Boundary-Aware Clustering of Spatial Transcriptomics Data via Fourier Feature Mapping and Dynamic Self-Supervision.

Abstract

Accurate identification of fine-grained spatial domains within tissues using spatial transcriptomics data is critical for understanding tissue development, disease pathology, and cellular interactions. However, inherent spatial heterogeneity in spatial transcriptomic data, characterized by significant discontinuity in spatial gradients of gene expression, makes it difficult for existing clustering methods to precisely delineate fine-grained structures and produce ambiguous spatial boundaries. To address this challenge, this paper proposes FPS-MGCN - a multi-view graph convolutional network integrating Fourier feature mapping with dynamic pseudo-label self-supervision. In detail, to tackle boundary ambiguity caused by spatial heterogeneity, we introduce a Fourier sine-cosine feature mapping that explicitly constructs high-frequency feature channels to enhance sensitivity to high-frequency spatial gradients such as tissue boundaries. In addition, a dynamic pseudo-label self-supervision strategy is further designed, providing progressive semantic constraints that smooth noise interference and enhance recognition in spatial boundary regions. The model integrates raw gene expression, Fourier-mapped features, and spatial adjacency information through a multi-view GCN encoder, employing an attention mechanism for adaptive fusion. Extensive experimental results demonstrate that the proposed FPS-MGCN identifies critical fine-grained structures difficult to resolve by traditional methods and outperforms other state-of-the-art methods in spatial domain identification.