基于分数的去噪技术轻松实现冰相分类

IF 5.3 2区 化学 Q1 CHEMISTRY, MEDICINAL
Hong Sun, Sebastien Hamel, Tim Hsu, Babak Sadigh, Vincenzo Lordi* and Fei Zhou*, 
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引用次数: 0

摘要

准确识别冰相对于理解各种物理化学现象至关重要。然而,由于冰的多态性和热波动具有复杂的对称性,因此对分子动力学模拟的结构进行分类非常复杂。为此,人们采用了传统的阶次参数和数据驱动的机器学习方法,但这些方法往往依赖于专家的直觉、特定的几何信息或大量的训练数据集。在这项工作中,我们提出了一种无监督冰相分类框架,该框架将基于分数的去噪器模型与随后的无模型分类方法相结合,以准确识别冰相。去噪模型在理想参考结构的扰动合成数据上进行训练,无需大型数据集和标记工作。分类步骤利用原子位置平滑重叠(SOAP)描述符作为原子指纹,确保了欧氏对称性和对各种结构系统的可移植性。我们的方法仅使用七个理想的冰相参考结构作为模型输入,就能在区分测试轨迹的冰相方面达到惊人的 100%准确率。这证明了基于分数的去噪模型在促进复杂分子系统相位识别方面的通用性。所提出的分类策略可广泛应用于研究各种材料的结构演变和相识别,为从根本上理解水和其他复杂系统提供新的见解。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Ice Phase Classification Made Easy with Score-Based Denoising

Ice Phase Classification Made Easy with Score-Based Denoising

Accurate identification of ice phases is essential for understanding various physicochemical phenomena. However, such classification for structures simulated with molecular dynamics is complicated by the complex symmetries of ice polymorphs and thermal fluctuations. For this purpose, both traditional order parameters and data-driven machine learning approaches have been employed, but they often rely on expert intuition, specific geometric information, or large training data sets. In this work, we present an unsupervised phase classification framework that combines a score-based denoiser model with a subsequent model-free classification method to accurately identify ice phases. The denoiser model is trained on perturbed synthetic data of ideal reference structures, eliminating the need for large data sets and labeling efforts. The classification step utilizes the smooth overlap of atomic position (SOAP) descriptors as the atomic fingerprint, ensuring Euclidean symmetries and transferability to various structural systems. Our approach achieves a remarkable 100% accuracy in distinguishing ice phases of test trajectories using only seven ideal reference structures of ice phases as model inputs. This demonstrates the generalizability of the score-based denoiser model in facilitating phase identification for complex molecular systems. The proposed classification strategy can be broadly applied to investigate structural evolution and phase identification for a wide range of materials, offering new insights into the fundamental understanding of water and other complex systems.

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来源期刊
CiteScore
9.80
自引率
10.70%
发文量
529
审稿时长
1.4 months
期刊介绍: The Journal of Chemical Information and Modeling publishes papers reporting new methodology and/or important applications in the fields of chemical informatics and molecular modeling. Specific topics include the representation and computer-based searching of chemical databases, molecular modeling, computer-aided molecular design of new materials, catalysts, or ligands, development of new computational methods or efficient algorithms for chemical software, and biopharmaceutical chemistry including analyses of biological activity and other issues related to drug discovery. Astute chemists, computer scientists, and information specialists look to this monthly’s insightful research studies, programming innovations, and software reviews to keep current with advances in this integral, multidisciplinary field. As a subscriber you’ll stay abreast of database search systems, use of graph theory in chemical problems, substructure search systems, pattern recognition and clustering, analysis of chemical and physical data, molecular modeling, graphics and natural language interfaces, bibliometric and citation analysis, and synthesis design and reactions databases.
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