MedCore: Boundary-Preserving Medical Core Pruning for MedSAM

Medical segmentation foundation models such as SAM and MedSAM provide strong prompt-driven segmentation, but their image encoders are still too large for many clinical settings. Compression is also risky in medicine because a model can keep high Dice while losing boundary fidelity. We propose MedCore, a structured pruning framework for MedSAM. The main idea is to preserve two kinds of structures: structures that became important during SAM-to-MedSAM adaptation, and structures that have high boundary leverage. We identify the first type by a dual-intervention score comparing zeroing a group with resetting it to its original SAM weights. We identify the second type by boundary-aware Fisher estimation. We also introduce a boundary leverage principle, which relates first-order boundary displacement to boundary logit perturbation divided by the spatial gradient norm. This principle explains why boundary metrics can degrade even when Dice remains high. On polyp segmentation benchmarks, MedCore reduces parameters by 60.0% and FLOPs by 58.4% while achieving Dice 0.9549, Boundary F1 0.6388, and HD95 5.14 after post-pruning fine-tuning. It also reaches 86.6% parameter reduction and 90.4G FLOPs, retaining Dice and HD95 near the fine-tuned MedSAM reference, with lower BF1. Our analysis shows that MedSAM lies in a head-fragile boundary regime: the median 95th-percentile boundary leverage is 2.887 times as high for head-pruning as for MLP-pruning steps, consistent with BF1 and HD95 degradation. Our code is available at https://anonymous.4open.science/r/MedCore-8461.