# MedCore: Boundary-Preserving Medical Core Pruning for MedSAM

arXiv: https://arxiv.org/abs/2605.13688 · HTML: https://mlsanity.com/paper/2605.13688/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 24 of its 41 references that are in the map.
- First posted on arXiv 13 May 2026.

## Builds on (most cited first, 24 of 24)

- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [Deep Compression: Compressing Deep Neural Networks with Pruning, Trained Quantization and Huffman Coding](https://mlsanity.com/paper/1510.00149/) (2015)
- [Learning both Weights and Connections for Efficient Neural Networks](https://mlsanity.com/paper/1506.02626/) (2015)
- [Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2105.05537/) (2021)
- [Analyzing Multi-Head Self-Attention: Specialized Heads Do the Heavy Lifting, the Rest Can Be Pruned](https://mlsanity.com/paper/1905.09418/) (2019)
- [Are Sixteen Heads Really Better than One?](https://mlsanity.com/paper/1905.10650/) (2019)
- [Skin Lesion Analysis Toward Melanoma Detection 2018: A Challenge Hosted by the International Skin Imaging Collaboration (ISIC)](https://mlsanity.com/paper/1902.03368/) (2019)
- [Kvasir-SEG: A Segmented Polyp Dataset](https://mlsanity.com/paper/1911.07069/) (2019)
- [Movement Pruning: Adaptive Sparsity by Fine-Tuning](https://mlsanity.com/paper/2005.07683/) (2020)
- [clDice -- A Novel Topology-Preserving Loss Function for Tubular Structure Segmentation](https://mlsanity.com/paper/2003.07311/) (2020)
- [A Benchmark for Endoluminal Scene Segmentation of Colonoscopy Images](https://mlsanity.com/paper/1612.00799/) (2016)
- [Boundary loss for highly unbalanced segmentation](https://mlsanity.com/paper/1812.07032/) (2018)
- [Group Fisher Pruning for Practical Network Compression](https://mlsanity.com/paper/2108.00708/) (2021)
- [Reducing the Hausdorff Distance in Medical Image Segmentation with Convolutional Neural Networks](https://mlsanity.com/paper/1904.10030/) (2019)
- [Global Vision Transformer Pruning with Hessian-Aware Saliency](https://mlsanity.com/paper/2110.04869/) (2021)
- [Polyp-SAM: Transfer SAM for Polyp Segmentation](https://mlsanity.com/paper/2305.00293/) (2023)
- [EMCAD: Efficient Multi-scale Convolutional Attention Decoding for Medical Image Segmentation](https://mlsanity.com/paper/2405.06880/) (2024)
- [Revisiting Random Channel Pruning for Neural Network Compression](https://mlsanity.com/paper/2205.05676/) (2022)
- [EdgeSAM: Prompt-In-the-Loop Distillation for SAM](https://mlsanity.com/paper/2312.06660/) (2023)
- [I-MedSAM: Implicit Medical Image Segmentation with Segment Anything](https://mlsanity.com/paper/2311.17081/) (2023)
- [Polyper: Boundary Sensitive Polyp Segmentation](https://mlsanity.com/paper/2312.08735/) (2023)
- [Efficient Quantization-Aware Training on Segment Anything Model in Medical Images and Its Deployment](https://mlsanity.com/paper/2412.11186/) (2024)

## Built on by (most cited first, 1 of 1)

- [ST-ColoNet: Spatio-Temporal Colon Segment Recognition via Hybrid Attention and Edge-Guided Feature Learning](https://mlsanity.com/paper/2605.28119/) (2026)

## Abstract (arXiv)

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 that compares zeroing a group with resetting it to its original SAM weight. We identify the second type by boundary-aware Fisher estimation. We also introduce a boundary leverage principle, which shows that compression-induced boundary displacement is controlled by logit perturbation on the boundary divided by the logit spatial gradient. 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 recovery fine-tuning. It also reaches 86.6% parameter reduction and 90.4G FLOPs with strong boundary quality. Our analysis further shows that MedSAM lies in a head-fragile boundary regime: head-pruning steps have 2.887 times larger 95th-percentile boundary leverage than MLP-pruning steps, and this logit-level effect is consistent with BF1 and HD95 degradation. Our code is available at https://github.com/cenweizhang/MedCore.