SUMIN/HuggingFace_transformer
1
0
Fork 0
Code Issues Pull Requests Actions 7 Packages Projects Releases Wiki Activity

Add BioGPT (#20420)

Browse Source 
* biogpt initial commit

* updated init

* fix faster decoding with use_cache

* 1. fix input_ids and input_embeds with correct device
2. added _keys_to_ignore_on_load_missing
3. updated prepare_inputs_for_generation

* add activation_dropout and scale_embedding

* replace fsmt attention with bart attention

* added test

* run make fix-copies

* doc init and fix build

* updated README with proper information

* 1. added tips to docs
2. updated BioGptTokenizer func

* 1. added tokenizer test
2. refactor tokenizer

* make fixup

* add biogpt fairseq to hf converter

* updated layer names more
similar to original checkpoints

* config update doc string and set defaults

* added "#copied" from bart model and
updated doc strings

* enable model_input_names in tokenizer

* 1.  positionalembedding depending on attention_mask
2. added attention mask to prepare for generation

* added test to verify past and generation

* BioGptLMHeadModel -> BioGptForCausalLM

* fix typo

* tokenization and test
Copyright and updated assertion

* updated Copyright and
one func at time in line

* Copyright updates and
minor doc fix

* replace assertion with ValueError

* rm extra space

* added code syntax

* revert cmnt position change

* add tokenizer to auto

* updated doc string

* tokenizer doc string update

* biogpt hub model update to microsoft/biogpt

* make fixup

* rm cmnt to fix flake8 5.0.4 vs 6 error
This commit is contained in:
Kamal Raj Kanakarajan
2022-12-05 20:42:03 +05:30
committed by GitHub
parent 91182e3a70
commit 13e736685a
23 changed files with 2189 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
docs/source/en/_toctree.yml
View File

@@ -209,6 +209,8 @@
title: BigBird
- local: model_doc/bigbird_pegasus
title: BigBirdPegasus
- local: model_doc/biogpt
title: BioGpt
- local: model_doc/blenderbot
title: Blenderbot
- local: model_doc/blenderbot-small

2
docs/source/en/index.mdx
View File

@@ -60,6 +60,7 @@ The documentation is organized into five sections:
1. **[BERTweet](model_doc/bertweet)** (from VinAI Research) released with the paper [BERTweet: A pre-trained language model for English Tweets](https://aclanthology.org/2020.emnlp-demos.2/) by Dat Quoc Nguyen, Thanh Vu and Anh Tuan Nguyen.
1. **[BigBird-Pegasus](model_doc/bigbird_pegasus)** (from Google Research) released with the paper [Big Bird: Transformers for Longer Sequences](https://arxiv.org/abs/2007.14062) by Manzil Zaheer, Guru Guruganesh, Avinava Dubey, Joshua Ainslie, Chris Alberti, Santiago Ontanon, Philip Pham, Anirudh Ravula, Qifan Wang, Li Yang, Amr Ahmed.
1. **[BigBird-RoBERTa](model_doc/big_bird)** (from Google Research) released with the paper [Big Bird: Transformers for Longer Sequences](https://arxiv.org/abs/2007.14062) by Manzil Zaheer, Guru Guruganesh, Avinava Dubey, Joshua Ainslie, Chris Alberti, Santiago Ontanon, Philip Pham, Anirudh Ravula, Qifan Wang, Li Yang, Amr Ahmed.
1. **[BioGpt](model_doc/biogpt)** (from Microsoft Research AI4Science) released with the paper [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.
1. **[Blenderbot](model_doc/blenderbot)** (from Facebook) released with the paper [Recipes for building an open-domain chatbot](https://arxiv.org/abs/2004.13637) by Stephen Roller, Emily Dinan, Naman Goyal, Da Ju, Mary Williamson, Yinhan Liu, Jing Xu, Myle Ott, Kurt Shuster, Eric M. Smith, Y-Lan Boureau, Jason Weston.
1. **[BlenderbotSmall](model_doc/blenderbot-small)** (from Facebook) released with the paper [Recipes for building an open-domain chatbot](https://arxiv.org/abs/2004.13637) by Stephen Roller, Emily Dinan, Naman Goyal, Da Ju, Mary Williamson, Yinhan Liu, Jing Xu, Myle Ott, Kurt Shuster, Eric M. Smith, Y-Lan Boureau, Jason Weston.
1. **[BLOOM](model_doc/bloom)** (from BigScience workshop) released by the [BigScience Workshop](https://bigscience.huggingface.co/).
@@ -229,6 +230,7 @@ Flax), PyTorch, and/or TensorFlow.
| Bert Generation | ✅ | ❌ | ✅ | ❌ | ❌ |
| BigBird | ✅ | ✅ | ✅ | ❌ | ✅ |
| BigBird-Pegasus | ❌ | ❌ | ✅ | ❌ | ❌ |
| BioGpt | ✅ | ❌ | ✅ | ❌ | ❌ |
| Blenderbot | ✅ | ✅ | ✅ | ✅ | ✅ |
| BlenderbotSmall | ✅ | ✅ | ✅ | ✅ | ✅ |
| BLOOM | ❌ | ✅ | ✅ | ❌ | ❌ |

52
docs/source/en/model_doc/biogpt.mdx Normal file
View File

@@ -0,0 +1,52 @@
<!--Copyright 2022 The HuggingFace Team. All rights reserved.
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with
the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on
an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the
specific language governing permissions and limitations under the License.
-->
# 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).
## BioGptConfig
[[autodoc]] BioGptConfig
## BioGptTokenizer
[[autodoc]] BioGptTokenizer
- save_vocabulary
## BioGptModel
[[autodoc]] BioGptModel
- forward
## BioGptForCausalLM
[[autodoc]] BioGptForCausalLM
- forward