# A Comparative Study of Graph Neural Networks for Shape Classification in Neuroimaging

arXiv: https://arxiv.org/abs/2210.16670 · HTML: https://mlsanity.com/paper/2210.16670/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 16 of its 38 references that are in the map.
- First posted on arXiv 29 Oct 2022.

## Builds on (most cited first, 16 of 16)

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [A Comprehensive Survey on Graph Neural Networks](https://mlsanity.com/paper/1901.00596/) (2019)
- [Graph Neural Networks: A Review of Methods and Applications](https://mlsanity.com/paper/1812.08434/) (2018)
- [Relational inductive biases, deep learning, and graph networks](https://mlsanity.com/paper/1806.01261/) (2018)
- [Energy and Policy Considerations for Deep Learning in NLP](https://mlsanity.com/paper/1906.02243/) (2019)
- [Geometric Deep Learning: Grids, Groups, Graphs, Geodesics, and Gauges](https://mlsanity.com/paper/2104.13478/) (2021)
- [Weisfeiler and Leman Go Neural: Higher-order Graph Neural Networks](https://mlsanity.com/paper/1810.02244/) (2018)
- [DropEdge: Towards Deep Graph Convolutional Networks on Node Classification](https://mlsanity.com/paper/1907.10903/) (2019)
- [Measuring and Relieving the Over-smoothing Problem for Graph Neural Networks from the Topological View](https://mlsanity.com/paper/1909.03211/) (2019)
- [SplineCNN: Fast Geometric Deep Learning with Continuous B-Spline Kernels](https://mlsanity.com/paper/1711.08920/) (2017)
- [Data Augmentation for Deep Graph Learning: A Survey](https://mlsanity.com/paper/2202.08235/) (2022)
- [Learning Dynamic Graph Representation of Brain Connectome with Spatio-Temporal Attention](https://mlsanity.com/paper/2105.13495/) (2021)
- [Learning Graph-Level Representation for Drug Discovery](https://mlsanity.com/paper/1709.03741/) (2017)
- [Data Augmentation for Graph Classification](https://mlsanity.com/paper/2009.09863/) (2020)

## Built on by (most cited first, 3 of 3)

- [The Importance of Model Inspection for Better Understanding Performance Characteristics of Graph Neural Networks](https://mlsanity.com/paper/2405.01270/) (2024)
- [Attention Maps in 3D Shape Classification for Dental Stage Estimation with Class Node Graph Attention Networks](https://mlsanity.com/paper/2509.07581/) (2025)
- [Spectral Vision Transformer for Efficient Tokenization with Limited Data](https://mlsanity.com/paper/2605.12026/) (2026)

## Abstract (arXiv)

Graph neural networks have emerged as a promising approach for the analysis of non-Euclidean data such as meshes. In medical imaging, mesh-like data plays an important role for modelling anatomical structures, and shape classification can be used in computer aided diagnosis and disease detection. However, with a plethora of options, the best architectural choices for medical shape analysis using GNNs remain unclear. We conduct a comparative analysis to provide practitioners with an overview of the current state-of-the-art in geometric deep learning for shape classification in neuroimaging. Using biological sex classification as a proof-of-concept task, we find that using FPFH as node features substantially improves GNN performance and generalisation to out-of-distribution data; we compare the performance of three alternative convolutional layers; and we reinforce the importance of data augmentation for graph based learning. We then confirm these results hold for a clinically relevant task, using the classification of Alzheimer's disease.