# Self-Supervised Graph Representation Learning for Neuronal Morphologies

arXiv: https://arxiv.org/abs/2112.12482 · HTML: https://mlsanity.com/paper/2112.12482/

## Key facts

- Cited by 5 papers in the map (data through 14 Oct 2026).
- Builds on 35 of its 77 references that are in the map.
- First posted on arXiv 23 Dec 2021.

## Builds on (most cited first, 30 of 35)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [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)
- [Representation Learning with Contrastive Predictive Coding](https://mlsanity.com/paper/1807.03748/) (2018)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Exploring Simple Siamese Representation Learning](https://mlsanity.com/paper/2011.10566/) (2020)
- [BEiT: BERT Pre-Training of Image Transformers](https://mlsanity.com/paper/2106.08254/) (2021)
- [Reformer: The Efficient Transformer](https://mlsanity.com/paper/2001.04451/) (2020)
- [Rethinking Attention with Performers](https://mlsanity.com/paper/2009.14794/) (2020)
- [Linformer: Self-Attention with Linear Complexity](https://mlsanity.com/paper/2006.04768/) (2020)
- [Graph Contrastive Learning with Augmentations](https://mlsanity.com/paper/2010.13902/) (2020)
- [Deep Graph Infomax](https://mlsanity.com/paper/1809.10341/) (2018)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [Gated Graph Sequence Neural Networks](https://mlsanity.com/paper/1511.05493/) (2015)
- [Convolutional Networks on Graphs for Learning Molecular Fingerprints](https://mlsanity.com/paper/1509.09292/) (2015)
- [Benchmarking Graph Neural Networks](https://mlsanity.com/paper/2003.00982/) (2020)
- [A Generalization of Transformer Networks to Graphs](https://mlsanity.com/paper/2012.09699/) (2020)
- [Contrastive Multi-View Representation Learning on Graphs](https://mlsanity.com/paper/2006.05582/) (2020)
- [SE(3)-Transformers: 3D Roto-Translation Equivariant Attention Networks](https://mlsanity.com/paper/2006.10503/) (2020)
- [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)
- [Diffusion Improves Graph Learning](https://mlsanity.com/paper/1911.05485/) (2019)
- [graph2vec: Learning Distributed Representations of Graphs](https://mlsanity.com/paper/1707.05005/) (2017)

## Built on by (most cited first, 5 of 5)

- [RedMotion: Motion Prediction via Redundancy Reduction](https://mlsanity.com/paper/2306.10840/) (2023)
- [Know Thyself by Knowing Others: Learning Neuron Identity from Population Context](https://mlsanity.com/paper/2512.01199/) (2025)
- [GraPHFormer: A Multimodal Graph Persistent Homology Transformer for the Analysis of Neuroscience Morphologies](https://mlsanity.com/paper/2603.20970/) (2026)
- [Identifying Influential nodes in Brain Networks via Self-Supervised Graph-Transformer](https://mlsanity.com/paper/2409.11174/) (2024)
- [CLEARMIND: Closed-Form Laplacian Embeddings of Arakelov-Green Resistance for Morphological Intrinsic Neuronal Distances](https://mlsanity.com/paper/2608.04460/) (2026)

## Abstract (arXiv)

Unsupervised graph representation learning has recently gained interest in several application domains such as neuroscience, where modeling the diverse morphology of cell types in the brain is one of the key challenges. It is currently unknown how many excitatory cortical cell types exist and what their defining morphological features are. Here we present GraphDINO, a purely data-driven approach to learn low-dimensional representations of 3D neuronal morphologies from unlabeled large-scale datasets. GraphDINO is a novel transformer-based representation learning method for spatially-embedded graphs. To enable self-supervised learning on transformers, we (1) developed data augmentation strategies for spatially-embedded graphs, (2) adapted the positional encoding and (3) introduced a novel attention mechanism, AC-Attention, which combines attention-based global interaction between nodes and classic graph convolutional processing. We show, in two different species and across multiple brain areas, that this method yields morphological cell type clusterings that are on par with manual feature-based classification by experts, but without using prior knowledge about the structural features of neurons. Moreover, it outperforms previous approaches on quantitative benchmarks predicting expert labels. Our method could potentially enable data-driven discovery of novel morphological features and cell types in large-scale datasets. It is applicable beyond neuroscience in settings where samples in a dataset are graphs and graph-level embeddings are desired.