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.
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 …
New features for quantum calculations learn N-center Hamiltonian matrix elements.
Unified theory linking atom-centered and message-passing models for molecular properties.
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…
New neural network predicts accurate protein complex structures.
Geometric GNNs model 3D atomic systems with rotations and translations.
NucleusDiff models atomic nuclei interactions to prevent separation violations in drug design.
EBM predicts protein conformations at atomic scale using crystallized data.
Proteins are the major building blocks of life, and actuators of almost all chemical and biophysical events in living organisms. Their native structures in turn enable their biological functions which have a fundamental role in drug design. This motivates predicting the structure of a protein from its sequence of amino…
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…
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…
Graph neural networks fail to distinguish certain 3D atom configurations.
Efficiently representing real world data in a succinct and parsimonious manner is of central importance in many fields. We present a generalized greedy pursuit framework, allowing us to efficiently solve structured matrix factorization problems, where the factors are allowed to be from arbitrary sets of structured vect…
VecMol generates 3D molecules as continuous vector fields, overcoming modality and geometry constraints.
A new machine-learned CG model predicts protein structures efficiently.
Proposes an algorithm for infinite-dimensional sparse learning in system identification.
Deep neural network predicts molecular wave functions in minimal basis.
Normalizing flows model atomic solids without needing ground-truth samples.
Optimizes basis for density-based atomic representations to enhance compactness and accuracy.
New method selects variables in groups with few nonzeros, improving support recovery.
Atoms and molecules are important conceptual entities we invented to understand the physical world around us. The key to their usefulness lies in the organization of nuclear and electronic degrees of freedom into a single dynamical variable whose time evolution we can better imagine. The use of such effective variables…
AniDS improves molecular force field modeling by learning anisotropic noise.
Despite an explosion in the number of experimentally determined, atomically detailed structures of biomolecules, many critical tasks in structural biology remain data-limited. Whether performance in such tasks can be improved by using large repositories of tangentially related structural data remains an open question. …
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…
DiAMoNDBack models protein backmapping from coarse-grained Cα traces.
Proves log-concavity of cluster algebra coefficients for type .
A new method predicts electron density accurately from atom-centered models.
In this paper, we propose a way to combine two acceleration techniques for the -regularized least squares problem: safe screening tests, which allow to eliminate useless dictionary atoms; and the use of fast structured approximations of the dictionary matrix. To do so, we introduce a new family of screening …
Nuclear magnetic resonance (NMR) spectroscopy is one of the leading techniques for protein studies. The method features a number of properties, allowing to explain macromolecular interactions mechanistically and resolve structures with atomic resolution. However, due to laborious data analysis, a full potential of NMR …
Study compares atom representations in graph neural networks for molecular properties.
Neural network learns atomic coordinates from Patterson maps in a simplified case.
Complex activity recognition is challenging due to the inherent uncertainty and diversity of performing a complex activity. Normally, each instance of a complex activity has its own configuration of atomic actions and their temporal dependencies. We propose in this paper an atomic action-based Bayesian model that const…
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…
Ancient grain boundaries resemble atoms in their formation and properties.
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.
AbDiffuser generates full-atom antibodies with sequence and structure fidelity.
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.
Improves latent variable learning for complex data.
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…
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…
Discovery of atomistic systems with desirable properties is a major challenge in chemistry and material science. Here we introduce a novel, autoregressive, convolutional deep neural network architecture that generates molecular equilibrium structures by sequentially placing atoms in three-dimensional space. The model e…
Sparse coding consists in representing signals as sparse linear combinations of atoms selected from a dictionary. We consider an extension of this framework where the atoms are further assumed to be embedded in a tree. This is achieved using a recently introduced tree-structured sparse regularization norm, which has pr…
ShotgunCSP predicts crystal structures using machine learning, achieving high accuracy with minimal computation.