论文标题

图形神经网络的分子图生成

Molecular graph generation with Graph Neural Networks

论文作者

Bongini, Pietro, Bianchini, Monica, Scarselli, Franco

论文摘要

药物发现是一个基本且不断发展的研究领域。新候选分子的设计需要大量的时间和金钱,并且越来越多地使用计算方法来削减这些成本。机器学习方法是设计大量潜在的新候选分子的理想选择,这些分子自然表示为图。深度学习方法正在彻底改变图形,而分子产生是其最有前途的应用之一。在本文中,我们基于一组图神经网络模块引入了一个顺序分子图生成器,我们称之为mg^2n^2。在每个步骤中,将一个节点或一组节点及其连接添加到图。模块化体系结构简化了训练步骤,还允许单个模块独立地进行重新培训。顺序和模块化使生成过程可解释。图形神经网络的使用最大化了每个生成步骤中输入中的信息,该步骤由前一步中产生的子图组成。 QM9和锌数据集中无条件产生的实验表明,我们的模型能够概括在训练阶段看到的分子模式,而无需过度拟合。结果表明,我们的方法具有竞争力,并且优于无条件生成的基准挑战基线。

Drug Discovery is a fundamental and ever-evolving field of research. The design of new candidate molecules requires large amounts of time and money, and computational methods are being increasingly employed to cut these costs. Machine learning methods are ideal for the design of large amounts of potential new candidate molecules, which are naturally represented as graphs. Graph generation is being revolutionized by deep learning methods, and molecular generation is one of its most promising applications. In this paper, we introduce a sequential molecular graph generator based on a set of graph neural network modules, which we call MG^2N^2. At each step, a node or a group of nodes is added to the graph, along with its connections. The modular architecture simplifies the training procedure, also allowing an independent retraining of a single module. Sequentiality and modularity make the generation process interpretable. The use of graph neural networks maximizes the information in input at each generative step, which consists of the subgraph produced during the previous steps. Experiments of unconditional generation on the QM9 and Zinc datasets show that our model is capable of generalizing molecular patterns seen during the training phase, without overfitting. The results indicate that our method is competitive, and outperforms challenging baselines for unconditional generation.

扫码加入交流群

加入微信交流群

微信交流群二维码

扫码加入学术交流群,获取更多资源