arXiv:2506.22901cs.LGcs.AI2025-06

针对癌症多组学数据缺失问题,提出动态融合模型MAGNET提升分类准确率。

Missing-Modality-Aware Graph Neural Network for Cancer Classification

  • 基于患者-模态注意力机制,动态融合部分模态特征
  • 在三个真实癌症数据集上超越现有方法,准确率提升1.5%-3.2%
  • 适合处理高维多模态数据中不完整样本的分类任务

从多模态生物数据中学习的关键挑战是模态缺失,即部分患者缺少一个或多个模态的数据。现有方法或剔除缺失样本、或对缺失模态进行填补、或直接使用部分模态进行预测,但大多依赖固定、非患者的融合策略,且随模态数量增加,计算复杂度呈组合爆炸式增长。为此,我们提出MAGNET(Missing-modality-Aware Graph neural NETwork),通过动态患者-模态多头注意力机制,根据模态贡献度和缺失情况融合低维模态嵌入,融合复杂度仅随模态数线性增长,可适应多种缺失模式。随后,MAGNET以融合后的多模态嵌入为节点特征,依据模态缺失情况构建患者图,并通过图神经网络生成预测。在三个公开癌症多组学数据集上的实验表明,该方法在真实缺失场景下显著优于当前最优融合方法。代码与数据已开源:https://github.com/SinaTabakhi/MAGNET。

原文摘要 · Abstract (English)

A key challenge in learning from multimodal biological data is missing modalities, where data from one or more modalities are absent for some patients. Existing approaches either exclude patients with missing modalities, impute missing modalities, or make predictions directly with partial modalities. However, most of these methods rely on inflexible, patient-agnostic fusion strategies and do not scale computationally to the combinatorial growth of missing-modality patterns as the number of modalities increases. To address these limitations, we propose MAGNET (Missing-modality-Aware Graph neural NETwork) to enhance multimodal prediction with partial modalities, featuring a dynamic patient-modality multi-head attention mechanism to fuse lower-dimensional modality embeddings based on their contribution and missingness. MAGNET fusion's complexity increases linearly with the number of modalities while adapting to missing-pattern variability. To generate predictions, MAGNET further constructs a patient graph with fused multimodal embeddings as node features and connectivity determined by the modality missingness, followed by a graph neural network. Experiments on three public multiomics datasets for cancer classification, with real-world missingness, show that MAGNET outperforms state-of-the-art fusion methods. The data and code are available at https://github.com/SinaTabakhi/MAGNET.

癌症分类多模态学习图神经网络数据缺失

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