Sparse Attention-based Hierarchical Node Representation for Spatial Domain Identification

Using deep learning models on spatial transcriptomics data to identify the spatial domain is crucial for uncovering the spatial distribution of cells and gene expression patterns within tissues, essential for understanding complex biological processes and disease mechanisms. Existing methods for spatial domain partitioning often rely on predefined adjacency relationships at a single scale, overlooking the hierarchical structure and functional characteristics of biological tissues. In this paper, we propose SpaNFM, a novel method that leverages sparse attention-based hierarchical node representation and multi-view contrastive learning for spatial domain identification in spatial transcriptomics data. The SpaNFM first treats each spot as a node and constructs two views using different data augmentation techniques based on tissue image information, gene expression profiles, and spatial coordinates of cells. Subsequently, SpaNFM utilizes a sparse attention-based hierarchical node fusion module to generate coarse-grained node representations. This fine-to-coarse hierarchical structure integrates complementary information from multi-granularity node features and reduces model complexity due to the decreased node size. The model parameters are updated using gene expression reconstruction loss and contrastive loss on the coarse-grained node representations from the two views. Finally, the learned node features are subjected to downstream clustering using the Leiden algorithm. We tested SpaNFM on the human dorsolateral prefrontal cortex dataset. The results demonstrate that SpaNFM outperforms other state-of-the-art methods in most cases. The data and code are available at: https://github.com/weiba/SpaNFM