Ewoud Smit

Jan Tagscherer, Sarah de Boer, Lena Philipp et al.

Developing foundation models in medical imaging requires continuous monitoring of downstream performance. Researchers are burdened with tracking numerous experiments, design choices, and their effects on performance, often relying on ad-hoc, manual workflows that are inherently slow and error-prone. We introduce EvalBlocks, a modular, plug-and-play framework for efficient evaluation of foundation models during development. Built on Snakemake, EvalBlocks supports seamless integration of new datasets, foundation models, aggregation methods, and evaluation strategies. All experiments and results are tracked centrally and are reproducible with a single command, while efficient caching and parallel execution enable scalable use on shared compute infrastructure. Demonstrated on five state-of-the-art foundation models and three medical imaging classification tasks, EvalBlocks streamlines model evaluation, enabling researchers to iterate faster and focus on model innovation rather than evaluation logistics. The framework is released as open source software at https://github.com/DIAGNijmegen/eval-blocks.

Niels Rocholl, Ewoud Smit, Mathias Prokop et al.

Longitudinal lesion analysis is crucial for oncological care, yet automated tools often struggle with temporal consistency. While universal lesion segmentation models have advanced, they are typically designed for single time points. This paper investigates the performance of the ULS23 segmentation model in a longitudinal context. Using a public clinical dataset of baseline and follow-up CT scans, we evaluated the model's ability to segment and track lesions over time. We identified two critical, interconnected failure modes: a sharp degradation in segmentation quality in follow-up cases due to inter-scan registration errors, and a subsequent breakdown of the lesion correspondence process. To systematically probe this vulnerability, we conducted a controlled experiment where we artificially displaced the input volume relative to the true lesion center. Our results demonstrate that the model's performance is highly dependent on its assumption of a centered lesion; segmentation accuracy collapses when the lesion is sufficiently displaced. These findings reveal a fundamental limitation of applying single-timepoint models to longitudinal data. We conclude that robust oncological tracking requires a paradigm shift away from cascading single-purpose tools towards integrated, end-to-end models inherently designed for temporal analysis.