PGST: A prototype-guided parameter-efficient network for spatial transcriptomics prediction.

Abstract

Spatial transcriptomics (ST) aims to decode spatially resolved gene expression patterns while preserving tissue morphology. Current methods tend to use lower-cost deep learning approaches for gene expression prediction, yet face severe challenges. First, existing methods fail to give sufficient consideration to the spatial specificity of positional encoding inherent in ST; second, they neglect to leverage spatially coherent co-expression patterns across different domains; third, their reliance on linearly weighted aggregation induces vulnerability to noise and distribution shifts; and finally, these architectures exhibit limited parameter efficiency. To address these issues, we introduce prototype-guided network for spatial transcriptomics (PGST), which includes four parts: (1) oriented signal propagation through polar embedding strategy for spatial transcriptomics (PEST); (2) prototype-guided aggregation for global co-feature preservation; (3) global consistency enforcement via shared decoder with reconstruction loss; and (4) lightweight architectural design. Our framework integrates contrastive learning with graph neural networks to balance local-global spatial dependencies and cross-modal consistency. Experimental results on multiple datasets from ST demonstrate the superior performance of our PGST model than existing methods. Our source code is available at: https://github.com/RanSuLab/PGST https://github.com/RanSuLab/PGST.