Self-supervision drives representational convergence in medical foundation models more than clinical supervision

Self-supervised pre-training methods in medical imaging typically treat each individual as an isolated instance, learning representations through augmentation-based objectives or masked reconstruction. They often do not adequately capitalize on a key characteristic of physiological features: anatomical structures maintain consistent spatial relationships across individuals (instances), such as the thalamus being medial to the basal ganglia, regardless of variations in brain size, shape, or pathology. We propose leveraging this cross-instance topological consistency as a supervisory signal. The challenge arises from the inherent variability in medical imaging, which can differ significantly across instances and modalities. To tackle this, we focus on two alignment regimes. (i) Intra-instance: with pixel-level correspondences available, a cross-modal triplet objective explicitly preserves local neighborhood topology. (ii) Inter-instance: without such supervision, we derive pseudo-correspondences to control partial neighborhood alignment and prevent topology collapse across modalities. We validate our approach across 7 downstream multi-modal tasks, achieving average improvements of 1.1% and 5.94% in segmentation and classification tasks, respectively, and demonstrating significantly better robustness when modalities are missing at test time.

Radiology foundation models (RFMs) have largely inherited the scale-first recipe of natural-image vision--language pre-training. This recipe is difficult to deploy in 3D radiology, where training corpora are smaller, reports vary across institutions, and receiving hospitals often need local adaptation under privacy and compute constraints. We ask whether routine radiology reports can instead be converted into auditable diagnostic supervision that shapes the image encoder, text encoder, aligned space, and local-adaptation procedure. We develop GreenRFM, a supervision-centric pre-training framework organized around four empirical principles: More distilled, Ubiquitous, Semantic-enforcing, and Task-aligning (MUST) supervision. These principles convert noisy reports into structured diagnostic signals and use them to learn discriminative unimodal encoders plus an aligned image--text space for diagnosis-centered multimodal use. GreenRFM requires 24 GPU-hours on a single 24GB GPU (lightweight variant: 6GB VRAM, 4~hours) and reaches a zero-shot CT-RATE AUC of 84.8. Evaluations using more than 200,000 volumes from six institutions and two modalities show transfer to private clinical cohorts and to musculoskeletal MRI. On a local institutional cohort, computationally feasible retraining raises macro-AUC from 70.5 to 82.1. The aligned space also improves hepatocellular-carcinoma microvascular-invasion prediction and trans-arterial chemoembolization response analysis over established clinical scores. These results support supervision-centric pre-training as a practical route to resource-efficient, locally adaptable, diagnosis-centered radiology vision--language representations.

Building foundation models for medical imaging requires pooling data across institutions, yet privacy regulations prohibit centralized aggregation. Existing Federated Foundation Models either fine-tune natural-image models with poor medical-domain transfer, or train from scratch within a single modality, lacking the flexibility to unify tasks. We identify an under-explored challenge, Imaging Modality Heterogeneity, where clients operate under two structural regimes: Overlapped (shared modalities with heterogeneous label distributions) and Non-overlapped (fully disjoint modalities per client). We propose FM$^2$, a unified framework that trains the core backbone from scratch to preserve medical domain fidelity while optionally incorporating biomedical pretrained encoders for vision-language alignment. FM$^2$ equips each client with dual Mixture-of-Experts modules (a Class-wise MoE for personalized category knowledge and a Domain-wise MoE for shared cross-modality representations), coupled with a Heterogeneous Modality Alignment (HMA) regularizer that explicitly aligns modality-specific expert parameters, admitting provable $O(1/\sqrt{T})$ convergence and generalization guarantees. FM$^2$ further incorporates Caption-Enhanced Learning (CEL), where locally retained GPT-4o-generated captions serve as a textual semantic bridge enabling representation transfer across clients with disjoint modalities, and demonstrates extensibility to Federated Medical VQA. Experiments on our MIMH benchmark (classification and CEL) and real-world medical VQA datasets confirm consistent superiority over state-of-the-art federated baselines and strong out-of-modality generalization across all three tasks.