Spatial transcriptomics captures molecular states within cells and their organisation in tissue. However, integrating fine-grained gene information with spatial context at scale remains challenging for existing foundation models. Here we present NexuST, a hierarchical foundation model that repeatedly interleaves gene-l...
Hai-Ping Liu, Qian Zhao, Li-Jing Lin et al.· bioRxiv· 0 citations
This review systematically analyzes the emerging landscape of FMs in omics research, spanning sequence modeling, cell state characterization, and multimodal integration, and proposes a roadmap for the next generation of FMs, advocating for architectures that move beyond statistical correlation to incorporate causal rea...
Haozhe Liu, Wenhao Cai, Yizheng Sun et al.· Briefings in Bioinformatics· 0 citations
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