# How Important is Domain Specificity in Language Models and Instruction Finetuning for Biomedical Relation Extraction?

arXiv: https://arxiv.org/abs/2402.13470 · HTML: https://mlsanity.com/paper/2402.13470/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 31 of its 55 references that are in the map.
- First posted on arXiv 21 Feb 2024.

## Builds on (most cited first, 30 of 31)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [Training language models to follow instructions with human feedback](https://mlsanity.com/paper/2203.02155/) (2022)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [Llama 2: Open Foundation and Fine-Tuned Chat Models](https://mlsanity.com/paper/2307.09288/) (2023)
- [BART: Denoising Sequence-to-Sequence Pre-training for Natural Language Generation, Translation, and Comprehension](https://mlsanity.com/paper/1910.13461/) (2019)
- [Deep reinforcement learning from human preferences](https://mlsanity.com/paper/1706.03741/) (2017)
- [Finetuned Language Models Are Zero-Shot Learners](https://mlsanity.com/paper/2109.01652/) (2021)
- [Scaling Instruction-Finetuned Language Models](https://mlsanity.com/paper/2210.11416/) (2022)
- [Self-Instruct: Aligning Language Models with Self-Generated Instructions](https://mlsanity.com/paper/2212.10560/) (2022)
- [Learning to summarize from human feedback](https://mlsanity.com/paper/2009.01325/) (2020)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Megatron-LM: Training Multi-Billion Parameter Language Models Using Model Parallelism](https://mlsanity.com/paper/1909.08053/) (2019)
- [Don't Stop Pretraining: Adapt Language Models to Domains and Tasks](https://mlsanity.com/paper/2004.10964/) (2020)
- [Multitask Prompted Training Enables Zero-Shot Task Generalization](https://mlsanity.com/paper/2110.08207/) (2021)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [Exploiting Cloze Questions for Few Shot Text Classification and Natural Language Inference](https://mlsanity.com/paper/2001.07676/) (2020)
- [BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining](https://mlsanity.com/paper/2210.10341/) (2022)
- [Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets](https://mlsanity.com/paper/1906.05474/) (2019)
- [Span-based Joint Entity and Relation Extraction with Transformer Pre-training](https://mlsanity.com/paper/1909.07755/) (2019)
- [SciFive: a text-to-text transformer model for biomedical literature](https://mlsanity.com/paper/2106.03598/) (2021)
- [BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model](https://mlsanity.com/paper/2204.03905/) (2022)
- [BioMegatron: Larger Biomedical Domain Language Model](https://mlsanity.com/paper/2010.06060/) (2020)
- [Effective Modeling of Encoder-Decoder Architecture for Joint Entity and Relation Extraction](https://mlsanity.com/paper/1911.09886/) (2019)
- [CopyMTL: Copy Mechanism for Joint Extraction of Entities and Relations with Multi-Task Learning](https://mlsanity.com/paper/1911.10438/) (2019)
- [An End-to-end Model for Entity-level Relation Extraction using Multi-instance Learning](https://mlsanity.com/paper/2102.05980/) (2021)
- [Drug Repurposing for COVID-19 via Knowledge Graph Completion](https://mlsanity.com/paper/2010.09600/) (2020)
- [A sequence-to-sequence approach for document-level relation extraction](https://mlsanity.com/paper/2204.01098/) (2022)
- [Discovering Drug-Target Interaction Knowledge from Biomedical Literature](https://mlsanity.com/paper/2109.13187/) (2021)

## Built on by (most cited first, 1 of 1)

- [LLMs are not Zero-Shot Reasoners for Biomedical Information Extraction](https://mlsanity.com/paper/2408.12249/) (2024)

## Abstract (arXiv)

Cutting edge techniques developed in the general NLP domain are often subsequently applied to the high-value, data-rich biomedical domain. The past few years have seen generative language models (LMs), instruction finetuning, and few-shot learning become foci of NLP research. As such, generative LMs pretrained on biomedical corpora have proliferated and biomedical instruction finetuning has been attempted as well, all with the hope that domain specificity improves performance on downstream tasks. Given the nontrivial effort in training such models, we investigate what, if any, benefits they have in the key biomedical NLP task of relation extraction. Specifically, we address two questions: (1) Do LMs trained on biomedical corpora outperform those trained on general domain corpora? (2) Do models instruction finetuned on biomedical datasets outperform those finetuned on assorted datasets or those simply pretrained? We tackle these questions using existing LMs, testing across four datasets. In a surprising result, general-domain models typically outperformed biomedical-domain models. However, biomedical instruction finetuning improved performance to a similar degree as general instruction finetuning, despite having orders of magnitude fewer instructions. Our findings suggest it may be more fruitful to focus research effort on larger-scale biomedical instruction finetuning of general LMs over building domain-specific biomedical LMs