VESTIGE: A Knowledge-Guided Masking Strategy for Corruption-Aware Fine-Tuning of Genomic Transformers, Validated on Ancient DNA Reconstruction
Standard masked-language-model fine-tuning applies a uniform masking probability across every token position, assuming reconstruction difficulty is position-agnostic. When the degradation process is characterised and concentrated at predictable positions, this assumption fails: at peak damage sites the model can underperform a frequency-matched random predictor. We introduce VESTIGE, a parameter-free, drop-in replacement for the standard MLM collator that aligns the masking distribution with an empirically measured per-position corruption profile. We apply it to ancient DNA (aDNA) reconstruction, where cytosine deamination produces a position-dependent C-to-T / G-to-A gradient quantified ...
| Authors | Angshuman Chakravertty, Rahul Maheshwari |
|---|---|
| Primary category | cs.LG |
| Published | 30 July 2026 |
| Last updated at source | 30 July 2026 |
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