Paper2Agent：將研究論文重塑為互動且可靠的AI代理

摘要

我們介紹了Paper2Agent，這是一個將研究論文自動轉化為AI代理的框架。Paper2Agent將研究成果從被動的靜態產物轉變為能加速下游應用、採納與發現的主動系統。傳統的研究論文要求讀者投入大量精力來理解並將論文的代碼、數據和方法應用於自身工作，這造成了傳播與重用的障礙。Paper2Agent通過自動將論文轉化為一個知識淵博的研究助手AI代理來應對這一挑戰。它利用多個代理系統地分析論文及其相關代碼庫，構建一個模型上下文協議（MCP）服務器，然後迭代生成並運行測試以精煉和強化最終的MCP。這些論文MCP隨後可以靈活地連接到聊天代理（如Claude Code），通過自然語言執行複雜的科學查詢，同時調用原始論文中的工具和工作流程。我們通過深入的案例研究展示了Paper2Agent在創建可靠且能力強大的論文代理方面的有效性。Paper2Agent創建了一個利用AlphaGenome解釋基因組變異的代理，以及基於ScanPy和TISSUE的代理來執行單細胞和空間轉錄組學分析。我們驗證了這些論文代理能夠重現原始論文的結果，並能正確執行新的用戶查詢。通過將靜態論文轉變為動態、互動的AI代理，Paper2Agent引入了一種新的知識傳播範式，並為AI協作科學家的生態系統奠定了基礎。

English

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. 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.

Paper2Agent：將研究論文重塑為互動且可靠的AI代理

Paper2Agent: Reimagining Research Papers As Interactive and Reliable AI Agents

摘要

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