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.
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48 results for “3D molecular design”
DECAF optimizes molecular graphs for ensemble properties, improving drug design accuracy.
problem Designing molecules with ensemble properties rather than single conformations.
method DECAF uses Boltzmann-expected design with decoupled annealing flows to optimize molecular graphs.
result DECAF optimizes molecular graphs to shift ensemble properties towards targets, improving accuracy over single-conformer methods.
Generative neural network designs novel 3D molecules with specified properties.
problem Designing molecules with desired properties in chemistry.
method Conditional generative neural network for 3D molecular structures.
result Demonstrated utility in generating novel molecules with specified motifs or composition.
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.
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.
GCDM generates valid large 3D molecules and optimizes existing molecules.
problem Lack of geometric properties in 3D molecule generation models.
method Introduces Geometry-Complete Diffusion Model (GCDM) using equivariant GNNs.
result Significantly outperforms existing models in 3D molecule generation and optimization.
GCPNet improves molecular graph learning for protein structure and binding.
problem Learning from 3D molecular graphs for protein structure and binding.
method SE(3)-equivariant graph neural network for 3D molecular graphs.
result GCPNet achieves state-of-the-art performance in multiple molecular tasks.
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.
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.
Constructing of molecular structural models from Cryo-Electron Microscopy (Cryo-EM) density volumes is the critical last step of structure determination by Cryo-EM technologies. Methods have evolved from manual construction by structural biologists to perform 6D translation-rotation searching, which is extremely comput…
Improved 3D generative models for drug design reduce bias and enhance data efficiency.
problem Data sparsity and bias in 3D molecular design models.
method Multi-level contrastive learning protocol for bias control and data efficiency.
result Hierarchical generative models that are topologically unbiased and explainable.
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.
We present a three-dimensional graph convolutional network (3DGCN), which predicts molecular properties and biochemical activities, based on 3D molecular graph. In the 3DGCN, graph convolution is unified with learning operations on the vector to handle the spatial information from molecular topology. The 3DGCN model ex…
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.
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.
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 …
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.
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.
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.
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…
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.
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.
Molecular generative model based on conditional variational autoencoder for de novo molecular designcs.LG
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…
SchNetPack 2.0 enhances atomistic machine learning with improved neural networks.
problem Improving atomistic machine learning methods and applications.
method Improved data pipeline, equivariant neural networks, PyTorch implementation, PyTorch Lightning, Hydra configuration framework.
result Easy extension and complex training tasks support.
Paper proposes a self-training method to generate molecular targets.
problem Challenges in training generative models for complex molecular design.
method Iterative target augmentation using a property predictor and EM iterations.
result Significant gains in molecular design, outperforming previous methods.
Gradient GA uses gradient information to improve molecular design.
problem Random walk exploration limits genetic algorithms' quality and speed in molecular design.
method Gradient GA incorporates gradient information from the objective function into genetic algorithms, using a differentiable neural network and Discrete Langevin Proposal.
result Significantly improves convergence speed and solution quality over traditional genetic algorithms.
Solving Newton's Equations of Motion with Large Timesteps using Recurrent Neural Networks based Operatorsphysics.comp-ph
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.
Physics-Constrained Predictive Molecular Latent Space Discovery with Graph Scattering Variational Autoencoderphysics.chem-ph
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.
Automates GNN design for molecular property prediction.
problem Designing and tuning GNN architectures for molecular property prediction is labor-intensive.
method Developed a NAS approach to automatically discover high-performing GNN architectures for MPNNs.
result Automatically discovered MPNNs outperform manually designed GNNs in molecular property prediction.
Autodock is a widely used molecular modeling tool which predicts how small molecules bind to a receptor of known 3D structure. The current version of AutoDock uses meta-heuristic algorithms in combination with local search methods for doing the conformation search. Appropriate settings of hyperparameters in these algor…
Enhancing Generative Molecular Design via Uncertainty-guided Fine-tuning of Variational Autoencoderscs.LG
Enhances molecular design models by fine-tuning uncertainty-guided VAEs.
problem Fine-tuning pre-trained generative models for specific molecular property optimization.
method Uncertainty-guided fine-tuning of variational autoencoders in an active learning setting.
result Uncertainty-guided fine-tuning improves model performance across multiple molecular properties.
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.
Polynomial invariants classify molecular chains based on their contact arrangements.
problem No established invariants for molecular chains with both hard and soft contacts.
method Developed polynomial invariants for circuit topology of molecular chains.
result Polynomial invariants efficiently classify chains with various contact types.
Molecular Design in Synthetically Accessible Chemical Space via Deep Reinforcement Learningphysics.chem-ph
A new RL framework optimizes drug-like molecules synthetically.
problem Optimizing drug-like molecules for specific criteria.
method Deep Reinforcement Learning framework for chemical space optimization.
result Outperforms existing methods in pharmacological optimization.
EHVI outperforms scalarized EI in MOBO for molecule design.
problem Benchmarking MOBO strategies for molecule design.
method Compared EHVI against fixed-weight scalarized EI in MOBO.
result EHVI consistently outperforms scalarized EI in molecular optimization tasks.
Materials discovery is decisive for tackling urgent challenges related to energy, the environment, health care and many others. In chemistry, conventional methodologies for innovation usually rely on expensive and incremental strategies to optimize properties from molecular structures. On the other hand, inverse approa…
New method generates molecular conformations efficiently.
problem Generating accurate molecular conformations efficiently.
method Variational approximation of rotatable bond torsion angles as a mixture of von Mises distributions.
result VonMisesNet generates conformations orders of magnitude faster than existing methods.
GEGL uses genetic experts to improve deep learning for molecular design.
problem Designing molecules with desired properties using deep learning.
method Genetic expert-guided learning (GEGL) framework for training DNN.
result Significantly improves molecular design, achieving high scores on benchmarks.
This work improves molecular design by efficiently selecting diverse candidate molecules.
problem Designing molecules that satisfy multiple conflicting objectives.
method A modular 'generate-then-optimize' framework using generative models and a novel acquisition function.
result Significant improvements in sample efficiency across synthetic and application-driven tasks.
Single-particle electron cryomicroscopy is an essential tool for high-resolution 3D reconstruction of proteins and other biological macromolecules. An important challenge in cryo-EM is the reconstruction of non-rigid molecules with parts that move and deform. Traditional reconstruction methods fail in these cases, resu…
MolHF generates complex molecules with hierarchical flow-based model.
problem Designing novel molecular structures with desired properties.
method MolHF is a hierarchical normalizing flow model that generates molecular graphs in a coarse-to-fine manner.
result MolHF achieves state-of-the-art performance in random generation and property optimization.
Cellular Electron Cryo-Tomography (CECT) is a powerful 3D imaging tool for studying the native structure and organization of macromolecules inside single cells. For systematic recognition and recovery of macromolecular structures captured by CECT, methods for several important tasks such as subtomogram classification a…
DESMILES uses deep learning to improve drug discovery by optimizing molecule properties.
problem Improving the efficiency and accuracy of drug discovery through better molecular design.
method DESMILES is a deep neural network model that optimizes molecular properties for drug discovery.
result DESMILES achieved a 77% lower failure rate in modifying molecules to inhibit the dopamine receptor D2 compared to state-of-the-art models.
Advanced GNNs improve molecular generation models.
problem Generating complete graphs with multiple nodes and edges based on labels.
method Replaced standard GNNs with more expressive GNNs in autoregressive and one-shot generation models.
result Advanced GNNs can improve performance of graph generative models, but expressiveness is not a necessity.
A Graph Neural Network model for generating molecular graphs.
problem Designing new drug molecules efficiently and cost-effectively.
method Sequential molecular graph generator based on Graph Neural Networks.
result The model can generate molecular graphs without overfitting and outperforms existing methods.
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…
DeepGG generates graph distributions for drug discovery and molecular design.
problem Learning graph distributions for various applications.
method Improved deep graph generator based on deep state machines with graph and node embeddings.
result The state machine design favors specific graph distributions.
Bayesian optimization improves molecule design by addressing three pitfalls.
problem Bayesian optimization pitfalls cause poor performance in molecule design.
method Identified and addressed three pitfalls: incorrect prior width, over-smoothing, and inadequate acquisition function maximization.
result Basic BO setup achieves highest performance on PMO benchmark.