# WeakMedSAM: Weakly-Supervised Medical Image Segmentation via SAM with Sub-Class Exploration and Prompt Affinity Mining

arXiv: https://arxiv.org/abs/2503.04106 · HTML: https://mlsanity.com/paper/2503.04106/

## Key facts

- Cited by 8 papers in the map (data through 14 Oct 2026).
- Builds on 48 of its 68 references that are in the map.
- First posted on arXiv 6 Mar 2025.

## Builds on (most cited first, 30 of 48)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [SAM 2: Segment Anything in Images and Videos](https://mlsanity.com/paper/2408.00714/) (2024)
- [Learning Deep Features for Discriminative Localization](https://mlsanity.com/paper/1512.04150/) (2015)
- [The Medical Segmentation Decathlon](https://mlsanity.com/paper/2106.05735/) (2021)
- [Medical SAM Adapter: Adapting Segment Anything Model for Medical Image Segmentation](https://mlsanity.com/paper/2304.12620/) (2023)
- [Learning Pixel-level Semantic Affinity with Image-level Supervision for Weakly Supervised Semantic Segmentation](https://mlsanity.com/paper/1803.10464/) (2018)
- [Self-supervised Equivariant Attention Mechanism for Weakly Supervised Semantic Segmentation](https://mlsanity.com/paper/2004.04581/) (2020)
- [Segment Anything Model for Medical Image Analysis: an Experimental Study](https://mlsanity.com/paper/2304.10517/) (2023)
- [Customized Segment Anything Model for Medical Image Segmentation](https://mlsanity.com/paper/2304.13785/) (2023)
- [AbdomenCT-1K: Is Abdominal Organ Segmentation A Solved Problem?](https://mlsanity.com/paper/2010.14808/) (2020)
- [Conditional Random Fields as Recurrent Neural Networks](https://mlsanity.com/paper/1502.03240/) (2015)
- [Object Region Mining with Adversarial Erasing: A Simple Classification to Semantic Segmentation Approach](https://mlsanity.com/paper/1703.08448/) (2017)
- [EfficientSAM: Leveraged Masked Image Pretraining for Efficient Segment Anything](https://mlsanity.com/paper/2312.00863/) (2023)
- [Swin-UMamba: Mamba-based UNet with ImageNet-based pretraining](https://mlsanity.com/paper/2402.03302/) (2024)
- [Mining Cross-Image Semantics for Weakly Supervised Semantic Segmentation](https://mlsanity.com/paper/2007.01947/) (2020)
- [Multi-class Token Transformer for Weakly Supervised Semantic Segmentation](https://mlsanity.com/paper/2203.02891/) (2022)
- [Railroad is not a Train: Saliency as Pseudo-pixel Supervision for Weakly Supervised Semantic Segmentation](https://mlsanity.com/paper/2105.08965/) (2021)
- [Causality-inspired Single-source Domain Generalization for Medical Image Segmentation](https://mlsanity.com/paper/2111.12525/) (2021)
- [Learning Affinity from Attention: End-to-End Weakly-Supervised Semantic Segmentation with Transformers](https://mlsanity.com/paper/2203.02664/) (2022)
- [Interactive Medical Image Segmentation using Deep Learning with Image-specific Fine-tuning](https://mlsanity.com/paper/1710.04043/) (2017)
- [Foundational Models Defining a New Era in Vision: A Survey and Outlook](https://mlsanity.com/paper/2307.13721/) (2023)
- [Non-Salient Region Object Mining for Weakly Supervised Semantic Segmentation](https://mlsanity.com/paper/2103.14581/) (2021)
- [Self-supervised Image-specific Prototype Exploration for Weakly Supervised Semantic Segmentation](https://mlsanity.com/paper/2203.02909/) (2022)
- [Weakly Supervised Semantic Segmentation by Pixel-to-Prototype Contrast](https://mlsanity.com/paper/2110.07110/) (2021)
- [DeepCut: Object Segmentation from Bounding Box Annotations using Convolutional Neural Networks](https://mlsanity.com/paper/1605.07866/) (2016)
- [Delving into Masked Autoencoders for Multi-Label Thorax Disease Classification](https://mlsanity.com/paper/2210.12843/) (2022)
- [Token Contrast for Weakly-Supervised Semantic Segmentation](https://mlsanity.com/paper/2303.01267/) (2023)
- [Regional Semantic Contrast and Aggregation for Weakly Supervised Semantic Segmentation](https://mlsanity.com/paper/2203.09653/) (2022)

## Built on by (most cited first, 8 of 8)

- [Steady Progress Beats Stagnation: Mutual Aid of Foundation and Conventional Models in Mixed Domain Semi-Supervised Medical Image Segmentation](https://mlsanity.com/paper/2503.16997/) (2025)
- [Background Matters: A Cross-view Bidirectional Modeling Framework for Semi-supervised Medical Image Segmentation](https://mlsanity.com/paper/2505.16625/) (2025)
- [Prompt Mechanisms in Medical Imaging: A Comprehensive Survey](https://mlsanity.com/paper/2507.01055/) (2025)
- [Weakly Supervised Food Image Segmentation using Vision Transformers and Segment Anything Model](https://mlsanity.com/paper/2509.19028/) (2025)
- [TWLR: Text-Guided Weakly-Supervised Lesion Localization and Severity Regression for Explainable Diabetic Retinopathy Grading](https://mlsanity.com/paper/2512.13008/) (2025)
- [Weakly-Supervised Lung Nodule Segmentation via Training-Free Guidance of 3D Rectified Flow](https://mlsanity.com/paper/2604.08313/) (2026)
- [Learning Where to Look: A Reinforcement Learning Framework for Robust Micro-Ultrasound Prostate Cancer Detection](https://mlsanity.com/paper/2606.30951/) (2026)
- [From Spatial Semantics to Temporal Context: Leveraging Gaze Trajectory for Weakly Supervised Medical Image Segmentation](https://mlsanity.com/paper/2607.26542/) (2026)

## Abstract (arXiv)

We have witnessed remarkable progress in foundation models in vision tasks. Currently, several recent works have utilized the segmenting anything model (SAM) to boost the segmentation performance in medical images, where most of them focus on training an adaptor for fine-tuning a large amount of pixel-wise annotated medical images following a fully supervised manner. In this paper, to reduce the labeling cost, we investigate a novel weakly-supervised SAM-based segmentation model, namely WeakMedSAM. Specifically, our proposed WeakMedSAM contains two modules: 1) to mitigate severe co-occurrence in medical images, a sub-class exploration module is introduced to learn accurate feature representations. 2) to improve the quality of the class activation maps, our prompt affinity mining module utilizes the prompt capability of SAM to obtain an affinity map for random-walk refinement. Our method can be applied to any SAM-like backbone, and we conduct experiments with SAMUS and EfficientSAM. The experimental results on three popularly-used benchmark datasets, i.e., BraTS 2019, AbdomenCT-1K, and MSD Cardiac dataset, show the promising results of our proposed WeakMedSAM. Our code is available at https://github.com/wanghr64/WeakMedSAM.