# BioCoref: Benchmarking Biomedical Coreference Resolution with LLMs

arXiv: https://arxiv.org/abs/2510.25087 · HTML: https://mlsanity.com/paper/2510.25087/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 12 of its 31 references that are in the map.
- First posted on arXiv 29 Oct 2025.

## Builds on (most cited first, 12 of 12)

- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [SpanBERT: Improving Pre-training by Representing and Predicting Spans](https://mlsanity.com/paper/1907.10529/) (2019)
- [Stanza: A Python Natural Language Processing Toolkit for Many Human Languages](https://mlsanity.com/paper/2003.07082/) (2020)
- [End-to-end Neural Coreference Resolution](https://mlsanity.com/paper/1707.07045/) (2017)
- [Higher-order Coreference Resolution with Coarse-to-fine Inference](https://mlsanity.com/paper/1804.05392/) (2018)
- [Coreference Resolution as Query-based Span Prediction](https://mlsanity.com/paper/1911.01746/) (2019)
- [Deep Reinforcement Learning for Mention-Ranking Coreference Models](https://mlsanity.com/paper/1609.08667/) (2016)
- [An Annotated Dataset of Coreference in English Literature](https://mlsanity.com/paper/1912.01140/) (2019)
- [Word-Level Coreference Resolution](https://mlsanity.com/paper/2109.04127/) (2021)
- [Bridging Context Gaps: Leveraging Coreference Resolution for Long Contextual Understanding](https://mlsanity.com/paper/2410.01671/) (2024)
- [Coreference Resolution for the Biomedical Domain: A Survey](https://mlsanity.com/paper/2109.12424/) (2021)
- [ARKref: a rule-based coreference resolution system](https://mlsanity.com/paper/1310.1975/) (2013)

## Abstract (arXiv)

Coreference resolution in biomedical texts presents unique challenges due to complex domain-specific terminology, high ambiguity in mention forms, and long-distance dependencies between coreferring expressions. In this work, we present a comprehensive evaluation of generative large language models (LLMs) for coreference resolution in the biomedical domain. Using the CRAFT corpus as our benchmark, we assess the LLMs' performance with four prompting experiments that vary in their use of local, contextual enrichment, and domain-specific cues such as abbreviations and entity dictionaries. We benchmark these approaches against a discriminative span-based encoder, SpanBERT, to compare the efficacy of generative versus discriminative methods. Our results demonstrate that while LLMs exhibit strong surface-level coreference capabilities, especially when supplemented with domain-grounding prompts, their performance remains sensitive to long-range context and mentions ambiguity. Notably, the LLaMA 8B and 17B models show superior precision and F1 scores under entity-augmented prompting, highlighting the potential of lightweight prompt engineering for enhancing LLM utility in biomedical NLP tasks.