biogpt.md

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*This model was released on 2022-10-19 and added to Hugging Face Transformers on 2022-12-05.*

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# 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`], [`AutoModel`], and also from the command line.

<hfoptions id="usage">
<hfoption id="Pipeline">

```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)
```

</hfoption>
<hfoption id="AutoModel">

```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)
```

</hfoption>
<hfoption id="transformers CLI">

```bash
echo -e "Ibuprofen is best used for" | transformers run --task text-generation --model microsoft/biogpt --device 0
```

</hfoption>
</hfoptions>

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

[[autodoc]] BioGptConfig

## BioGptTokenizer

[[autodoc]] BioGptTokenizer
    - save_vocabulary

## BioGptModel

[[autodoc]] BioGptModel
    - forward

## BioGptForCausalLM

[[autodoc]] BioGptForCausalLM
    - forward

## BioGptForTokenClassification

[[autodoc]] BioGptForTokenClassification
    - forward

## BioGptForSequenceClassification

[[autodoc]] BioGptForSequenceClassification
    - forward