论文标题

Hignn:分子属性预测的分层信息图神经网络,配备了特征注意

HiGNN: Hierarchical Informative Graph Neural Networks for Molecular Property Prediction Equipped with Feature-Wise Attention

论文作者

Zhu, Weimin, Zhang, Yi, Zhao, DuanCheng, Xu, Jianrong, Wang, Ling

论文摘要

阐明并准确预测分子的吸毒性和生物活性在药物设计和发现中起关键作用,并且仍然是一个开放的挑战。最近,图神经网络(GNN)在基于图的分子属性预测中取得了显着进步。但是,当前基于图的深度学习方法忽略了分子的分层信息以及特征通道之间的关系。在这项研究中,我们提出了一个精心设计的分层信息图神经网络框架(称为Hignn),用于通过利用分子图和化学综合的可可构成的无限元素片段来预测分子特性。此外,首先在Hignn体系结构中设计了插件功能的注意块,以适应消息传递阶段后自适应重新校准原子特征。广泛的实验表明,Hignn在许多具有挑战性的药物发现相关基准数据集上实现了最先进的预测性能。此外,我们设计了一种分子碎片相似性机制,以全面研究Hignn模型在子图水平上的解释性,表明Hignn作为强大的深度学习工具可以帮助化学家和药剂师确定用于设计具有所需特性或功能的更好分子的关键分子的关键成分。源代码可在https://github.com/idruglab/hignn上公开获得。

Elucidating and accurately predicting the druggability and bioactivities of molecules plays a pivotal role in drug design and discovery and remains an open challenge. Recently, graph neural networks (GNN) have made remarkable advancements in graph-based molecular property prediction. However, current graph-based deep learning methods neglect the hierarchical information of molecules and the relationships between feature channels. In this study, we propose a well-designed hierarchical informative graph neural networks framework (termed HiGNN) for predicting molecular property by utilizing a co-representation learning of molecular graphs and chemically synthesizable BRICS fragments. Furthermore, a plug-and-play feature-wise attention block is first designed in HiGNN architecture to adaptively recalibrate atomic features after the message passing phase. Extensive experiments demonstrate that HiGNN achieves state-of-the-art predictive performance on many challenging drug discovery-associated benchmark datasets. In addition, we devise a molecule-fragment similarity mechanism to comprehensively investigate the interpretability of HiGNN model at the subgraph level, indicating that HiGNN as a powerful deep learning tool can help chemists and pharmacists identify the key components of molecules for designing better molecules with desired properties or functions. The source code is publicly available at https://github.com/idruglab/hignn.

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