arXiv:2503.22939cs.LGq-bio.QM2025-03被引 11

用图神经网络整合多组学数据,精准识别31种癌症的生物标志物。

Interpretable Graph Kolmogorov-Arnold Networks for Multi-Cancer Classification and Biomarker Identification using Multi-Omics Data

  • 基于柯尔莫哥洛夫-阿诺德定理构建可解释模型,融合基因、miRNA与甲基化数据。
  • 在31种癌症上实现96.28%分类准确率,实验波动小,优于现有深度学习模型。
  • 识别出的标志物经功能富集分析验证为癌症相关,适合临床转化研究者使用。

整合异质性多组学数据以支持精准癌症诊断仍是系统级分析的挑战。本文提出多组学图柯尔莫哥洛夫-阿诺德网络(MOGKAN),结合mRNA、miRNA序列及DNA甲基化数据,并利用蛋白质-蛋白质相互作用(PPI)网络对31种癌症类型进行分类。该方法通过DESeq2、LIMMA和LASSO回归降低数据维度,同时保留关键生物学特征。模型架构基于柯尔莫哥洛夫-阿诺德定理,采用可训练的单变量函数,提升可解释性与特征分析能力。MOGKAN达到96.28%的分类准确率,且实验变异低,优于同类深度学习模型。经基因本体(GO)与京都基因与基因组百科全书(KEGG)富集分析,所识别的生物标志物被证实与癌症相关。该方法融合多组学与图神经网络,在保持高预测性能的同时具备强可解释性,有望推动复杂多组学数据向临床可操作诊断转化。

原文摘要 · Abstract (English)

The integration of heterogeneous multi-omics datasets at a systems level remains a central challenge for developing analytical and computational models in precision cancer diagnostics. This paper introduces Multi-Omics Graph Kolmogorov-Arnold Network (MOGKAN), a deep learning framework that utilizes messenger-RNA, micro-RNA sequences, and DNA methylation samples together with Protein-Protein Interaction (PPI) networks for cancer classification across 31 different cancer types. The proposed approach combines differential gene expression with DESeq2, Linear Models for Microarray (LIMMA), and Least Absolute Shrinkage and Selection Operator (LASSO) regression to reduce multi-omics data dimensionality while preserving relevant biological features. The model architecture is based on the Kolmogorov-Arnold theorem principle and uses trainable univariate functions to enhance interpretability and feature analysis. MOGKAN achieves classification accuracy of 96.28 percent and exhibits low experimental variability in comparison to related deep learning-based models. The biomarkers identified by MOGKAN were validated as cancer-related markers through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. By integrating multi-omics data with graph-based deep learning, our proposed approach demonstrates robust predictive performance and interpretability with potential to enhance the translation of complex multi-omics data into clinically actionable cancer diagnostics.

癌症分类多组学可解释性图神经网络

Thank you to arXiv for use of its open access interoperability. PaperDance 不是 arXiv 官方产品;中文卡片由大模型生成,请以原文为准。