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…
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48 results for “atomic environments”
Optimal Invariant Bases for Atomistic Machine Learningphysics.chem-ph
Optimizes atomic descriptors to reduce redundancy and improve machine learning models.
problem Redundant descriptors in atomistic machine learning models increase computational burden and limit model expressivity.
method Employing techniques from pattern recognition, we refine and augment existing atomistic representations to produce optimal sets of descriptors.
result New architectures recognize up to 5-body patterns with low computational cost and high accuracy.
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.
A novel method computes Wigner kernels for atomic environments, achieving state-of-the-art accuracy.
problem Efficiently describing local atomic environments in materials science.
method Computes fully equivariant and body-ordered kernels iteratively, independent of basis.
result Achieves state-of-the-art accuracy on the QM9 benchmark dataset.
Equivariant representations for molecular Hamiltonians and N-center atomic-scale propertiesphysics.chem-ph
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.
Learning molecular energies using localized graph kernelsphysics.comp-ph
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…
A new graph model HMG and neural network HMGNN improve molecule property predictions.
problem Predicting quantum mechanical properties of molecules with limited consideration of many-body interactions.
method Introducing heterogeneous molecular graphs (HMG) and building HMGNN on neural message passing scheme.
result HMGNN achieves state-of-the-art performance in 9 out of 12 tasks on the QM9 dataset.
Graph neural networks fail to distinguish certain 3D atom configurations.
problem Graph neural networks (GNN) fail to distinguish certain 3D atom configurations.
method Construction of degenerate 3D atom configurations that are indistinguishable by first-order GNNs.
result First-order GNNs are incomplete for 3D atom configurations.
Spectral/Spatial Tensor Atomic Cluster Expansion with Universal Embeddings in Cartesian Spacestat.ML
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.
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.
A set of molecular descriptors whose length is independent of molecular size is developed for machine learning models that target thermodynamic and electronic properties of molecules. These features are evaluated by monitoring performance of kernel ridge regression models on well-studied data sets of small organic mole…
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…
Framework tackles OOD challenges in molecule property prediction by modeling environments.
problem Challenges in modeling OOD samples for molecule property prediction.
method Soft causal learning framework incorporating chemistry theories and cross-attention mechanisms.
result Demonstrates well generalization ability on seven datasets.
Hierarchical Deep Reinforcement Learning: Integrating Temporal Abstraction and Intrinsic Motivationcs.LG
Learning goal-directed behavior in environments with sparse feedback is a major challenge for reinforcement learning algorithms. The primary difficulty arises due to insufficient exploration, resulting in an agent being unable to learn robust value functions. Intrinsically motivated agents can explore new behavior for …
Comparison of Atom Representations in Graph Neural Networks for Molecular Property Predictionphysics.chem-ph
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.
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.
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…
Machine Learning Prediction of Accurate Atomization Energies of Organic Molecules from Low-Fidelity Quantum Chemical Calculationsphysics.comp-ph
Recent studies illustrate how machine learning (ML) can be used to bypass a core challenge of molecular modeling: the tradeoff between accuracy and computational cost. Here, we assess multiple ML approaches for predicting the atomization energy of organic molecules. Our resulting models learn the difference between low…
We prove that the introduction of the class of geometrically atomic bundle maps by Harvey and Lawson in their theory of singular connections is not necessary because an arbitrary map satisfies the conditions of geometric atomicity.
PAM models generate dependent random distributions across groups with overlapping clusters.
problem Generating dependent random distributions across multiple groups.
method Atom skipping in an infinite mixture model.
result Interpretable posterior inference of cluster exclusivity and sharing.
Non-atomic arbitrage exploits price differences on Ethereum and other blockchains, accounting for over 10% of Ethereum's block value.
problem Price differences on decentralized exchanges and centralized exchanges lead to MEV.
method Analyzed non-atomic arbitrage on Ethereum's largest DEXes, identifying its prevalence and impact.
result More than 10% of Ethereum's block value is attributed to non-atomic arbitrage, involving over $132 billion.
Atomistic structure learningcond-mat.mtrl-sci
One endeavour of modern physical chemistry is to use bottom-up approaches to design materials and drugs with desired properties. Here we introduce an atomistic structure learning algorithm (ASLA) that utilizes a convolutional neural network to build 2D compounds and layered structures atom by atom. The algorithm takes …
Four-dimensional scanning transmission electron microscopy (4D-STEM) of local atomic diffraction patterns is emerging as a powerful technique for probing intricate details of atomic structure and atomic electric fields. However, efficient processing and interpretation of large volumes of data remain challenging, especi…
Distributed model training suffers from communication overheads due to frequent gradient updates transmitted between compute nodes. To mitigate these overheads, several studies propose the use of sparsified stochastic gradients. We argue that these are facets of a general sparsification method that can operate on any p…
Atoms meet symbolsmath.AG
Unified approach to invariants in equivariant geometry.
problem Constructing invariants in -equivariant birational geometry.
method Combining atom theory and modular symbols.
result Developed new geometric invariants for orbifolds and surfaces.
Site-specific graph neural network for predicting protonation energy of oxygenate moleculesphysics.chem-ph
Bio-oil molecule assessment is essential for the sustainable development of chemicals and transportation fuels. These oxygenated molecules have adequate carbon, hydrogen, and oxygen atoms that can be used for developing new value-added molecules (chemicals or transportation fuels). One motivation for our study stems fr…
Wasserstein Dictionary Learning: Optimal Transport-based unsupervised non-linear dictionary learningstat.ML
This paper introduces a new nonlinear dictionary learning method for histograms in the probability simplex. The method leverages optimal transport theory, in the sense that our aim is to reconstruct histograms using so-called displacement interpolations (a.k.a. Wasserstein barycenters) between dictionary atoms; such at…
Develops conformal Bayes for two-sided censored Gaussian regression under label shift.
problem Prediction under label shift with censored responses.
method Combines posterior predictive tilting with weighted conformal calibration.
result Restores marginal coverage with smaller prediction sets.
Machine learning is often used in virtual screening to find compounds that are pharmacologically active on a target protein. The weave module is a type of graph convolutional deep neural network that uses not only features focusing on atoms alone (atom features) but also features focusing on atom pairs (pair features);…
In many signal processing applications, the aim is to reconstruct a signal that has a simple representation with respect to a certain basis or frame. Fundamental elements of the basis known as "atoms" allow us to define "atomic norms" that can be used to formulate convex regularizations for the reconstruction problem. …
Geometric GNNs model 3D atomic systems with rotations and translations.
problem Modeling 3D atomic systems with geometric graphs and machine learning.
method Invariant, equivariant, and unconstrained GNN architectures.
result Geometric GNNs leverage physical symmetries and chemical properties.
Proposes an algorithm for infinite-dimensional sparse learning in system identification.
problem System identification without known model structures.
method Atomic norm regularization and greedy algorithm for solving an infinite-dimensional group lasso problem.
result The proposed algorithm outperforms benchmark methods in impulse response fitting and pole location estimation.
Robust method for finding sparse solutions to linear inverse problems using an L2 regularizationmath.NA
We analyzed the performance of a biologically inspired algorithm called the Corrected Projections Algorithm (CPA) when a sparseness constraint is required to unambiguously reconstruct an observed signal using atoms from an overcomplete dictionary. By changing the geometry of the estimation problem, CPA gives an analyti…
Predicting molecular dipole moments by combining atomic partial charges and atomic dipolesphysics.chem-ph
MuML models predict molecular dipole moments using atomic partial charges and dipoles.
problem Predicting molecular dipole moments accurately and efficiently.
method Combining atomic partial charges and atomic dipoles within a physically inspired ML model.
result MuML models achieve excellent transferability and accuracy, approaching DFT results at a fraction of the computational cost.
Optimizes basis for density-based atomic representations to enhance compactness and accuracy.
problem Improving the efficiency and accuracy of machine learning models for atomic properties.
method An unsupervised approach to determine the optimal basis set for atom density representations using splines.
result Optimal basis sets that encode structural information more compactly and accurately.
Generative models have achieved impressive results in many domains including image and text generation. In the natural sciences, generative models have led to rapid progress in automated drug discovery. Many of the current methods focus on either 1-D or 2-D representations of typically small, drug-like molecules. Howev…
Compressed Sensing of Scanning Transmission Electron Microscopy (STEM) on Non-Rectangular Scansphysics.ins-det
Scanning Transmission Electron Microscopy (STEM) has become the main stay for materials characterization on atomic level, with applications ranging from visualization of localized and extended defects to mapping order parameter fields. In the last several years, attention was attracted by potential of STEM to explore b…
Recent research in off-the-grid compressed sensing (CS) has demonstrated that, under certain conditions, one can successfully recover a spectrally sparse signal from a few time-domain samples even though the dictionary is continuous. In particular, atomic norm minimization was proposed in \cite{tang2012csotg} to recove…
We consider the asymptotic behavior of the implied volatility in stochastic asset price models with atoms. In such models, the asset price distribution has a singular component at zero. Examples of models with atoms include the constant elasticity of variance model, jump-to-default models, and stochastic models describ…
Convexifying Sparse Interpolation with Infinitely Wide Neural Networks: An Atomic Norm Approachcs.LG
This study uses neural networks to solve interpolation problems with sparse, infinitely wide layers.
problem Exact data interpolation using sparse, infinitely wide neural networks.
method Atomic norm framework to derive convex hulls and equivalent convex formulations.
result Simple characterizations of convex hulls for different constraints on network weights and biases.
In signal analysis and synthesis, linear approximation theory considers a linear decomposition of any given signal in a set of atoms, collected into a so-called dictionary. Relevant sparse representations are obtained by relaxing the orthogonality condition of the atoms, yielding overcomplete dictionaries with an exten…
Normalizing flows for atomic solidsphysics.comp-ph
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.
Hydrogen atom confined inside an inverted-Gaussian potentialphysics.atom-ph
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.
Electronic-structure properties from atom-centered predictions of the electron densityphysics.chem-ph
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.
Bayesian control prepares GHZ states in Rydberg atoms.
problem Preparing non-classical states robustly for quantum sensors.
method Bayesian optimal control of trapped Rydberg atoms.
result Control pulses drive atoms into GHZ states with scalable preparation times.
The answers to many unsolved problems lie in the intractable chemical space of molecules and materials. Machine learning techniques are rapidly growing in popularity as a way to compress and explore chemical space efficiently. One of the most important aspects of machine learning techniques is representation through th…
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.
ATOM improves robust OOD detection by mining informative auxiliary examples.
problem Robust OOD detection in open-world settings is challenging due to adversarial inputs.
method ATOM combines adversarial training with outlier mining to improve robustness.
result ATOM achieves state-of-the-art performance in OOD detection, reducing FPR by up to 57.99%.