# Biomedical Nested NER with Large Language Model and UMLS Heuristics

arXiv: https://arxiv.org/abs/2407.05480 · HTML: https://mlsanity.com/paper/2407.05480/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 7 of its 12 references that are in the map.
- First posted on arXiv 7 Jul 2024.

## Builds on (most cited first, 7 of 7)

- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [Mixtral of Experts](https://mlsanity.com/paper/2401.04088/) (2024)
- [A Prompt Pattern Catalog to Enhance Prompt Engineering with ChatGPT](https://mlsanity.com/paper/2302.11382/) (2023)
- [A Unified MRC Framework for Named Entity Recognition](https://mlsanity.com/paper/1910.11476/) (2019)
- [Opportunities and Challenges for ChatGPT and Large Language Models in Biomedicine and Health](https://mlsanity.com/paper/2306.10070/) (2023)
- [Nested Named Entity Recognition via Second-best Sequence Learning and Decoding](https://mlsanity.com/paper/1909.02250/) (2019)
- [NEREL-BIO: A Dataset of Biomedical Abstracts Annotated with Nested Named Entities](https://mlsanity.com/paper/2210.11913/) (2022)

## Built on by (most cited first, 3 of 3)

- [Overview of BioASQ 2024: The twelfth BioASQ challenge on Large-Scale Biomedical Semantic Indexing and Question Answering](https://mlsanity.com/paper/2508.20532/) (2025)
- [A Guideline-Augmented Multi-Agent Framework for Schema-as-Code Biomedical Named Entity Recognition](https://mlsanity.com/paper/2610.02970/) (2026)
- [Opioid Named Entity Recognition (ONER-2025) from Reddit](https://mlsanity.com/paper/2504.00027/) (2025)

## Abstract (arXiv)

In this paper, we present our system for the BioNNE English track, which aims to extract 8 types of biomedical nested named entities from biomedical text. We use a large language model (Mixtral 8x7B instruct) and ScispaCy NER model to identify entities in an article and build custom heuristics based on unified medical language system (UMLS) semantic types to categorize the entities. We discuss the results and limitations of our system and propose future improvements. Our system achieved an F1 score of 0.39 on the BioNNE validation set and 0.348 on the test set.