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---
license: apache-2.0
language: en
datasets:
- pubmed
tags:
- bert
- exbert
- linkbert
- biolinkbert
- feature-extraction
- fill-mask
- question-answering
- text-classification
- token-classification
widget:
- text: "Sunitinib is a tyrosine kinase inhibitor"
---
## BioLinkBERT-base
BioLinkBERT-base model pretrained on [PubMed](https://pubmed.ncbi.nlm.nih.gov/) abstracts along with citation link information. It is introduced in the paper [LinkBERT: Pretraining Language Models with Document Links (ACL 2022)](https://arxiv.org/abs/2203.15827). The code and data are available in [this repository](https://github.com/michiyasunaga/LinkBERT).
This model achieves state-of-the-art performance on several biomedical NLP benchmarks such as [BLURB](https://microsoft.github.io/BLURB/) and [MedQA-USMLE](https://github.com/jind11/MedQA).
## Model description
LinkBERT is a transformer encoder (BERT-like) model pretrained on a large corpus of documents. It is an improvement of BERT that newly 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 a single document.
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).
## Intended uses & limitations
The model can be used by fine-tuning on a downstream task, such as question answering, sequence classification, and token classification.
You can also use the raw model for feature extraction (i.e. obtaining embeddings for input text).
### How to use
To use the model to get the features of a given text in PyTorch:
```python
from transformers import AutoTokenizer, AutoModel
tokenizer = AutoTokenizer.from_pretrained('michiyasunaga/BioLinkBERT-base')
model = AutoModel.from_pretrained('michiyasunaga/BioLinkBERT-base')
inputs = tokenizer("Sunitinib is a tyrosine kinase inhibitor", return_tensors="pt")
outputs = model(**inputs)
last_hidden_states = outputs.last_hidden_state
```
For fine-tuning, you can use [this repository](https://github.com/michiyasunaga/LinkBERT) or follow any other BERT fine-tuning codebases.
## Evaluation results
When fine-tuned on downstream tasks, LinkBERT achieves the following results.
**Biomedical benchmarks ([BLURB](https://microsoft.github.io/BLURB/), [MedQA](https://github.com/jind11/MedQA), [MMLU](https://github.com/hendrycks/test), 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** |
## Citation
If you find LinkBERT useful in your project, please cite the following:
```bibtex
@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)},
}
```
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