用有向线图建模化学反应,提升分类精度。
DLGNet: Hyperedge Classification through Directed Line Graphs for Chemical Reactions
- 将化学反应转为有向超边,构建有向线图进行建模。
- 在真实数据集上平均提升33.01%,最高达37.71%。
- 首个基于谱方法的超图神经网络,适合分子反应研究。
图与超图为建模多实体间交互提供了强大抽象,在化学、生物等领域广泛应用,尤其在药物发现与分子生成中迅速发展。化学反应可自然表示为有向超边。本文提出有向线图(DGL)表示,并构建首个专用于超图的谱域图神经网络DLGNet。其核心是新的埃尔米特矩阵——有向线图拉普拉斯算子,能紧凑编码超边内互动的方向性。该算子具有特征分解和半正定性,适用于谱域GNN。在多个真实化学反应数据集上实验表明,DLGNet显著优于现有方法,平均相对提升33.01%,最大提升达37.71%。
原文摘要 · Abstract (English)
Graphs and hypergraphs provide powerful abstractions for modeling interactions among a set of entities of interest and have been attracting a growing interest in the literature thanks to many successful applications in several fields. In particular, they are rapidly expanding in domains such as chemistry and biology, especially in the areas of drug discovery and molecule generation. One of the areas witnessing the fasted growth is the chemical reactions field, where chemical reactions can be naturally encoded as directed hyperedges of a hypergraph. In this paper, we address the chemical reaction classification problem by introducing the notation of a Directed Line Graph (DGL) associated with a given directed hypergraph. On top of it, we build the Directed Line Graph Network (DLGNet), the first spectral-based Graph Neural Network (GNN) expressly designed to operate on a hypergraph via its DLG transformation. The foundation of DLGNet is a novel Hermitian matrix, the Directed Line Graph Laplacian, which compactly encodes the directionality of the interactions taking place within the directed hyperedges of the hypergraph thanks to the DLG representation. The Directed Line Graph Laplacian enjoys many desirable properties, including admitting an eigenvalue decomposition and being positive semidefinite, which make it well-suited for its adoption within a spectral-based GNN. Through extensive experiments on chemical reaction datasets, we show that DGLNet significantly outperforms the existing approaches, achieving on a collection of real-world datasets an average relative-percentage-difference improvement of 33.01%, with a maximum improvement of 37.71%.
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