GraphGANFed: A Federated Generative Framework for Graph-Structured Molecules Towards Efficient Drug Discovery

• URL: http://arxiv.org/abs/2304.05498v1
• Date: Tue, 11 Apr 2023 21:15:28 GMT
• Title: GraphGANFed: A Federated Generative Framework for Graph-Structured Molecules Towards Efficient Drug Discovery
• Authors: Daniel Manu, Jingjing Yao, Wuji Liu, and Xiang Sun
• Abstract summary: We propose a Graph convolutional network in Generative Adversarial Networks via Federated learning (GraphGANFed) framework to generate novel molecules without sharing local data sets. The molecules generated by GraphGANFed can achieve high novelty (=100) and diversity (> 0.9)
• Score: 2.309914459672556
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: Recent advances in deep learning have accelerated its use in various applications, such as cellular image analysis and molecular discovery. In molecular discovery, a generative adversarial network (GAN), which comprises a discriminator to distinguish generated molecules from existing molecules and a generator to generate new molecules, is one of the premier technologies due to its ability to learn from a large molecular data set efficiently and generate novel molecules that preserve similar properties. However, different pharmaceutical companies may be unwilling or unable to share their local data sets due to the geo-distributed and sensitive nature of molecular data sets, making it impossible to train GANs in a centralized manner. In this paper, we propose a Graph convolutional network in Generative Adversarial Networks via Federated learning (GraphGANFed) framework, which integrates graph convolutional neural Network (GCN), GAN, and federated learning (FL) as a whole system to generate novel molecules without sharing local data sets. In GraphGANFed, the discriminator is implemented as a GCN to better capture features from molecules represented as molecular graphs, and FL is used to train both the discriminator and generator in a distributive manner to preserve data privacy. Extensive simulations are conducted based on the three bench-mark data sets to demonstrate the feasibility and effectiveness of GraphGANFed. The molecules generated by GraphGANFed can achieve high novelty (=100) and diversity (> 0.9). The simulation results also indicate that 1) a lower complexity discriminator model can better avoid mode collapse for a smaller data set, 2) there is a tradeoff among different evaluation metrics, and 3) having the right dropout ratio of the generator and discriminator can avoid mode collapse.

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