TotalFM: An Organ-Separated 3D-CT Foundation Model Leveraging Large-Scale Routine Clinical Radiology Data

CT vision-language foundation models have demonstrated promising performance across downstream tasks, but are typically trained with whole-volume representations that dilute fine-grained anatomical signals. Fine-grained vision-language pre-training addresses this by aligning anatomy-level visual features with anatomy-specific text, but in doing so discards the global context that whole-volume models provide. Furthermore, existing fine-grained approaches train from scratch, making them computationally expensive. We introduce Anatomy Contextualized Adaptation (ACA), a lightweight framework that adapts frozen CT foundation model representations for anatomy-level vision-language alignment while enhancing global contextualization. ACA uses TotalSegmentator to decompose CT volumes into anatomy-level embeddings, which are refined via a transformer that captures cross-anatomy relationships, and aligned to both per-anatomy and scan-level text extracted from radiology reports. Evaluated on Merlin and CT-RATE, ACA consistently outperforms both the frozen foundation model baselines and existing fine-grained methods in zero-shot finding classification, while requiring less than one hour of training once embeddings are cached. The attention weights learned by ACA's inter-anatomy transformer additionally indicate plausible cross-anatomy context routing. Altogether, these results support ACA as a lightweight approach for adapting CT foundation models to anatomically grounded vision-language alignment while preserving and enhancing global anatomical context.

The rapid proliferation of open-source medical foundation models (FMs) raises a practical question: how well do their pre-trained representations transfer to clinically relevant but data-scarce classification tasks? Particularly in CT-based renal lesion classification, a push toward greater generalizability would be meaningful, as the field is constrained by inherently limited training data. We addressed this through a benchmark of three medical FMs on this specific task. This six-class problem spans common entities like cysts and clear cell renal cell carcinoma, alongside rare subtypes. Using a frozen feature-probing protocol, we compared FM embeddings against a handcrafted radiomics classifier and a 3D ResNet-50 trained from scratch. Models were trained on a composite dataset of 2,854 lesions and evaluated on an external test set of 234 lesions from The Cancer Imaging Archive. Our results reveal two key findings. First, FM performance (AUC 0.70-0.77) matched the from-scratch ResNet (AUC 0.72) while drastically reducing hardware demand, requiring only seconds on a CPU after feature extraction. However, the conventional radiomics baseline significantly outperformed all deep learning approaches, achieving an AUC of 0.88 (all p $\leq$ 0.002). This suggests that current generalist FM embeddings do not yet capture the fine-grained texture and shape heterogeneity driving histological subtype discrimination. Despite their potential in data-scarce settings, medical FMs did not surpass established models for renal lesion stratification, leaving radiomics as the current state-of-the-art.

Chest computed tomography (CT) is central to the detection and management of thoracic disease, yet the growing scale and complexity of volumetric imaging increasingly exceed what can be addressed by scan-level prediction alone. Clinically useful AI for CT must not only recognize disease across the whole volume, but also localize abnormalities and provide interpretable visual evidence. Existing vision-language foundation models typically compress scans and reports into global image-text representations, limiting their ability to preserve spatial evidence and support clinically meaningful interpretation. Here we developed EXACT, an explainable anomaly-aware foundation model for three-dimensional chest CT that learns spatially resolved representations from paired clinical scans and radiology reports. EXACT was pre-trained on 25,692 CT-reports pairs using anatomy-aware weak supervision, jointly learning organ segmentation and multi-instance anomaly localization without manual voxel-level annotations. The resulting organ-specific anomaly-aware maps assign each voxel a disease-specific anomaly score confined to its corresponding anatomy, jointly encoding lesion extent and organ-level context. In retrospective multinational and multi-center evaluations, EXACT showed broad and consistent improvements across clinically relevant CT tasks, spanning multi-disease diagnosis, zero-shot anomaly localization, downstream adaptation, and visually grounded report generation, outperforming existing three-dimensional medical foundation models. By transforming routine clinical CT scans and free-text reports into explainable voxel-level representations, EXACT establishes a scalable paradigm for trustworthy volumetric medical AI.