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UTH-Olympia@BC8 Track 3: Adapting GPT-4 for Entity Extraction and Normalizing Responses to Detect Key Findings in Dysmorphology Physical Examination Observations

Authors: Soysal, Ekin; Roberts, Kirk;

UTH-Olympia@BC8 Track 3: Adapting GPT-4 for Entity Extraction and Normalizing Responses to Detect Key Findings in Dysmorphology Physical Examination Observations

Abstract

Abstract In this paper, we present our approach for the Biocreative VIII Track 3: Genetic Phenotype Extraction from Dysmorphology Physical Examination Entries (genetic conditions in pediatric patients). The aim of this track is to extract and normalize key findings present in dysmorphology physical examinations. We report an automated system relying on OpenAI's most recent large language model (LLM): GPT-4 to retrieve named entities and their spans from observations and normalize retrieved entities to Human Phenotype Ontology (HPO) concepts using dictionary matching algorithms. Our reported systems achieved an F1 score of 0.82 for standard matching in subtask 3a and an F1 score of 0.72 for exact matching in subtask 3b. This article is part of the Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models.

Keywords

ner, phenotypes, entity linking, bionlp

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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average
Green