arXiv:2603.25247cs.CVcs.AI2026-03被引 1

用全连接注意力建模基因表达空间关系,提升病理图像预测精度。

FEAST: Fully Connected Expressive Attention for Spatial Transcriptomics

  • 构建全连接图捕捉所有基因位点间交互,突破传统稀疏图限制。
  • 引入负向感知注意力,识别生物中的抑制性相互作用,提升模型解释性。
  • 采用非网格采样策略,获取更丰富的组织形态上下文信息,减少信息丢失。

空间转录组学(Spatial Transcriptomics, ST)可提供具有空间分辨率的基因表达数据,对理解组织结构和复杂疾病至关重要。然而其高昂成本限制了广泛应用,因此研究重点转向从易获取的全切片图像推断空间基因表达。尽管图神经网络被用于建模组织区域间的交互,但其依赖预定义的稀疏图,无法考虑潜在的位点对交互,制约了复杂生物关系的捕捉。为此,我们提出FEAST(Fully connected Expressive Attention for Spatial Transcriptomics),一种基于注意力机制的框架,将组织建模为全连接图,从而考虑所有成对交互。为更好反映生物互作,引入负向感知注意力,同时建模兴奋性和抑制性交互,捕捉标准注意力常忽略的负向关系。此外,为缓解标准位点图像提取中截断或忽略上下文导致的信息损失,提出非网格采样策略,从中间区域收集额外图像,使模型能捕获更丰富的形态上下文。在公开的ST数据集上实验表明,FEAST在基因表达预测上优于现有最先进方法,并生成符合生物学意义的注意力图,清晰揭示正负向交互。代码已开源:https://github.com/starforTJ/FEAST。

原文摘要 · Abstract (English)

Spatial Transcriptomics (ST) provides spatially-resolved gene expression, offering crucial insights into tissue architecture and complex diseases. However, its prohibitive cost limits widespread adoption, leading to significant attention on inferring spatial gene expression from readily available whole slide images. While graph neural networks have been proposed to model interactions between tissue regions, their reliance on pre-defined sparse graphs prevents them from considering potentially interacting spot pairs, resulting in a structural limitation in capturing complex biological relationships. To address this, we propose FEAST (Fully connected Expressive Attention for Spatial Transcriptomics), an attention-based framework that models the tissue as a fully connected graph, enabling the consideration of all pairwise interactions. To better reflect biological interactions, we introduce negative-aware attention, which models both excitatory and inhibitory interactions, capturing essential negative relationships that standard attention often overlooks. Furthermore, to mitigate the information loss from truncated or ignored context in standard spot image extraction, we introduce an off-grid sampling strategy that gathers additional images from intermediate regions, allowing the model to capture a richer morphological context. Experiments on public ST datasets show that FEAST surpasses state-of-the-art methods in gene expression prediction while providing biologically plausible attention maps that clarify positive and negative interactions. Our code is available at https://github.com/starforTJ/ FEAST.

空间转录组注意力机制生物信息

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。