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.
Geometric GNNs model 3D atomic systems with rotations and translations.
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…
VecMol generates 3D molecules as continuous vector fields, overcoming modality and geometry constraints.
AniDS improves molecular force field modeling by learning anisotropic noise.
New neural network predicts accurate protein complex structures.
Equivariant diffusion model generates 3D molecules efficiently.
Graph neural networks fail to distinguish certain 3D atom configurations.
Wavelet scattering predicts material properties beyond training 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…
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…
Transformer-M learns molecular data in 2D or 3D formats.
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…
Neural network learns atomic coordinates from Patterson maps in a simplified case.
AbDiffuser generates full-atom antibodies with sequence and structure fidelity.
Proposes an algorithm for infinite-dimensional sparse learning in system identification.
HLTF generates chemically valid 3D molecules with improved topology control.
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…
A general machine learning architecture is introduced that uses wavelet scattering coefficients of an inputted three dimensional signal as features. Solid harmonic wavelet scattering transforms of three dimensional signals were previously introduced in a machine learning framework for the regression of properties of sm…
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 …
New 3D protein analysis methods improve accuracy.
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. …
New framework for 3D spatial topology enumeration and identification.
Bayesian control prepares GHZ states in Rydberg atoms.
New method uses scalar-based models to approximate spherical tensors efficiently.
DECAF optimizes molecular graphs for ensemble properties, improving drug design accuracy.
Non-trivialization probability of arc system in 3D space
Normalizing flows model atomic solids without needing ground-truth samples.
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…
NT probability measures knotting in 3D arc systems.
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 …
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…
V-SysId identifies keypoints and 3D system from unlabeled videos.
Hydrogen atom confined in an inverted-Gaussian potential, with detailed numerical methods and results.
MuML models predict molecular dipole moments using atomic partial charges and dipoles.
The rising use of deep learning and other big-data algorithms has led to an increasing demand for hardware platforms that are computationally powerful, yet energy-efficient. Due to the amount of data parallelism in these algorithms, high-performance 3D manycore platforms that incorporate both CPUs and GPUs present a pr…
Unified theory linking atom-centered and message-passing models for molecular properties.
This paper considers object detection and 3D estimation using an FMCW radar. The state-of-the-art deep learning framework is employed instead of using traditional signal processing. In preparing the radar training data, the ground truth of an object orientation in 3D space is provided by conducting image analysis, of w…
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…
Optimizes master faces for 2D and 3D face verification using evolutionary algorithms and neural networks.
Cryo-electron microscopy (cryo-EM) is capable of producing reconstructed 3D images of biomolecules at near-atomic resolution. As such, it represents one of the most promising imaging techniques in structural biology. However, raw cryo-EM images are only highly corrupted - noisy and band-pass filtered - 2D projections o…
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…
New algorithm efficiently trains machine learning models to atomic forces data.
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…
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…
LSS learns molecular trajectories from MD data.
In the area of traditional physics the atomic nucleus belongs to the most complex systems. It involves essentially all elements that characterize complexity including the most distinctive one whose essence is a permanent coexistence of coherent patterns and of randomness. From a more interdisciplinary perspective, thes…
This paper proposes a geometry-aware active learning framework for spatiotemporal dynamic systems.
3D Convolutional Neural Networks (3D-CNN) have been used for object recognition based on the voxelized shape of an object. However, interpreting the decision making process of these 3D-CNNs is still an infeasible task. In this paper, we present a unique 3D-CNN based Gradient-weighted Class Activation Mapping method (3D…