# What does this PR do?

This updates the top-level readme files say the project has been tested with Python 3.8+ (instead of 3.7+) and PyTorch 1.10+ (instead of 1.9+). Versions prior to those are no longer supported as of [v4.31.0](https://github.com/huggingface/transformers/releases/tag/v4.31.0). It also updates some other versions in those lists, that had become out of date earlier. The non-English readme files were less up to date than the English readme file `README.md`.

I allowed my editor to remove trailing whitespace, since it does not appear to have been intentional. Rendered Markdown does not appear changed. After editing all seven READMEs, running `make fix-copies` (required to pass CI) propagated this whitespace removal to (just) one of the `index.md` files, which is why that is also changed. However, I understand if whitespace removal may be viewed as best done separately; if requested, I'd be pleased to modify this PR to retain the trailing whitespace.

## Rationale

My reasoning is similar as the reasoning that was given for the previous update to these versions in #24307. As of [**v4.31.0**](https://github.com/huggingface/transformers/releases/tag/v4.31.0), 🤗 Transformers has dropped support for Python 3.7 (#24091) and for PyTorch 1.9 (#24080). Because of that:

- If the version ranges noted in the readme files are not changed, some users are likely to be mislead into expecting new releases of 🤗 Transformers to support those versions.
- A lesser issue is that the claim that this repository is tested on all those versions will gradually become inaccurate as further contributions are made to the repository, now that those versions are not supported.

## Before submitting

- [x] This PR fixes a typo or improves the docs (you can dismiss the other checks if that's the case).
- [x] Did you read the [contributor guideline](https://github.com/huggingface/transformers/blob/main/CONTRIBUTING.md#start-contributing-pull-requests), Pull Request section?
- [ ] Was this discussed/approved via a Github issue or the [forum](https://discuss.huggingface.co/)? Please add a link to it if that's the case.

<!-- I'm sure who, if anyone, I should ping for this. I may edit in a ping later.

## Who can review?

Anyone in the community is free to review the PR once the tests have passed. Feel free to tag
members/contributors who may be interested in your PR.

Your PR will be replied to more quickly if you can figure out the right person to tag with @

 If you know how to use git blame, that is the easiest way, otherwise, here is a rough guide of **who to tag**.
 Please tag fewer than 3 people.

Models:

- text models: @ArthurZucker and @younesbelkada
- vision models: @amyeroberts
- speech models: @sanchit-gandhi
- graph models: @clefourrier

Library:

- flax: @sanchit-gandhi
- generate: @gante
- pipelines: @Narsil
- tensorflow: @gante and @Rocketknight1
- tokenizers: @ArthurZucker
- trainer: @sgugger

Integrations:

- deepspeed: HF Trainer/Accelerate: @pacman100
- ray/raytune: @richardliaw, @amogkam

Documentation: @sgugger, @stevhliu and @MKhalusova

HF projects:

- accelerate: [different repo](https://github.com/huggingface/accelerate)
- datasets: [different repo](https://github.com/huggingface/datasets)
- diffusers: [different repo](https://github.com/huggingface/diffusers)
- rust tokenizers: [different repo](https://github.com/huggingface/tokenizers)

Maintained examples (not research project or legacy):

- Flax: @sanchit-gandhi
- PyTorch: @sgugger
- TensorFlow: @Rocketknight1

 -->

Update tested versions in READMEs. # What does this PR do?

This updates the top-level readme files say the project has been tested with Python 3.8+ (instead of 3.7+) and PyTorch 1.10+ (instead of 1.9+). Versions prior to those are no longer supported as of [v4.31.0](https://github.com/huggingface/transformers/releases/tag/v4.31.0). It also updates some other versions in those lists, that had become out of date earlier. The non-English readme files were less up to date than the English readme file `README.md`.

I allowed my editor to remove trailing whitespace, since it does not appear to have been intentional. Rendered Markdown does not appear changed. After editing all seven READMEs, running `make fix-copies` (required to pass CI) propagated this whitespace removal to (just) one of the `index.md` files, which is why that is also changed. However, I understand if whitespace removal may be viewed as best done separately; if requested, I'd be pleased to modify this PR to retain the trailing whitespace.

## Rationale

My reasoning is similar as the reasoning that was given for the previous update to these versions in #24307. As of [**v4.31.0**](https://github.com/huggingface/transformers/releases/tag/v4.31.0), 🤗 Transformers has dropped support for Python 3.7 (#24091) and for PyTorch 1.9 (#24080). Because of that:

- If the version ranges noted in the readme files are not changed, some users are likely to be mislead into expecting new releases of 🤗 Transformers to support those versions.
- A lesser issue is that the claim that this repository is tested on all those versions will gradually become inaccurate as further contributions are made to the repository, now that those versions are not supported.

## Before submitting

- [x] This PR fixes a typo or improves the docs (you can dismiss the other checks if that's the case).
- [x] Did you read the [contributor guideline](https://github.com/huggingface/transformers/blob/main/CONTRIBUTING.md#start-contributing-pull-requests), Pull Request section?
- [ ] Was this discussed/approved via a Github issue or the [forum](https://discuss.huggingface.co/)? Please add a link to it if that's the case.

<!-- I'm sure who, if anyone, I should ping for this. I may edit in a ping later.

## Who can review?

Anyone in the community is free to review the PR once the tests have passed. Feel free to tag
members/contributors who may be interested in your PR.

Your PR will be replied to more quickly if you can figure out the right person to tag with @

 If you know how to use git blame, that is the easiest way, otherwise, here is a rough guide of **who to tag**.
 Please tag fewer than 3 people.

Models:

- text models: @ArthurZucker and @younesbelkada
- vision models: @amyeroberts
- speech models: @sanchit-gandhi
- graph models: @clefourrier

Library:

- flax: @sanchit-gandhi
- generate: @gante
- pipelines: @Narsil
- tensorflow: @gante and @Rocketknight1
- tokenizers: @ArthurZucker
- trainer: @sgugger

Integrations:

- deepspeed: HF Trainer/Accelerate: @pacman100
- ray/raytune: @richardliaw, @amogkam

Documentation: @sgugger, @stevhliu and @MKhalusova

HF projects:

- accelerate: [different repo](https://github.com/huggingface/accelerate)
- datasets: [different repo](https://github.com/huggingface/datasets)
- diffusers: [different repo](https://github.com/huggingface/diffusers)
- rust tokenizers: [different repo](https://github.com/huggingface/tokenizers)

Maintained examples (not research project or legacy):

- Flax: @sanchit-gandhi
- PyTorch: @sgugger
- TensorFlow: @Rocketknight1

 -->

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rendered properly in your Markdown viewer.

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# BioGPT

## Overview

The BioGPT model was proposed in [BioGPT: generative pre-trained transformer for biomedical text generation and mining
](https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbac409/6713511?guestAccessKey=a66d9b5d-4f83-4017-bb52-405815c907b9) 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](https://huggingface.co/kamalkraj). The original code can be found [here](https://github.com/microsoft/BioGPT).

## Documentation resources

- [Causal language modeling task guide](../tasks/language_modeling)

## BioGptConfig

[[autodoc]] BioGptConfig


## BioGptTokenizer

[[autodoc]] BioGptTokenizer
    - save_vocabulary


## BioGptModel

[[autodoc]] BioGptModel
    - forward


## BioGptForCausalLM

[[autodoc]] BioGptForCausalLM
    - forward

    
## BioGptForTokenClassification

[[autodoc]] BioGptForTokenClassification
    - forward


## BioGptForSequenceClassification

[[autodoc]] BioGptForSequenceClassification
    - forward
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Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on
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⚠️ Note that this file is in Markdown but contain specific syntax for our doc-builder (similar to MDX) that may not be
rendered properly in your Markdown viewer.

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# BioGPT

## Overview

The BioGPT model was proposed in [BioGPT: generative pre-trained transformer for biomedical text generation and mining
](https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbac409/6713511?guestAccessKey=a66d9b5d-4f83-4017-bb52-405815c907b9) 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](https://huggingface.co/kamalkraj). The original code can be found [here](https://github.com/microsoft/BioGPT).

## Documentation resources

- [Causal language modeling task guide](../tasks/language_modeling)

## BioGptConfig

[[autodoc]] BioGptConfig


## BioGptTokenizer

[[autodoc]] BioGptTokenizer
    - save_vocabulary


## BioGptModel

[[autodoc]] BioGptModel
    - forward


## BioGptForCausalLM

[[autodoc]] BioGptForCausalLM
    - forward

    
## BioGptForTokenClassification

[[autodoc]] BioGptForTokenClassification
    - forward


## BioGptForSequenceClassification

[[autodoc]] BioGptForSequenceClassification
    - forward