arXiv:2411.12570cond-mat.mtrl-scics.LG2024-11被引 7

通过数据驱动方法评估描述符在噪声轨迹中提取物理信息的效率。

A data driven approach to classify descriptors based on their efficiency in translating noisy trajectories into physically-relevant information

  • 用洋葱聚类法分析单点时间序列,量化不同描述符的信息提取能力。
  • 先进描述符如SOAP、LENS因信噪比高表现更优,简单描述符经去噪后可超越。
  • 适用于研究含复杂内部结构的分子动力学系统,尤其关注噪声影响。

重构多体动力系统物理复杂性具有挑战性。从组分粒子轨迹(原始数据)出发,传统方法需选择合适描述符将其转化为时间序列以提取可解释信息,但高效描述符的识别常不明确。本文提出一种数据驱动方法,比较多种描述符在从噪声轨迹中提取信息并转化为物理洞察方面的效率。以冰水共存、接近固液相变温度的原子系统为原型,对比了通用与特定于水体系的描述符:邻域数、分子速度、平滑原子位置重叠(SOAP)、局部环境与邻居置换(LENS)、取向四面体序及第五邻近距离(d₅)。采用洋葱聚类——一种高效的无监督单点时间序列分析方法——评估各描述符的最大可提取信息,并通过高维度度量进行排序。结果表明,如SOAP和LENS等高级描述符因更高信噪比而优于经典描述符;然而,即使简单描述符在局部信号去噪后也能媲美甚至超过高级描述符。例如,最初表现最弱的d₅,在去噪后成为解析系统非局域动力学复杂性的最优工具。本工作凸显了噪声在分子轨迹信息提取中的关键作用,并提供了一种数据驱动方法,用于识别具有特征内部复杂性的系统的最优描述符。

原文摘要 · Abstract (English)

Reconstructing the physical complexity of many-body dynamical systems can be challenging. Starting from the trajectories of their constitutive units (raw data), typical approaches require selecting appropriate descriptors to convert them into time-series, which are then analyzed to extract interpretable information. However, identifying the most effective descriptor is often non-trivial. Here, we report a data-driven approach to compare the efficiency of various descriptors in extracting information from noisy trajectories and translating it into physically relevant insights. As a prototypical system with non-trivial internal complexity, we analyze molecular dynamics trajectories of an atomistic system where ice and water coexist in equilibrium near the solid/liquid transition temperature. We compare general and specific descriptors often used in aqueous systems: number of neighbors, molecular velocities, Smooth Overlap of Atomic Positions (SOAP), Local Environments and Neighbors Shuffling (LENS), Orientational Tetrahedral Order, and distance from the fifth neighbor ($d_5$). Using Onion Clustering -- an efficient unsupervised method for single-point time-series analysis -- we assess the maximum extractable information for each descriptor and rank them via a high-dimensional metric. Our results show that advanced descriptors like SOAP and LENS outperform classical ones due to higher signal-to-noise ratios. Nonetheless, even simple descriptors can rival or exceed advanced ones after local signal denoising. For example, $d_5$, initially among the weakest, becomes the most effective at resolving the system's non-local dynamical complexity after denoising. This work highlights the critical role of noise in information extraction from molecular trajectories and offers a data-driven approach to identify optimal descriptors for systems with characteristic internal complexity.

分子动力学描述符去噪

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