mlsanityData to 7 Oct 2026

Graph Neural Networks in Network Neuroscience

arXiv 2106.03535 ↗First posted 7 Jun 2021cs.LG q-bio.NCcited by 91

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Abstract (arXiv)

Noninvasive medical neuroimaging has yielded many discoveries about the brain connectivity. Several substantial techniques mapping morphological, structural and functional brain connectivities were developed to create a comprehensive road map of neuronal activities in the human brain -namely brain graph. Relying on its non-Euclidean data type, graph neural network (GNN) provides a clever way of learning the deep graph structure and it is rapidly becoming the state-of-the-art leading to enhanced performance in various network neuroscience tasks. Here we review current GNN-based methods, highlighting the ways that they have been used in several applications related to brain graphs such as missing brain graph synthesis and disease classification. We conclude by charting a path toward a better application of GNN models in network neuroscience field for neurological disorder diagnosis and population graph integration. The list of papers cited in our work is available at https://github.com/basiralab/GNNs-in-Network-Neuroscience.

Key facts. Cited by 91 papers in the map (data through 7 Oct 2026). Builds on 44 of its 127 references that are in the map. First posted on arXiv 7 Jun 2021.

Builds on

44 of 127 references.

References · 44

  1. 2016Semi-Supervised Classification with Graph Convolutional Networkscited by 11,282
  2. 2017Graph Attention Networkscited by 8,854
  3. 2017Neural Message Passing for Quantum Chemistrycited by 3,460
  4. 2019A Comprehensive Survey on Graph Neural Networkscited by 2,906
  5. 2018Graph Neural Networks: A Review of Methods and Applicationscited by 1,571
  6. 2016Geometric deep learning: going beyond Euclidean datacited by 1,042
  7. 2019GNNExplainer: Generating Explanations for Graph Neural Networkscited by 735
  8. 2020Benchmarking Graph Neural Networkscited by 672
  9. 2016Geometric deep learning on graphs and manifolds using mixture model CNNscited by 468
  10. 2019Generalizing from a Few Examples: A Survey on Few-Shot Learningcited by 462
  11. 2018Deep Learning on Graphs: A Surveycited by 393
  12. 2020Explainability in Graph Neural Networks: A Taxonomic Surveycited by 383
32 more
  1. 2017Few-Shot Learning with Graph Neural Networkscited by 324
  2. 2017Dynamic Edge-Conditioned Filters in Convolutional Neural Networks on Graphscited by 307
  3. 2019A Fair Comparison of Graph Neural Networks for Graph Classificationcited by 244
  4. 2020GraphLIME: Local Interpretable Model Explanations for Graph Neural Networkscited by 209
  5. 2020Graph Structure of Neural Networkscited by 67
  6. 2017Spectral Graph Convolutions for Population-based Disease Predictioncited by 42
  7. 2019Graph Neural Network for Interpreting Task-fMRI Biomarkerscited by 40
  8. 2019InceptionGCN: Receptive Field Aware Graph Convolutional Network for Disease Predictioncited by 39
  9. 2020Pooling Regularized Graph Neural Network for fMRI Biomarker Analysiscited by 25
  10. 2020Few-Shot Anomaly Detection for Polyp Frames from Colonoscopycited by 19
  11. 2016Multi-scale brain networkscited by 16
  12. 2020Deep Graph Normalizer: A Geometric Deep Learning Approach for Estimating Connectional Brain Templatescited by 16
  13. 2020Deep Representation Learning For Multimodal Brain Networkscited by 12
  14. 2020Foreseeing Brain Graph Evolution Over Time Using Deep Adversarial Network Normalizercited by 11
  15. 2020Deep EvoGraphNet Architecture For Time-Dependent Brain Graph Data Synthesis From a Single Timepointcited by 11
  16. 2020GSR-Net: Graph Super-Resolution Network for Predicting High-Resolution from Low-Resolution Functional Brain Connectomescited by 10
  17. 2017Geometric Convolutional Neural Network for Analyzing Surface-Based Neuroimaging Datacited by 8
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  19. 2019DS-GCNs: Connectome Classification Using Dynamic Spectral Graph Convolution Networks with Assistant Task Trainingcited by 6
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  24. 2020Supervised Multi-topology Network Cross-diffusion for Population-driven Brain Network Atlas Estimationcited by 4
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  26. 2018Navigable maps of structural brain networks across speciescited by 3
  27. 2020Deep Hypergraph U-Net for Brain Graph Embedding and Classificationcited by 3
  28. 2017Coalescent embedding in the hyperbolic space unsupervisedly discloses the hidden geometry of the braincited by 2
  29. 2020Deep Modeling of Growth Trajectories for Longitudinal Prediction of Missing Infant Cortical Surfacescited by 2
  30. 2020Multi-Scale Profiling of Brain Multigraphs by Eigen-based Cross-Diffusion and Heat Tracing for Brain State Profilingcited by 2
  31. 2020Multi-View Brain HyperConnectome AutoEncoder For Brain State Classificationcited by 2
  32. 2019Navigability evaluation of complex networks by greedy routing efficiencycited by 1

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Cited by year (2026 to 7 Oct)

Citing papers per year: 2021: 7; 2022: 17; 2023: 16; 2024: 17; 2025: 25; 2026: 9.

91 papers.

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  1. 2022BrainGB: A Benchmark for Brain Network Analysis with Graph Neural Networkscited by 73
  2. 2022Transformers in Medical Image Analysis: A Reviewcited by 41
  3. 2024A Review of Graph Neural Networks in Epidemic Modelingcited by 31
  4. 2024Towards Effective and General Graph Unlearning via Mutual Evolutioncited by 29
  5. 2023A Survey on Spectral Graph Neural Networkscited by 26
  6. 2023From Continuous Dynamics to Graph Neural Networks: Neural Diffusion and Beyondcited by 26
  7. 2024AdaFGL: A New Paradigm for Federated Node Classification with Topology Heterogeneitycited by 25
  8. 2023Graph Neural Network-based EEG Classification: A Surveycited by 21
  9. 2022GATE: Graph CCA for Temporal SElf-supervised Learning for Label-efficient fMRI Analysiscited by 19
  10. 2023Breaking the Entanglement of Homophily and Heterophily in Semi-supervised Node Classificationcited by 19
  11. 2022coVariance Neural Networkscited by 18
  12. 2022Forecasting Unobserved Node States with spatio-temporal Graph Neural Networkscited by 9
38 more
  1. 2024MM-GTUNets: Unified Multi-Modal Graph Deep Learning for Brain Disorders Predictioncited by 9
  2. 2025Biologically Plausible Brain Graph Transformercited by 9
  3. 2025OpenGU: A Comprehensive Benchmark for Graph Unlearningcited by 8
  4. 2021Predicting cognitive scores with graph neural networks through sample selection learningcited by 7
  5. 2023Learning Dynamic Graph Embeddings with Neural Controlled Differential Equationscited by 7
  6. 2023MMGPL: Multimodal Medical Data Analysis with Graph Prompt Learningcited by 7
  7. 2023A graph neural network-based model with Out-of-Distribution Robustness for enhancing Antiretroviral Therapy Outcome Prediction for HIV-1cited by 7
  8. 2022A Topological Deep Learning Framework for Neural Spike Decodingcited by 6
  9. 2023Fast Temporal Wavelet Graph Neural Networkscited by 6
  10. 2024Fair CoVariance Neural Networkscited by 6
  11. 2024NeuroPath: A Neural Pathway Transformer for Joining the Dots of Human Connectomescited by 6
  12. 2024Sparse Covariance Neural Networkscited by 6
  13. 2022Modern Views of Machine Learning for Precision Psychiatrycited by 5
  14. 2022Towards better Interpretable and Generalizable AD detection using Collective Artificial Intelligencecited by 5
  15. 2022Comparative Survey of Multigraph Integration Methods for Holistic Brain Connectivity Mappingcited by 4
  16. 2023Leveraging Brain Modularity Prior for Interpretable Representation Learning of fMRIcited by 4
  17. 2024A Primer on Temporal Graph Learningcited by 4
  18. 2021Recurrent Multigraph Integrator Network for Predicting the Evolution of Population-Driven Brain Connectivity Templatescited by 3
  19. 2021StairwayGraphNet for Inter- and Intra-modality Multi-resolution Brain Graph Alignment and Synthesiscited by 3
  20. 2021One Representative-Shot Learning Using a Population-Driven Template with Application to Brain Connectivity Classification and Evolution Predictioncited by 3
  21. 2022Contrastive Graph Learning for Population-based fMRI Classificationcited by 3
  22. 2022HIRE: Distilling High-order Relational Knowledge From Heterogeneous Graph Neural Networkscited by 2
  23. 2022Deep Cross-Modality and Resolution Graph Integration for Universal Brain Connectivity Mapping and Augmentationcited by 2
  24. 2023Body Fat Estimation from Surface Meshes using Graph Neural Networkscited by 2
  25. 2024Scalable Graph Compressed Convolutionscited by 2
  26. 2024DuoGNN: Topology-aware Graph Neural Network with Homophily and Heterophily Interaction-Decouplingcited by 2
  27. 2024Towards Data-centric Machine Learning on Directed Graphs: a Surveycited by 2
  28. 2025Information Bottleneck-Guided Heterogeneous Graph Learning for Interpretable Neurodevelopmental Disorder Diagnosiscited by 2
  29. 2025Deterministic Certification of Graph Neural Networks against Graph Poisoning Attacks with Arbitrary Perturbationscited by 2
  30. 2026Learning beyond Site Bias for OOD Generalization in Brain Networkscited by 2
  31. 2021Quantifying the Reproducibility of Graph Neural Networks using Multigraph Brain Datacited by 1
  32. 2021A Few-shot Learning Graph Multi-Trajectory Evolution Network for Forecasting Multimodal Baby Connectivity Development from a Baseline Timepointcited by 1
  33. 2022An explainability framework for cortical surface-based deep learningcited by 1
  34. 2022Investigating the Predictive Reproducibility of Federated Graph Neural Networks using Medical Datasetscited by 1
  35. 2022Meta-RegGNN: Predicting Verbal and Full-Scale Intelligence Scores using Graph Neural Networks and Meta-Learningcited by 1
  36. 2022Population Template-Based Brain Graph Augmentation for Improving One-Shot Learning Classificationcited by 1
  37. 2023mSPD-NN: A Geometrically Aware Neural Framework for Biomarker Discovery from Functional Connectomics Manifoldscited by 1
  38. 2023Transformer and Snowball Graph Convolution Learning for Brain functional network Classificationcited by 1

50 most cited of 91 All 91 (JSON)