将压缩数据直接转为满足生化约束的DNA序列,提升存储效率
SCONE: A Practical, Constraint-Aware Plug-in for Latent Encoding in Learned DNA Storage
- 直接在潜在空间进行四进制算术编码,一步完成压缩与编码
- 动态调整概率分布,确保鸟嘌呤-胞嘧啶含量均衡且抑制同聚物
- 计算开销极小,适合接入各类神经压缩模型
DNA存储已从概念走向实用,但其与神经压缩流水线的集成仍不高效。早期编码器在原始二进制数据上叠加冗余约束层,虽可行但原始。近期神经编解码器将数据压缩为具有丰富统计结构的潜在表示,却仍通过朴素的二进制到四进制转换生成DNA,忽略熵模型优化。这种错配削弱压缩效率并复杂化编码流程。SCONE提出一个插件模块,将潜在压缩与DNA编码合并为单一步骤。它在潜空间直接执行四进制算术编码,其约束感知自适应编码模块动态调整熵编码器的分布,以确定性方式实现鸟嘌呤-胞嘧啶(GC)平衡和同聚物抑制,无需事后修正。设计保持完全可逆性,并未修改超先验模型的先验。实验表明,SCONE实现近乎完美的约束满足,计算开销极低(延迟增加小于2%),为端到端兼容DNA的神经编码器提供无感接口。
原文摘要 · Abstract (English)
DNA storage has matured from concept to practical stage, yet its integration with neural compression pipelines remains inefficient. Early DNA encoders applied redundancy-heavy constraint layers atop raw binary data - workable but primitive. Recent neural codecs compress data into learned latent representations with rich statistical structure, yet still convert these latents to DNA via naive binary-to-quaternary transcoding, discarding the entropy model's optimization. This mismatch undermines compression efficiency and complicates the encoding stack. A plug-in module that collapses latent compression and DNA encoding into a single step. SCONE performs quaternary arithmetic coding directly on the latent space in DNA bases. Its Constraint-Aware Adaptive Coding module dynamically steers the entropy encoder's learned probability distribution to enforce biochemical constraints - Guanine-Cytosine (GC) balance and homopolymer suppression - deterministically during encoding, eliminating post-hoc correction. The design preserves full reversibility and exploits the hyperprior model's learned priors without modification. Experiments show SCONE achieves near-perfect constraint satisfaction with negligible computational overhead (<2% latency), establishing a latent-agnostic interface for end-to-end DNA-compatible learned codecs.
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