Multi-Slice Spatial Transcriptomics Data Integration Analysis with STG3Net

TL;DR

STG3Net is a novel deep learning framework that effectively integrates multi-slice spatial transcriptomics data by correcting batch effects and identifying spatial domains, outperforming existing methods.

Contribution

We introduce STG3Net, a new method combining graph autoencoders and adversarial learning for robust multi-slice SRT data integration and batch effect correction.

Findings

STG3Net outperforms existing methods in accuracy and consistency.

It effectively preserves biological variability across slices.

Demonstrated on three diverse SRT datasets.

Abstract

With the rapid development of the latest Spatially Resolved Transcriptomics (SRT) technology, which allows for the mapping of gene expression within tissue sections, the integrative analysis of multiple SRT data has become increasingly important. However, batch effects between multiple slices pose significant challenges in analyzing SRT data. To address these challenges, we have developed a plug-and-play batch correction method called Global Nearest Neighbor (G2N) anchor pairs selection. G2N effectively mitigates batch effects by selecting representative anchor pairs across slices. Building upon G2N, we propose STG3Net, which cleverly combines masked graph convolutional autoencoders as backbone modules. These autoencoders, integrated with generative adversarial learning, enable STG3Net to achieve robust multi-slice spatial domain identification and batch correction. We comprehensively evaluate the feasibility of STG3Net on three multiple SRT datasets from different platforms, considering accuracy, consistency, and the F1LISI metric (a measure of batch effect correction efficiency). Compared to existing methods, STG3Net achieves the best overall performance while preserving the biological variability and connectivity between slices. Source code and all public datasets used in this paper are available at https://github.com/wenwenmin/STG3Net and https://zenodo.org/records/12737170.