Abstract
Recent methods for generating novel molecules use graph representations of molecules and employ various forms of graph convolutional neural networks for inference. However, training requires solving an expensive graph isomorphism problem, which previous approaches do not address or solve only approximately. In this work, we propose ALMGIG, a likelihood-free adversarial learning framework for inference and de novo molecule generation that avoids explicitly computing a reconstruction loss. Our approach extends generative adversarial networks by including an adversarial cycle-consistency loss to implicitly enforce the reconstruction property. To capture properties unique to molecules, such as valence, we extend the Graph Isomorphism Network to multi-graphs. To quantify the performance of models, we propose to compute the distance between distributions of physicochemical properties with the 1-Wasserstein distance. We demonstrate that ALMGIG more accurately learns the distribution over the space of molecules than all baselines. Moreover, it can be utilized for drug discovery by efficiently searching the space of molecules using molecules’ continuous latent representation. Our code is available at https://github.com/ai-med/almgig.
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Acknowledgements
This research was partially supported by the Bavarian State Ministry of Education, Science and the Arts in the framework of the Centre Digitisation.Bavaria (ZD.B), and the Federal Ministry of Education and Research in the call for Computational Life Sciences (DeepMentia, 031L0200A).
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Pölsterl, S., Wachinger, C. (2021). Adversarial Learned Molecular Graph Inference and Generation. In: Hutter, F., Kersting, K., Lijffijt, J., Valera, I. (eds) Machine Learning and Knowledge Discovery in Databases. ECML PKDD 2020. Lecture Notes in Computer Science(), vol 12458. Springer, Cham. https://doi.org/10.1007/978-3-030-67661-2_11
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