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.
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.
Research predicts XRP price anomalies using graph topologies.
problem Forecasting extreme price movements in XRP cryptoasset.
method Analyzed topological features of XRP transaction graphs.
result Topological features indicate extreme price surges.
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 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 readout layer improves graph property prediction.
problem Graph property prediction challenges due to information loss.
method Introduces a novel generalized global pooling layer for Message-Passing Neural Networks.
result New state-of-the-art results in graph property prediction.
Graph hypernetworks improve molecule property prediction and classification.
problem Improving molecule property prediction and classification using graph neural networks.
method Replacing underlying networks with hypernetworks and addressing training instability.
result Demonstrated state-of-the-art performance in various benchmarks.
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.
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.
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…
Paper tackles multi-task learning for molecular property prediction with limited data.
problem Limited labeled data for each molecular property task in drug discovery.
method Proposes SGNN-EBM method to utilize relation graph between tasks and improve multi-task learning performance.
result Empirical results show the effectiveness of SGNN-EBM.
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.
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.
Neural message passing on molecular graphs is one of the most promising methods for predicting formation energy and other properties of molecules and materials. In this work we extend the neural message passing model with an edge update network which allows the information exchanged between atoms to depend on the hidde…
SGRNN models evolving graph data for better property prediction.
problem Modeling evolving graph data for property prediction.
method SGRNN uses stochastic latent variables to capture both node attribute and topology evolution, with semi-implicit variational inference and KL-divergence simplification.
result SGRNN improves property prediction on real-world datasets.
Graph networks struggle with multi-task learning due to varying property loss surface curvatures.
problem Graph networks underperform in multi-task learning for crystal and molecule properties.
method Assessed curvature of property loss surfaces via spectral properties of Hessians, matrix-free using randomized numerical linear algebra.
result Varying curvature of property loss surfaces explains graph networks' multi-task learning inefficiency.
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.
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.
AWARE improves graph prediction by aggregating walks with attention schemes.
problem Improving graph prediction accuracy using walk aggregation.
method Integrates attention schemes into walk-aggregating GNNs.
result AWARE outperforms existing methods in graph-level prediction tasks.
This paper classifies chiral graphs up to size 12.
problem Understanding the chirality of simple graphs to predict molecular behavior.
method Classifying minor minimal intrinsically chiral graphs among simple graphs of size up to 12.
result Complete set of minor minimal graphs for intrinsic properties of chiral molecules.
Two ML frameworks predict antibody properties using structural data.
problem Predicting antibody properties using sequence and structural data.
method ANTIPASTI and INFUSSE models using graph representations and neural networks.
result ANTIPASTI predicts binding affinity; INFUSSE predicts residue flexibility.
Data-driven prediction of molecular properties presents unique challenges to the design of machine learning methods concerning data structure/dimensionality, symmetry adaption, and confidence management. In this paper, we present a kernel-based pipeline that can learn and predict the atomization energy of molecules wit…
A new triad decoder improves graph auto-encoders' performance.
problem Graph auto-encoders ignore edge interactions, leading to suboptimal predictions.
method Integrates triadic closure property to predict three edges in a local triad.
result Triad decoder leads to more accurate predictions, clustering, and graph characteristics preservation.
The study evaluates GRL approaches and finds limitations in their applicability.
problem Challenges in applying GRL approaches to real-world graphs with varying structural differences.
method Empirical data-driven framework and theoretical analysis of GRL approaches.
result Existing GRL approaches are insufficient for real-world graphs with diverse structural patterns.
CHILI datasets tackle inorganic nanomaterials, advancing graph machine learning.
problem Challenges in modelling inorganic crystalline materials and nanomaterials with graph ML.
method Presented two large-scale datasets of inorganic nanomaterials, defined property and structure prediction tasks.
result Benchmarked performance of graph ML methods on inorganic nanomaterials, highlighting areas for future work.
Persistent homology enhances graph classification by capturing long-range graph properties.
problem Lack of formal assessment of persistent homology in graph learning.
method Brief introduction and theoretical discussion of persistent homology in graph context, followed by empirical analysis.
result Persistent homology improves graph classification, especially for data with prominent topological structures.
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.
In the paper, we consider the problem of link prediction in time-evolving graphs. We assume that certain graph features, such as the node degree, follow a vector autoregressive (VAR) model and we propose to use this information to improve the accuracy of prediction. Our strategy involves a joint optimization procedure …
Proposes a novel approach using vector cross product to preserve directional edges in directed graphs.
problem Preserving directional edges in directed graphs for tasks like link prediction and node recommendation.
method Integrates the non-commutative property of vector cross product into a Siamese neural network to learn N-dimensional embeddings.
result Low-dimensional embeddings effectively preserve directional properties and outperform state-of-the-art methods.
GraphOpt learns the formation mechanism of graphs from observed structures.
problem Learning formation mechanisms from observed graphs with complex structural properties.
method GraphOpt uses maximum entropy inverse reinforcement learning to solve the link formation problem in a sequential decision-making process.
result GraphOpt discovers a latent objective function that can explain and transfer across different graphs.
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.
Graph neural networks improve with affinity measures from random walks.
problem Limited expressivity of GNNs due to small receptive field.
method Introduced affinity measures from random walks into GNNs.
result Affinity measures enhance GNN performance on various tasks.
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.
GNNs learn graph representations, with new theory on their power and limitations.
problem Understanding the capabilities and limitations of GNNs.
method Theoretical analysis of GNNs, focusing on approximation and learning properties.
result New insights into the representation, generalization, and extrapolation of GNNs.
Framework tackles OOD challenges in molecule property prediction by modeling environments.
problem Challenges in modeling OOD samples for molecule property prediction.
method Soft causal learning framework incorporating chemistry theories and cross-attention mechanisms.
result Demonstrates well generalization ability on seven datasets.
We propose a framework for the completely unsupervised learning of latent object properties from their interactions: the perception-prediction network (PPN). Consisting of a perception module that extracts representations of latent object properties and a prediction module that uses those extracted properties to simula…
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%.
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.
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…
Study the averaging estimator on graphs with labeled nodes.
problem Understanding the quality of averaging estimators on graph data.
method Rigorously study concentration properties, variance bounds, and risk bounds.
result Contributes to theoretical understanding of graph learning.
A new algorithm learns graph embeddings considering directionality, improving multiple tasks.
problem Lack of directionality in graph embedding algorithms affects performance across tasks.
method DIAGRAM, a multi-objective model that preserves direction, textual features, and graph context.
result DIAGRAM significantly outperforms state-of-the-art baselines on link prediction and node classification.
Proposes a graph-based approach for better stock prediction.
problem Long-range dependencies and chaotic property in stock prediction.
method Transforms time series into graphs, extracting structural information to resolve issues.
result Obtains the best performance among state-of-the-art benchmarks and highest cumulative profits in trading simulations.
We model GitHub interactions as a temporal knowledge graph for software engineering questions.
problem Insufficient performance of existing temporal models on extrapolated queries and time prediction.
method Introduced an extension to current temporal models using relative temporal information.
result Improved performance on extrapolated queries and time prediction.
DeeperGCN tackles deep GCNs by overcoming vanishing gradient and over-smoothing issues.
problem Vanishing gradient, over-smoothing, and over-fitting issues in deep GCNs.
method DeeperGCN uses differentiable generalized aggregation functions and a novel normalization layer (MsgNorm) to train deep GCNs.
result DeeperGCN significantly boosts performance on large-scale graph learning tasks.
We study the problem of prediction for evolving graph data. We formulate the problem as the minimization of a convex objective encouraging sparsity and low-rank of the solution, that reflect natural graph properties. The convex formulation allows to obtain oracle inequalities and efficient solvers. We provide empirical…
PanRep learns universal node embeddings for heterogeneous graphs.
problem Learning universal node embeddings for heterogeneous graphs.
method Graph Neural Network (GNN) model with four decoders capturing different properties.
result PanRep outperforms unsupervised and supervised methods in node classification and link prediction.
Machine learning predicts criminal networks' missing partnerships and future behavior.
problem Predicting and understanding criminal networks' properties and future behavior.
method Combining graph representation learning and machine learning methods.
result Outstanding accuracy in predicting missing criminal partnerships and future behavior.
Fairness constraints improve exact recovery in structured prediction models.
problem Exact recovery of fair binary node labels from noisy observations.
method Analyzed Globerson et al. (2015) model with fairness constraints and improved exact recovery for graphs with poor expansion properties.
result Fairness constraints improve the probability of exact recovery from noisy observations.