论文标题
分子图的定向消息传递
Directional Message Passing for Molecular Graphs
论文作者
论文摘要
图神经网络最近在预测分子的量子机械性能方面取得了巨大成功。这些模型仅使用原子之间的距离(节点)表示分子作为图。但是,尽管方向信息在分子的经验潜力中起着核心作用,例如在角电位中。为了减轻这一限制,我们提出了定向信息传递,其中我们将传递的信息嵌入到原子本身之间。每个消息都与坐标空间中的方向相关联。这些定向消息的嵌入是旋转的旋转均值,因为相关的方向与分子旋转。我们提出了一个类似于信念传播的消息传递方案的消息,该消息通过基于它们之间的角度转换消息来使用方向信息。此外,我们使用球形贝塞尔函数和球形谐波来构建理论上有良好的正交表示,这些表示的性能比当前普遍存在的高斯径向基础表示更好,同时使用少于1/4的参数。我们利用这些创新来构建传递神经网络(Dimenet)的定向消息。 Dimenet在MD17上的表现平均优于先前的GNN,而QM9的表现平均比31%。我们的实施可在线提供。
Graph neural networks have recently achieved great successes in predicting quantum mechanical properties of molecules. These models represent a molecule as a graph using only the distance between atoms (nodes). They do not, however, consider the spatial direction from one atom to another, despite directional information playing a central role in empirical potentials for molecules, e.g. in angular potentials. To alleviate this limitation we propose directional message passing, in which we embed the messages passed between atoms instead of the atoms themselves. Each message is associated with a direction in coordinate space. These directional message embeddings are rotationally equivariant since the associated directions rotate with the molecule. We propose a message passing scheme analogous to belief propagation, which uses the directional information by transforming messages based on the angle between them. Additionally, we use spherical Bessel functions and spherical harmonics to construct theoretically well-founded, orthogonal representations that achieve better performance than the currently prevalent Gaussian radial basis representations while using fewer than 1/4 of the parameters. We leverage these innovations to construct the directional message passing neural network (DimeNet). DimeNet outperforms previous GNNs on average by 76% on MD17 and by 31% on QM9. Our implementation is available online.