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

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

Contents

• Surveys
• Prediction-Based Static Brain Graph Learning
• Interpretation-Based Static Brain Graph Learning
• Prediction-Based Dynamic Brain Graph Learning
• Interpretation-Based Dynamic Brain Graph Learning
• Prediction-Based Multi-Modal Brain Graph Learning
• Interpretation-Based Multi-Modal Brain Graph Learning
• Brain Neuroimaging Datasets
• Brain Graph Analysis Tools

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The framework of brain graph learning based on GNNs

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	-

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The toy example of different types of brain graph generated

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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]

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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	-

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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]

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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	-

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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	-

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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	-	-

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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]

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Brain Graph Analysis Tools

fMRI Preprocessing Tools

• SPM https://www.fil.ion.ucl.ac.uk/spm/software/spm12
• AFNI https://afni.nimh.nih.gov
• FSL https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL
• FreeSurfer https://surfer.nmr.mgh.harvard.edu
• CONN https://web.conn-toolbox.org/home
• Nilearn https://nilearn.github.io/stable/index.html

DTI Preprocessing Tools

• AFNI https://afni.nimh.nih.gov
• FSL https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL
• DSI Studio https://dsi-studio.labsolver.org
• MRtrix3 https://www.mrtrix.org/

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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.