arXiv:2510.16082q-bio.QMcs.AI2025-10被引 1

BIOGEN通过多智能体协作,让基因表达结果有据可查、零幻觉。

BIOGEN: Evidence-Grounded Multi-Agent Reasoning Framework for Transcriptomic Interpretation in Antimicrobial Resistance

  • 用检索+推理+多评审机制,生成带证据和置信度的解释
  • 在五组细菌数据上实现0%幻觉,比大模型基线提升显著
  • 适合需要可追溯生物解释的研究者,如耐药性机制探索

解读RNA测序中的基因簇仍具挑战,尤其在抗生素耐药性研究中,机制洞察对假说生成至关重要。现有通路富集方法虽能总结共表达模块,但常缺乏针对特定簇的解释,且与文献支持连接薄弱。我们提出BIOGEN——一种面向转录模块事后解释的证据根基多智能体框架。BIOGEN结合生物医学检索、结构化推理与多评审验证,生成可追踪的簇级解释,附带明确证据与置信度标签。在主样本沙门氏菌数据集上,BIOGEN表现优异:BERTScore为0.689,语义对齐得分0.715,KEGG功能相似度0.342,幻觉率为0.000;而仅用大模型的基线幻觉率达0.100。在另外四个细菌RNA-seq数据集上,BIOGEN在相同固定流程下也保持零幻觉。相比代表性开源智能体基线,BIOGEN是唯一在全部五个数据集上均维持零幻觉的框架。结果表明,仅靠检索不足以实现可靠生物学解释,证据根基的协同调度对透明、可溯源的转录组推理至关重要。

原文摘要 · Abstract (English)

Interpreting gene clusters from RNA sequencing (RNA-seq) remains challenging, especially in antimicrobial resistance studies where mechanistic insight is important for hypothesis generation. Existing pathway enrichment methods can summarize co-expressed modules, but they often provide limited cluster-specific explanations and weak connections to supporting literature. We present BIOGEN, an evidence-grounded multi-agent framework for post hoc interpretation of RNA-seq transcriptional modules. BIOGEN combines biomedical retrieval, structured reasoning, and multi-critic verification to generate traceable cluster-level explanations with explicit evidence and confidence labels. On a primary Salmonella enterica dataset, BIOGEN achieved strong biological grounding, including BERTScore 0.689, Semantic Alignment Score 0.715, KEGG Functional Similarity 0.342, and a hallucination rate of 0.000, compared with 0.100 for an LLM-only baseline. Across four additional bacterial RNA-seq datasets, BIOGEN also maintained zero hallucination under the same fixed pipeline. In comparisons with representative open-source agentic AI baselines, BIOGEN was the only framework that consistently preserved zero hallucination across all five datasets. These findings suggest that retrieval alone is not enough for reliable biological interpretation, and that evidence-grounded orchestration is important for transparent and source-traceable transcriptomic reasoning.

基因解释多智能体抗药性零幻觉

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