ESM-2 outperforms all tested single-sequence protein language models across a range of structure prediction tasks, and enables atomic resolution structure prediction. It was released with the paper Language models of protein sequences at the scale of evolution enable accurate structure prediction by Zeming Lin, Halil Akin, Roshan Rao, Brian Hie, Zhongkai Zhu, Wenting Lu, Allan dos Santos Costa, Maryam Fazel-Zarandi, Tom Sercu, Sal Candido and Alexander Rives.
The abstract from “Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences” is
In the field of artificial intelligence, a combination of scale in data and model capacity enabled by unsupervised learning has led to major advances in representation learning and statistical generation. In the life sciences, the anticipated growth of sequencing promises unprecedented data on natural sequence diversity. Protein language modeling at the scale of evolution is a logical step toward predictive and generative artificial intelligence for biology. To this end, we use unsupervised learning to train a deep contextual language model on 86 billion amino acids across 250 million protein sequences spanning evolutionary diversity. The resulting model contains information about biological properties in its representations. The representations are learned from sequence data alone. The learned representation space has a multiscale organization reflecting structure from the level of biochemical properties of amino acids to remote homology of proteins. Information about secondary and tertiary structure is encoded in the representations and can be identified by linear projections. Representation learning produces features that generalize across a range of applications, enabling state-of-the-art supervised prediction of mutational effect and secondary structure and improving state-of-the-art features for long-range contact prediction.
The abstract from “Language models of protein sequences at the scale of evolution enable accurate structure prediction” is
Large language models have recently been shown to develop emergent capabilities with scale, going beyond simple pattern matching to perform higher level reasoning and generate lifelike images and text. While language models trained on protein sequences have been studied at a smaller scale, little is known about what they learn about biology as they are scaled up. In this work we train models up to 15 billion parameters, the largest language models of proteins to be evaluated to date. We find that as models are scaled they learn information enabling the prediction of the three-dimensional structure of a protein at the resolution of individual atoms. We present ESMFold for high accuracy end-to-end atomic level structure prediction directly from the individual sequence of a protein. ESMFold has similar accuracy to AlphaFold2 and RoseTTAFold for sequences with low perplexity that are well understood by the language model. ESMFold inference is an order of magnitude faster than AlphaFold2, enabling exploration of the structural space of metagenomic proteins in practical timescales.
Tips:
The original code can be found here and was was developed by the Fundamental AI Research team at Meta AI. This model was contributed to huggingface by jasonliu and Matt.
( 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_act = 'gelu' 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 classifier_dropout = None emb_layer_norm_before = None token_dropout = False **kwargs )
Parameters
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
.
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.
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.
int
, optional, defaults to 768) —
Dimensionality of the encoder layers and the pooler layer.
int
, optional, defaults to 12) —
Number of hidden layers in the Transformer encoder.
int
, optional, defaults to 12) —
Number of attention heads for each attention layer in the Transformer encoder.
int
, optional, defaults to 3072) —
Dimensionality of the “intermediate” (often named feed-forward) layer in the Transformer encoder.
str
or Callable
, optional, defaults to "gelu"
) —
The non-linear activation function (function or string) in the encoder and pooler. If string, "gelu"
,
"relu"
, "silu"
and "gelu_new"
are supported.
float
, optional, defaults to 0.1) —
The dropout probability for all fully connected layers in the embeddings, encoder, and pooler.
float
, optional, defaults to 0.1) —
The dropout ratio for the attention probabilities.
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).
float
, optional, defaults to 0.02) —
The standard deviation of the truncated_normal_initializer for initializing all weight matrices.
float
, optional, defaults to 1e-12) —
The epsilon used by the layer normalization layers.
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.).
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
.
float
, optional) —
The dropout ratio for the classification head.
bool
, optional) —
Whether to apply layer normalization after embeddings but before the main stem of the network.
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
esm-base-uncased 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 esm-base-uncased style configuration >>> configuration = EsmConfig()
>>> # Initializing a model from the configuration >>> model = ESMModel(configuration)
>>> # Accessing the model configuration >>> configuration = model.config
Constructs an ESM tokenizer.
( token_ids_0: typing.List[int] token_ids_1: typing.Optional[typing.List[int]] = None )
( 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
List[int]
) —
List of ids of the first sequence.
List[int]
, optional) —
List of ids of the second sequence.
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.
(
token_ids_0: typing.List[int]
token_ids_1: typing.Optional[typing.List[int]] = None
)
→
List[int]
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.
( config add_pooling_layer = True )
Parameters
The bare ESM Model transformer 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.
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 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.
(
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
torch.LongTensor
of shape ((batch_size, sequence_length))
) —
Indices of input sequence tokens in the vocabulary.
Indices can be obtained using EsmTokenizer. See PreTrainedTokenizer.encode() and PreTrainedTokenizer.call() for details.
torch.FloatTensor
of shape ((batch_size, sequence_length))
, optional) —
Mask to avoid performing attention on padding token indices. Mask values selected in [0, 1]
:
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.max_position_embeddings - 1]
.
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]
:
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.
bool
, optional) —
Whether or not to return the attentions tensors of all attention layers. See attentions
under returned
tensors for more detail.
bool
, optional) —
Whether or not to return the hidden states of all layers. See hidden_states
under returned tensors for
more detail.
bool
, optional) —
Whether or not to return a ModelOutput instead of a plain tuple.
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.
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]
:
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)
.
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
).
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 (tuple(tuple(torch.FloatTensor))
, optional, returned when use_cache=True
is passed or when config.use_cache=True
) — 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)
) and optionally if
config.is_encoder_decoder=True
2 additional tensors of shape (batch_size, num_heads, encoder_sequence_length, embed_size_per_head)
.
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.
Example:
>>> from transformers import EsmTokenizer, EsmModel
>>> import torch
>>> tokenizer = EsmTokenizer.from_pretrained("facebook/esm2_t6_8M_UR50D")
>>> model = EsmModel.from_pretrained("facebook/esm2_t6_8M_UR50D")
>>> inputs = tokenizer("Hello, my dog is cute", return_tensors="pt")
>>> outputs = model(**inputs)
>>> last_hidden_states = outputs.last_hidden_state
( config )
Parameters
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.
(
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
torch.LongTensor
of shape (batch_size, sequence_length)
) —
Indices of input sequence tokens in the vocabulary.
Indices can be obtained using EsmTokenizer. See PreTrainedTokenizer.encode() and PreTrainedTokenizer.call() for details.
torch.FloatTensor
of shape (batch_size, sequence_length)
, optional) —
Mask to avoid performing attention on padding token indices. Mask values selected in [0, 1]
:
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.max_position_embeddings - 1]
.
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]
:
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.
bool
, optional) —
Whether or not to return the attentions tensors of all attention layers. See attentions
under returned
tensors for more detail.
bool
, optional) —
Whether or not to return the hidden states of all layers. See hidden_states
under returned tensors for
more detail.
bool
, optional) —
Whether or not to return a ModelOutput instead of a plain tuple.
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]
Dict[str, any]
, optional, defaults to {}) —
Used to hide legacy arguments that have been deprecated.
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 EsmTokenizer, EsmForMaskedLM
>>> import torch
>>> tokenizer = EsmTokenizer.from_pretrained("facebook/esm2_t6_8M_UR50D")
>>> model = EsmForMaskedLM.from_pretrained("facebook/esm2_t6_8M_UR50D")
>>> 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)
( config )
Parameters
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.
(
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
torch.LongTensor
of shape (batch_size, sequence_length)
) —
Indices of input sequence tokens in the vocabulary.
Indices can be obtained using EsmTokenizer. See PreTrainedTokenizer.encode() and PreTrainedTokenizer.call() for details.
torch.FloatTensor
of shape (batch_size, sequence_length)
, optional) —
Mask to avoid performing attention on padding token indices. Mask values selected in [0, 1]
:
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.max_position_embeddings - 1]
.
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]
:
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.
bool
, optional) —
Whether or not to return the attentions tensors of all attention layers. See attentions
under returned
tensors for more detail.
bool
, optional) —
Whether or not to return the hidden states of all layers. See hidden_states
under returned tensors for
more detail.
bool
, optional) —
Whether or not to return a ModelOutput instead of a plain tuple.
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).
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 EsmTokenizer, EsmForSequenceClassification
>>> tokenizer = EsmTokenizer.from_pretrained("facebook/esm2_t6_8M_UR50D")
>>> model = EsmForSequenceClassification.from_pretrained("facebook/esm2_t6_8M_UR50D")
>>> 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/esm2_t6_8M_UR50D", 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 EsmTokenizer, EsmForSequenceClassification
>>> tokenizer = EsmTokenizer.from_pretrained("facebook/esm2_t6_8M_UR50D")
>>> model = EsmForSequenceClassification.from_pretrained("facebook/esm2_t6_8M_UR50D", 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_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/esm2_t6_8M_UR50D", num_labels=num_labels, problem_type="multi_label_classification"
... )
>>> labels = torch.nn.functional.one_hot(torch.tensor([predicted_class_id]), num_classes=num_labels).to(
... torch.float
... )
>>> loss = model(**inputs, labels=labels).loss
>>> loss.backward()
( config )
Parameters
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 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.
(
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
torch.LongTensor
of shape (batch_size, sequence_length)
) —
Indices of input sequence tokens in the vocabulary.
Indices can be obtained using EsmTokenizer. See PreTrainedTokenizer.encode() and PreTrainedTokenizer.call() for details.
torch.FloatTensor
of shape (batch_size, sequence_length)
, optional) —
Mask to avoid performing attention on padding token indices. Mask values selected in [0, 1]
:
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.max_position_embeddings - 1]
.
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]
:
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.
bool
, optional) —
Whether or not to return the attentions tensors of all attention layers. See attentions
under returned
tensors for more detail.
bool
, optional) —
Whether or not to return the hidden states of all layers. See hidden_states
under returned tensors for
more detail.
bool
, optional) —
Whether or not to return a ModelOutput instead of a plain tuple.
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]
.
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 EsmTokenizer, EsmForTokenClassification
>>> import torch
>>> tokenizer = EsmTokenizer.from_pretrained("facebook/esm2_t6_8M_UR50D")
>>> model = EsmForTokenClassification.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="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
( *args **kwargs )
Parameters
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.
(
input_ids: typing.Union[typing.List[tensorflow.python.framework.ops.Tensor], typing.List[numpy.ndarray], typing.List[tensorflow.python.keras.engine.keras_tensor.KerasTensor], typing.Dict[str, tensorflow.python.framework.ops.Tensor], typing.Dict[str, numpy.ndarray], typing.Dict[str, tensorflow.python.keras.engine.keras_tensor.KerasTensor], tensorflow.python.framework.ops.Tensor, numpy.ndarray, tensorflow.python.keras.engine.keras_tensor.KerasTensor, NoneType] = None
attention_mask: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
position_ids: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
head_mask: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
inputs_embeds: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
encoder_hidden_states: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
encoder_attention_mask: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
past_key_values: typing.Union[typing.Tuple[typing.Tuple[typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor]]], NoneType] = 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
training: typing.Optional[bool] = False
)
→
transformers.modeling_tf_outputs.TFBaseModelOutputWithPoolingAndCrossAttentions or tuple(tf.Tensor)
Parameters
tf.Tensor
of shape (batch_size, sequence_length)
) —
Indices of input sequence tokens in the vocabulary.
Indices can be obtained using EsmTokenizer. See PreTrainedTokenizer.encode() and PreTrainedTokenizer.call() for details.
tf.Tensor
of shape (batch_size, sequence_length)
, optional) —
Mask to avoid performing attention on padding token indices. Mask values selected in [0, 1]
:
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]
.
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]
:
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.
bool
, optional) —
Whether or not to return the attentions tensors of all attention layers. See attentions
under returned
tensors for more detail.
bool
, optional) —
Whether or not to return the hidden states of all layers. See hidden_states
under returned tensors for
more detail.
bool
, optional) —
Whether or not to return a ModelOutput instead of a plain tuple.
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.
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]
:
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)
.
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 EsmTokenizer, TFEsmModel
>>> import tensorflow as tf
>>> tokenizer = EsmTokenizer.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
( *args **kwargs )
Parameters
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.
(
input_ids: typing.Union[typing.List[tensorflow.python.framework.ops.Tensor], typing.List[numpy.ndarray], typing.List[tensorflow.python.keras.engine.keras_tensor.KerasTensor], typing.Dict[str, tensorflow.python.framework.ops.Tensor], typing.Dict[str, numpy.ndarray], typing.Dict[str, tensorflow.python.keras.engine.keras_tensor.KerasTensor], tensorflow.python.framework.ops.Tensor, numpy.ndarray, tensorflow.python.keras.engine.keras_tensor.KerasTensor, NoneType] = None
attention_mask: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
position_ids: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
head_mask: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
inputs_embeds: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
encoder_hidden_states: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
encoder_attention_mask: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
labels: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
output_attentions: typing.Optional[bool] = None
output_hidden_states: typing.Optional[bool] = None
return_dict: typing.Optional[bool] = None
training: bool = False
)
→
transformers.modeling_tf_outputs.TFMaskedLMOutput or tuple(tf.Tensor)
Parameters
tf.Tensor
of shape (batch_size, sequence_length)
) —
Indices of input sequence tokens in the vocabulary.
Indices can be obtained using EsmTokenizer. See PreTrainedTokenizer.encode() and PreTrainedTokenizer.call() for details.
tf.Tensor
of shape (batch_size, sequence_length)
, optional) —
Mask to avoid performing attention on padding token indices. Mask values selected in [0, 1]
:
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]
.
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]
:
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.
bool
, optional) —
Whether or not to return the attentions tensors of all attention layers. See attentions
under returned
tensors for more detail.
bool
, optional) —
Whether or not to return the hidden states of all layers. See hidden_states
under returned tensors for
more detail.
bool
, optional) —
Whether or not to return a ModelOutput instead of a plain tuple.
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]
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 EsmTokenizer, TFEsmForMaskedLM
>>> import tensorflow as tf
>>> tokenizer = EsmTokenizer.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)
>>> tokenizer.decode(predicted_token_id)
( *args **kwargs )
Parameters
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.
(
input_ids: typing.Union[typing.List[tensorflow.python.framework.ops.Tensor], typing.List[numpy.ndarray], typing.List[tensorflow.python.keras.engine.keras_tensor.KerasTensor], typing.Dict[str, tensorflow.python.framework.ops.Tensor], typing.Dict[str, numpy.ndarray], typing.Dict[str, tensorflow.python.keras.engine.keras_tensor.KerasTensor], tensorflow.python.framework.ops.Tensor, numpy.ndarray, tensorflow.python.keras.engine.keras_tensor.KerasTensor, NoneType] = None
attention_mask: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
position_ids: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
head_mask: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
inputs_embeds: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
labels: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
output_attentions: typing.Optional[bool] = None
output_hidden_states: typing.Optional[bool] = None
return_dict: typing.Optional[bool] = None
training: bool = False
)
→
transformers.modeling_tf_outputs.TFSequenceClassifierOutput or tuple(tf.Tensor)
Parameters
tf.Tensor
of shape (batch_size, sequence_length)
) —
Indices of input sequence tokens in the vocabulary.
Indices can be obtained using EsmTokenizer. See PreTrainedTokenizer.encode() and PreTrainedTokenizer.call() for details.
tf.Tensor
of shape (batch_size, sequence_length)
, optional) —
Mask to avoid performing attention on padding token indices. Mask values selected in [0, 1]
:
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]
.
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]
:
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.
bool
, optional) —
Whether or not to return the attentions tensors of all attention layers. See attentions
under returned
tensors for more detail.
bool
, optional) —
Whether or not to return the hidden states of all layers. See hidden_states
under returned tensors for
more detail.
bool
, optional) —
Whether or not to return a ModelOutput instead of a plain tuple.
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 EsmTokenizer, TFEsmForSequenceClassification
>>> import tensorflow as tf
>>> tokenizer = EsmTokenizer.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])
>>> 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 = TFEsmForSequenceClassification.from_pretrained("facebook/esm2_t6_8M_UR50D", num_labels=num_labels)
>>> labels = tf.constant(1)
>>> loss = model(**inputs, labels=labels).loss
>>> round(float(loss), 2)
( *args **kwargs )
Parameters
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.
(
input_ids: typing.Union[typing.List[tensorflow.python.framework.ops.Tensor], typing.List[numpy.ndarray], typing.List[tensorflow.python.keras.engine.keras_tensor.KerasTensor], typing.Dict[str, tensorflow.python.framework.ops.Tensor], typing.Dict[str, numpy.ndarray], typing.Dict[str, tensorflow.python.keras.engine.keras_tensor.KerasTensor], tensorflow.python.framework.ops.Tensor, numpy.ndarray, tensorflow.python.keras.engine.keras_tensor.KerasTensor, NoneType] = None
attention_mask: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
position_ids: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
head_mask: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
inputs_embeds: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
labels: typing.Union[numpy.ndarray, tensorflow.python.framework.ops.Tensor, NoneType] = None
output_attentions: typing.Optional[bool] = None
output_hidden_states: typing.Optional[bool] = None
return_dict: typing.Optional[bool] = None
training: bool = False
)
→
transformers.modeling_tf_outputs.TFTokenClassifierOutput or tuple(tf.Tensor)
Parameters
tf.Tensor
of shape (batch_size, sequence_length)
) —
Indices of input sequence tokens in the vocabulary.
Indices can be obtained using EsmTokenizer. See PreTrainedTokenizer.encode() and PreTrainedTokenizer.call() for details.
tf.Tensor
of shape (batch_size, sequence_length)
, optional) —
Mask to avoid performing attention on padding token indices. Mask values selected in [0, 1]
:
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]
.
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]
:
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.
bool
, optional) —
Whether or not to return the attentions tensors of all attention layers. See attentions
under returned
tensors for more detail.
bool
, optional) —
Whether or not to return the hidden states of all layers. See hidden_states
under returned tensors for
more detail.
bool
, optional) —
Whether or not to return a ModelOutput instead of a plain tuple.
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 EsmTokenizer, TFEsmForTokenClassification
>>> import tensorflow as tf
>>> tokenizer = EsmTokenizer.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()]
>>> predicted_tokens_classes