GraphGANFed: A Federated Generative Framework for Graph-Structured Molecules Towards Efficient Drug Discovery
Daniel Manu, Jingjing Yao, Wuji Liu, Xiang Sun
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 <underline xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Graph</u> convolutional network in <underline xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</u> enerative <underline xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">A</u> dversarial <underline xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</u> etworks via <underline xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Fed</u> erated 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 benchmark data sets to demonstrate the feasibility and effectiveness of GraphGANFed. The molecules generated by GraphGANFed can achieve high novelty <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$(\approx 100 )$</tex-math></inline-formula> and diversity <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$(\gt 0.9)$</tex-math></inline-formula> . 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.