A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
The study shows that certain graphs are regular at boundary points.
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…
Graphs with bounded anisotropic mean curvature are regular almost everywhere.
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…
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…
EBM predicts protein conformations at atomic scale using crystallized data.
Study compares atom representations in graph neural networks for molecular properties.
Normalizing flows model atomic solids without needing ground-truth samples.
A2I Transformer predicts atom energies from coordinates, avoiding heavy featurization.
New bin-wise scaling methods improve prediction uncertainty calibration for machine learning.
Proposes linking energy and force uncertainty in deep learning potentials.
A new method predicts electron density accurately from atom-centered models.
New algorithm efficiently trains machine learning models to atomic forces data.
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 …
Machine learning predicts electronic density of states for condensed matter.
Novel ML model predicts solvation free energies from atom interactions.
ShotgunCSP predicts crystal structures using machine learning, achieving high accuracy with minimal computation.
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.
New method trains deep neural networks for non-interacting kinetic-energy functionals in DFT.
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.
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.
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.
Deep neural network predicts molecular wave functions in minimal basis.
We propose Cormorant, a rotationally covariant neural network architecture for learning the behavior and properties of complex many-body physical systems. We apply these networks to molecular systems with two goals: learning atomic potential energy surfaces for use in Molecular Dynamics simulations, and learning ground…
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. …
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.
GDML learns effective CG models from all-atom data.
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…
TACE unifies scalar and tensorial modeling in Cartesian space for accurate, stable, and efficient atomistic predictions.
Proposes an algorithm for infinite-dimensional sparse learning in system identification.
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…
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.
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…
Improved covariance matrix estimation for portfolio optimization with guaranteed PSD and controlled conditioning.
Michael-Simon inequality proven for anisotropic energies close to area.
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…
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…
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.
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…