用神经符号框架解析结直肠癌耐药机制,发现关键基因的隐藏调控关系。
Contextual Invertible World Models: A Neuro-Symbolic Agentic Framework for Colorectal Cancer Drug Response
- 融合机器学习与大模型推理,构建可逆世界模型分析药物反应。
- 在83个样本中发现突变KRAS主导5-氟尿嘧啶耐药,影响度Δ=-0.0469。
- 揭示PIK3CA修复反而增强耐药性,适合肿瘤机制研究者阅读。
精准肿瘤学受限于小样本、高维度的困境:基因组数据丰富但药理响应样本稀少。深度学习虽具高预测精度,却常缺乏临床所需的机制解释力。本文提出上下文可逆世界模型(CIWM),一种神经符号代理框架,通过整合量化机器学习模拟器与大语言模型推理层,弥合此鸿沟。基于对桑格GDSC数据集(N=83)的严格数据工程,剔除体外假信号,建立复杂转录组预测相关性基准(r=0.268)。通过逆向推理,在结直肠癌谱系中进行虚拟CRISPR扰动。框架自主推翻经典机制假设,发现突变KRAS在驱动5-氟尿嘧啶耐药中具有层级主导地位(Δ=-0.0469),其“KRAS护盾”映射至MAPK/PI3K通路。此外,代理层识别出“PIK3CA悖论”:修复PIK3CA反而提升化疗耐药性(Δ=+0.0085),因触发补偿性反馈回路,过度激活主导的MAPK生存通路。
原文摘要 · Abstract (English)
Precision oncology is currently limited by the small-N, large-P paradox, where high-dimensional genomic data is abundant but pharmacological response samples are sparse. While deep learning achieves predictive accuracy, it frequently fails to provide the mechanistic clarity required for clinical adoption. We present the Contextual Invertible World Model (CIWM), a Neuro-Symbolic Agentic Framework that bridges this gap by integrating a quantitative machine learning emulator with a Large Language Model reasoning layer. Utilising a stringently curated, high-fidelity data engineering pipeline on the Sanger GDSC dataset (\( N=83 \)), we isolate true biological signals from in vitro artifacts to establish a rigorous baseline predictive correlation for complex transcriptomics (\( r=0.268 \)). Through Inverse Reasoning, we perform in silico CRISPR perturbations across the colorectal landscape. The framework autonomously overturns classical mechanistic assumptions, identifying a hierarchical dominance of mutant KRAS over the APC/Wnt-axis in driving 5-fluorouracil resistance (\( Δ=-0.0469 \)) via a "KRAS Shield" mapped to MAPK/PI3K networks. Furthermore, the agentic layer identified a "PIK3CA Paradox", revealing that repairing PIK3CA inadvertently increases chemoresistance (\( Δ=+0.0085 \)) by triggering a compensatory feedback loop that hyperactivates the dominant MAPK survival pathway.
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