.tie_word_embeddings = False
        self.attn_backend = attn_backend


### Rotary Embeddings
def rotate_half(x: torch.Tensor, interleaved: bool = False) -> torch.Tensor:
    """Rotates half the hidden dims of the input."""
    if not interleaved:
        x1, x2 = x.chunk(2, dim=-1)
        return torch.cat((-x2, x1), dim=-1)
    else:
        x1, x2 = x[..., ::2], x[..., 1::2]
        return rearrange(
            torch.stack((-x2, x1), dim=-1), "... d two -> ... (d two)", two=2
        )


def apply_rotary_emb_torch(
    x: torch.Tensor,
    cos: torch.Tensor,
    sin: torch.Tensor,
    interleaved: bool = False,
    _inplace: bool = False,
) -> torch.Tensor:
    """Apply rotary embeddings to input based on cos and sin."""
    ro_dim = cos.shape[-1] * 2
    assert ro_dim <= x.shape[-1]
    seqlen = x.size(1)
    cos = cos[:seqlen]
    sin = sin[:seqlen]
    cos = repeat(cos, "s d -> s 1 (2 d)")
    sin = repeat(sin, "s d -> s 1 (2 d)")
    return torch.cat(
        [
            x[..., :ro_dim] * cos + rotate_half(x[..., :ro_dim], interleaved) * sin,
            x[..., ro_dim:],
        ],
        dim=-1,
    )


class RotaryEmbedding(torch.nn.Module):
    """Rotary position embeddings.
    
    Based on the paper "RoFormer: Enhanced Transformer with Rotary Position Embedding"
    
    Args:
        dim: Dimension of the embedding
        base: Base for computing angular frequencies
        interleaved: Whether to use interleaved rotations
        scale_base: Base for scaling
        scaling_factor: Factor for scaling positions
        pos_idx_in_fp32: Whether to compute position indices in fp32
        device: Computation device
    """
    def __init__(
        self,
        dim: int,
        base: float = 10000.0,
        interleaved: bool = False,
        scale_base: Optional[float] = None,
        scaling_factor: float = 1.0,
        pos_idx_in_fp32: bool = True,
        device: Optional[torch.device] = None,
    ):
        super().__init__()
        self.dim = dim
        self.base = float(base)
        self.pos_idx_in_fp32 = pos_idx_in_fp32
        self.interleaved = interleaved
        self.scale_base = scale_base
        self.scaling_factor = scaling_factor
        self.device = device

        self._seq_len_cached = 0
        self._cos_cached = None
        self._sin_cached = None
        self._cos_k_cached = None
        self._sin_k_cached = None
        self.reset_parameters()

    def reset_parameters(self):
        """Reset the parameters of the embedding."""
        inv_freq = self._compute_inv_freq(self.device)
        self.register_buffer("inv_freq", inv_freq, persistent=False)
        arange = torch.arange(0, self.dim, 2, device=self.device, dtype=torch.float32)
        scale = (
            (arange + 0.4 * self.dim) / (1.4 * self.dim)
            if self.scale_base is not None
            else None
        )
        self.register_buffer("scale", scale)

    def _compute_inv_freq(self, device: Optional[torch.device] = None) -> torch.Tensor:
        """Compute inverse frequency bands."""
        return 1 / (
            self.base
            ** (
                torch.arange(0, self.dim, 2, device=device, dtype=torch.float32)
                / self.dim
            )
        )

    def _update_cos_sin_cache(self, seqlen: int, device: Optional[torch.device] = None, dtype: Optional[torch.dtype] = None):
        """Update the cached cosine and sine values."""
        if (
            seqlen > self._seq_len_cached
            or self._cos_cached is None
            or self._cos_cached.device != device
            or self._cos_cached.dtype != dtype
            or (self.training and self._cos_cached.is_inference())
        ):
            self._seq_len_cached = seqlen
            if self.pos_idx_in_fp32:
                t = torch.arange(seqlen, device=device, dtype=torch.float32)
                t /= self.scaling_factor
                if self.inv_freq.dtype != torch.float32:
                    inv_freq = self.inv_freq.to(torch.float32)
                else:
                    inv_freq = self.inv_freq
            else:
                t = torch.arange(seqlen, device=device, dtype=self.inv_freq.dtype)
                t /= self.scaling_factor
                inv_freq = self.inv_freq
            freqs = torch.outer(t, inv_freq)

            if self.scale is None:
                self._cos_cached = torch.cos(freqs).to(dtype)
                self._sin_cached = torch.sin(freqs).to(dtype)
            else:
                power = (
                    torch.arange(
                        seqlen, dtype=self.scale.dtype, device=self.scale.device
                    )
                    - seqlen // 2
                ) / self.scale_base
                scale = self.scale.to(device=power.device) ** power.unsqueeze(-1)
                self._cos_cached = (torch.cos(freqs) * scale).to(dtype)
                self._sin_cached = (torch.sin(freqs) * scale).to(dtype)
                self._cos_k_cached = (torch.cos(freqs) / scale).to(dtype)
                self._sin_k_cached = (torch.sin(freqs) / scale).to(dtype)

    def forward(self, q: torch.Tensor, k: torch.Tensor) -> Tuple[torch.Tensor, torch.Tensor]:
        """Apply rotary embeddings to queries and keys.
        
        Args:
            q: Query tensor of shape (batch, seqlen, nheads, headdim)
            k: Key tensor of shape (batch, seqlen, nheads, headdim)
            
        Returns:
            Tuple of rotated query and key tensors
        """
        self._update_cos_sin_cache(q.shape[1], device=q.device, dtype=q.dtype)
        assert self._cos_cached is not None
        assert self._sin_cached is not None
        if self.scale is None:
            return (
                apply_rotary_emb_torch(
                    q,
                    self._cos_cached,
                    self._sin_cached,
                    self.interleaved,
                    True,  # inplace=True
                ),
                apply_rotary_emb_torch(
                    k,
                    self._cos_cached,
                    self._sin_cached,
                    self.interleaved,
                    True,  # inplace=True
                ),
            )  # type: ignore
        else:
            assert False


### Feedforward Network Components
def swiglu_correction_fn(expansion_ratio: float, d_model: int) -> int:
    """Compute corrected dimension for SwiGLU."""
    return int(((expansion_ratio * d_model) + 255) // 256 * 256)


class SwiGLU(nn.Module):
    """SwiGLU activation function."""
    def __init__(self):
        super(SwiGLU, self).__init__()

    def forward(self, x: torch.Tensor) -> torch.Tensor:
        x1, x2 = x.chunk(2, dim=-1)
        return F.silu(x1) * x2


def swiglu_ln_ffn(d_model: int, expansion_ratio: float) -> nn.Sequential:
    """Create SwiGLU feedforward network with layer normalization."""
    return nn.Sequential(
        nn.LayerNorm(d_model),
        nn.Linear(
            d_model, swiglu_correction_fn(expansion_ratio, d_model) * 2, bias=False
        ),
        SwiGLU(),
        nn.Linear(swiglu_correction_fn(expansion_ratio, d_model), d_model, bias=False),
    )


### Attention
class MultiHeadAttention(nn.Module):
    """Multi-head attention with rotary embeddings.
    
    Args:
        d_model: Model dimension
        n_heads: Number of attention heads
    """
    def __init__(
        self,
        d_model: int,
        n_heads: int,
        attn_backend: str = "sdpa",
    ):
        super().__init__()
        self.d_model = d_model
        self.n_heads = n_heads
        self.d_head = self.d_model // self.n_heads
        self.attn_backend = attn_backend
        self._warned_flex_fallback = False
        self.layernorm_qkv = nn.Sequential(
            nn.LayerNorm(d_model), nn.Linear(d_model, d_model * 3, bias=False)
        )
        self.out_proj = nn.Linear(d_model, d_model, bias=False)
        self.q_ln = nn.LayerNorm(d_model, bias=False)
        self.k_ln = nn.LayerNorm(d_model, bias=False)
        self.reshaper = partial(rearrange, pattern="b s (h d) -> b h s d", h=n_heads)
        self.rotary = RotaryEmbedding(d_model // n_heads)

    def _apply_rotary(self, q: torch.Tensor, k: torch.Tensor) -> Tuple[torch.Tensor, torch.Tensor]:
        """Apply rotary embeddings to query and key."""
        q = q.unflatten(-1, (self.n_heads, self.d_head))
        k = k.unflatten(-1, (self.n_heads, self.d_head))
        q, k = self.rotary(q, k)
        q = q.flatten(-2, -1)
        k = k.flatten(-2, -1)
        return q, k

    def forward(
        self,
        x: torch.Tensor,
        attention_mask: Optional[torch.Tensor] = None,
        flex_block_mask: Optional[object] = None,
        output_attentions: bool = False,
    ) -> Union[torch.Tensor, Tuple[torch.Tensor, torch.Tensor]]:
        """
        Args:
            x: Input tensor
            attention_mask: Optional attention mask
            output_attentions: Whether to return attention weights
            
        Returns:
            Output tensor after self attention, and optionally attention weights
        """
        attn_weights = None
        qkv_BLD3 = self.layernorm_qkv(x)
        query_BLD, key_BLD, value_BLD = torch.chunk(qkv_BLD3, 3, dim=-1)
        query_BLD, key_BLD = (
            self.q_ln(query_BLD).to(query_BLD.dtype),
            self.k_ln(key_BLD).to(query_BLD.dtype),
        )
        query_BLD, key_BLD = self._apply_rotary(query_BLD, key_BLD)
        query_BHLD, key_BHLD, value_BHLD = map(self.reshaper, (query_BLD, key_BLD, value_BLD))
        scale = 1 / math.sqrt(self.d_head)

        if output_attentions: # Manual attention computation
            b, h, l, _ = query_BHLD.shape
            attn_bias = torch.zeros(b, h, l, l, dtype=query_BLD.dtype, device=query_BLD.device)
            if attention_mask is not None:
                attn_bias.masked_fill_(attention_mask.logical_not(), float('-inf'))
            attn_weights = torch.matmul(query_BHLD, key_BHLD.transpose(-2, -1)) * scale
            attn_weights += attn_bias
            attn_weights = F.softmax(attn_weights, dim=-1)
            context_BHLD = torch.matmul(attn_weights, value_BHLD)
        else:
            sdpa_mask = None
            if attention_mask is not None:
                sdpa_mask = torch.zeros_like(attention_mask, dtype=query_BHLD.dtype)
                sdpa_mask.masked_fill_(attention_mask.logical_not(), float("-inf"))
            use_flex = (
                self.attn_backend == "flex"
                and (attention_mask is None or flex_block_mask is not None)
            )
            if use_flex:
                try:
                    context_BHLD = flex_attention(
                        query_BHLD,
                        key_BHLD,
                        value_BHLD,
                        block_mask=flex_block_mask,
                        scale=scale,
                    )
                except Exception as exc:
                    if not self._warned_flex_fallback:
                        warnings.warn(
                            f"Flex attention failed in ESM++ attention; falling back to SDPA. Error: {exc}",
                            RuntimeWarning,
                        )
                        self._warned_flex_fallback = True
                    context_BHLD = F.scaled_dot_product_attention(
                        query_BHLD,
                        key_BHLD,
                        value_BHLD,
                        attn_mask=sdpa_mask,
                        scale=scale,
                    )
            else:
                context_BHLD = F.scaled_dot_product_attention(
                    query_BHLD,
                    key_BHLD,
                    value_BHLD,
                    attn_mask=sdpa_mask,
                    scale=scale,
                )
            
        context_BLD = rearrange(context_BHLD, "b h s d -> b s (h d)")
        output = self.out_proj(context_BLD)
        return output, attn_weights


### Regression Head
def RegressionHead(d_model: int, output_dim: int, hidden_dim: Optional[int] = None) -> nn.Module:
    """Create a regression head with optional hidden dimension.
    
    Args:
        d_model: Input dimension
        output_dim: Output dimension
        hidden_dim: Optional hidden dimension (defaults to d_model)
    """
    hidden_dim = hidden_dim if hidden_dim is not None else d_model
    return nn.Sequential(
        nn.Linear(d_model, hidden_dim),
        nn.GELU(),
        nn.LayerNorm(hidden_dim),
        nn.Linear(hidden_dim, output_dim),
    )


### Transformer Block
class UnifiedTransformerBlock(nn.Module):
    """Transformer block with attention and feedforward layers.
    
    Args:
        d_model: Model dimension
        n_heads: Number of attention heads
        residue_scaling_factor: Factor for scaling residual connections
        expansion_ratio: Expansion ratio for feedforward network
    """
    def __init__(
        self,
        d_model: int,
        n_heads: int,
        residue_scaling_factor: float = 1,
        expansion_ratio: float = 8 / 3,
        dropout: float = 0.0,
        attn_backend: str = "sdpa",
    ):
        super().__init__()
        self.attn = MultiHeadAttention(
            d_model=d_model,
            n_heads=n_heads,
            attn_backend=attn_backend,
        )
        self.ffn = swiglu_ln_ffn(d_model, expansion_ratio)
        self.scaling_factor = residue_scaling_factor
        self.dropout = nn.Dropout(dropout)

    def forward(
        self,
        x: torch.Tensor,
        attention_mask: Optional[torch.Tensor] = None,
        flex_block_mask: Optional[object] = None,
        output_attentions: bool = False,
    ) -> Union[torch.Tensor, Tuple[torch.Tensor, torch.Tensor]]:
        """
        Args:
            x: Input tensor
            attention_mask: Optional attention mask
            output_attentions: Whether to return attention weights
            
        Returns:
            Output tensor after transformer block, and optionally attention weights
        """
        attn_output, attn_weights = self.attn(
            x,
            attention_mask,
            flex_block_mask,
            output_attentions,
        )
        x = x + self.dropout(attn_output) / self.scaling_factor
        x = x + self.dropout(self.ffn(x)) / self.scaling_factor
        return x, attn_weights


### Model Outputs
@dataclass
class TransformerOutput(ModelOutput):
    """Output type for transformer encoder."""
    last_hidden_state: Optional[torch.Tensor] = None
    hidden_states: Optional[Tuple[torch.Tensor]] = None
    attentions: Optional[Tuple[torch.Tensor]] = None


@dataclass
class ESMplusplusOutput(ModelOutput):
    """Output type for ESM++ models."""
    loss: Optional[torch.Tensor] = None
    logits: Optional[torch.Tensor] = None
    last_hidden_state: Optional[torch.Tensor] = None
    hidden_states: Optional[Tuple[torch.Tensor]] = None
    attentions: Optional[Tuple[torch.Tensor]] = None


### Transformer Stack
class TransformerStack(nn.Module):
    """Stack of transformer blocks.
    
    Args:
        d_model: Model dimension
        n_heads: Number of attention heads
        n_layers: Number of transformer layers
        dropout: Dropout rate
    """
    def __init__(
        self,
        d_model: int,
        n_heads: int,
        n_layers: int,
        dropout: float = 0.0,
        attn_backend: str = "sdpa",
    ):
        super().__init__()
        self.attn_backend = attn_backend
        self.blocks = nn.ModuleList(
            [
                UnifiedTransformerBlock(
                    d_model,
                    n_heads,
                    residue_scaling_factor=math.sqrt(n_layers / 36),
                    dropout=dropout,
                    attn_backend=attn_backend,
                )
                for i in range(n_layers)
            ]
        )
        self.norm = nn.LayerNorm(d_model, bias=False)
        self.gradient_checkpointing = False

    def forward(
        self,
        x: torch.Tensor,
        attention_mask: Optional[torch.Tensor] = None,
        output_hidden_states: bool = False,
        output_attentions: bool = False,
    ) -> TransformerOutput:
        """
        Args:
            x: Input tensor
            attention_mask: Optional attention mask
            output_hidden_states: Whether to return all hidden states
            output_attentions: Whether to return attention weights
            
        Returns:
            TransformerOutput containing last hidden state and optionally all hidden states and attention weights
        """
        hidden_states = () if output_hidden_states else None
        attentions = () if output_attentions else None
        
        if attention_mask is not None:
            assert attention_mask.ndim == 2, f"Expected 2D token attention mask, got shape {attention_mask.shape}."
            token_attention_mask = attention_mask.bool()
            pairwise_attention_mask = token_attention_mask.unsqueeze(-1) & token_attention_mask.unsqueeze(-2)
            attention_mask = pairwise_attention_mask.unsqueeze(1)
            if self.attn_backend == "flex" and not output_attentions:
                flex_block_mask = _create_pad_block_mask(token_attention_mask)
            else:
                flex_block_mask = None
        else:
            flex_block_mask = None
            
        for block in self.blocks:
            if self.gradient_checkpointing and self.training:
                x, attn_weights = self._gradient_checkpointing_func(
                    block.__call__,
                    x,
                    attention_mask,
                    flex_block_mask,
                    output_attentions,
                )
            else:
                x, attn_weights = block(x, attention_mask, flex_block_mask, output_attentions)

            if attentions is not None:
                attentions += (attn_weights,)
                
            if output_hidden_states:
                assert hidden_states is not None
                hidden_states += (x,)
                
        return TransformerOutput(
            last_hidden_state=self.norm(x), 
            hidden_states=hidden_states,
            attentions=attentions
        )


class PreTrainedESMplusplusModel(PreTrainedModel):
    """
    init weights for ESM++ models
    """
    config_class = ESMplusplusConfig
    base_model_prefix = "esm++"
    supports_gradient_checkpointing = True
    all_tied_weights_keys = {}

    def _init_weights(self, module):
        """Initialize the weights"""
        if isinstance(module, nn.Linear):
            module.weight.data.normal_(mean=0.0, std=self.config.initializer_range)
            if module.bias is not None:
                module.bias.data.zero_()
        elif isinstance(module, nn.Embedding):
            module.weight.data.normal_(mean=0.0, std=self.config.initializer_range)
            if module.padding_idx is not None:
                module.weight.data[module.padding_idx].zero_()
        elif isinstance(module, nn.LayerNorm):
            if module.bias is not None:
                module.bias.data.zero_()
            module.weight.data.fill_(1.0)

    @classmethod
    def from_pretrained_esm(cls, model_name: str):
        """Load a pretrained ESM++ model."""
        if '300' in model_name:
            return ESMplusplus_300M()
        elif '600' in model_name:
            return ESMplusplus_600M()
        else:
            raise ValueError(f"Invalid model name: {model_name}")


### ESM++ Models
class ESMplusplusModel(PreTrainedESMplusplusModel, EmbeddingMixin):
    """
    ESM++ model. transformer model with no heads
    """
    config_class = ESMplusplusConfig
    def __init__(self, config: ESMplusplusConfig, **kwargs):
        PreTrainedESMplusplusModel.__init__(self, config, **kwargs)
        self.config = config
        self.vocab_size = config.vocab_size
        self.embed = nn.Embedding(self.vocab_size, config.hidden_size)
        self.transformer = TransformerStack(
            d_model=config.hidden_size,
            n_heads=config.num_attention_heads,
            n_layers=config.num_hidden_layers,
            dropout=config.dropout,
            attn_backend=config.attn_backend,
        )
        self.tokenizer = EsmSequenceTokenizer()
        self.init_weights()

    def get_input_embeddings(self):
        return self.embed

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

    def _embed(self, input_ids: torch.Tensor, attention_mask: Optional[torch.Tensor] = None) -> torch.Tensor:
        x = self.embed(input_ids)
        return self.transformer(x, attention_mask, output_hidden_states=False, output_attentions=False).last_hidden_state

    def forward(
        self,
        input_ids: Optional[torch.Tensor] = None,
        attention_mask: Optional[torch.Tensor] = None,
        inputs_embeds: Optional[torch.Tensor] = None,
        output_attentions: Optional[bool] = None,
        output_hidden_states: Optional[bool] = None,
        return_dict: Optional[bool] = None, # to play nice with HF adjacent packages
        **kwargs,
    ) -> TransformerOutput:
        """Forward pass for masked language modeling.
        
        Args:
            input_ids: Input token IDs
            attention_mask: Attention mask
            inputs_embeds: Optional precomputed embeddings
            output_hidden_states: Whether to return all hidden states
            output_attentions: Whether to return attention weights
            
        Returns:
            TransformerOutput containing last hidden state and optionally all hidden states and attention weights
        """
        if inputs_embeds is None:
            x = self.embed(input_ids)
        else:
            x = inputs_embeds
        return self.transformer(x, attention_mask, output_hidden_states, output_attentions)
        

class ESMplusplusForMaskedLM(PreTrainedESMplusplusModel, EmbeddingMixin):
    """
    ESM++ model for masked language modeling.
    Implements the base ESM++ architecture with a masked language modeling head.
    """
    config_class = ESMplusplusConfig
    def __init__(self, config: ESMplusplusConfig, **kwargs):
        PreTrainedESMplusplusModel.__init__(self, config, **kwargs)
        self.config = config
        self.vocab_size = config.vocab_size
        self.embed = nn.Embedding(self.vocab_size, config.hidden_size)
        self.transformer = TransformerStack(
            d_model=config.hidden_size,
            n_heads=config.num_attention_heads,
            n_layers=config.num_hidden_layers,
            dropout=config.dropout,
            attn_backend=config.attn_backend,
        )
        self.sequence_head = RegressionHead(config.hidden_size, self.vocab_size)
        self.ce_loss = nn.CrossEntropyLoss()
        self.tokenizer = EsmSequenceTokenizer()
        self.init_weights()

    def get_input_embeddings(self):
        return self.embed

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

    def get_output_embeddings(self):
        return self.sequence_head[-1]

    def set_output_embeddings(self, new_embeddings):
        self.sequence_head[-1] = new_embeddings

    def _embed(self, input_ids: torch.Tensor, attention_mask: Optional[torch.Tensor] = None) -> torch.Tensor:
        x = self.embed(input_ids)
        return self.transformer(x, attention_mask, output_hidden_states=False, output_attentions=False).last_hidden_state

    def forward(
        self,
        input_ids: Optional[torch.Tensor] = None,
        attention_mask: Optional[torch.Tensor] = None,
        inputs_embeds: Optional[torch.Tensor] = None,
        labels: Optional[torch.Tensor] = None,
        output_attentions: Optional[bool] = None,
        output_hidden_states: Optional[bool] = None,
        return_dict: Optional[bool] = None, # to play nice with HF adjacent packages
        **kwargs,
    ) -> ESMplusplusOutput:
        """Forward pass for masked language modeling.
        
        Args:
            input_ids: Input token IDs
            attention_mask: Attention mask
            inputs_embeds: Optional precomputed embeddings
            labels: Optional labels for masked tokens
            output_hidden_states: Whether to return all hidden states
            output_attentions: Whether to return attention weights
            
        Returns:
            ESMplusplusOutput containing loss, logits, hidden states and attention weights
        """
        if inputs_embeds is None:
            x = self.embed(input_ids)
        else:
            x = inputs_embeds
        output = self.transformer(x, attention_mask, output_hidden_states, output_attentions)
        x = output.last_hidden_state
        logits = self.sequence_head(x)
        loss = None
        if labels is not None:
            loss = self.ce_loss(logits.view(-1, self.vocab_size), labels.view(-1))
        return ESMplusplusOutput(
            loss=loss,
            logits=logits,
            last_hidden_state=x,
            hidden_states=output.hidden_states,
            attentions=output.attentions,
        )


class ESMplusplusForSequenceClassification(ESMplusplusForMaskedLM, EmbeddingMixin):
    """
    ESM++ model for sequence classification.
    Extends the base ESM++ model with a classification head.
    """
    def __init__(self, config: ESMplusplusConfig, **kwargs):
        ESMplusplusForMaskedLM.__init__(self, config, **kwargs)
        self.config = config
        self.num_labels = config.num_labels
        self.classifier = RegressionHead(config.hidden_size * 2, config.num_labels, config.hidden_size * 4)
        # Large intermediate projections help with sequence classification tasks (*4)
        self.mse = nn.MSELoss()
        self.ce = nn.CrossEntropyLoss()
        self.bce = nn.BCEWithLogitsLoss()
        # if kwargs has pooling_types, use them, otherwise use ['cls', 'mean']
        if 'pooling_types' in kwargs and isinstance(kwargs['pooling_types'], List[str]) and len(kwargs['pooling_types']) > 0:
            pooling_types = kwargs['pooling_types']
        else:
            pooling_types = ['cls', 'mean']
        self.pooler = Pooler(pooling_types)
        self.init_weights()

    def _embed(self, input_ids: torch.Tensor, attention_mask: Optional[torch.Tensor] = None) -> torch.Tensor:
        x = self.embed(input_ids)
        return self.transformer(x, attention_mask, output_hidden_states=False, output_attentions=False).last_hidden_state

    def forward(
        self,
        input_ids: Optional[torch.Tensor] = None,
        attention_mask: Optional[torch.Tensor] = None,
        inputs_embeds: Optional[torch.Tensor] = None,
        labels: Optional[torch.Tensor] = None,
        output_attentions: Optional[bool] = None,
        output_hidden_states: Optional[bool] = None,
        return_dict: Optional[bool] = None, # to play nice with HF adjacent packages
        **kwargs,
    ) -> ESMplusplusOutput:
        """Forward pass for sequence classification.
        
        Args:
            input_ids: Input token IDs
            attention_mask: Attention mask
            inputs_embeds: Optional precomputed embeddings
            labels: Optional labels for classification
            output_hidden_states: Whether to return all hidden states
            output_attentions: Whether to return attention weights
            
        Returns:
            ESMplusplusOutput containing loss, logits, and hidden states
        """
        output = super().forward(
            input_ids=input_ids,
            attention_mask=attention_mask,
            inputs_embeds=inputs_embeds,
            labels=None,
            output_attentions=output_attentions,
            output_hidden_states=output_hidden_states
        )
        x = output.last_hidden_state
        features = self.pooler(x, attention_mask)
        logits = self.classifier(features)
        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":
                if self.num_labels == 1:
                    loss = self.mse(logits.flatten(), labels.flatten())
                else:
                    loss = self.mse(logits, labels)
            elif self.config.problem_type == "single_label_classification":
                loss = self.ce(logits.view(-1, self.num_labels), labels.view(-1))
            elif self.config.problem_type == "multi_label_classification":
                loss = self.bce(logits, labels)

        return ESMplusplusOutput(
            loss=loss,
            logits=logits,
            last_hidden_state=x,
            hidden_states=output.hidden_states,
            attentions=output.attentions,
        )


class ESMplusplusForTokenClassification(ESMplusplusForMaskedLM, EmbeddingMixin):
    """
    ESM++ model for token classification.
    Extends the base ESM++ model with a token classification head.
    """
    def __init__(self, config: ESMplusplusConfig, **kwargs):
        ESMplusplusForMaskedLM.__init__(self, config, **kwargs)
        self.config = config
        self.num_labels = config.num_labels
        self.classifier = RegressionHead(config.hidden_size, config.num_labels, config.hidden_size * 4)
        # Large intermediate projections help with sequence classification tasks (*4)
        self.loss_fct = nn.CrossEntropyLoss()
        self.init_weights()

    def _embed(self, input_ids: torch.Tensor, attention_mask: Optional[torch.Tensor] = None) -> torch.Tensor:
        x = self.embed(input_ids)
        return self.transformer(x, attention_mask, output_hidden_states=False, output_attentions=False).last_hidden_state

    def forward(
        self,
        input_ids: Optional[torch.Tensor] = None,
        attention_mask: Optional[torch.Tensor] = None,
        inputs_embeds: Optional[torch.Tensor] = None,
        labels: Optional[torch.Tensor] = None,
        output_attentions: Optional[bool] = None,
        output_hidden_states: Optional[bool] = None,
        return_dict: Optional[bool] = None, # to play nice with HF adjacent packages
        **kwargs,
    ) -> ESMplusplusOutput:
        """Forward pass for token classification.
        
        Args:
            input_ids: Input token IDs
            attention_mask: Attention mask
            inputs_embeds: Optional precomputed embeddings
            labels: Optional labels for token classification
            output_hidden_states: Whether to return all hidden states
            output_attentions: Whether to return attention weights
            
        Returns:
            ESMplusplusOutput containing loss, logits, and hidden states
        """
        output = super().forward(
            input_ids=input_ids,
            attention_mask=attention_mask,
            inputs_embeds=inputs_embeds,
            labels=None,
            output_attentions=output_attentions,
            output_hidden_states=output_hidden_states
        )
        x = output.last_hidden_state
        logits = self.classifier(x)
        loss = None
        if labels is not None:
            loss = self.loss_fct(logits.view(-1, self.num_labels), labels.view(-1))
        return ESMplusplusOutput(
            loss=loss,
            logits=logits,
            last_hidden_state=x,
            hidden_states=output.hidden_states,
            attentions=output.attentions,
        )


### Loading from EvolutionaryScale
_ESMC_CHECKPOINT_SPECS = {
    "esmc-300": {
        "repo_id": "EvolutionaryScale/esmc-300m-2024-12",
        "weights_relpath": "data/weights/esmc_300m_2024_12_v0.pth",
        "hidden_size": 960,
        "num_attention_heads": 15,
        "num_hidden_layers": 30,
    },
    "esmc-600": {
        "repo_id": "EvolutionaryScale/esmc-600m-2024-12",
        "weights_relpath": "data/weights/esmc_600m_2024_12_v0.pth",
        "hidden_size": 1152,
        "num_attention_heads": 18,
        "num_hidden_layers": 36,
    },
}


def _resolve_esmc_checkpoint_key(model: str) -> str:
    if "esmc-300" in model:
        return "esmc-300"
    if "esmc-600" in model:
        return "esmc-600"
    raise ValueError(f"{model=} is an invalid ESMC model name.")


@staticmethod
@cache
def data_root(model: str):
    if "INFRA_PROVIDER" in os.environ:
        return Path("")
    key = _resolve_esmc_checkpoint_key(model)
    return Path(snapshot_download(repo_id=_ESMC_CHECKPOINT_SPECS[key]["repo_id"]))


def get_esmc_checkpoint_path(model: str) -> Path:
    key = _resolve_esmc_checkpoint_key(model)
    return data_root(key) / _ESMC_CHECKPOINT_SPECS[key]["weights_relpath"]


def _load_esmc_checkpoint_model(
    config: ESMplusplusConfig,
    model: str,
    device: torch.device | str = "cpu",
) -> ESMplusplusForMaskedLM:
    key = _resolve_esmc_checkpoint_key(model)
    spec = _ESMC_CHECKPOINT_SPECS[key]
    assert config.hidden_size == spec["hidden_size"], (
        f"ESMC loader expected hidden_size={spec['hidden_size']} for {key}, "
        f"but got {config.hidden_size}."
    )
    assert config.num_attention_heads == spec["num_attention_heads"], (
        f"ESMC loader expected num_attention_heads={spec['num_attention_heads']} for {key}, "
        f"but got {config.num_attention_heads}."
    )
    assert config.num_hidden_layers == spec["num_hidden_layers"], (
        f"ESMC loader expected num_hidden_layers={spec['num_hidden_layers']} for {key}, "
        f"but got {config.num_hidden_layers}."
    )
    with torch.device(device):
        model_obj = ESMplusplusForMaskedLM(config)
    state_dict = torch.load(get_esmc_checkpoint_path(key), map_location=device)
    model_obj.load_state_dict(state_dict)
    return model_obj


def ESMplusplus_300M(device: torch.device | str = "cpu"):
    config = ESMplusplusConfig(
        hidden_size=960,
        num_attention_heads=15,
        num_hidden_layers=30,
    )
    return _load_esmc_checkpoint_model(config=config, model="esmc-300", device=device)


def ESMplusplus_600M(device: torch.device | str = "cpu"):
    config = ESMplusplusConfig(
        hidden_size=1152,
        num_attention_heads=18,
        num_hidden_layers=36,
    )
    return _load_esmc_checkpoint_model(config=config, model="esmc-600", device=device)


### Tokenization
SEQUENCE_VOCAB = [
    "<cls>", "<pad>", "<eos>", "<unk>",
    "L", "A", "G", "V", "S", "E", "R", "T", "I", "D", "P", "K",
    "Q", "N", "F", "Y", "M", "H", "W", "C", "X", "B", "U", "Z",
    "O", ".", "-", "|",
    "<mask>",
]

class EsmSequenceTokenizer(PreTrainedTokenizerFast):
    model_input_names = ["input_ids", "attention_mask"]

    def __init__(
        self,
        unk_token="<unk>",
        cls_token="<cls>",
        pad_token="<pad>",
        mask_token="<mask>",
        eos_token="<eos>",
        chain_break_token="|",
        **kwargs,
    ):
        all_tokens = SEQUENCE_VOCAB
        token_to_id = {tok: ind for ind, tok in enumerate(all_tokens)}

        # a character-level tokenizer is the same as BPE with no token merges
        bpe = BPE(token_to_id, merges=[], unk_token=unk_token)
        tokenizer = Tokenizer(bpe)
        special_tokens = [
            cls_token,
            pad_token,
            mask_token,
            eos_token,
            chain_break_token,
        ]
        self.cb_token = chain_break_token
        additional_special_tokens = [chain_break_token]

        tokenizer.add_special_tokens(special_tokens)

        # This is where we configure the automatic addition of special tokens when we call
        # tokenizer(text, add_special_tokens=True). Note that you can also configure how two
        # sequences are merged if you want.
        tokenizer.post_processor = TemplateProcessing(  # type: ignore
            single="<cls> $A <eos>",
            pair="<cls>:0 $A:0 <eos>:0 $B:1 <eos>:1",
            special_tokens=[
                ("<cls>", tokenizer.token_to_id("<cls>")),
                ("<eos>", tokenizer.token_to_id("<eos>")),
            ],
        )
        super().__init__(
            tokenizer_object=tokenizer,
            unk_token=unk_token,
            cls_token=cls_token,
            pad_token=pad_token,
            mask_token=mask_token,
            eos_token=eos_token,
            additional_special_tokens=additional_special_tokens,
            **kwargs,
        )

    # These are a footgun, we never use the `bos` token anywhere so we're just overriding it here.
    @property
    def bos_token(self):
        return self.cls_token

    @property
    def bos_token_id(self):
        return self.cls_token_id

    @property
    def chain_break_token(self):
        return self.cb_token

    @property
    def chain_break_token_id(self):
        return self.convert_tokens_to_ids(self.chain_break_token)

    @property
    def all_token_ids(self):
        return list(range(self.vocab_size))

    @property
    def special_token_ids(self):
        return self.all_special_ids


if __name__ == "__main__":    
    # Set device to CPU for testing
    device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
    print(f"Using device: {device}")
    
    # Test tokenizer
    tokenizer = EsmSequenceTokenizer()
    sample_sequence = "MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG"
    encoding = tokenizer(sample_sequence, return_tensors="pt")
    print(f"Input sequence length: {len(sample_sequence)}")
    print(f"Tokenized sequence: {encoding['input_ids'].shape}")
    
    # Prepare inputs
    input_ids = encoding['input_ids'].to(device)
    attention_mask = encoding['attention_mask'].to(device)
    
    # Test base model with smaller config for quick testing
    print("\n=== Testing ESMplusplus Base Model ===")
    base_config = ESMplusplusConfig(
        hidden_size=384,
        num_attention_heads=6,
        num_hidden_layers=4
    )
    base_model = ESMplusplusModel(base_config).to(device)
    
    with torch.no_grad():
        outputs = base_model(input_ids=input_ids, attention_mask=attention_mask)
    
    print(f"Last hidden state shape: {outputs.last_hidden_state.shape}")
    
    # Test embedding functionality
    print("\nTesting embedding functionality:")
    with torch.no_grad():
        embeddings = base_model._embed(input_ids, attention_mask)
    print(f"Embedding shape: {embeddings.shape}")
    
    # Test masked language modeling
    print("\n=== Testing ESMplusplus For Masked LM ===")
    mlm_model = ESMplusplusForMaskedLM(base_config).to(device)
    
    with torch.no_grad():
        outputs = mlm_model(input_ids=input_ids, attention_mask=attention_mask)
    
    print(f"Last hidden state shape: {outputs.last_hidden_state.shape}")
    print(f"Logits shape: {outputs.logits.shape}")
    
    # Test sequence classification model
    print("\n=== Testing Sequence Classification Model ===")
    classification_model = ESMplusplusForSequenceClassification(base_config).to(device)
    
    with torch.no_grad():
        outputs = classification_model(input_ids=input_ids, attention_mask=attention_mask)
    
    print(f"Last hidden state shape: {outputs.last_hidden_state.shape}")
    print(f"Logits shape: {outputs.logits.shape}")
    
    # Test token classification model
    print("\n=== Testing Token Classification Model ===")
    token_model = ESMplusplusForTokenClassification(base_config).to(device)
    
    with torch.no_grad():
        outputs = token_model(input_ids=input_ids, attention_mask=attention_mask)
    
    print(f"Last hidden state shape: {outputs.last_hidden_state.shape}")
    print(f"Logits shape: {outputs.logits.shape}")
    
    # Test embedding dataset functionality with a mini dataset
    print("\n=== Testing Embed Dataset Functionality ===")
    mini_dataset = [sample_sequence, sample_sequence[:50], sample_sequence[:30]]
    print(f"Creating embeddings for {len(mini_dataset)} sequences")
    
    # Only run this if save path doesn't exist to avoid overwriting
    if not os.path.exists("test_embeddings.pth"):
        embeddings = mlm_model.embed_dataset(
            sequences=mini_dataset,
            tokenizer=tokenizer,
            batch_size=2,
            max_len=100,
            full_embeddings=False,
            pooling_types=['mean'],
            save_path="test_embeddings.pth"
        )
        if embeddings:
            print(f"Embedding dictionary size: {len(embeddings)}")
            for seq, emb in embeddings.items():
                print(f"Sequence length: {len(seq)}, Embedding shape: {emb.shape}")
                break
    else:
        print("Skipping embedding test as test_embeddings.pth already exists")
    
    print("\nAll tests completed successfully!")