# Benchmarking Large Language Models for Biomedical Relation Extraction

arXiv: https://arxiv.org/abs/2609.19071 · HTML: https://mlsanity.com/paper/2609.19071/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 4 of its 11 references that are in the map.
- First posted on arXiv 23 Jul 2026.

## Builds on (most cited first, 4 of 4)

- [Unsupervised Cross-lingual Representation Learning at Scale](https://mlsanity.com/paper/1911.02116/) (2019)
- [Qwen Technical Report](https://mlsanity.com/paper/2309.16609/) (2023)
- [DeBERTa: Decoding-enhanced BERT with Disentangled Attention](https://mlsanity.com/paper/2006.03654/) (2020)
- [Named Entity Recognition with Bidirectional LSTM-CNNs](https://mlsanity.com/paper/1511.08308/) (2015)

## Abstract (arXiv)

Extracting SNP-phenotype associations from biomedical literature is vital but challenging. We benchmarked diverse NLP models, including MLMs, hybrid architectures, and state-of-the-art LLMs (Gemini 2.0, OpenAI O-series, Qwen, Mistral), on the SNPPhenA corpus across three tasks: sentence-level, abstract-level, and association strength classification. OpenAI O1 achieved state-of-the-art (SOTA) results using few-shot learning for non-finetuned sentence-level classification (F1 0.89) and established a new SOTA for abstract-level classification (F1 0.82). Association strength classification proved difficult, though fine-tuned Gemini 2.0 Pro performed best (F1 0.60) in the first LLM evaluation of this task. Proprietary LLMs, especially in few-shot (O1) or fine-tuned (Gemini 2.0 Pro) settings, significantly outperformed other models. These findings confirm the power of modern LLMs for genomic knowledge extraction.