# Pre-training data selection for biomedical domain adaptation using journal impact metrics

arXiv: https://arxiv.org/abs/2409.02725 · HTML: https://mlsanity.com/paper/2409.02725/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 13 of its 33 references that are in the map.
- First posted on arXiv 4 Sep 2024.

## Builds on (most cited first, 13 of 13)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [LIMA: Less Is More for Alignment](https://mlsanity.com/paper/2305.11206/) (2023)
- [Galactica: A Large Language Model for Science](https://mlsanity.com/paper/2211.09085/) (2022)
- [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)
- [BioMedGPT: Open Multimodal Generative Pre-trained Transformer for BioMedicine](https://mlsanity.com/paper/2308.09442/) (2023)
- [A Corpus with Multi-Level Annotations of Patients, Interventions and Outcomes to Support Language Processing for Medical Literature](https://mlsanity.com/paper/1806.04185/) (2018)
- [Results of the seventh edition of the BioASQ Challenge](https://mlsanity.com/paper/2006.09174/) (2020)
- [NLU on Data Diets: Dynamic Data Subset Selection for NLP Classification Tasks](https://mlsanity.com/paper/2306.03208/) (2023)

## Built on by (most cited first, 2 of 2)

- [From Learning to Unlearning: Biomedical Security Protection in Multimodal Large Language Models](https://mlsanity.com/paper/2508.04192/) (2025)
- [Tracing Multilingual Knowledge Acquisition Dynamics in Domain Adaptation: A Case Study of English-Japanese Biomedical Adaptation](https://mlsanity.com/paper/2510.12115/) (2025)

## Abstract (arXiv)

Domain adaptation is a widely used method in natural language processing (NLP) to improve the performance of a language model within a specific domain. This method is particularly common in the biomedical domain, which sees regular publication of numerous scientific articles. PubMed, a significant corpus of text, is frequently used in the biomedical domain. The primary objective of this study is to explore whether refining a pre-training dataset using specific quality metrics for scientific papers can enhance the performance of the resulting model. To accomplish this, we employ two straightforward journal impact metrics and conduct experiments by continually pre-training BERT on various subsets of the complete PubMed training set, we then evaluate the resulting models on biomedical language understanding tasks from the BLURB benchmark. Our results show that pruning using journal impact metrics is not efficient. But we also show that pre-training using fewer abstracts (but with the same number of training steps) does not necessarily decrease the resulting model's performance.