modeling_omnigenome.py

# coding=utf-8
# Copyright 2022 ColaLab-UoE (https://colalab.ai/), Meta and The HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
""" PyTorch OmniGenome model."""

import math
import random
import warnings
from typing import List, Optional, Tuple, Union

import numpy as np
import torch
import torch.utils.checkpoint
from torch import nn
from torch.nn import BCEWithLogitsLoss, CrossEntropyLoss, MSELoss
from transformers import add_start_docstrings, PreTrainedModel

from transformers.modeling_outputs import (
    BaseModelOutputWithPastAndCrossAttentions,
    BaseModelOutputWithPoolingAndCrossAttentions,
    MaskedLMOutput,
    SequenceClassifierOutput,
    TokenClassifierOutput,
)

from transformers.pytorch_utils import (
    find_pruneable_heads_and_indices,
    prune_linear_layer,
)

from transformers.utils import (
    logging,
    add_code_sample_docstrings,
    add_start_docstrings_to_model_forward,
)

from .configuration_omnigenome import OmniGenomeConfig

logger = logging.get_logger(__name__)

_CHECKPOINT_FOR_DOC = "yangheng/OmniGenome-52M"
_CONFIG_FOR_DOC = "OmniGenomeConfig"

OmniGenome_PRETRAINED_MODEL_ARCHIVE_LIST = [
    "yangheng/OmniGenome-52M",
    # This is not a complete list of all OmniGenome models!
    # See all OmniGenome models at https://huggingface.co/models?filter=OmniGenome
]


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


def symmetrize(x):
    "Make layer symmetric in final two dimensions, used for contact prediction."
    return x + x.transpose(-1, -2)


def average_product_correct(x):
    "Perform average product correct, used for contact prediction."
    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)  # in-place to reduce memory
    normalized = x - avg
    return normalized


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

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

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

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

        return self._cos_cached, self._sin_cached

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

        return (
            apply_rotary_pos_emb(q, self._cos_cached, self._sin_cached),
            apply_rotary_pos_emb(k, self._cos_cached, self._sin_cached),
        )


# Copied from transformers.models.esm.modeling_esm.EsmContactPredictionHead with Esm->OmniGenome
class OmniGenomeContactPredictionHead(nn.Module):
    """Performs symmetrization, apc, and computes a logistic regression on the output features"""

    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):
        # remove eos token 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]
        # remove cls token attentions
        attentions = attentions[..., 1:, 1:]
        batch_size, layers, heads, seqlen, _ = attentions.size()
        attentions = attentions.view(batch_size, layers * heads, seqlen, seqlen)

        # features: batch x channels x tokens x tokens (symmetric)
        attentions = attentions.to(
            self.regression.weight.device
        )  # attentions always float32, may need to convert to float16
        attentions = average_product_correct(symmetrize(attentions))
        attentions = attentions.permute(0, 2, 3, 1)
        return self.activation(self.regression(attentions).squeeze(3))


# Copied from transformers.models.esm.modeling_esm.EsmEmbeddings with Esm->OmniGenome
class OmniGenomeEmbeddings(nn.Module):
    """
    Same as BertEmbeddings with a tiny tweak for positional embeddings indexing.
    """

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

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

        self.padding_idx = config.pad_token_id
        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:
                # Create the position ids from the input token ids. Any padded tokens remain padded.
                position_ids = create_position_ids_from_input_ids(
                    input_ids, self.padding_idx, 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)

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

        # Matt: OmniGenome has the option to handle masking in MLM in a slightly unusual way. If the token_dropout
        # flag is False then it is handled in the same was as BERT/RoBERTa. If it is set to True, however,
        # masked tokens are treated as if they were selected for input dropout and zeroed out.
        # This "mask-dropout" is compensated for when masked tokens are not present, by scaling embeddings by
        # a factor of (fraction of unmasked tokens during training) / (fraction of unmasked tokens in sample).
        # This is analogous to the way that dropout layers scale down outputs during evaluation when not
        # actually dropping out values (or, equivalently, scale up their un-dropped outputs in training).
        if self.token_dropout:
            embeddings = embeddings.masked_fill(
                (input_ids == self.mask_token_id).unsqueeze(-1), 0.0
            )
            mask_ratio_train = (
                    0.15 * 0.8
            )  # Hardcoded as the ratio used in all OmniGenome model training runs
            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
            )
        # Matt: I think this line was copied incorrectly from BERT, disabling it for now.
        # embeddings = self.dropout(embeddings)
        return embeddings

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

        Args:
            inputs_embeds: torch.Tensor

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

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


# Copied from transformers.models.esm.modeling_esm.EsmSelfAttention with Esm->OmniGenome
class OmniGenomeSelfAttention(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 "
                f"heads ({config.num_attention_heads})"
            )

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

        self.query = nn.Linear(config.hidden_size, self.all_head_size)
        self.key = nn.Linear(config.hidden_size, self.all_head_size)
        self.value = nn.Linear(config.hidden_size, self.all_head_size)

        self.dropout = 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)

        # If this is instantiated as a cross-attention module, the keys
        # and values come from an encoder; the attention mask needs to be
        # such that the encoder's padding tokens are not attended to.
        is_cross_attention = encoder_hidden_states is not None

        if is_cross_attention and past_key_value is not None:
            # reuse k,v, cross_attentions
            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)

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

        if self.is_decoder:
            # if cross_attention save Tuple(torch.Tensor, torch.Tensor) of all cross attention key/value_states.
            # Further calls to cross_attention layer can then reuse all cross-attention
            # key/value_states (first "if" case)
            # if uni-directional self-attention (decoder) save Tuple(torch.Tensor, torch.Tensor) of
            # all previous decoder key/value_states. Further calls to uni-directional self-attention
            # can concat previous decoder key/value_states to current projected key/value_states (third "elif" case)
            # if encoder bi-directional self-attention `past_key_value` is always `None`
            past_key_value = (key_layer, value_layer)

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

        # Take the dot product between "query" and "key" to get the raw attention scores.
        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:
            # Apply the attention mask is (precomputed for all layers in OmniGenomeModel forward() function)
            attention_scores = attention_scores + attention_mask

        # Normalize the attention scores to probabilities.
        attention_probs = nn.functional.softmax(attention_scores, dim=-1)

        # This is actually dropping out entire tokens to attend to, which might
        # seem a bit unusual, but is taken from the original Transformer paper.
        attention_probs = self.dropout(attention_probs)

        # Mask heads if we want to
        if head_mask is not None:
            attention_probs = attention_probs * head_mask

        context_layer = torch.matmul(attention_probs, 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


# Copied from transformers.models.esm.modeling_esm.EsmSelfOutput with Esm->OmniGenome
class OmniGenomeSelfOutput(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


# Copied from transformers.models.esm.modeling_esm.EsmAttention with Esm->OmniGenome
class OmniGenomeAttention(nn.Module):
    def __init__(self, config):
        super().__init__()
        self.self = OmniGenomeSelfAttention(config)
        self.output = OmniGenomeSelfOutput(config)
        self.pruned_heads = set()
        self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)

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

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

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

    def forward(
            self,
            hidden_states,
            attention_mask=None,
            head_mask=None,
            encoder_hidden_states=None,
            encoder_attention_mask=None,
            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:
                                        ]  # add attentions if we output them
        return outputs


# Copied from transformers.models.esm.modeling_esm.EsmIntermediate with Esm->OmniGenome
class OmniGenomeIntermediate(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


# Copied from transformers.models.esm.modeling_esm.EsmOutput with Esm->OmniGenome
class OmniGenomeOutput(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


# Copied from transformers.models.esm.modeling_esm.EsmLayer with Esm->OmniGenome
class OmniGenomeLayer(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 = OmniGenomeAttention(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 = OmniGenomeAttention(config)
        self.intermediate = OmniGenomeIntermediate(config)
        self.output = OmniGenomeOutput(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,
    ):
        # decoder uni-directional self-attention cached key/values tuple is at positions 1,2
        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 decoder, the last output is tuple of self-attn cache
        if self.is_decoder:
            outputs = self_attention_outputs[1:-1]
            present_key_value = self_attention_outputs[-1]
        else:
            outputs = self_attention_outputs[
                      1:
                      ]  # add self attentions if we output attention weights

        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 cached key/values tuple is at positions 3,4 of past_key_value tuple
            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]
            )  # add cross attentions if we output attention weights

            # add cross-attn cache to positions 3,4 of present_key_value tuple
            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 decoder, return the attn key/values as the last output
        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


# Copied from transformers.models.esm.modeling_esm.EsmEncoder with Esm->OmniGenome
class OmniGenomeEncoder(nn.Module):
    def __init__(self, config):
        super().__init__()
        self.config = config
        self.layer = nn.ModuleList(
            [OmniGenomeLayer(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,
        )


# Copied from transformers.models.bert.modeling_bert.BertPooler with Bert->OmniGenome
class OmniGenomePooler(nn.Module):
    def __init__(self, config):
        super().__init__()
        self.dense = nn.Linear(config.hidden_size, config.hidden_size)
        self.activation = nn.Tanh()

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


# Copied from transformers.models.esm.modeling_esm.EsmPreTrainedModel with Esm->OmniGenome
class OmniGenomePreTrainedModel(PreTrainedModel):
    """
    An abstract class to handle weights initialization and a simple interface for downloading and loading pretrained
    models.
    """

    config_class = OmniGenomeConfig
    base_model_prefix = "OmniGenome"
    supports_gradient_checkpointing = True
    _no_split_modules = [
        "OmniGenomeLayer",
        "OmniGenomeFoldTriangularSelfAttentionBlock",
        "OmniGenomeEmbeddings",
    ]

    # Copied from transformers.models.bert.modeling_bert.BertPreTrainedModel._init_weights
    def _init_weights(self, module):
        """Initialize the weights"""
        if isinstance(module, nn.Linear):
            # Slightly different from the TF version which uses truncated_normal for initialization
            # cf https://github.com/pytorch/pytorch/pull/5617
            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)


OmniGenome_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 ([`OmniGenomeConfig`]): 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.
"""

OmniGenome_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 OmniGenome Model transformer outputting raw hidden-states without any specific head on top.",
    OmniGenome_START_DOCSTRING,
)
# Copied from transformers.models.esm.modeling_esm.EsmModel with Esm->OmniGenome
class OmniGenomeModel(OmniGenomePreTrainedModel):
    """

    The model can behave as an encoder (with only self-attention) as well as a decoder, in which case a layer of
    cross-attention is added between the self-attention layers, following the architecture described in [Attention is
    all you need](https://arxiv.org/abs/1706.03762) by Ashish Vaswani, Noam Shazeer, Niki Parmar, Jakob Uszkoreit,
    Llion Jones, Aidan N. Gomez, Lukasz Kaiser and Illia Polosukhin.

    To behave as an decoder the model needs to be initialized with the `is_decoder` argument of the configuration set
    to `True`. To be used in a Seq2Seq model, the model needs to initialized with both `is_decoder` argument and
    `add_cross_attention` set to `True`; an `encoder_hidden_states` is then expected as an input to the forward pass.
    """

    def __init__(self, config, add_pooling_layer=True):
        super().__init__(config)
        self.config = config

        self.embeddings = OmniGenomeEmbeddings(config)
        self.encoder = OmniGenomeEncoder(config)

        self.pooler = OmniGenomePooler(config) if add_pooling_layer else None

        self.contact_head = OmniGenomeContactPredictionHead(
            in_features=config.num_hidden_layers * config.num_attention_heads, bias=True
        )

        # Initialize weights and apply final processing
        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):
        """
        Prunes heads of the model. heads_to_prune: dict of {layer_num: list of heads to prune in this layer} See base
        class PreTrainedModel
        """
        for layer, heads in heads_to_prune.items():
            self.encoder.layer[layer].attention.prune_heads(heads)

    @add_start_docstrings_to_model_forward(
        OmniGenome_INPUTS_DOCSTRING.format("(batch_size, sequence_length)")
    )
    @add_code_sample_docstrings(
        checkpoint=_CHECKPOINT_FOR_DOC,
        output_type=BaseModelOutputWithPoolingAndCrossAttentions,
        config_class=_CONFIG_FOR_DOC,
    )
    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]:
        r"""
        encoder_hidden_states  (`torch.FloatTensor` of shape `(batch_size, sequence_length, hidden_size)`, *optional*):
            Sequence of hidden-states at the output of the last layer of the encoder. Used in the cross-attention if
            the model is configured as a decoder.
        encoder_attention_mask (`torch.FloatTensor` of shape `(batch_size, sequence_length)`, *optional*):
            Mask to avoid performing attention on the padding token indices of the encoder input. This mask is used in
            the cross-attention if the model is configured as a decoder. Mask values selected in `[0, 1]`:

            - 1 for tokens that are **not masked**,
            - 0 for tokens that are **masked**.
        past_key_values (`tuple(tuple(torch.FloatTensor))` of length `config.n_layers` with each tuple having 4 tensors of shape `(batch_size, num_heads, sequence_length - 1, embed_size_per_head)`):
            Contains precomputed key and value hidden states of the attention blocks. Can be used to speed up decoding.

            If `past_key_values` are used, the user can optionally input only the last `decoder_input_ids` (those that
            don't have their past key value states given to this model) of shape `(batch_size, 1)` instead of all
            `decoder_input_ids` of shape `(batch_size, sequence_length)`.
        use_cache (`bool`, *optional*):
            If set to `True`, `past_key_values` key value states are returned and can be used to speed up decoding (see
            `past_key_values`).
        """
        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_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
            )

        # We can provide a self-attention mask of dimensions [batch_size, from_seq_length, to_seq_length]
        # ourselves in which case we just need to make it broadcastable to all heads.
        extended_attention_mask: torch.Tensor = self.get_extended_attention_mask(
            attention_mask, input_shape
        )

        # If a 2D or 3D attention mask is provided for the cross-attention
        # we need to make broadcastable to [batch_size, num_heads, seq_length, seq_length]
        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

        # Prepare head mask if needed
        # 1.0 in head_mask indicate we keep the head
        # attention_probs has shape bsz x n_heads x N x N
        # input head_mask has shape [num_heads] or [num_hidden_layers x num_heads]
        # and head_mask is converted to shape [num_hidden_layers x batch x num_heads x seq_length x seq_length]
        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)  # Matches the original model layout
        # In the original model, attentions for padding tokens are completely zeroed out.
        # This makes no difference most of the time because the other tokens won't attend to them,
        # but it does for the contact prediction task, which takes attentions as input,
        # so we have to mimic that here.
        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(
    """OmniGenome Model with a `language modeling` head on top.""", OmniGenome_START_DOCSTRING
)
# Copied from transformers.models.esm.modeling_esm.EsmForMaskedLM with Esm->OmniGenome
class OmniGenomeForMaskedLM(OmniGenomePreTrainedModel):
    _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 `OmniGenomeForMaskedLM` make sure `config.is_decoder=False` for "
                "bi-directional self-attention."
            )

        self.OmniGenome = OmniGenomeModel(config, add_pooling_layer=False)
        self.lm_head = OmniGenomeLMHead(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(
        OmniGenome_INPUTS_DOCSTRING.format("batch_size, sequence_length")
    )
    @add_code_sample_docstrings(
        checkpoint=_CHECKPOINT_FOR_DOC,
        output_type=MaskedLMOutput,
        config_class=_CONFIG_FOR_DOC,
        mask="<mask>",
    )
    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]:
        r"""
        labels (`torch.LongTensor` of shape `(batch_size, sequence_length)`, *optional*):
            Labels for computing the masked language modeling loss. Indices should be in `[-100, 0, ...,
            config.vocab_size]` (see `input_ids` docstring) Tokens with indices set to `-100` are ignored (masked), the
            loss is only computed for the tokens with labels in `[0, ..., config.vocab_size]`
        kwargs (`Dict[str, any]`, optional, defaults to *{}*):
            Used to hide legacy arguments that have been deprecated.
        """
        return_dict = (
            return_dict if return_dict is not None else self.config.use_return_dict
        )

        outputs = self.OmniGenome(
            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.OmniGenome.predict_contacts(tokens, attention_mask=attention_mask)


# Copied from transformers.models.esm.modeling_esm.EsmLMHead with Esm->OmniGenome
class OmniGenomeLMHead(nn.Module):
    """OmniGenome Head for masked language modeling."""

    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)

        # project back to size of vocabulary with bias
        x = self.decoder(x) + self.bias
        return x


@add_start_docstrings(
    """
    OmniGenome Model transformer with a sequence classification/regression head on top (a linear layer on top of the pooled
    output) e.g. for GLUE tasks.
    """,
    OmniGenome_START_DOCSTRING,
)
class OmniGenomeForSequenceClassification(OmniGenomePreTrainedModel):
    def __init__(self, config):
        super().__init__(config)
        self.num_labels = config.num_labels
        self.config = config
        self.OmniGenome = OmniGenomeModel(config, add_pooling_layer=False)
        self.classifier = OmniGenomeClassificationHead(config)
        self.init_weights()

    @add_start_docstrings_to_model_forward(
        OmniGenome_INPUTS_DOCSTRING.format("batch_size, sequence_length")
    )
    @add_code_sample_docstrings(
        checkpoint=_CHECKPOINT_FOR_DOC,
        output_type=SequenceClassifierOutput,
        config_class=_CONFIG_FOR_DOC,
    )
    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]:
        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
        )

        outputs = self.OmniGenome(
            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,
        )
        last_hidden_state = outputs[0]
        logits = self.classifier(last_hidden_state)

        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(
    """
    OmniGenome Model with a token classification head on top (a linear layer on top of the hidden-states output) 
    Note that this model is pre-trained for RNA secondary structure prediction and can be used for zero-shot RNA
    secondary structure prediction. Please find more advanced usages at https://github.com/yangheng95/OmniGenome
    This model can be fine-tuned for other token classification tasks.
    """,
    OmniGenome_START_DOCSTRING,
)
# Copied from transformers.models.esm.modeling_esm.EsmForTokenClassification with Esm->OmniGenome
class OmniGenomeForTokenClassification(OmniGenomePreTrainedModel):
    def __init__(self, config):
        super().__init__(config)
        self.num_labels = config.num_labels
        self.OmniGenome = OmniGenomeModel(config, add_pooling_layer=False)
        self.dense = torch.nn.Linear(config.hidden_size, config.hidden_size)
        self.classifier = torch.nn.Linear(self.config.hidden_size, self.num_labels)
        self.softmax = nn.Softmax(dim=-1)
        self.init_weights()

    @add_start_docstrings_to_model_forward(
        OmniGenome_INPUTS_DOCSTRING.format("batch_size, sequence_length")
    )
    @add_code_sample_docstrings(
        checkpoint=_CHECKPOINT_FOR_DOC,
        output_type=TokenClassifierOutput,
        config_class=_CONFIG_FOR_DOC,
    )
    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]:
        r"""
        labels (`torch.LongTensor` of shape `(batch_size, sequence_length)`, *optional*):
            Labels for computing the token classification loss. Indices should be in `[0, ..., config.num_labels - 1]`.
        """

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

        outputs = self.OmniGenome(
            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,
        )

        last_hidden_state = outputs[0]
        last_hidden_state = self.dense(last_hidden_state)
        logits = self.classifier(last_hidden_state)
        logits = self.softmax(logits)

        loss = None
        if labels is not None:
            loss_fct = CrossEntropyLoss()
            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,
        )

    @staticmethod
    def verify_secondary_structure(structure):
        structure = list(structure)
        left_brackets = []
        right_brackets = []
        for i, char in enumerate(structure):
            if char == "(":
                left_brackets.append(i)
            elif char == ")":
                if left_brackets:
                    left_brackets.pop()
                else:
                    right_brackets.append(i)

        for i in left_brackets:
            structure[i] = "."
        for i in right_brackets:
            structure[i] = "."

        structure = "".join(structure)

        return structure

    def predict_rna_structure(
            self,
            sequence: str,
            **kwargs
    ) -> List[str]:
        r"""
        Load the pretrained OmniGenome Model to do zero-shot prediction of the secondary structure
         of a sequence given the sequence
        """
        if self.tokenizer is None:
            tokenizer = kwargs.get("tokenizer", None)
            if tokenizer is None:
                from transformers import AutoTokenizer
                self.tokenizer = AutoTokenizer.from_pretrained(self.config.name_or_path)
            else:
                self.tokenizer = tokenizer

        inputs = self.tokenizer(sequence, return_tensors="pt", padding="max_length", truncation=True)
        input_ids = inputs["input_ids"]
        attention_mask = inputs["attention_mask"]
        outputs = self.forward(input_ids, attention_mask, **kwargs)

        logits = torch.argmax(outputs.logits, dim=-1)
        lengths = torch.sum(torch.ne(torch.tensor(0), attention_mask), dim=-1)
        structures = []
        for i, length in enumerate(lengths):
            structure = logits[i, :length].cpu().numpy()
            structure = "".join(self.config.id2label[label] for label in structure)
            if self.config.verify_ss:
                structure = self.verify_secondary_structure(structure)
            structures.append(structure)
        return structures


@add_start_docstrings(
    """
    This is not a standard Seq2Seq model. Instead, this model is designed for RNA design tasks.
    This is the OmniGenome Model with a simple genetic algorithm based RNA design head on top. 
    """,
    OmniGenome_START_DOCSTRING,
)
class OmniGenomeModelForSeq2SeqLM(OmniGenomePreTrainedModel):
    def __init__(self, config):
        super().__init__(config)
        self.num_labels = config.num_labels
        self.OmniGenome = OmniGenomeModel(config, add_pooling_layer=False)
        self.lm_head = OmniGenomeLMHead(config)
        self.num_generation = config.num_generation
        self.num_population = config.num_population
        self.init_weights()

        self.tokenizer = None
        self.predict_structure = None

        warnings.warn(f"This model {self.__class__.__name__} is not a real Seq2Seq model. "
                      f"Instead, this model is designed for RNA design tasks")

    @add_start_docstrings_to_model_forward(
        OmniGenome_INPUTS_DOCSTRING.format("batch_size, sequence_length")
    )
    @add_code_sample_docstrings(
        checkpoint=_CHECKPOINT_FOR_DOC,
        output_type=TokenClassifierOutput,
        config_class=_CONFIG_FOR_DOC,
    )
    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] = True,
            return_dict: Optional[bool] = None,
    ) -> Union[Tuple, TokenClassifierOutput]:
        r"""
        labels (`torch.LongTensor` of shape `(batch_size, sequence_length)`, *optional*):
            Labels for computing the token classification loss. Indices should be in `[0, ..., config.num_labels - 1]`.
        """
        raise NotImplementedError("This model is not designed for standard Seq2Seq tasks. "
                                  "Use model.rna_sequence_design() for RNA sequences design instead.")

    def rna_sequence_design(
            self,
            structure: str,
            predict_structure_func=None,
            **kwargs
    ) -> List[str]:
        """
        Assemble the RNA sequence given the reference sequence structure
        """
        if self.tokenizer is None:
            tokenizer = kwargs.get("tokenizer", None)
            if tokenizer is None:
                from transformers import AutoTokenizer
                self.tokenizer = AutoTokenizer.from_pretrained(self.config.name_or_path)
            else:
                self.tokenizer = tokenizer

        candidates = self.genetic_algorithm_for_rna_design(structure, predict_structure_func=None, **kwargs)

        return candidates

    def genetic_algorithm_for_rna_design(self, structure, predict_structure_func=None, **kwargs):
        if predict_structure_func is None:
            import ViennaRNA

            def predict_structure(sequence):
                return ViennaRNA.fold(sequence)[0]

            predict_structure_func = predict_structure

        self.predict_structure = predict_structure_func
        mutation_ratio = kwargs.get("mutation_ratio", 0.5)
        num_population = kwargs.get("num_population", self.num_population)
        num_generation = kwargs.get("num_generation", self.num_generation)
        import tqdm
        population = self.init_population(structure, num_population)
        population = self.mlm_mutate(population, structure, mutation_ratio=mutation_ratio)
        for generation_id in tqdm.tqdm(range(num_generation), desc="Designing RNA Sequence"):
            population_fitness = self.sequence_fitness(population, structure)[:num_population]
            population = sorted(zip(population, population_fitness), key=lambda x: x[1])[:num_population]
            population = [x[0] for x in population]
            next_generation = population  # Elitism
            next_generation += self.crossover(population, structure)
            next_generation += self.mlm_mutate(next_generation, structure, mutation_ratio)
            fitness_values = self.sequence_fitness(next_generation, structure)
            next_generation = sorted(zip(next_generation, fitness_values), key=lambda x: x[1])

            candidate_sequences = []
            for sequence, fitness in next_generation:
                if fitness == 0:
                    candidate_sequences.append(sequence)
                else:
                    break
            if candidate_sequences:
                return candidate_sequences
            print(f"Generation {generation_id}: {next_generation[0][0]} with fitness {next_generation[0][1]}")
            population = [x[0] for x in next_generation[:num_population]]

        return []

    def init_population(self, structure, num_population):
        # Initialize lists to store population data and inputs for masked language model
        population = []
        mlm_inputs = []
        # Iterate over the number of individuals in the population
        for _ in range(num_population):  # Changed from self.num_population to num_population
            # Create a sequence by randomly choosing nucleotides or a mask token for each position in the structure
            masked_sequence = [
                random.choice(["A", "G", "C", "T", "<mask>"])
                for _ in range(len(structure))
            ]
            masked_sequence_str = "".join(masked_sequence)
            mlm_inputs.append(f"{masked_sequence_str}<eos>{''.join(structure)}")

        # Call a function to predict outputs using the masked language model
        outputs = self.mlm_predict(mlm_inputs, structure)

        # Decode the mlm outputs and construct the initial population
        for i in range(len(outputs)):
            sequence = self.tokenizer.convert_ids_to_tokens(outputs[i].tolist())
            fixed_sequence = [
                x if x in "AGCT" else random.choice(["G", "C"])
                for x, y in zip(sequence, list(mlm_inputs[i].replace('<mask>', '$')))
            ]
            population.append("".join(fixed_sequence))

        return population

    def mlm_mutate(self, population, structure, mutation_ratio):
        def mutate(sequence, mutation_rate):
            sequence = np.array(list(sequence), dtype=np.str_)
            probability_matrix = np.full(sequence.shape, mutation_rate)
            masked_indices = np.random.rand(*sequence.shape) < probability_matrix
            sequence[masked_indices] = "$"
            mut_seq = "".join(sequence.tolist()).replace("$", "<mask>")
            return mut_seq

        # Initialize lists to store population data and inputs for masked language model
        mlm_inputs = []
        masked_sequences = []

        # Iterate over the number of individuals in the population
        for sequence in population:
            # Create a sequence by randomly choosing nucleotides or a mask token for each position in the structure
            masked_sequence = mutate(sequence, mutation_ratio)
            masked_sequences.append(masked_sequence)
            mlm_inputs.append(f"{masked_sequence}<eos>{''.join(structure)}")

        # Call a function to predict outputs using the masked language model
        outputs = self.mlm_predict(mlm_inputs, structure)

        mut_population = []

        # Decode the mlm outputs and construct the initial population
        for i in range(len(outputs)):
            sequence = self.tokenizer.convert_ids_to_tokens(outputs[i].tolist())
            fixed_sequence = [
                x if x in "AGCT" else random.choice(["G", "C"])
                for x, y in zip(sequence, list(masked_sequences[i].replace('<mask>', '$')))
            ]
            mut_population.append("".join(fixed_sequence))

        return mut_population

    def crossover(self, population, structure):
        crossover_population = []
        batch_crossover_inputs = []
        for i in range(len(population)):
            parent1, parent2 = random.choices(population, k=2)
            pos = random.randint(1, len(parent1) - 1)
            child1 = parent1[:pos] + "<mask>" * len(parent2[pos:])
            child2 = "<mask>" * len(parent1[:pos]) + parent2[pos:]
            batch_crossover_inputs.append(f"{child1}<eos>{structure}")
            batch_crossover_inputs.append(f"{child2}<eos>{structure}")

        outputs = self.mlm_predict(batch_crossover_inputs, structure)

        for i in range(len(outputs)):
            sequence = self.tokenizer.convert_ids_to_tokens(outputs[i].tolist())
            fixed_sequence = [
                x if x in "AGCT" else random.choice(["G", "C"])
                for x, y in zip(sequence, list(batch_crossover_inputs[i].replace('<mask>', '$')))
            ]
            crossover_population.append("".join(fixed_sequence))

        return crossover_population

    def sequence_fitness(self, sequences, structure):
        fitness_values = []
        structures = [self.predict_structure(sequence) for sequence in sequences]
        for predicted_structure in structures:
            scores = []
            for i in range(len(predicted_structure)):
                if predicted_structure[i] == structure[i]:
                    scores.append(1)
                elif (
                        predicted_structure[i] == ")"
                        and structure[i] == "("
                        or predicted_structure[i] == "("
                        and structure[i] == ")"
                ):
                    scores.append(-3)
                else:
                    scores.append(0)
            score = 1 - sum(scores) / len(structure)
            fitness_values.append(score)
        return fitness_values

    def mlm_predict(self, mlm_inputs, structure):
        batch_size = 4
        all_outputs = []
        from transformers import set_seed
        set_seed(random.randint(0, 99999999), deterministic=False)

        with torch.no_grad():
            for i in range(0, len(mlm_inputs), batch_size):
                batch_mlm_inputs = self.tokenizer(
                    mlm_inputs[i:i + batch_size],
                    padding=True,
                    max_length=len(mlm_inputs[0]) // 2,
                    truncation=True,
                    return_tensors="pt",
                )
                batch_mlm_inputs = batch_mlm_inputs.to(self.device)
                outputs = self.OmniGenome(**batch_mlm_inputs)[0]
                outputs = self.lm_head(outputs)
                outputs = outputs.argmax(dim=-1)
                all_outputs.append(outputs)
        outputs = torch.cat(all_outputs, dim=0)
        return outputs[:, 1:1 + len(structure)]


# Copied from transformers.models.esm.modeling_esm.EsmClassificationHead with Esm->OmniGenome
class OmniGenomeClassificationHead(nn.Module):
    """Head for sentence-level classification tasks."""

    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, :]  # take <s> token (equiv. to [CLS])
        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
):
    """
    Replace non-padding symbols with their position numbers. Position numbers begin at padding_idx+1. Padding symbols
    are ignored. This is modified from fairseq's `utils.make_positions`.

    Args:
        x: torch.Tensor x:

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