Paper2Agent: Reimagining Research Papers As Interactive and Reliable AI Agents
Summary
Paper2Agent is an automated framework that converts research papers into interactive AI agents to enhance knowledge dissemination and enable complex scientific queries through natural language.
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Paper page - Paper2Agent: Reimagining Research Papers As Interactive and Reliable AI Agents
Source: https://huggingface.co/papers/2509.06917 Published on Sep 8, 2025
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Submitted byhttps://huggingface.co/taesiri
taesirion Sep 9, 2025
Abstract
Paper2Agent converts research papers into interactive AI agents to facilitate knowledge dissemination and enable complex scientific queries through natural language.
We introduce Paper2Agent, an automated framework that converts research papers intoAI agents. Paper2Agent transforms research output from passive artifacts into active systems that can accelerate downstream use, adoption, and discovery. Conventional research papers require readers to invest substantial effort to understand and adapt a paper’s code, data, and methods to their own work, creating barriers to dissemination and reuse. Paper2Agent addresses this challenge by automatically converting a paper into an AI agent that acts as a knowledgeable research assistant. It systematically analyzes the paper and the associated codebase using multiple agents to construct a Model Context Protocol (MCP) server, then iteratively generates and runs tests to refine and robustify the resulting MCP. These paper MCPs can then be flexibly connected to a chat agent (e.g. Claude Code) to carry out complex scientific queries through natural language while invoking tools and workflows from the original paper. We demonstrate Paper2Agent’s effectiveness in creating reliable and capable paper agents through in-depth case studies. Paper2Agent created an agent that leveragesAlphaGenometo interpret genomic variants and agents based onScanPyandTISSUEto carry out single-cell andspatial transcriptomicsanalyses. We validate that these paper agents can reproduce the original paper’s results and can correctly carry out novel user queries. By turning static papers into dynamic, interactiveAI agents, Paper2Agent introduces a new paradigm for knowledge dissemination and a foundation for the collaborative ecosystem of AI co-scientists.
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