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Compressing physics with an autoencoder: Creating an atomic species representation to improve machine learning models in the chemical sciences.

John E. Herr,Kevin J Koh,Kun Yao,John A. Parkhill

Published 2018 in Journal of Chemical Physics

ABSTRACT

We define a vector quantity which corresponds to atomic species identity by compressing a set of physical properties with an autoencoder. This vector, referred to here as the elemental modes, provides many advantages in downstream machine learning tasks. Using the elemental modes directly as the feature vector, we trained a neural network to predict formation energies of elpasolites with improved accuracy over previous works on the same task. Combining the elemental modes with geometric features used in high-dimensional neural network potentials (HD-NNPs) solves many problems of scaling and efficiency in the development of such neural network potentials. Whereas similar models in the past have been limited to typically four atomic species (H, C, N, and O), our implementation does not scale in cost by adding more atomic species and allows us to train an HD-NNP model which treats molecules containing H, C, N, O, F, P, S, Cl, Se, Br, and I. Finally, we establish that our implementation allows us to define feature vectors for alchemical intermediate states in the HD-NNP model, which opens up new possibilities for performing alchemical free energy calculations on systems where bond breaking/forming is important.

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