LA-MARRVEL: A Knowledge-Grounded and Language-Aware LLM Reranker for AI-MARRVEL in Rare Disease Diagnosis

arXiv:2511.02263v3 Announce Type: replace
Abstract: Diagnosing rare diseases requires linking gene findings with often unstructured reference text. Current pipelines collect many candidate genes, but clinicians still spend a lot of time filtering false positives and combining evidence from papers and databases. A key challenge is language: phenotype descriptions and inheritance patterns are written in prose, not fully captured by tables. Large language models (LLMs) can read such text, but clinical use needs grounding in citable knowledge and stable, repeatable behavior. We explore a knowledge-grounded and language-aware reranking layer on top of a high-recall first-stage pipeline. The goal is to improve precision and explainability, not to replace standard bioinformatics steps. We use expert-built context and a consensus method to reduce LLM variability, producing shorter, better-justified gene lists for expert review. LA-MARRVEL achieves the highest accuracy, outperforming other methods — including traditional bioinformatics diagnostic tools (AI-MARRVEL, Exomiser, LIRICAL) and naive large language models (e.g., Anthropic Claude) — with an average Recall@5 of 94.10%, a +3.65 percentage-point improvement over AI-MARRVEL. The LLM-generated reasoning provides clear prose on phenotype matching and inheritance patterns, making clinical review faster and easier. LA-MARRVEL has three parts: expert-engineered context that enriches phenotype and disease information; a ranked voting algorithm that combines multiple LLM runs to choose a consensus ranked gene list; and the AI-MARRVEL pipeline that provides first-stage ranks and gene annotations, already known as a state-of-the-art method in Rare Disease Diagnosis on BG, DDD, and UDN cohorts. The online AI-MARRVEL includes LA-MARRVEL as an LLM feature at https://ai.marrvel.org . We evaluate LA-MARRVEL on three datasets from independent cohorts of real-world diagnosed patients.