Marta Kersten-Oertel

Mumu Aktar, Hassan Rivaz, Marta Kersten-Oertel et al.

Angiography is widely used to detect, diagnose, and treat cerebrovascular diseases. While numerous techniques have been proposed to segment the vascular network from different imaging modalities, deep learning (DL) has emerged as a promising approach. However, existing DL methods often depend on proprietary datasets and extensive manual annotation. Moreover, the availability of pre-trained networks specifically for medical domains and 3D volumes is limited. To overcome these challenges, we propose a few-shot learning approach called VesselShot for cerebrovascular segmentation. VesselShot leverages knowledge from a few annotated support images and mitigates the scarcity of labeled data and the need for extensive annotation in cerebral blood vessel segmentation. We evaluated the performance of VesselShot using the publicly available TubeTK dataset for the segmentation task, achieving a mean Dice coefficient (DC) of 0.62(0.03).

Bahar Jahani, Matsanga Leyila Kaseka, Marta Kersten-Oertel et al.

Stroke remains a leading cause of mortality and disability worldwide, requiring rapid and informed clinical decision-making. A solid spatial understanding of cerebrovascular anatomy and vascular territories in relation to stroke symptoms and severity is critical for timely clinical decision and patient care. However, this knowledge is typically conveyed through static 2D diagrams and printed materials, which can hinder mastery of the complex neurovascular system and their clinical implications. Mobile augmented reality (AR) offers an accessible medium for delivering intuitive 3D anatomical education, yet applications focused on the neurovascular system and stroke remain limited despite the demand. To address this, we propose NeuroVase, a tablet-based mobile AR platform within a structured pedagogical framework that enhances stroke-related neuroanatomy learning by providing an interactive, engaging, and accessible alternative to traditional methods. NeuroVase features a dual-mode setup, using tangible cue cards as standalone study aids while also serving as interactive markers for AR content delivery. A custom learning curriculum focused on cerebrovascular anatomy and stroke supports exploration of vascular territories, stroke syndromes, and arterial occlusions, in the context of annotated 3D anatomical models in NeuroVase. A controlled user study with 40 participants revealed that NeuroVase is an effective and user-friendly AR platform to facilitate complex anatomical and physiological education, compared with traditional learning.

Pascal Spiegler, Taha Koleilat, Arash Harirpoush et al.

Pancreatic cancer carries a poor prognosis and relies on endoscopic ultrasound (EUS) for targeted biopsy and radiotherapy. However, the speckle noise, low contrast, and unintuitive appearance of EUS make segmentation of pancreatic tumors with fully supervised deep learning (DL) models both error-prone and dependent on large, expert-curated annotation datasets. To address these challenges, we present TextSAM-EUS, a novel, lightweight, text-driven adaptation of the Segment Anything Model (SAM) that requires no manual geometric prompts at inference. Our approach leverages text prompt learning (context optimization) through the BiomedCLIP text encoder in conjunction with a LoRA-based adaptation of SAM's architecture to enable automatic pancreatic tumor segmentation in EUS, tuning only 0.86% of the total parameters. On the public Endoscopic Ultrasound Database of the Pancreas, TextSAM-EUS with automatic prompts attains 82.69% Dice and 85.28% normalized surface distance (NSD), and with manual geometric prompts reaches 83.10% Dice and 85.70% NSD, outperforming both existing state-of-the-art (SOTA) supervised DL models and foundation models (e.g., SAM and its variants). As the first attempt to incorporate prompt learning in SAM-based medical image segmentation, TextSAM-EUS offers a practical option for efficient and robust automatic EUS segmentation. Code is available at https://github.com/HealthX-Lab/TextSAM-EUS .

Arash Harirpoush, Amirhossein Rasoulian, Marta Kersten-Oertel et al.

Recent rising interests in patient-specific thoracic surgical planning and simulation require efficient and robust creation of digital anatomical models from automatic medical image segmentation algorithms. Deep learning (DL) is now state-of-the-art in various radiological tasks, and U-shaped DL models have particularly excelled in medical image segmentation since the inception of the 2D UNet. To date, many variants of U-shaped models have been proposed by the integration of different attention mechanisms and network configurations. Systematic benchmark studies which analyze the architecture of these models by leveraging the recent development of the multi-label databases, can provide valuable insights for clinical deployment and future model designs, but such studies are still rare. We conduct the first systematic benchmark study for variants of 3D U-shaped models (3DUNet, STUNet, AttentionUNet, SwinUNETR, FocalSegNet, and a novel 3D SwinUnet with four variants) with a focus on CT-based anatomical segmentation for thoracic surgery. Our study systematically examines the impact of different attention mechanisms, the number of resolution stages, and network configurations on segmentation accuracy and computational complexity. To allow cross-reference with other recent benchmarking studies, we also included a performance assessment of the BTCV abdominal structural segmentation. With the STUNet ranking at the top, our study demonstrated the value of CNN-based U-shaped models for the investigated tasks and the benefit of residual blocks in network configuration designs to boost segmentation performance.

Mehrdad Asadi, Komi Sodoké, Ian J. Gerard et al.

In this work, we present a novel approach to multi-label chest X-ray (CXR) image classification that enhances clinical interpretability while maintaining a streamlined, single-model, single-run training pipeline. Leveraging the CheXpert dataset and VisualCheXbert-derived labels, we incorporate hierarchical label groupings to capture clinically meaningful relationships between diagnoses. To achieve this, we designed a custom hierarchical binary cross-entropy (HBCE) loss function that enforces label dependencies using either fixed or data-driven penalty types. Our model achieved a mean area under the receiver operating characteristic curve (AUROC) of 0.903 on the test set. Additionally, we provide visual explanations and uncertainty estimations to further enhance model interpretability. All code, model configurations, and experiment details are made available.

Simon Joseph Clément Crête, Marta Kersten-Oertel, Yiming Xiao

MRI-based brain age estimation models aim to assess a subject's biological brain age based on information, such as neuroanatomical features. Various factors, including neurodegenerative diseases, can accelerate brain aging and measuring this phenomena could serve as a potential biomarker for clinical applications. While deep learning (DL)-based regression has recently attracted major attention, existing approaches often fail to capture the continuous nature of neuromorphological changes, potentially resulting in sub-optimal feature representation and results. To address this, we propose to use supervised contrastive learning with the recent Rank-N-Contrast (RNC) loss to estimate brain age based on widely used T1w structural MRI for the first time and leverage Grad-RAM to visually explain regression results. Experiments show that our proposed method achieves a mean absolute error (MAE) of 4.27 years and an $R^2$ of 0.93 with a limited dataset of training samples, significantly outperforming conventional deep regression with the same ResNet backbone while performing better or comparably with the state-of-the-art methods with significantly larger training data. Furthermore, Grad-RAM revealed more nuanced features related to age regression with the RNC loss than conventional deep regression. As an exploratory study, we employed the proposed method to estimate the gap between the biological and chronological brain ages in Alzheimer's Disease and Parkinson's disease patients, and revealed the correlation between the brain age gap and disease severity, demonstrating its potential as a biomarker in neurodegenerative disorders.

Jonatan Reyes, Lisa Di Jorio, Cecile Low-Kam et al.

Federated Learning using the Federated Averaging algorithm has shown great advantages for large-scale applications that rely on collaborative learning, especially when the training data is either unbalanced or inaccessible due to privacy constraints. We hypothesize that Federated Averaging underestimates the full extent of heterogeneity of data when the aggregation is performed. We propose Precision-weighted Federated Learning a novel algorithm that takes into account the variance of the stochastic gradients when computing the weighted average of the parameters of models trained in a Federated Learning setting. With Precision-weighted Federated Learning, we provide an alternate averaging scheme that leverages the heterogeneity of the data when it has a large diversity of features in its composition. Our method was evaluated using standard image classification datasets with two different data partitioning strategies (IID/non-IID) to measure the performance and speed of our method in resource-constrained environments, such as mobile and IoT devices. We obtained a good balance between computational efficiency and convergence rates with Precision-weighted Federated Learning. Our performance evaluations show 9% better predictions with MNIST, 18% with Fashion-MNIST, and 5% with CIFAR-10 in the non-IID setting. Further reliability evaluations ratify the stability in our method by reaching a 99% reliability index with IID partitions and 96% with non-IID partitions. In addition, we obtained a 20x speedup on Fashion-MNIST with only 10 clients and up to 37x with 100 clients participating in the aggregation concurrently per communication round. The results indicate that Precision-weighted Federated Learning is an effective and faster alternative approach for aggregating private data, especially in domains where data is highly heterogeneous.