Graph Neural Networks in Network Neuroscience

In Geometric Deep Learning (GDL), one of the most popular learning methods is the Graph Neural Network (GNN), which applies convolutional layers to learn the topological structure of the input graph. GNNs have recently been used for the analysis of different types of the human connectome, such as structural, functional, and morphological networks derived respectively from Diffusion Tensor Imaging (DTI), functional magnetic resonance imaging (fMRI), and T1-w MRI data. Such a nascent field has achieved significant performance improvements over traditional deep neural networks in the early diagnosis of brain disorders. Thus, we list here all MICCAI papers of 4 years (2017-2020), some journals, and IPMI (2017-2019) papers focusing on different learning tasks:

• Predicting one or multiple modalities from a single or different modalities (e.g., data synthesis)
• Predicting high-resolution data from low-resolution data
• Predicting the brain evolution trajectory
• Population network integration and fusion
• Computer-aided prognostic methods (e.g., for brain diseases)
• Biomarker identification
• Extra works related to machine learning

If you like to update the file by adding the unlisted open-source articles, feel free to open an issue or submit a pull requests. You can also directly contact Alaa Bessadok at alaa.bessadok@gmail.com. All contributions are very welcome!

arXiv link

The full paper is downloadable at https://arxiv.org/pdf/2106.03535.pdf

Cross-domain graph prediction

Single graph prediction

Title	Paper	Author	Dataset	Code	Youtube Video	Proceeding/Journal/Year
Recovering Brain Structural Connectivity from Functional Connectivity via Multi-GCN Based Generative Adversarial Network	LNCS	Lu Zhang	HCP	__	__	MICCAI 2020
Topology-Guided Cyclic Brain Connectivity Generation using Geometric Deep Learning	ScienceDirect	Abubakhari Sserwadda	ABIDE	Python	__	Journal of Neuroscience Methods 2020
Deep Representation Learning for Multimodal Brain Networks	ARXIV	Wen Zhang	WU-Minn HCP	__	__	MICCAI 2020
Symmetric Dual Adversarial Connectomic Domain Alignment for Predicting Isomorphic Brain Graph from a Baseline Graph	LNCS	Alaa Bessadok	ABIDE	__	__	MICCAI 2019
Hierarchical Adversarial Connectomic Domain Alignment for Target Brain Graph Prediction and Classification from a Source Graph	LNCS	Alaa Bessadok	ABIDE	Python	14min	PRIME-MICCAI 2019
Brain graph synthesis by dual adversarial domain alignment and target graph prediction from a source graph	LNCS	Alaa Bessadok	ABIDE	__	__	Medical Image Analysis Journal 2021

Multi-graph prediction

Title	Paper	Author	Dataset	Code	Youtube Video	Proceeding/Journal/Year
Topology-Aware Generative Adversarial Network for Joint Prediction of Multiple Brain Graphs from a Single Brain Graph	ARXIV	Alaa Bessadok	ABIDE	Python	10min	MICCAI 2020

Cross-resolution graph prediction

Title	Paper	Author	Dataset	Code	Youtube Video	Proceeding/Journal/Year
GSR-Net: Graph Super-Resolution Network for Predicting High-Resolution from Low-Resolution Functional Brain Connectomes	ARXIV	Megi Isallari	Southwest University Longitudinal Imaging Multimodal (SLIM) study	Python	11min	MLMI-MICCAI 2020

Cross-time graph prediction

Title	Paper	Author	Dataset	Code	Youtube Video	Proceeding/Journal/Year
Deep EvoGraphNet Architecture for Time-Dependent Brain Graph Data Synthesis from a Single Timepoint	ARXIV	Ahmed Nebli	OASIS-2	Python	6min	PRIME-MICCAI 2020
Residual Embedding Similarity-Based Network Selection for Predicting Brain Network Evolution Trajectory from a Single Observation	ARXIV	Ahmet Serkan Goktas	ADNI GO	Python	6min	PRIME-MICCAI 2020
Foreseeing Brain Graph Evolution over Time Using Deep Adversarial Network Normalizer	ARXIV	Zeynep Gurler	OASIS-2	Python	6min	PRIME-MICCAI 2020

Integration/Fusion

Title	Paper	Author	Dataset	Code	Youtube Video	Proceeding/Journal/Year
Deep Graph Normalizer: A Geometric Deep Learning Approach for Estimating Connectional Brain Templates	LNCS	Mustafa Burak Gurbuz	ADNI ABIDE	Python	10min	MICCAI 2020
Clustering-Based Deep Brain MultiGraph Integrator Network for Learning Connectional Brain Templates	LNCS	Uğur Demir	ABIDE	Python	__	GRAIL-MICCAI 2020

Brain graph classification

Graph embedding-based methods

Title	Paper	Author	Dataset	Code	Youtube Video	Proceeding/Journal/Year
Multi-view Brain HyperConnectome AutoEncoder for Brain State Classification	LNCS	Alin Banka	ADNI GO	Python	6min	PRIME-MICCAI 2020
Adversarial Connectome Embedding for Mild Cognitive Impairment Identification Using Cortical Morphological Networks	LNCS	Alin Banka	ADNI GO	__	__	CIN-MICCAI 2019
Deep Hypergraph U-Net for Brain Graph Embedding and Classification	ARXIV	Mert Lostar	ADNI GO	Python	__	2020
Interpretable Multimodality Embedding of Cerebral Cortex Using Attention Graph Network for Identifying Bipolar Disorder	LNCS	Huzheng Yang	__	__	__	MICCAI 2019
New Graph-Blind Convolutional Network for Brain Connectome Data Analysis	LNCS	Yanfu Zhang	HCP	__	__	IPMI 2019
Attention-Diffusion-Bilinear Neural Network for Brain Network Analysis	PubMed	Jiashuang Huang	Epilepsy dataset	__	__	IEEE Transactions on Medical Imaging 2020

Graph-based methods

Title	Paper	Author	Dataset	Code	Youtube Video	Proceeding/Journal/Year
Metric learning with spectral graph convolutions on brain connectivity networks	ScienceDirect	Sofia Ira Ktena	ABIDE [UK Biobank]	Python	__	Neuroimage Journal 2018
Dynamic Spectral Graph Convolution Networks with Assistant Task Training for Early MCI Diagnosis	LNCS	Xiaodan Xing	ADNI2	__	__	MICCAI 2019
A Cascaded Multi-modality Analysis in Mild Cognitive Impairment	LNCS	Lu Zhang	ADNI 3	__	__	MLMI-MICCAI 2019
DS-GCNs: Connectome Classification Using Dynamic Spectral Graph Convolution Networks with Assistant Task Training	ARXIV	Xiaodan Xing	ABIDE	__	__	Cerebral Cortex 2021
Multi-Hops Functional Connectivity Improves Individual Prediction of Fusiform Face Activation via a Graph Neural Network	Journal website	Dongya Wu	HCP	__	__	Frontiers in Neuroscience 2021

Population-based methods

Title	Paper	Author	Dataset	Code	Youtube Video	Proceeding/Journal/Year
Integrating Similarity Awareness and Adaptive Calibration in Graph Convolution Network to Predict Disease	LNCS	Xuegang Song	ADNI	__	__	MICCAI 2020
Spectral Graph Convolutions for Population-Based Disease Prediction	ARXIV	Sarah Parisot	ADNI ABIDE	Python	__	MICCAI 2017
InceptionGCN: Receptive Field Aware Graph Convolutional Network for Disease Prediction	ARXIV	Anees Kazi	ABIDE TADPOLE	__	__	IPMI 2019

Biomarker identification

Title	Paper	Author	Dataset	Code	Youtube Video	Proceeding/Journal/Year
Graph Neural Network for Interpreting Task-fMRI Biomarkers	ARXIV	Xiaoxiao Li	UNC/UMN Baby Connectome Project	[Yale Child Study Center]	__	MICCAI 2019
Pooling Regularized Graph Neural Network for fMRI Biomarker Analysis	ARXIV	Xiaoxiao Li	multi-modal epilepsy dataset	__	__	MICCAI 2020
Interpretable Multimodality Embedding of Cerebral Cortex Using Attention Graph Network for Identifying Bipolar Disorder	LNCS	Huzheng Yang	__	__	__	MICCAI 2019
BrainGNN: Interpretable Brain Graph NeuralNetwork for fMRI Analysis	bioRxiv	Xiaoxiao Li	Biopoint HCP	__	__	bioRxiv 2020

Machine Learning and other types of algorithm for Network Neuroscience

Single/Multi-view prediction

Title	Paper	Author	Dataset	Code	Youtube Video	Proceeding/Journal/Year
Multi-view Brain Network Prediction from a Source View Using Sample Selection via CCA-Based Multi-kernel Connectomic Manifold Learning	LNCS	Minghui Zhu	ABIDE	__	__	PRIME-MICCAI 2018

Integration/Fusion

Title	Paper	Author	Dataset	Code	Youtube Video	Proceeding/Journal/Year
Supervised Multi-topology Network Cross-Diffusion for Population-Driven Brain Network Atlas Estimation	ARXIV	Islem Mhiri	ABIDE	Python MATLAB	10min	MICCAI 2020
Multi-scale Profiling of Brain Multigraphs by Eigen-Based Cross-diffusion and Heat Tracing for Brain State Profiling	ARXIV	Mustafa Saglam	ABIDE	__	8min	GRAIL-MICCAI 2020
Estimation of Brain Network Atlases UsingDiffusive-Shrinking Graphs:Application to Developing Brains	LNCS	Islem Rekik	UNC/UMN Baby Connectome dataset	__	__	IPMI 2017

Resolution

Title	Paper	Author	Dataset	Code	Youtube Video	Proceeding/Journal/Year
Predicting High-Resolution Brain Networks Using Hierarchically Embedded and Aligned Multi-resolution Neighborhoods	LNCS	Kübra Cengiz	ABIDE	__	__	PRIME-MICCAI 2019

Time-dependent

Title	Paper	Author	Dataset	Code	Youtube Video	Proceeding/Journal/Year
Progressive Infant Brain Connectivity Evolution Prediction from Neonatal MRI Using Bidirectionally Supervised Sample Selection	LNCS	Olfa Ghribi	__	__	__	MICCAI 2019
Learning-Guided Infinite Network Atlas Selection for Predicting Longitudinal Brain Network Evolution from a Single Observation	LNCS	Baha Eddine Ezzine	ADNI GO	__	__	MICCAI 2019

Disease classification

Title	Paper	Author	Dataset	Code	Youtube Video	Proceeding/Journal/Year
Graph Morphology-Based Genetic Algorithm for Classifying Late Dementia States	LNCS	Oumaima Ben Khelifa	__	__	__	CNI-MICCAI 2019
Joint Correlational and Discriminative Ensemble Classifier Learning for Dementia Stratification Using Shallow Brain Multiplexes	LNCS	Rory Raeper	ABIDE	__	__	PRIME-MICCAI 2018

Other predictions

Title	Paper	Author	Dataset	Code	Youtube Video	Proceeding/Journal/Year
Predicting Emotional Intelligence Scores from Multi-session Functional Brain Connectomes	LNCS	Anna Lisowska	SLIM	__	__	PRIME-MICCAI 2018

Please cite the following paper when using our work:

@article{bessadok2022graph,
  title={Graph neural networks in network neuroscience},
  author={Bessadok, Alaa and Mahjoub, Mohamed Ali and Rekik, Islem},
  journal={IEEE Transactions on Pattern Analysis and Machine Intelligence},
  year={2022},
  publisher={IEEE}
}