STFormer: Learning to Explore Spot Relationships for Spatial Transcriptomics Prediction from Histology of Colorectal Cancer

Spatial transcriptomics (ST) offers insights into gene expression patterns within tumor microenvironments, but its widespread application is impeded by cost constraints. To address this, predicting ST from Histology emerges as a cost-effective alternative. However, current methods such as STNet, HistoGene, and Hist2ST exhibit limitations, either overlooking stain variation across datasets or failing to well explore inter-spot correlations in scenarios with limited Whole Slide Image (WSI) data. In response, we present STFormer, a deep learning approach that incorporates the Style-Aug module to enhance feature generalization through medically-irrelevant style transfer augmentation. Additionally, the Cross-WSI Transformer module is introduced to capture Cross-WSI spot relationships efficiently. Our experimental results, conducted on both internal and external datasets, demonstrate that STFormer surpasses existing methods by a substantial margin. This showcases its potential as a powerful tool for spatial transcriptomics predictions, addressing critical gaps in current methodologies.