/GNNs-in-Network-Neuroscience

A review of papers proposing novel GNN methods with application to brain connectivity published in 2017-2020.

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:

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}
}