#
ESM

##
개요

이 페이지는 Meta AI의 Fundamental AI Research 팀에서 제공하는 Transformer 단백질 언어 모델에 대한 코드와 사전 훈련된 가중치를 제공합니다. 여기에는 최첨단인 ESMFold와 ESM-2, 그리고 이전에 공개된 ESM-1b와 ESM-1v가 포함됩니다. Transformer 단백질 언어 모델은 Alexander Rives, Joshua Meier, Tom Sercu, Siddharth Goyal, Zeming Lin, Jason Liu, Demi Guo, Myle Ott, C. Lawrence Zitnick, Jerry Ma, Rob Fergus의 논문 Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences에서 소개되었습니다. 이 논문의 첫 번째 버전은 2019년에 출판 전 논문 형태로 공개되었습니다.

ESM-2는 다양한 구조 예측 작업에서 테스트된 모든 단일 시퀀스 단백질 언어 모델을 능가하며, 원자 수준의 구조 예측을 가능하게 합니다. 이 모델은 Zeming Lin, Halil Akin, Roshan Rao, Brian Hie, Zhongkai Zhu, Wenting Lu, Allan dos Santos Costa, Maryam Fazel-Zarandi, Tom Sercu, Sal Candido, Alexander Rives의 논문 Language models of protein sequences at the scale of evolution enable accurate structure prediction에서 공개되었습니다.

이 논문에서 함께 소개된 ESMFold는 ESM-2 스템을 사용하며, 최첨단의 정확도로 단백질 접힘 구조를 예측할 수 있는 헤드를 갖추고 있습니다. AlphaFold2와 달리, 이는 대형 사전 훈련된 단백질 언어 모델 스템의 토큰 임베딩에 의존하며, 추론 시 다중 시퀀스 정렬(MSA) 단계를 수행하지 않습니다. 이는 ESMFold 체크포인트가 완전히 “독립적”이며, 예측을 위해 알려진 단백질 시퀀스와 구조의 데이터베이스, 그리고 그와 관련 외부 쿼리 도구를 필요로 하지 않는다는 것을 의미합니다. 그리고 그 결과, 훨씬 빠릅니다.

“Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences”의 초록은 다음과 같습니다:

인공지능 분야에서는 대규모의 데이터와 모델 용량을 갖춘 비지도 학습의 조합이 표현 학습과 통계적 생성에서 주요한 발전을 이끌어냈습니다. 생명 과학에서는 시퀀싱 기술의 성장이 예상되며, 자연 시퀀스 다양성에 대한 전례 없는 데이터가 나올 것으로 기대됩니다. 진화적 단계에서 볼 때, 단백질 언어 모델링은 생물학을 위한 예측 및 생성 인공지능을 향한 논리적인 단계에 있습니다. 이를 위해 우리는 진화적 다양성을 아우르는 2억 5천만 개의 단백질 시퀀스에서 추출한 860억 개의 아미노산에 대해 심층 컨텍스트 언어 모델을 비지도 학습으로 훈련합니다. 그 결과 모델은 그 표현에서 생물학적 속성에 대한 정보를 포함합니다. 이 표현은 시퀀스 데이터만으로 학습됩니다. 학습된 표현 공간은 아미노산의 생화학적 특성 수준에서부터 단백질의 원거리 상동성까지 구조를 반영하는 다중 규모의 조직을 가지고 있습니다. 이 표현에는 2차 및 3차 구조에 대한 정보가 인코딩되어 있으며, 선형 전사에 의해 식별 될 수 있습니다. 표현 학습은 돌연변이에 의한 효과와 2차 구조의 최첨단 지도 예측을 가능하게 하고, 넓은 범위의 접촉 부위 예측을 위한 최첨단 특징을 향상시킵니다.

“Language models of protein sequences at the scale of evolution enable accurate structure prediction”의 초록은 다음과 같습니다:

대형 언어 모델은 최근 규모가 커짐에 따라 긴급한 기능을 개발하여 단순한 패턴 매칭을 넘어 더 높은 수준의 추론을 수행하고 생생한 이미지와 텍스트를 생성하는 것으로 나타났습니다. 더 작은 규모에서 훈련된 단백질 시퀀스의 언어 모델이 연구되었지만, 그들이 규모가 커짐에 따라 생물학에 대해 무엇을 배우는지는 거의 알려져 있지 않습니다. 이 연구에서 우리는 현재까지 평가된 가장 큰 150억 개의 매개변수를 가진 모델을 훈련합니다. 우리는 모델이 규모가 커짐에 따라 단일 아미노산의 해상도로 단백질의 3차원 구조를 예측할 수 있는 정보를 학습한다는 것을 발견했습니다. 우리는 개별 단백질 시퀀스로부터 직접 고정밀 원자 수준의 엔드-투-엔드 구조 예측을 하기 위한 ESMFold를 제시합니다. ESMFold는 언어 모델에 잘 이해되는 낮은 퍼플렉서티를 가진 시퀀스에 대해 AlphaFold2와 RoseTTAFold와 유사한 정확도를 가지고 있습니다. ESMFold의 추론은 AlphaFold2보다 한 자릿수 빠르며, 메타게놈 단백질의 구조적 공간을 실용적인 시간 내에 탐색할 수 있게 합니다.

원본 코드는 여기에서 찾을 수 있으며, Meta AI의 Fundamental AI Research 팀에서 개발되었습니다. ESM-1b, ESM-1v, ESM-2는 jasonliu와 Matt에 의해 HuggingFace에 기여되었습니다.

ESMFold는 Matt와 Sylvain에 의해 HuggingFace에 기여되었으며, 이 과정에서 많은 도움을 준 Nikita Smetanin, Roshan Rao, Tom Sercu에게 큰 감사를 드립니다!

##
사용 팁

- ESM 모델은 마스크드 언어 모델링(MLM) 목표로 훈련되었습니다.
- HuggingFace의 ESMFold 포트는 openfold 라이브러리의 일부를 사용합니다. `openfold` 라이브러리는 Apache License 2.0에 따라 라이선스가 부여됩니다.

##
리소스

- 텍스트 분류 작업 가이드
- 토큰 분류 작업 가이드
- 마스킹드 언어 모델링 작업 가이드

##
EsmConfig

###
class transformers.EsmConfig

< source >

( vocab_size = None mask_token_id = None pad_token_id = None hidden_size = 768 num_hidden_layers = 12 num_attention_heads = 12 intermediate_size = 3072 hidden_dropout_prob = 0.1 attention_probs_dropout_prob = 0.1 max_position_embeddings = 1026 initializer_range = 0.02 layer_norm_eps = 1e-12 position_embedding_type = 'absolute' use_cache = True emb_layer_norm_before = None token_dropout = False is_folding_model = False esmfold_config = None vocab_list = None **kwargs )

Parameters

- vocab_size (`int`, optional) — Vocabulary size of the ESM model. Defines the number of different tokens that can be represented by the `inputs_ids` passed when calling `ESMModel`.
- mask_token_id (`int`, optional) — The index of the mask token in the vocabulary. This must be included in the config because of the “mask-dropout” scaling trick, which will scale the inputs depending on the number of masked tokens.
- pad_token_id (`int`, optional) — The index of the padding token in the vocabulary. This must be included in the config because certain parts of the ESM code use this instead of the attention mask.
- hidden_size (`int`, optional, defaults to 768) — Dimensionality of the encoder layers and the pooler layer.
- num_hidden_layers (`int`, optional, defaults to 12) — Number of hidden layers in the Transformer encoder.
- num_attention_heads (`int`, optional, defaults to 12) — Number of attention heads for each attention layer in the Transformer encoder.
- intermediate_size (`int`, optional, defaults to 3072) — Dimensionality of the “intermediate” (often named feed-forward) layer in the Transformer encoder.
- hidden_dropout_prob (`float`, optional, defaults to 0.1) — The dropout probability for all fully connected layers in the embeddings, encoder, and pooler.
- attention_probs_dropout_prob (`float`, optional, defaults to 0.1) — The dropout ratio for the attention probabilities.
- max_position_embeddings (`int`, optional, defaults to 1026) — The maximum sequence length that this model might ever be used with. Typically set this to something large just in case (e.g., 512 or 1024 or 2048).
- initializer_range (`float`, optional, defaults to 0.02) — The standard deviation of the truncated_normal_initializer for initializing all weight matrices.
- layer_norm_eps (`float`, optional, defaults to 1e-12) — The epsilon used by the layer normalization layers.
- position_embedding_type (`str`, optional, defaults to `"absolute"`) — Type of position embedding. Choose one of `"absolute"`, `"relative_key"`, `"relative_key_query", "rotary"`. For positional embeddings use `"absolute"`. For more information on `"relative_key"`, please refer to Self-Attention with Relative Position Representations (Shaw et al.). For more information on `"relative_key_query"`, please refer to Method 4 in Improve Transformer Models with Better Relative Position Embeddings (Huang et al.).
- is_decoder (`bool`, optional, defaults to `False`) — Whether the model is used as a decoder or not. If `False`, the model is used as an encoder.
- use_cache (`bool`, optional, defaults to `True`) — Whether or not the model should return the last key/values attentions (not used by all models). Only relevant if `config.is_decoder=True`.
- emb_layer_norm_before (`bool`, optional) — Whether to apply layer normalization after embeddings but before the main stem of the network.
- token_dropout (`bool`, defaults to `False`) — When this is enabled, masked tokens are treated as if they had been dropped out by input dropout.

This is the configuration class to store the configuration of a `ESMModel`. It is used to instantiate a ESM model according to the specified arguments, defining the model architecture. Instantiating a configuration with the defaults will yield a similar configuration to that of the ESM facebook/esm-1b architecture.

Configuration objects inherit from PretrainedConfig and can be used to control the model outputs. Read the documentation from PretrainedConfig for more information.

Examples:

    >>> from transformers import EsmModel, EsmConfig

    >>> # Initializing a ESM facebook/esm-1b style configuration
    >>> configuration = EsmConfig(vocab_size=33)

    >>> # Initializing a model from the configuration
    >>> model = EsmModel(configuration)

    >>> # Accessing the model configuration
    >>> configuration = model.config

####
to_dict

< source >

( ) →
`Dict[str, any]`

Returns

`Dict[str, any]`

Dictionary of all the attributes that make up this configuration instance,

Serializes this instance to a Python dictionary. Override the default to_dict().

##
EsmTokenizer

###
class transformers.EsmTokenizer

< source >

( vocab_file unk_token = '<unk>' cls_token = '<cls>' pad_token = '<pad>' mask_token = '<mask>' eos_token = '<eos>' **kwargs )

Constructs an ESM tokenizer.

####
build_inputs_with_special_tokens

< source >

( token_ids_0: typing.List[int] token_ids_1: typing.Optional[typing.List[int]] = None )

####
get_special_tokens_mask

< source >

( token_ids_0: typing.List token_ids_1: typing.Optional[typing.List] = None already_has_special_tokens: bool = False ) →
A list of integers in the range [0, 1]

Parameters

- token_ids_0 (`List[int]`) — List of ids of the first sequence.
- token_ids_1 (`List[int]`, optional) — List of ids of the second sequence.
- already_has_special_tokens (`bool`, optional, defaults to `False`) — Whether or not the token list is already formatted with special tokens for the model.

Returns

A list of integers in the range [0, 1]

1 for a special token, 0 for a sequence token.

Retrieves sequence ids from a token list that has no special tokens added. This method is called when adding special tokens using the tokenizer `prepare_for_model` or `encode_plus` methods.

####
create_token_type_ids_from_sequences

< source >

( token_ids_0: typing.List[int] token_ids_1: typing.Optional[typing.List[int]] = None ) →
`List[int]`

Parameters

- token_ids_0 (`List[int]`) — The first tokenized sequence.
- token_ids_1 (`List[int]`, optional) — The second tokenized sequence.

Returns

`List[int]`

The token type ids.

Create the token type IDs corresponding to the sequences passed. What are token type IDs?

Should be overridden in a subclass if the model has a special way of building those.

####
save_vocabulary

< source >

( save_directory filename_prefix )

Pytorch
Hide Pytorch content

##
EsmModel

###
class transformers.EsmModel

< source >

( config add_pooling_layer = True )

Parameters

- config (EsmModel) — 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 from_pretrained() method to load the model weights.
- add_pooling_layer (`bool`, optional, defaults to `True`) — Whether to add a pooling layer

The bare Esm Model outputting raw hidden-states without any specific head on top.

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 subclass. Use it as a regular PyTorch Module and refer to the PyTorch documentation for all matter related to general usage and behavior.

####
forward

< source >

( input_ids: typing.Optional[torch.Tensor] = None attention_mask: typing.Optional[torch.Tensor] = None position_ids: typing.Optional[torch.Tensor] = None head_mask: typing.Optional[torch.Tensor] = None inputs_embeds: typing.Optional[torch.Tensor] = None encoder_hidden_states: typing.Optional[torch.Tensor] = None encoder_attention_mask: typing.Optional[torch.Tensor] = None past_key_values: typing.Optional[typing.List[torch.FloatTensor]] = None use_cache: typing.Optional[bool] = None output_attentions: typing.Optional[bool] = None output_hidden_states: typing.Optional[bool] = None return_dict: typing.Optional[bool] = None ) →
transformers.modeling_outputs.BaseModelOutputWithPoolingAndCrossAttentions or `tuple(torch.FloatTensor)`

Parameters

- input_ids (`torch.Tensor` of shape `((batch_size, sequence_length))`) — 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?

- attention_mask (`torch.Tensor` of shape `(batch_size, sequence_length)`, 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?

- position_ids (`torch.Tensor` of shape `((batch_size, sequence_length))`, 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?

- head_mask (`torch.Tensor` 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.Tensor` of shape `((batch_size, sequence_length), 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.
- encoder_hidden_states (`torch.Tensor` 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.Tensor` 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 (`List[torch.FloatTensor]`, optional) — Pre-computed hidden-states (key and values in the self-attention blocks and in the cross-attention blocks) that can be used to speed up sequential decoding. This typically consists in the `past_key_values` returned by the model at a previous stage of decoding, when `use_cache=True` or `config.use_cache=True`.

  Two formats are allowed:

  - a Cache instance, see our kv cache guide;
  - Tuple of `tuple(torch.FloatTensor)` of length `config.n_layers`, with each tuple having 2 tensors of shape `(batch_size, num_heads, sequence_length, embed_size_per_head)`). This is also known as the legacy cache format.

  The model will output the same cache format that is fed as input. If no `past_key_values` are passed, the legacy cache format will be returned.

  If `past_key_values` are used, the user can optionally input only the last `input_ids` (those that don’t have their past key value states given to this model) of shape `(batch_size, 1)` instead of all `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 (`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 ModelOutput instead of a plain tuple.

Returns

transformers.modeling_outputs.BaseModelOutputWithPoolingAndCrossAttentions or `tuple(torch.FloatTensor)`

A transformers.modeling_outputs.BaseModelOutputWithPoolingAndCrossAttentions or a tuple of `torch.FloatTensor` (if `return_dict=False` is passed or when `config.return_dict=False`) comprising various elements depending on the configuration (EsmConfig) and inputs.

- last_hidden_state (`torch.FloatTensor` of shape `(batch_size, sequence_length, hidden_size)`) — Sequence of hidden-states at the output of the last layer of the model.

- pooler_output (`torch.FloatTensor` of shape `(batch_size, hidden_size)`) — Last layer hidden-state of the first token of the sequence (classification token) after further processing through the layers used for the auxiliary pretraining task. E.g. for BERT-family of models, this returns the classification token after processing through a linear layer and a tanh activation function. The linear layer weights are trained from the next sentence prediction (classification) objective during pretraining.

- hidden_states (`tuple(torch.FloatTensor)`, optional, returned when `output_hidden_states=True` is passed or when `config.output_hidden_states=True`) — Tuple of `torch.FloatTensor` (one for the output of the embeddings, if the model has an embedding layer, + one for the output of each layer) of shape `(batch_size, sequence_length, hidden_size)`.

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

- attentions (`tuple(torch.FloatTensor)`, optional, returned when `output_attentions=True` is passed or when `config.output_attentions=True`) — Tuple of `torch.FloatTensor` (one for each layer) of shape `(batch_size, num_heads, sequence_length, sequence_length)`.

  Attentions weights after the attention softmax, used to compute the weighted average in the self-attention heads.

- cross_attentions (`tuple(torch.FloatTensor)`, optional, returned when `output_attentions=True` and `config.add_cross_attention=True` is passed or when `config.output_attentions=True`) — Tuple of `torch.FloatTensor` (one for each layer) of shape `(batch_size, num_heads, sequence_length, sequence_length)`.

  Attentions weights of the decoder’s cross-attention layer, after the attention softmax, used to compute the weighted average in the cross-attention heads.

- past_key_values (`Cache`, optional, returned when `use_cache=True` is passed or when `config.use_cache=True`) — It is a Cache instance. For more details, see our kv cache guide.

  Contains pre-computed hidden-states (key and values in the self-attention blocks and optionally if `config.is_encoder_decoder=True` in the cross-attention blocks) that can be used (see `past_key_values` input) to speed up sequential decoding.

The EsmModel forward method, overrides the `__call__` special method.

Although the recipe for forward pass needs to be defined within this function, one should call the `Module` instance afterwards instead of this since the former takes care of running the pre and post processing steps while the latter silently ignores them.

##
EsmForMaskedLM

###
class transformers.EsmForMaskedLM

< source >

( config )

Parameters

- config (EsmForMaskedLM) — 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 from_pretrained() method to load the model weights.

The Esm Model with a `language modeling` head on top.”

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 subclass. Use it as a regular PyTorch Module and refer to the PyTorch documentation for all matter related to general usage and behavior.

####
forward

< source >

( input_ids: typing.Optional[torch.LongTensor] = None attention_mask: typing.Optional[torch.Tensor] = None position_ids: typing.Optional[torch.LongTensor] = None head_mask: typing.Optional[torch.Tensor] = None inputs_embeds: typing.Optional[torch.FloatTensor] = None encoder_hidden_states: typing.Optional[torch.FloatTensor] = None encoder_attention_mask: typing.Optional[torch.Tensor] = None labels: typing.Optional[torch.LongTensor] = None output_attentions: typing.Optional[bool] = None output_hidden_states: typing.Optional[bool] = None return_dict: typing.Optional[bool] = None ) →
transformers.modeling_outputs.MaskedLMOutput or `tuple(torch.FloatTensor)`

Parameters

- input_ids (`torch.LongTensor` of shape `(batch_size, sequence_length)`, optional) — Indices of input sequence tokens in the vocabulary. Padding will be ignored by default.

  Indices can be obtained using AutoTokenizer. See PreTrainedTokenizer.encode() and PreTrainedTokenizer.call() for details.

  What are input IDs?

- attention_mask (`torch.Tensor` of shape `(batch_size, sequence_length)`, 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?

- position_ids (`torch.LongTensor` of shape `(batch_size, sequence_length)`, optional) — Indices of positions of each input sequence tokens in the position embeddings. Selected in the range `[0, config.n_positions - 1]`.

  What are position IDs?

- head_mask (`torch.Tensor` 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 `(batch_size, sequence_length, 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.
- 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.Tensor` 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.
- 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]`
- 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 ModelOutput instead of a plain tuple.

Returns

transformers.modeling_outputs.MaskedLMOutput or `tuple(torch.FloatTensor)`

A transformers.modeling_outputs.MaskedLMOutput or a tuple of `torch.FloatTensor` (if `return_dict=False` is passed or when `config.return_dict=False`) comprising various elements depending on the configuration (EsmConfig) and inputs.

- loss (`torch.FloatTensor` of shape `(1,)`, optional, returned when `labels` is provided) — Masked language modeling (MLM) loss.

- logits (`torch.FloatTensor` of shape `(batch_size, sequence_length, config.vocab_size)`) — Prediction scores of the language modeling head (scores for each vocabulary token before SoftMax).

- hidden_states (`tuple(torch.FloatTensor)`, optional, returned when `output_hidden_states=True` is passed or when `config.output_hidden_states=True`) — Tuple of `torch.FloatTensor` (one for the output of the embeddings, if the model has an embedding layer, + one for the output of each layer) of shape `(batch_size, sequence_length, hidden_size)`.

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

- attentions (`tuple(torch.FloatTensor)`, optional, returned when `output_attentions=True` is passed or when `config.output_attentions=True`) — Tuple of `torch.FloatTensor` (one for each layer) of shape `(batch_size, num_heads, sequence_length, sequence_length)`.

  Attentions weights after the attention softmax, used to compute the weighted average in the self-attention heads.

The EsmForMaskedLM forward method, overrides the `__call__` special method.

Although the recipe for forward pass needs to be defined within this function, one should call the `Module` instance afterwards instead of this since the former takes care of running the pre and post processing steps while the latter silently ignores them.

Example:

    >>> from transformers import AutoTokenizer, EsmForMaskedLM
    >>> import torch

    >>> tokenizer = AutoTokenizer.from_pretrained("facebook/esm-1b")
    >>> model = EsmForMaskedLM.from_pretrained("facebook/esm-1b")

    >>> inputs = tokenizer("The capital of France is <mask>.", return_tensors="pt")

    >>> with torch.no_grad():
    ...     logits = model(**inputs).logits

    >>> # retrieve index of <mask>
    >>> mask_token_index = (inputs.input_ids == tokenizer.mask_token_id)[0].nonzero(as_tuple=True)[0]

    >>> predicted_token_id = logits[0, mask_token_index].argmax(axis=-1)
    >>> tokenizer.decode(predicted_token_id)
    ...

    >>> labels = tokenizer("The capital of France is Paris.", return_tensors="pt")["input_ids"]
    >>> # mask labels of non-<mask> tokens
    >>> labels = torch.where(inputs.input_ids == tokenizer.mask_token_id, labels, -100)

    >>> outputs = model(**inputs, labels=labels)
    >>> round(outputs.loss.item(), 2)
    ...

##
EsmForSequenceClassification

###
class transformers.EsmForSequenceClassification

< source >

( config )

Parameters

- config (EsmForSequenceClassification) — 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 from_pretrained() method to load the model weights.

ESM Model transformer with a sequence classification/regression head on top (a linear layer on top of the pooled output) e.g. for GLUE tasks.

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 subclass. Use it as a regular PyTorch Module and refer to the PyTorch documentation for all matter related to general usage and behavior.

####
forward

< source >

( input_ids: typing.Optional[torch.LongTensor] = None attention_mask: typing.Optional[torch.Tensor] = None position_ids: typing.Optional[torch.LongTensor] = None head_mask: typing.Optional[torch.Tensor] = None inputs_embeds: typing.Optional[torch.FloatTensor] = None labels: typing.Optional[torch.LongTensor] = None output_attentions: typing.Optional[bool] = None output_hidden_states: typing.Optional[bool] = None return_dict: typing.Optional[bool] = None ) →
transformers.modeling_outputs.SequenceClassifierOutput or `tuple(torch.FloatTensor)`

Parameters

- input_ids (`torch.LongTensor` of shape `(batch_size, sequence_length)`, optional) — Indices of input sequence tokens in the vocabulary. Padding will be ignored by default.

  Indices can be obtained using AutoTokenizer. See PreTrainedTokenizer.encode() and PreTrainedTokenizer.call() for details.

  What are input IDs?

- attention_mask (`torch.Tensor` of shape `(batch_size, sequence_length)`, 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?

- position_ids (`torch.LongTensor` of shape `(batch_size, sequence_length)`, optional) — Indices of positions of each input sequence tokens in the position embeddings. Selected in the range `[0, config.n_positions - 1]`.

  What are position IDs?

- head_mask (`torch.Tensor` 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 `(batch_size, sequence_length, 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.
- 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).
- 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 ModelOutput instead of a plain tuple.

Returns

transformers.modeling_outputs.SequenceClassifierOutput or `tuple(torch.FloatTensor)`

A transformers.modeling_outputs.SequenceClassifierOutput or a tuple of `torch.FloatTensor` (if `return_dict=False` is passed or when `config.return_dict=False`) comprising various elements depending on the configuration (EsmConfig) and inputs.

- loss (`torch.FloatTensor` of shape `(1,)`, optional, returned when `labels` is provided) — Classification (or regression if config.num_labels==1) loss.

- logits (`torch.FloatTensor` of shape `(batch_size, config.num_labels)`) — Classification (or regression if config.num_labels==1) scores (before SoftMax).

- hidden_states (`tuple(torch.FloatTensor)`, optional, returned when `output_hidden_states=True` is passed or when `config.output_hidden_states=True`) — Tuple of `torch.FloatTensor` (one for the output of the embeddings, if the model has an embedding layer, + one for the output of each layer) of shape `(batch_size, sequence_length, hidden_size)`.

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

- attentions (`tuple(torch.FloatTensor)`, optional, returned when `output_attentions=True` is passed or when `config.output_attentions=True`) — Tuple of `torch.FloatTensor` (one for each layer) of shape `(batch_size, num_heads, sequence_length, sequence_length)`.

  Attentions weights after the attention softmax, used to compute the weighted average in the self-attention heads.

The EsmForSequenceClassification forward method, overrides the `__call__` special method.

Although the recipe for forward pass needs to be defined within this function, one should call the `Module` instance afterwards instead of this since the former takes care of running the pre and post processing steps while the latter silently ignores them.

Example of single-label classification:

    >>> import torch
    >>> from transformers import AutoTokenizer, EsmForSequenceClassification

    >>> tokenizer = AutoTokenizer.from_pretrained("facebook/esm-1b")
    >>> model = EsmForSequenceClassification.from_pretrained("facebook/esm-1b")

    >>> inputs = tokenizer("Hello, my dog is cute", return_tensors="pt")

    >>> with torch.no_grad():
    ...     logits = model(**inputs).logits

    >>> predicted_class_id = logits.argmax().item()
    >>> model.config.id2label[predicted_class_id]
    ...

    >>> # To train a model on `num_labels` classes, you can pass `num_labels=num_labels` to `.from_pretrained(...)`
    >>> num_labels = len(model.config.id2label)
    >>> model = EsmForSequenceClassification.from_pretrained("facebook/esm-1b", num_labels=num_labels)

    >>> labels = torch.tensor([1])
    >>> loss = model(**inputs, labels=labels).loss
    >>> round(loss.item(), 2)
    ...

Example of multi-label classification:

    >>> import torch
    >>> from transformers import AutoTokenizer, EsmForSequenceClassification

    >>> tokenizer = AutoTokenizer.from_pretrained("facebook/esm-1b")
    >>> model = EsmForSequenceClassification.from_pretrained("facebook/esm-1b", problem_type="multi_label_classification")

    >>> inputs = tokenizer("Hello, my dog is cute", return_tensors="pt")

    >>> with torch.no_grad():
    ...     logits = model(**inputs).logits

    >>> predicted_class_ids = torch.arange(0, logits.shape[-1])[torch.sigmoid(logits).squeeze(dim=0) > 0.5]

    >>> # To train a model on `num_labels` classes, you can pass `num_labels=num_labels` to `.from_pretrained(...)`
    >>> num_labels = len(model.config.id2label)
    >>> model = EsmForSequenceClassification.from_pretrained(
    ...     "facebook/esm-1b", num_labels=num_labels, problem_type="multi_label_classification"
    ... )

    >>> labels = torch.sum(
    ...     torch.nn.functional.one_hot(predicted_class_ids[None, :].clone(), num_classes=num_labels), dim=1
    ... ).to(torch.float)
    >>> loss = model(**inputs, labels=labels).loss

##
EsmForTokenClassification

###
class transformers.EsmForTokenClassification

< source >

( config )

Parameters

- config (EsmForTokenClassification) — 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 from_pretrained() method to load the model weights.

The Esm transformer 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.

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 subclass. Use it as a regular PyTorch Module and refer to the PyTorch documentation for all matter related to general usage and behavior.

####
forward

< source >

( input_ids: typing.Optional[torch.LongTensor] = None attention_mask: typing.Optional[torch.Tensor] = None position_ids: typing.Optional[torch.LongTensor] = None head_mask: typing.Optional[torch.Tensor] = None inputs_embeds: typing.Optional[torch.FloatTensor] = None labels: typing.Optional[torch.LongTensor] = None output_attentions: typing.Optional[bool] = None output_hidden_states: typing.Optional[bool] = None return_dict: typing.Optional[bool] = None ) →
transformers.modeling_outputs.TokenClassifierOutput or `tuple(torch.FloatTensor)`

Parameters

- input_ids (`torch.LongTensor` of shape `(batch_size, sequence_length)`, optional) — Indices of input sequence tokens in the vocabulary. Padding will be ignored by default.

  Indices can be obtained using AutoTokenizer. See PreTrainedTokenizer.encode() and PreTrainedTokenizer.call() for details.

  What are input IDs?

- attention_mask (`torch.Tensor` of shape `(batch_size, sequence_length)`, 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?

- position_ids (`torch.LongTensor` of shape `(batch_size, sequence_length)`, optional) — Indices of positions of each input sequence tokens in the position embeddings. Selected in the range `[0, config.n_positions - 1]`.

  What are position IDs?

- head_mask (`torch.Tensor` 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 `(batch_size, sequence_length, 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.
- 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]`.
- 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 ModelOutput instead of a plain tuple.

Returns

transformers.modeling_outputs.TokenClassifierOutput or `tuple(torch.FloatTensor)`

A transformers.modeling_outputs.TokenClassifierOutput or a tuple of `torch.FloatTensor` (if `return_dict=False` is passed or when `config.return_dict=False`) comprising various elements depending on the configuration (EsmConfig) and inputs.

- loss (`torch.FloatTensor` of shape `(1,)`, optional, returned when `labels` is provided) — Classification loss.

- logits (`torch.FloatTensor` of shape `(batch_size, sequence_length, config.num_labels)`) — Classification scores (before SoftMax).

- hidden_states (`tuple(torch.FloatTensor)`, optional, returned when `output_hidden_states=True` is passed or when `config.output_hidden_states=True`) — Tuple of `torch.FloatTensor` (one for the output of the embeddings, if the model has an embedding layer, + one for the output of each layer) of shape `(batch_size, sequence_length, hidden_size)`.

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

- attentions (`tuple(torch.FloatTensor)`, optional, returned when `output_attentions=True` is passed or when `config.output_attentions=True`) — Tuple of `torch.FloatTensor` (one for each layer) of shape `(batch_size, num_heads, sequence_length, sequence_length)`.

  Attentions weights after the attention softmax, used to compute the weighted average in the self-attention heads.

The EsmForTokenClassification forward method, overrides the `__call__` special method.

Although the recipe for forward pass needs to be defined within this function, one should call the `Module` instance afterwards instead of this since the former takes care of running the pre and post processing steps while the latter silently ignores them.

Example:

    >>> from transformers import AutoTokenizer, EsmForTokenClassification
    >>> import torch

    >>> tokenizer = AutoTokenizer.from_pretrained("facebook/esm-1b")
    >>> model = EsmForTokenClassification.from_pretrained("facebook/esm-1b")

    >>> inputs = tokenizer(
    ...     "HuggingFace is a company based in Paris and New York", add_special_tokens=False, return_tensors="pt"
    ... )

    >>> with torch.no_grad():
    ...     logits = model(**inputs).logits

    >>> predicted_token_class_ids = logits.argmax(-1)

    >>> # Note that tokens are classified rather then input words which means that
    >>> # there might be more predicted token classes than words.
    >>> # Multiple token classes might account for the same word
    >>> predicted_tokens_classes = [model.config.id2label[t.item()] for t in predicted_token_class_ids[0]]
    >>> predicted_tokens_classes
    ...

    >>> labels = predicted_token_class_ids
    >>> loss = model(**inputs, labels=labels).loss
    >>> round(loss.item(), 2)
    ...

##
EsmForProteinFolding

###
class transformers.EsmForProteinFolding

< source >

( config )

Parameters

- config (EsmForProteinFolding) — 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 from_pretrained() method to load the model weights.

ESMForProteinFolding is the HuggingFace port of the original ESMFold model. It consists of an ESM-2 “stem” followed by a protein folding “head”, although unlike most other output heads, this “head” is similar in size and runtime to the rest of the model combined! It outputs a dictionary containing predicted structural information about the input protein(s).

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 subclass. Use it as a regular PyTorch Module and refer to the PyTorch documentation for all matter related to general usage and behavior.

####
forward

< source >

( input_ids: Tensor attention_mask: typing.Optional[torch.Tensor] = None position_ids: typing.Optional[torch.Tensor] = None masking_pattern: typing.Optional[torch.Tensor] = None num_recycles: typing.Optional[int] = None output_hidden_states: typing.Optional[bool] = False ) →
`transformers.models.esm.modeling_esmfold.EsmForProteinFoldingOutput` or `tuple(torch.FloatTensor)`

Parameters

- input_ids (`torch.Tensor` of shape `(batch_size, sequence_length)`) — Indices of input sequence tokens in the vocabulary. Padding will be ignored by default.

  Indices can be obtained using AutoTokenizer. See PreTrainedTokenizer.encode() and PreTrainedTokenizer.call() for details.

  What are input IDs?

- attention_mask (`torch.Tensor` of shape `(batch_size, sequence_length)`, 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?

- position_ids (`torch.Tensor` of shape `(batch_size, sequence_length)`, optional) — Indices of positions of each input sequence tokens in the position embeddings. Selected in the range `[0, config.n_positions - 1]`.

  What are position IDs?

- masking_pattern (`torch.Tensor` of shape `(batch_size, sequence_length)`, optional) — Locations of tokens to mask during training as a form of regularization. Mask values selected in `[0, 1]`.
- num_recycles (`int`, optional, defaults to `None`) — Number of times to recycle the input sequence. If `None`, defaults to `config.num_recycles`. “Recycling” consists of passing the output of the folding trunk back in as input to the trunk. During training, the number of recycles should vary with each batch, to ensure that the model learns to output valid predictions after each recycle. During inference, num_recycles should be set to the highest value that the model was trained with for maximum accuracy. Accordingly, when this value is set to `None`, config.max_recycles is used.
- output_hidden_states (`bool`, optional, defaults to `False`) — Whether or not to return the hidden states of all layers. See `hidden_states` under returned tensors for more detail.

Returns

`transformers.models.esm.modeling_esmfold.EsmForProteinFoldingOutput` or `tuple(torch.FloatTensor)`

A `transformers.models.esm.modeling_esmfold.EsmForProteinFoldingOutput` or a tuple of `torch.FloatTensor` (if `return_dict=False` is passed or when `config.return_dict=False`) comprising various elements depending on the configuration (EsmConfig) and inputs.

- frames (`torch.FloatTensor`) — Output frames.
- sidechain_frames (`torch.FloatTensor`) — Output sidechain frames.
- unnormalized_angles (`torch.FloatTensor`) — Predicted unnormalized backbone and side chain torsion angles.
- angles (`torch.FloatTensor`) — Predicted backbone and side chain torsion angles.
- positions (`torch.FloatTensor`) — Predicted positions of the backbone and side chain atoms.
- states (`torch.FloatTensor`) — Hidden states from the protein folding trunk.
- s_s (`torch.FloatTensor`) — Per-residue embeddings derived by concatenating the hidden states of each layer of the ESM-2 LM stem.
- s_z (`torch.FloatTensor`) — Pairwise residue embeddings.
- distogram_logits (`torch.FloatTensor`) — Input logits to the distogram used to compute residue distances.
- lm_logits (`torch.FloatTensor`) — Logits output by the ESM-2 protein language model stem.
- aatype (`torch.FloatTensor`) — Input amino acids (AlphaFold2 indices).
- atom14_atom_exists (`torch.FloatTensor`) — Whether each atom exists in the atom14 representation.
- residx_atom14_to_atom37 (`torch.FloatTensor`) — Mapping between atoms in the atom14 and atom37 representations.
- residx_atom37_to_atom14 (`torch.FloatTensor`) — Mapping between atoms in the atom37 and atom14 representations.
- atom37_atom_exists (`torch.FloatTensor`) — Whether each atom exists in the atom37 representation.
- residue_index (`torch.FloatTensor`) — The index of each residue in the protein chain. Unless internal padding tokens are used, this will just be a sequence of integers from 0 to `sequence_length`.
- lddt_head (`torch.FloatTensor`) — Raw outputs from the lddt head used to compute plddt.
- plddt (`torch.FloatTensor`) — Per-residue confidence scores. Regions of low confidence may indicate areas where the model’s prediction is uncertain, or where the protein structure is disordered.
- ptm_logits (`torch.FloatTensor`) — Raw logits used for computing ptm.
- ptm (`torch.FloatTensor`) — TM-score output representing the model’s high-level confidence in the overall structure.
- aligned_confidence_probs (`torch.FloatTensor`) — Per-residue confidence scores for the aligned structure.
- predicted_aligned_error (`torch.FloatTensor`) — Predicted error between the model’s prediction and the ground truth.
- max_predicted_aligned_error (`torch.FloatTensor`) — Per-sample maximum predicted error.

The EsmForProteinFolding forward method, overrides the `__call__` special method.

Although the recipe for forward pass needs to be defined within this function, one should call the `Module` instance afterwards instead of this since the former takes care of running the pre and post processing steps while the latter silently ignores them.

Example:

    >>> from transformers import AutoTokenizer, EsmForProteinFolding

    >>> model = EsmForProteinFolding.from_pretrained("facebook/esmfold_v1")
    >>> tokenizer = AutoTokenizer.from_pretrained("facebook/esmfold_v1")
    >>> inputs = tokenizer(["MLKNVQVQLV"], return_tensors="pt", add_special_tokens=False)  # A tiny random peptide
    >>> outputs = model(**inputs)
    >>> folded_positions = outputs.positions

TensorFlow
Hide TensorFlow content

##
TFEsmModel

###
class transformers.TFEsmModel

< source >

( config: EsmConfig add_pooling_layer = True *inputs **kwargs )

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 from_pretrained() method to load the model weights.

The bare ESM Model transformer outputting raw hidden-states without any specific head on top.

This model inherits from TFPreTrainedModel. 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 Keras Model subclass. Use it as a regular Keras model and refer to the TF/Keras documentation for all matters related to general usage and behavior.

####
call

< source >

( input_ids: TFModelInputType | None = None attention_mask: np.ndarray | tf.Tensor | None = None position_ids: np.ndarray | tf.Tensor | None = None head_mask: np.ndarray | tf.Tensor | None = None inputs_embeds: np.ndarray | tf.Tensor | None = None encoder_hidden_states: np.ndarray | tf.Tensor | None = None encoder_attention_mask: np.ndarray | tf.Tensor | None = None past_key_values: Optional[Tuple[Tuple[Union[np.ndarray, tf.Tensor]]]] = None use_cache: Optional[bool] = None output_attentions: Optional[bool] = None output_hidden_states: Optional[bool] = None return_dict: Optional[bool] = None training: Optional[bool] = False ) →
transformers.modeling_tf_outputs.TFBaseModelOutputWithPoolingAndCrossAttentions or `tuple(tf.Tensor)`

Parameters

- input_ids (`tf.Tensor` of shape `(batch_size, sequence_length)`) — 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?

- attention_mask (`tf.Tensor` of shape `(batch_size, sequence_length)`, 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?

- position_ids (`tf.Tensor` of shape `(batch_size, sequence_length)`, 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?

- head_mask (`tf.Tensor` 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 (`tf.Tensor` of shape `(batch_size, sequence_length, 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 ModelOutput instead of a plain tuple.
- encoder_hidden_states (`tf.Tensor` 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 (`tf.Tensor` 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[tf.Tensor]]` of length `config.n_layers`) — 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, defaults to `True`) — If set to `True`, `past_key_values` key value states are returned and can be used to speed up decoding (see `past_key_values`). Set to `False` during training, `True` during generation

Returns

transformers.modeling_tf_outputs.TFBaseModelOutputWithPoolingAndCrossAttentions or `tuple(tf.Tensor)`

A transformers.modeling_tf_outputs.TFBaseModelOutputWithPoolingAndCrossAttentions or a tuple of `tf.Tensor` (if `return_dict=False` is passed or when `config.return_dict=False`) comprising various elements depending on the configuration (EsmConfig) and inputs.

- last_hidden_state (`tf.Tensor` of shape `(batch_size, sequence_length, hidden_size)`) — Sequence of hidden-states at the output of the last layer of the model.

- pooler_output (`tf.Tensor` of shape `(batch_size, hidden_size)`) — Last layer hidden-state of the first token of the sequence (classification token) further processed by a Linear layer and a Tanh activation function. The Linear layer weights are trained from the next sentence prediction (classification) objective during pretraining.

  This output is usually not a good summary of the semantic content of the input, you’re often better with averaging or pooling the sequence of hidden-states for the whole input sequence.

- past_key_values (`List[tf.Tensor]`, optional, returned when `use_cache=True` is passed or when `config.use_cache=True`) — List of `tf.Tensor` of length `config.n_layers`, with each tensor of shape `(2, batch_size, num_heads, sequence_length, embed_size_per_head)`).

  Contains pre-computed hidden-states (key and values in the attention blocks) that can be used (see `past_key_values` input) to speed up sequential decoding.

- hidden_states (`tuple(tf.Tensor)`, optional, returned when `output_hidden_states=True` is passed or when `config.output_hidden_states=True`) — Tuple of `tf.Tensor` (one for the output of the embeddings + one for the output of each layer) of shape `(batch_size, sequence_length, hidden_size)`.

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

- attentions (`tuple(tf.Tensor)`, optional, returned when `output_attentions=True` is passed or when `config.output_attentions=True`) — Tuple of `tf.Tensor` (one for each layer) of shape `(batch_size, num_heads, sequence_length, sequence_length)`.

  Attentions weights after the attention softmax, used to compute the weighted average in the self-attention heads.

- cross_attentions (`tuple(tf.Tensor)`, optional, returned when `output_attentions=True` is passed or when `config.output_attentions=True`) — Tuple of `tf.Tensor` (one for each layer) of shape `(batch_size, num_heads, sequence_length, sequence_length)`.

  Attentions weights of the decoder’s cross-attention layer, after the attention softmax, used to compute the weighted average in the cross-attention heads.

The TFEsmModel forward method, overrides the `__call__` special method.

Although the recipe for forward pass needs to be defined within this function, one should call the `Module` instance afterwards instead of this since the former takes care of running the pre and post processing steps while the latter silently ignores them.

Example:

    >>> from transformers import AutoTokenizer, TFEsmModel
    >>> import tensorflow as tf

    >>> tokenizer = AutoTokenizer.from_pretrained("facebook/esm2_t6_8M_UR50D")
    >>> model = TFEsmModel.from_pretrained("facebook/esm2_t6_8M_UR50D")

    >>> inputs = tokenizer("Hello, my dog is cute", return_tensors="tf")
    >>> outputs = model(inputs)

    >>> last_hidden_states = outputs.last_hidden_state

##
TFEsmForMaskedLM

###
class transformers.TFEsmForMaskedLM

< source >

( config )

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 from_pretrained() method to load the model weights.

ESM Model with a `language modeling` head on top.

This model inherits from TFPreTrainedModel. 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 Keras Model subclass. Use it as a regular Keras model and refer to the TF/Keras documentation for all matters related to general usage and behavior.

####
call

< source >

( input_ids: TFModelInputType | None = None attention_mask: np.ndarray | tf.Tensor | None = None position_ids: np.ndarray | tf.Tensor | None = None head_mask: np.ndarray | tf.Tensor | None = None inputs_embeds: np.ndarray | tf.Tensor | None = None encoder_hidden_states: np.ndarray | tf.Tensor | None = None encoder_attention_mask: np.ndarray | tf.Tensor | None = None labels: np.ndarray | tf.Tensor | None = None output_attentions: Optional[bool] = None output_hidden_states: Optional[bool] = None return_dict: Optional[bool] = None training: bool = False ) →
transformers.modeling_tf_outputs.TFMaskedLMOutput or `tuple(tf.Tensor)`

Parameters

- input_ids (`tf.Tensor` of shape `(batch_size, sequence_length)`) — 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?

- attention_mask (`tf.Tensor` of shape `(batch_size, sequence_length)`, 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?

- position_ids (`tf.Tensor` of shape `(batch_size, sequence_length)`, 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?

- head_mask (`tf.Tensor` 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 (`tf.Tensor` of shape `(batch_size, sequence_length, 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 ModelOutput instead of a plain tuple.
- labels (`tf.Tensor` 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.

Returns

transformers.modeling_tf_outputs.TFMaskedLMOutput or `tuple(tf.Tensor)`

A transformers.modeling_tf_outputs.TFMaskedLMOutput or a tuple of `tf.Tensor` (if `return_dict=False` is passed or when `config.return_dict=False`) comprising various elements depending on the configuration (EsmConfig) and inputs.

- loss (`tf.Tensor` of shape `(n,)`, optional, where n is the number of non-masked labels, returned when `labels` is provided) — Masked language modeling (MLM) loss.

- logits (`tf.Tensor` of shape `(batch_size, sequence_length, config.vocab_size)`) — Prediction scores of the language modeling head (scores for each vocabulary token before SoftMax).

- hidden_states (`tuple(tf.Tensor)`, optional, returned when `output_hidden_states=True` is passed or when `config.output_hidden_states=True`) — Tuple of `tf.Tensor` (one for the output of the embeddings + one for the output of each layer) of shape `(batch_size, sequence_length, hidden_size)`.

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

- attentions (`tuple(tf.Tensor)`, optional, returned when `output_attentions=True` is passed or when `config.output_attentions=True`) — Tuple of `tf.Tensor` (one for each layer) of shape `(batch_size, num_heads, sequence_length, sequence_length)`.

  Attentions weights after the attention softmax, used to compute the weighted average in the self-attention heads.

The TFEsmForMaskedLM forward method, overrides the `__call__` special method.

Although the recipe for forward pass needs to be defined within this function, one should call the `Module` instance afterwards instead of this since the former takes care of running the pre and post processing steps while the latter silently ignores them.

Example:

    >>> from transformers import AutoTokenizer, TFEsmForMaskedLM
    >>> import tensorflow as tf

    >>> tokenizer = AutoTokenizer.from_pretrained("facebook/esm2_t6_8M_UR50D")
    >>> model = TFEsmForMaskedLM.from_pretrained("facebook/esm2_t6_8M_UR50D")

    >>> inputs = tokenizer("The capital of France is <mask>.", return_tensors="tf")
    >>> logits = model(**inputs).logits

    >>> # retrieve index of <mask>
    >>> mask_token_index = tf.where((inputs.input_ids == tokenizer.mask_token_id)[0])
    >>> selected_logits = tf.gather_nd(logits[0], indices=mask_token_index)

    >>> predicted_token_id = tf.math.argmax(selected_logits, axis=-1)

    >>> labels = tokenizer("The capital of France is Paris.", return_tensors="tf")["input_ids"]
    >>> # mask labels of non-<mask> tokens
    >>> labels = tf.where(inputs.input_ids == tokenizer.mask_token_id, labels, -100)

    >>> outputs = model(**inputs, labels=labels)

##
TFEsmForSequenceClassification

###
class transformers.TFEsmForSequenceClassification

< source >

( config )

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 from_pretrained() method to load the model weights.

ESM Model transformer with a sequence classification/regression head on top (a linear layer on top of the pooled output) e.g. for GLUE tasks.

This model inherits from TFPreTrainedModel. 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 Keras Model subclass. Use it as a regular Keras model and refer to the TF/Keras documentation for all matters related to general usage and behavior.

####
call

< source >

( input_ids: TFModelInputType | None = None attention_mask: np.ndarray | tf.Tensor | None = None position_ids: np.ndarray | tf.Tensor | None = None head_mask: np.ndarray | tf.Tensor | None = None inputs_embeds: np.ndarray | tf.Tensor | None = None labels: np.ndarray | tf.Tensor | None = None output_attentions: Optional[bool] = None output_hidden_states: Optional[bool] = None return_dict: Optional[bool] = None training: bool = False ) →
transformers.modeling_tf_outputs.TFSequenceClassifierOutput or `tuple(tf.Tensor)`

Parameters

- input_ids (`tf.Tensor` of shape `(batch_size, sequence_length)`) — 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?

- attention_mask (`tf.Tensor` of shape `(batch_size, sequence_length)`, 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?

- position_ids (`tf.Tensor` of shape `(batch_size, sequence_length)`, 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?

- head_mask (`tf.Tensor` 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 (`tf.Tensor` of shape `(batch_size, sequence_length, 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 ModelOutput instead of a plain tuple.
- labels (`tf.Tensor` 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).

Returns

transformers.modeling_tf_outputs.TFSequenceClassifierOutput or `tuple(tf.Tensor)`

A transformers.modeling_tf_outputs.TFSequenceClassifierOutput or a tuple of `tf.Tensor` (if `return_dict=False` is passed or when `config.return_dict=False`) comprising various elements depending on the configuration (EsmConfig) and inputs.

- loss (`tf.Tensor` of shape `(batch_size, )`, optional, returned when `labels` is provided) — Classification (or regression if config.num_labels==1) loss.

- logits (`tf.Tensor` of shape `(batch_size, config.num_labels)`) — Classification (or regression if config.num_labels==1) scores (before SoftMax).

- hidden_states (`tuple(tf.Tensor)`, optional, returned when `output_hidden_states=True` is passed or when `config.output_hidden_states=True`) — Tuple of `tf.Tensor` (one for the output of the embeddings + one for the output of each layer) of shape `(batch_size, sequence_length, hidden_size)`.

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

- attentions (`tuple(tf.Tensor)`, optional, returned when `output_attentions=True` is passed or when `config.output_attentions=True`) — Tuple of `tf.Tensor` (one for each layer) of shape `(batch_size, num_heads, sequence_length, sequence_length)`.

  Attentions weights after the attention softmax, used to compute the weighted average in the self-attention heads.

The TFEsmForSequenceClassification forward method, overrides the `__call__` special method.

Although the recipe for forward pass needs to be defined within this function, one should call the `Module` instance afterwards instead of this since the former takes care of running the pre and post processing steps while the latter silently ignores them.

Example:

    >>> from transformers import AutoTokenizer, TFEsmForSequenceClassification
    >>> import tensorflow as tf

    >>> tokenizer = AutoTokenizer.from_pretrained("facebook/esm2_t6_8M_UR50D")
    >>> model = TFEsmForSequenceClassification.from_pretrained("facebook/esm2_t6_8M_UR50D")

    >>> inputs = tokenizer("Hello, my dog is cute", return_tensors="tf")

    >>> logits = model(**inputs).logits

    >>> predicted_class_id = int(tf.math.argmax(logits, axis=-1)[0])

    >>> # To train a model on `num_labels` classes, you can pass `num_labels=num_labels` to `.from_pretrained(...)`
    >>> num_labels = len(model.config.id2label)
    >>> model = TFEsmForSequenceClassification.from_pretrained("facebook/esm2_t6_8M_UR50D", num_labels=num_labels)

    >>> labels = tf.constant(1)
    >>> loss = model(**inputs, labels=labels).loss

##
TFEsmForTokenClassification

###
class transformers.TFEsmForTokenClassification

< source >

( config )

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 from_pretrained() method to load the model weights.

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.

This model inherits from TFPreTrainedModel. 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 Keras Model subclass. Use it as a regular Keras model and refer to the TF/Keras documentation for all matters related to general usage and behavior.

####
call

< source >

( input_ids: TFModelInputType | None = None attention_mask: np.ndarray | tf.Tensor | None = None position_ids: np.ndarray | tf.Tensor | None = None head_mask: np.ndarray | tf.Tensor | None = None inputs_embeds: np.ndarray | tf.Tensor | None = None labels: np.ndarray | tf.Tensor | None = None output_attentions: Optional[bool] = None output_hidden_states: Optional[bool] = None return_dict: Optional[bool] = None training: bool = False ) →
transformers.modeling_tf_outputs.TFTokenClassifierOutput or `tuple(tf.Tensor)`

Parameters

- input_ids (`tf.Tensor` of shape `(batch_size, sequence_length)`) — 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?

- attention_mask (`tf.Tensor` of shape `(batch_size, sequence_length)`, 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?

- position_ids (`tf.Tensor` of shape `(batch_size, sequence_length)`, 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?

- head_mask (`tf.Tensor` 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 (`tf.Tensor` of shape `(batch_size, sequence_length, 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 ModelOutput instead of a plain tuple.
- labels (`tf.Tensor` of shape `(batch_size, sequence_length)`, optional) — Labels for computing the token classification loss. Indices should be in `[0, ..., config.num_labels - 1]`.

Returns

transformers.modeling_tf_outputs.TFTokenClassifierOutput or `tuple(tf.Tensor)`

A transformers.modeling_tf_outputs.TFTokenClassifierOutput or a tuple of `tf.Tensor` (if `return_dict=False` is passed or when `config.return_dict=False`) comprising various elements depending on the configuration (EsmConfig) and inputs.

- loss (`tf.Tensor` of shape `(n,)`, optional, where n is the number of unmasked labels, returned when `labels` is provided) — Classification loss.

- logits (`tf.Tensor` of shape `(batch_size, sequence_length, config.num_labels)`) — Classification scores (before SoftMax).

- hidden_states (`tuple(tf.Tensor)`, optional, returned when `output_hidden_states=True` is passed or when `config.output_hidden_states=True`) — Tuple of `tf.Tensor` (one for the output of the embeddings + one for the output of each layer) of shape `(batch_size, sequence_length, hidden_size)`.

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

- attentions (`tuple(tf.Tensor)`, optional, returned when `output_attentions=True` is passed or when `config.output_attentions=True`) — Tuple of `tf.Tensor` (one for each layer) of shape `(batch_size, num_heads, sequence_length, sequence_length)`.

  Attentions weights after the attention softmax, used to compute the weighted average in the self-attention heads.

The TFEsmForTokenClassification forward method, overrides the `__call__` special method.

Although the recipe for forward pass needs to be defined within this function, one should call the `Module` instance afterwards instead of this since the former takes care of running the pre and post processing steps while the latter silently ignores them.

Example:

    >>> from transformers import AutoTokenizer, TFEsmForTokenClassification
    >>> import tensorflow as tf

    >>> tokenizer = AutoTokenizer.from_pretrained("facebook/esm2_t6_8M_UR50D")
    >>> model = TFEsmForTokenClassification.from_pretrained("facebook/esm2_t6_8M_UR50D")

    >>> inputs = tokenizer(
    ...     "HuggingFace is a company based in Paris and New York", add_special_tokens=False, return_tensors="tf"
    ... )

    >>> logits = model(**inputs).logits
    >>> predicted_token_class_ids = tf.math.argmax(logits, axis=-1)

    >>> # Note that tokens are classified rather then input words which means that
    >>> # there might be more predicted token classes than words.
    >>> # Multiple token classes might account for the same word
    >>> predicted_tokens_classes = [model.config.id2label[t] for t in predicted_token_class_ids[0].numpy().tolist()]

    >>> labels = predicted_token_class_ids
    >>> loss = tf.math.reduce_mean(model(**inputs, labels=labels).loss)

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