arXiv:2505.01696q-bio.GNcs.AI2025-05综述被引 3

首篇系统综述可解释图模型在多模态生物医学数据中的应用,助力精准医疗落地。

Interpretable graph-based models on multimodal biomedical data integration: A technical review and benchmarking

  • 按可解释性分类四类方法,梳理图构建与解释技术演进趋势。
  • 在阿尔茨海默病数据上对比四种解释方法,发现SHAP和敏感性分析覆盖更广生物通路。
  • 提供流程图指导研究者平衡计算成本与解释深度,适合临床转化研究者。

整合影像、组学与临床记录等异构生物医学数据有助于精准诊断与个性化治疗。图模型通过捕捉非欧几里得数据的空间与关系结构实现融合,但临床应用需满足监管级可解释性要求。本文首次系统回顾2019年1月至2024年9月间发表的26项可解释图模型研究,多数聚焦癌症等疾病分类,采用基于简单相似度的静态图结构,图原生解释器罕见,主流仍为梯度显著性、SHAP等非图领域后处理方法。我们归纳四类可解释性范式,指出图中图层次、知识图谱边、动态拓扑学习等趋势,并在阿尔茨海默病队列中开展实证基准测试。结果表明,SHAP与敏感性分析能恢复最广泛的已知AD通路及基因本体术语,而梯度显著性与图掩码揭示互补的代谢与转运特征。置换检验显示四者均优于随机基因集,但各有权衡:SHAP与图掩码揭示更深生物学意义,但计算成本高;梯度显著性与敏感性分析更快但分辨率较低。我们还提供涵盖图构建、解释器选择与资源分配的步骤流程图,帮助研究者在透明性与性能间取舍。本综述总结了多模态医学中可解释图学习现状,基准化领先技术,并指明未来方向,包括先进XAI工具与未充分研究疾病,为方法开发者与转化科学家提供简洁参考。

原文摘要 · Abstract (English)

Integrating heterogeneous biomedical data including imaging, omics, and clinical records supports accurate diagnosis and personalised care. Graph-based models fuse such non-Euclidean data by capturing spatial and relational structure, yet clinical uptake requires regulator-ready interpretability. We present the first technical survey of interpretable graph based models for multimodal biomedical data, covering 26 studies published between Jan 2019 and Sep 2024. Most target disease classification, notably cancer and rely on static graphs from simple similarity measures, while graph-native explainers are rare; post-hoc methods adapted from non-graph domains such as gradient saliency, and SHAP predominate. We group existing approaches into four interpretability families, outline trends such as graph-in-graph hierarchies, knowledge-graph edges, and dynamic topology learning, and perform a practical benchmark. Using an Alzheimer disease cohort, we compare Sensitivity Analysis, Gradient Saliency, SHAP and Graph Masking. SHAP and Sensitivity Analysis recover the broadest set of known AD pathways and Gene-Ontology terms, whereas Gradient Saliency and Graph Masking surface complementary metabolic and transport signatures. Permutation tests show all four beat random gene sets, but with distinct trade-offs: SHAP and Graph Masking offer deeper biology at higher compute cost, while Gradient Saliency and Sensitivity Analysis are quicker though coarser. We also provide a step-by-step flowchart covering graph construction, explainer choice and resource budgeting to help researchers balance transparency and performance. This review synthesises the state of interpretable graph learning for multimodal medicine, benchmarks leading techniques, and charts future directions, from advanced XAI tools to under-studied diseases, serving as a concise reference for method developers and translational scientists.

可解释性图神经网络多模态生物医学

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。