# Automated Labeling of Intracranial Arteries with Uncertainty Quantification Using Deep Learning

arXiv: https://arxiv.org/abs/2509.17726 · HTML: https://mlsanity.com/paper/2509.17726/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 15 of its 55 references that are in the map.
- First posted on arXiv 22 Sep 2025.

## Builds on (most cited first, 15 of 15)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [On Calibration of Modern Neural Networks](https://mlsanity.com/paper/1706.04599/) (2017)
- [Can You Trust Your Model's Uncertainty? Evaluating Predictive Uncertainty Under Dataset Shift](https://mlsanity.com/paper/1906.02530/) (2019)
- [The Medical Segmentation Decathlon](https://mlsanity.com/paper/2106.05735/) (2021)
- [MONAI: An open-source framework for deep learning in healthcare](https://mlsanity.com/paper/2211.02701/) (2022)
- [Aleatoric uncertainty estimation with test-time augmentation for medical image segmentation with convolutional neural networks](https://mlsanity.com/paper/1807.07356/) (2018)
- [nnU-Net Revisited: A Call for Rigorous Validation in 3D Medical Image Segmentation](https://mlsanity.com/paper/2404.09556/) (2024)
- [Assessing Reliability and Challenges of Uncertainty Estimations for Medical Image Segmentation](https://mlsanity.com/paper/1907.03338/) (2019)
- [Trustworthy clinical AI solutions: a unified review of uncertainty quantification in deep learning models for medical image analysis](https://mlsanity.com/paper/2210.03736/) (2022)
- [CS2-Net: Deep Learning Segmentation of Curvilinear Structures in Medical Imaging](https://mlsanity.com/paper/2010.07486/) (2020)
- [Automated Intracranial Artery Labeling using a Graph Neural Network and Hierarchical Refinement](https://mlsanity.com/paper/2007.14472/) (2020)
- [Average Calibration Losses for Reliable Uncertainty in Medical Image Segmentation](https://mlsanity.com/paper/2506.03942/) (2025)
- [Deep Feature Fusion via Graph Convolutional Network for Intracranial Artery Labeling](https://mlsanity.com/paper/2205.10757/) (2022)
- [Efficient Epistemic Uncertainty Estimation in Cerebrovascular Segmentation](https://mlsanity.com/paper/2503.22271/) (2025)

## Abstract (arXiv)

Accurate anatomical labeling of intracranial arteries is essential for cerebrovascular diagnosis and hemodynamic analysis but remains time-consuming and subject to interoperator variability. We present a deep learning-based framework for automated artery labeling from 3D Time-of-Flight Magnetic Resonance Angiography (3D ToF-MRA) segmentations (n=35), incorporating uncertainty quantification to enhance interpretability and reliability. We evaluated three convolutional neural network architectures: (1) a UNet with residual encoder blocks, reflecting commonly used baselines in vascular labeling; (2) CS-Net, an attention-augmented UNet incorporating channel and spatial attention mechanisms for enhanced curvilinear structure recognition; and (3) nnUNet, a self-configuring framework that automates preprocessing, training, and architectural adaptation based on dataset characteristics. Among these, nnUNet achieved the highest labeling performance (average Dice score: 0.922; average surface distance: 0.387 mm), with improved robustness in anatomically complex vessels. To assess predictive confidence, we implemented test-time augmentation (TTA) and introduced a novel coordinate-guided strategy to reduce interpolation errors during augmented inference. The resulting uncertainty maps reliably indicated regions of anatomical ambiguity, pathological variation, or manual labeling inconsistency. We further validated clinical utility by comparing flow velocities derived from automated and manual labels in co-registered 4D Flow MRI datasets, observing close agreement with no statistically significant differences. Our framework offers a scalable, accurate, and uncertainty-aware solution for automated cerebrovascular labeling, supporting downstream hemodynamic analysis and facilitating clinical integration.