# Improving biomedical entity linking with generative relevance feedback

## TL;DR

This paper introduces a new method using large language models to improve the accuracy of linking biomedical text to standardized identifiers.

## Contribution

The first systematic evaluation of Generative Relevance Feedback (GRF) for enhancing candidate retrieval in biomedical entity linking.

## Key findings

- GRF significantly improves both accuracy and recall in biomedical entity linking.
- GRF is effective across multiple corpora and knowledge bases.
- GRF is an efficient, model-agnostic solution for enhancing BEL systems.

## Abstract

Biomedical Entity Linking (BEL) maps mentions in biomedical text to standardized identifiers, enabling structured data integration and downstream knowledge discovery. However, current BEL systems remain fundamentally constrained by the recall of the initial candidate pool, where suboptimal retrieval limits the overall effectiveness of the normalization pipeline.

We present the first systematic evaluation of Generative Relevance Feedback (GRF) for enhancing candidate retrieval in state-of-the-art BEL systems. GRF leverages large language models (LLMs) to enrich the expressiveness of the mention in a zero-shot fashion. We assess GRF’s impact under two scenarios—direct linking prediction and candidate generation in cascading normalization pipelines—and analyze its sensitivity to different LLMs, feedback types, and integration strategies. Experiments across eight corpora and four biomedical knowledge bases demonstrate that integrating GRF significantly improves both accuracy and recall, thereby increasing the upper bound on normalization performance. Our findings highlight GRF as an efficient, model-agnostic solution and underscore its potential as a key component for advancing BEL.

The code to reproduce our experiments can be found at: https://doi.org/10.5281/zenodo.17853541.