Rare disease diagnosis is inherently challenging due to heterogeneous symptoms, limited clinical familiarity, and fragmented evidence across specialties. Recent large language model (LLM)-based agentic systems have shown promise by simulating multidisciplinary team discussions to generate and evaluate diagnostic hypotheses. However, fully automated diagnosis remains unrealistic, and existing human-in-the-loop approaches provide limited support for effective clinician-agent collaboration. In practice, clinicians are often presented with final diagnostic outputs and lengthy, unstructured agent discussion logs, making it difficult to inspect reasoning, intervene in a timely manner, or guide agent deliberation effectively. To address these challenges, we developed MDTRoom, an interactive system that transforms multi-agent discussions from linear transcripts into a structured, inspectable workspace. The system externalizes patient data, evidence provenance, hypothesis evolution, and inter-agent conflicts as interconnected visual objects, enabling clinicians to efficiently examine, intervene in, and guide agent reasoning. Our evaluation demonstrates the effectiveness of MDTRoom in supporting clinician-agent collaboration.

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