Whole Brain Vessel Graphs: A Dataset and Benchmark for Graph Learning and Neuroscience

Johannes C. Paetzold, Julian McGinnis, Suprosanna Shit, Ivan Ezhov, Paul Büschl, Chinmay Prabhakar, Anjany Sekuboyina, Mihail Todorov, Georgios Kaissis, Ali Ertürk, Stephan Günnemann, bjoern menze

Keywords: Graph Learning, Brain Vessels, Graph Extraction, Node Classification, Link Prediction, GNN, Neuroscience

Abstract:

Biological neural networks define the brain function and intelligence of humans and other mammals, and form ultra-large, spatial, structured graphs. Their neuronal organization is closely interconnected with the spatial organization of the brain's microvasculature, which supplies oxygen to the neurons and builds a complementary spatial graph. This vasculature (or the vessel structure) plays an important role in neuroscience; for example, the organization of (and changes to) vessel structure can represent early signs of various pathologies, e.g. Alzheimer's disease or stroke. Recently, advances in tissue clearing have enabled whole brain imaging and segmentation of the entirety of the mouse brain's vasculature.

Building on these advances in imaging, we are presenting an extendable dataset of whole-brain vessel graphs based on specific imaging protocols. Specifically, we extract vascular graphs using a refined graph extraction scheme leveraging the volume rendering engine Voreen and provide them in an accessible and adaptable form through the OGB and PyTorch Geometric dataloaders. Moreover, we benchmark numerous state-of-the-art graph learning algorithms on the biologically relevant tasks of vessel prediction and vessel classification using the introduced vessel graph dataset.

Our work paves a path towards advancing graph learning research into the field of neuroscience. Complementarily, the presented dataset raises challenging graph learning research questions for the machine learning community, in terms of incorporating biological priors into learning algorithms, or in scaling these algorithms to handle sparse,spatial graphs with millions of nodes and edges.

URL: https://github.com/jocpae/VesselGraph

TL;DR: We are presenting a large dataset of whole-brain vessel graphs to advance graph learning research in the field of neuroscience.

Contribution Process Agreement: Yes

Dataset Url: https://github.com/jocpae/VesselGraph

License: Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) license

Author Statement: Yes

Community Implementations: [ 2 code implementations](https://www.catalyzex.com/paper/whole-brain-vessel-graphs-a-dataset-and/code)