62,774 research outputs found

    Machine-learning of atomic-scale properties based on physical principles

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    We briefly summarize the kernel regression approach, as used recently in materials modelling, to fitting functions, particularly potential energy surfaces, and highlight how the linear algebra framework can be used to both predict and train from linear functionals of the potential energy, such as the total energy and atomic forces. We then give a detailed account of the Smooth Overlap of Atomic Positions (SOAP) representation and kernel, showing how it arises from an abstract representation of smooth atomic densities, and how it is related to several popular density-based representations of atomic structure. We also discuss recent generalisations that allow fine control of correlations between different atomic species, prediction and fitting of tensorial properties, and also how to construct structural kernels---applicable to comparing entire molecules or periodic systems---that go beyond an additive combination of local environments

    Detecting periodic time scales in temporal networks

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    Temporal networks are commonly used to represent dynamical complex systems like social networks, simultaneous firing of neurons, human mobility or public transportation. Their dynamics may evolve on multiple time scales characterising for instance periodic activity patterns or structural changes. The detection of these time scales can be challenging from the direct observation of simple dynamical network properties like the activity of nodes or the density of links. Here we propose two new methods, which rely on already established static representations of temporal networks, namely supra-adjacency matrices and temporal event graphs. We define dissimilarity metrics extracted from these representations and compute their Fourier Transform to effectively identify dominant periodic time scales characterising the original temporal network. We demonstrate our methods using synthetic and real-world data sets describing various kinds of temporal networks. We find that while in all cases the two methods outperform the reference measures, the supra-adjacency based method identifies more easily periodic changes in network density, while the temporal event graph based method is better suited to detect periodic changes in the group structure of the network. Our methodology may provide insights into different phenomena occurring at multiple time-scales in systems represented by temporal networks.Comment: 19 pages, 11 figure

    Alchemical and structural distribution based representation for improved QML

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    We introduce a representation of any atom in any chemical environment for the generation of efficient quantum machine learning (QML) models of common electronic ground-state properties. The representation is based on scaled distribution functions explicitly accounting for elemental and structural degrees of freedom. Resulting QML models afford very favorable learning curves for properties of out-of-sample systems including organic molecules, non-covalently bonded protein side-chains, (H2_2O)40_{40}-clusters, as well as diverse crystals. The elemental components help to lower the learning curves, and, through interpolation across the periodic table, even enable "alchemical extrapolation" to covalent bonding between elements not part of training, as evinced for single, double, and triple bonds among main-group elements

    Crystal Structure Representations for Machine Learning Models of Formation Energies

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    We introduce and evaluate a set of feature vector representations of crystal structures for machine learning (ML) models of formation energies of solids. ML models of atomization energies of organic molecules have been successful using a Coulomb matrix representation of the molecule. We consider three ways to generalize such representations to periodic systems: (i) a matrix where each element is related to the Ewald sum of the electrostatic interaction between two different atoms in the unit cell repeated over the lattice; (ii) an extended Coulomb-like matrix that takes into account a number of neighboring unit cells; and (iii) an Ansatz that mimics the periodicity and the basic features of the elements in the Ewald sum matrix by using a sine function of the crystal coordinates of the atoms. The representations are compared for a Laplacian kernel with Manhattan norm, trained to reproduce formation energies using a data set of 3938 crystal structures obtained from the Materials Project. For training sets consisting of 3000 crystals, the generalization error in predicting formation energies of new structures corresponds to (i) 0.49, (ii) 0.64, and (iii) 0.37 eV/atom for the respective representations

    Alchemical and structural distribution based representation for improved QML

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    We introduce a representation of any atom in any chemical environment for the generation of efficient quantum machine learning (QML) models of common electronic ground-state properties. The representation is based on scaled distribution functions explicitly accounting for elemental and structural degrees of freedom. Resulting QML models afford very favorable learning curves for properties of out-of-sample systems including organic molecules, non-covalently bonded protein side-chains, (H2_2O)40_{40}-clusters, as well as diverse crystals. The elemental components help to lower the learning curves, and, through interpolation across the periodic table, even enable "alchemical extrapolation" to covalent bonding between elements not part of training, as evinced for single, double, and triple bonds among main-group elements

    Representations of molecules and materials for interpolation of quantum-mechanical simulations via machine learning

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    Computational study of molecules and materials from first principles is a cornerstone of physics, chemistry and materials science, but limited by the cost of accurate and precise simulations. In settings involving many simulations, machine learning can reduce these costs, sometimes by orders of magnitude, by interpolating between reference simulations. This requires representations that describe any molecule or material and support interpolation. We review, discuss and benchmark state-of-the-art representations and relations between them, including smooth overlap of atomic positions, many-body tensor representation, and symmetry functions. For this, we use a unified mathematical framework based on many-body functions, group averaging and tensor products, and compare energy predictions for organic molecules, binary alloys and Al-Ga-In sesquioxides in numerical experiments controlled for data distribution, regression method and hyper-parameter optimization

    Structural and electronic properties of p-doped silicon clathrates

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    We present an ab initio study of the structural and electronic properties of type-I and type-II silicon clathrates doped by elements chosen to be more electronegative than silicon. Depending on the intercalated element, we show that the electronic properties of doped silicon clathrates can exhibit metallic, semiconducting, or insulating behavior. It is found in particular that doping can lead to silicon-based materials with a band gap in the visible range and that, in type-II clathrates, the gap can be direct. However, the analysis of the selection rules show that the optical transitions are forbidden in type-I and type-II clathrates. Concerning the structural properties, the bonding between the dopant atom and silicon can significantly decrease the compressibility of the host network to values equivalent to the one of the much denser diamond phase. The present results are complemented and rationalized by the study of endohedrally doped SinHn n=20,24,28 silicon clusters
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