Improving Automated Deep Phenotyping Through Large Language Models Using Retrieval Augmented Generation

Abstract

BackgroundDiagnosing rare genetic disorders relies on precise phenotypic and genotypic analysis, with the Human Phenotype Ontology (HPO) providing a standardized language for capturing clinical phenotypes. Traditional HPO tools, such as Doc2HPO and ClinPhen, employ concept recognition to automate phenotype extraction but struggle with incomplete phenotype assignment, often requiring intensive manual review. While large language models (LLMs) hold promise for more context-driven phenotype extraction, they are prone to errors and "hallucinations," making them less reliable without further refinement. We present RAG-HPO, a Python-based tool that leverages Retrieval-Augmented Generation (RAG) to elevate LLM accuracy in HPO term assignment, bypassing the limitations of baseline models while avoiding the time and resource intensive process of fine-tuning. RAG-HPO integrates a dynamic vector database, allowing real-time retrieval and contextual matching. MethodsThe high-dimensional vector database utilized by RAG-HPO includes >54,000 phenotypic phrases mapped to HPO IDs, derived from the HPO database and supplemented with additional validated phrases. The RAG-HPO workflow uses an LLM to first extract phenotypic phrases that are then matched via semantic similarity to entries within a vector database before providing best term matches back to the LLM as context for final HPO term assignment. A benchmarking dataset of 120 published case reports with 1,792 manually-assigned HPO terms was developed, and the performance of RAG-HPO measured against existing published tools Doc2HPO, ClinPhen, and FastHPOCR. ResultsIn evaluations, RAG-HPO, powered by Llama-3 70B and applied to a set of 120 case reports, achieved a mean precision of 0.84, recall of 0.78, and an F1 score of 0.80--significantly surpassing conventional tools (p<0.00001). False positive HPO term identification occurred for 15.8% (256/1,624) of terms, of which only 2.7% (7/256) represented hallucinations, and 33.6% (86/256) unrelated terms; the remainder of false positives (63.7%, 163/256) were relative terms of the target term. ConclusionsRAG-HPO is a user-friendly, adaptable tool designed for secure evaluation of clinical text and outperforms standard HPO-matching tools in precision, recall, and F1. Its enhanced precision and recall represent a substantial advancement in phenotypic analysis, accelerating the identification of genetic mechanisms underlying rare diseases and driving progress in genetic research and clinical genomics.