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Reimagining research papers as interactive and reliable AI agents

nature.com5 points1 comments
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Paper2Agent is an automated framework that converts research papers and their associated code, data and workflows into interactive AI agents, effectively turning static manuscripts into virtual corresponding authors. The system extracts a paper’s key contributions with multiple helper agents, packages executable functions, static resources and structured workflow prompts into a Model Context Protocol (MCP) server, and wraps that server with LLM-based agents for natural-language interaction and autonomous execution. Users can ask complex scientific questions or request analyses without installing environments or parsing APIs: MCP tools run validated code, MCP resources expose manuscripts and datasets, and MCP prompts orchestrate reproducible multi-step workflows. Demonstrations include agents that reproduce and extend results from AlphaGenome, Scanpy and TISSUE, and a multi-agent collaboration that prioritized a causal gene for psoriasis.

The framework emphasizes reliability and reproducibility by validating tools against reported figures and example datasets, locking tested tool implementations, and including explicit code references to prevent “code hallucination” and limit randomness in code generation. Building on MCP as an industry interface, Paper2Agent generalizes prior executable-paper and containerization efforts by agentifying full research outputs so methods can be applied, adapted and composed via dialogue. This reframes scientific dissemination from static documents to interactive, interoperable AI co‑scientists that lower technical barriers and accelerate reuse.

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