Bioinfoysis让生物信息分析全程可追溯,避免错误证据重复使用。
Bioinfoysis Technical Report

- 用多智能体架构持久化分析过程,每步结果绑定责任人和步骤
- 在BixBench上达到82.4%准确率,比基线平均提升36.3个百分点
- 适合需要可复现、可验证的长周期生物信息分析任务
大语言模型代理在生物信息学中展现潜力,但现有系统多聚焦最终答案,将规划、工具调用和代码执行视为短暂交互。这种设计不适用于长周期任务,因结论难以关联支撑数据与中间证据。我们提出 extbf{Bioinfoysis},一个将每个请求表示为持久化、基于成果的分析运行的多智能体框架。它结合全局规划与逐步证据驱动的重规划:规划器维护可执行清单,并根据每个工作者执行后的结构化交接信息修订待办步骤。这些交接将中间结果与负责智能体、清单步骤及计划生成绑定,防止重规划后过时证据被无声复用。受控运行时在用于下游分析或报告前验证生成的脚本、表格和图表;角色特定上下文、持久记忆和受控生物信息技能支持长分析轨迹中的可靠执行。我们在BixBench和LAB-Bench 2的两个问答任务上评估Bioinfoysis。在BixBench上,其准确率达到82.4%的业界领先水平。在四个底层语言模型下,其在SeqQA2上的平均准确率从27.81%提升至64.13%,在DbQA2上从3.13%提升至31.25%。结果表明,可靠的生物信息自动化不仅依赖模型能力,更取决于对规划、执行、记忆和证据流的管控机制。我们希望Bioinfoysis能推动生物信息学社区的发展。演示网站见https://report.bioinfoysis.com/。
原文摘要 · Abstract (English)
Large language model agents have shown promise in bioinformatics, but most existing systems focus primarily on producing final answers, treating planning, tool use, and code execution as transient interactions. This design is poorly suited to long-horizon bioinformatics tasks, where conclusions must remain connected to the data, computations, and intermediate evidence that support them. We introduce \textbf{Bioinfoysis}, a multi-agent harness that represents each request as a persistent, artifact-grounded analysis run. Bioinfoysis combines global planning with step-wise, evidence-driven replanning: the planner maintains an executable checklist and revises pending steps using structured handoffs returned after each worker execution. These handoffs bind intermediate results to their responsible agent, checklist step, and plan generation, preventing stale evidence from being silently reused after replanning. A controlled runtime validates generated scripts, tables, and figures before they are used in downstream analysis or reporting, while role-specific context, persistent memory, and governed bioinformatics skills support reliable execution over long analysis trajectories. We evaluate Bioinfoysis on BixBench and two question-answering tracks of LAB-Bench 2. On BixBench, Bioinfoysis achieves state-of-the-art accuracy of 82.4\%. Across four underlying language models, Bioinfoysis increases average accuracy from 27.81\% to 64.13\% on SeqQA2 and from 3.13\% to 31.25\% on DbQA2. These results demonstrate that reliable bioinformatics automation depends not only on model capability, but also on the harness that governs planning, execution, memory, and evidence flow. We hope that the emergence of Bioinfoysis will play a driving and leading role in the development of the bioinformatics community. Our demo website can be seen in https://report.bioinfoysis.com/.
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