Machine learning predicts atomization energies accurately from low-fidelity calculations.
problem Predicting accurate atomization energies of organic molecules efficiently.
method Machine learning models trained on low-fidelity B3LYP energies to predict high-fidelity G4MP2 energies.
result Predicted G4MP2 atomization energies within 0.012 eV for molecules with 10-14 heavy atoms.
We introduce a machine learning model to predict atomization energies of a diverse set of organic molecules, based on nuclear charges and atomic positions only. The problem of solving the molecular Schrödinger equation is mapped onto a non-linear statistical regression problem of reduced complexity. Regression models a…
Graph neural network predicts protonation energies of oxygen atoms in bio-oil molecules.
problem Predicting protonation energies of oxygen atoms in bio-oil molecules for chemical upgrading.
method Site-specific graph neural network approach using iterative local nonlinear embedding.
result Effective prediction of protonation energies of individual oxygen atoms in bio-oil molecules.
Recent machine learning methods make it possible to model potential energy of atomic configurations with chemical-level accuracy (as calculated from ab-initio calculations) and at speeds suitable for molecular dynam- ics simulation. Best performance is achieved when the known physical constraints are encoded in the mac…
EBM predicts protein conformations at atomic scale using crystallized data.
problem Predicting the conformation of a side chain from its context within a protein structure.
method Energy-based model trained on crystallized protein data, evaluating performance on rotamer recovery task.
result EBM achieves performance close to state-of-the-art methods, including Rosetta energy function.
Study compares atom representations in graph neural networks for molecular properties.
problem Incorrect attribution of results in molecular property prediction due to varying atom features.
method Evaluated multiple atom representations on free energy, solubility, and metabolic stability predictions.
result Different atom representations can lead to varying predictive performance in graph neural networks.
Normalizing flows model atomic solids without needing ground-truth samples.
problem Modeling atomic solids without ground-truth samples.
method Normalizing flows to transform a base distribution into the target solid.
result Excellent agreement between model estimates and literature values for Helmholtz free energy.
The study shows that certain graphs are regular at boundary points.
problem Boundary regularity of anisotropic minimal Lipschitz graphs.
method Proves regularity for graphs with bounded anisotropic mean curvature and atomic energy condition.
result Regularity at boundary points with density bounded above by 1/2 + σ.
Proposes linking energy and force uncertainty in deep learning potentials.
problem Uncertainty in predicted energies and forces in machine learning models.
method Introduces a spatially correlated noise process to link energy and force uncertainty.
result Demonstrates the approach on molecular datasets, linking energy and force uncertainties.
A new method predicts electron density accurately from atom-centered models.
problem Predicting electron density accurately from atom-centered models.
method Gradient-based approach to minimize loss function in an optimized sparse feature space.
result Extremely accurate predictions of electron density and total energies.
New algorithm efficiently trains machine learning models to atomic forces data.
problem Efficiently training machine learning models to large amounts of force data.
method Developed an efficient algorithm for training machine learning models to all available force data.
result Training to all available force data is only a few times more expensive than training to energies alone.
We introduce a novel class of localized atomic environment representations, based upon the Coulomb matrix. By combining these functions with the Gaussian approximation potential approach, we present LC-GAP, a new system for generating atomic potentials through machine learning (ML). Tests on the QM7, QM7b and GDB9 biom…
The calculation of minimum energy paths for transitions such as atomic and/or spin re-arrangements is an important task in many contexts and can often be used to determine the mechanism and rate of transitions. An important challenge is to reduce the computational effort in such calculations, especially when ab initio …
Novel ML model predicts solvation free energies from atom interactions.
problem Predicting solvation free energies from atomistic interactions.
method Two encoding functions extract atomic feature vectors, interactions calculated by inner product.
result Outstanding performance and transferability on 6,493 experimental measurements.
ShotgunCSP predicts crystal structures using machine learning, achieving high accuracy with minimal computation.
problem Predicting stable or metastable crystal structures of large systems.
method Noniterative screening using transfer learning and generative models.
result ShotgunCSP achieves 93.3% accuracy in benchmark tests with 90 different crystal structures.
Empirical scoring functions based on either molecular force fields or cheminformatics descriptors are widely used, in conjunction with molecular docking, during the early stages of drug discovery to predict potency and binding affinity of a drug-like molecule to a given target. These models require expert-level knowled…
New method uses geometric moments for accurate machine learning potentials.
problem Creating high-dimensional potential energy surfaces efficiently.
method Feed-forward neural networks with invariant local molecular descriptors based on geometric moments.
result Accuracy comparable to established models, high efficiency.
Graphs with bounded anisotropic mean curvature are regular almost everywhere.
problem Understanding the regularity of graphs with anisotropic mean curvature.
method Proving regularity for m-dimensional Lipschitz graphs with anisotropic mean curvature bounded in Lp. result Graphs with bounded anisotropic mean curvature are regular almost everywhere.
New method trains deep neural networks for non-interacting kinetic-energy functionals in DFT.
problem Lack of exact relationship between electron density and non-interacting kinetic energy.
method Variational principle to regularize machine-learned density functionals.
result Excellent results on kinetic-energy functionals for various systems.
A2I Transformer predicts atom energies from coordinates, avoiding heavy featurization.
problem Efficiently predicting atom energies from molecular coordinates with minimal featurization.
method End-to-end model using self-attention, permutation-equivariant.
result Stable predictions with significantly smaller errors than molecular dynamics simulations.
Minimum energy paths for transitions such as atomic and/or spin rearrangements in thermalized systems are the transition paths of largest statistical weight. Such paths are frequently calculated using the nudged elastic band method, where an initial path is iteratively shifted to the nearest minimum energy path. The co…
Neural message passing on molecular graphs is one of the most promising methods for predicting formation energy and other properties of molecules and materials. In this work we extend the neural message passing model with an edge update network which allows the information exchanged between atoms to depend on the hidde…
Hydrogen atom confined in an inverted-Gaussian potential, with detailed numerical methods and results.
problem Studying hydrogen atom in a specific potential.
method Three numerical methods: Lagrange-mesh, fourth order finite differences, and finite element method.
result Accurate numerical results for hydrogen atom energies and eigenfunctions, improving previous literature.
Computational materials screening studies require fast calculation of the properties of thousands of materials. The calculations are often performed with Density Functional Theory (DFT), but the necessary computer time sets limitations for the investigated material space. Therefore, the development of machine learning …
Large GNNs trained with Graph Parallelism improve atomic simulation accuracy.
problem Training memory-intensive GNNs for high-order atomic interactions.
method Graph Parallelism to distribute graphs across GPUs.
result Graph-parallelized models achieve state-of-the-art results on catalyst datasets.
New bin-wise scaling methods improve prediction uncertainty calibration for machine learning.
problem Improving prediction uncertainty calibration for machine learning regression.
method Adaptations of Binwise Variance Scaling (BVS) with alternative loss functions and feature-based binning.
result Improved adaptivity and consistency in prediction uncertainty calibration.
Deep neural network predicts molecular wave functions in minimal basis.
problem Improving accuracy and efficiency in quantum chemistry calculations.
method Adapted SchNet for Orbitals (SchNOrb) model in quasi-atomic minimal basis.
result Model accurately predicts molecular orbital energies and wavefunctions for large molecules.
Macromolecular and biomolecular folding landscapes typically contain high free energy barriers that impede efficient sampling of configurational space by standard molecular dynamics simulation. Biased sampling can artificially drive the simulation along pre-specified collective variables (CVs), but success depends crit…
Wavelet scattering predicts material properties beyond training data.
problem Predict material properties beyond training data.
method Atomic orbital wavelet scattering transform.
result Extrapolation of material properties achieved.
GDML learns effective CG models from all-atom data.
problem Learning effective coarse-grained force fields efficiently.
method Ensemble learning with stratified sampling and GDML.
result GDML yields smaller free energy error than neural networks.
Cormorant learns molecular properties via rotationally covariant neural networks.
problem Learning molecular potential energy surfaces and properties.
method Rotationally covariant neural network architecture with tensor products and Clebsch-Gordan decomposition.
result Significantly outperforms competing algorithms in learning molecular Potential Energy Surfaces.
We introduce multiscale invariant dictionaries to estimate quantum chemical energies of organic molecules, from training databases. Molecular energies are invariant to isometric atomic displacements, and are Lipschitz continuous to molecular deformations. Similarly to density functional theory (DFT), the molecule is re…
Machine learning predicts electronic density of states for condensed matter.
problem Predicting the electronic density of states (DOS) in complex condensed matter systems.
method Developed a machine learning framework to predict DOS from density functional theory data, considering geometric configurations of atoms.
result Demonstrated the model's effectiveness in predicting DOS and its components for various silicon configurations.
TACE unifies scalar and tensorial modeling in Cartesian space for accurate, stable, and efficient atomistic predictions.
problem Complexity and challenges in equivariant atomistic machine learning models.
method Tensor Atomic Cluster Expansion (TACE) in Cartesian space, decomposing local environments into irreducible Cartesian tensors (ICT).
result Universal invariant and equivariant embeddings, enabling explicit control at inference.
With the rise of deep neural networks for quantum chemistry applications, there is a pressing need for architectures that, beyond delivering accurate predictions of chemical properties, are readily interpretable by researchers. Here, we describe interpretation techniques for atomistic neural networks on the example of …
A multi-scale model predicts atomic-scale properties using both local and long-range information.
problem Inability of machine-learning schemes to capture long-range physical effects.
method Combines local and non-local information in a multipole expansion framework.
result Demonstrates the ability to model electrostatics, polarization, and dispersion.
Data-driven prediction of molecular properties presents unique challenges to the design of machine learning methods concerning data structure/dimensionality, symmetry adaption, and confidence management. In this paper, we present a kernel-based pipeline that can learn and predict the atomization energy of molecules wit…
This article addresses the issue of representing electroencephalographic (EEG) signals in an efficient way. While classical approaches use a fixed Gabor dictionary to analyze EEG signals, this article proposes a data-driven method to obtain an adapted dictionary. To reach an efficient dictionary learning, appropriate s…
We introduce weighted atom-centered symmetry functions (wACSFs) as descriptors of a chemical system's geometry for use in the prediction of chemical properties such as enthalpies or potential energies via machine learning. The wACSFs are based on conventional atom-centered symmetry functions (ACSFs) but overcome the un…
Unified theory linking atom-centered and message-passing models for molecular properties.
problem Combining atom-centered and message-passing models for accurate molecular property prediction.
method Generalizing ACDC framework to include multi-centered information, providing a complete linear basis for regression.
result Unified understanding of atom-centered and message-passing models, providing a coherent foundation.
We consider few-body bound state systems and provide precise definitions of Borromean and Brunnian systems. The initial concepts are more than a hundred years old and originated in mathematical knot-theory as purely geometric considerations. About thirty years ago they were generalized and applied to the binding of sys…
Functionals involving surface curvature are important across a range of scientific disciplines, and their extrema are representative of physically meaningful objects such as atomic lattices and biomembranes. Inspired in particular by the relationship of the Willmore energy to lipid bilayers, we consider a general funct…
DenSNet learns electron densities for molecular dynamics, enabling accurate spectroscopic predictions.
problem Lack of accurate electronic observables in MLIPs for molecular dynamics.
method DenSNet uses SE(3)-equivariant neural networks to predict electron densities and total energy.
result DenSNet predicts infrared spectra with excellent agreement to experimental data.
The atomic swap protocol allows for the exchange of cryptocurrencies on different blockchains without the need to trust a third-party. However, market participants who desire to hold derivative assets such as options or futures would also benefit from trustless exchange. In this paper I propose the atomic swaption, whi…
TeaNet uses GCNs to model complex atomic interactions inspired by electronic relaxation.
problem Creating a universal interatomic potential for all elements.
method Tensor-embedded atom network (TeaNet) using graph convolutional neural networks (GCNs).
result TeaNet achieves good performance (19 meV/atom) for structures and reactions involving elements from H to Ar.
New features for quantum calculations learn N-center Hamiltonian matrix elements.
problem Quantum calculations need features for N-center Hamiltonians, not just atom-centered ones.
method Developed fully equivariant N-center features for machine learning.
result Learned matrix elements of N-center Hamiltonians efficiently.
DNPUs improve neural network performance with high-capacity nanoelectronic nodes.
problem Limited performance of single DNPUs in solving complex classification problems.
method Developed DNPUs as high-capacity neurons and implemented multi-DNPU networks.
result Feed-forward DNPU networks improve single DNPU performance from 77% to 94% test accuracy.
Neural network learns atomic coordinates from Patterson maps in a simplified case.
problem Training a neural network to infer atomic coordinates from Patterson maps.
method Synthetic data training, centering output maps, removing centrosymmetric inversion, and adding empty space.
result The network can generalize to infer atom positions from Patterson maps not in the training set.