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Yanlin Zhang

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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
Preprint Aug 2026

GenomeHarness: Harnessing Al Agents for Reliable Adaptation of Genome Language Models

GenomeHarness, an agentic harness for adapting genome language models through controlled search over fine-tuning recipes, improves mean test MCC in 47 settings, and shows gains on Genomic Benchmarks and on tasks where the root recipe is unstable or poorly matched.

Weicai Long, Yusen Hou, Houcheng Su et al. · 0 citations

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