Comparing the Performance of Foundation Model Derived Embeddings with Traditional Approaches for Distant Metastasis Prediction in Head and Neck Cancer

Background: Early prediction of distant metastasis (DM) risk in head and neck cancer (HNC) can enable timely interventions that may improve treatment outcomes. Many current machine learning methods rely on prior knowledge of the region of interest such as tumor segmentations, which require expert knowledge, is time-consuming and introduces user-dependent variability. Medical image-based foundation models have recently been developed for specific imaging modalities to streamline down-stream prediction tasks by extracting modality-relevant features. Purpose: In this study, we evaluate the effectiveness of using a foundation model as the feature extractor to predict DM risk in HNC patients and compare its performance with traditional approaches that require prior knowledge on the regions of interest. Methods: Preoperative CT images of 2327 patients from the RADCURE dataset were used. Three features-sets were created including radiomics, deep-learning based features, and CT Foundation derived features. The feature-sets were used individually in a multi-layer perceptron (MLP) to predict DM risk. Results: The model using CT Foundation embeddings outperformed the radiomics and deep learning-based models, achieving a Receiver Operating Characteristic Area Under the Curve (AUC) of 0.791, compared to AUC values of 0.772 and 0.753 for the radiomics and deep learning-based models, respectively. The CT Foundation based model had similar performance to a model that combined the use of radiomics and deep learning-based features that achieved an AUC of 0.794. Conclusions: Features based on foundation models offer a promising alternative to traditional radiomics while reducing the need for domain expertise and extensively annotated datasets. Their minimal preprocessing requirements also make them a more accessible and scalable option.

Jolia: Concept-Level Vision-Language Alignment for 3D CT Contrastive Learning

Vision-language contrastive pretraining has become the dominant recipe for 3D medical foundation models, leveraging the large volumes of paired scans and reports produced in clinical practice. However, medical images usually span dozens of organs, and radiological reports are much longer than typical natural image captions and are composed of multiple structured sections. CLIP-style pretraining compresses this structure by encoding each modality into a single global token, at the risk of losing important details. We introduce ConQuer (Concept Queries), an image-text pretraining method that augments CLIP's global alignment with a set of localized alignments, one per concept. ConQuer splits the report into concept-specific sections and learns cross-attention queries that pool the matching image features without using any segmentation mask or spatial supervision. Contrastive learning is then applied independently for each concept. Concepts can be any unit of semantic localization; here, they are anatomical regions, one query per organ or gross body region. As a byproduct, each query learns attention maps focused on its concept, providing built-in spatial interpretability. We use ConQuer to train Jolia, a 3D CT foundation model on chest and abdominal CT. Jolia consistently outperforms a CLIP baseline on findings classification, report generation, and cross-center transfer, and sets a new state of the art across multiple public benchmarks. Jolia's weights will be released upon acceptance.