Graph neural networks struggle with structural noise.
problem Robustness of graph neural networks to structural noise.
method Controlled experiments with a representative GNN model.
result Graph neural networks are not robust to structural noise.
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48 results for “Graph Structured Prediction”
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.
Investigates how neural network graph structure impacts predictive performance.
problem Lack of understanding between neural network graph structure and predictive performance.
method Developed relational graph representation to analyze neural networks, identifying a 'sweet spot' for improved performance.
result Identified a 'sweet spot' in relational graph structure that significantly improves neural network predictive performance.
A new conformal prediction framework for graph-valued outputs using Z-Gromov-Wasserstein distances.
problem Lack of principled uncertainty quantification for graph-valued supervised prediction.
method Proposes a conformal prediction framework using Z-Gromov-Wasserstein distances for graph-valued outputs.
result Provides distribution-free coverage guarantees for graph-valued outputs.
New method predicts graph structure changes over time.
problem Existing graph prediction methods assume static vertices, limiting their applicability.
method Combines time series prediction with adapted FBA for growing graphs.
result Efficacy demonstrated on synthetic and real datasets.
Paper predicts future graph structures using time series methods.
problem Forecasting dynamic graph structures with unseen nodes and edges.
method Time series forecasting for node degree prediction combined with flux balance analysis.
result Demonstrated utility and applicability of the approach on synthetic and real-world datasets.
Study shows gMPNNs struggle with OOD link prediction in larger test graphs.
problem Inductive out-of-distribution link prediction in larger test graphs.
method Theoretical analysis and development of a gMPNN with structural pairwise embeddings.
result Structural node embeddings from gMPNNs converge to random guessing as test graphs grow.
Recently, graph neural networks (GNNs) have proved to be suitable in tasks on unstructured data. Particularly in tasks as community detection, node classification, and link prediction. However, most GNN models still operate with static relationships. We propose the Graph Learning Network (GLN), a simple yet effective p…
New method learns graph structure and uncertainty from data.
problem Learning latent graph structures and their uncertainty from data.
method Proposes a sampling-based method to learn latent graph structure and uncertainty simultaneously.
result Proves that suitable loss functions on stochastic model outputs solve both learning latent graph structure and achieving optimal predictions.
This work benchmarks neural embeddings for link prediction in evolving knowledge graphs.
problem Evaluating the robustness of neural embeddings in changing knowledge graphs.
method Proposes an open-source evaluation pipeline using relation-centric connectivity measures.
result Demonstrates the importance of simulating embedding accuracy for frequently updated knowledge graphs.
GTDL methods fail to accurately model feature interactions in tabular data.
problem Accurate modeling of feature interactions in tabular data.
method Graph-based tabular deep learning methods using attention mechanisms and message-passing schemes.
result Current GTDL methods fail to recover meaningful feature interactions due to poor edge recovery.
Graph Structured Prediction Energy Networks model correlations for joint inference.
problem Joint inference over multiple variables with high-order correlations.
method Energy Networks for modeling explicit local and implicit higher-order correlations.
result Tractable inference with explicit modeling of correlations.
This work investigates how GCNs should handle local structure discrepancies in testing nodes.
problem GCNs assume homophily but real graphs often have discrepancies in local structure.
method Using causal graph analysis, the study intervenes the graph structure to assess the local structure's impact on predictions.
result The method effectively enhances GCN predictions by eliminating local structure discrepancies.
Graph Neural Networks (GNNs) are a powerful tool for machine learning on graphs.GNNs combine node feature information with the graph structure by recursively passing neural messages along edges of the input graph. However, incorporating both graph structure and feature information leads to complex models, and explainin…
Improves GNN prediction sets with conformal prediction for node classification.
problem Lack of predictive uncertainty for GNN models.
method Adapted conformal prediction for graph data, weighting scores based on graph structure.
result Better calibrated and tighter prediction sets than naive conformal prediction.
DArtNet predicts time series data using graph structure and dynamic attributes.
problem Predicting time series data using graph structure and dynamic attributes.
method DArtNet learns static and dynamic embeddings for graph nodes and encodes history information using RNN for joint link and attribute prediction.
result Improved time series prediction accuracy on five datasets.
Bi-GNN models drug interactions using a bi-level graph approach.
problem Predicting drug-drug interactions using machine learning.
method Bi-level graph neural networks that consider both interaction graph and representation graphs of drugs.
result Bi-GNN model improves DDI prediction accuracy compared to existing methods.
We consider the two problems of predicting links in a dynamic graph sequence and predicting functions defined at each node of the graph. In many applications, the solution of one problem is useful for solving the other. Indeed, if these functions reflect node features, then they are related through the graph structure.…
Eigen-GNN enhances GNNs by preserving graph structures.
problem Existing shallow GNNs fail to effectively preserve graph structures.
method Integrates eigenspace of graph structures into GNNs as a dimensionality reduction module.
result Eigen-GNN boosts GNNs' ability to preserve graph structures without increasing depth.
We introduce the variational graph auto-encoder (VGAE), a framework for unsupervised learning on graph-structured data based on the variational auto-encoder (VAE). This model makes use of latent variables and is capable of learning interpretable latent representations for undirected graphs. We demonstrate this model us…
RR-GNN improves GNN prediction intervals by accounting for graph heteroscedasticity and structural biases.
problem Uncertainty quantification in GNNs for high-stakes domains.
method Graph-Structured Mondrian CP, Residual-Adaptive Nonconformity Scores, Cross-Training Protocol.
result Improved efficiency and no loss of coverage compared to CP baselines.
DynDepNet learns dynamic brain graphs from fMRI data for better prediction performance.
problem Static brain graphs from fMRI data lead to poor GNN performance.
method Dynamic Graph Structure Learning for time-varying brain connectivity.
result DynDepNet achieves state-of-the-art sex classification accuracy on real-world fMRI data.
We study the effect of structural variation in graph data on the predictive performance of graph kernels. To this end, we introduce a novel, noise-robust adaptation of the GraphHopper kernel and validate it on benchmark data, obtaining modestly improved predictive performance on a range of datasets. Next, we investigat…
Graph-augmented CNN predicts drug interactions with high accuracy.
problem Predicting drug-drug interactions (DDIs) with high accuracy.
method Combining graph CNN with an attentive pooling network to extract structural relations between drug pairs.
result Desirable performance with ROC 0.988, F1-score 0.956, and AUPR 0.986.
We examine two fundamental tasks associated with graph representation learning: link prediction and semi-supervised node classification. We present a novel autoencoder architecture capable of learning a joint representation of both local graph structure and available node features for the multi-task learning of link pr…
Financial Default Prediction via Motif-preserving Graph Neural Network with Curriculum Learningq-fin.RM
Proposes a motif-preserving Graph Neural Network for financial default prediction.
problem Weak connectivity and imbalance in motif patterns in graph-based models.
method MotifGNN with curriculum learning to capture higher-order topology structures.
result Significantly improved financial default prediction accuracy on public and industrial datasets.
New metrics improve uncertainty estimation on graph data.
problem Current GNNs focus only on nodewise scores, limiting uncertainty estimation.
method Proposed edgewise metrics for uncertainty estimation on graphs.
result GNN models with structured prediction perform better in uncertainty estimation.
CF-GNN provides reliable uncertainty estimates for graph data.
problem Lack of rigorous uncertainty estimates in GNNs.
method Conformal prediction extended to graph-based models (CF-GNN).
result CF-GNN produces prediction sets with provable coverage probability.
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.
Graph Convolutional Gaussian Processes predict missing links.
problem Link prediction in large graphs.
method Simplified graph convolutions and variational inducing point method.
result Consistent improvements over existing models and competitive performance.
This paper introduces Graph Convolutional Recurrent Network (GCRN), a deep learning model able to predict structured sequences of data. Precisely, GCRN is a generalization of classical recurrent neural networks (RNN) to data structured by an arbitrary graph. Such structured sequences can represent series of frames in v…
We present a general theoretical analysis of structured prediction with a series of new results. We give new data-dependent margin guarantees for structured prediction for a very wide family of loss functions and a general family of hypotheses, with an arbitrary factor graph decomposition. These are the tightest margin…
Graphs are general and powerful data representations which can model complex real-world phenomena, ranging from chemical compounds to social networks; however, effective feature extraction from graphs is not a trivial task, and much work has been done in the field of machine learning and data mining. The recent advance…
Generative model predicts multiple brain graphs from one, preserving topology.
problem Predicting multiple brain graphs from a single one, preserving topology.
method MultiGraphGAN architecture, graph adversarial auto-encoder, cluster-specific decoders, topological loss.
result Significantly outperformed variants in multi-view brain graph generation.
MR-GNN: Multi-Resolution and Dual Graph Neural Network for Predicting Structured Entity Interactionscs.LG
Predicting interactions between structured entities lies at the core of numerous tasks such as drug regimen and new material design. In recent years, graph neural networks have become attractive. They represent structured entities as graphs and then extract features from each individual graph using graph convolution op…
Graph transformers outperform graph convolutions by preserving community information.
problem Understanding why graph transformers perform well in node-level prediction tasks.
method Analyzing the Gaussian process limits of graph transformers with infinite width and infinite heads.
result Graph transformers maintain discriminative node representations even in deep layers, preventing oversmoothing.
New method models aptamer libraries as Boltzmann-weighted graph ensembles for better affinity predictions.
problem Anomalous candidates in SELEX datasets obscure true aptamer-ligand affinity.
method Boltzmann graph ensemble embeddings for thermodynamically parameterized exponential-family random graphs.
result Proposed embedding enables robust community detection and subgraph-level explanations for aptamer ligand affinity.
A new framework explains GNN predictions by simulating graph structure and feature changes.
problem Lack of transparency in GNN predictions hinders understanding.
method TraP2 framework using a three-layer architecture: Translation, Perturbation, and Paraphrase layers.
result TraP2 achieves 10.2% higher explanation accuracy than state-of-the-art methods.
New method explains GNN predictions using walks.
problem GNNs are black-boxes and hard to explain.
method Nested attribution scheme using relevant walks.
result Extracts meaningful explanations from GNNs.
Graph data augmentation improves GNN performance in node classification.
problem Improving generalizability of graph neural networks (GNNs) in semi-supervised node classification.
method Introduces GAug framework for graph data augmentation using neural edge predictors.
result GAug framework improves GNN-based node classification performance across various architectures and datasets.
Recursive prediction of graph signals with new nodes added.
problem Predicting graph signals with new nodes added over time.
method Recursive prediction of graph signals using incoming nodes.
result Recursive method results in good prediction performance close to full graph knowledge.
Paper tackles uncertainty in GNNs for graph data.
problem Uncertainty in GNNs' predictions for graph data.
method CF-T2NN, tensor decomposition, topological learning.
result CF-T2NN improves reliability and interpretability of GNN outcomes.
Trading Graph Neural Networkq-fin.TR
TGNN combines GNN and SMM for better trading network predictions.
problem Predicting asset prices in trading networks with structural impact factors.
method Combines GNN and SMM for asset price prediction.
result TGNN outperforms existing methods in prediction accuracy.
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…
Generates low-dimensional node vectors for graphs with privacy while preserving structural preferences.
problem Publishing graph node vectors can leak sensitive individual information.
method SE-PrivGEmb, a skip-gram based technique with a unified noise tolerance mechanism and negative sampling probabilities.
result Our method outperforms existing methods in structural equivalence and link prediction tasks.
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.
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.
Accurate prediction of drug-target interaction (DTI) is essential for in silico drug design. For the purpose, we propose a novel approach for predicting DTI using a GNN that directly incorporates the 3D structure of a protein-ligand complex. We also apply a distance-aware graph attention algorithm with gate augmentatio…