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MUSS: A Multi-scale and Sequence-based Model for Single-cell Gene Regulation
MUSS is a sequence-based multi-scale model that jointly represents DNA sequence, chromatin accessibility, and gene expression at single-cell resolution. It uses a frozen pre-trained sequence encoder and integrates peak and gene representations via self-attention and distance-biased interactions. The model achieves strong performance on gene expression prediction, enhancer-gene linking, and zero-shot cell clustering.
Why it matters: Introduces a novel sequence-grounded multi-scale representation approach that outperforms baselines in single-cell regulatory modeling, with practical code and data release.
gene regulationsingle-cell omicsdeep learning