stEnTrans: Transformer-Based Deep Learning for Spatial Transcriptomics Enhancement

The spatial position of cells within tissues and organs is crucial for the manifestation of their specific functions. Spatial transcriptomics technology enables comprehensive measurement of the gene expression patterns in tissues while retaining spatial information. However, current popular spatial transcriptomics techniques either have shallow sequencing depth or low resolution. We present stEnTrans, a deep learning method based on Transformer architecture that provides comprehensive predictions for gene expression in unmeasured or unexpectedly lost areas and enhances gene expression in original and imputed spots. Utilizing self-supervised learning approach, stEnTrans establishes proxy tasks on gene expression profiles without requiring additional data, mining intrinsic features of the tissues as supervisory information. We evaluate stEnTrans on six datasets and the results indicate superior performance in enhancing spatial resolution and predicting gene expression in unmeasured areas compared to other deep learning and traditional interpolation methods. Additionally, stEnTrans can also help the discovery of spatial patterns in spatial transcriptomics and enrich to more biologically significant pathways. Our source code is available at https://github.com/shuailinxue/stEnTrans .