提出基于影响半径的3D分子图解释方法,提升模型可解释性。
RISE: Radius of Influence based Subgraph Extraction for 3D Molecular Graph Explanation
- 以节点为中心定义影响半径,聚焦局部空间区域进行解释。
- 通过限制子图范围,增强对3D分子结构依赖性的刻画能力。
- 适用于需要透明决策过程的药物设计与分子性质预测场景。
三维几何图神经网络(GNN)已成为建模分子数据的有力工具。尽管其具备强大预测能力,但模型可解释性有限,制约了其在科学应用中的可信度。现有方法多集中于2D GNN的子结构解释,而3D GNN面临新挑战,如由截断半径生成的隐式密集边结构。为此,我们提出一种专为3D GNN设计的新解释方法,将解释范围限定在每个节点的3D空间邻域内。每个节点被赋予一个影响半径,定义消息传递所捕捉空间与结构相互作用的关键局部区域。该方法利用3D图固有的空间和几何特性,通过约束子图至局部影响半径,不仅提升可解释性,也契合分子学习等3D图应用中的物理与结构依赖关系。
原文摘要 · Abstract (English)
3D Geometric Graph Neural Networks (GNNs) have emerged as transformative tools for modeling molecular data. Despite their predictive power, these models often suffer from limited interpretability, raising concerns for scientific applications that require reliable and transparent insights. While existing methods have primarily focused on explaining molecular substructures in 2D GNNs, the transition to 3D GNNs introduces unique challenges, such as handling the implicit dense edge structures created by a cut-off radius. To tackle this, we introduce a novel explanation method specifically designed for 3D GNNs, which localizes the explanation to the immediate neighborhood of each node within the 3D space. Each node is assigned an radius of influence, defining the localized region within which message passing captures spatial and structural interactions crucial for the model's predictions. This method leverages the spatial and geometric characteristics inherent in 3D graphs. By constraining the subgraph to a localized radius of influence, the approach not only enhances interpretability but also aligns with the physical and structural dependencies typical of 3D graph applications, such as molecular learning.
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