aiqbench analysis
This paper proposes LOCOGEN, a sampling-time method that guides a frozen diffusion model to design regulatory DNA with high predicted activity while keeping sequences novel and plausible. Its main contribution is a locality-aware approach: it protects learned motif positions and damps guidance only on background positions. Readers should note that the evaluation rests on predicted activity from models rather than wet-lab validation, so the gains are provisional until experimentally confirmed.
Locality-Controlled Out-of-Distribution Guidance for Robust Regulatory DNA Sequence Design
arXiv:2610.41736v1 Announce Type: new Abstract: Designing regulatory DNA sequences for targeted gene-expression control is an important challenge. Recent approaches frame this task as property-conditioned generation, where diffusion models trained on natural sequences are guided toward high predicted activity through reward-based fine-tuning or sampling-time guidance. We show that single-reward evaluation can obscure reward-hacking behavior. By decomposing evaluation into property, novelty, and plausibility, we identify an empirically underexplored region of the evaluation space in which all three objectives are satisfied, but no existing baseline succeeds. We postulate that this gap arises because prior methods treat guidance primarily as a matter of magnitude. In regulatory DNA, however, sequence grammar is spatially nonuniform: motif positions are sensitive to perturbation, while background regions allow more exploration. We therefore propose LOCOGEN by reformulating guidance as a problem of locality. LOCOGEN learns an invariant motif mask through sequence-level invariance learning to protect motif positions, while applying OOD damping only to background positions. It operates at sampling time on a frozen diffusion backbone, without retraining the backbone. Across HepG2, K562, and SK-N-SH, LOCOGEN reaches this previously underexplored region of the property-novelty-plausibility space. Code is available at https://github.com/Lotfollahi-lab/LocoGen.
Abstract:Designing regulatory DNA sequences for targeted gene-expression control is an important challenge. Recent approaches frame this task as property-conditioned generation, where diffusion models trained on natural sequences are guided toward high predicted activity through reward-based fine-tuning or sampling-time guidance. We show that single-reward evaluation can obscure reward-hacking behavior. By decomposing evaluation into property, novelty, and plausibility, we identify an empirically underexplored region of the evaluation space in which all three objectives are satisfied, but no existing baseline succeeds. We postulate that this gap arises because prior methods treat guidance primarily as a matter of magnitude. In regulatory DNA, however, sequence grammar is spatially nonuniform: motif positions are sensitive to perturbation, while background regions allow more exploration. We therefore propose LOCOGEN by reformulating guidance as a problem of locality. LOCOGEN learns an invariant motif mask through sequence-level invariance learning to protect motif positions, while applying OOD damping only to background positions. It operates at sampling time on a frozen diffusion backbone, without retraining the backbone. Across HepG2, K562, and SK-N-SH, LOCOGEN reaches this previously underexplored region of the property-novelty-plausibility space. Code is available at this https URL.
Machine Learning (cs.LG); Genomics (q-bio.GN)
arXiv:2610.41736 [cs.LG]
(or arXiv:2610.41736v1 [cs.LG] for this version)
https://doi.org/10.48550/arXiv.2610.41736 Focus to learn more arXiv-issued DOI via DataCite (pending registration)
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Full text under the publisher's open licence · 282 words