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BioGPT

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BioGPT

Overview

The BioGPT model was proposed in BioGPT: generative pre-trained transformer for biomedical text generation and mining by Renqian Luo, Liai Sun, Yingce Xia, Tao Qin, Sheng Zhang, Hoifung Poon and Tie-Yan Liu. BioGPT is a domain-specific generative pre-trained Transformer language model for biomedical text generation and mining. BioGPT follows the Transformer language model backbone, and is pre-trained on 15M PubMed abstracts from scratch.

The abstract from the paper is the following:

Pre-trained language models have attracted increasing attention in the biomedical domain, inspired by their great success in the general natural language domain. Among the two main branches of pre-trained language models in the general language domain, i.e. BERT (and its variants) and GPT (and its variants), the first one has been extensively studied in the biomedical domain, such as BioBERT and PubMedBERT. While they have achieved great success on a variety of discriminative downstream biomedical tasks, the lack of generation ability constrains their application scope. In this paper, we propose BioGPT, a domain-specific generative Transformer language model pre-trained on large-scale biomedical literature. We evaluate BioGPT on six biomedical natural language processing tasks and demonstrate that our model outperforms previous models on most tasks. Especially, we get 44.98%, 38.42% and 40.76% F1 score on BC5CDR, KD-DTI and DDI end-to-end relation extraction tasks, respectively, and 78.2% accuracy on PubMedQA, creating a new record. Our case study on text generation further demonstrates the advantage of BioGPT on biomedical literature to generate fluent descriptions for biomedical terms.

Tips:

  • BioGPT is a model with absolute position embeddings so it’s usually advised to pad the inputs on the right rather than the left.
  • BioGPT was trained with a causal language modeling (CLM) objective and is therefore powerful at predicting the next token in a sequence. Leveraging this feature allows BioGPT to generate syntactically coherent text as it can be observed in the run_generation.py example script.
  • The model can take the past_key_values (for PyTorch) as input, which is the previously computed key/value attention pairs. Using this (past_key_values or past) value prevents the model from re-computing pre-computed values in the context of text generation. For PyTorch, see past_key_values argument of the BioGptForCausalLM.forward() method for more information on its usage.

This model was contributed by kamalkraj. The original code can be found here.

Documentation resources

BioGptConfig

class transformers.BioGptConfig

< >

( vocab_size = 42384 hidden_size = 1024 num_hidden_layers = 24 num_attention_heads = 16 intermediate_size = 4096 hidden_act = 'gelu' hidden_dropout_prob = 0.1 attention_probs_dropout_prob = 0.1 max_position_embeddings = 1024 initializer_range = 0.02 layer_norm_eps = 1e-12 scale_embedding = True use_cache = True layerdrop = 0.0 activation_dropout = 0.0 pad_token_id = 1 bos_token_id = 0 eos_token_id = 2 **kwargs )

Parameters

  • vocab_size (int, optional, defaults to 42384) — Vocabulary size of the BioGPT model. Defines the number of different tokens that can be represented by the inputs_ids passed when calling BioGptModel.
  • hidden_size (int, optional, defaults to 1024) — Dimension of the encoder layers and the pooler layer.
  • num_hidden_layers (int, optional, defaults to 24) — Number of hidden layers in the Transformer encoder.
  • num_attention_heads (int, optional, defaults to 16) — Number of attention heads for each attention layer in the Transformer encoder.
  • intermediate_size (int, optional, defaults to 4096) — Dimension of the “intermediate” (i.e., feed-forward) layer in the Transformer encoder.
  • hidden_act (str or function, optional, defaults to "gelu") — The non-linear activation function (function or string) in the encoder and pooler. If string, "gelu", "relu", "selu" and "gelu_new" are supported.
  • hidden_dropout_prob (float, optional, defaults to 0.1) — The dropout probabilitiy 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 1024) — 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.
  • scale_embedding (bool, optional, defaults to True) — Scale embeddings by diving by sqrt(d_model).
  • 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.
  • layerdrop (float, optional, defaults to 0.0) — Please refer to the paper about LayerDrop: https://arxiv.org/abs/1909.11556 for further details
  • activation_dropout (float, optional, defaults to 0.0) — The dropout ratio for activations inside the fully connected layer.
  • pad_token_id (int, optional, defaults to 1) — Padding token id.
  • bos_token_id (int, optional, defaults to 0) — Beginning of stream token id.
  • eos_token_id (int, optional, defaults to 2) — End of stream token id. Example —

This is the configuration class to store the configuration of a BioGptModel. It is used to instantiate an BioGPT 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 BioGPT microsoft/biogpt architecture.

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

>>> from transformers import BioGptModel, BioGptConfig

>>> # Initializing a BioGPT microsoft/biogpt style configuration
>>> configuration = BioGptConfig()

>>> # Initializing a model from the microsoft/biogpt style configuration
>>> model = BioGptModel(configuration)

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

BioGptTokenizer

class transformers.BioGptTokenizer

< >

( vocab_file merges_file unk_token = '<unk>' bos_token = '<s>' eos_token = '</s>' sep_token = '</s>' pad_token = '<pad>' **kwargs )

Parameters

  • vocab_file (str) — Path to the vocabulary file.
  • merges_file (str) — Merges file.
  • unk_token (str, optional, defaults to "<unk>") — The unknown token. A token that is not in the vocabulary cannot be converted to an ID and is set to be this token instead.
  • bos_token (str, optional, defaults to "<s>") — The beginning of sequence token that was used during pretraining. Can be used a sequence classifier token.

    When building a sequence using special tokens, this is not the token that is used for the beginning of sequence. The token used is the cls_token.
  • eos_token (str, optional, defaults to "</s>") — The end of sequence token.

    When building a sequence using special tokens, this is not the token that is used for the end of sequence. The token used is the sep_token.
  • sep_token (str, optional, defaults to "</s>") — The separator token, which is used when building a sequence from multiple sequences, e.g. two sequences for sequence classification or for a text and a question for question answering. It is also used as the last token of a sequence built with special tokens.
  • pad_token (str, optional, defaults to "<pad>") — The token used for padding, for example when batching sequences of different lengths.

Construct an FAIRSEQ Transformer tokenizer. Moses tokenization followed by Byte-Pair Encoding.

This tokenizer inherits from PreTrainedTokenizer which contains most of the main methods. Users should refer to this superclass for more information regarding those methods.

save_vocabulary

< >

( save_directory: str filename_prefix: typing.Optional[str] = None )

BioGptModel

class transformers.BioGptModel

< >

( config: BioGptConfig )

Parameters

  • config (~BioGptConfig) — 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 BioGPT Model transformer outputting raw hidden-states without any specific head on top. This model is a PyTorch torch.nn.Module sub-class. Use it as a regular PyTorch Module and refer to the PyTorch documentation for all matter related to general usage and behavior.

forward

< >

( input_ids: typing.Optional[torch.LongTensor] = None attention_mask: typing.Optional[torch.FloatTensor] = None head_mask: typing.Optional[torch.FloatTensor] = None inputs_embeds: typing.Optional[torch.FloatTensor] = None past_key_values: typing.Optional[typing.Tuple[typing.Tuple[torch.Tensor]]] = 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.BaseModelOutputWithPastAndCrossAttentions or tuple(torch.FloatTensor)

Parameters

  • input_ids (torch.LongTensor 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.FloatTensor 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?

  • head_mask (torch.FloatTensor of shape (num_heads,) or (num_layers, num_heads), optional) — Mask to nullify selected heads of the self-attention modules. Mask values selected in [0, 1]:

    • 1 indicates the head is not masked,
    • 0 indicates the head is masked.
  • inputs_embeds (torch.FloatTensor of shape (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.
  • 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 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 in the cross-attention blocks) that can be used (see past_key_values input) to speed up sequential 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). 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.

  • 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.BaseModelOutputWithPastAndCrossAttentions or tuple(torch.FloatTensor)

A transformers.modeling_outputs.BaseModelOutputWithPastAndCrossAttentions 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 (BioGptConfig) 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.

    If past_key_values is used only the last hidden-state of the sequences of shape (batch_size, 1, hidden_size) is output.

  • 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.

  • 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.

The BioGptModel 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, BioGptModel
>>> import torch

>>> tokenizer = AutoTokenizer.from_pretrained("microsoft/biogpt")
>>> model = BioGptModel.from_pretrained("microsoft/biogpt")

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

>>> last_hidden_states = outputs.last_hidden_state

BioGptForCausalLM

class transformers.BioGptForCausalLM

< >

( config )

Parameters

  • config (~BioGptConfig) — 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.

BioGPT Model with a language modeling head on top for CLM fine-tuning. This model is a PyTorch torch.nn.Module sub-class. Use it as a regular PyTorch Module and refer to the PyTorch documentation for all matter related to general usage and behavior.

forward

< >

( input_ids: typing.Optional[torch.LongTensor] = None attention_mask: typing.Optional[torch.FloatTensor] = None head_mask: typing.Optional[torch.FloatTensor] = None inputs_embeds: typing.Optional[torch.FloatTensor] = None past_key_values: typing.Optional[typing.Tuple[typing.Tuple[torch.Tensor]]] = None labels: typing.Optional[torch.LongTensor] = 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.CausalLMOutputWithCrossAttentions or tuple(torch.FloatTensor)

Parameters

  • input_ids (torch.LongTensor 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.FloatTensor 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?

  • head_mask (torch.FloatTensor of shape (num_heads,) or (num_layers, num_heads), optional) — Mask to nullify selected heads of the self-attention modules. Mask values selected in [0, 1]:

    • 1 indicates the head is not masked,
    • 0 indicates the head is masked.
  • inputs_embeds (torch.FloatTensor of shape (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.
  • 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 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 in the cross-attention blocks) that can be used (see past_key_values input) to speed up sequential 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). 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.

  • 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.
  • labels (torch.LongTensor of shape (batch_size, sequence_length), optional) — Labels for language modeling. Note that the labels are shifted inside the model, i.e. you can set labels = input_ids Indices are selected in [-100, 0, ..., config.vocab_size] All labels set to -100 are ignored (masked), the loss is only computed for labels in [0, ..., config.vocab_size]

Returns

transformers.modeling_outputs.CausalLMOutputWithCrossAttentions or tuple(torch.FloatTensor)

A transformers.modeling_outputs.CausalLMOutputWithCrossAttentions 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 (BioGptConfig) and inputs.

  • loss (torch.FloatTensor of shape (1,), optional, returned when labels is provided) — Language modeling loss (for next-token prediction).

  • 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.

  • cross_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).

    Cross attentions weights 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 torch.FloatTensor tuples of length config.n_layers, with each tuple containing the cached key, value states of the self-attention and the cross-attention layers if model is used in encoder-decoder setting. Only relevant if config.is_decoder = True.

    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.

The BioGptForCausalLM 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:

>>> import torch
>>> from transformers import AutoTokenizer, BioGptForCausalLM

>>> tokenizer = AutoTokenizer.from_pretrained("microsoft/biogpt")
>>> model = BioGptForCausalLM.from_pretrained("microsoft/biogpt")

>>> inputs = tokenizer("Hello, my dog is cute", return_tensors="pt")
>>> outputs = model(**inputs, labels=inputs["input_ids"])
>>> loss = outputs.loss
>>> logits = outputs.logits
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