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BioManus is an MCP-native biomedical agent system that uses graph-scaffolded planning over structured biological capabilities instead of flat prompt-based tool retrieval, achieving better context efficiency and execution accuracy on biomedical benchmarks. The system introduces a BioinfoMCP Compiler to standardize heterogeneous bioinformatics tools and organizes them as a typed heterogeneous MCP graph for scalable reasoning.
CoHyDE introduces an iterative co-training procedure for an LLM rewriter and a dense encoder to improve tool retrieval from large API catalogs. It outperforms single-component baselines, especially on vague queries, by training both components together using InfoNCE and DPO.