GenoTrace: Inheritable Watermarks for Genome Foundation Model Distillation
Can a genome model retain a detectable record of the synthetic sequences used to train it? We study watermark inheritance through distillation with GenoTrace, a codon-aware extension of green-list watermarking. Two token-level factors modulate the teacher's generation bias using codon position and organism-specific codon usage. The resulting sequences train a smaller student, whose outputs are audited without an active watermark processor. In a three-seed GenomeOcean-500M-to-100M experiment, the joint configuration achieves a mean audit score of 17.88 and 94.5% detection at a fixed threshold. It retains 49.0% detection after key-aware token substitution, compared with 0% for the available...
| Authors | Guang Yang, Fengchen Liu |
|---|---|
| Primary category | cs.CR |
| Published | 27 September 2026 |
| Last updated at source | 1 October 2026 |
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