# PTGB: Pre-Train Graph Neural Networks for Brain Network Analysis

arXiv: https://arxiv.org/abs/2305.14376 · HTML: https://mlsanity.com/paper/2305.14376/

## Key facts

- Cited by 10 papers in the map (data through 14 Oct 2026).
- Builds on 62 of its 100 references that are in the map.
- First posted on arXiv 20 May 2023.

## Builds on (most cited first, 30 of 62)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Momentum Contrast for Unsupervised Visual Representation Learning](https://mlsanity.com/paper/1911.05722/) (2019)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [SGDR: Stochastic Gradient Descent with Warm Restarts](https://mlsanity.com/paper/1608.03983/) (2016)
- [Model-Agnostic Meta-Learning for Fast Adaptation of Deep Networks](https://mlsanity.com/paper/1703.03400/) (2017)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [BLIP: Bootstrapping Language-Image Pre-training for Unified Vision-Language Understanding and Generation](https://mlsanity.com/paper/2201.12086/) (2022)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [node2vec: Scalable Feature Learning for Networks](https://mlsanity.com/paper/1607.00653/) (2016)
- [Barlow Twins: Self-Supervised Learning via Redundancy Reduction](https://mlsanity.com/paper/2103.03230/) (2021)
- [Modeling Relational Data with Graph Convolutional Networks](https://mlsanity.com/paper/1703.06103/) (2017)
- [DeepWalk: Online Learning of Social Representations](https://mlsanity.com/paper/1403.6652/) (2014)
- [Variational Graph Auto-Encoders](https://mlsanity.com/paper/1611.07308/) (2016)
- [Learning deep representations by mutual information estimation and maximization](https://mlsanity.com/paper/1808.06670/) (2018)
- [Graph Contrastive Learning with Augmentations](https://mlsanity.com/paper/2010.13902/) (2020)
- [Deep Graph Infomax](https://mlsanity.com/paper/1809.10341/) (2018)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [Hierarchical Graph Representation Learning with Differentiable Pooling](https://mlsanity.com/paper/1806.08804/) (2018)
- [GNNExplainer: Generating Explanations for Graph Neural Networks](https://mlsanity.com/paper/1903.03894/) (2019)
- [FILIP: Fine-grained Interactive Language-Image Pre-Training](https://mlsanity.com/paper/2111.07783/) (2021)
- [Graph Contrastive Learning with Adaptive Augmentation](https://mlsanity.com/paper/2010.14945/) (2020)
- [GCC: Graph Contrastive Coding for Graph Neural Network Pre-Training](https://mlsanity.com/paper/2006.09963/) (2020)
- [InfoGraph: Unsupervised and Semi-supervised Graph-Level Representation Learning via Mutual Information Maximization](https://mlsanity.com/paper/1908.01000/) (2019)
- [Parameterized Explainer for Graph Neural Network](https://mlsanity.com/paper/2011.04573/) (2020)

## Built on by (most cited first, 10 of 10)

- [Graph Neural Networks for Brain Graph Learning: A Survey](https://mlsanity.com/paper/2406.02594/) (2024)
- [R-Mixup: Riemannian Mixup for Biological Networks](https://mlsanity.com/paper/2306.02532/) (2023)
- [Weakly-Supervised Scientific Document Classification via Retrieval-Augmented Multi-Stage Training](https://mlsanity.com/paper/2306.07193/) (2023)
- [RSEA-MVGNN: Multi-View Graph Neural Network with Reliable Structural Enhancement and Aggregation](https://mlsanity.com/paper/2408.07331/) (2024)
- [NeuroMambaLLM: Dynamic Graph Learning of fMRI Functional Connectivity in Autistic Brains Using Mamba and Language Model Reasoning](https://mlsanity.com/paper/2602.13770/) (2026)
- [Exploring Graph Mamba: A Comprehensive Survey on State-Space Models for Graph Learning](https://mlsanity.com/paper/2412.18322/) (2024)
- [A Survey of Cross-domain Graph Learning: Progress and Future Directions](https://mlsanity.com/paper/2503.11086/) (2025)
- [A Note on Graphon-Signal Analysis of Graph Neural Networks](https://mlsanity.com/paper/2508.18564/) (2025)
- [FCN-LLM: Empower LLM for Brain Functional Connectivity Network Understanding via Graph-level Multi-task Instruction Tuning](https://mlsanity.com/paper/2603.01135/) (2026)
- [Toward a Multi-View Brain Network Foundation Model: Cross-View Consistency Learning Across Arbitrary Atlases](https://mlsanity.com/paper/2603.20348/) (2026)

## Abstract (arXiv)

The human brain is the central hub of the neurobiological system, controlling behavior and cognition in complex ways. Recent advances in neuroscience and neuroimaging analysis have shown a growing interest in the interactions between brain regions of interest (ROIs) and their impact on neural development and disorder diagnosis. As a powerful deep model for analyzing graph-structured data, Graph Neural Networks (GNNs) have been applied for brain network analysis. However, training deep models requires large amounts of labeled data, which is often scarce in brain network datasets due to the complexities of data acquisition and sharing restrictions. To make the most out of available training data, we propose PTGB, a GNN pre-training framework that captures intrinsic brain network structures, regardless of clinical outcomes, and is easily adaptable to various downstream tasks. PTGB comprises two key components: (1) an unsupervised pre-training technique designed specifically for brain networks, which enables learning from large-scale datasets without task-specific labels; (2) a data-driven parcellation atlas mapping pipeline that facilitates knowledge transfer across datasets with different ROI systems. Extensive evaluations using various GNN models have demonstrated the robust and superior performance of PTGB compared to baseline methods.