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

Published: 11 Oct 2021, Last Modified: 23 May 2023NeurIPS 2021 Datasets and Benchmarks Track (Round 2)Readers: Everyone
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.
Supplementary Material: pdf
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
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