# Diffusion-Guided Pretraining for Brain Graph Foundation Models

arXiv: https://arxiv.org/abs/2602.09437 · HTML: https://mlsanity.com/paper/2602.09437/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 21 of its 31 references that are in the map.
- First posted on arXiv 10 Feb 2026.

## Builds on (most cited first, 21 of 21)

- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Contrastive Learning with Augmentations](https://mlsanity.com/paper/2010.13902/) (2020)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [Hypergraph Neural Networks](https://mlsanity.com/paper/1809.09401/) (2018)
- [GCC: Graph Contrastive Coding for Graph Neural Network Pre-Training](https://mlsanity.com/paper/2006.09963/) (2020)
- [GraphMAE: Self-Supervised Masked Graph Autoencoders](https://mlsanity.com/paper/2205.10803/) (2022)
- [Diffusion Improves Graph Learning](https://mlsanity.com/paper/1911.05485/) (2019)
- [GRAND: Graph Neural Diffusion](https://mlsanity.com/paper/2106.10934/) (2021)
- [Data Augmentation for Deep Graph Learning: A Survey](https://mlsanity.com/paper/2202.08235/) (2022)
- [GraphMAE2: A Decoding-Enhanced Masked Self-Supervised Graph Learner](https://mlsanity.com/paper/2304.04779/) (2023)
- [Brain Network Transformer](https://mlsanity.com/paper/2210.06681/) (2022)
- [DIFFormer: Scalable (Graph) Transformers Induced by Energy Constrained Diffusion](https://mlsanity.com/paper/2301.09474/) (2023)
- [Brain-JEPA: Brain Dynamics Foundation Model with Gradient Positioning and Spatiotemporal Masking](https://mlsanity.com/paper/2409.19407/) (2024)
- [Graph Data Augmentation for Graph Machine Learning: A Survey](https://mlsanity.com/paper/2202.08871/) (2022)
- [BrainMass: Advancing Brain Network Analysis for Diagnosis with Large-scale Self-Supervised Learning](https://mlsanity.com/paper/2403.01433/) (2024)
- [Graph Neural Networks with Adaptive Readouts](https://mlsanity.com/paper/2211.04952/) (2022)
- [Long-range Brain Graph Transformer](https://mlsanity.com/paper/2501.01100/) (2025)
- [Multi-modal Cross-domain Self-supervised Pre-training for fMRI and EEG Fusion](https://mlsanity.com/paper/2409.19130/) (2024)
- [Supercharging Graph Transformers with Advective Diffusion](https://mlsanity.com/paper/2310.06417/) (2023)

## Abstract (arXiv)

With the growing interest in foundation models for brain signals, graph-based pretraining has emerged as a promising paradigm for learning transferable representations from connectome data. However, existing contrastive and masked autoencoder methods typically rely on naive random dropping or masking for augmentation, which is ill-suited for brain graphs and hypergraphs as it disrupts semantically meaningful connectivity patterns. Moreover, commonly used graph-level readout and reconstruction schemes fail to capture global structural information, limiting the robustness of learned representations. In this work, we propose a unified diffusion-based pretraining framework that addresses both limitations. First, diffusion is designed to guide structure-aware dropping and masking strategies, preserving brain graph semantics while maintaining effective pretraining diversity. Second, diffusion enables topology-aware graph-level readout and node-level global reconstruction by allowing graph embeddings and masked nodes to aggregate information from globally related regions. Extensive experiments across multiple neuroimaging datasets with over 25,000 subjects and 60,000 scans involving various mental disorders and brain atlases demonstrate consistent performance improvements.