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.
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.
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.
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…
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.
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…
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. …
The answers to many unsolved problems lie in the intractable chemical space of molecules and materials. Machine learning techniques are rapidly growing in popularity as a way to compress and explore chemical space efficiently. One of the most important aspects of machine learning techniques is representation through th…
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.
Deep neural network predicts molecular wave functions in minimal basis.
problem Improving accuracy and efficiency in quantum chemistry calculations.
method Adapted SchNet for Orbitals (SchNOrb) model in quasi-atomic minimal basis.
result Model accurately predicts molecular orbital energies and wavefunctions for large molecules.
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.
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.
Improved CG force-field learning from all-atom data.
problem Training accurate coarse-grained models from all-atom simulations is challenging.
method Optimized force mapping to improve statistical efficiency of force-field learning.
result Substantially improved CG force-fields can be learned from the same simulation data.
In the last decade, traditional dictionary learning methods have been successfully applied to various pattern classification tasks. Although these methods produce sparse representations of signals which are robust against distortions and missing data, such representations quite often turn out to be unsuitable if the fi…
Machine learning is often used in virtual screening to find compounds that are pharmacologically active on a target protein. The weave module is a type of graph convolutional deep neural network that uses not only features focusing on atoms alone (atom features) but also features focusing on atom pairs (pair features);…
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.
HiGraphDTI learns drug and target representations from molecular graphs to predict DTIs.
problem Inaccurate drug-target interaction prediction due to insufficient chemical information extraction.
method Hierarchical graph representation learning to extract chemical information from atoms, motifs, and molecules.
result HiGraphDTI outperforms state-of-the-art methods in DTI prediction and interaction interpretation.
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…
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.
EBM predicts protein conformations at atomic scale using crystallized data.
problem Predicting the conformation of a side chain from its context within a protein structure.
method Energy-based model trained on crystallized protein data, evaluating performance on rotamer recovery task.
result EBM achieves performance close to state-of-the-art methods, including Rosetta energy function.
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.
Docking is an important tool in computational drug discovery that aims to predict the binding pose of a ligand to a target protein through a combination of pose scoring and optimization. A scoring function that is differentiable with respect to atom positions can be used for both scoring and gradient-based optimization…
Improved molecular property prediction using WL embedding in GNNs.
problem Limited performance of GNNs in predicting molecular properties.
method Explored Weisfeiler-Lehman (WL) embedding to replace GNN layers, enhancing representability and performance.
result WL embedding consistently improves GNN performance across multiple datasets.
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.
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.
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…
Sparse learning has been shown to be effective in solving many real-world problems. Finding sparse representations is a fundamentally important topic in many fields of science including signal processing, computer vision, genome study and medical imaging. One important issue in applying sparse representation is to find…
A novel method computes Wigner kernels for atomic environments, achieving state-of-the-art accuracy.
problem Efficiently describing local atomic environments in materials science.
method Computes fully equivariant and body-ordered kernels iteratively, independent of basis.
result Achieves state-of-the-art accuracy on the QM9 benchmark dataset.
Proves log-concavity of cluster algebra coefficients for type An.
problem Log-concavity of cluster algebra coefficients.
method Introduced atomic theta basis and proved log-concavity for type An. result Proved log-concavity of coefficients for cluster algebra variables of type An. Improves latent variable learning for complex data.
problem Expressive latent variables for model prediction on multi-component data.
method Dynamic Latent Separation method that distances data samples in the latent space.
result Enhances output diversity and provides interpretable representations.
This paper addresses law invariant coherent risk measures and their Kusuoka representations. By elaborating the existence of a minimal representation we show that every Kusuoka representation can be reduced to its minimal representation. Uniqueness -- in a sense specified in the paper -- of the risk measure's Kusuoka r…
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…
TACE unifies scalar and tensorial modeling in Cartesian space for accurate, stable, and efficient atomistic predictions.
problem Complexity and challenges in equivariant atomistic machine learning models.
method Tensor Atomic Cluster Expansion (TACE) in Cartesian space, decomposing local environments into irreducible Cartesian tensors (ICT).
result Universal invariant and equivariant embeddings, enabling explicit control at inference.
Tiered latent representations and latent spaces for molecular graphs provide a simple but effective way to explicitly represent and utilize groups (e.g., functional groups), which consist of the atom (node) tier, the group tier and the molecule (graph) tier. They can be learned using the tiered graph autoencoder archit…
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…
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.
A multi-scale model predicts atomic-scale properties using both local and long-range information.
problem Inability of machine-learning schemes to capture long-range physical effects.
method Combines local and non-local information in a multipole expansion framework.
result Demonstrates the ability to model electrostatics, polarization, and dispersion.
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…
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 consider deep feedforward neural networks with rectified linear units from a signal processing perspective. In this view, such representations mark the transition from using a single (data-driven) linear representation to utilizing a large collection of affine linear representations tailored to particular regions of…
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.
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 …
Sparse coding, which is the decomposition of a vector using only a few basis elements, is widely used in machine learning and image processing. The basis set, also called dictionary, is learned to adapt to specific data. This approach has proven to be very effective in many image processing tasks. Traditionally, the di…
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…
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.
problem Constructing invariants in G-equivariant birational geometry. method Combining atom theory and modular symbols.
result Developed new geometric invariants for orbifolds and surfaces.