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.
The need for advanced materials has led to the development of complex, multi-component alloys or solid-solution alloys. These materials have shown exceptional properties like strength, toughness, ductility, electrical and electronic properties. Current development of such material systems are hindered by expensive expe…
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.
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.
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.
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.
LSS learns molecular trajectories from MD data.
problem Limited integration time steps in MD simulations.
method Three deep learning networks for slow collective variables, dynamics, and configuration reconstruction.
result Generates ultra-long synthetic folding trajectories.
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…
Transformer-M learns molecular data in 2D or 3D formats.
problem Learning models for molecules are limited to specific data formats.
method Developed a Transformer-based model that can handle 2D and 3D molecular data.
result Transformer-M achieves strong performance on both 2D and 3D molecular tasks.
Motivation: Prediction of ligands for proteins of known 3D structure is important to understand structure-function relationship, predict molecular function, or design new drugs. Results: We explore a new approach for ligand prediction in which binding pockets are represented by atom clouds. Each target pocket is compar…
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.
Ancient grain boundaries resemble atoms in their formation and properties.
problem Understanding the formation and properties of ancient grain boundaries.
method Analyzing ancient grain boundaries as analogous to atoms and using geometric flow techniques.
result New examples of convex ancient and translating solutions to mean curvature flow.
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…
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.
AbDiffuser generates full-atom antibodies with sequence and structure fidelity.
problem Generating high-fidelity antibodies with both structure and sequence information.
method Equivariant and physics-informed diffusion model with novel protein structure representation.
result AbDiffuser generates antibodies with sequence and structural properties matching a reference set.
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.
New method describes entanglement of straight lines in 3D space.
problem Tackles the geometry and topology of configurations of straight lines.
method Introduces direction matrices and a discrete motion principle.
result Shows n-crosses as links of pairwise connected unknots.
Study on planar graph braid groups' second homology.
problem Characterize the second homology of planar graph braid groups.
method Analyzing configuration spaces of planar graphs under specific operations.
result The second homology is generated by three specific graphs.
The paper explores different perspectives on rhombile tilings.
problem None explicitly stated, focuses on different viewpoints.
method Four ways of looking at rhombile tilings: cubes, groups, lines, and points.
result Different methods provide insights into rhombile tilings.
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…
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…
New framework for 3D spatial topology enumeration and identification.
problem Efficient navigation through complex engineering system topologies.
method Mathematical spatial graph theory to represent, enumerate, and identify unique topological classes.
result Identification of distinctive 3D topological classes for engineering systems.
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.
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.
New invariant counts graph configurations in 3D manifolds.
problem Counting graph configurations in 3D manifolds.
method Using combings instead of parallelizations for a more flexible definition.
result Universal finite type invariant of three-manifolds.
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…
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 …
The abstract formulates and proves a categorification of Robertson's conjecture.
problem The homology of graph braid groups and their universal finite generation.
method Categorification of Robertson's conjecture and analysis of configuration spaces of graphs.
result Existence of a finite list of atomic graphs generating the homology of configuration spaces of graphs.
New 3D protein analysis methods improve accuracy.
problem Lack of suitable learning algorithms for protein data.
method Intrinsic-Extrinsic Convolution and Pooling for 3D protein structures.
result Outperforms state-of-the-art methods on protein analysis tasks.
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. …
WILD-SCAV benchmarks AI in complex 3D FPS environments.
problem Lack of complexity and diversity in RL environments.
method Developed a 3D open-world FPS game environment.
result Demonstrates effectiveness in benchmarking RL algorithms.
We study supersymmetric probe M5-branes in the AdS_4 solution that arises from M5-branes wrapped on a hyperbolic 3-manifold M_3. This amounts to introducing internal defects within the framework of the 3d-3d correspondence. The BPS condition for a probe M5-brane extending along all of AdS_4 requires it to wrap a surfac…
New method generates equilibrium glass configurations efficiently.
problem Sampling equilibrium configurations of amorphous materials is slow and difficult.
method Riemannian stochastic interpolation framework combining Riemannian stochastic interpolant and equivariant flow matching.
result Enforcing geometric and symmetry constraints significantly improves generative performance.
Flows are exact-likelihood generative neural networks that transform samples from a simple prior distribution to the samples of the probability distribution of interest. Boltzmann Generators (BG) combine flows and statistical mechanics to sample equilibrium states of strongly interacting many-body systems such as prote…
We study geometric consistency relations between angles on 3-dimensional (3D) circular quadrilateral lattices -- lattices whose faces are planar quadrilaterals inscribable into a circle. We show that these relations generate canonical transformations of a remarkable ``ultra-local'' Poisson bracket algebra defined on di…
Rapid overlay of chemical structures (ROCS) is a standard tool for the calculation of 3D shape and chemical ("color") similarity. ROCS uses unweighted sums to combine many aspects of similarity, yielding parameter-free models for virtual screening. In this report, we decompose the ROCS color force field into "color com…
Graph neural networks predict solid-state NMR parameters from atomic structures.
problem Efficiently predicting NMR parameters from atomic structures for complex materials.
method Graph neural networks applied to tensor quantities for anisotropic magnetic shielding and electric field gradient.
result Improved accuracy in predicting NMR properties from diverse and complex materials.
New method uses geometric moments for accurate machine learning potentials.
problem Creating high-dimensional potential energy surfaces efficiently.
method Feed-forward neural networks with invariant local molecular descriptors based on geometric moments.
result Accuracy comparable to established models, high efficiency.
New method uses scalar-based models to approximate spherical tensors efficiently.
problem Efficiently approximating spherical tensors with equivariant functions.
method Expressing equivariant functions as the product of a scalar function and a small tensor basis.
result Approximations are fast, simple to implement, and accurate in practical settings.
Computes knot types using HOMFLY-PT polynomial.
problem Determining chiral knot and link types with small crossing numbers.
method Uses the HOMFLY-PT polynomial to compute knot types from 3D coordinates.
result Efficacy of HOMFLY-PT for knot types up to crossing number 16.
Machine learning predicts electronic density of states for condensed matter.
problem Predicting the electronic density of states (DOS) in complex condensed matter systems.
method Developed a machine learning framework to predict DOS from density functional theory data, considering geometric configurations of atoms.
result Demonstrated the model's effectiveness in predicting DOS and its components for various silicon configurations.
Geodesics spiral around Reeb orbits in 3D contact manifolds.
problem Understanding geodesics in sub-Riemannian geometry.
method Normal form along Reeb orbits due to Melrose.
result Sub-Riemannian geodesics spiral around Reeb orbits in both phase and configuration spaces.
Structure based ligand discovery is one of the most successful approaches for augmenting the drug discovery process. Currently, there is a notable shift towards machine learning (ML) methodologies to aid such procedures. Deep learning has recently gained considerable attention as it allows the model to "learn" to extra…
By using two different invariants for the Rubik's Magic puzzle, one of metric type, the other of topological type, we can dramatically reduce the universe of constructible configurations of the puzzle. Finding the set of actually constructible shapes remains however a challenging task, that we tackle by first reducing …
Wavelet scattering predicts material properties beyond training data.
problem Predict material properties beyond training data.
method Atomic orbital wavelet scattering transform.
result Extrapolation of material properties achieved.
Gradient-based training and pruning for radial basis function networks in materials physics.
problem Interpretable and robust machine learning for materials physics problems.
method Gradient-based training and pruning of radial basis function networks with closed-form optimization criteria.
result Pruned models provide compact and interpretable versions of larger models, offering insights into atom-level migration processes.
Machine learning methods have shown promise in predicting molecular properties, and given sufficient training data machine learning approaches can enable rapid high-throughput virtual screening of large libraries of compounds. Graph-based neural network architectures have emerged in recent years as the most successful …