AutoPCR: Automated Phenotype Concept Recognition by Prompting

ACL ARR 2025 May Submission4637 Authors

Abstract: Phenotype concept recognition (CR) is a fundamental task in biomedical text mining, enabling applications such as clinical diagnostics and knowledge graph construction. However, existing methods often require ontology-specific training and struggle to generalize across diverse text types and evolving biomedical terminology. We present AutoPCR, a prompt-based phenotype CR method that does not require ontology-specific training. AutoPCR performs CR in three stages: entity extraction using a hybrid of rule-based and neural tagging strategies, candidate retrieval via SapBERT, and entity linking through prompting a large language model. Experiments on four benchmark datasets show that AutoPCR achieves the best average and most robust performance across both mention-level and document-level evaluations, surpassing prior state-of-the-art methods. Further ablation and transfer studies demonstrate its inductive capability and generalizability to new ontologies.

Paper Type: Long

Research Area: Information Extraction

Research Area Keywords: named entity recognition and relation extraction; entity linking/disambiguation; zero/few-shot extraction

Contribution Types: NLP engineering experiment

Languages Studied: English

Submission Number: 4637