DAHGT-CCI: Dynamic Heterogeneous Graph Transformer for Spatial Transcriptomics Cell-Cell Interaction Inference

Abstract

Spatial transcriptomics has significantly advanced tissue biology and makes it possible to study the spatial interactions of cells in the microenvironment of complex tissues. However, accurately inferring intercellular communication from these data remains challenging due to the need to effectively integrate spatial topology with high-dimensional gene expression information. To address this challenge, we propose DAHGT-CCI, a novel method for inferring intercellular communication from spatial transcriptomics data. By fusing multimodal heterogeneous features to construct a unified node representation and introducing a meta-relation-aware dynamic attention mechanism, DAHGT-CCI can adaptively learn the weights of edges in the graph, thereby achieving superior precision and fine-grained inference of intercellular interactions. We evaluated the performance of DAHGT-CCI on six different spatial transcriptomics datasets. In these benchmarks, DAHGT-CCI outperformed existing graph-based learning methods and cell-cell communication inference models in terms of accuracy, AUROC, recall, and F1 score. These results demonstrate that DAHGT-CCI can more accurately reconstruct cell communication networks in complex tissue microenvironments, offering an indispensable computational tool for studying developmental processes, disease mechanisms, and potential therapeutic targets from a spatially resolved perspective.