# Harnessing Large Language Models for Biomedical Named Entity Recognition

arXiv: https://arxiv.org/abs/2512.22738 · HTML: https://mlsanity.com/paper/2512.22738/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 16 of its 31 references that are in the map.
- First posted on arXiv 28 Dec 2025.

## Builds on (most cited first, 16 of 16)

- [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)
- [Qwen3 Technical Report](https://mlsanity.com/paper/2505.09388/) (2025)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [Super-NaturalInstructions: Generalization via Declarative Instructions on 1600+ NLP Tasks](https://mlsanity.com/paper/2204.07705/) (2022)
- [BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining](https://mlsanity.com/paper/2210.10341/) (2022)
- [InstructUIE: Multi-task Instruction Tuning for Unified Information Extraction](https://mlsanity.com/paper/2304.08085/) (2023)
- [GPT-NER: Named Entity Recognition via Large Language Models](https://mlsanity.com/paper/2304.10428/) (2023)
- [Superfiltering: Weak-to-Strong Data Filtering for Fast Instruction-Tuning](https://mlsanity.com/paper/2402.00530/) (2024)
- [UniversalNER: Targeted Distillation from Large Language Models for Open Named Entity Recognition](https://mlsanity.com/paper/2308.03279/) (2023)
- [How Robust is GPT-3.5 to Predecessors? A Comprehensive Study on Language Understanding Tasks](https://mlsanity.com/paper/2303.00293/) (2023)
- [Taiyi: A Bilingual Fine-Tuned Large Language Model for Diverse Biomedical Tasks](https://mlsanity.com/paper/2311.11608/) (2023)
- [LLMs in Biomedicine: A study on clinical Named Entity Recognition](https://mlsanity.com/paper/2404.07376/) (2024)
- [llmNER: (Zero|Few)-Shot Named Entity Recognition, Exploiting the Power of Large Language Models](https://mlsanity.com/paper/2406.04528/) (2024)
- [Demonstration-based learning for few-shot biomedical named entity recognition under machine reading comprehension](https://mlsanity.com/paper/2308.06454/) (2023)

## Abstract (arXiv)

Background and Objective: Biomedical Named Entity Recognition (BioNER) is a foundational task in medical informatics, crucial for downstream applications like drug discovery and clinical trial matching. However, adapting general-domain Large Language Models (LLMs) to this task is often hampered by their lack of domain-specific knowledge and the performance degradation caused by low-quality training data. To address these challenges, we introduce BioSelectTune, a highly efficient, data-centric framework for fine-tuning LLMs that prioritizes data quality over quantity. Methods and Results: BioSelectTune reformulates BioNER as a structured JSON generation task and leverages our novel Hybrid Superfiltering strategy, a weak-to-strong data curation method that uses a homologous weak model to distill a compact, high-impact training dataset. Conclusions: Through extensive experiments, we demonstrate that BioSelectTune achieves state-of-the-art (SOTA) performance across multiple BioNER benchmarks. Notably, our model, trained on only 50% of the curated positive data, not only surpasses the fully-trained baseline but also outperforms powerful domain-specialized models like BioMedBERT.