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arXiv · 2509.06917

Paper2Agent: Reimagining Research Papers As Interactive and Reliable AI Agents

Jiacheng Miao·Joe R. Davis·Yaohui Zhang·Jonathan K. Pritchard·James Zou
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Abstract

We introduce Paper2Agent, an automated framework that converts research papers into AI 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 leverages AlphaGenome to interpret genomic variants and agents based on ScanPy and TISSUE to carry out single-cell and spatial transcriptomics analyses. We validate that these paper agents can reproduce the original paper's results and can correctly carry out novel user queries. Paper2Agent automatically created AI co-scientist that identified new splicing variant associated with ADHD risk. By turning static papers into dynamic, interactive AI agents, Paper2Agent introduces a new paradigm for knowledge dissemination and a foundation for the collaborative ecosystem of AI co-scientists.

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BibTeXRIS

Jiacheng Miao, Joe R. Davis, Yaohui Zhang, Jonathan K. Pritchard, James Zou. 2025-09-08. Paper2Agent: Reimagining Research Papers As Interactive and Reliable AI Agents. https://arxiv.org/abs/2509.06917

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