DeepRare Agent Tops Doctors in Rare Disease Diagnosis

• Multi-agent system architecture powered by large language models with specialized tool integration (40+ tools) • Processes heterogeneous clinical inputs: free-text clinical descriptions, structured Human Phenotype Ontology (HPO) terms, and genetic testing results • Agentic workflow implements System 2 reasoning: forms diagnostic hypotheses, tests against medical evidence, revises conclusions iteratively • Integrates up-to-date knowledge sources and enables traceable reasoning linked to verifiable medical evidence • Evaluated across nine datasets spanning 14 medical specialties with 2,919 diseases across Asia, North America, and Europe • Achieves 95.4% expert validation rate on reasoning chains, confirming transparency and traceability of diagnostic logic

DeepRare represents a significant shift in clinical AI deployment by demonstrating that agentic systems with transparent reasoning can match or exceed specialist performance in complex diagnostic tasks. The system's 600+ institutional registrations since July 2025 indicate rapid adoption potential in healthcare systems lacking routine genetic testing access. The research team's planned global rare disease diagnostic alliance and validation using 20,000 real-world cases suggests scaling toward standardized international deployment. This advancement could reduce the documented 4.26-year diagnostic odyssey and 42% misdiagnosis rate, potentially reshaping clinical workflows for rare disease diagnosis across healthcare systems worldwide. The success of LLM-driven agentic systems in this domain may accelerate similar applications in other complex medical decision-making areas.