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Publication# Local Kernel Regression and Neural Network Approaches to the Conformational Landscapes of Oligopeptides

Abstract

The application of machine learning to theoretical chemistry has made it possible to combine the accuracy of quantum chemical energetics with the thorough sampling of finite-temperature fluctuations. To reach this goal, a diverse set of methods has been proposed, ranging from simple linear models to kernel regression and highly nonlinear neural networks. Here we apply two widely different approaches to the same, challenging problem: the sampling of the conformational landscape of polypeptides at finite temperature. We develop a local kernel regression (LKR) coupled with a supervised sparsity method and compare it with a more established approach based on Behler-Parrinello type neural networks. In the context of the LKR, we discuss how the supervised selection of the reference pool of environments is crucial to achieve accurate potential energy surfaces at a competitive computational cost and leverage the locality of the model to infer which chemical environments are poorly described by the DFTB baseline. We then discuss the relative merits of the two frameworks and perform Hamiltonian-reservoir replica-exchange Monte Carlo sampling and metadynamics simulations, respectively, to demonstrate that both frameworks can achieve converged and transferable sampling of the conformational landscape of complex and flexible biomolecules with comparable accuracy and computational cost.

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Related concepts (33)

Artificial neural network

Artificial neural networks (ANNs, also shortened to neural networks (NNs) or neural nets) are a branch of machine learning models that are built using principles of neuronal organization discovered by connectionism in the biological neural networks constituting animal brains. An ANN is based on a collection of connected units or nodes called artificial neurons, which loosely model the neurons in a biological brain. Each connection, like the synapses in a biological brain, can transmit a signal to other neurons.

Kernel regression

In statistics, kernel regression is a non-parametric technique to estimate the conditional expectation of a random variable. The objective is to find a non-linear relation between a pair of random variables X and Y. In any nonparametric regression, the conditional expectation of a variable relative to a variable may be written: where is an unknown function. Nadaraya and Watson, both in 1964, proposed to estimate as a locally weighted average, using a kernel as a weighting function.

Nonparametric regression

Nonparametric regression is a category of regression analysis in which the predictor does not take a predetermined form but is constructed according to information derived from the data. That is, no parametric form is assumed for the relationship between predictors and dependent variable. Nonparametric regression requires larger sample sizes than regression based on parametric models because the data must supply the model structure as well as the model estimates.

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