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Constrained Graph Variational Autoencoders for Molecule Design
Qi Liu · Miltiadis Allamanis · Marc Brockschmidt · Alexander Gaunt

Thu Dec 06 02:00 PM -- 04:00 PM (PST) @ Room 517 AB #103

Graphs are ubiquitous data structures for representing interactions between entities. With an emphasis on applications in chemistry, we explore the task of learning to generate graphs that conform to a distribution observed in training data. We propose a variational autoencoder model in which both encoder and decoder are graph-structured. Our decoder assumes a sequential ordering of graph extension steps and we discuss and analyze design choices that mitigate the potential downsides of this linearization. Experiments compare our approach with a wide range of baselines on the molecule generation task and show that our method is successful at matching the statistics of the original dataset on semantically important metrics. Furthermore, we show that by using appropriate shaping of the latent space, our model allows us to design molecules that are (locally) optimal in desired properties.

Author Information

Qi Liu (Facebook AI Research)
Miltiadis Allamanis (Microsoft Research)
Marc Brockschmidt (Microsoft Research)
Alexander Gaunt (Microsoft Research)

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