arXiv research

MuML models predict molecular dipole moments using atomic partial charges and dipoles.

Despite being studied for over a century, the use of quadrupoles have been limited to Cartesian coordinates in flat spacetime due to the incorrect transformation rules used to define them. Here the correct transformation rules are derived, which are particularly unusual as they involve second derivatives of the coordin…

DenSNet learns electron densities for molecular dynamics, enabling accurate spectroscopic predictions.

Paper explores ML for UV spectra, showing transferability in chemical space.

In this work we simulate null geodesics for the Bonnor massive dipole metric by implementing a symbolic-numerical algorithm in Sage and Python. This program is also capable of visualizing in 3D, in principle, the geodesics for any given metric. Geodesics are launched from a common point, collectively forming a cone of …

Paper proposes a novel SVM method for creating survival trees.

CycleQSM uses deep learning to accurately map tissue magnetic susceptibility without needing paired data.

Quantitative susceptibility mapping (QSM) is a powerful MRI technique that has shown great potential in quantifying tissue susceptibility in numerous neurological disorders. However, the intrinsic ill-posed dipole inversion problem greatly affects the accuracy of the susceptibility map. We propose QSMGAN: a 3D deep con…

A variational equation of the fourth order for the free relativistic top is developed starting from the Dixon's system of equations for the motion of the relativistic dipole. The obtained equation is then cast into the homogeneous space-time Hamiltonian form.

Rotationally equivariant convolutions improve molecular property prediction.

Unified theory linking atom-centered and message-passing models for molecular properties.

We study the problem of stationary bi-axially symmetric solutions of the $5$-dimensional minimal supergravity equations. Essentially all possible solutions with nondegenerate horizons are produced, having the allowed horizon cross-sectional topologies of the sphere $S^3$, ring $S^1\times S^2$, and lens $L(p,q)$, as wel…

We propose Nonlinear Dipole Inversion (NDI) for high-quality Quantitative Susceptibility Mapping (QSM) without regularization tuning, while matching the image quality of state-of-the-art reconstruction techniques. In addition to avoiding over-smoothing that these techniques often suffer from, we also obviate the need f…

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…

New features for quantum calculations learn N-center Hamiltonian matrix elements.

Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for vibrational anharmonic and dynamical effects -- typically neglected by conventional quan…

Study compares atom representations in graph neural networks for molecular properties.

Neural network learns atomic coordinates from Patterson maps in a simplified case.

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…

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.

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…

PAM models generate dependent random distributions across groups with overlapping clusters.

Non-atomic arbitrage exploits price differences on Ethereum and other blockchains, accounting for over 10% of Ethereum's block value.

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 …

We prove existence of all possible bi-axisymmetric near-horizon geometries of 5-dimensional minimal supergravity. These solutions possess the cross-sectional horizon topology $S^3$, $S^1\times S^2$, or $L(p,q)$ and come with prescribed electric charge, two angular momenta, and a dipole charge (in the ring case). Moreov…

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…

Study on bending energy of surfaces with curvature concentration, deriving new lower bounds.

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…

Unified approach to invariants in equivariant geometry.

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…

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.

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.

Proposes an algorithm for infinite-dimensional sparse learning in system identification.

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…

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…

Optimizes basis for density-based atomic representations to enhance compactness and accuracy.

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…

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 study the Seifert surfaces of a link by relating the embeddings of graphs by using induced graphs. As applications, we prove that every link $L$ is the boundary of an oriented surface which is obtained from a graph embedding of a complete bipartite graph $K_{2,n}$, where all voltage assignments on the edges of $K_{2…

A new graph model HMG and neural network HMGNN improve molecule property predictions.

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…

This study uses neural networks to solve interpolation problems with sparse, infinitely wide layers.

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…