Atom-Density Representations for Machine Learning

The applications of machine learning techniques to chemistry and materials science become more numerous by the day. The main challenge is to devise representations of atomic systems that are at the same time complete and concise, so as to reduce the number of reference calculations that are needed to predict the properties of different types of materials reliably. This has led to a proliferation of alternative ways to convert an atomic structure into an input for a machine-learning model. We introduce an abstract definition of chemical environments that is based on a smoothed atomic density, using a bra-ket notation to emphasize basis set independence and to highlight the connections with some popular choices of representations for describing atomic systems. The correlations between the spatial distribution of atoms and their chemical identities are computed as inner products between these feature kets, which can be given an explicit representation in terms of the expansion of the atom density on orthogonal basis functions, that is equivalent to the smooth overlap of atomic positions (SOAP) power spectrum, but also in real space, corresponding to $n$-body correlations of the atom density. This formalism lays the foundations for a more systematic tuning of the behavior of the representations, by introducing operators that represent the correlations between structure, composition, and the target properties. It provides a unifying picture of recent developments in the field and indicates a way forward towards more effective and computationally affordable machine-learning schemes for molecules and materials

Feature Optimization for Atomistic Machine Learning Yields A Data-Driven Construction of the Periodic Table of the Elements

Machine-learning of atomic-scale properties amounts to extracting correlations between structure, composition and the quantity that one wants to predict. Representing the input structure in a way that best reflects such correlations makes it possible to improve the accuracy of the model for a given amount of reference data. When using a description of the structures that is transparent and well-principled, optimizing the representation might reveal insights into the chemistry of the data set. Here we show how one can generalize the SOAP kernel to introduce a distance-dependent weight that accounts for the multi-scale nature of the interactions, and a description of correlations between chemical species. We show that this improves substantially the performance of ML models of molecular and materials stability, while making it easier to work with complex, multi-component systems and to extend SOAP to coarse-grained intermolecular potentials. The element correlations that give the best performing model show striking similarities with the conventional periodic table of the elements, providing an inspiring example of how machine learning can rediscover, and generalize, intuitive concepts that constitute the foundations of chemistry.Comment: 9 pages, 4 figure

Efficient implementation of atom-density representations

Physically motivated and mathematically robust atom-centered representations of molecular structures are key to the success of modern atomistic machine learning. They lie at the foundation of a wide range of methods to predict the properties of both materials and molecules and to explore and visualize their chemical structures and compositions. Recently, it has become clear that many of the most effective representations share a fundamental formal connection. They can all be expressed as a discretization of n-body correlation functions of the local atom density, suggesting the opportunity of standardizing and, more importantly, optimizing their evaluation. We present an implementation, named librascal, whose modular design lends itself both to developing refinements to the density-based formalism and to rapid prototyping for new developments of rotationally equivariant atomistic representations. As an example, we discuss smooth overlap of atomic position (SOAP) features, perhaps the most widely used member of this family of representations, to show how the expansion of the local density can be optimized for any choice of radial basis sets. We discuss the representation in the context of a kernel ridge regression model, commonly used with SOAP features, and analyze how the computational effort scales for each of the individual steps of the calculation. By applying data reduction techniques in feature space, we show how to reduce the total computational cost by a factor of up to 4 without affecting the model’s symmetry properties and without significantly impacting its accuracy

Boltzmann-conserving classical dynamics in quantum time-correlation functions: "Matsubara dynamics".

We show that a single change in the derivation of the linearized semiclassical-initial value representation (LSC-IVR or "classical Wigner approximation") results in a classical dynamics which conserves the quantum Boltzmann distribution. We rederive the (standard) LSC-IVR approach by writing the (exact) quantum time-correlation function in terms of the normal modes of a free ring-polymer (i.e., a discrete imaginary-time Feynman path), taking the limit that the number of polymer beads N → ∞, such that the lowest normal-mode frequencies take their "Matsubara" values. The change we propose is to truncate the quantum Liouvillian, not explicitly in powers of ħ(2) at ħ(0) (which gives back the standard LSC-IVR approximation), but in the normal-mode derivatives corresponding to the lowest Matsubara frequencies. The resulting "Matsubara" dynamics is inherently classical (since all terms O(ħ(2)) disappear from the Matsubara Liouvillian in the limit N → ∞) and conserves the quantum Boltzmann distribution because the Matsubara Hamiltonian is symmetric with respect to imaginary-time translation. Numerical tests show that the Matsubara approximation to the quantum time-correlation function converges with respect to the number of modes and gives better agreement than LSC-IVR with the exact quantum result. Matsubara dynamics is too computationally expensive to be applied to complex systems, but its further approximation may lead to practical methods.T.J.H.H., M.J.W., and S.C.A. acknowledge funding from the U.K. Engineering and Physical Sciences Research Council. A.M. acknowledges the European Lifelong Learning Programme (LLP) for an Erasmus student placement scholarship. T.J.H.H. also acknowledges a Research Fellowship from Jesus College, Cambridge and helpful discussions with Dr. Adam Harper.This is the author accepted manuscript. The final version is available from AIP via http://dx.doi.org/10.1063/1.491631

Path-integral dynamics of water using curvilinear centroids

We develop a path-integral dynamics method for water that resembles centroid molecular dynamics (CMD), except that the centroids are averages of curvilinear, rather than cartesian, bead coordinates. The curvilinear coordinates are used explicitly only when computing the potential of mean force, the components of which are re-expressed in terms of cartesian 'quasi-centroids' (so-called because they are close to the cartesian centroids). Cartesian equations of motion are obtained by making small approximations to the quantum Boltzmann distribution. Simulations of the infrared spectra of various water models over 150-600 K show these approximations to be justified: for a two-dimensional OH-bond model, the quasi-centroid molecular dynamics (QCMD) spectra lie close to the exact quantum spectra, and almost on top of the Matsubara dynamics spectra; for gas-phase water, the QCMD spectra are close to the exact quantum spectra; for liquid water and ice (using the q-TIP4P/F surface), the QCMD spectra are close to the CMD spectra at 600 K, and line up with the results of thermostatted ring-polymer molecular dynamics and approximate quantum calculations at 300 and 150 K. The QCMD spectra show no sign of the CMD 'curvature problem' (of erroneous red shifts and broadening). In the liquid and ice simulations, the potential of mean force was evaluated on the fly by generalising an adiabatic CMD algorithm to curvilinear coordinates; the full limit of adiabatic separation needed to be taken, which made the QCMD calculations 8 times more expensive than partially adiabatic CMD at 300 K, and 32 times at 150 K (and the intensities may still not be converged at this temperature). The QCMD method is probably generalisable to many other systems, provided collective bead-coordinates can be identified that yield compact mean-field ring-polymer distributions.Cambridge University Vice Chancellor's award

Approximating Matsubara dynamics using the planetary model: Tests on liquid water and ice.

Matsubara dynamics is the quantum-Boltzmann-conserving classical dynamics which remains when real-time coherences are taken out of the exact quantum Liouvillian [T. J. H. Hele et al., J. Chem. Phys. 142, 134103 (2015)]; because of a phase-term, it cannot be used as a practical method without further approximation. Recently, Smith et al. [J. Chem. Phys. 142, 244112 (2015)] developed a "planetary" model dynamics which conserves the Feynman-Kleinert (FK) approximation to the quantum-Boltzmann distribution. Here, we show that for moderately anharmonic potentials, the planetary dynamics gives a good approximation to Matsubara trajectories on the FK potential surface by decoupling the centroid trajectory from the locally harmonic Matsubara fluctuations, which reduce to a single phase-less fluctuation particle (the "planet"). We also show that the FK effective frequency can be approximated by a direct integral over these fluctuations, obviating the need to solve iterative equations. This modification, together with use of thermostatted ring-polymer molecular dynamics, allows us to test the planetary model on water (gas-phase, liquid, and ice) using the q-TIP4P/F potential surface. The "planetary" fluctuations give a poor approximation to the rotational/librational bands in the infrared spectrum, but a good approximation to the bend and stretch bands, where the fluctuation lineshape is found to be motionally narrowed by the vibrations of the centroid

Fast and Accurate Uncertainty Estimation in Chemical Machine Learning

We present a scheme to obtain an inexpensive and reliable estimate of the uncertainty associated with the predictions of a machine-learning model of atomic and molecular properties. The scheme is based on resampling, with multiple models being generated based on subsampling of the same training data. The accuracy of the uncertainty prediction can be benchmarked by maximum likelihood estimation, which can also be used to correct for correlations between resampled models and to improve the performance of the uncertainty estimation by a cross-validation procedure. In the case of sparse Gaussian Process Regression models, this resampled estimator can be evaluated at negligible cost. We demonstrate the reliability of these estimates for the prediction of molecular and materials energetics and for the estimation of nuclear chemical shieldings in molecular crystals. Extension to estimate the uncertainty in energy differences, forces, or other correlated predictions is straightforward. This method can be easily applied to other machine-learning schemes and will be beneficial to make data-driven predictions more reliable and to facilitate training-set optimization and active-learning strategies

Communication: Relation of centroid molecular dynamics and ring-polymer molecular dynamics to exact quantum dynamics.

We recently obtained a quantum-Boltzmann-conserving classical dynamics by making a single change to the derivation of the "Classical Wigner" approximation. Here, we show that the further approximation of this "Matsubara dynamics" gives rise to two popular heuristic methods for treating quantum Boltzmann time-correlation functions: centroid molecular dynamics (CMD) and ring-polymer molecular dynamics (RPMD). We show that CMD is a mean-field approximation to Matsubara dynamics, obtained by discarding (classical) fluctuations around the centroid, and that RPMD is the result of discarding a term in the Matsubara Liouvillian which shifts the frequencies of these fluctuations. These findings are consistent with previous numerical results and give explicit formulae for the terms that CMD and RPMD leave out.TJHH, MJW and SCA acknowledge funding from the UK Science and Engineering Research Council. AM acknowledges the European Lifelong Learning Programme (LLP) for an Erasmus student placement scholarship. TJHH also acknowledges a Research Fellowship from Jesus College, Cambridge.This is the author accepted manuscript. The final version is available from AIP via http://dx.doi.org/10.1063/1.492123