SpaMFG: a Spatial Multi-omics Integration Method based on Feature Grouping
Zilin Li, Litian Ma, Jingtao Liu, Wei Sun, Yan Li, Chenguang Zhao, Liang YuAbstract
Motivation
The rapid development of spatial multi-omics technology enables the simultaneous measurement of gene and protein expression alongside spatial location, providing valuable insights into tissue heterogeneity. However, challenges such as low spatial resolution and high feature dimensionality complicate data integration and biological interpretation.
Results
To address these issues, we propose SpaMFG, an innovative feature-group-level framework for interpretable spatial multi-omics integration. SpaMFG leverages spatial location information and introduces a spatial proximity weighting method to improve feature grouping accuracy. Additionally, it employs a new cross-omics feature group matching method that combines spatial location and Jaccard similarity to construct a weighted cost matrix, which is optimized using the Hungarian algorithm. This approach enhances the biological interpretability of cross-omics feature relationships. We evaluated SpaMFG's performance through comparative analysis on the human lymph node dataset, demonstrating its effectiveness. Further applications on human tonsils, mouse spleens, and mouse thymus datasets confirmed the robustness of SpaMFG in various biological contexts.
Availability
The source code for SpaMFG is available at https://github.com/LiangYu-Xidian/SpaMFG
Supplementary information
Supplementary data are available at Bioinformatics online.