3DGCN predicts molecular properties and biochemical activities using 3D molecular graph.
problem Predicting molecular properties and biochemical activities from 3D molecular graphs.
method Unified graph convolution with learning operations to handle spatial information, distinguishing 3D rotations.
result Significantly higher performance on various molecular tasks compared to other deep-learning models.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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 …
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.
New method reconstructs moving parts of proteins in cryo-EM.
problem Reconstructing non-rigid molecules with moving parts in cryo-EM.
method Graph Laplacian construction from multiple projection images, followed by spectral volume expansion.
result High-resolution visualization of molecular dynamics using spectral volumes.
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.
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.
RL-VAE uses RL to decode molecular graphs from latent embeddings.
problem Efficiently decoding molecular graphs from latent embeddings.
method Repurposed simple graph generator for efficient decoding.
result Decoding molecular graphs from latent embeddings is possible with a simple graph generator.
Tiered graph autoencoders improve molecular graph representation.
problem Representing and utilizing groups in molecular graphs.
method Adapting tiered graph autoencoders for PyTorch Geometric.
result Molecular graphs have tiered latent representations.
A^2-Net learns to estimate molecular structures from Cryo-EM data.
problem Estimating molecular structures from Cryo-EM density volumes.
method Learning-based approach using 3D detection and pose estimation.
result Achieves 91% coverage on new dataset and is hundreds of times faster.
GraphNVP generates molecular graphs efficiently and reversibly.
problem Generating valid molecular graphs with desired properties.
method Decomposes graph generation into adjacency tensor and node attributes, using reversible flows.
result Efficiently generates valid molecular graphs with minimal duplicates and latent space for property generation.
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 learns diverse molecular transformations for optimization.
problem Optimizing molecules in various ways.
method Junction tree encoder-decoder with adversarial training.
result Model outperforms previous methods on molecular optimization tasks.
PAGTN improves molecular property prediction by leveraging longer-range graph dependencies.
problem Local aggregation in GCNs misses higher-order graph properties.
method PAGTN uses path features and global attention layers to capture longer-range dependencies.
result PAGTN outperforms GCNs on various molecular property prediction datasets.
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.
Generative model for 3D molecules respects symmetry for targeted properties.
problem Infeasibility of exhaustive exploration in chemical space.
method Symmetry-adapted 3D point set generation neural network.
result Model generates molecules with desired properties like small HOMO-LUMO gap.
LaPool improves molecular graph representation learning by capturing interaction importance.
problem Lack of efficient intermediate pooling steps in GNNs leads to poor molecular substructure representation.
method LaPool is a novel, data-driven, and interpretable hierarchical graph pooling method that considers node features and graph structure.
result LaPool outperforms recent GNNs on molecular graph prediction and understanding tasks.
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.
Graph neural networks improve molecular property prediction.
problem Efficiently predicting molecular properties with high accuracy and scalability.
method Gated Graph Recursive Neural Networks (GGNN) with skip connections.
result GGNN achieves state-of-the-art performance on molecular property prediction benchmarks.
Enhances drug discovery by optimizing molecular structures.
problem Accelerate drug discovery through better optimization of precursor molecules.
method Integrates substructure components with atom-level encoding in a fully autoregressive graph decoder.
result Significantly outperforms previous state-of-the-art baselines on molecular optimization tasks.
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 …
A new neural network model for molecular graphs that learns efficiently and accurately.
problem Learning on molecular graphs with cycles and complex structures.
method Hierarchical inter-message passing using raw graph and junction tree representations.
result The model outperforms classical GNNs in detecting cycles and is efficient to train.
E-NFs generate molecules and their positions while preserving Euclidean symmetries.
problem Generating molecules with their positions while preserving Euclidean symmetries.
method Integrating E(n) graph neural networks into a differential equation to create an invertible equivariant function.
result E-NFs significantly outperform baselines and existing methods in log-likelihood for particle systems and molecules.
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.
Neural network learns from higher-order connections in molecules.
problem Graph neural networks fail to account for local and hidden structures in graphs.
method Developed a neural network that can pass messages and aggregate information across higher-order paths.
result The model improves molecular property prediction.
A new flow-based model for molecular graphs achieves better performance with fewer parameters.
problem Generating molecular graphs efficiently and accurately.
method Graph residual flow (GRF) based on residual flows for molecular graphs, with invertibility conditions derived.
result The GRF model achieves comparable performance to existing models with significantly fewer parameters.
Boosts GNN performance on molecular graphs.
problem Current GNNs struggle with training set and scalability.
method Proposes an auxiliary module to enhance GNNs.
result Improves GNN performance on molecular datasets.
Graph neural networks outperform fixed molecular descriptors in property prediction.
problem Comparing graph neural networks to fixed molecular descriptors for property prediction.
method Benchmarked graph convolutional neural networks on public and proprietary datasets.
result Graph convolutional model consistently matches or outperforms existing models on both public and proprietary datasets.
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.
Generative model learns molecular geometry from graph representations.
problem Generating equilibrium states for molecular systems is computationally expensive.
method Probabilistic model based on Euclidean distance geometry.
result Generative model achieves state-of-the-art accuracy in molecular conformation generation.
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.
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.
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.
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.
Model learns molecular structures from graphs without explicit rules.
problem Learning molecular structures from graphs without explicit rules.
method Adapted Transformer model for undirected molecular graphs.
result Transformer model can learn complex molecular structures.
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.
Two new minor minimal intrinsically chiral graphs identified.
problem Identifying intrinsically chiral graphs in molecular structures.
method Analyzing graph symmetry and embedding properties.
result Found two new minor minimal intrinsically chiral graphs Γ7 and Γ8. Improved molecular property prediction using multitask learning.
problem Predicting molecular properties from chemical data is challenging.
method Multitask learning applied to graph neural networks.
result Multitask learning significantly improves model performance and reduces variance.