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Open access Oct 2026

Alignment-Aware Genomic Coordinate Encoding for Long-Range DNA Modeling

Current genomic foundation models (GFMs) largely inherit the language-modeling paradigm over contiguous token sequences, treating DNA as ordinary text. The genome, however, is a coordinate-based system of sparse signals: the entities that matter, such as individual variants, regulatory elements, and distal gene interac...

Xu Yang, Chen-Chen Qin, Fang Wang et al. · 0 citations
Open access Sep 2026

scTransMIL bridges patient-level disease states and single-cell transcriptomics for cancer screening and heterogeneity inference

Single-cell sequencing offers profound insights into tumor complexity. However, reliably linking individual cellular profiles to overall sample-level phenotypes remains computationally challenging, particularly when cell-specific annotations are absent. This disconnect limits the technology’s utility in studying underl...

Zhen-Chao Tang, Fang Wang, Fan Yang et al. · 2 citations

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