# MAGNET: Manifold-Aware Graph Diffusion Network for Connectome Generation

arXiv: https://arxiv.org/abs/2610.17014 · HTML: https://mlsanity.com/paper/2610.17014/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 54 of its 88 references that are in the map.
- First posted on arXiv 12 Oct 2026.

## Builds on (most cited first, 30 of 54)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [Distilling the Knowledge in a Neural Network](https://mlsanity.com/paper/1503.02531/) (2015)
- [Denoising Diffusion Implicit Models](https://mlsanity.com/paper/2010.02502/) (2020)
- [Diffusion Models Beat GANs on Image Synthesis](https://mlsanity.com/paper/2105.05233/) (2021)
- [Scalable Diffusion Models with Transformers](https://mlsanity.com/paper/2212.09748/) (2022)
- [Classifier-Free Diffusion Guidance](https://mlsanity.com/paper/2207.12598/) (2022)
- [Flow Matching for Generative Modeling](https://mlsanity.com/paper/2210.02747/) (2022)
- [Improved Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2102.09672/) (2021)
- [FiLM: Visual Reasoning with a General Conditioning Layer](https://mlsanity.com/paper/1709.07871/) (2017)
- [GLU Variants Improve Transformer](https://mlsanity.com/paper/2002.05202/) (2020)
- [Spectral Normalization for Generative Adversarial Networks](https://mlsanity.com/paper/1802.05957/) (2018)
- [Deep Sets](https://mlsanity.com/paper/1703.06114/) (2017)
- [Relational inductive biases, deep learning, and graph networks](https://mlsanity.com/paper/1806.01261/) (2018)
- [Geometric Deep Learning: Grids, Groups, Graphs, Geodesics, and Gauges](https://mlsanity.com/paper/2104.13478/) (2021)
- [Geometric deep learning: going beyond Euclidean data](https://mlsanity.com/paper/1611.08097/) (2016)
- [On Layer Normalization in the Transformer Architecture](https://mlsanity.com/paper/2002.04745/) (2020)
- [Decoupling Representation and Classifier for Long-Tailed Recognition](https://mlsanity.com/paper/1910.09217/) (2019)
- [Spectrally-normalized margin bounds for neural networks](https://mlsanity.com/paper/1706.08498/) (2017)
- [DiGress: Discrete Denoising diffusion for graph generation](https://mlsanity.com/paper/2209.14734/) (2022)
- [A systematic study of the class imbalance problem in convolutional neural networks](https://mlsanity.com/paper/1710.05381/) (2017)
- [Analog Bits: Generating Discrete Data using Diffusion Models with Self-Conditioning](https://mlsanity.com/paper/2208.04202/) (2022)
- [Invariant and Equivariant Graph Networks](https://mlsanity.com/paper/1812.09902/) (2018)
- [NIPS 2016 Tutorial: Generative Adversarial Networks](https://mlsanity.com/paper/1701.00160/) (2016)
- [Score-based Generative Modeling of Graphs via the System of Stochastic Differential Equations](https://mlsanity.com/paper/2202.02514/) (2022)
- [Query-Key Normalization for Transformers](https://mlsanity.com/paper/2010.04245/) (2020)
- [Applying Guidance in a Limited Interval Improves Sample and Distribution Quality in Diffusion Models](https://mlsanity.com/paper/2404.07724/) (2024)
- [What is the Effect of Importance Weighting in Deep Learning?](https://mlsanity.com/paper/1812.03372/) (2018)
- [Riemannian Score-Based Generative Modelling](https://mlsanity.com/paper/2202.02763/) (2022)
- [How Faithful is your Synthetic Data? Sample-level Metrics for Evaluating and Auditing Generative Models](https://mlsanity.com/paper/2102.08921/) (2021)

## Abstract (arXiv)

Functional brain connectome represents neural connectivity as a matrix of pairwise interactions between brain regions. Generation of functional connectomes is not only a question of validity; rather, having satisfied the constraints on the correlation matrix, the next step is to recover the class-conditional geometry buried under coarse labels. We propose MAGNET, a Manifold-Aware Graph Diffusion Network which uses a normalized-Cholesky representation of the manifold of correlation matrices that guarantees validity. MAGNET lifts noisy latent states into ROI-level region tokens and performs denoising with a relational inductive bias over brain atlas regions. To deal with structural problems induced by coarse labels, MAGNET employs class-anchored conditioning, amortized structural bridge, and relevance-preserving corruption. Across ABIDE, ADNI, and OASIS-3, MAGNET consistently achieves favorable results compared to previous manifold-aware approaches, demonstrating improvements of 7-21% in class-conditional fidelity (α,β-F1) across three cohorts and better sampling efficiency. Moreover, while training only with strict binary labels, MAGNET is capable of maintaining clinical heterogeneity through fine substructure of the connectomes in a zero-shot setting, improving subclass covariance alignment (λ-MSE) by over 30%. These results suggest that geometric validity is a necessary but insufficient condition for clinical utility in connectome synthesis. Moreover, efforts in making the diffusion denoising class-conditional manifold aware finds utility beyond the highly curved brain connectome generation as this is a critical problem in various general settings. The code repository can be found at https://github.com/protyayofficial/MAGNET.