Molecular Hypergraph Grammar with Its Application to Molecular Optimization

Hiroshi Kajino
; Proceedings of the 36th International Conference on Machine Learning, PMLR 97:3183-3191, 2019.

Abstract

Molecular optimization aims to discover novel molecules with desirable properties, and its two fundamental challenges are: (i) it is not trivial to generate valid molecules in a controllable way due to hard chemical constraints such as the valency conditions, and (ii) it is often costly to evaluate a property of a novel molecule, and therefore, the number of property evaluations is limited. These challenges are to some extent alleviated by a combination of a variational autoencoder (VAE) and Bayesian optimization (BO), where VAE converts a molecule into/from its latent continuous vector, and BO optimizes a latent continuous vector (and its corresponding molecule) within a limited number of property evaluations. While the most recent work, for the first time, achieved 100% validity, its architecture is rather complex due to auxiliary neural networks other than VAE, making it difficult to train. This paper presents a molecular hypergraph grammar variational autoencoder (MHG-VAE), which uses a single VAE to achieve 100% validity. Our idea is to develop a graph grammar encoding the hard chemical constraints, called molecular hypergraph grammar (MHG), which guides VAE to always generate valid molecules. We also present an algorithm to construct MHG from a set of molecules.

Cite this Paper


BibTeX
@InProceedings{pmlr-v97-kajino19a, title = {Molecular Hypergraph Grammar with Its Application to Molecular Optimization}, author = {Kajino, Hiroshi}, pages = {3183--3191}, year = {2019}, editor = {Kamalika Chaudhuri and Ruslan Salakhutdinov}, volume = {97}, series = {Proceedings of Machine Learning Research}, address = {Long Beach, California, USA}, month = {09--15 Jun}, publisher = {PMLR}, pdf = {http://proceedings.mlr.press/v97/kajino19a/kajino19a.pdf}, url = {http://proceedings.mlr.press/v97/kajino19a.html}, abstract = {Molecular optimization aims to discover novel molecules with desirable properties, and its two fundamental challenges are: (i) it is not trivial to generate valid molecules in a controllable way due to hard chemical constraints such as the valency conditions, and (ii) it is often costly to evaluate a property of a novel molecule, and therefore, the number of property evaluations is limited. These challenges are to some extent alleviated by a combination of a variational autoencoder (VAE) and Bayesian optimization (BO), where VAE converts a molecule into/from its latent continuous vector, and BO optimizes a latent continuous vector (and its corresponding molecule) within a limited number of property evaluations. While the most recent work, for the first time, achieved 100% validity, its architecture is rather complex due to auxiliary neural networks other than VAE, making it difficult to train. This paper presents a molecular hypergraph grammar variational autoencoder (MHG-VAE), which uses a single VAE to achieve 100% validity. Our idea is to develop a graph grammar encoding the hard chemical constraints, called molecular hypergraph grammar (MHG), which guides VAE to always generate valid molecules. We also present an algorithm to construct MHG from a set of molecules.} }
Endnote
%0 Conference Paper %T Molecular Hypergraph Grammar with Its Application to Molecular Optimization %A Hiroshi Kajino %B Proceedings of the 36th International Conference on Machine Learning %C Proceedings of Machine Learning Research %D 2019 %E Kamalika Chaudhuri %E Ruslan Salakhutdinov %F pmlr-v97-kajino19a %I PMLR %J Proceedings of Machine Learning Research %P 3183--3191 %U http://proceedings.mlr.press %V 97 %W PMLR %X Molecular optimization aims to discover novel molecules with desirable properties, and its two fundamental challenges are: (i) it is not trivial to generate valid molecules in a controllable way due to hard chemical constraints such as the valency conditions, and (ii) it is often costly to evaluate a property of a novel molecule, and therefore, the number of property evaluations is limited. These challenges are to some extent alleviated by a combination of a variational autoencoder (VAE) and Bayesian optimization (BO), where VAE converts a molecule into/from its latent continuous vector, and BO optimizes a latent continuous vector (and its corresponding molecule) within a limited number of property evaluations. While the most recent work, for the first time, achieved 100% validity, its architecture is rather complex due to auxiliary neural networks other than VAE, making it difficult to train. This paper presents a molecular hypergraph grammar variational autoencoder (MHG-VAE), which uses a single VAE to achieve 100% validity. Our idea is to develop a graph grammar encoding the hard chemical constraints, called molecular hypergraph grammar (MHG), which guides VAE to always generate valid molecules. We also present an algorithm to construct MHG from a set of molecules.
APA
Kajino, H.. (2019). Molecular Hypergraph Grammar with Its Application to Molecular Optimization. Proceedings of the 36th International Conference on Machine Learning, in PMLR 97:3183-3191

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