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.
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.
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.
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.
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…
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.
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.
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.
GemNet improves molecular predictions by overcoming graph neural network limitations.
problem Graph neural networks struggle with distinguishing certain types of molecular graphs.
method Discretized geometric message passing neural network (GemNet) with spherical representations.
result GemNet outperforms previous models on molecular datasets by 34-20%.
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.
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.
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.
Sparse molecular representations improve interpretability in graph neural networks.
problem Difficulty in understanding which molecular graph aspects drive deep learning predictions.
method Constrain weights in a graph convolutional neural network using the Gini index to maximize representation inequality.
result The Gini-constrained approach does not degrade evaluation metrics and allows for interpretable representation combination.
Two regularization techniques improve GCNN explainability and preference from chemists.
problem Difficulty in rationalizing molecular graph neural network predictions.
method Batch Representation Orthonormalization (BRO) and Gini regularization applied during GCNN training.
result Regularization improves GCNN attribution methods and preference from chemists.
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.
MV-GNN improves molecular property prediction by integrating atom and bond information.
problem Accurately predicting molecular properties using graph neural networks.
method Multi-View Graph Neural Network (MV-GNN) architecture with shared self-attentive readout and cross-dependent message passing.
result MV-GNN achieves superior performance on molecular property prediction benchmarks.
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.
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.
Deep learning predicts drug side-effects from molecular graphs.
problem Predicting drug side-effects from molecular structures.
method Recurrent Graph Neural Networks for multi-class multi-label graph-focused classification.
result Improved classification capability compared to previous methods.
Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular fingerprints or expert-crafted descriptors, and graph convolutional neural networks that…
Rotationally equivariant convolutions improve molecular property prediction.
problem Predicting molecular properties using graph neural networks.
method Ablation study with rotationally equivariant and invariant convolutions on QM9 data set.
result Rotationally equivariant layers decrease test error by an average of 23%.
We introduce a convolutional neural network that operates directly on graphs. These networks allow end-to-end learning of prediction pipelines whose inputs are graphs of arbitrary size and shape. The architecture we present generalizes standard molecular feature extraction methods based on circular fingerprints. We sho…
Graph Neural Network (GNN) is a popular architecture for the analysis of chemical molecules, and it has numerous applications in material and medicinal science. Current lines of GNNs developed for molecular analysis, however, do not fit well on the training set, and their performance does not scale well with the comple…
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.
Optimal Transport Graph Neural Networks (OT-GNN) improves graph embeddings by using optimal transport.
problem Graph Neural Networks (GNN) often lose structural or semantic information when aggregating node embeddings.
method Combines optimal transport (OT) with parametric graph models to compute graph embeddings from Wasserstein distances between node embeddings and prototype point clouds.
result OT-GNN outperforms popular methods on molecular property prediction tasks and produces smoother graph representations.
Enhances graph neural networks with random walks to improve performance.
problem Limited input to graph neural networks, especially for molecular data.
method Random walk data processing to enrich graph neural network input.
result Shallow network outperforms deep GNNs using only node features.
Derives formulae for general permutation equivariant layers and presents a second order graph variational encoder.
problem Tackles the limitation of previous equivariant neural networks by considering permutations of matrices.
method Derives formulae for general permutation equivariant layers, including matrix permutations. Presents a second order graph variational encoder.
result Latent distribution of equivariant generative models must be exchangeable.
CW Networks leverage cell complexes to enhance GNNs, achieving state-of-the-art results on molecular datasets.
problem Graph Neural Networks struggle with long-range interactions and lack principled ways to model higher-order structures.
method CW Networks use cell complexes to decouple computational and input graph structures, enabling flexible hierarchical message passing.
result CW Networks achieve state-of-the-art results on molecular datasets.
Introduces P-tensors for generalized higher-order message passing in graph neural networks.
problem Expanding the expressive power of graph neural networks through higher-order structures.
method Introduces P-tensors to define the most general form of permutation equivariant message passing.
result Achieves state-of-the-art performance on molecular datasets.
Machine learning generates coarse-grained force fields for molecular dynamics.
problem Creating thermodynamically consistent coarse-grained models for larger systems.
method Hybrid architecture using graph neural networks to learn molecular features.
result Framework reproduces thermodynamics for small biomolecular systems.
Recent work in graph neural networks (GNNs) has led to improvements in molecular activity and property prediction tasks. Unfortunately, GNNs often fail to capture the relative importance of interactions between molecular substructures, in part due to the absence of efficient intermediate pooling steps. To address these…
Enhances graph neural networks by creating virtual data examples.
problem Lack of examples to identify optimal graph rationales in graph applications.
method Introduces environment replacement to create virtual data examples and proposes a framework for rationale-environment separation and representation learning.
result Demonstrates the effectiveness and efficiency of the augmentation-based graph rationalization framework on molecular and polymer datasets.
Graph Neural Networks (GNNs) achieve an impressive performance on structured graphs by recursively updating the representation vector of each node based on its neighbors, during which parameterized transformation matrices should be learned for the node feature updating. However, existing propagation schemes are far fro…
Most of the successful deep neural network architectures are structured, often consisting of elements like convolutional neural networks and gated recurrent neural networks. Recently, graph neural networks have been successfully applied to graph structured data such as point cloud and molecular data. These networks oft…
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.
New model learns graph neural networks equivariant to various transformations.
problem Learning equivariant graph neural networks for complex transformations.
method E(n)-Equivariant Graph Neural Networks (EGNNs) that are computationally efficient and scalable.
result Achieves competitive or better performance without higher-order representations.
Functional groups (FGs) are molecular substructures that are served as a foundation for analyzing and predicting chemical properties of molecules. Automatic discovery of FGs will impact various fields of research, including medicinal chemistry and material sciences, by reducing the amount of lab experiments required fo…
HGNet improves GNNs' ability to handle long-range interactions in graphs.
problem Insufficiency of GNNs in capturing long-range interactions.
method Introduces hierarchical message passing models with multi-resolution graph representations.
result HGNet outperforms conventional GNNs in molecular property prediction.
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.
Combines neural networks and probabilistic graphical models for efficient higher-order inference.
problem Lack of efficient higher-order relational information in graph neural networks and probabilistic graphical models.
method Derives efficient approximate sum-product loopy belief propagation for higher-order PGMs, embeds into neural network, proposes methods for constructing higher-order factors.
result Substantially outperforms state-of-the-art k-order graph neural networks in molecular datasets.
Graphs predict reaction conditions for organic chemistry.
problem Predicting specific reaction conditions in organic chemistry.
method Graph Neural Networks (GNNs) for modeling reaction graphs.
result GNNs can identify specific graph features affecting reaction conditions.
Graph neural network predicts optimal coarse-grained mapping operators.
problem Optimal coarse-grained mapping operators selection for molecular dynamics simulations.
method Graph Neural Network (DSGPM) trained on expert-annotated data.
result DSGPM outperforms state-of-the-art methods in graph segmentation.
Graph Convolutional Neural Networks (Graph CNNs) are generalizations of classical CNNs to handle graph data such as molecular data, point could and social networks. Current filters in graph CNNs are built for fixed and shared graph structure. However, for most real data, the graph structures varies in both size and con…
JAX MD enables differentiable physics simulations for molecular dynamics.
problem Performing efficient and differentiable physics simulations for molecular dynamics.
method Differentiable physics simulation environments, interaction potentials, neural networks, flexible primitives.
result Differentiable physics simulations can be used for meta-optimization and scaling to large particle systems.
Much of the recent work on learning molecular representations has been based on Graph Convolution Networks (GCN). These models rely on local aggregation operations and can therefore miss higher-order graph properties. To remedy this, we propose Path-Augmented Graph Transformer Networks (PAGTN) that are explicitly built…
Proposes a new model to predict polymer properties by integrating various data types.
problem Inaccurate polymer property prediction due to separate modeling of different data types.
method Multi-modal cascade feature transfer using GCN for chemical structure and molecular descriptors.
result Empirically evaluated model shows higher predictive performance than single-feature approaches.
GraphDETR detects subgraphs in large graphs using deep learning.
problem Detecting subgraphs in large graphs efficiently and accurately.
method Formulates subgraph detection as a set prediction problem using GraphDETR, a deep learning framework.
result GraphDETR can detect diverse patterns in large graphs, achieving strong performance on molecular functional group detection.
A new aggregation strategy improves GNN performance and learning dynamics.
problem Improving expressivity and learning dynamics of GNNs.
method Proposes a variance-preserving aggregation function (VPA) for GNNs.
result VPA leads to increased predictive performance and improved learning dynamics.