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Awesome-Graph-Neural-Networks-for-Brain-Graph-Learning

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🔥🔥 This is a collection of awesome papers about graph neural networks for brain graph learning, datasets and tools.

Contents

The framework of brain graph learning based on GNNs

framework

Surveys

Paper Title Venue Year Code
Benchmarking Graph Neural Networks for FMRI analysis Arxiv 2022 [Code]
Graph neural networks for image‐guided disease diagnosis: A review iRADIOLOGY 2023 -
NeuroGraph: Benchmarks for Graph Machine Learning in Brain Connectomics Arxiv 2023 [Code]
GNN4EEG: A Benchmark and Toolkit for Electroencephalography Classification with Graph Neural Network Arxiv 2023 [Code]
A Survey of EEG Analysis based on Graph Neural Network CECIT Conference 2021 -
BrainGB: A Benchmark for Brain Network Analysis With Graph Neural Networks IEEE TMI 2022 [Code]
Graph Neural Networks and Their Current Applications in Bioinformatics Frontiers in genetics 2021 -
Graph Neural Networks in Network Neuroscience IEEE TPAMI 2022 -

The toy example of different types of brain graph generated

brain

Prediction-Based Static Brain Graph Learning

Paper Title Venue Year Model Code
EEG-Based Graph Neural Network Classification of Alzheimer’s Disease: An Empirical Evaluation of Functional Connectivity Methods IEEE TNSRE 2022 - -
Effective and Interpretable fMRI Analysis via Functional Brain Network Generation ICML Workshop 2021 - -
Multi-Level Graph Neural Network With Sparsity Pooling for Recognizing Parkinson’s Disease IEEE TNSRE 2023 SparsityATopK -
Balanced Graph Structure Information for Brain Disease Detection PKAW 2023 Bargrain -
Brain network classification based on dynamic graph attention information bottleneck Comput. Meth. Programs Biomed. 2024 DGAIB -
TRANSFORMER-BASED HIERARCHICAL CLUSTERING FOR BRAIN NETWORK ANALYSIS ISBI 2023 THC -
Graph Neural Network based Alzheimer’s Disease Classification using Structural Brain Network ICTer 2022 -
GRAPH CONVOLUTIONAL NEURAL NETWORKS FOR ALZHEIMER’S DISEASE CLASSIFICATION ISBI 2019 GCNN -
TSEN: TRANSFORMER AND SNOWBALL GRAPH CONVOLUTION LEARNING FOR BRAIN FUNCTIONAL NETWORK CLASSIFICATION Arxiv 2023 TSEN [Code]
GNEA: A Graph Neural Network with ELM Aggregator for Brain Network Classification Complexity Journal 2020 GNEA -
Hi-GCN: A hierarchical graph convolution network for graph embedding learning of brain network and brain disorders prediction Comput. Biol. Med. 2020 Hi-GCN [Code]
A Graph Attention Neural Network for Diagnosing ASD with fMRI Data BIBM 2021 - -
BrainMixup: Data Augmentation for GNN-based Functional Brain Network Analysis Big Data 2022 - -
BRAIN NETWORK TRANSFORMER NeurIPS 2022 BRAINNETTF [Code]
BrainVGAE: End-to-End Graph Neural Networks for Noisy fMRI Dataset BIBM 2022 - -
Classification of First-Episode Schizophrenia, Chronic Schizophrenia and Healthy Control Based on Brain Network of Mismatch Negativity by Graph Neural Network TNSRE 2021 - -
Deep reinforcement learning guided graph neural networks for brain network analysis Neural Networks 2022 BN-GNN [Code]
EEG-GNN: Graph Neural Networks for Classification of Electroencephalogram (EEG) Signals EMBC 2021 - -
PTGB: Pre-Train Graph Neural Networks for Brain Network Analysis CHIL 2023 PTGB [Code]
Data-Efficient Brain Connectome Analysis via Multi-Task Meta-Learning KDD 2022 MML [Code]
Population Graph GNNs for Brain Age Prediction ICML Workshop 2020 - [Code]

Interpretation-Based Static Brain Graph Learning

Paper Title Venue Year Model Code
An Interpretable Brain Graph Contrastive Learning Framework for Brain Disorder Analysis WSDM 2024 BraGCL [Code]
Knowledge Distillation Guided Interpretable Brain Subgraph Neural Networks for Brain Disorder Exploration (early accept) TNNLS 2024 - [Code]
TOWARDS A MORE STABLE AND GENERAL SUBGRAPH INFORMATION BOTTLENECK ICASSP 2023 - [Code]
Deep dag learning of effective brain connectivity for fmri analysis ISBI 2023 DABNet -
GAT LI: a graph attention network based learning and interpreting method for functional brain network classification BMC Bioinformatics 2021 GAT-LI -
Pooling Regularized Graph Neural Network for fMRI Biomarker Analysis MICCAI 2020 PR-GNN -
Investigating Brain Connectivity with Graph Neural Networks and GNNExplainer ICPR 2022 - -
Interpretable Graph Neural Networks for Connectome-Based Brain Disorder Analysis MICCAI 2022 IBGNN [Code]
Adaptive Gated Graph Convolutional Network for Explainable Diagnosis of Alzheimer’s Disease using EEG Data Arxiv 2023 AGGCN -
Interpretable Sparsification of Brain Graphs: Better Practices and Effective Designs for Graph Neural Networks KDD 2023 IGS [Code]
Contrastive Graph Pooling for Explainable Classification of Brain Networks Arxiv 2023 ContrastPool -
Brain Networks and Intelligence: A Graph Neural Network Based Approach to Resting State fMRI Data Arxiv 2023 BrainRGIN [Code]
Classification of Brain Disorders in rs-fMRI via Local-to-Global Graph Neural Networks TMI 2023 LG-GNN [Code]
Dementia analysis from functional connectivity network with graph neural networks IPM 2022 - -
Graph Neural Network for Interpreting Task-fMRI Biomarkers MICCAI 2019 t-fMRI -
Community-Aware Transformer for Autism Prediction in fMRI Connectome MICCAI 2023 Com-BrainTF [Code]
FC–HAT: Hypergraph attention network for functional brain network classification Information Sciences 2022 FC–HAT [Code]
BrainGNN: Interpretable Brain Graph Neural Network for fMRI Analysis Med. Image Anal. 2021 BrainGNN [Code]
BrainIB: Interpretable Brain Network-based Psychiatric Diagnosis with Graph Information Bottleneck Arxiv 2023 BrainIB -
FBNetGen: Task-aware GNN-based fMRI Analysis via Functional Brain Network Generation MIDL 2022 FBNetGen [Code]
BRAINNPT: PRE-TRAINING TRANSFORMER NETWORKS FOR BRAIN FUNCTIONAL NETWORK CLASSIFICATION Arxiv 2023 BrainNPT -

Prediction-Based Dynamic Brain Graph Learning

Paper Title Venue Year Model Code
Multi-Scale Dynamic Graph Learning for Brain Disorder Detection With Functional MRI IEEE TNSRE 2023 MDGL -
Modeling spatio-temporal patterns of holistic functional brain networks via multi-head guided attention graph neural networks Med. Image Anal. 2022 Multi-Head GAGNN [Code]
Spatio-Temporal Graph Convolution for Resting-State fMRI Analysis MICCAI 2020 STGCN [Code]

Interpretation-Based Dynamic Brain Graph Learning

Paper Title Venue Year Model Code
Explainable fMRI-based brain decoding via spatial temporal-pyramid graph convolutional network Hum. Brain Mapp. 2023 STpGCN -
HDGL: A HIERARCHICAL DYNAMIC GRAPH REPRESENTATION LEARNING MODEL FOR BRAIN DISORDER CLASSIFICATION Arxiv 2023 HDGL -

Prediction-Based Multi-Modal Brain Graph Learning

Paper Title Venue Year Model Code
Multi-View Multi-Graph Embedding for Brain Network Clustering Analysis AAAI 2018 M2E [Code]
Brain multigraph prediction using topology-aware adversarial graph neural Med. Image Anal. 2021 TopoGAN [Code]
Community-preserving Graph Convolutions for Structural and Functional Joint Embedding of Brain Networks Big Data 2019 SCP-GCN -
Heterogeneous Graph-Based Multimodal Brain Network Learning Arxiv 2021 HebrainGNN [Code]
Joint Embedding of Structural and Functional Brain Networks with Graph Neural Networks for Mental Illness Diagnosis EMBC 2022 BrainNN -
Multi-Modal Graph Learning for Disease Prediction TMI 2022 MMGL [Code]
Multi-Modal Non-Euclidean Brain Network Analysis With Community Detection and Convolutional Autoencoder TETCI 2022 M2CDCA -
Multiplex Graph Networks for Multimodal Brain Network Analysis Arxiv 2021 MGNet [Code]
Multi-View Brain Network Analysis with Cross-View Missing Network Generation BIBM 2022 GroGen [Code]
Multi-view Graph Embedding with Hub Detection for Brain Network Analysis ICDM 2017 MVGE-HD -
Multi-View Tensor Graph Neural Networks Through Reinforced Aggregation TKDE 2023 RTGNN [Code]
Overlapping Community Detection in Multi view Brain Network BIBM 2018 oComm -

Interpretation-Based Multi-Modal Brain Graph Learning

Paper Title Venue Year Model Code
Autistic Spectrum Disorders Diagnose with Graph Neural Networks MM 2023 - -
A graph neural network framework for causal inference in brain networks Scientific Reports 2021 DCRNN -
Multimodal Triplet Attention Network for Brain Disease Diagnosis TMI 2022 - -
Multimodal graph coarsening for interpretable, MRI-based brain graph neural network MLSP Workshop 2021 MM-GNN -
MSTGC: Multi-Channel Spatio-Temporal Graph Convolution Network for Multi-Modal Brain Networks Fusion TNSRE 2023 MSTGC -
Mapping Multi-modal Brain Connectome for Brain Disorder Diagnosis via Cross-modal Mutual Learning TMI 2023 Cross-GNN -
Interpretable graph convolutional network of multi-modality brain imaging for alzheimer's disease diagnosis ISBI 2022 - -
Multimodal Brain Connectomics-Based Prediction of Parkinson’s Disease Using Graph Attention Networks Frontiers in genetics 2022 - -
Deep Representation Learning for Multimodal Brain Networks MICCAI 2020 DMBN -
BraceNet: Graph-Embedded Neural Network for Brain Network Analysis Big Data 2022 BraceNet -
Multi-modal Graph Neural Network for Early Diagnosis of Alzheimer's Disease from sMRI and PET Scans Comput. Biol. Med. 2023 - -

Brain Neuroimaging Datasets

Dataset Data Source Modality Type Data Link
ABIDE Autism Spectrum Disorder fMRI [Link]
ADNI Alzheimer Disorder fMRI, PET [Link]
PPMI Parkinson Disorder fMRI [Link]
HIV Human Immunodeficiency Virus Disorder fMRI, DTI -
BP Bipolar Disorder fMRI, DTI -
HCP Human Connectome Project fMRI [Link]
ABCD Adolescent Brain Cognitive Development Study fMRI [Link]
ADHD Attention Deficit Hyperactivity Disorder fMRI -
Biopoint Autism Spectrum Disorder fMRI -
HIV Human Immunodeficiency Virus Disorder fMRI, DTI -
UKB The United Kingdom Biobank fMRI [Link]
NCANDA The national consortium on alcohol and neurodevelopment in adolescence fMRI -
PNC Philadelphia Neuroimaging Cohort fMRI [Link]

Brain Graph Analysis Tools

fMRI Preprocessing Tools

DTI Preprocessing Tools

Disclaimer

If you have any inquiries or updates regarding brain graph learning with GNNs, please do not hesitate to contact us. We also extend an invitation to researchers interested in brain graph learning with GNNs to join this project as contributors and contribute to advancing research in this field.

Emails: xuexiong.luo@hdr.mq.edu.au, jia.wu@mq.edu.au.