arXiv:2502.21011cs.CV2025-02被引 10

MagNet通过多级注意力图网络,实现高分辨率空间转录组的精准预测。

MagNet: Multi-Level Attention Graph Network for Predicting High-Resolution Spatial Transcriptomics

  • 构建多级注意力图网络,融合多分辨率图像特征
  • 在三种分辨率下均达当前最优性能,尤其在高分辨率上优势显著
  • 适合从事高分辨率空间转录组研究的生物医学与计算领域学者

空间转录组学(ST)的快速发展为探索组织微环境中的基因表达模式提供了新机遇。现有研究通过整合病理图像来推断基因表达,以应对生成空间转录组数据成本高、耗时长的问题。然而,随着空间转录组分辨率持续提升,现有方法仍主要聚焦于低分辨率点级基因表达预测,面对高分辨率(HD)数据时面临严重的信息瓶颈。为此,本文提出MagNet,一种用于高分辨率HD数据精准预测的多级注意力图网络。MagNet采用跨注意力层分层整合多分辨率图像块特征,并利用GAT-Transformer模块聚合邻域信息。通过融合多层级特征,有效克服了低分辨率输入对高分辨率基因表达预测的限制。我们在私有和公开两个空间转录组数据集上,分别在三个不同分辨率水平下系统评估了MagNet及现有模型。结果表明,MagNet在点级与高分辨率区块级预测中均达到当前最优表现,为高分辨率HD级空间转录组研究提供新方法与基准。代码已开源:https://github.com/Junchao-Zhu/MagNet。

原文摘要 · Abstract (English)

The rapid development of spatial transcriptomics (ST) offers new opportunities to explore the gene expression patterns within the spatial microenvironment. Current research integrates pathological images to infer gene expression, addressing the high costs and time-consuming processes to generate spatial transcriptomics data. However, as spatial transcriptomics resolution continues to improve, existing methods remain primarily focused on gene expression prediction at low-resolution spot levels. These methods face significant challenges, especially the information bottleneck, when they are applied to high-resolution HD data. To bridge this gap, this paper introduces MagNet, a multi-level attention graph network designed for accurate prediction of high-resolution HD data. MagNet employs cross-attention layers to integrate features from multi-resolution image patches hierarchically and utilizes a GAT-Transformer module to aggregate neighborhood information. By integrating multilevel features, MagNet overcomes the limitations posed by low-resolution inputs in predicting high-resolution gene expression. We systematically evaluated MagNet and existing ST prediction models on both a private spatial transcriptomics dataset and a public dataset at three different resolution levels. The results demonstrate that MagNet achieves state-of-the-art performance at both spot level and high-resolution bin levels, providing a novel methodology and benchmark for future research and applications in high-resolution HD-level spatial transcriptomics. Code is available at https://github.com/Junchao-Zhu/MagNet.

空间转录组多级注意力高分辨率图神经网络

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