Fast Graph Representation Learning with PyTorch Geometric
2019/03/06 by Matthias Fey, Jan Eric Lenssen, Fey, Matthias +1 · 1,260 citations
Computer Science · Mathematics · #Advanced Graph Neural Networks #Artificial intelligence #CUDA #Computational science #Computer science #Data Visualization and Analytics #Deep learning #Graph #Graph Theory and Algorithms #Parallel computing #Point cloud #Theoretical computer science #cs.LG #stat.ML
paper · pdf · doi:10.48550/arxiv.1903.02428
published in arXiv (Cornell University) (Cornell University) · ICLR 2019 (RLGM Workshop)
openalex publication_date 2019/03/06 · openalex created_date 2019/03/11 · arxiv created 2019/04/25 · arxiv updated 2019/04/26 · openalex updated_date 2026/07/28
Abstract
We introduce PyTorch Geometric, a library for deep learning on irregularly structured input data such as graphs, point clouds and manifolds, built upon PyTorch. In addition to general graph data structures and processing methods, it contains a variety of recently published methods from the domains of relational learning and 3D data processing. PyTorch Geometric achieves high data throughput by leveraging sparse GPU acceleration, by providing dedicated CUDA kernels and by introducing efficient mini-batch handling for input examples of different size. In this work, we present the library in detail and perform a comprehensive comparative study of the implemented methods in homogeneous evaluation scenarios.
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- PeakWeather: MeteoSwiss Weather Station Measurements for Spatiotemporal Deep Learning
- DiffGCN: Graph Convolutional Networks via Differential Operators and Algebraic Multigrid Pooling
- Quantum-Informed Contrastive Learning with Dynamic Mixup Augmentation for Class-Imbalanced Expert Systems
- A Fair Comparison of Graph Neural Networks for Graph Classification
- INT: An Inequality Benchmark for Evaluating Generalization in Theorem Proving
- ICLR 2021 Challenge for Computational Geometry & Topology: Design and Results
- Delving into Instance-Dependent Label Noise in Graph Data: A Comprehensive Study and Benchmark
- HYPER: A Foundation Model for Inductive Link Prediction with Knowledge Hypergraphs
- Geometry-Aware Edge Pooling for Graph Neural Networks
- How do Probabilistic Graphical Models and Graph Neural Networks Look at Network Data?
- Subgraph Neural Networks
- Graph Semi-Supervised Learning for Point Classification on Data Manifolds
- Principled Approaches for Extending Neural Architectures to Function Spaces for Operator Learning
- Guided Graph Compression for Quantum Graph Neural Networks
- Benchmarking Quantum Architecture Search with Surrogate Assistance
- Demystifying Topological Message-Passing with Relational Structures: A Case Study on Oversquashing in Simplicial Message-Passing
- Masked Language Models are Good Heterogeneous Graph Generalizers
- Simplicial Complex Representation Learning
- Tri-graph Information Propagation for Polypharmacy Side Effect Prediction
- Pruning Spurious Subgraphs for Graph Out-of-Distribution Generalization
- Large Language Models are Good Relational Learners
- Graph Neural Networks for Natural Language Processing: A Survey
- Graph Persistence goes Spectral
- Mitigating Degree Bias Adaptively with Hard-to-Learn Nodes in Graph Contrastive Learning
- The Oversmoothing Fallacy: A Misguided Narrative in GNN Research
- EnGN: A High-Throughput and Energy-Efficient Accelerator for Large Graph Neural Networks
- Positional Encoder Graph Neural Networks for Geographic Data
- Integrating Sensing and Communication in Cellular Networks via NR Sidelink
- Degree-Quant: Quantization-Aware Training for Graph Neural Networks
- Are Powerful Graph Neural Nets Necessary? A Dissection on Graph Classification
- Deep Graph Library: A Graph-Centric, Highly-Performant Package for Graph Neural Networks
- Adapted and Oversegmenting Graphs: Application to Geometric Deep Learning
- Graph Convolutional Memory using Topological Priors
- Improving Graph Property Prediction with Generalized Readout Functions
- Short-term Hourly Streamflow Prediction with Graph Convolutional GRU Networks
- Reconstructing nodal pressures in water distribution systems with graph neural networks
- Learning from Noise: Enhancing DNNs for Event-Based Vision through Controlled Noise Injection
- Deep Learning on Graphs: A Survey
- Tiered Graph Autoencoders with PyTorch Geometric for Molecular Graphs
- Framework GNN-AID: Graph Neural Network Analysis Interpretation and Defense
- Self-supervised Representation Learning for Evolutionary Neural Architecture Search
- Graph Convolution for Semi-Supervised Classification: Improved Linear Separability and Out-of-Distribution Generalization
- BenLOC: A Benchmark for Learning to Configure MIP Optimizers
- Equivariant Subgraph Aggregation Networks
- RDB2G-Bench: A Comprehensive Benchmark for Automatic Graph Modeling of Relational Databases
- Understanding and Improving Laplacian Positional Encodings For Temporal GNNs
- From Features to Structure: Task-Aware Graph Construction for Relational and Tabular Learning with GNNs
- Hierarchical Inter-Message Passing for Learning on Molecular Graphs
- Bridging Quantum and Classical Computing in Drug Design: Architecture Principles for Improved Molecule Generation
- Probing Neural Topology of Large Language Models
- Boosting Bot Detection via Heterophily-Aware Representation Learning and Prototype-Guided Cluster Discovery
- Spatial Graph Attention and Curiosity-driven Policy for Antiviral Drug Discovery
- DeGLIF for Label Noise Robust Node Classification using GNNs
- Weisfeiler and Leman Follow the Arrow of Time: Expressive Power of Message Passing in Temporal Event Graphs
- Point Cloud Instance Segmentation using Probabilistic Embeddings
- Recurrent Brain Graph Mapper for Predicting Time-Dependent Brain Graph Evaluation Trajectory
- Inductive Representation Learning on Temporal Graphs
- Hyperbolic-PDE GNN: Spectral Graph Neural Networks in the Perspective of A System of Hyperbolic Partial Differential Equations
- PLAID: A Unified Data Model for Machine Learning on Heterogeneous Physics Simulations
- Hybrid-graph neural network method for muon fast reconstruction in neutrino telescopes
- Grasp the Graph (GtG) 2.0: Ensemble of Graph Neural Networks for High-Precision Grasp Pose Detection in Clutter
- Bridging Source and Target Domains via Link Prediction for Unsupervised Domain Adaptation on Graphs
- Uncertainty Estimation for Heterophilic Graphs Through the Lens of Information Theory
- Multivariate de Bruijn Graphs: A Symbolic Graph Framework for Time Series Forecasting
- Graph Classification by Mixture of Diverse Experts
- Directed Homophily-Aware Graph Neural Network
- Geoopt: Riemannian Optimization in PyTorch
- Learnable Kernel Density Estimation for Graphs
- Bridging Arbitrary and Tree Metrics via Differentiable Gromov Hyperbolicity
- Identifying Super Spreaders in Multilayer Networks
- Dynamical Data for More Efficient and Generalizable Learning: A Case Study in Disordered Elastic Networks
- Adaptive Frontier Exploration on Graphs with Applications to Network-Based Disease Testing
- xChemAgents: Agentic AI for Explainable Quantum Chemistry
- Graph Wave Networks
- PCDCNet: A Surrogate Model for Air Quality Forecasting with Physical-Chemical Dynamics and Constraints
- OCN: Effectively Utilizing Higher-Order Common Neighbors for Better Link Prediction
- Geometric Graph Representations and Geometric Graph Convolutions for Deep Learning on Three-Dimensional (3D) Graphs
- Learning for Dynamic Combinatorial Optimization without Training Data
- Information Obfuscation of Graph Neural Networks
- Walk2Map: Extracting Floor Plans from Indoor Walk Trajectories
- Robustness questions the interpretability of graph neural networks: what to do?
- When to Talk: Chatbot Controls the Timing of Talking during Multi-turn Open-domain Dialogue Generation
- Convexified Message-Passing Graph Neural Networks
- Early-Exit Graph Neural Networks
- Aiding Medical Diagnosis Through the Application of Graph Neural Networks to Functional MRI Scans
- On Graph Classification Networks, Datasets and Baselines
- Few-Shot Learning from Gigapixel Images via Hierarchical Vision-Language Alignment and Modeling
- Learning Flexible Forward Trajectories for Masked Molecular Diffusion
- Joint Relational Database Generation via Graph-Conditional Diffusion Models
- An Empirical Study of Graph Contrastive Learning
- Efficient and Interpretable Robot Manipulation with Graph Neural Networks
- Survey of Image Based Graph Neural Networks
- Graph Data Selection for Domain Adaptation: A Model-Free Approach
- SCENIR: Visual Semantic Clarity through Unsupervised Scene Graph Retrieval
- TELLER: Non-intrusive Cross-Layer Root-Cause Analysis for LLM Inference
- Network Information Enhances Unreliable News Domain Detection
- p-Laplacian Based Graph Neural Networks
- Relationship Analysis of Image-Text Pair in SNS Posts
- A Semi-Supervised Approach for Abnormal Event Prediction on Large Operational Network Time-Series Data
- Khan-GCL: Kolmogorov-Arnold Network Based Graph Contrastive Learning with Hard Negatives
- Train on Small, Play the Large: Scaling Up Board Games with AlphaZero and GNN
- Partition-wise Graph Filtering: A Unified Perspective Through the Lens of Graph Coarsening
- Towards Comprehensive and Prerequisite-Free Explainer for Graph Neural Networks
- RainfalLTE: A Zero-effect Rainfall Sensing System Utilizing Existing LTE Infrastructure
- Node Attribute Completion in Knowledge Graphs with Multi-Relational Propagation
- DIG: A Turnkey Library for Diving into Graph Deep Learning Research
- Self-Reinforced Graph Contrastive Learning
- Learning (Approximately) Equivariant Networks via Constrained Optimization
- RECON: Robust symmetry discovery via Explicit Canonical Orientation Normalization
- Multi-Level Monte Carlo Training of Neural Operators
- How Benchmarks and Evaluation Protocols Shape Conclusions in Provenance-Based Intrusion Detection
- Wireless 3D Point Cloud Delivery Using Deep Graph Neural Networks
- A method for the systematic generation of graph XAI benchmarks via Weisfeiler-Leman coloring
- Neurospectrum: A Geometric and Topological Deep Learning Framework for Uncovering Spatiotemporal Signatures in Neural Activity
- Neural Graduated Assignment for Maximum Common Edge Subgraphs
- Ripple: Scalable Incremental GNN Inferencing on Large Streaming Graphs
- Differentiable Lifting for Topological Neural Networks
- Understanding the Capabilities of Molecular Graph Neural Networks in Materials Science Through Multimodal Learning and Physical Context Encoding
- Deep Iterative Surface Normal Estimation
- ProtFun: A Protein Function Prediction Model Using Graph Attention Networks with a Protein Large Language Model
- Space Group Equivariant Crystal Diffusion
- OpenGraphGym-MG: Using Reinforcement Learning to Solve Large Graph Optimization Problems on MultiGPU Systems
- Graph and Simplicial Complex Prediction Gaussian Process via the Hodgelet Representations
- Graph Representational Learning: When Does More Expressivity Hurt Generalization?
- Relational Graph Transformer
- Learning traffic flows: Graph Neural Networks for Metamodelling Traffic Assignment
- Conditional grain-graph diffusion for property-guided inverse design of polycrystalline microstructures
- GNN-Suite: a Graph Neural Network Benchmarking Framework for Biomedical Informatics
- Uniform Loss vs. Specialized Optimization: A Comparative Analysis in Multi-Task Learning
- Geometric Deep Reinforcement Learning for Dynamic DAG Scheduling
- Quotient Complex Transformer (QCformer) for Perovskite Data Analysis
- Modeling Global and Local Node Contexts for Text Generation from Knowledge Graphs
- Accelerating Training and Inference of Graph Neural Networks with Fast Sampling and Pipelining
- Fused3S: Fast Sparse Attention on Tensor Cores
- Towards a Taxonomy of Graph Learning Datasets
- Transformer-based Machine Learning for Fast SAT Solvers and Logic Synthesis
- Wide & Deep Learning for Node Classification
- RISE: Radius of Influence based Subgraph Extraction for 3D Molecular Graph Explanation
- ForgeEDA: A Comprehensive Multimodal Dataset for Advancing EDA
- Isometric Transformation Invariant and Equivariant Graph Convolutional Networks
- Node2Seq: Towards Trainable Convolutions in Graph Neural Networks
- Vision Transformers and Graph Neural Networks for Charged Particle Tracking in the ATLAS Muon Spectrometer
- Graph Convolutional Networks for traffic anomaly
- Global Attention Improves Graph Networks Generalization
- TeLoGraF: Temporal Logic Planning via Graph-encoded Flow Matching
- Hierarchical Graph Learning for Calendar Spread Strategies in Commodity Futures Markets
- Querying Counterfactuals on Tissue Graphs with Supervised Disentanglement
- Balancing Multi-level Interactions for Session-based Recommendation
- Semi-Supervised Deep Learning for Multiplex Networks
- MAGNET: an open-source library for mesh agglomeration by Graph Neural Networks
- Frequency-Space Mechanics: A Sequence and Coordinate-Free Representation for Protein Function Prediction
- Heterophily-informed Message Passing
- GraphNetz: Statistical Benchmarking of Graph Neural Networks with Paired Tests and Rank Aggregation
- Neuro-Relational Programs: Unifying Queries and Neural Computation over Structured Data
- Learning Hierarchical Interaction for Accurate Molecular Property Prediction
- Learning Efficiency Meets Symmetry Breaking
- PUFFIN: Protein Unit Discovery with Functional Supervision
- Efficient GNN Training Through Structure-Aware Randomized Mini-Batching
- Utilising Graph Machine Learning within Drug Discovery and Development
- Disentangling multispecific antibody function with graph neural networks
- Optimizing Memory Efficiency of Graph Neural Networks on Edge Computing Platforms
- Message Passing Query Embedding
- TAG-HGT: A Scalable and Cost-Effective Framework for Inductive Cold-Start Academic Recommendation
- Unveiling the Hidden: Movie Genre and User Bias in Spoiler Detection
- PTCL: Pseudo-Label Temporal Curriculum Learning for Label-Limited Dynamic Graph
- Speaker Attribution with Voice Profiles by Graph-Based Semi-Supervised Learning
- ARENA: Asynchronous Reconfigurable Accelerator Ring to Enable Data-Centric Parallel Computing
- Embedding Signals on Knowledge Graphs with Unbalanced Diffusion Earth Mover's Distance
- Benchmarking machine learning models for predicting aerofoil performance
- Optimization of a Triangular Delaunay Mesh Generator using Reinforcement Learning
- Mitigating Degree Bias in Graph Representation Learning with Learnable Structural Augmentation and Structural Self-Attention
- Event2Vec: Processing Neuromorphic Events Directly by Representations in Vector Space
- Scalable Graph Neural Networks for Heterogeneous Graphs
- Beamforming Design and Association Scheme for Multi-RIS Multi-User mmWave Systems Through Graph Neural Networks
- Fairness-Aware Node Representation Learning
- A Comparison of Neural Network Architectures for Data-Driven Reduced-Order Modeling
- 3D Meta Point Signature: Learning to Learn 3D Point Signature for 3D Dense Shape Correspondence
- When Contrastive Learning Meets Active Learning: A Novel Graph Active Learning Paradigm with Self-Supervision
- Scalable Graph Neural Network Training
- Explainable Scene Understanding with Qualitative Representations and Graph Neural Networks
- Inference-friendly Graph Compression for Graph Neural Networks
- H3GNNs: Harmonizing Heterophily and Homophily in GNNs via Joint Structural Node Encoding and Self-Supervised Learning
- The Impact of Dimensionality on the Stability of Node Embeddings
- Subset-Contrastive Multi-Omics Network Embedding
- Ember: A Compiler for Efficient Embedding Operations on Decoupled Access-Execute Architectures
- Optimizing Data Distribution and Kernel Performance for Efficient Training of Chemistry Foundation Models: A Case Study with MACE
- Landmark-Based Node Representations for Shortest Path Distance Approximations in Random Graphs
- Prediction of Usage Probabilities of Shopping-Mall Corridors Using Heterogeneous Graph Neural Networks
- Leveraging GCN-based Action Recognition for Teleoperation in Daily Activity Assistance
- InfoGain Wavelets: Furthering the Design of Graph Diffusion Wavelets
- Graph Neural Networks for Enhancing Ensemble Forecasts of Extreme Rainfall
- Scaling Graph Neural Networks for Particle Track Reconstruction
- Boosting Relational Deep Learning with Pretrained Tabular Models
- Optimizing Quantum Circuits via ZX Diagrams using Reinforcement Learning and Graph Neural Networks
- Graphically Speaking: Unmasking Abuse in Social Media with Conversation Insights
- MLKV: Efficiently Scaling up Large Embedding Model Training with Disk-based Key-Value Storage
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