RNN operators solve Newton's equations with large timesteps for molecular dynamics.
problem Solving Newton's equations of motion with large timesteps for molecular dynamics simulations.
method Recurrent Neural Networks (RNN) operators to solve Newton's equations using past trajectory data.
result Significant speedup in molecular dynamics simulations with timesteps up to 4000 times larger.
New method uses normalizing flows to improve force fields for coarse-grained molecular dynamics.
problem Lack of reference atomistic forces makes force matching infeasible for MLCG force fields.
method Introduces noise-based kernels adapted to low-data regimes using normalizing flows.
result Flow-based kernels reduce local distortions while preserving global accuracy.
A microscopic model is established for financial Brownian motion from the direct observation of the dynamics of high-frequency traders (HFTs) in a foreign exchange market. Furthermore, a theoretical framework parallel to molecular kinetic theory is developed for the systematic description of the financial market from m…
Generative models accelerate molecular dynamics by four orders of magnitude.
problem Femtosecond time steps limit access to slow molecular processes.
method Deep generative modeling framework that accelerates sampling.
result Quantitative characterization of equilibrium ensembles and dynamical relaxation processes.
New normalizing flows model molecular crystal structures.
problem Modeling positions and orientations of molecules in crystals.
method Smooth flows on unit quaternions for rigid body motion, using double cover property.
result Trained flows can generate Boltzmann distributions of molecules.
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.
Timewarp accelerates molecular dynamics by learning to simulate long timescales.
problem Efficiently simulating long timescales in molecular dynamics.
method Uses a normalizing flow to learn large time steps in Markov chain Monte Carlo.
result Generalizes to unseen small peptides, accelerating sampling.
The success of enhanced sampling molecular simulations that accelerate along collective variables (CVs) is predicated on the availability of variables coincident with the slow collective motions governing the long-time conformational dynamics of a system. It is challenging to intuit these slow CVs for all but the simpl…
The paper extends manifold learning to arbitrary norms, improving molecular motion mapping.
problem Improving manifold learning for non-Euclidean norms.
method Determines the limiting differential operator for graph Laplacians using any norm.
result A modified Laplacian eigenmaps algorithm using Earthmover's distance outperforms Euclidean methods in molecular motion mapping.
Recent technological development has enabled researchers to study social phenomena scientifically in detail and financial markets has particularly attracted physicists since the Brownian motion has played the key role as in physics. In our previous report (arXiv:1703.06739; to appear in Phys. Rev. Lett.), we have prese…
Survey and new results link hydrodynamics, molecular physics, and financial engineering.
problem Understanding financial engineering topics like Asian options and volatility swaps.
method Linking Kevin waves, Klein-Kramers, and Kolmogorov equations to financial models.
result Corrected the original solution of the Kolmogorov equation.
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…
We provide a proof and analyze the asymptotic behavior of a formula for the linking number of line segments.
problem The invariant formula for the linking number of line segments and its asymptotic behavior.
method Detailed proof and asymptotic analysis of the formula.
result We provide a proof and analyze the asymptotic behavior of the formula for the linking number of line segments.
Optimizes electric field to control molecule states in Hartree-Fock theory.
problem Optimizing electric field to drive molecule from initial to target state.
method Trust region optimization with gradients from adjoint state method.
result Achieves desired target states with minimal control effort.
Physics-informed machine learning models improve biomolecular system simulations.
problem Modeling unresolved interactions beyond classical force fields.
method Physics-informed neural networks and operator learning.
result Accurate, mechanistic, generalizable models for long-timescale kinetics.
Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and spatial scales involved in thermodynamic and kinetic phenomena in materials, atomis…
The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. It is clear, that gene expression patterns cannot explain the development of the precise geometry of an organism and its parts in space. Here, we suggest a set of …
This paper deals with a general method for the reduction of quantum systems with symmetry. For a Riemannian manifold M admitting a compact Lie group G as an isometry group, the quotient space Q = M/G is not a smooth manifold in general but stratified into a collection of smooth manifolds of various dimensions. If the a…
Reduces field theories on principal bundles by a subgroup, deriving reduced equations.
problem Hamiltonian field theories on principal G-bundles with invariant densities.
method Lie-Poisson reduction using covariant bracket formulation.
result Derives reduced observables, brackets, and equations of motion for field theories.
A new model designs molecular latent vectors for drug discovery.
problem Designing effective molecular descriptors from molecular structures.
method Proposes a denoising diffusion probabilistic model (DDPM) for variational autoencoding molecular graphs.
result Demonstrates superior prediction performance and robustness compared to existing approaches.
MoFlow generates chemically valid molecular graphs from latent representations.
problem Generating chemically valid molecular graphs from latent representations is challenging.
method MoFlow uses a flow-based approach with Glow for bond generation and a novel graph conditional flow for atom generation, ensuring chemical validity and efficiency.
result MoFlow achieves state-of-the-art performance in molecular graph generation and optimization.
Study compares GNNs and classical molecular featurisations for molecular property and cliff prediction.
problem Comparing GNNs and classical featurisations for molecular property and cliff prediction.
method Systematic exploration and comparison of PDVs, ECFPs, and GNNs; introduction of substructure pooling.
result Sort & Slice outperforms hash-based folding in ECFP vectorization.
We propose a molecular generative model based on the conditional variational autoencoder for de novo molecular design. It is specialized to control multiple molecular properties simultaneously by imposing them on a latent space. As a proof of concept, we demonstrate that it can be used to generate drug-like molecules w…
Generative models are becoming a tool of choice for exploring the molecular space. These models learn on a large training dataset and produce novel molecular structures with similar properties. Generated structures can be utilized for virtual screening or training semi-supervised predictive models in the downstream tas…
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.
Machine learning models simulate molecular spectra and reactions in solvents.
problem Accurate simulation of molecular spectra and reactions in solvent environments.
method Introduced FieldSchNet, a deep neural network for modeling molecular interactions with external fields.
result Demonstrated significant lowering of Claisen rearrangement reaction activation barrier using FieldSchNet.
In this paper, we propose a novel approach for manifold learning that combines the Earthmover's distance (EMD) with the diffusion maps method for dimensionality reduction. We demonstrate the potential benefits of this approach for learning shape spaces of proteins and other flexible macromolecules using a simulated dat…
Framework for training-free guidance in discrete diffusion models for molecular generation.
problem No equivalent training-free guidance methods for discrete diffusion models.
method Framework using guidance functions for discrete data.
result Demonstrated utility on molecular graph generation tasks.
Optimizes molecular generation for chemist preferences.
problem Models lack inherent preferences for chemist-desired structures.
method Fine-tuning with Direct Preference Optimization.
result Approach is simple, efficient, and highly effective.
New RL method designs 3D molecules with improved symmetry.
problem Lack of 3D information in molecular design.
method Symmetry-aware actor-critic architecture using spherical harmonics.
result Improves generalization and molecule quality.
FlowMO uses Gaussian Processes for molecular property prediction with uncertainty.
problem Predicting molecular properties with uncertainty for small datasets.
method Gaussian Processes implemented in FlowMO, built on GPflow and RDKit.
result Comparable predictive performance to deep learning but superior uncertainty calibration.
In a range of fields including the geosciences, molecular biology, robotics and computer vision, one encounters problems that involve random variables on manifolds. Currently, there is a lack of flexible probabilistic models on manifolds that are fast and easy to train. We define an extremely flexible class of exponent…
Automating molecular design using deep reinforcement learning (RL) holds the promise of accelerating the discovery of new chemical compounds. Existing approaches work with molecular graphs and thus ignore the location of atoms in space, which restricts them to 1) generating single organic molecules and 2) heuristic rew…
Framework learns surrogates for molecular dynamics across multiple time-scales.
problem Stable molecular dynamics simulations require small time-steps, but long-time-scale moments need repeated simulations.
method Implicit Transfer Operator Learning with denoising diffusion probabilistic models and SE(3) equivariant architecture.
result Models can generate self-consistent stochastic dynamics across multiple time-scales.
Paper improves molecular property prediction using denoising autoencoders.
problem Limited data for molecular property prediction from 3D structures.
method Pre-training via denoising for learning molecular force fields.
result Achieves new state-of-the-art performance on QM9 dataset.
Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the molecular structure while ignoring others, rather than allowing the model to make data-d…
Model predicts stable molecules with AI and physics constraints.
problem Designing stable molecules with limited data.
method Graph Scattering Variational Autoencoder with physical constraints.
result Model generates stable molecules with desired properties.
Researchers use active subspaces to quantify uncertainty in deep generative models for molecular design.
problem Uncertainty quantification in deep generative models for molecular design due to high parameter space.
method Leveraging active subspaces to approximate posterior distribution over low-dimensional parameters.
result The proposed UQ scheme effectively estimates epistemic uncertainty in high-dimensional parameter space without altering model architecture.
Molecule property prediction is a fundamental problem for computer-aided drug discovery and materials science. Quantum-chemical simulations such as density functional theory (DFT) have been widely used for calculating the molecule properties, however, because of the heavy computational cost, it is difficult to search a…
GAGA accelerates 3D molecular generation by replacing long trajectories with Gaussian approximations.
problem High computational cost of long generative trajectories in 3D molecular generation.
method GAGA identifies a characteristic step where molecular data becomes sufficiently Gaussian, replacing the trajectory with a Gaussian approximation.
result Significant improvement in both generation quality and computational efficiency.
Molecular structure-property relationships are key to molecular engineering for materials and drug discovery. The rise of deep learning offers a new viable solution to elucidate the structure-property relationships directly from chemical data. Here we show that the performance of graph convolutional networks (GCNs) for…
Graph Polish optimizes molecular structures by minimizing changes and maximizing preservation.
problem Error-prone traditional molecular optimization methods.
method Graph Polish transforms optimization into a polishing task, focusing on optimization centers and minimizing changes.
result Significant advantage over state-of-the-art methods on multiple optimization tasks.
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory computations or the limited accuracy of classical empirical force fields. Machine l…
ASGN uses active semi-supervised learning to predict molecular properties efficiently.
problem Predicting molecular properties with scarce labeled data and high computational cost.
method ASGN combines a teacher-student framework with active learning to handle joint representation and property learning.
result ASGN achieves remarkable performance in property prediction on public datasets.
We seek to automate the design of molecules based on specific chemical properties. In computational terms, this task involves continuous embedding and generation of molecular graphs. Our primary contribution is the direct realization of molecular graphs, a task previously approached by generating linear SMILES strings …
XIMP improves molecular property prediction by integrating multiple graph representations.
problem Graph neural networks struggle in data-scarce regimes and fail to surpass traditional methods.
method Cross-graph inter-message passing with multiple graph abstractions.
result XIMP outperforms state-of-the-art baselines across diverse molecular property tasks.
RC flow learns molecular kinetics in low dimensions.
problem Discovering interpretable low-dimensional models of molecular kinetics.
method Normalizing flow for coordinate transformation and Brownian dynamics for kinetics approximation.
result Tractable and trainable model of reduced kinetics in continuous time and space.
This paper reviews deep learning and knowledge-based methods for molecular design.
problem Optimizing molecular properties for scientific advances and process performance.
method Survey of deep learning and knowledge-based methods for molecular design.
result Deep learning models show promise in overcoming computational challenges.