scholarly journals A universal framework for featurization of atomistic systems

Author(s):  
Xiangyun Lei ◽  
Andrew Medford

Abstract Molecular dynamics simulations are an invaluable tool in numerous scientific fields. However, the ubiquitous classical force fields cannot describe reactive systems, and quantum molecular dynamics are too computationally demanding to treat large systems or long timescales. Reactive force fields based on physics or machine learning can be used to bridge the gap in time and length scales, but these force fields require substantial effort to construct and are highly specific to a given chemical composition and application. A significant limitation of machine learning models is the use of element-specific features, leading to models that scale poorly with the number of elements. This work introduces the Gaussian multipole (GMP) featurization scheme that utilizes physically-relevant multipole expansions of the electron density around atoms to yield feature vectors that interpolate between element types and have a fixed dimension regardless of the number of elements present. We combine GMP with neural networks to directly compare it to the widely used Behler-Parinello symmetry functions for the MD17 dataset, revealing that it exhibits improved accuracy and computational efficiency. Further, we demonstrate that GMP-based models can achieve chemical accuracy for the QM9 dataset, and their accuracy remains reasonable even when extrapolating to new elements. Finally, we test GMP-based models for the Open Catalysis Project (OCP) dataset, revealing comparable performance to graph convolutional deep learning models. The results indicate that this featurization scheme fills a critical gap in the construction of efficient and transferable machine-learned force fields.

2019 ◽  
Vol 10 (8) ◽  
pp. 2298-2307 ◽  
Author(s):  
Florian Häse ◽  
Ignacio Fdez. Galván ◽  
Alán Aspuru-Guzik ◽  
Roland Lindh ◽  
Morgane Vacher

Machine learning models, trained to reproduce molecular dynamics results, help interpreting simulations and extracting new understanding of chemistry.


2021 ◽  
Vol 11 (3) ◽  
pp. 1323
Author(s):  
Medard Edmund Mswahili ◽  
Min-Jeong Lee ◽  
Gati Lother Martin ◽  
Junghyun Kim ◽  
Paul Kim ◽  
...  

Cocrystals are of much interest in industrial application as well as academic research, and screening of suitable coformers for active pharmaceutical ingredients is the most crucial and challenging step in cocrystal development. Recently, machine learning techniques are attracting researchers in many fields including pharmaceutical research such as quantitative structure-activity/property relationship. In this paper, we develop machine learning models to predict cocrystal formation. We extract descriptor values from simplified molecular-input line-entry system (SMILES) of compounds and compare the machine learning models by experiments with our collected data of 1476 instances. As a result, we found that artificial neural network shows great potential as it has the best accuracy, sensitivity, and F1 score. We also found that the model achieved comparable performance with about half of the descriptors chosen by feature selection algorithms. We believe that this will contribute to faster and more accurate cocrystal development.


1994 ◽  
Vol 101 (8) ◽  
pp. 7048-7057 ◽  
Author(s):  
D. L. Lynch ◽  
N. Troullier ◽  
J. D. Kress ◽  
L. A. Collins

2014 ◽  
Vol 140 (18) ◽  
pp. 18A529 ◽  
Author(s):  
Fuyuki Shimojo ◽  
Shinnosuke Hattori ◽  
Rajiv K. Kalia ◽  
Manaschai Kunaseth ◽  
Weiwei Mou ◽  
...  

Sign in / Sign up

Export Citation Format

Share Document