Gene co-expression maps transcriptome-wide gene-gene relationships, yet high-quality estimates cover less than half the genome. Meanwhile, spatial omics either profiles restricted in situ panels or lacks cellular resolution. Extending co-expression transcriptome-wide could overcome these limitations by inferring unassa...
Concord is a novel single-cell FM that explicitly models relationships between gene identities and expression levels through a collaborative rotary attention (CRA) mechanism, and employs two collaborative attention modes: a gene-to-expression rotational attention that produces gene-enhanced expression representations,...
Kaichen Xu, Mianpeng Liu, Hao Wu et al.· Proceedings of the 32nd ACM...· 0 citations
Cell type standardization plays a central role in integrating biological knowledge across single-cell studies. While standardized resources (e.g., Cell Ontology, Nomenclature Frameworks) provide unified vocabularies of cell populations, scientific publications and public datasets continue to use heterogeneous study-spe...
Peng Xie, Rongjia Zhou, Zhi-Li Ou et al.· arXiv.org· 0 citations
DiffPro, a novel framework that integrates a Latent Diffusion Model (LDM) as a structural prior, confirms that the diffusion prior successfully regularizes the latent space, mitigating task representation collapse and enabling robust, high-precision predictions for combination therapy design.
Shu-Ting Jin, Xu Guo, An-Qi Huang et al.· Proceedings of the 32nd ACM...· 0 citations
Foundation models (FMs) have recently transformed single-cell genomics by learning transferable representations from large-scale single-cell data, enabling a wide range of downstream biomedical applications. Inspired by natural language processing, existing single-cell FMs adapt transformer architectures by treating ge...
Kaichen Xu, Mianpeng Liu, Hao Wu et al.· Proceedings of the 32nd ACM...· 0 citations
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