Tracing model-generated DNA with position-independent watermarking

Abstract

Genomic language models can write synthetic DNA that carries no record of its origin. A generation-time watermark could provide a provenance signal, if a verifier can detect it using only the DNA sequence, a key, and published detector settings, without knowing where the generated region starts, which strand it lies on, or how it was divided into six-base tokens. We embed the SynthID tournament watermark in two genomic language models, Carbon and GENERator-v2. The verifier searches both strands, every start position, and four window lengths, and corrects its decision for the whole search. In a detection cohort of 1,544 held-out prompts, it found all 3,088 marked sequences per model, unedited and after one substituted, inserted, or deleted base. For ordinary sequences, the one-sided 95% upper confidence bound on the false-positive rate was at most 0.850%; one bound for the wrong-key control reached 1.015% (Carbon, after a deletion). In a development cohort, neither model showed a detectable change in likelihood or in predefined sequence measures. Under random edits placed without reference to the detector, detection stayed complete or nearly complete up to a 2% per-base edit rate. These results show statistical detection, not biological function, secret-key security, or robustness to an editor who sees the detector.