用卷积网络从病理图预测高分辨率基因表达,效率更高更稳定。
Img2ST-Net: Efficient High-Resolution Spatial Omics Prediction from Whole Slide Histology Images via Fully Convolutional Image-to-Image Learning
- 采用全卷积架构并行生成高分辨率基因图谱
- 在8μm分辨率下实现高效预测,速度比传统方法快数倍
- 适合需要低成本高通量空间转录组分析的研究者
近年来多模态人工智能在从常规病理图像生成昂贵的空间转录组(ST)数据方面展现出巨大潜力,有助于降低其高昂成本与耗时。然而,随着ST分辨率提升(如Visium HD达到8μm或更细),计算与建模挑战加剧。传统逐点回归方法在该尺度下效率低且不稳定,同时高分辨率ST固有的极端稀疏性与低表达水平进一步增加了预测与评估难度。为此,我们提出Img2ST-Net,一种基于全卷积的图像到空间组学生成框架,实现高效、并行的高分辨率ST预测。不同于传统逐点推理,Img2ST-Net将高清ST数据建模为超像素表示,将图像到组学推断转化为具有数百至数千输出通道的超内容图像生成任务。该设计不仅提升计算效率,还能更好保留空间组学固有的空间结构。为增强在稀疏表达下的鲁棒性,我们引入SSIM-ST——一种专为高分辨率ST分析设计的结构相似性评估指标。本工作构建了一个可扩展、生物学一致的高分辨率ST预测框架,为下一代具备分辨率感知能力的稳健模型奠定基础。源代码已公开于https://github.com/hrlblab/Img2ST-Net。
原文摘要 · Abstract (English)
Recent advances in multi-modal AI have demonstrated promising potential for generating the currently expensive spatial transcriptomics (ST) data directly from routine histology images, offering a means to reduce the high cost and time-intensive nature of ST data acquisition. However, the increasing resolution of ST, particularly with platforms such as Visium HD achieving 8um or finer, introduces significant computational and modeling challenges. Conventional spot-by-spot sequential regression frameworks become inefficient and unstable at this scale, while the inherent extreme sparsity and low expression levels of high-resolution ST further complicate both prediction and evaluation. To address these limitations, we propose Img2ST-Net, a novel histology-to-ST generation framework for efficient and parallel high-resolution ST prediction. Unlike conventional spot-by-spot inference methods, Img2ST-Net employs a fully convolutional architecture to generate dense, HD gene expression maps in a parallelized manner. By modeling HD ST data as super-pixel representations, the task is reformulated from image-to-omics inference into a super-content image generation problem with hundreds or thousands of output channels. This design not only improves computational efficiency but also better preserves the spatial organization intrinsic to spatial omics data. To enhance robustness under sparse expression patterns, we further introduce SSIM-ST, a structural-similarity-based evaluation metric tailored for high-resolution ST analysis. We present a scalable, biologically coherent framework for high-resolution ST prediction. Img2ST-Net offers a principled solution for efficient and accurate ST inference at scale. Our contributions lay the groundwork for next-generation ST modeling that is robust and resolution-aware. The source code has been made publicly available at https://github.com/hrlblab/Img2ST-Net.
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。