"""
    #################################################################################################################################################################################################
    # This code library is an adaptation of the original Transformers and was designed, developed and programmed by Sapiens Technology®.                                                            #
    # Any alteration and/or disclosure of this code without prior authorization is strictly prohibited and is subject to legal action that will be forwarded by the Sapiens Technology® legal team. #
    # This set of algorithms aims to download, train, fine-tune and/or infer large language models from various sources and slopes.                                                                 #
    #################################################################################################################################################################################################
"""
import math
from typing import List, Optional, Tuple, Union
import torch
import torch.utils.checkpoint
from torch import nn
from torch.nn import BCEWithLogitsLoss, CrossEntropyLoss, MSELoss
from ...file_utils import add_code_sample_docstrings, add_start_docstrings, add_start_docstrings_to_model_forward
from ...modeling_outputs import (BaseModelOutputWithPastAndCrossAttentions, BaseModelOutputWithPoolingAndCrossAttentions, MaskedLMOutput, SequenceClassifierOutput, TokenClassifierOutput)
from ...modeling_utils import PreTrainedModel, find_pruneable_heads_and_indices, prune_linear_layer
from ...utils import logging
from .configuration_esm import EsmConfig
logger = logging.get_logger(__name__)
_CHECKPOINT_FOR_DOC = "facebook/esm2_t6_8M_UR50D"
_CONFIG_FOR_DOC = "EsmConfig"
def rotate_half(x):
    x1, x2 = x.chunk(2, dim=-1)
    return torch.cat((-x2, x1), dim=-1)
def apply_rotary_pos_emb(x, cos, sin):
    cos = cos[:, :, : x.shape[-2], :]
    sin = sin[:, :, : x.shape[-2], :]
    return (x * cos) + (rotate_half(x) * sin)
def gelu(x): return x * 0.5 * (1.0 + torch.erf(x / math.sqrt(2.0)))
def symmetrize(x): return x + x.transpose(-1, -2)
def average_product_correct(x):
    a1 = x.sum(-1, keepdims=True)
    a2 = x.sum(-2, keepdims=True)
    a12 = x.sum((-1, -2), keepdims=True)
    avg = a1 * a2
    avg.div_(a12)
    normalized = x - avg
    return normalized
class RotaryEmbedding(torch.nn.Module):
    def __init__(self, dim: int):
        super().__init__()
        inv_freq = 1.0 / (10000 ** (torch.arange(0, dim, 2, dtype=torch.int64).float() / dim))
        inv_freq = inv_freq
        self.register_buffer("inv_freq", inv_freq)
        self._seq_len_cached = None
        self._cos_cached = None
        self._sin_cached = None
    def _update_cos_sin_tables(self, x, seq_dimension=2):
        seq_len = x.shape[seq_dimension]
        if seq_len != self._seq_len_cached or self._cos_cached.device != x.device:
            self._seq_len_cached = seq_len
            t = torch.arange(x.shape[seq_dimension], device=x.device).type_as(self.inv_freq)
            freqs = torch.outer(t, self.inv_freq)
            emb = torch.cat((freqs, freqs), dim=-1).to(x.device)
            self._cos_cached = emb.cos()[None, None, :, :]
            self._sin_cached = emb.sin()[None, None, :, :]
        return self._cos_cached, self._sin_cached
    def forward(self, q: torch.Tensor, k: torch.Tensor) -> Tuple[torch.Tensor, torch.Tensor]:
        self._cos_cached, self._sin_cached = self._update_cos_sin_tables(k, seq_dimension=-2)
        return (apply_rotary_pos_emb(q, self._cos_cached, self._sin_cached), apply_rotary_pos_emb(k, self._cos_cached, self._sin_cached),)
class EsmContactPredictionHead(nn.Module):
    def __init__(self, in_features: int, bias=True, eos_idx: int = 2):
        super().__init__()
        self.in_features = in_features
        self.eos_idx = eos_idx
        self.regression = nn.Linear(in_features, 1, bias)
        self.activation = nn.Sigmoid()
    def forward(self, tokens, attentions):
        eos_mask = tokens.ne(self.eos_idx).to(attentions)
        eos_mask = eos_mask.unsqueeze(1) * eos_mask.unsqueeze(2)
        attentions = attentions * eos_mask[:, None, None, :, :]
        attentions = attentions[..., :-1, :-1]
        attentions = attentions[..., 1:, 1:]
        batch_size, layers, heads, seqlen, _ = attentions.size()
        attentions = attentions.view(batch_size, layers * heads, seqlen, seqlen)
        attentions = attentions.to(self.regression.weight.device)
        attentions = average_product_correct(symmetrize(attentions))
        attentions = attentions.permute(0, 2, 3, 1)
        return self.activation(self.regression(attentions).squeeze(3))
class EsmEmbeddings(nn.Module):
    def __init__(self, config):
        super().__init__()
        self.word_embeddings = nn.Embedding(config.vocab_size, config.hidden_size, padding_idx=config.pad_token_id)
        if config.emb_layer_norm_before: self.layer_norm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
        else: self.layer_norm = None
        self.dropout = nn.Dropout(config.hidden_dropout_prob)
        self.position_embedding_type = getattr(config, "position_embedding_type", "absolute")
        self.register_buffer("position_ids", torch.arange(config.max_position_embeddings).expand((1, -1)), persistent=False)
        self.padding_idx = config.pad_token_id
        self.position_embeddings = nn.Embedding(config.max_position_embeddings, config.hidden_size, padding_idx=self.padding_idx)
        self.token_dropout = config.token_dropout
        self.mask_token_id = config.mask_token_id
    def forward(self, input_ids=None, attention_mask=None, position_ids=None, inputs_embeds=None, past_key_values_length=0):
        if position_ids is None:
            if input_ids is not None: position_ids = create_position_ids_from_input_ids(input_ids, self.padding_idx, past_key_values_length)
            else: position_ids = self.create_position_ids_from_inputs_embeds(inputs_embeds)
        if inputs_embeds is None: inputs_embeds = self.word_embeddings(input_ids)
        embeddings = inputs_embeds
        if self.token_dropout:
            embeddings = embeddings.masked_fill((input_ids == self.mask_token_id).unsqueeze(-1), 0.0)
            mask_ratio_train = 0.15 * 0.8
            src_lengths = attention_mask.sum(-1)
            mask_ratio_observed = (input_ids == self.mask_token_id).sum(-1).float() / src_lengths
            embeddings = (embeddings * (1 - mask_ratio_train) / (1 - mask_ratio_observed)[:, None, None]).to(embeddings.dtype)
        if self.position_embedding_type == "absolute":
            position_embeddings = self.position_embeddings(position_ids)
            embeddings = embeddings + position_embeddings
        if self.layer_norm is not None: embeddings = self.layer_norm(embeddings)
        if attention_mask is not None: embeddings = (embeddings * attention_mask.unsqueeze(-1)).to(embeddings.dtype)
        return embeddings
    def create_position_ids_from_inputs_embeds(self, inputs_embeds):
        input_shape = inputs_embeds.size()[:-1]
        sequence_length = input_shape[1]
        position_ids = torch.arange(self.padding_idx + 1, sequence_length + self.padding_idx + 1, dtype=torch.long, device=inputs_embeds.device)
        return position_ids.unsqueeze(0).expand(input_shape)
class EsmSelfAttention(nn.Module):
    def __init__(self, config, position_embedding_type=None):
        super().__init__()
        if config.hidden_size % config.num_attention_heads != 0 and not hasattr(config, "embedding_size"): raise ValueError(f"The hidden size ({config.hidden_size}) is not a multiple of the number of attention heads ({config.num_attention_heads})")
        self.num_attention_heads = config.num_attention_heads
        self.attention_head_size = int(config.hidden_size / config.num_attention_heads)
        self.all_head_size = self.num_attention_heads * self.attention_head_size
        self.query = nn.Linear(config.hidden_size, self.all_head_size)
        self.key = nn.Linear(config.hidden_size, self.all_head_size)
        self.value = nn.Linear(config.hidden_size, self.all_head_size)
        self.dropout = nn.Dropout(config.attention_probs_dropout_prob)
        self.position_embedding_type = position_embedding_type or getattr(config, "position_embedding_type", "absolute")
        self.rotary_embeddings = None
        if self.position_embedding_type == "relative_key" or self.position_embedding_type == "relative_key_query":
            self.max_position_embeddings = config.max_position_embeddings
            self.distance_embedding = nn.Embedding(2 * config.max_position_embeddings - 1, self.attention_head_size)
        elif self.position_embedding_type == "rotary": self.rotary_embeddings = RotaryEmbedding(dim=self.attention_head_size)
        self.is_decoder = config.is_decoder
    def transpose_for_scores(self, x: torch.Tensor) -> torch.Tensor:
        new_x_shape = x.size()[:-1] + (self.num_attention_heads, self.attention_head_size)
        x = x.view(new_x_shape)
        return x.permute(0, 2, 1, 3)
    def forward(self, hidden_states: torch.Tensor, attention_mask: Optional[torch.FloatTensor] = None, head_mask: Optional[torch.FloatTensor] = None, encoder_hidden_states: Optional[torch.FloatTensor] = None,
    encoder_attention_mask: Optional[torch.FloatTensor] = None, past_key_value: Optional[Tuple[Tuple[torch.FloatTensor]]] = None, output_attentions: Optional[bool] = False) -> Tuple[torch.Tensor]:
        mixed_query_layer = self.query(hidden_states)
        is_cross_attention = encoder_hidden_states is not None
        if is_cross_attention and past_key_value is not None:
            key_layer = past_key_value[0]
            value_layer = past_key_value[1]
            attention_mask = encoder_attention_mask
        elif is_cross_attention:
            key_layer = self.transpose_for_scores(self.key(encoder_hidden_states))
            value_layer = self.transpose_for_scores(self.value(encoder_hidden_states))
            attention_mask = encoder_attention_mask
        elif past_key_value is not None:
            key_layer = self.transpose_for_scores(self.key(hidden_states))
            value_layer = self.transpose_for_scores(self.value(hidden_states))
            key_layer = torch.cat([past_key_value[0], key_layer], dim=2)
            value_layer = torch.cat([past_key_value[1], value_layer], dim=2)
        else:
            key_layer = self.transpose_for_scores(self.key(hidden_states))
            value_layer = self.transpose_for_scores(self.value(hidden_states))
        query_layer = self.transpose_for_scores(mixed_query_layer)
        query_layer = query_layer * self.attention_head_size**-0.5
        if self.is_decoder: past_key_value = (key_layer, value_layer)
        if self.position_embedding_type == "rotary": query_layer, key_layer = self.rotary_embeddings(query_layer, key_layer)
        attention_scores = torch.matmul(query_layer, key_layer.transpose(-1, -2))
        if self.position_embedding_type == "relative_key" or self.position_embedding_type == "relative_key_query":
            seq_length = hidden_states.size()[1]
            position_ids_l = torch.arange(seq_length, dtype=torch.long, device=hidden_states.device).view(-1, 1)
            position_ids_r = torch.arange(seq_length, dtype=torch.long, device=hidden_states.device).view(1, -1)
            distance = position_ids_l - position_ids_r
            positional_embedding = self.distance_embedding(distance + self.max_position_embeddings - 1)
            positional_embedding = positional_embedding.to(dtype=query_layer.dtype)  # fp16 compatibility
            if self.position_embedding_type == "relative_key":
                relative_position_scores = torch.einsum("bhld,lrd->bhlr", query_layer, positional_embedding)
                attention_scores = attention_scores + relative_position_scores
            elif self.position_embedding_type == "relative_key_query":
                relative_position_scores_query = torch.einsum("bhld,lrd->bhlr", query_layer, positional_embedding)
                relative_position_scores_key = torch.einsum("bhrd,lrd->bhlr", key_layer, positional_embedding)
                attention_scores = attention_scores + relative_position_scores_query + relative_position_scores_key
        if attention_mask is not None: attention_scores = attention_scores + attention_mask
        attention_probs = nn.functional.softmax(attention_scores, dim=-1)
        attention_probs = self.dropout(attention_probs)
        if head_mask is not None: attention_probs = attention_probs * head_mask
        context_layer = torch.matmul(attention_probs.to(value_layer.dtype), value_layer)
        context_layer = context_layer.permute(0, 2, 1, 3).contiguous()
        new_context_layer_shape = context_layer.size()[:-2] + (self.all_head_size,)
        context_layer = context_layer.view(new_context_layer_shape)
        outputs = (context_layer, attention_probs) if output_attentions else (context_layer,)
        if self.is_decoder: outputs = outputs + (past_key_value,)
        return outputs
class EsmSelfOutput(nn.Module):
    def __init__(self, config):
        super().__init__()
        self.dense = nn.Linear(config.hidden_size, config.hidden_size)
        self.dropout = nn.Dropout(config.hidden_dropout_prob)
    def forward(self, hidden_states, input_tensor):
        hidden_states = self.dense(hidden_states)
        hidden_states = self.dropout(hidden_states)
        hidden_states = hidden_states + input_tensor
        return hidden_states
class EsmAttention(nn.Module):
    def __init__(self, config):
        super().__init__()
        self.self = EsmSelfAttention(config)
        self.output = EsmSelfOutput(config)
        self.pruned_heads = set()
        self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
    def prune_heads(self, heads):
        if len(heads) == 0: return
        heads, index = find_pruneable_heads_and_indices(heads, self.self.num_attention_heads, self.self.attention_head_size, self.pruned_heads)
        self.self.query = prune_linear_layer(self.self.query, index)
        self.self.key = prune_linear_layer(self.self.key, index)
        self.self.value = prune_linear_layer(self.self.value, index)
        self.output.dense = prune_linear_layer(self.output.dense, index, dim=1)
        self.self.num_attention_heads = self.self.num_attention_heads - len(heads)
        self.self.all_head_size = self.self.attention_head_size * self.self.num_attention_heads
        self.pruned_heads = self.pruned_heads.union(heads)
    def forward(self, hidden_states, attention_mask=None, head_mask=None, encoder_hidden_states=None, encoder_attention_mask=None, past_key_value=None, output_attentions=False):
        hidden_states_ln = self.LayerNorm(hidden_states)
        self_outputs = self.self(hidden_states_ln, attention_mask, head_mask, encoder_hidden_states, encoder_attention_mask, past_key_value, output_attentions)
        attention_output = self.output(self_outputs[0], hidden_states)
        outputs = (attention_output,) + self_outputs[1:]
        return outputs
class EsmIntermediate(nn.Module):
    def __init__(self, config):
        super().__init__()
        self.dense = nn.Linear(config.hidden_size, config.intermediate_size)
    def forward(self, hidden_states: torch.Tensor) -> torch.Tensor:
        hidden_states = self.dense(hidden_states)
        hidden_states = gelu(hidden_states)
        return hidden_states
class EsmOutput(nn.Module):
    def __init__(self, config):
        super().__init__()
        self.dense = nn.Linear(config.intermediate_size, config.hidden_size)
        self.dropout = nn.Dropout(config.hidden_dropout_prob)
    def forward(self, hidden_states, input_tensor):
        hidden_states = self.dense(hidden_states)
        hidden_states = self.dropout(hidden_states)
        hidden_states = hidden_states + input_tensor
        return hidden_states
class EsmLayer(nn.Module):
    def __init__(self, config):
        super().__init__()
        self.chunk_size_feed_forward = config.chunk_size_feed_forward
        self.seq_len_dim = 1
        self.attention = EsmAttention(config)
        self.is_decoder = config.is_decoder
        self.add_cross_attention = config.add_cross_attention
        if self.add_cross_attention:
            if not self.is_decoder: raise RuntimeError(f"{self} should be used as a decoder model if cross attention is added")
            self.crossattention = EsmAttention(config)
        self.intermediate = EsmIntermediate(config)
        self.output = EsmOutput(config)
        self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
    def forward(self, hidden_states, attention_mask=None, head_mask=None, encoder_hidden_states=None, encoder_attention_mask=None, past_key_value=None, output_attentions=False):
        self_attn_past_key_value = past_key_value[:2] if past_key_value is not None else None
        self_attention_outputs = self.attention(hidden_states, attention_mask, head_mask, output_attentions=output_attentions, past_key_value=self_attn_past_key_value)
        attention_output = self_attention_outputs[0]
        if self.is_decoder:
            outputs = self_attention_outputs[1:-1]
            present_key_value = self_attention_outputs[-1]
        else: outputs = self_attention_outputs[1:]
        cross_attn_present_key_value = None
        if self.is_decoder and encoder_hidden_states is not None:
            if not hasattr(self, "crossattention"): raise AttributeError(f"If `encoder_hidden_states` are passed, {self} has to be instantiated with cross-attention layers by setting `config.add_cross_attention=True`")
            cross_attn_past_key_value = past_key_value[-2:] if past_key_value is not None else None
            cross_attention_outputs = self.crossattention(attention_output, attention_mask, head_mask, encoder_hidden_states, encoder_attention_mask, cross_attn_past_key_value, output_attentions)
            attention_output = cross_attention_outputs[0]
            outputs = outputs + cross_attention_outputs[1:-1]
            cross_attn_present_key_value = cross_attention_outputs[-1]
            present_key_value = present_key_value + cross_attn_present_key_value
        layer_output = self.feed_forward_chunk(attention_output)
        outputs = (layer_output,) + outputs
        if self.is_decoder: outputs = outputs + (present_key_value,)
        return outputs
    def feed_forward_chunk(self, attention_output):
        attention_output_ln = self.LayerNorm(attention_output)
        intermediate_output = self.intermediate(attention_output_ln)
        layer_output = self.output(intermediate_output, attention_output)
        return layer_output
class EsmEncoder(nn.Module):
    def __init__(self, config):
        super().__init__()
        self.config = config
        self.layer = nn.ModuleList([EsmLayer(config) for _ in range(config.num_hidden_layers)])
        self.emb_layer_norm_after = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
        self.gradient_checkpointing = False
    def forward(self, hidden_states, attention_mask=None, head_mask=None, encoder_hidden_states=None, encoder_attention_mask=None, past_key_values=None,
    use_cache=None, output_attentions=False, output_hidden_states=False, return_dict=True):
        if self.gradient_checkpointing and self.training:
            if use_cache:
                logger.warning_once("`use_cache=True` is incompatible with `config.gradient_checkpointing=True`. Setting `use_cache=False`...")
                use_cache = False
        all_hidden_states = () if output_hidden_states else None
        all_self_attentions = () if output_attentions else None
        all_cross_attentions = () if output_attentions and self.config.add_cross_attention else None
        next_decoder_cache = () if use_cache else None
        for i, layer_module in enumerate(self.layer):
            if output_hidden_states: all_hidden_states = all_hidden_states + (hidden_states,)
            layer_head_mask = head_mask[i] if head_mask is not None else None
            past_key_value = past_key_values[i] if past_key_values is not None else None
            if self.gradient_checkpointing and self.training:
                layer_outputs = self._gradient_checkpointing_func(layer_module.__call__, hidden_states, attention_mask, layer_head_mask, encoder_hidden_states,
                encoder_attention_mask, past_key_value, output_attentions)
            else: layer_outputs = layer_module(hidden_states, attention_mask, layer_head_mask, encoder_hidden_states, encoder_attention_mask, past_key_value, output_attentions)
            hidden_states = layer_outputs[0]
            if use_cache: next_decoder_cache = next_decoder_cache + (layer_outputs[-1],)
            if output_attentions:
                all_self_attentions = all_self_attentions + (layer_outputs[1],)
                if self.config.add_cross_attention: all_cross_attentions = all_cross_attentions + (layer_outputs[2],)
        if self.emb_layer_norm_after: hidden_states = self.emb_layer_norm_after(hidden_states)
        if output_hidden_states: all_hidden_states = all_hidden_states + (hidden_states,)
        if not return_dict: return tuple(v for v in [hidden_states, next_decoder_cache, all_hidden_states, all_self_attentions, all_cross_attentions] if v is not None)
        return BaseModelOutputWithPastAndCrossAttentions(last_hidden_state=hidden_states, past_key_values=next_decoder_cache, hidden_states=all_hidden_states,
        attentions=all_self_attentions, cross_attentions=all_cross_attentions)
class EsmPooler(nn.Module):
    def __init__(self, config):
        super().__init__()
        self.dense = nn.Linear(config.hidden_size, config.hidden_size)
        self.activation = nn.Tanh()
    def forward(self, hidden_states: torch.Tensor) -> torch.Tensor:
        first_token_tensor = hidden_states[:, 0]
        pooled_output = self.dense(first_token_tensor)
        pooled_output = self.activation(pooled_output)
        return pooled_output
class EsmPreTrainedModel(PreTrainedModel):
    config_class = EsmConfig
    base_model_prefix = "esm"
    supports_gradient_checkpointing = True
    _no_split_modules = ["EsmLayer", "EsmFoldTriangularSelfAttentionBlock", "EsmEmbeddings"]
    def _init_weights(self, module):
        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):
            module.bias.data.zero_()
            module.weight.data.fill_(1.0)
ESM_START_DOCSTRING = r"""
    This model inherits from [`PreTrainedModel`]. Check the superclass documentation for the generic methods the
    library implements for all its model (such as downloading or saving, resizing the input embeddings, pruning heads
    etc.)
    This model is also a PyTorch [torch.nn.Module](https://pytorch.org/docs/stable/nn.html#torch.nn.Module) subclass.
    Use it as a regular PyTorch Module and refer to the PyTorch documentation for all matter related to general usage
    and behavior.
    Parameters:
        config ([`EsmConfig`]): Model configuration class with all the parameters of the
            model. Initializing with a config file does not load the weights associated with the model, only the
            configuration. Check out the [`~PreTrainedModel.from_pretrained`] method to load the model weights.
"""
ESM_INPUTS_DOCSTRING = r"""
    Args:
        input_ids (`torch.LongTensor` of shape `(0)`):
            Indices of input sequence tokens in the vocabulary.
            Indices can be obtained using [`AutoTokenizer`]. See [`PreTrainedTokenizer.encode`] and
            [`PreTrainedTokenizer.__call__`] for details.
            [What are input IDs?](../glossary#input-ids)
        attention_mask (`torch.FloatTensor` of shape `(0)`, *optional*):
            Mask to avoid performing attention on padding token indices. Mask values selected in `[0, 1]`:
            - 1 for tokens that are *not masked*,
            - 0 for tokens that are *masked*.
            [What are attention masks?](../glossary#attention-mask)
        position_ids (`torch.LongTensor` of shape `(0)`, *optional*):
            Indices of positions of each input sequence tokens in the position embeddings. Selected in the range `[0,
            config.max_position_embeddings - 1]`.
            [What are position IDs?](../glossary#position-ids)
        head_mask (`torch.FloatTensor` of shape `(num_heads,)` or `(num_layers, num_heads)`, *optional*):
            Mask to nullify selected heads of the self-attention modules. Mask values selected in `[0, 1]`:
            - 1 indicates the head is *not masked*,
            - 0 indicates the head is *masked*.
        inputs_embeds (`torch.FloatTensor` of shape `(0, hidden_size)`, *optional*):
            Optionally, instead of passing `input_ids` you can choose to directly pass an embedded representation. This
            is useful if you want more control over how to convert `input_ids` indices into associated vectors than the
            model's internal embedding lookup matrix.
        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_hidden_states (`bool`, *optional*):
            Whether or not to return the hidden states of all layers. See `hidden_states` under returned tensors for
            more detail.
        return_dict (`bool`, *optional*):
            Whether or not to return a [`~file_utils.ModelOutput`] instead of a plain tuple.
"""
@add_start_docstrings("The bare ESM Model transformer outputting raw hidden-states without any specific head on top.", ESM_START_DOCSTRING)
class EsmModel(EsmPreTrainedModel):
    def __init__(self, config, add_pooling_layer=True):
        super().__init__(config)
        self.config = config
        self.embeddings = EsmEmbeddings(config)
        self.encoder = EsmEncoder(config)
        self.pooler = EsmPooler(config) if add_pooling_layer else None
        self.contact_head = EsmContactPredictionHead(in_features=config.num_hidden_layers * config.num_attention_heads, bias=True)
        self.post_init()
    def get_input_embeddings(self): return self.embeddings.word_embeddings
    def set_input_embeddings(self, value): self.embeddings.word_embeddings = value
    def _prune_heads(self, heads_to_prune):
        for layer, heads in heads_to_prune.items(): self.encoder.layer[layer].attention.prune_heads(heads)
    @add_start_docstrings_to_model_forward(ESM_INPUTS_DOCSTRING.format("(batch_size, sequence_length)"))
    def forward(self, input_ids: Optional[torch.Tensor] = None, attention_mask: Optional[torch.Tensor] = None, position_ids: Optional[torch.Tensor] = None, head_mask: Optional[torch.Tensor] = None,
    inputs_embeds: Optional[torch.Tensor] = None, encoder_hidden_states: Optional[torch.Tensor] = None, encoder_attention_mask: Optional[torch.Tensor] = None,
    past_key_values: Optional[List[torch.FloatTensor]] = None, use_cache: Optional[bool] = None, output_attentions: Optional[bool] = None,
    output_hidden_states: Optional[bool] = None, return_dict: Optional[bool] = None) -> Union[Tuple[torch.Tensor], BaseModelOutputWithPoolingAndCrossAttentions]:
        output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
        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
        if self.config.is_decoder: use_cache = use_cache if use_cache is not None else self.config.use_cache
        else: use_cache = False
        if input_ids is not None and inputs_embeds is not None: raise ValueError("You cannot specify both input_ids and inputs_embeds at the same time")
        elif input_ids is not None:
            self.warn_if_padding_and_no_attention_mask(input_ids, attention_mask)
            input_shape = input_ids.size()
        elif inputs_embeds is not None: input_shape = inputs_embeds.size()[:-1]
        else: raise ValueError("You have to specify either input_ids or inputs_embeds")
        batch_size, seq_length = input_shape
        device = input_ids.device if input_ids is not None else inputs_embeds.device
        past_key_values_length = past_key_values[0][0].shape[2] if past_key_values is not None else 0
        if attention_mask is None: attention_mask = torch.ones(((batch_size, seq_length + past_key_values_length)), device=device)
        extended_attention_mask: torch.Tensor = self.get_extended_attention_mask(attention_mask, input_shape)
        if self.config.is_decoder and encoder_hidden_states is not None:
            encoder_batch_size, encoder_sequence_length, _ = encoder_hidden_states.size()
            encoder_hidden_shape = (encoder_batch_size, encoder_sequence_length)
            if encoder_attention_mask is None: encoder_attention_mask = torch.ones(encoder_hidden_shape, device=device)
            encoder_extended_attention_mask = self.invert_attention_mask(encoder_attention_mask)
        else: encoder_extended_attention_mask = None
        head_mask = self.get_head_mask(head_mask, self.config.num_hidden_layers)
        embedding_output = self.embeddings(input_ids=input_ids, position_ids=position_ids, attention_mask=attention_mask, inputs_embeds=inputs_embeds, past_key_values_length=past_key_values_length)
        encoder_outputs = self.encoder(embedding_output, attention_mask=extended_attention_mask, head_mask=head_mask, encoder_hidden_states=encoder_hidden_states,
        encoder_attention_mask=encoder_extended_attention_mask, past_key_values=past_key_values, use_cache=use_cache, output_attentions=output_attentions,
        output_hidden_states=output_hidden_states, return_dict=return_dict)
        sequence_output = encoder_outputs[0]
        pooled_output = self.pooler(sequence_output) if self.pooler is not None else None
        if not return_dict: return (sequence_output, pooled_output) + encoder_outputs[1:]
        return BaseModelOutputWithPoolingAndCrossAttentions(last_hidden_state=sequence_output, pooler_output=pooled_output, past_key_values=encoder_outputs.past_key_values,
        hidden_states=encoder_outputs.hidden_states, attentions=encoder_outputs.attentions, cross_attentions=encoder_outputs.cross_attentions)
    def predict_contacts(self, tokens, attention_mask):
        attns = self(tokens, attention_mask=attention_mask, return_dict=True, output_attentions=True).attentions
        attns = torch.stack(attns, dim=1)
        attns *= attention_mask.unsqueeze(1).unsqueeze(2).unsqueeze(3)
        attns *= attention_mask.unsqueeze(1).unsqueeze(2).unsqueeze(4)
        return self.contact_head(tokens, attns)
@add_start_docstrings("ESM Model with a `language modeling` head on top.", ESM_START_DOCSTRING)
class EsmForMaskedLM(EsmPreTrainedModel):
    _tied_weights_keys = ["lm_head.decoder.weight"]
    def __init__(self, config):
        super().__init__(config)
        if config.is_decoder: logger.warning("If you want to use `EsmForMaskedLM` make sure `config.is_decoder=False` for bi-directional self-attention.")
        self.esm = EsmModel(config, add_pooling_layer=False)
        self.lm_head = EsmLMHead(config)
        self.init_weights()
    def get_output_embeddings(self): return self.lm_head.decoder
    def set_output_embeddings(self, new_embeddings): self.lm_head.decoder = new_embeddings
    @add_start_docstrings_to_model_forward(ESM_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
    def forward(self, input_ids: Optional[torch.LongTensor] = None, attention_mask: Optional[torch.Tensor] = None, position_ids: Optional[torch.LongTensor] = None,
    head_mask: Optional[torch.Tensor] = None, inputs_embeds: Optional[torch.FloatTensor] = None, encoder_hidden_states: Optional[torch.FloatTensor] = None,
    encoder_attention_mask: Optional[torch.Tensor] = None, labels: Optional[torch.LongTensor] = None, output_attentions: Optional[bool] = None,
    output_hidden_states: Optional[bool] = None, return_dict: Optional[bool] = None) -> Union[Tuple, MaskedLMOutput]:
        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
        outputs = self.esm(input_ids, attention_mask=attention_mask, position_ids=position_ids, head_mask=head_mask, inputs_embeds=inputs_embeds, encoder_hidden_states=encoder_hidden_states,
        encoder_attention_mask=encoder_attention_mask, output_attentions=output_attentions, output_hidden_states=output_hidden_states, return_dict=return_dict)
        sequence_output = outputs[0]
        prediction_scores = self.lm_head(sequence_output)
        masked_lm_loss = None
        if labels is not None:
            loss_fct = CrossEntropyLoss()
            labels = labels.to(prediction_scores.device)
            masked_lm_loss = loss_fct(prediction_scores.view(-1, self.config.vocab_size), labels.view(-1))
        if not return_dict:
            output = (prediction_scores,) + outputs[2:]
            return ((masked_lm_loss,) + output) if masked_lm_loss is not None else output
        return MaskedLMOutput(loss=masked_lm_loss, logits=prediction_scores, hidden_states=outputs.hidden_states, attentions=outputs.attentions)
    def predict_contacts(self, tokens, attention_mask): return self.esm.predict_contacts(tokens, attention_mask=attention_mask)
class EsmLMHead(nn.Module):
    def __init__(self, config):
        super().__init__()
        self.dense = nn.Linear(config.hidden_size, config.hidden_size)
        self.layer_norm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
        self.decoder = nn.Linear(config.hidden_size, config.vocab_size, bias=False)
        self.bias = nn.Parameter(torch.zeros(config.vocab_size))
    def forward(self, features, **kwargs):
        x = self.dense(features)
        x = gelu(x)
        x = self.layer_norm(x)
        x = self.decoder(x) + self.bias
        return x
@add_start_docstrings("ESM Model transformer with a sequence classification/regression head on top (a linear layer on top of the poole output) e.g. for GLUE tasks.", ESM_START_DOCSTRING)
class EsmForSequenceClassification(EsmPreTrainedModel):
    def __init__(self, config):
        super().__init__(config)
        self.num_labels = config.num_labels
        self.config = config
        self.esm = EsmModel(config, add_pooling_layer=False)
        self.classifier = EsmClassificationHead(config)
        self.init_weights()
    @add_start_docstrings_to_model_forward(ESM_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
    def forward(self, input_ids: Optional[torch.LongTensor] = None, attention_mask: Optional[torch.Tensor] = None, position_ids: Optional[torch.LongTensor] = None,
    head_mask: Optional[torch.Tensor] = None, inputs_embeds: Optional[torch.FloatTensor] = None, labels: Optional[torch.LongTensor] = None, output_attentions: Optional[bool] = None,
    output_hidden_states: Optional[bool] = None, return_dict: Optional[bool] = None) -> Union[Tuple, SequenceClassifierOutput]:
        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
        outputs = self.esm(input_ids, attention_mask=attention_mask, position_ids=position_ids, head_mask=head_mask, inputs_embeds=inputs_embeds, output_attentions=output_attentions,
        output_hidden_states=output_hidden_states, return_dict=return_dict)
        sequence_output = outputs[0]
        logits = self.classifier(sequence_output)
        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 = MSELoss()
                if self.num_labels == 1: loss = loss_fct(logits.squeeze(), labels.squeeze())
                else: loss = loss_fct(logits, labels)
            elif self.config.problem_type == "single_label_classification":
                loss_fct = CrossEntropyLoss()
                loss = loss_fct(logits.view(-1, self.num_labels), labels.view(-1))
            elif self.config.problem_type == "multi_label_classification":
                loss_fct = BCEWithLogitsLoss()
                loss = loss_fct(logits, labels)
        if not return_dict:
            output = (logits,) + outputs[2:]
            return ((loss,) + output) if loss is not None else output
        return SequenceClassifierOutput(loss=loss, logits=logits, hidden_states=outputs.hidden_states, attentions=outputs.attentions)
@add_start_docstrings("ESM Model with a token classification head on top (a linear layer on top of the hidden-states output) e.g. for Named-Entity-Recognition (NER) tasks.", ESM_START_DOCSTRING)
class EsmForTokenClassification(EsmPreTrainedModel):
    def __init__(self, config):
        super().__init__(config)
        self.num_labels = config.num_labels
        self.esm = EsmModel(config, add_pooling_layer=False)
        self.dropout = nn.Dropout(config.hidden_dropout_prob)
        self.classifier = nn.Linear(config.hidden_size, config.num_labels)
        self.init_weights()
    @add_start_docstrings_to_model_forward(ESM_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
    def forward(self, input_ids: Optional[torch.LongTensor] = None, attention_mask: Optional[torch.Tensor] = None, position_ids: Optional[torch.LongTensor] = None,
    head_mask: Optional[torch.Tensor] = None, inputs_embeds: Optional[torch.FloatTensor] = None, labels: Optional[torch.LongTensor] = None, output_attentions: Optional[bool] = None,
    output_hidden_states: Optional[bool] = None, return_dict: Optional[bool] = None) -> Union[Tuple, TokenClassifierOutput]:
        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
        outputs = self.esm(input_ids, attention_mask=attention_mask, position_ids=position_ids, head_mask=head_mask, inputs_embeds=inputs_embeds, output_attentions=output_attentions,
        output_hidden_states=output_hidden_states, return_dict=return_dict)
        sequence_output = outputs[0]
        sequence_output = self.dropout(sequence_output)
        logits = self.classifier(sequence_output)
        loss = None
        if labels is not None:
            loss_fct = CrossEntropyLoss()
            labels = labels.to(logits.device)
            loss = loss_fct(logits.view(-1, self.num_labels), labels.view(-1))
        if not return_dict:
            output = (logits,) + outputs[2:]
            return ((loss,) + output) if loss is not None else output
        return TokenClassifierOutput(loss=loss, logits=logits, hidden_states=outputs.hidden_states, attentions=outputs.attentions)
class EsmClassificationHead(nn.Module):
    def __init__(self, config):
        super().__init__()
        self.dense = nn.Linear(config.hidden_size, config.hidden_size)
        self.dropout = nn.Dropout(config.hidden_dropout_prob)
        self.out_proj = nn.Linear(config.hidden_size, config.num_labels)
    def forward(self, features, **kwargs):
        x = features[:, 0, :]
        x = self.dropout(x)
        x = self.dense(x)
        x = torch.tanh(x)
        x = self.dropout(x)
        x = self.out_proj(x)
        return x
def create_position_ids_from_input_ids(input_ids, padding_idx, past_key_values_length=0):
    mask = input_ids.ne(padding_idx).int()
    incremental_indices = (torch.cumsum(mask, dim=1).type_as(mask) + past_key_values_length) * mask
    return incremental_indices.long() + padding_idx
"""
    #################################################################################################################################################################################################
    # This code library is an adaptation of the original Transformers and was designed, developed and programmed by Sapiens Technology®.                                                            #
    # Any alteration and/or disclosure of this code without prior authorization is strictly prohibited and is subject to legal action that will be forwarded by the Sapiens Technology® legal team. #
    # This set of algorithms aims to download, train, fine-tune and/or infer large language models from various sources and slopes.                                                                 #
    #################################################################################################################################################################################################
"""
