Specializing Foundation Models via Mixture of Low-Rank Experts for Comprehensive Head CT Analysis

Adapting deep learning models to profound clinical heterogeneity typically relies on parameter-efficient fine-tuning (PEFT) to avoid the severe overfitting associated with full end-to-end network updates. Although PEFT successfully navigates limited data scenarios, it inherently forces the training of a separate, isolated adapter for every specific diagnostic task. Consolidating these isolated adapters into a single generalist network risks negative transfer, as optimization gradients from conflicting visual domains interfere. To address this, we propose MoPET, a mixture-of-experts (MoE) method that uses a learned sparse router to direct each input through a small subset of low-rank PEFT experts injected into a frozen foundation model, sharing capacity across datasets while limiting cross-domain gradient conflict. Through selected evaluations on the MedMNIST benchmark, we first establish that PEFT outperforms full network updates, improving average accuracy from 86.50% to 88.97%. We then show that a single MoPET model consolidates four heterogeneous datasets into one network, improving average accuracy over the best isolated PEFT adapters (93.46% versus 92.83%). Finally, we show that co-training with auxiliary datasets improves accuracy on data-constrained clinical targets, raising average target accuracy over the strongest isolated adapter from 81.58% to 83.58%. Our source code is publicly available at https://github.com/sdoerrich97/mopet.

Deploying a medical imaging model that must later accommodate a modality it has never seen is a recurring practical problem: retraining the shared representation is expensive and destroys performance on the modalities already in service. We study this onboarding problem under a strict leave-one-domain-out protocol, in which a convolutional backbone is pre-trained on source modalities (Kidney CT and Brain MRI), frozen permanently, and then required to accommodate an unseen modality (Chest X-ray). Under this protocol we establish three findings. First, decision-layer parameter-efficient fine-tuning is insufficient when the backbone has never observed the target modality: a linear probe and fully-connected LoRA both fall well short, whereas convolutional LoRA recovers most of the achievable accuracy, showing that adaptation must reach the convolutional features. Second, and centrally, the low-rank convolutional basis learned on the source modalities transfers: freezing that basis and training only its up-projections onboards the unseen modality using just $0.78\%$ of full fine-tuning's parameters, at an accuracy $6.11$ percentage points above a random basis of identical size, while an equivalent decision-layer basis exhibits no reliable transfer. Third, adapter-based onboarding leaves source-modality accuracy exactly unchanged ($Δ= 0.00$ pp), whereas full fine-tuning reaches the highest target accuracy only by catastrophically degrading the source modalities. A Mahalanobis score on frozen backbone features detects the unseen modality with high sensitivity at a strict source-retention threshold, providing a practical trigger for when onboarding is required. All results are reported over three seeds with paired bootstrap confidence intervals.

Medical foundation models improve generalization when training AI models with limited labeled data, but remain confined to a single specialty, such as pathology or radiology, and to either sparse or dense outputs, such as classification or segmentation. Here, we present CoM$^3$eT (Co-representation Multidimensional Multitask Medical Transformer), a medical vision foundation model that unifies pathology and radiology, sparse and dense predictions, and two- and higher-dimensional inputs by modeling multidimensional context with attention. CoM$^3$eT outperformed other medical foundation models in an open competition spanning five tomographic, four whole-specimen, and three two-dimensional datasets, covering sparse and dense prediction tasks as well as report generation. When adapted across diverse clinical applications, training fewer than 2.5% of parameters achieved performance comparable to full fine-tuning, enabling research without access to high-performance GPU clusters. Applied to federated learning across hospitals, this approach achieved performance comparable to pooled-data training over internet connections and with consumer-grade hardware.