arXiv:2510.16253cs.LGcs.AI2025-10被引 1

用微分方程重写蛋白质折叠模型,更省资源且可调精度。

Protein Folding with Neural Ordinary Differential Equations

  • 将48层离散结构改为连续时间微分方程建模,保留注意力机制核心。
  • 单卡训练仅需17.5小时,内存恒定,推理时可动态调节速度与准确率。
  • 适合追求高效、可解释的生物分子建模研究者使用。

近期蛋白结构预测进展(如AlphaFold)表明,深度神经网络(如Evoformer)能有效捕捉蛋白构象中的复杂空间与进化约束。然而,其48层堆叠结构带来高计算开销和固定层间离散化问题。受神经微分方程(Neural ODEs)启发,我们提出连续深度版Evoformer,以神经微分方程替代原有48个离散块,同时保留核心注意力操作。该连续时间模型通过伴随法实现恒定内存开销(随深度),并借助自适应微分方程求解器实现运行时与精度间的合理权衡。在蛋白结构预测任务上,该模型生成结构合理且能可靠捕获α-螺旋等二级结构元素的预测结果,尽管未完全达到原始架构精度。但其仅需单卡17.5小时训练,凸显连续深度模型在生物分子建模中作为轻量、可解释替代方案的巨大潜力。本工作为高效、自适应的蛋白结构预测框架开辟新方向。

原文摘要 · Abstract (English)

Recent advances in protein structure prediction, such as AlphaFold, have demonstrated the power of deep neural architectures like the Evoformer for capturing complex spatial and evolutionary constraints on protein conformation. However, the depth of the Evoformer, comprising 48 stacked blocks, introduces high computational costs and rigid layerwise discretization. Inspired by Neural Ordinary Differential Equations (Neural ODEs), we propose a continuous-depth formulation of the Evoformer, replacing its 48 discrete blocks with a Neural ODE parameterization that preserves its core attention-based operations. This continuous-time Evoformer achieves constant memory cost (in depth) via the adjoint method, while allowing a principled trade-off between runtime and accuracy through adaptive ODE solvers. Benchmarking on protein structure prediction tasks, we find that the Neural ODE-based Evoformer produces structurally plausible predictions and reliably captures certain secondary structure elements, such as alpha-helices, though it does not fully replicate the accuracy of the original architecture. However, our model achieves this performance using dramatically fewer resources, just 17.5 hours of training on a single GPU, highlighting the promise of continuous-depth models as a lightweight and interpretable alternative for biomolecular modeling. This work opens new directions for efficient and adaptive protein structure prediction frameworks.

蛋白质折叠神经微分方程高效建模

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