mlsanityData to 7 Oct 2026

BrainGB: A Benchmark for Brain Network Analysis with Graph Neural Networks

arXiv 2204.07054 ↗First posted 17 Mar 2022q-bio.NC cs.LG cs.NEcited by 73

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Abstract (arXiv)

Mapping the connectome of the human brain using structural or functional connectivity has become one of the most pervasive paradigms for neuroimaging analysis. Recently, Graph Neural Networks (GNNs) motivated from geometric deep learning have attracted broad interest due to their established power for modeling complex networked data. Despite their superior performance in many fields, there has not yet been a systematic study of how to design effective GNNs for brain network analysis. To bridge this gap, we present BrainGB, a benchmark for brain network analysis with GNNs. BrainGB standardizes the process by (1) summarizing brain network construction pipelines for both functional and structural neuroimaging modalities and (2) modularizing the implementation of GNN designs. We conduct extensive experiments on datasets across cohorts and modalities and recommend a set of general recipes for effective GNN designs on brain networks. To support open and reproducible research on GNN-based brain network analysis, we host the BrainGB website at https://braingb.us with models, tutorials, examples, as well as an out-of-box Python package. We hope that this work will provide useful empirical evidence and offer insights for future research in this novel and promising direction.

Key facts. Cited by 73 papers in the map (data through 7 Oct 2026). Builds on 31 of its 112 references that are in the map. First posted on arXiv 17 Mar 2022.

Builds on

31 of 112 references.

References · 31

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  3. 2021Learning Transferable Visual Models From Natural Language Supervisioncited by 33,456
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  5. 2016Semi-Supervised Classification with Graph Convolutional Networkscited by 11,282
  6. 2017Graph Attention Networkscited by 8,854
  7. 2018How Powerful are Graph Neural Networks?cited by 4,355
  8. 2019Fast Graph Representation Learning with PyTorch Geometriccited by 2,414
  9. 2020Conformer: Convolution-augmented Transformer for Speech Recognitioncited by 1,838
  10. 2017Modeling Relational Data with Graph Convolutional Networkscited by 1,684
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  12. 2018Hierarchical Graph Representation Learning with Differentiable Poolingcited by 786
19 more
  1. 2018Session-based Recommendation with Graph Neural Networkscited by 312
  2. 2019A Fair Comparison of Graph Neural Networks for Graph Classificationcited by 244
  3. 2021Attention Mechanisms in Computer Vision: A Surveycited by 232
  4. 2019Position-aware Graph Neural Networkscited by 203
  5. 2020Combining Label Propagation and Simple Models Out-performs Graph Neural Networkscited by 199
  6. 2021Graph Neural Networks in Network Neurosciencecited by 91
  7. 2020Rethinking pooling in graph neural networkscited by 73
  8. 2021Understanding Pooling in Graph Neural Networkscited by 69
  9. 2021On Positional and Structural Node Features for Graph Neural Networks on Non-attributed Graphscited by 49
  10. 2019Graph Neural Network for Interpreting Task-fMRI Biomarkerscited by 40
  11. 2019On Node Features for Graph Neural Networkscited by 20
  12. 2021Joint Embedding of Structural and Functional Brain Networks with Graph Neural Networks for Mental Illness Diagnosiscited by 20
  13. 2018Understanding Regularized Spectral Clustering via Graph Conductancecited by 14
  14. 2018Multi-View Multi-Graph Embedding for Brain Network Clustering Analysiscited by 14
  15. 2021BrainNNExplainer: An Interpretable Graph Neural Network Framework for Brain Network based Disease Analysiscited by 13
  16. 2019Learnable Pooling in Graph Convolution Networks for Brain Surface Analysiscited by 11
  17. 2018Boosted Sparse and Low-Rank Tensor Regressioncited by 9
  18. 2021Edges in Brain Networks: Contributions to Models of Structure and Functioncited by 9
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Cited by year (2026 to 7 Oct)

Citing papers per year: 2022: 5; 2023: 18; 2024: 17; 2025: 23; 2026: 10.

73 papers.

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  1. 2022Brain Network Transformercited by 92
  2. 2024Brain-JEPA: Brain Dynamics Foundation Model with Gradient Positioning and Spatiotemporal Maskingcited by 64
  3. 2022Interpretable Graph Neural Networks for Connectome-Based Brain Disorder Analysiscited by 58
  4. 2024A Comprehensive Survey of Foundation Models in Medicinecited by 56
  5. 2025QoQ-Med: Building Multimodal Clinical Foundation Models with Domain-Aware GRPO Trainingcited by 38
  6. 2023NeuroGraph: Benchmarks for Graph Machine Learning in Brain Connectomicscited by 33
  7. 2024Learning on Multimodal Graphs: A Surveycited by 22
  8. 2023CF-GODE: Continuous-Time Causal Inference for Multi-Agent Dynamical Systemscited by 16
  9. 2022Data-Efficient Brain Connectome Analysis via Multi-Task Meta-Learningcited by 15
  10. 2024Graph Neural Networks for Brain Graph Learning: A Surveycited by 13
  11. 2025CLIMB: Data Foundations for Large Scale Multimodal Clinical Foundation Modelscited by 13
  12. 2022Learning Task-Aware Effective Brain Connectivity for fMRI Analysis with Graph Neural Networkscited by 12
38 more
  1. 2024BrainODE: Dynamic Brain Signal Analysis via Graph-Aided Neural Ordinary Differential Equationscited by 12
  2. 2025Long-range Brain Graph Transformercited by 11
  3. 2023PTGB: Pre-Train Graph Neural Networks for Brain Network Analysiscited by 10
  4. 2023Learning High-Order Relationships of Brain Regionscited by 10
  5. 2023BrainNPT: Pre-training of Transformer networks for brain network classificationcited by 9
  6. 2024Multi-modal Cross-domain Self-supervised Pre-training for fMRI and EEG Fusioncited by 9
  7. 2025Biologically Plausible Brain Graph Transformercited by 9
  8. 2023Transformer-Based Hierarchical Clustering for Brain Network Analysiscited by 8
  9. 2023R-Mixup: Riemannian Mixup for Biological Networkscited by 8
  10. 2025Rethinking Functional Brain Connectome Analysis: Do Graph Deep Learning Models Helpcited by 8
  11. 2023Dynamic Brain Transformer with Multi-level Attention for Functional Brain Network Analysiscited by 7
  12. 2023A graph neural network-based model with Out-of-Distribution Robustness for enhancing Antiretroviral Therapy Outcome Prediction for HIV-1cited by 7
  13. 2024DSAM: A Deep Learning Framework for Analyzing Temporal and Spatial Dynamics in Brain Networkscited by 7
  14. 2023Beyond the Snapshot: Brain Tokenized Graph Transformer for Longitudinal Brain Functional Connectome Embeddingcited by 6
  15. 2024NeuroPath: A Neural Pathway Transformer for Joining the Dots of Human Connectomescited by 6
  16. 2023An Explainable Geometric-Weighted Graph Attention Network for Identifying Functional Networks Associated with Gait Impairmentcited by 5
  17. 2022DynDepNet: Learning Time-Varying Dependency Structures from fMRI Data via Dynamic Graph Structure Learningcited by 4
  18. 2023Leveraging Brain Modularity Prior for Interpretable Representation Learning of fMRIcited by 4
  19. 2025Unified Cross-Modal Attention-Mixer Based Structural-Functional Connectomics Fusion for Neuropsychiatric Disorder Diagnosiscited by 3
  20. 2025A Brain Graph Foundation Model: Pre-Training and Prompt-Tuning across Broad Atlases and Disorderscited by 3
  21. 2023Source-Free Collaborative Domain Adaptation via Multi-Perspective Feature Enrichment for Functional MRI Analysiscited by 2
  22. 2024Spatial Craving Patterns in Marijuana Users: Insights from fMRI Brain Connectivity Analysis with High-Order Graph Attention Neural Networkscited by 2
  23. 2024Multimodal MRI Accurately Identifies Amyloid Status in Unbalanced Cohorts in Alzheimer's Disease Continuumcited by 2
  24. 2024Multi-atlas Ensemble Graph Neural Network Model For Major Depressive Disorder Detection Using Functional MRI Datacited by 2
  25. 2025BrainMAP: Multimodal Graph Learning For Efficient Brain Disease Localizationcited by 2
  26. 2025RTGMFF: Enhanced fMRI-based Brain Disorder Diagnosis via ROI-driven Text Generation and Multimodal Feature Fusioncited by 2
  27. 2023Momentum Gradient-based Untargeted Attack on Hypergraph Neural Networkscited by 1
  28. 2023Balanced Graph Structure Information for Brain Disease Detectioncited by 1
  29. 2024Advancing Graph Neural Networks with HL-HGAT: A Hodge-Laplacian and Attention Mechanism Approach for Heterogeneous Graph-Structured Datacited by 1
  30. 2024Discovering robust biomarkers of psychiatric disorders from resting-state functional MRI via graph neural networks: A systematic reviewcited by 1
  31. 20253DViT-GAT: A Unified Atlas-Based 3D Vision Transformer and Graph Learning Framework for Major Depressive Disorder Detection Using Structural MRI Datacited by 1
  32. 2025Brain-HGCN: A Hyperbolic Graph Convolutional Network for Brain Functional Network Analysiscited by 1
  33. 2025Interpretable Neuropsychiatric Diagnosis via Concept-Guided Graph Neural Networkscited by 1
  34. 2025Causal Graph Neural Networks for Healthcarecited by 1
  35. 2023Oversmoothing: A Nightmare for Graph Contrastive Learning?cited by 0
  36. 2023Video-Instrument Synergistic Network for Referring Video Instrument Segmentation in Robotic Surgerycited by 0
  37. 2023TiBGL: Template-induced Brain Graph Learning for Functional Neuroimaging Analysiscited by 0
  38. 2024Imbalanced Graph-Level Anomaly Detection via Counterfactual Augmentation and Feature Learningcited by 0

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