STINR: Deciphering Spatial Transcriptomics via Implicit Neural Representation

Spatial transcriptomics (ST) are emerging technologies that reveal spatial distributions of gene expressions within tissues, serving as important ways to uncover biological insights. However, the irregular spatial profiles and variability of genes make it challenging to integrate spatial information with gene expression under a computational framework. Current algorithms mostly utilize spatial graph neural networks to encode spatial information, which may incur increased computational costs and may not be flexible enough to depict complex spatial configurations. In this study, we introduce a concise yet effective representation framework, STINR, for deciphering ST data. STINR leverages an implicit neural representation (INR) to continuously represent ST data, which efficiently characterizes spatial and slice-wise correlations of ST data by inheriting the implicit smoothness of INR. STINR allows easier integration of multiple slices and multi-omics without any alignment, and serves as a potent tool for various biological tasks including gene imputation, gene denoising, spatial domain detection, and cell-type deconvolution stemed from ST data. In particular, STINR identifies the thinnest cortex layer in the dorsolateral prefrontal cortex which previous methods were unable to achieve, and more accurately identifies tumor regions in the human squamous cell carcinoma, showcasing its practical value for biological discoveries. Code at https://github.com/YisiLuo/STINR.