Deep Spatial Learning with Molecular Vibration

Chemical Science, 2022

Machine learning techniques including neural networks are popular tools for chemical, physical and materials applications searching for viable alternative methods in the analysis of structure and energetics of systems ranging from crystals to biomolecules. Efforts are less abundant for prediction of kinetics and dynamics. Here we explore the ability of three well established recurrent neural network architectures for reproducing and forecasting the energetics of a liquid solution of ethyl acetate containing a macromolecular polymer-lipid aggregate at ambient conditions. Data models from three recurrent neural networks, ERNN, LSTM and GRU, are trained and tested on half million points time series of the macromolecular aggregate potential energy and its interaction energy with the solvent obtained from molecular dynamics simulations. Our exhaustive analyses convey that the recurrent neural network architectures investigated generate data models that reproduce excellently the time series although their capability of yielding short or long term energetics forecasts with expected statistical distributions of the time points is limited. We propose an in silico protocol by extracting time patterns of the original series and utilizing these patterns to create an ensemble of artificial network models trained on an ensemble of time series seeded by the additional time patters. The energetics forecast improve, predicting a band of forecasted time series with a spread of values consistent with the molecular dynamics energy fluctuations span. Although the distribution of points from the band of energy forecasts is not optimal, the proposed in silico protocol provides useful estimates of the solvated macromolecular aggregate fate. Given the growing application of artificial networks in materials design, the data-based protocol presented here expands the realm of science areas where supervised machine learning serves as a decision making tool aiding the simulation practitioner to assess when long simulations are worth to be continued.

Computational Materials Science, 2021

Simulation of reasonable timescales for any long physical process using molecular dynamics (MD) is a major challenge in computational physics. In this study, we have implemented an approach based on multi-fidelity physics informed neural network (MPINN) to achieve long-range MD simulation results over a large sample space with significantly less computational cost. The fidelity of our present multi-fidelity study is based on the integration timestep size of MD simulations. While MD simulations with larger timestep produce results with lower level of accuracy, it can provide enough computationally cheap training data for the MPINN to learn an accurate relationship between these low-fidelity results and high-fidelity MD results obtained using smaller simulation timestep. We have performed two benchmark studies, involving one and two component Lennard-Jones systems, to determine the optimum percentage of high-fidelity training data required to achieve accurate results with high computational saving. The results show that important system properties such as system energy per atom, system pressure and diffusion coefficients can be determined with high accuracy while saving 68% computational costs. Finally, as a demonstration of the applicability of our present methodology in practical MD studies, we have studied the viscosity of argon-copper nanofluid and its variation with temperature and volume fraction by MD simulation using MPINN. Then we have compared them with numerous previous studies and theoretical models. Our results indicate that MPINN can predict accurate nanofluid viscosity at a wide range of sample space with significantly small number of MD simulations. Our present methodology is the first implementation of MPINN in conjunction with MD simulation for predicting nanoscale properties. This can pave pathways to investigate more complex engineering problems that demand long-range MD simulations.

Nanotechnology, 2017

Single-molecule experiments typically produce large datasets, which can be challenging to analyse. Hypothesis-driven data exploration, informed by an expectation of the signal characteristics, can lead to interpretation bias or loss of information. The latest developments in Machine Learning, so-called Deep Learning (DL) methods offer an interesting, new avenue to address such challenges. A DL algorithm 'learns' certain data features towards an optimal prediction (e.g., a base call in DNA sequencing). In some applications, such as speech and image recognition, DL has been able to outperform conventional Machine Learning strategies and even human performance. However, to date DL has not been applied in single-molecule science, to the best of our knowledge. We illustrate how it can be used, and discuss some of the strengths and weaknesses of the approach. In particular, a 'deep' neural network has many features of a 'black box', which marks a significant departure from hypothesis-led data interpretation. Single-molecule sensing, sequencing and characterisation based on electric or optical techniques can generate very large datasets, in some cases in a (semi-) automated fashion 1-4. This data is typically one-dimensional, in the sense that the conductance, intensity or current is being recorded as a function of a single, independent variable, for example time or electrode distance, as illustrated in Fig. 1. The analysis can be very challenging, not only because of the sheer size of the dataset, but also due to insufficient knowledge about the characteristic signal features and poor signal-tonoise ratio (S/N). Some hypothesis-driven data exploration and selection is often required: Led by an expectation that may for example be informed by a physical model or even intuition, the experimenter inspects the data either manually or

2019

Recent advances in artificial intelligence along with development of large datasets of energies calculated using quantum mechanical (QM)/density functional theory (DFT) methods have enabled prediction of accurate molecular energies at reasonably low computational cost. However, machine learning models that have been reported so far requires the atomic positions obtained from geometry optimizations using high level QM/DFT methods as input in order to predict the energies, and do not allow for geometry optimization. In this paper, a transferable and molecule-size independent machine learning model (BAND NN) based on a chemically intuitive representation inspired by molecular mechanics force fields is presented. The model predicts the atomization energies of equilibrium and non-equilibrium structures as sum of energy contributions from bonds (B), angles (A), nonbonds (N) and dihedrals (D) at remarkable accuracy. The robustness of the proposed model is further validated by calculations ...

Journal of Physical Chemistry Letters, 2015

Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective manybody interactions proves to be essential for approaching the "holy grail" of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. In addition, the same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies.

Cornell University - arXiv, 2020

Precise physical descriptions of molecules can be obtained by solving the Schrodinger equation; however, these calculations are intractable and even approximations can be cumbersome. Force fields, which estimate interatomic potentials based on empirical data, are also time-consuming. This paper proposes a new methodology for modeling a set of physical parameters by taking advantage of the restricted Boltzmann machine's fast learning capacity and representational power. By training the machine on ab initio data, we can predict new data in the distribution of molecular configurations matching the ab initio distribution. In this paper we introduce a new RBM based on the Tanh activation function, and conduct a comparison of RBMs with different activation functions, including sigmoid, Gaussian, and (Leaky) ReLU. Finally we demonstrate the ability of Gaussian RBMs to model small molecules such as water and ethane.

Journal of Membrane Science, 2021

A phase III, open-label, randomised multicentre study to evaluate the immunogenicity and safety of a booster dose of two different reduced antigen diphtheria-tetanus-acellular pertussis-polio vaccines, when coadministered with measles-mumps-rubella vaccine in 3 and 4-year-old healthy children in the UK

arXiv (Cornell University), 2022

From AlexNet to Inception, autoencoders to diffusion models, the development of novel and powerful deep learning models and learning algorithms has proceeded at breakneck speeds. In part, we believe that rapid iteration of model architecture and learning techniques by a large community of researchers over a common representation of the underlying entities has resulted in transferable deep learning knowledge. As a result, model scale, accuracy, fidelity, and compute performance have dramatically increased in computer vision and natural language processing. On the other hand, the lack of a common representation for chemical structure has hampered similar progress. To enable transferable deep learning, we identify the need for a robust 3-dimensional representation of materials such as molecules and crystals. The goal is to enable both materials property prediction and materials generation with 3D structures. While computationally costly, such representations can model a large set of chemical structures. We propose ParticleGrid, a SIMD-optimized library for 3D structures, that is designed for deep learning applications and to seamlessly integrate with deep learning frameworks. Our highly optimized grid generation allows for generating grids on the fly on the CPU, reducing storage and GPU compute and memory requirements. We show the efficacy of 3D grids generated via ParticleGrid and accurately predict molecular energy properties using a 3D convolutional neural network. Our model is able to get 0.006 mean square error and nearly match the values calculated using computationally costly density functional theory at a fraction of the time.

2021

The generalization accuracy of machine learning models of potential energy surfaces (PES) and force fields (FF) for large polyatomic molecules can be generally improved either by increasing the number of training points or by improving the models. In order to build accurate models based on expensive high-level ab initio calculations, much of recent work has focused on the latter. In particular, it has been shown that gradient domain machine learning (GDML) models produce accurate results for high-dimensional molecular systems with a small number of ab initio calculations. The present work extends GDML to models with complex kernels built to maximize inference from a small number of molecular geometries. We illustrate that GDML models can be improved by increasing the complexity of underlying kernels through a greedy search algorithm using Bayesian information criterion as the model selection metric. We show that this requires including anisotropy into kernel functions and produces m...

ML4Chem is an open-source machine learning library for chemistry and materials science. It provides an extendable platform to develop and deploy machine learning models and pipelines and is targeted to the non-expert and expert users. ML4Chem follows user-experience design and offers the needed tools to go from data preparation to inference. Here we introduce its atomistic module for the implementation, deployment, and reproducibility of atom-centered models. This module is composed of six core building blocks: data, featurization, models, model optimization, inference, and visualization. We present their functionality and ease of use with demonstrations utilizing neural networks and kernel ridge regression algorithms.