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ancient dna reconstruction 1corruption-aware training 1genomic transformers 1knowledge-guided masking 1masked language modeling 1

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cs.LG2026

VESTIGE: A Knowledge-Guided Masking Strategy for Corruption-Aware Fine-Tuning of Genomic Transformers, Validated on Ancient DNA Reconstruction

Angshuman Chakravertty, Rahul Maheshwari

The paper presents VESTIGE, a parameter‑free masking strategy that aligns masked language model training with measured per‑position DNA damage profiles, improving ancient DNA recon…