Large Language Model (LLM)-based agents have recently demonstrated remarkable capabilities in deep research tasks, yet their application to the medical domain remains challenging. The leading proprietary systems achieve only modest results on complex medical benchmarks. This exposes two key bottlenecks: (i) limited clinical-reasoning capability in the underlying model, and (ii) unreliable access to authoritative medical evidence when constrained to open-web retrieval. To address these limitations and equip agents with robust clinical reasoning capabilities, we present MedResearcher-R1, a medical deep research agent featuring two core innovations. First, we propose Knowledge-Informed Trajectory Synthesis (KISA), a novel approach that builds medical knowledge graphs to construct complex multi-hop question-answer pairs centered on rare medical entities, overcoming the scarcity of high-quality domain-specific training data. Second, we integrate a medical retrieval engine alongside general-purpose tools, enabling precise and reliable synthesis of medical evidence. Through this methodology, we yield over 2,100 diverse trajectories spanning 12 medical specialties. Trained with supervised fine-tuning and reinforcement learning, our MedResearcher-R1-32B achieves state-of-the-art performance on MedBrowseComp (27.5/50 vs. 25.5/50 for o3-deepresearch) while demonstrating strong general performance on GAIA and xBench benchmarks. To the best of our knowledge, we present the first high-quality, tool-augmented medical dataset paired with a domain-specialized deep-research agent, demonstrating that smaller open-source models can surpass substantially larger proprietary systems on specialized medical tasks.

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