arXiv:2512.15923cs.LG2025-12被引 2

统一离散、高斯与单纯形扩散,让一个模型通吃多种序列生成任务。

A Unification of Discrete, Gaussian, and Simplicial Diffusion

  • 基于沃伊特-费舍尔种群模型,统一看似不同的扩散方法。
  • 单纯形扩散更稳定,在条件DNA生成上超越现有模型。
  • 单个模型可跨域推理,无需在训练时预设数据类型。

为建模如DNA、蛋白质和语言等离散序列,从业者需在三种主要方法间抉择:离散空间扩散、欧氏空间高斯扩散,或单纯形上的扩散。尽管目标一致,这些模型算法、理论结构和权衡各异:离散扩散领域最自然,高斯扩散算法更成熟,而单纯形扩散理论上结合二者优势,但实践中因数值不稳定的随机过程受限。理想情况下,应将三者视为同一基础框架的不同参数化形式,并使从业者能灵活切换下游应用。然而此前理论仅覆盖特殊情形。本文构建了一个统一理论,将三类离散扩散视为同一过程——沃伊特-费舍尔种群遗传模型的不同参数化形式。特别地,单纯形与高斯扩散均为大种群极限情形。该理论正式连接了各模型的似然与超参数,并借助数十年数学遗传学文献实现稳定单纯形扩散。最终,我们证明可通过训练单一模型,在测试时任意执行三类扩散,免除模型权衡之苦。实验表明,沃伊特-费舍尔单纯形扩散更稳定,且在条件DNA生成上优于先前模型;同时,多域联合训练模型性能可媲美单一领域专用模型。

原文摘要 · Abstract (English)

To model discrete sequences such as DNA, proteins, and language using diffusion, practitioners must choose between three major methods: diffusion in discrete space, Gaussian diffusion in Euclidean space, or diffusion on the simplex. Despite their shared goal, these models have disparate algorithms, theoretical structures, and tradeoffs: discrete diffusion has the most natural domain, Gaussian diffusion has more mature algorithms, and diffusion on the simplex in principle combines the strengths of the other two but in practice suffers from a numerically unstable stochastic processes. Ideally we could see each of these models as instances of the same underlying framework, and enable practitioners to switch between models for downstream applications. However previous theories have only considered connections in special cases. Here we build a theory unifying all three methods of discrete diffusion as different parameterizations of the same underlying process: the Wright-Fisher population genetics model. In particular, we find simplicial and Gaussian diffusion as two large-population limits. Our theory formally connects the likelihoods and hyperparameters of these models and leverages decades of mathematical genetics literature to unlock stable simplicial diffusion. Finally, we relieve the practitioner of balancing model trade-offs by demonstrating it is possible to train a single model that can perform diffusion in any of these three domains at test time. Our experiments show that Wright-Fisher simplicial diffusion is more stable and outperforms previous simplicial diffusion models on conditional DNA generation. We also show that we can train models on multiple domains at once that are competitive with models trained on any individual domain.

扩散模型序列生成统一理论生物序列

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