@inproceedings{xiang-etal-2025-knowledge,
title = "From Knowledge to Treatment: Large Language Model Assisted Biomedical Concept Representation for Drug Repurposing",
author = "Xiang, Chengrui and
Ma, Tengfei and
Fu, Xiangzheng and
Liu, Yiping and
Song, Bosheng and
Zeng, Xiangxiang",
editor = "Christodoulopoulos, Christos and
Chakraborty, Tanmoy and
Rose, Carolyn and
Peng, Violet",
booktitle = "Findings of the Association for Computational Linguistics: EMNLP 2025",
month = nov,
year = "2025",
address = "Suzhou, China",
publisher = "Association for Computational Linguistics",
url = "https://aclanthology.org/2025.findings-emnlp.751/",
pages = "13967--13982",
ISBN = "979-8-89176-335-7",
abstract = "Drug repurposing plays a critical role in accelerating treatment discovery, especially for complex and rare diseases. Biomedical knowledge graphs (KGs), which encode rich clinical associations, have been widely adopted to support this task. However, existing methods largely overlook common-sense biomedical concept knowledge in real-world labs, such as mechanistic priors indicating that certain drugs are fundamentally incompatible with specific treatments. To address this gap, we propose LLaDR, a Large Language Model-assisted framework for Drug Repurposing, which improves the representation of biomedical concepts within KGs. Specifically, we extract semantically enriched treatment-related textual representations of biomedical entities from large language models (LLMs) and use them to fine-tune knowledge graph embedding (KGE) models. By injecting treatment-relevant knowledge into KGE, LLaDR largely improves the representation of biomedical concepts, enhancing semantic understanding of under-studied or complex indications. Experiments based on benchmarks demonstrate that LLaDR achieves state-of-the-art performance across different scenarios, with case studies on Alzheimer{'}s disease further confirming its robustness and effectiveness."
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<abstract>Drug repurposing plays a critical role in accelerating treatment discovery, especially for complex and rare diseases. Biomedical knowledge graphs (KGs), which encode rich clinical associations, have been widely adopted to support this task. However, existing methods largely overlook common-sense biomedical concept knowledge in real-world labs, such as mechanistic priors indicating that certain drugs are fundamentally incompatible with specific treatments. To address this gap, we propose LLaDR, a Large Language Model-assisted framework for Drug Repurposing, which improves the representation of biomedical concepts within KGs. Specifically, we extract semantically enriched treatment-related textual representations of biomedical entities from large language models (LLMs) and use them to fine-tune knowledge graph embedding (KGE) models. By injecting treatment-relevant knowledge into KGE, LLaDR largely improves the representation of biomedical concepts, enhancing semantic understanding of under-studied or complex indications. Experiments based on benchmarks demonstrate that LLaDR achieves state-of-the-art performance across different scenarios, with case studies on Alzheimer’s disease further confirming its robustness and effectiveness.</abstract>
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%0 Conference Proceedings
%T From Knowledge to Treatment: Large Language Model Assisted Biomedical Concept Representation for Drug Repurposing
%A Xiang, Chengrui
%A Ma, Tengfei
%A Fu, Xiangzheng
%A Liu, Yiping
%A Song, Bosheng
%A Zeng, Xiangxiang
%Y Christodoulopoulos, Christos
%Y Chakraborty, Tanmoy
%Y Rose, Carolyn
%Y Peng, Violet
%S Findings of the Association for Computational Linguistics: EMNLP 2025
%D 2025
%8 November
%I Association for Computational Linguistics
%C Suzhou, China
%@ 979-8-89176-335-7
%F xiang-etal-2025-knowledge
%X Drug repurposing plays a critical role in accelerating treatment discovery, especially for complex and rare diseases. Biomedical knowledge graphs (KGs), which encode rich clinical associations, have been widely adopted to support this task. However, existing methods largely overlook common-sense biomedical concept knowledge in real-world labs, such as mechanistic priors indicating that certain drugs are fundamentally incompatible with specific treatments. To address this gap, we propose LLaDR, a Large Language Model-assisted framework for Drug Repurposing, which improves the representation of biomedical concepts within KGs. Specifically, we extract semantically enriched treatment-related textual representations of biomedical entities from large language models (LLMs) and use them to fine-tune knowledge graph embedding (KGE) models. By injecting treatment-relevant knowledge into KGE, LLaDR largely improves the representation of biomedical concepts, enhancing semantic understanding of under-studied or complex indications. Experiments based on benchmarks demonstrate that LLaDR achieves state-of-the-art performance across different scenarios, with case studies on Alzheimer’s disease further confirming its robustness and effectiveness.
%U https://aclanthology.org/2025.findings-emnlp.751/
%P 13967-13982
Markdown (Informal)
[From Knowledge to Treatment: Large Language Model Assisted Biomedical Concept Representation for Drug Repurposing](https://aclanthology.org/2025.findings-emnlp.751/) (Xiang et al., Findings 2025)
ACL