arXiv:2606.17668cs.LGcs.AI2026-06

用Transformer直接预测分子动力学多步原子坐标,省去传统迭代计算。

ASTEROID: A Spatiotemporal Information Transformer for Forecasting Multi-Step Time Series of Molecular Dynamics

  • 将分子轨迹转为时空序列,结合局部全局注意力捕捉多尺度依赖。
  • 在多个数据集上实现更高预测精度,且计算成本远低于传统方法。
  • 适合需要快速模拟长时程分子行为的研究者,如材料设计与药物研发。

分子动力学(MD)模拟计算成本高,尤其对大规模系统需长期分析。本文提出数据驱动框架ASTEROID(Advanced Spatiotemporal TransformER fOr Inferring Dynamics),可直接预测多步原子坐标,无需传统迭代积分。ASTEROID将MD轨迹建模为高维时空序列,将时空信息变换方程融入Transformer架构。核心创新在于建模多尺度时空依赖:空间上采用局部-全局自注意力机制捕获短距与长距相互作用;时间上通过编码器-解码器结构融合全局上下文并实现自回归预测。在多个基于量子力学的分子数据集上评估表明,ASTEROID在多种基准测试中不仅显著优于现有方法的多步预测精度,还大幅降低传统MD模拟的计算开销。模型支持长时间尺度的迭代多步预测。本工作建立了一种高效、通用的数据驱动范式,加速分子动力学模拟。

原文摘要 · Abstract (English)

Molecular dynamics (MD) simulation is computationally demanding, particularly for large-scale systems requiring long-term analysis. Accurate forecast of the outcomes of a MD simulation is not only an attractive scientific challenge but also has substantial practical value. In this work, we developed a data-driven framework, termed ASTEROID (Advanced Spatiotemporal TransformER fOr Inferring Dynamics), that can directly predict multi-step atomic coordinates, avoiding conventional iterative integration. For this purpose, our ASTEROID reformulates MD trajectories as high-dimensional spatiotemporal sequences and integrates the Spatiotemporal Information (STI) Transformation equation into a Transformer architecture. The core innovation of ASTEROID lies in its ability to model multiscale spatiotemporal dependencies. In particular, for spatial dependencies, a local-global self-attention mechanism captures both short- and long-range interactions. For temporal dependencies, an encoder-decoder structure integrates global context with autoregressive forecasting. ASTEROID was evaluated on several quantum-mechanics derived molecular datasets. Our results indicate that ASTEROID achieved not only a higher level of accuracy in multi-step prediction than existing methods on various benchmarks, but also significantly reduced computational cost of conventional MD simulation. Moreover, the model supports iterative multi-step forecasting over an extended time scale. This work establishes a robust and generalizable data-driven paradigm for accelerating MD simulations.

分子动力学时空建模Transformer预测

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