# BioGPT

[BioGPT](https://huggingface.co/papers/2210.10341) is a generative Transformer model based on [GPT-2](./gpt2) and pretrained on 15 million PubMed abstracts. It is designed for biomedical language tasks.

You can find all the original BioGPT checkpoints under the [Microsoft](https://huggingface.co/microsoft?search_models=biogpt) organization.

> [!TIP]
> Click on the BioGPT models in the right sidebar for more examples of how to apply BioGPT to different language tasks.

The example below demonstrates how to generate biomedical text with [Pipeline](/docs/transformers/v5.6.2/en/main_classes/pipelines#transformers.Pipeline), [AutoModel](/docs/transformers/v5.6.2/en/model_doc/auto#transformers.AutoModel), and also from the command line.

```py
import torch
from transformers import pipeline

generator = pipeline(
    task="text-generation",
    model="microsoft/biogpt",
    dtype=torch.float16,
    device=0,
)
result = generator("Ibuprofen is best used for", truncation=True, max_length=50, do_sample=True)[0]["generated_text"]
print(result)
```

```py
import torch
from transformers import AutoModelForCausalLM, AutoTokenizer

tokenizer = AutoTokenizer.from_pretrained("microsoft/biogpt")
model = AutoModelForCausalLM.from_pretrained(
    "microsoft/biogpt",
    dtype=torch.float16,
    device_map="auto",
    attn_implementation="sdpa"
)

input_text = "Ibuprofen is best used for"
inputs = tokenizer(input_text, return_tensors="pt").to(model.device)

with torch.no_grad():
    generated_ids = model.generate(**inputs, max_length=50)

output = tokenizer.decode(generated_ids[0], skip_special_tokens=True)
print(output)
```

Quantization reduces the memory burden of large models by representing the weights in a lower precision. Refer to the [Quantization](../quantization/overview) overview for more available quantization backends.

The example below uses [bitsandbytes](../quantization/bitsandbytes) to only quantize the weights to 4-bit precision.

```py
import torch
from transformers import AutoTokenizer, AutoModelForCausalLM, BitsAndBytesConfig

bnb_config = BitsAndBytesConfig(
    load_in_4bit=True,
    bnb_4bit_quant_type="nf4",
    bnb_4bit_compute_dtype=torch.bfloat16,
    bnb_4bit_use_double_quant=True
)

tokenizer = AutoTokenizer.from_pretrained("microsoft/BioGPT-Large")
model = AutoModelForCausalLM.from_pretrained(
    "microsoft/BioGPT-Large",
    quantization_config=bnb_config,
    dtype=torch.bfloat16,
    device_map="auto"
)

input_text = "Ibuprofen is best used for"
inputs = tokenizer(input_text, return_tensors="pt").to(model.device)
with torch.no_grad():
    generated_ids = model.generate(**inputs, max_length=50)
output = tokenizer.decode(generated_ids[0], skip_special_tokens=True)
print(output)
```

## Notes

- Pad inputs on the right because BioGPT uses absolute position embeddings.
- BioGPT can reuse previously computed key-value attention pairs. Access this feature with the [past_key_values](https://huggingface.co/docs/transformers/main/en/model_doc/biogpt#transformers.BioGptModel.forward.past_key_values) parameter in `BioGPTModel.forward`.

   ```py
   from transformers import AutoModelForCausalLM

   model = AutoModelForCausalLM.from_pretrained(
      "microsoft/biogpt",
      attn_implementation="eager"
   )

## BioGptConfig[[transformers.BioGptConfig]]

#### transformers.BioGptConfig[[transformers.BioGptConfig]]

[Source](https://github.com/huggingface/transformers/blob/v5.6.2/src/transformers/models/biogpt/configuration_biogpt.py#L24)

This is the configuration class to store the configuration of a BioGptModel. It is used to instantiate a 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 [microsoft/biogpt](https://huggingface.co/microsoft/biogpt)

Configuration objects inherit from [PreTrainedConfig](/docs/transformers/v5.6.2/en/main_classes/configuration#transformers.PreTrainedConfig) and can be used to control the model outputs. Read the
documentation from [PreTrainedConfig](/docs/transformers/v5.6.2/en/main_classes/configuration#transformers.PreTrainedConfig) for more information.

Example:

```python
>>> 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
```

**Parameters:**

vocab_size (`int`, *optional*, defaults to `42384`) : Vocabulary size of the model. Defines the number of different tokens that can be represented by the `input_ids`.

hidden_size (`int`, *optional*, defaults to `1024`) : Dimension of the hidden representations.

num_hidden_layers (`int`, *optional*, defaults to `24`) : Number of hidden layers in the Transformer decoder.

num_attention_heads (`int`, *optional*, defaults to `16`) : Number of attention heads for each attention layer in the Transformer decoder.

intermediate_size (`int`, *optional*, defaults to `4096`) : Dimension of the MLP representations.

hidden_act (`str`, *optional*, defaults to `gelu`) : The non-linear activation function (function or string) in the decoder. For example, `"gelu"`, `"relu"`, `"silu"`, etc.

hidden_dropout_prob (`Union[float, int]`, *optional*, defaults to `0.1`) : The dropout probability for all fully connected layers in the embeddings, encoder, and pooler.

attention_probs_dropout_prob (`Union[float, int]`, *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.

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`) : Whether to scale embeddings by dividing 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` or when the model is a decoder-only generative model.

layerdrop (`Union[float, int]`, *optional*, defaults to `0.0`) : The LayerDrop probability. See the [LayerDrop paper](see https://huggingface.co/papers/1909.11556) for more details.

activation_dropout (`Union[float, int]`, *optional*, defaults to `0.0`) : The dropout ratio for activations inside the fully connected layer.

pad_token_id (`int`, *optional*, defaults to `1`) : Token id used for padding in the vocabulary.

bos_token_id (`int`, *optional*, defaults to `0`) : Token id used for beginning-of-stream in the vocabulary.

eos_token_id (`Union[int, list[int]]`, *optional*, defaults to `2`) : Token id used for end-of-stream in the vocabulary.

tie_word_embeddings (`bool`, *optional*, defaults to `True`) : Whether to tie weight embeddings according to model's `tied_weights_keys` mapping.

## BioGptTokenizer[[transformers.BioGptTokenizer]]

#### transformers.BioGptTokenizer[[transformers.BioGptTokenizer]]

[Source](https://github.com/huggingface/transformers/blob/v5.6.2/src/transformers/models/biogpt/tokenization_biogpt.py#L44)

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

This tokenizer inherits from [PreTrainedTokenizer](/docs/transformers/v5.6.2/en/main_classes/tokenizer#transformers.PythonBackend) which contains most of the main methods. Users should refer to
this superclass for more information regarding those methods.

save_vocabularytransformers.BioGptTokenizer.save_vocabularyhttps://github.com/huggingface/transformers/blob/v5.6.2/src/transformers/models/biogpt/tokenization_biogpt.py#L282[{"name": "save_directory", "val": ": str"}, {"name": "filename_prefix", "val": ": str | None = None"}]

**Parameters:**

vocab_file (`str`) : Path to the vocabulary file.

merges_file (`str`) : Merges file.

unk_token (`str`, *optional*, defaults to `""`) : 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 `""`) : 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 `""`) : 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 `""`) : 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 `""`) : The token used for padding, for example when batching sequences of different lengths.

## BioGptModel[[transformers.BioGptModel]]

#### transformers.BioGptModel[[transformers.BioGptModel]]

[Source](https://github.com/huggingface/transformers/blob/v5.6.2/src/transformers/models/biogpt/modeling_biogpt.py#L321)

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

This model inherits from [PreTrainedModel](/docs/transformers/v5.6.2/en/main_classes/model#transformers.PreTrainedModel). Check the superclass documentation for the generic methods the
library implements for all its model (such as downloading or saving, resizing the input embeddings, pruning heads
etc.)

This model is also a PyTorch [torch.nn.Module](https://pytorch.org/docs/stable/nn.html#torch.nn.Module) subclass.
Use it as a regular PyTorch Module and refer to the PyTorch documentation for all matter related to general usage
and behavior.

forwardtransformers.BioGptModel.forwardhttps://github.com/huggingface/transformers/blob/v5.6.2/src/transformers/models/biogpt/modeling_biogpt.py#L343[{"name": "input_ids", "val": ": torch.LongTensor | None = None"}, {"name": "attention_mask", "val": ": torch.FloatTensor | None = None"}, {"name": "inputs_embeds", "val": ": torch.FloatTensor | None = None"}, {"name": "past_key_values", "val": ": transformers.cache_utils.Cache | None = None"}, {"name": "use_cache", "val": ": bool | None = None"}, {"name": "position_ids", "val": ": torch.LongTensor | None = None"}, {"name": "**kwargs", "val": ": typing_extensions.Unpack[transformers.utils.generic.TransformersKwargs]"}]- **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](/docs/transformers/v5.6.2/en/model_doc/auto#transformers.AutoTokenizer). See [PreTrainedTokenizer.encode()](/docs/transformers/v5.6.2/en/internal/tokenization_utils#transformers.PreTrainedTokenizerBase.encode) and
  [PreTrainedTokenizer.__call__()](/docs/transformers/v5.6.2/en/internal/tokenization_utils#transformers.PreTrainedTokenizerBase.__call__) for details.

  [What are input IDs?](../glossary#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?](../glossary#attention-mask)
- **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** (`~cache_utils.Cache`, *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`.

  Only [Cache](/docs/transformers/v5.6.2/en/internal/generation_utils#transformers.Cache) instance is allowed as input, see our [kv cache guide](https://huggingface.co/docs/transformers/en/kv_cache).
  If no `past_key_values` are passed, [DynamicCache](/docs/transformers/v5.6.2/en/internal/generation_utils#transformers.DynamicCache) will be initialized by default.

  The model will output the same cache format that is fed as input.

  If `past_key_values` are used, the user is expected to input only unprocessed `input_ids` (those that don't
  have their past key value states given to this model) of shape `(batch_size, unprocessed_length)` 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`).
- **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?](../glossary#position-ids)0[BaseModelOutputWithPastAndCrossAttentions](/docs/transformers/v5.6.2/en/main_classes/output#transformers.modeling_outputs.BaseModelOutputWithPastAndCrossAttentions) or `tuple(torch.FloatTensor)`A [BaseModelOutputWithPastAndCrossAttentions](/docs/transformers/v5.6.2/en/main_classes/output#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](/docs/transformers/v5.6.2/en/model_doc/biogpt#transformers.BioGptConfig)) and inputs.
The [BioGptModel](/docs/transformers/v5.6.2/en/model_doc/biogpt#transformers.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.

- **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** (`Cache`, *optional*, returned when `use_cache=True` is passed or when `config.use_cache=True`) -- It is a [Cache](/docs/transformers/v5.6.2/en/internal/generation_utils#transformers.Cache) instance. For more details, see our [kv cache guide](https://huggingface.co/docs/transformers/en/kv_cache).

  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.

**Parameters:**

config ([BioGptConfig](/docs/transformers/v5.6.2/en/model_doc/biogpt#transformers.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()](/docs/transformers/v5.6.2/en/main_classes/model#transformers.PreTrainedModel.from_pretrained) method to load the model weights.

**Returns:**

`[BaseModelOutputWithPastAndCrossAttentions](/docs/transformers/v5.6.2/en/main_classes/output#transformers.modeling_outputs.BaseModelOutputWithPastAndCrossAttentions) or `tuple(torch.FloatTensor)``

A [BaseModelOutputWithPastAndCrossAttentions](/docs/transformers/v5.6.2/en/main_classes/output#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](/docs/transformers/v5.6.2/en/model_doc/biogpt#transformers.BioGptConfig)) and inputs.

## BioGptForCausalLM[[transformers.BioGptForCausalLM]]

#### transformers.BioGptForCausalLM[[transformers.BioGptForCausalLM]]

[Source](https://github.com/huggingface/transformers/blob/v5.6.2/src/transformers/models/biogpt/modeling_biogpt.py#L420)

BioGPT Model with a `language modeling` head on top for CLM fine-tuning.

This model inherits from [PreTrainedModel](/docs/transformers/v5.6.2/en/main_classes/model#transformers.PreTrainedModel). Check the superclass documentation for the generic methods the
library implements for all its model (such as downloading or saving, resizing the input embeddings, pruning heads
etc.)

This model is also a PyTorch [torch.nn.Module](https://pytorch.org/docs/stable/nn.html#torch.nn.Module) subclass.
Use it as a regular PyTorch Module and refer to the PyTorch documentation for all matter related to general usage
and behavior.

forwardtransformers.BioGptForCausalLM.forwardhttps://github.com/huggingface/transformers/blob/v5.6.2/src/transformers/models/biogpt/modeling_biogpt.py#L438[{"name": "input_ids", "val": ": torch.LongTensor | None = None"}, {"name": "attention_mask", "val": ": torch.FloatTensor | None = None"}, {"name": "inputs_embeds", "val": ": torch.FloatTensor | None = None"}, {"name": "past_key_values", "val": ": transformers.cache_utils.Cache | None = None"}, {"name": "labels", "val": ": torch.LongTensor | None = None"}, {"name": "use_cache", "val": ": bool | None = None"}, {"name": "position_ids", "val": ": torch.LongTensor | None = None"}, {"name": "logits_to_keep", "val": ": int | torch.Tensor = 0"}, {"name": "**kwargs", "val": ": typing_extensions.Unpack[transformers.utils.generic.TransformersKwargs]"}]- **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](/docs/transformers/v5.6.2/en/model_doc/auto#transformers.AutoTokenizer). See [PreTrainedTokenizer.encode()](/docs/transformers/v5.6.2/en/internal/tokenization_utils#transformers.PreTrainedTokenizerBase.encode) and
  [PreTrainedTokenizer.__call__()](/docs/transformers/v5.6.2/en/internal/tokenization_utils#transformers.PreTrainedTokenizerBase.__call__) for details.

  [What are input IDs?](../glossary#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?](../glossary#attention-mask)
- **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** (`~cache_utils.Cache`, *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`.

  Only [Cache](/docs/transformers/v5.6.2/en/internal/generation_utils#transformers.Cache) instance is allowed as input, see our [kv cache guide](https://huggingface.co/docs/transformers/en/kv_cache).
  If no `past_key_values` are passed, [DynamicCache](/docs/transformers/v5.6.2/en/internal/generation_utils#transformers.DynamicCache) will be initialized by default.

  The model will output the same cache format that is fed as input.

  If `past_key_values` are used, the user is expected to input only unprocessed `input_ids` (those that don't
  have their past key value states given to this model) of shape `(batch_size, unprocessed_length)` instead of all `input_ids`
  of shape `(batch_size, sequence_length)`.
- **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]`
- **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`).
- **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?](../glossary#position-ids)
- **logits_to_keep** (`Union[int, torch.Tensor]`, *optional*, defaults to `0`) --
  If an `int`, compute logits for the last `logits_to_keep` tokens. If `0`, calculate logits for all
  `input_ids` (special case). Only last token logits are needed for generation, and calculating them only for that
  token can save memory, which becomes pretty significant for long sequences or large vocabulary size.
  If a `torch.Tensor`, must be 1D corresponding to the indices to keep in the sequence length dimension.
  This is useful when using packed tensor format (single dimension for batch and sequence length).0[CausalLMOutputWithCrossAttentions](/docs/transformers/v5.6.2/en/main_classes/output#transformers.modeling_outputs.CausalLMOutputWithCrossAttentions) or `tuple(torch.FloatTensor)`A [CausalLMOutputWithCrossAttentions](/docs/transformers/v5.6.2/en/main_classes/output#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](/docs/transformers/v5.6.2/en/model_doc/biogpt#transformers.BioGptConfig)) and inputs.
The [BioGptForCausalLM](/docs/transformers/v5.6.2/en/model_doc/biogpt#transformers.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.

- **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** (`Cache`, *optional*, returned when `use_cache=True` is passed or when `config.use_cache=True`) -- It is a [Cache](/docs/transformers/v5.6.2/en/internal/generation_utils#transformers.Cache) instance. For more details, see our [kv cache guide](https://huggingface.co/docs/transformers/en/kv_cache).

  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.

Example:

```python
```

**Parameters:**

config ([BioGptForCausalLM](/docs/transformers/v5.6.2/en/model_doc/biogpt#transformers.BioGptForCausalLM)) : 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()](/docs/transformers/v5.6.2/en/main_classes/model#transformers.PreTrainedModel.from_pretrained) method to load the model weights.

**Returns:**

`[CausalLMOutputWithCrossAttentions](/docs/transformers/v5.6.2/en/main_classes/output#transformers.modeling_outputs.CausalLMOutputWithCrossAttentions) or `tuple(torch.FloatTensor)``

A [CausalLMOutputWithCrossAttentions](/docs/transformers/v5.6.2/en/main_classes/output#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](/docs/transformers/v5.6.2/en/model_doc/biogpt#transformers.BioGptConfig)) and inputs.

## BioGptForTokenClassification[[transformers.BioGptForTokenClassification]]

#### transformers.BioGptForTokenClassification[[transformers.BioGptForTokenClassification]]

[Source](https://github.com/huggingface/transformers/blob/v5.6.2/src/transformers/models/biogpt/modeling_biogpt.py#L487)

The Biogpt 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](/docs/transformers/v5.6.2/en/main_classes/model#transformers.PreTrainedModel). Check the superclass documentation for the generic methods the
library implements for all its model (such as downloading or saving, resizing the input embeddings, pruning heads
etc.)

This model is also a PyTorch [torch.nn.Module](https://pytorch.org/docs/stable/nn.html#torch.nn.Module) subclass.
Use it as a regular PyTorch Module and refer to the PyTorch documentation for all matter related to general usage
and behavior.

forwardtransformers.BioGptForTokenClassification.forwardhttps://github.com/huggingface/transformers/blob/v5.6.2/src/transformers/models/biogpt/modeling_biogpt.py#L502[{"name": "input_ids", "val": ": torch.LongTensor | None = None"}, {"name": "token_type_ids", "val": ": torch.LongTensor | None = None"}, {"name": "attention_mask", "val": ": torch.FloatTensor | None = None"}, {"name": "past_key_values", "val": ": transformers.cache_utils.Cache | None = None"}, {"name": "inputs_embeds", "val": ": torch.FloatTensor | None = None"}, {"name": "labels", "val": ": torch.LongTensor | None = None"}, {"name": "use_cache", "val": ": bool | None = None"}, {"name": "position_ids", "val": ": torch.LongTensor | None = None"}, {"name": "**kwargs", "val": ""}]- **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](/docs/transformers/v5.6.2/en/model_doc/auto#transformers.AutoTokenizer). See [PreTrainedTokenizer.encode()](/docs/transformers/v5.6.2/en/internal/tokenization_utils#transformers.PreTrainedTokenizerBase.encode) and
  [PreTrainedTokenizer.__call__()](/docs/transformers/v5.6.2/en/internal/tokenization_utils#transformers.PreTrainedTokenizerBase.__call__) for details.

  [What are input IDs?](../glossary#input-ids)
- **token_type_ids** (`torch.LongTensor` of shape `(batch_size, sequence_length)`, *optional*) --
  Segment token indices to indicate first and second portions of the inputs. Indices are selected in `[0, 1]`:

  - 0 corresponds to a *sentence A* token,
  - 1 corresponds to a *sentence B* token.

  [What are token type IDs?](../glossary#token-type-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?](../glossary#attention-mask)
- **past_key_values** (`~cache_utils.Cache`, *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`.

  Only [Cache](/docs/transformers/v5.6.2/en/internal/generation_utils#transformers.Cache) instance is allowed as input, see our [kv cache guide](https://huggingface.co/docs/transformers/en/kv_cache).
  If no `past_key_values` are passed, [DynamicCache](/docs/transformers/v5.6.2/en/internal/generation_utils#transformers.DynamicCache) will be initialized by default.

  The model will output the same cache format that is fed as input.

  If `past_key_values` are used, the user is expected to input only unprocessed `input_ids` (those that don't
  have their past key value states given to this model) of shape `(batch_size, unprocessed_length)` instead of all `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.
- **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).
- **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`).
- **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?](../glossary#position-ids)0[TokenClassifierOutput](/docs/transformers/v5.6.2/en/main_classes/output#transformers.modeling_outputs.TokenClassifierOutput) or `tuple(torch.FloatTensor)`A [TokenClassifierOutput](/docs/transformers/v5.6.2/en/main_classes/output#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 ([BioGptConfig](/docs/transformers/v5.6.2/en/model_doc/biogpt#transformers.BioGptConfig)) and inputs.
The [BioGptForTokenClassification](/docs/transformers/v5.6.2/en/model_doc/biogpt#transformers.BioGptForTokenClassification) 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.

- **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.

Example:

```python
>>> from transformers import AutoTokenizer, BioGptForTokenClassification
>>> import torch

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

>>> 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)
...
```

**Parameters:**

config ([BioGptForTokenClassification](/docs/transformers/v5.6.2/en/model_doc/biogpt#transformers.BioGptForTokenClassification)) : 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()](/docs/transformers/v5.6.2/en/main_classes/model#transformers.PreTrainedModel.from_pretrained) method to load the model weights.

**Returns:**

`[TokenClassifierOutput](/docs/transformers/v5.6.2/en/main_classes/output#transformers.modeling_outputs.TokenClassifierOutput) or `tuple(torch.FloatTensor)``

A [TokenClassifierOutput](/docs/transformers/v5.6.2/en/main_classes/output#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 ([BioGptConfig](/docs/transformers/v5.6.2/en/model_doc/biogpt#transformers.BioGptConfig)) and inputs.

## BioGptForSequenceClassification[[transformers.BioGptForSequenceClassification]]

#### transformers.BioGptForSequenceClassification[[transformers.BioGptForSequenceClassification]]

[Source](https://github.com/huggingface/transformers/blob/v5.6.2/src/transformers/models/biogpt/modeling_biogpt.py#L571)

The BioGpt Model transformer with a sequence classification head on top (linear layer).

[BioGptForSequenceClassification](/docs/transformers/v5.6.2/en/model_doc/biogpt#transformers.BioGptForSequenceClassification) uses the last token in order to do the classification, as other causal models
(e.g. GPT-2) do.

Since it does classification on the last token, it is required to know the position of the last token. If a
`pad_token_id` is defined in the configuration, it finds the last token that is not a padding token in each row. If
no `pad_token_id` is defined, it simply takes the last value in each row of the batch. Since it cannot guess the
padding tokens when `inputs_embeds` are passed instead of `input_ids`, it does the same (take the last value in
each row of the batch).

This model inherits from [PreTrainedModel](/docs/transformers/v5.6.2/en/main_classes/model#transformers.PreTrainedModel). Check the superclass documentation for the generic methods the
library implements for all its model (such as downloading or saving, resizing the input embeddings, pruning heads
etc.)

This model is also a PyTorch [torch.nn.Module](https://pytorch.org/docs/stable/nn.html#torch.nn.Module) subclass.
Use it as a regular PyTorch Module and refer to the PyTorch documentation for all matter related to general usage
and behavior.

forwardtransformers.BioGptForSequenceClassification.forwardhttps://github.com/huggingface/transformers/blob/v5.6.2/src/transformers/models/biogpt/modeling_biogpt.py#L581[{"name": "input_ids", "val": ": torch.LongTensor | None = None"}, {"name": "attention_mask", "val": ": torch.FloatTensor | None = None"}, {"name": "past_key_values", "val": ": transformers.cache_utils.Cache | None = None"}, {"name": "inputs_embeds", "val": ": torch.FloatTensor | None = None"}, {"name": "labels", "val": ": torch.LongTensor | None = None"}, {"name": "use_cache", "val": ": bool | None = None"}, {"name": "position_ids", "val": ": torch.LongTensor | None = None"}, {"name": "logits_to_keep", "val": ": int | torch.Tensor = 0"}, {"name": "**kwargs", "val": ""}]- **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](/docs/transformers/v5.6.2/en/model_doc/auto#transformers.AutoTokenizer). See [PreTrainedTokenizer.encode()](/docs/transformers/v5.6.2/en/internal/tokenization_utils#transformers.PreTrainedTokenizerBase.encode) and
  [PreTrainedTokenizer.__call__()](/docs/transformers/v5.6.2/en/internal/tokenization_utils#transformers.PreTrainedTokenizerBase.__call__) for details.

  [What are input IDs?](../glossary#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?](../glossary#attention-mask)
- **past_key_values** (`~cache_utils.Cache`, *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`.

  Only [Cache](/docs/transformers/v5.6.2/en/internal/generation_utils#transformers.Cache) instance is allowed as input, see our [kv cache guide](https://huggingface.co/docs/transformers/en/kv_cache).
  If no `past_key_values` are passed, [DynamicCache](/docs/transformers/v5.6.2/en/internal/generation_utils#transformers.DynamicCache) will be initialized by default.

  The model will output the same cache format that is fed as input.

  If `past_key_values` are used, the user is expected to input only unprocessed `input_ids` (those that don't
  have their past key value states given to this model) of shape `(batch_size, unprocessed_length)` instead of all `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.
- **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).
- **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`).
- **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?](../glossary#position-ids)
- **logits_to_keep** (`Union[int, torch.Tensor]`, *optional*, defaults to `0`) --
  If an `int`, compute logits for the last `logits_to_keep` tokens. If `0`, calculate logits for all
  `input_ids` (special case). Only last token logits are needed for generation, and calculating them only for that
  token can save memory, which becomes pretty significant for long sequences or large vocabulary size.
  If a `torch.Tensor`, must be 1D corresponding to the indices to keep in the sequence length dimension.
  This is useful when using packed tensor format (single dimension for batch and sequence length).0`SequenceClassifierOutputWithPast` or `tuple(torch.FloatTensor)`A `SequenceClassifierOutputWithPast` 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](/docs/transformers/v5.6.2/en/model_doc/biogpt#transformers.BioGptConfig)) and inputs.
The [BioGptForSequenceClassification](/docs/transformers/v5.6.2/en/model_doc/biogpt#transformers.BioGptForSequenceClassification) 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.

- **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).
- **past_key_values** (`Cache`, *optional*, returned when `use_cache=True` is passed or when `config.use_cache=True`) -- It is a [Cache](/docs/transformers/v5.6.2/en/internal/generation_utils#transformers.Cache) instance. For more details, see our [kv cache guide](https://huggingface.co/docs/transformers/en/kv_cache).

  Contains pre-computed hidden-states (key and values in the self-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.

Example of single-label classification:

```python
>>> import torch
>>> from transformers import AutoTokenizer, BioGptForSequenceClassification

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

>>> 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 = BioGptForSequenceClassification.from_pretrained("microsoft/biogpt", num_labels=num_labels)

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

Example of multi-label classification:

```python
>>> import torch
>>> from transformers import AutoTokenizer, BioGptForSequenceClassification

>>> tokenizer = AutoTokenizer.from_pretrained("microsoft/biogpt")
>>> model = BioGptForSequenceClassification.from_pretrained("microsoft/biogpt", 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 = BioGptForSequenceClassification.from_pretrained(
...     "microsoft/biogpt", 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
```

**Parameters:**

config ([BioGptConfig](/docs/transformers/v5.6.2/en/model_doc/biogpt#transformers.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()](/docs/transformers/v5.6.2/en/main_classes/model#transformers.PreTrainedModel.from_pretrained) method to load the model weights.

**Returns:**

``SequenceClassifierOutputWithPast` or `tuple(torch.FloatTensor)``

A `SequenceClassifierOutputWithPast` 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](/docs/transformers/v5.6.2/en/model_doc/biogpt#transformers.BioGptConfig)) and inputs.