LinkBERT: A Knowledgeable Language Model Pretrained with Document Links

This repo provides the model, code & data of our paper: LinkBERT: Pretraining Language Models with Document Links (ACL 2022). [PDF] [HuggingFace Models]

Overview

LinkBERT is a new pretrained language model (improvement of BERT) that captures document links such as hyperlinks and citation links to include knowledge that spans across multiple documents. Specifically, it was pretrained by feeding linked documents into the same language model context, besides using a single document as in BERT.

LinkBERT can be used as a drop-in replacement for BERT. It achieves better performance for general language understanding tasks (e.g. text classification), and is also particularly effective for knowledge-intensive tasks (e.g. question answering) and cross-document tasks (e.g. reading comprehension, document retrieval).

1. Pretrained Models

We release the pretrained LinkBERT (-base and -large sizes) for both the general domain and biomedical domain. These models have the same format as the HuggingFace BERT models, and you can easily switch them with LinkBERT models.

Model	Size	Domain	Pretraining Corpus	Download Link (🤗 HuggingFace)
LinkBERT-base	110M parameters	General	Wikipedia with hyperlinks	michiyasunaga/LinkBERT-base
LinkBERT-large	340M parameters	General	Wikipedia with hyperlinks	michiyasunaga/LinkBERT-large
BioLinkBERT-base	110M parameters	Biomedicine	PubMed with citation links	michiyasunaga/BioLinkBERT-base
BioLinkBERT-large	340M parameters	Biomedicine	PubMed with citation links	michiyasunaga/BioLinkBERT-large

To use these models in 🤗 Transformers:

from transformers import AutoTokenizer, AutoModel
tokenizer = AutoTokenizer.from_pretrained('michiyasunaga/LinkBERT-large')
model = AutoModel.from_pretrained('michiyasunaga/LinkBERT-large')
inputs = tokenizer("Hello, my dog is cute", return_tensors="pt")
outputs = model(**inputs)

To fine-tune the models, see Section 2 & 3 below. When fine-tuned on downstream tasks, LinkBERT achieves the following results.
General benchmarks (MRQA and GLUE):

	HotpotQA	TriviaQA	SearchQA	NaturalQ	NewsQA	SQuAD	GLUE
	F1	F1	F1	F1	F1	F1	Avg score
BERT-base	76.0	70.3	74.2	76.5	65.7	88.7	79.2
LinkBERT-base	78.2	73.9	76.8	78.3	69.3	90.1	79.6
BERT-large	78.1	73.7	78.3	79.0	70.9	91.1	80.7
LinkBERT-large	80.8	78.2	80.5	81.0	72.6	92.7	81.1

Biomedical benchmarks (BLURB, MedQA, MMLU, etc): BioLinkBERT attains new state-of-the-art 😊

	BLURB score	PubMedQA	BioASQ	MedQA-USMLE
PubmedBERT-base	81.10	55.8	87.5	38.1
BioLinkBERT-base	83.39	70.2	91.4	40.0
BioLinkBERT-large	84.30	72.2	94.8	44.6

	MMLU-professional medicine
GPT-3 (175 params)	38.7
UnifiedQA (11B params)	43.2
BioLinkBERT-large (340M params)	50.7

2. Set up environment and data

Environment

Run the following commands to create a conda environment:

conda create -n linkbert python=3.8
source activate linkbert
pip install torch==1.10.1+cu113 -f https://download.pytorch.org/whl/cu113/torch_stable.html
pip install transformers==4.9.1 datasets==1.11.0 fairscale==0.4.0 wandb sklearn seqeval

Data

You can download the preprocessed datasets on which we evaluated LinkBERT from [here]. Simply download this zip file and unzip it. This includes:

• MRQA question answering datasets (HotpotQA, TriviaQA, NaturalQuestions, SearchQA, NewsQA, SQuAD)
• BLURB biomedical NLP datasets (PubMedQA, BioASQ, HoC, Chemprot, PICO, etc.)
• MedQA-USMLE biomedical reasoning dataset.
• MMLU-professional medicine reasoning dataset.

They are all preprocessed in the HuggingFace dataset format.

If you would like to preprocess the raw data from scratch, you can take the following steps:

• First download the raw datasets from the original sources by following instructions in scripts/download_raw_data.sh
• Then run the preprocessing scripts scripts/preprocess_{mrqa,blurb,medqa,mmlu}.py.

3. Fine-tune LinkBERT

Change the working directory to src/, and follow the instructions below for each dataset.

MRQA

To fine-tune for the MRQA datasets (HotpotQA, TriviaQA, NaturalQuestions, SearchQA, NewsQA, SQuAD), run commands listed in run_examples_mrqa_linkbert-{base,large}.sh.

BLURB

To fine-tune for the BLURB biomedial datasets (PubMedQA, BioASQ, HoC, Chemprot, PICO, etc.), run commands listed in run_examples_blurb_biolinkbert-{base,large}.sh.

MedQA & MMLU

To fine-tune for the MedQA-USMLE dataset, run commands listed in run_examples_medqa_biolinkbert-{base,large}.sh.

To evaluate the fine-tuned model additionally on MMLU-professional medicine, run the commands listed at the bottom of run_examples_medqa_biolinkbert-large.sh.

Reproducibility

We also provide Codalab worksheet, on which we record our experiments. You may find it useful for replicating the experiments using the same model, code, data, and environment.

Citation

If you find our work helpful, please cite the following:

@InProceedings{yasunaga2022linkbert,
  author =  {Michihiro Yasunaga and Jure Leskovec and Percy Liang},
  title =   {LinkBERT: Pretraining Language Models with Document Links},
  year =    {2022},  
  booktitle = {Association for Computational Linguistics (ACL)},  
}