arXiv:2512.04333cs.LGcs.AI2025-12

用图神经网络递归筛选癌症标志基因,提升早期检测准确率。

RGE-GCN: Recursive Gene Elimination with Graph Convolutional Networks for RNA-seq based Early Cancer Detection

  • 构建基因表达图谱,用GCN联合选择与分类
  • 在肺癌等三类癌症数据中准确率超传统工具
  • 结果基因关联经典癌通路,适合生物标志物发现

早期癌症检测对提高生存率至关重要,但从RNA-seq数据中识别可靠生物标志物仍具挑战。数据维度高,传统统计方法难以捕捉基因间复杂关系。本文提出RGE-GCN(递归基因剔除结合图卷积网络),将特征选择与分类整合于统一流程。通过基因表达谱构建图结构,利用图卷积网络区分癌与正常样本,并采用集成梯度识别关键基因。通过递归剔除低贡献基因,模型收敛至紧凑且可解释的标志基因集。在合成数据及肺、肾、宫颈癌真实RNA-seq队列上评估,所有数据集均优于DESeq2、edgeR和limma-voom等标准工具。所选基因显著富集于PI3K-AKT、MAPK、SUMO化及免疫调控等已知癌通路。结果表明RGE-GCN在基于RNA-seq的早期癌症检测与标志物发现中具有普适潜力。

原文摘要 · Abstract (English)

Early detection of cancer plays a key role in improving survival rates, but identifying reliable biomarkers from RNA-seq data is still a major challenge. The data are high-dimensional, and conventional statistical methods often fail to capture the complex relationships between genes. In this study, we introduce RGE-GCN (Recursive Gene Elimination with Graph Convolutional Networks), a framework that combines feature selection and classification in a single pipeline. Our approach builds a graph from gene expression profiles, uses a Graph Convolutional Network to classify cancer versus normal samples, and applies Integrated Gradients to highlight the most informative genes. By recursively removing less relevant genes, the model converges to a compact set of biomarkers that are both interpretable and predictive. We evaluated RGE-GCN on synthetic data as well as real-world RNA-seq cohorts of lung, kidney, and cervical cancers. Across all datasets, the method consistently achieved higher accuracy and F1-scores than standard tools such as DESeq2, edgeR, and limma-voom. Importantly, the selected genes aligned with well-known cancer pathways including PI3K-AKT, MAPK, SUMOylation, and immune regulation. These results suggest that RGE-GCN shows promise as a generalizable approach for RNA-seq based early cancer detection and biomarker discovery (https://rce-gcn.streamlit.app/ ).

癌症检测图神经网络生物标志物RNA-seq

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