StereoMM: a graph fusion model for integrating spatial transcriptomic data and pathological images
Spatial omics technologies, generating high-throughput and multimodal data, have necessitated the development of advanced data integration methods to facilitate comprehensive biological and clinical treatment discoveries. Based on the cross-attention concept, we developed an AI learning based toolchain called StereoMM, a graph based fusion model that can incorporate omics data such as gene expression, histological images, and spatial location. StereoMM uses an attention module for omics data interaction and a graph autoencoder to integrate spatial positions and omics data in a self-supervised manner. Applying StereoMM across various cancer types and platforms has demonstrated its robust capability. StereoMM outperforms competitors in identifying spatial regions reflecting tumour progression and shows promise in classifying colorectal cancer patients into deficient mismatch repair and proficient mismatch repair groups. The comprehensive inter-modal integration and efficiency of StereoMM enable researchers to construct spatial views of integrated multimodal features efficiently, advancing thorough tissue and patient characterization.
Authors
- Guibo Li (ORCID: https://orcid.org/0000-0002-6141-4931)
- Sha Liao (ORCID: https://orcid.org/0000-0001-5825-5514)
- Weimiao Yu (ORCID: https://orcid.org/0000-0001-5092-1009)
- Min Jian (ORCID: https://orcid.org/0000-0003-4985-5520)
- Huaqiang Huang (ORCID: https://orcid.org/0009-0000-5844-1261)
- Weixuan Cen
- Mei Li (ORCID: https://orcid.org/0000-0003-3310-2911)
- Feng Xi (ORCID: https://orcid.org/0000-0002-4170-3023)
- Bingying Luo (ORCID: https://orcid.org/0009-0001-6344-2645)
- Chi Qu (ORCID: https://orcid.org/0000-0002-3776-5512)
- Ao Chen (ORCID: https://orcid.org/0000-0002-9699-8340)
- Xin Liu (ORCID: https://orcid.org/0000-0003-3256-2940)
- Xing Liu (ORCID: https://orcid.org/0000-0003-1741-3437)
- Xue Zhang (ORCID: https://orcid.org/0000-0002-8297-9931)
- Xun Xu (ORCID: https://orcid.org/0000-0002-5338-5173)
- Guo Tang
- Fei Teng (ORCID: https://orcid.org/0000-0003-4913-7094)
- Yu Feng (ORCID: https://orcid.org/0000-0001-8358-8740)
- Wenyan Jiang (ORCID: https://orcid.org/0000-0002-1089-3450)
- Jinmiao Chen (ORCID: https://orcid.org/0000-0001-7547-6423)
- Xuanzhu Liu
- Jiajun Zhang (ORCID: https://orcid.org/0009-0005-7336-992X)
Institutions
- Nanyang Technological University (SG)
- Shanxi Medical University (CN)
- Duke-NUS Medical School (SG)
- CE Technologies (United Kingdom) (GB)
- Botswana Geoscience Institute (BW)
- BGI Research (CN)
Publication Details
- Journal
- Briefings in Bioinformatics
- Published
- 2025-04-23
- DOI
- https://doi.org/10.1093/bib/bbaf210
- Citations
- 4
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 3.22
Funders
- Centre Scientifique et Technique du Bâtiment