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.
End-to-end model predicts protein interfaces from atomic coordinates.
problem Improving protein interface prediction using large datasets.
method Developed SASNet, an end-to-end learning model using only atomic coordinates.
result SASNet outperforms state-of-the-art methods trained on gold-standard data.
Improves molecular activity prediction using graph convolutional neural networks considering graph distances.
problem Predicting molecular activity using graph convolutional neural networks with improved distance representation.
method Proposed three improvements: modified graph distances, distance-dependent weight matrices, and weighted sum conversion.
result The proposed method slightly outperforms the original weave module in compound activity prediction.
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.
ATOMO reduces communication in distributed learning by sparsifying gradients.
problem Communication overheads in distributed model training.
method ATOMO framework for atomic sparsification of stochastic gradients.
result Sparsifying singular value decomposition can lead to faster distributed training.
Deep learning predicts protein structures accurately.
problem Predicting the 3D structure of proteins from amino acid sequences.
method Embeddings and deep learning models for backbone atom distance matrices and torsion angles.
result Competitive results in CASP13 and CASP12, surpassing previous winners.
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.
VecMol generates 3D molecules as continuous vector fields, overcoming modality and geometry constraints.
problem Challenges in generating 3D molecules, especially in drug discovery and materials science.
method VecMol reimagines molecular representation by modeling 3D molecules as continuous vector fields over Euclidean space, parameterized by a neural field and generated using a latent diffusion model.
result Vector-field-based representations show promise for 3D molecular generation, validated on benchmarks.
Equivariant diffusion model generates 3D molecules efficiently.
problem Generating high-quality 3D molecules efficiently.
method Equivariant Diffusion Model (EDM) that operates on atom coordinates and types.
result Significantly outperforms previous methods in molecule quality and training efficiency.
The paper tackles MSDA by learning dictionary atoms in Wasserstein space.
problem Mitigating data distribution shifts across multiple source domains to target domain.
method Dictionary learning and optimal transport in Wasserstein space; DaDiL algorithm for learning.
result Improved classification performance by 3.15%, 2.29%, and 7.71% in benchmarks.
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.
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…
New neural network predicts accurate protein complex structures.
problem Predicting accurate protein complex structures from atomic coordinates.
method Rotation-equivariant neural network combining point-based representation, equivariance, local convolutions, and hierarchical subsampling.
result Significant improvement in identifying accurate structural models.
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…
DimeNet uses directional message passing to improve molecular predictions.
problem Lack of directional information in graph neural networks for molecules.
method Directional message passing, rotationally equivariant embeddings, spherical functions.
result DimeNet outperforms previous GNNs by 76% on MD17 and 31% on QM9.
AniDS improves molecular force field modeling by learning anisotropic noise.
problem Molecular force field modeling suffers from oversimplified assumptions about atomic motions.
method AniDS introduces anisotropic noise generation for better modeling of directional and structural variability.
result AniDS outperforms existing methods on benchmarks, achieving significant improvements in force prediction accuracy.
DiAMoNDBack models protein backmapping from coarse-grained Cα traces.
problem Restoring all-atom details from coarse-grained protein representations.
method Autoregressive denoising diffusion model for residue-by-residue backmapping.
result Achieves state-of-the-art reconstruction performance in diverse applications.
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.
New algorithm combines gradient and coordinate descent steps for faster convergence.
problem Optimizing smooth convex functions over atom-spans.
method Blended matching pursuit combining coordinate descent and gradient descent.
result Derives linear convergence rates for non-strongly convex functions.
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.
Proposes atomic swaptions for trustless cryptocurrency derivatives.
problem Lack of trustless derivatives for cryptocurrency exchanges.
method Extends atomic swap protocol to include derivatives without oracles.
result Atomic swaptions enable trustless exchange of derivative assets.
Method estimates section thickness and XY anisotropy in ssEM images.
problem Accurate 3D reconstructions require precise section thickness and XY anisotropy estimates.
method Non-parametric Bayesian regression of image statistics.
result Method has lower estimation error compared to existing methods.
Researchers use manifold learning to analyze 4D-STEM data of graphene, revealing atomic structure details.
problem Challenges in processing and interpreting large 4D-STEM datasets, especially for light materials.
method Data-driven manifold learning approaches for visualization and exploration of 4D-STEM datasets.
result Extracted patterns relate to individual atom sites and sublattice structures, effectively discriminating single dopant anomalies.
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.
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.
Novel RL approach for molecular design using quantum mechanics.
problem Existing RL methods for molecular design are limited in scope and reward function.
method Formulation in Cartesian coordinates, direct use of quantum mechanics for reward function, translation and rotation invariant state-action space.
result Agent efficiently learns to solve molecular design tasks from scratch.
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.
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…
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…
ASLA learns atomic structures using neural networks and reinforcement learning.
problem Designing materials and drugs with desired properties.
method Atomistic structure learning algorithm (ASLA) using a convolutional neural network and reinforcement learning.
result ASLA can predict optimal structural arrangements of atoms for various target properties.
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.
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.
New algorithms improve computation of optimal transport and Wasserstein barycenter.
problem Computing optimal transport and Wasserstein barycenter for multiple probability distributions.
method Introduced APDRCD and APDGCD algorithms for efficient computation, demonstrating better performance than existing methods.
result New algorithms match or exceed the best known complexities for OT problems and improve practical performance.
Auto-encoders learn atomistic to coarse-grained mappings for molecular dynamics.
problem Simulating large systems in molecular dynamics is computationally expensive.
method Auto-encoders learn both atomistic to coarse-grained mappings and the coarse-grained potential energy function.
result Auto-encoders enable efficient simulation of larger systems in molecular dynamics.
Improved chemical predictions through compressed atomic species representations.
problem Intractable chemical space of molecules and materials.
method Introducing elemental modes for compressed representation of atomic species.
result Elemental modes enable improvements in machine learning tasks for chemical predictions.
Unified approach to invariants in equivariant geometry.
problem Constructing invariants in G-equivariant birational geometry. method Combining atom theory and modular symbols.
result Developed new geometric invariants for orbifolds and surfaces.
HLTF generates chemically valid 3D molecules with improved topology control.
problem Generating chemically valid 3D molecules is challenging due to bond topology errors.
method HLTF uses a latent multi-scale plan for global context and a constraint-aware sampler to suppress topology-driven failures.
result HLTF achieves high validity and uniqueness on QM9 and GEOM-DRUGS datasets.
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.
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…
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.
Finding a fixed point to a nonexpansive operator, i.e., x∗=Tx∗, abstracts many problems in numerical linear algebra, optimization, and other areas of scientific computing. To solve fixed-point problems, we propose ARock, an algorithmic framework in which multiple agents (machines, processors, or cores) update x i…
Selection of appropriate collective variables for enhancing sampling of molecular simulations remains an unsolved problem in computational biophysics. In particular, picking initial collective variables (CVs) is particularly challenging in higher dimensions. Which atomic coordinates or transforms there of from a list o…
Generative models encode and decode 3D crystal structures from a large dataset.
problem Challenges in encoding and decoding 3D crystal structures from large datasets.
method Training two neural networks on a dataset of over 120,000 crystal structures to encode and decode 3D atom positions.
result Ability to generate compressed, continuous latent space representations and decode molecules accurately.
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…