arXiv:2502.10848cs.LGq-bio.QM2025-02

用神经网络表示分子的向量场,实现高保真、可插值的分子建模。

Implicit Neural Representations of Molecular Vector-Valued Functions

  • 用神经网络参数化分子的多维向量场,替代传统离散表示。
  • 实现蛋白-配体复合物的超分辨率重建与构象时空插值。
  • 适合分子生成、结构优化及动态模拟任务,尤其擅长形状驱动设计。

分子有多种计算表示形式,包括数值描述符、字符串、图、点云和表面。每种表示方法都可配合从线性回归到图神经网络乃至大语言模型的各类机器学习方法。为补充现有表示,我们提出通过神经网络参数化的向量值函数(即n维向量场)来表示分子,称为分子神经场。相比表面表示,分子神经场能捕捉蛋白质等大分子的外部特征与疏水核心;相较离散图或点表示,分子神经场更紧凑、与分辨率无关,且天然适合空间与时间维度的插值。这些特性使其适用于基于期望形状、结构与组成生成分子,以及在空间和时间上对分子构象进行无分辨率依赖的插值。本文提供了分子神经场的框架与概念验证:利用自编码器架构实现蛋白-配体复合物的参数化与超分辨率重建,并通过自编码器架构将分子体积嵌入潜在空间。

原文摘要 · Abstract (English)

Molecules have various computational representations, including numerical descriptors, strings, graphs, point clouds, and surfaces. Each representation method enables the application of various machine learning methodologies from linear regression to graph neural networks paired with large language models. To complement existing representations, we introduce the representation of molecules through vector-valued functions, or $n$-dimensional vector fields, that are parameterized by neural networks, which we denote molecular neural fields. Unlike surface representations, molecular neural fields capture external features and the hydrophobic core of macromolecules such as proteins. Compared to discrete graph or point representations, molecular neural fields are compact, resolution independent and inherently suited for interpolation in spatial and temporal dimensions. These properties inherited by molecular neural fields lend themselves to tasks including the generation of molecules based on their desired shape, structure, and composition, and the resolution-independent interpolation between molecular conformations in space and time. Here, we provide a framework and proofs-of-concept for molecular neural fields, namely, the parametrization and superresolution reconstruction of a protein-ligand complex using an auto-decoder architecture and the embedding of molecular volumes in latent space using an auto-encoder architecture.

分子建模神经场生成模型结构预测

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