Interpretable high-resolution dimension reduction of spatial transcriptomics data by DeepFuseNMF

Junjie Tang, Zihao Chen, Kun Qian, Siyuan Huang, Yang He, Shenyi Yin, Xinyu He, Buqing Ye, Yan Zhuang, Hongxue Meng, Jianzhong Xi, Ruibin Xi
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Abstract

Spatial transcriptomics (ST) technologies have revolutionized tissue architecture studies by capturing gene expression with spatial context. However, high-dimensional ST data often have limited spatial resolution and exhibit considerable noise and sparsity, posing significant challenges in deciphering subtle spatial structures and underlying biological activities. Here, we introduce DeepFuseNMF, a multi-modal dimension reduction framework that enhances spatial resolution by integrating ST gene expression with high-resolution histology images. DeepFuseNMF incorporates non-negative matrix factorization into a neural network architecture, enabling the identification of interpretable, high resolution embeddings. Furthermore, DeepFuseNMF can simultaneously analyze multiple samples and is compatible with various types of histology images. Extensive evaluations on synthetic and real ST datasets from various technologies and tissue types demonstrate that DeepFuseNMF can effectively produce highly interpretable, high-resolution embeddings, and detects refined spatial structures. DeepFuseNMF represents a powerful approach for integrating ST data and histology images, offering deeper insights into complex tissue structures and functions.
利用 DeepFuseNMF 对空间转录组学数据进行可解释的高分辨率维度缩减
空间转录组学(ST)技术通过捕捉具有空间背景的基因表达,彻底改变了组织结构研究。然而,高维空间转录组学数据的空间分辨率往往有限,并表现出相当大的噪声和稀疏性,这给解读微妙的空间结构和潜在的生物活动带来了巨大挑战。在此,我们介绍一种多模态降维框架 DeepFuseNMF,它通过整合 ST 基因表达和高分辨率组织学图像来提高空间分辨率。DeepFuseNMF 将非负矩阵因式分解纳入神经网络架构,从而能够识别可解释的高分辨率嵌入。此外,DeepFuseNMF 还能同时分析多个样本,并兼容各种类型的组织学图像。在来自不同技术和组织类型的合成和真实 ST 数据集上进行的广泛评估表明,DeepFuseNMF 能有效生成可解释性高的高分辨率嵌入,并能检测到精细的空间结构。DeepFuseNMF 是一种整合 ST 数据和组织学图像的强大方法,能让人们更深入地了解复杂的组织结构和功能。
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