Kaouther Mouheb

Kaouther Mouheb, Marawan Elbatel, Stefan Klein et al.

Deep learning has achieved impressive performance across various medical imaging tasks. However, its inherent bias against specific groups hinders its clinical applicability in equitable healthcare systems. A recently discovered phenomenon, Neural Collapse (NC), has shown potential in improving the generalization of state-of-the-art deep learning models. Nonetheless, its implications on bias in medical imaging remain unexplored. Our study investigates deep learning fairness through the lens of NC. We analyze the training dynamics of models as they approach NC when training using biased datasets, and examine the subsequent impact on test performance, specifically focusing on label bias. We find that biased training initially results in different NC configurations across subgroups, before converging to a final NC solution by memorizing all data samples. Through extensive experiments on three medical imaging datasets -- PAPILA, HAM10000, and CheXpert -- we find that in biased settings, NC can lead to a significant drop in F1 score across all subgroups. Our code is available at https://gitlab.com/radiology/neuro/neural-collapse-fairness

Marawan Elbatel, Anbang Wang, Keyuan Liu et al.

This paper does not introduce a novel architecture; instead, it revisits a fundamental yet overlooked baseline: adapting human-centric foundation models for anatomical landmark detection in medical imaging. While landmark detection has traditionally relied on domain-specific models, the emergence of large-scale pre-trained vision models presents new opportunities. In this study, we investigate the adaptation of Sapiens, a human-centric foundation model designed for pose estimation, to medical imaging through multi-dataset pretraining, establishing a new state of the art across multiple datasets. Our proposed model, MedSapiens, demonstrates that human-centric foundation models, inherently optimized for spatial pose localization, provide strong priors for anatomical landmark detection, yet this potential has remained largely untapped. We benchmark MedSapiens against existing state-of-the-art models, achieving up to 5.26% improvement over generalist models and up to 21.81% improvement over specialist models in the average success detection rate (SDR). To further assess MedSapiens adaptability to novel downstream tasks with few annotations, we evaluate its performance in limited-data settings, achieving 2.69% improvement over the few-shot state of the art in SDR. Code and model weights are available at https://github.com/xmed-lab/MedSapiens .

Marawan Elbatel, Mohamed Ghonim, Jiaji Mao et al.

Automated segmentation of liver lesions on non-contrast computed tomography (NCCT) is clinically important but fundamentally challenging, particularly in low-resource settings across Africa and Asia where contrast agents are frequently unavailable. Progress has been limited by the absence of annotated NCCT benchmarks. Here we describe the TriALS challenge for automated liver lesion segmentation under contrast-limited conditions, supported by a multi-centre dataset of 150 cases with four-phase CT acquisitions (600 volumes) from Egyptian and Chinese institutions. Algorithms were evaluated on 70 cases from three institutions, including an independent external cohort. The top-performing method achieved a mean venous-phase Dice of 0.754, consistent with human-level performance, yet dropped to 0.57 on NCCT. On external validation, the leading method outperformed off-the-shelf models by up to 28% in Dice on NCCT. Algorithm performance was most strongly predicted by training data scale and pre-training strategy. A cross-year comparison exposed a persistent perceptual barrier on NCCT that scaling pre-training alone cannot overcome. Data, annotations, and code are available at https://github.com/xmed-lab/TriALS.

Douwe J. Spaanderman, Karthik Prathaban, Petr Zelina et al.

Large language models (LLMs) are increasingly used to extract structured information from free-text clinical records, but prior work often focuses on single tasks, limited models, and English-language reports. We evaluated 15 open-weight LLMs on pathology and radiology reports across six use cases, colorectal liver metastases, liver tumours, neurodegenerative diseases, soft-tissue tumours, melanomas, and sarcomas, at three institutes in the Netherlands, UK, and Czech Republic. Models included general-purpose and medical-specialised LLMs of various sizes, and six prompting strategies were compared: zero-shot, one-shot, few-shot, chain-of-thought, self-consistency, and prompt graph. Performance was assessed using task-appropriate metrics, with consensus rank aggregation and linear mixed-effects models quantifying variance. Top-ranked models achieved macro-average scores close to inter-rater agreement across tasks. Small-to-medium general-purpose models performed comparably to large models, while tiny and specialised models performed worse. Prompt graph and few-shot prompting improved performance by ~13%. Task-specific factors, including variable complexity and annotation variability, influenced results more than model size or prompting strategy. These findings show that open-weight LLMs can extract structured data from clinical reports across diseases, languages, and institutions, offering a scalable approach for clinical data curation.

Kaouther Mouheb, Mobina Ghojogh Nejad, Lavsen Dahal et al.

Accurate 3D modeling of human organs is critical for constructing digital phantoms in virtual imaging trials. However, organs such as the large intestine remain particularly challenging due to their complex geometry and shape variability. We propose CLAP, a novel Conditional LAtent Point-diffusion model that combines geometric deep learning with denoising diffusion models to enhance 3D representations of the large intestine. Given point clouds sampled from segmentation masks, we employ a hierarchical variational autoencoder to learn both global and local latent shape representations. Two conditional diffusion models operate within this latent space to refine the organ shape. A pretrained surface reconstruction model is then used to convert the refined point clouds into meshes. CLAP achieves substantial improvements in shape modeling accuracy, reducing Chamfer distance by 26% and Hausdorff distance by 36% relative to the initial suboptimal shapes. This approach offers a robust and extensible solution for high-fidelity organ modeling, with potential applicability to a wide range of anatomical structures.

Kaouther Mouheb, Marawan Elbatel, Janne Papma et al.

While foundation models (FMs) offer strong potential for AI-based dementia diagnosis, their integration into federated learning (FL) systems remains underexplored. In this benchmarking study, we systematically evaluate the impact of key design choices: classification head architecture, fine-tuning strategy, and aggregation method, on the performance and efficiency of federated FM tuning using brain MRI data. Using a large multi-cohort dataset, we find that the architecture of the classification head substantially influences performance, freezing the FM encoder achieves comparable results to full fine-tuning, and advanced aggregation methods outperform standard federated averaging. Our results offer practical insights for deploying FMs in decentralized clinical settings and highlight trade-offs that should guide future method development.