# Structural Connectome Harmonization Using Deep Learning: The Strength of Graph Neural Networks

arXiv: https://arxiv.org/abs/2507.13992 · HTML: https://mlsanity.com/paper/2507.13992/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 13 of its 58 references that are in the map.
- First posted on arXiv 18 Jul 2025.

## Builds on (most cited first, 13 of 13)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift](https://mlsanity.com/paper/1502.03167/) (2015)
- [A Style-Based Generator Architecture for Generative Adversarial Networks](https://mlsanity.com/paper/1812.04948/) (2018)
- [mixup: Beyond Empirical Risk Minimization](https://mlsanity.com/paper/1710.09412/) (2017)
- [Domain-Adversarial Training of Neural Networks](https://mlsanity.com/paper/1505.07818/) (2015)
- [Unsupervised Domain Adaptation by Backpropagation](https://mlsanity.com/paper/1409.7495/) (2014)
- [StarGAN: Unified Generative Adversarial Networks for Multi-Domain Image-to-Image Translation](https://mlsanity.com/paper/1711.09020/) (2017)
- [Distance Metric Learning using Graph Convolutional Networks: Application to Functional Brain Networks](https://mlsanity.com/paper/1703.02161/) (2017)
- [Graph Edge Convolutional Neural Networks for Skeleton Based Action Recognition](https://mlsanity.com/paper/1805.06184/) (2018)
- [ImUnity: a generalizable VAE-GAN solution for multicenter MR image harmonization](https://mlsanity.com/paper/2109.06756/) (2021)
- [Deep Graph Translation](https://mlsanity.com/paper/1805.09980/) (2018)
- [Brain Graph Super-Resolution Using Adversarial Graph Neural Network with Application to Functional Brain Connectivity](https://mlsanity.com/paper/2105.00425/) (2021)
- [IGUANe: a 3D generalizable CycleGAN for multicenter harmonization of brain MR images](https://mlsanity.com/paper/2402.03227/) (2024)

## Built on by (most cited first, 1 of 1)

- [Unsupervised learning of acquisition variability in structural connectomes via hybrid latent space modeling](https://mlsanity.com/paper/2605.13933/) (2026)

## Abstract (arXiv)

Small sample sizes in neuroimaging in general, and in structural connectome (SC) studies in particular limit the development of reliable biomarkers for neurological and psychiatric disorders - such as Alzheimer's disease and schizophrenia - by reducing statistical power, reliability, and generalizability. Large-scale multi-site studies have exist, but they have acquisition-related biases due to scanner heterogeneity, compromising imaging consistency and downstream analyses. While existing SC harmonization methods - such as linear regression (LR), ComBat, and deep learning techniques - mitigate these biases, they often rely on detailed metadata, traveling subjects (TS), or overlook the graph-topology of SCs. To address these limitations, we propose a site-conditioned deep harmonization framework that harmonizes SCs across diverse acquisition sites without requiring metadata or TS that we test in a simulated scenario based on the Human Connectome Dataset. Within this framework, we benchmark three deep architectures - a fully connected autoencoder (AE), a convolutional AE, and a graph convolutional AE - against a top-performing LR baseline. While non-graph models excel in edge-weight prediction and edge existence detection, the graph AE demonstrates superior preservation of topological structure and subject-level individuality, as reflected by graph metrics and fingerprinting accuracy, respectively. Although the LR baseline achieves the highest numerical performance by explicitly modeling acquisition parameters, it lacks applicability to real-world multi-site use cases as detailed acquisition metadata is often unavailable. Our results highlight the critical role of model architecture in SC harmonization performance and demonstrate that graph-based approaches are particularly well-suited for structure-aware, domain-generalizable SC harmonization in large-scale multi-site SC studies.