arXiv:2507.00846cs.LGphysics.bio-ph2025-07NeurIPS被引 10

用噪声对比估计加速玻尔兹曼生成的似然计算,提升分子模拟效率。

BoltzNCE: Learning Likelihoods for Boltzmann Generation with Stochastic Interpolants and Noise Contrastive Estimation

  • 用噪声对比估计与得分匹配联合训练能量模型近似似然值。
  • 在丙氨酸二肽上实现100倍提速,自由能曲线接近精确解。
  • 支持跨系统迁移,推理速度比标准分子动力学快6倍以上。

给定能量函数时高效采样玻尔兹曼分布是建模复杂物理系统(如分子)的关键挑战。玻尔兹曼生成器利用连续归一化流将简单先验转换为可重加权以匹配目标分布的分布,但获取似然值需在积分过程中计算高成本的雅可比行列式,对大型分子系统不实用。为此,我们训练一个能量基模型(EBM),结合噪声对比估计(NCE)和得分匹配来近似似然值,结果表明其性能优于单独使用任一目标。在二维合成系统中,NCE改善了模式权重分配;在丙氨酸二肽上,该方法获得的自由能分布与精确似然结果高度一致,且推理速度提升100倍。通过在多个二肽系统上训练,证明该方法具备有效迁移能力,在新系统推理时实现至少6倍于标准分子动力学的速度提升。本工作展示了加速似然计算的设计,使重加权方案能在大规模下保持无偏玻尔兹曼统计。代码已开源:https://github.com/RishalAggarwal/BoltzNCE。

原文摘要 · Abstract (English)

Efficient sampling from the Boltzmann distribution given its energy function is a key challenge for modeling complex physical systems such as molecules. Boltzmann Generators address this problem by leveraging continuous normalizing flows to transform a simple prior into a distribution that can be reweighted to match the target using sample likelihoods. Despite the elegance of this approach, obtaining these likelihoods requires computing costly Jacobians during integration, which is impractical for large molecular systems. To overcome this difficulty, we train an energy-based model (EBM) to approximate likelihoods using both noise contrastive estimation (NCE) and score matching, which we show outperforms the use of either objective in isolation. On 2d synthetic systems where failure can be easily visualized, NCE improves mode weighting relative to score matching alone. On alanine dipeptide, our method yields free energy profiles and energy distributions that closely match those obtained using exact likelihoods while achieving $100\times$ faster inference. By training on multiple dipeptide systems, we show that our approach also exhibits effective transfer learning, generalizing to new systems at inference time and achieving at least a $6\times$ speedup over standard MD. While many recent efforts in generative modeling have prioritized models with fast sampling, our work demonstrates the design of models with accelerated likelihoods, enabling the application of reweighting schemes that ensure unbiased Boltzmann statistics at scale. Our code is available at https://github.com/RishalAggarwal/BoltzNCE.

生成模型分子模拟似然计算能量模型

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