PiPMRE: A Pipeline Based on Language Model for Medical Relation Extraction

arXiv:2609.02896v1 Announce Type: new Abstract: Medical relation extraction (MRE) is commonly known for extracting entities and their relations jointly from a medical text, which has attracted considerable attention in recent years. Previous studies treat MRE as a sequence tagging task, which results in either a challenging design of the tagging schema or a failed extraction of multiple relations, due to intricate relationships among medical entities. In this work, we review the task from the linguistic perspective and propose a novel pipeline framework, PiPMRE, developed on language models to enhance MRE performance. Specifically, PiPMRE consists of a relation generator and a relation filter. Given a text, the generator first yields multiple relational triplets, and then the filter scores each triplet and retains only those that pass the borderline as the final results. Implementing PiPMRE requires no tagging schema; instead, we use a simple template to reformulate the input text, ensuring that entities and relations are generated in a contextual order. Extensive experimental results on two public datasets demonstrate the advancement of PiPMRE. It surpasses the previous state-of-the-art by an average of 5.6 recall points and 4.4 accuracy points. PiPMRE's superiority is also demonstrated in few-shot settings.

Abstract:Medical relation extraction (MRE) is commonly known for extracting entities and their relations jointly from a medical text, which has attracted considerable attention in recent years. Previous studies treat MRE as a sequence tagging task, which results in either a challenging design of the tagging schema or a failed extraction of multiple relations, due to intricate relationships among medical entities. In this work, we review the task from the linguistic perspective and propose a novel pipeline framework, PiPMRE, developed on language models to enhance MRE performance. Specifically, PiPMRE consists of a relation generator and a relation filter. Given a text, the generator first yields multiple relational triplets, and then the filter scores each triplet and retains only those that pass the borderline as the final results. Implementing PiPMRE requires no tagging schema; instead, we use a simple template to reformulate the input text, ensuring that entities and relations are generated in a contextual order. Extensive experimental results on two public datasets demonstrate the advancement of PiPMRE. It surpasses the previous state-of-the-art by an average of 5.6 recall points and 4.4 accuracy points. PiPMRE's superiority is also demonstrated in few-shot settings.

Computation and Language (cs.CL)

arXiv:2609.02896 [cs.CL]

(or arXiv:2609.02896v1 [cs.CL] for this version)

https://doi.org/10.48550/arXiv.2609.02896 Focus to learn more arXiv-issued DOI via DataCite

Proceedings of the Annual Meeting of the Cognitive Science Society, Vol. 47, No. 0 (2025)

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PiPMRE: A Pipeline Based on Language Model for Medical Relation Extraction

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