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Gourhari Jana

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JMLR Journal 2020 Journal Article

NEVAE: A Deep Generative Model for Molecular Graphs

  • Bidisha Samanta
  • Abir De
  • Gourhari Jana
  • Vicenç Gómez
  • Pratim Chattaraj
  • Niloy Ganguly
  • Manuel Gomez-Rodriguez

Deep generative models have been praised for their ability to learn smooth latent representations of images, text, and audio, which can then be used to generate new, plausible data. Motivated by these success stories, there has been a surge of interest in developing deep generative models for automated molecule design. However, these models face several difficulties due to the unique characteristics of molecular graphs—their underlying structure is not Euclidean or grid-like, they remain isomorphic under permutation of the nodes’ labels, and they come with a different number of nodes and edges. In this paper, we first propose a novel variational autoencoder for molecular graphs, whose encoder and decoder are specially designed to account for the above properties by means of several technical innovations. Moreover, in contrast with the state of the art, our decoder is able to provide the spatial coordinates of the atoms of the molecules it generates. Then, we develop a gradient-based algorithm to optimize the decoder of our model so that it learns to generate molecules that maximize the value of certain property of interest and, given any arbitrary molecule, it is able to optimize the spatial configuration of its atoms for greater stability. Experiments reveal that our variational autoencoder can discover plausible, diverse and novel molecules more effectively than several state of the art models. Moreover, for several properties of interest, our optimized decoder is able to identify molecules with property values 121% higher than those identified by several state of the art methods based on Bayesian optimization and reinforcement learning. [abs] [ pdf ][ bib ] &copy JMLR 2020. ( edit, beta )

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AAAI Conference 2019 Conference Paper

NeVAE: A Deep Generative Model for Molecular Graphs

  • Bidisha Samanta
  • Abir De
  • Gourhari Jana
  • Pratim Kumar Chattaraj
  • Niloy Ganguly
  • Manuel Gomez Rodriguez

Deep generative models have been praised for their ability to learn smooth latent representation of images, text, and audio, which can then be used to generate new, plausible data. However, current generative models are unable to work with molecular graphs due to their unique characteristics—their underlying structure is not Euclidean or grid-like, they remain isomorphic under permutation of the nodes labels, and they come with a different number of nodes and edges. In this paper, we propose NeVAE, a novel variational autoencoder for molecular graphs, whose encoder and decoder are specially designed to account for the above properties by means of several technical innovations. In addition, by using masking, the decoder is able to guarantee a set of valid properties in the generated molecules. Experiments reveal that our model can discover plausible, diverse and novel molecules more effectively than several state of the art methods. Moreover, by utilizing Bayesian optimization over the continuous latent representation of molecules our model finds, we can also find molecules that maximize certain desirable properties more effectively than alternatives.

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