An artificial intelligence framework for end-to-end rare disease phenotyping from clinical notes using large language models
Cathy Shyr, Yan Hu, Rory J. Tinker, Thomas A. Cassini, Kevin W. Byram, Rizwan Hamid · Feb 23, 2026
Citations: 0
Expert Verification Automatic Metrics Medicine
- Existing artificial intelligence approaches typically optimize individual components of phenotyping but do not operationalize the full clinical workflow of extracting features from clinical text, standardizing them to Human Phenotype…
- Using clinician-curated HPO terms as the gold standard, RARE-PHENIX consistently outperformed a state-of-the-art deep learning baseline (PhenoBERT) across ontology-based similarity and precision-recall-F1 metrics in end-to-end evaluation…