# Biomed-Enriched: A Biomedical Dataset Enriched with LLMs for Pretraining and Extracting Rare and Hidden Content

arXiv: https://arxiv.org/abs/2506.20331 · HTML: https://mlsanity.com/paper/2506.20331/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 11 of its 21 references that are in the map.
- First posted on arXiv 25 Jun 2025.

## Builds on (most cited first, 11 of 11)

- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [Measuring Massive Multitask Language Understanding](https://mlsanity.com/paper/2009.03300/) (2020)
- [Think you have Solved Question Answering? Try ARC, the AI2 Reasoning Challenge](https://mlsanity.com/paper/1803.05457/) (2018)
- [Unsupervised Cross-lingual Representation Learning at Scale](https://mlsanity.com/paper/1911.02116/) (2019)
- [Can a Suit of Armor Conduct Electricity? A New Dataset for Open Book Question Answering](https://mlsanity.com/paper/1809.02789/) (2018)
- [The FineWeb Datasets: Decanting the Web for the Finest Text Data at Scale](https://mlsanity.com/paper/2406.17557/) (2024)
- [DataComp-LM: In search of the next generation of training sets for language models](https://mlsanity.com/paper/2406.11794/) (2024)
- [BioMistral: A Collection of Open-Source Pretrained Large Language Models for Medical Domains](https://mlsanity.com/paper/2402.10373/) (2024)
- [MEDITRON-70B: Scaling Medical Pretraining for Large Language Models](https://mlsanity.com/paper/2311.16079/) (2023)
- [Organize the Web: Constructing Domains Enhances Pre-Training Data Curation](https://mlsanity.com/paper/2502.10341/) (2025)
- [FrenchMedMCQA: A French Multiple-Choice Question Answering Dataset for Medical domain](https://mlsanity.com/paper/2304.04280/) (2023)

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

- [A Causal Language Modeling Detour Improves Encoder Continued Pretraining](https://mlsanity.com/paper/2605.12438/) (2026)
- [MrBERT: Modern Multilingual Encoders via Vocabulary, Domain, and Dimensional Adaptation](https://mlsanity.com/paper/2602.21379/) (2026)

## Abstract (arXiv)

We introduce Biomed-Enriched, a biomedical text dataset constructed from PubMed via a two-stage annotation process. In the first stage, a large language model annotates 400K paragraphs from PubMed scientific articles, assigning scores for their type (review, study, clinical case, other), domain (clinical, biomedical, other), and educational quality. The educational quality score (rated 1 to 5) estimates how useful a paragraph is for college-level learning. These annotations are then used to fine-tune a small language model, which propagates the labels across the full PMC-OA corpus. The resulting metadata allows us to extract refined subsets, including 2M clinical case paragraphs with over 450K high-quality ones from articles with commercial-use licenses, and to construct several variants via quality filtering and domain upsampling. Clinical text is typically difficult to access due to privacy constraints, as hospital records cannot be publicly shared. Hence, our dataset provides an alternative large-scale, openly available collection of clinical cases from PubMed, making it a valuable resource for biomedical and clinical NLP. Preliminary continual-pretraining experiments with OLMo2 suggest these curated subsets enable targeted improvements, with clinical upsampling boosting performance by ~5% on MMLU ProfMed and educational quality filtering improving MedQA and MedMCQA by ~1%. Combinations of these techniques led to faster convergence, reaching same performance with a third of training tokens, indicating potential for more efficient and effective biomedical pretraining strategies.