Evaluating Multi-Agent LLM Architectures for Rare Disease Diagnosis

While large language models are capable diagnostic tools, the impact of multi-agent topology on diagnostic accuracy remains underexplored. This study evaluates four agent topologies, Control (single agent), Hierarchical, Adversarial, and Collaborative, across 302 cases spanning 33 rare disease categories. We introduce a Reasoning Gap metric to quantify the difference between internal knowledge retrieval and final diagnostic accuracy. Results indicate that the Hierarchical topology (50.0% accuracy) marginally outperforms Collaborative (49.8%) and Control (48.5%) configurations. In contrast, the Adversarial model significantly degrades performance (27.3%), exhibiting a massive Reasoning Gap where valid diagnoses were rejected due to artificial doubt. Across all architectures, performance was strongest in Allergic diseases and Toxic Effects categories but poorest in Cardiac Malformation and Respiratory cases. Critically, while the single-agent baseline was generally robust, all multi-agent systems, including the Adversarial model, yielded superior accuracy in Bone and Thoracic disease categories. These findings demonstrate that increasing system complexity does not guarantee better reasoning, supporting a shift toward dynamic topology selection.