# AutoSAM: Adapting SAM to Medical Images by Overloading the Prompt Encoder

arXiv: https://arxiv.org/abs/2306.06370 · HTML: https://mlsanity.com/paper/2306.06370/

## Key facts

- Cited by 70 papers in the map (data through 14 Oct 2026).
- Builds on 39 of its 59 references that are in the map.
- First posted on arXiv 10 Jun 2023.

## Builds on (most cited first, 30 of 39)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [Photorealistic Text-to-Image Diffusion Models with Deep Language Understanding](https://mlsanity.com/paper/2205.11487/) (2022)
- [Zero-Shot Text-to-Image Generation](https://mlsanity.com/paper/2102.12092/) (2021)
- [Prefix-Tuning: Optimizing Continuous Prompts for Generation](https://mlsanity.com/paper/2101.00190/) (2021)
- [UNet++: A Nested U-Net Architecture for Medical Image Segmentation](https://mlsanity.com/paper/1807.10165/) (2018)
- [SegNet: A Deep Convolutional Encoder-Decoder Architecture for Image Segmentation](https://mlsanity.com/paper/1511.00561/) (2015)
- [Making Pre-trained Language Models Better Few-shot Learners](https://mlsanity.com/paper/2012.15723/) (2020)
- [Segmenter: Transformer for Semantic Segmentation](https://mlsanity.com/paper/2105.05633/) (2021)
- [Universal Adversarial Triggers for Attacking and Analyzing NLP](https://mlsanity.com/paper/1908.07125/) (2019)
- [GPT Understands, Too](https://mlsanity.com/paper/2103.10385/) (2021)
- [Kvasir-SEG: A Segmented Polyp Dataset](https://mlsanity.com/paper/1911.07069/) (2019)
- [UNet++: Redesigning Skip Connections to Exploit Multiscale Features in Image Segmentation](https://mlsanity.com/paper/1912.05074/) (2019)
- [Medical SAM Adapter: Adapting Segment Anything Model for Medical Image Segmentation](https://mlsanity.com/paper/2304.12620/) (2023)
- [Structure-measure: A New Way to Evaluate Foreground Maps](https://mlsanity.com/paper/1708.00786/) (2017)
- [PraNet: Parallel Reverse Attention Network for Polyp Segmentation](https://mlsanity.com/paper/2006.11392/) (2020)
- [Enhanced-alignment Measure for Binary Foreground Map Evaluation](https://mlsanity.com/paper/1805.10421/) (2018)
- [Axial-DeepLab: Stand-Alone Axial-Attention for Panoptic Segmentation](https://mlsanity.com/paper/2003.07853/) (2020)
- [Medical Transformer: Gated Axial-Attention for Medical Image Segmentation](https://mlsanity.com/paper/2102.10662/) (2021)
- [Gland Segmentation in Colon Histology Images: The GlaS Challenge Contest](https://mlsanity.com/paper/1603.00275/) (2016)
- [UCTransNet: Rethinking the Skip Connections in U-Net from a Channel-wise Perspective with Transformer](https://mlsanity.com/paper/2109.04335/) (2021)
- [Polyp-PVT: Polyp Segmentation with Pyramid Vision Transformers](https://mlsanity.com/paper/2108.06932/) (2021)
- [ZeroCap: Zero-Shot Image-to-Text Generation for Visual-Semantic Arithmetic](https://mlsanity.com/paper/2111.14447/) (2021)
- [See More, Know More: Unsupervised Video Object Segmentation with Co-Attention Siamese Networks](https://mlsanity.com/paper/2001.06810/) (2020)
- [Salient Object Detection: A Benchmark](https://mlsanity.com/paper/1501.02741/) (2015)
- [Shallow Attention Network for Polyp Segmentation](https://mlsanity.com/paper/2108.00882/) (2021)
- [Video Polyp Segmentation: A Deep Learning Perspective](https://mlsanity.com/paper/2203.14291/) (2022)
- [Full-Duplex Strategy for Video Object Segmentation](https://mlsanity.com/paper/2108.03151/) (2021)

## Built on by (most cited first, 30 of 70)

- [RSPrompter: Learning to Prompt for Remote Sensing Instance Segmentation based on Visual Foundation Model](https://mlsanity.com/paper/2306.16269/) (2023)
- [Foundational Models Defining a New Era in Vision: A Survey and Outlook](https://mlsanity.com/paper/2307.13721/) (2023)
- [Segment Anything Model for Medical Image Segmentation: Current Applications and Future Directions](https://mlsanity.com/paper/2401.03495/) (2024)
- [Foundation Model for Advancing Healthcare: Challenges, Opportunities, and Future Directions](https://mlsanity.com/paper/2404.03264/) (2024)
- [Convolution Meets LoRA: Parameter Efficient Finetuning for Segment Anything Model](https://mlsanity.com/paper/2401.17868/) (2024)
- [MedCLIP-SAMv2: Towards Universal Text-Driven Medical Image Segmentation](https://mlsanity.com/paper/2409.19483/) (2024)
- [How to build the best medical image segmentation algorithm using foundation models: a comprehensive empirical study with Segment Anything Model](https://mlsanity.com/paper/2404.09957/) (2024)
- [Foundation Models for Biomedical Image Segmentation: A Survey](https://mlsanity.com/paper/2401.07654/) (2024)
- [AutoProSAM: Automated Prompting SAM for 3D Multi-Organ Segmentation](https://mlsanity.com/paper/2308.14936/) (2023)
- [MedSAM-U: Uncertainty-Guided Auto Multi-Prompt Adaptation for Reliable MedSAM](https://mlsanity.com/paper/2409.00924/) (2024)
- [On Efficient Variants of Segment Anything Model: A Survey](https://mlsanity.com/paper/2410.04960/) (2024)
- [nnSAM: Plug-and-play Segment Anything Model Improves nnUNet Performance](https://mlsanity.com/paper/2309.16967/) (2023)
- [ProtoSAM: One-Shot Medical Image Segmentation With Foundational Models](https://mlsanity.com/paper/2407.07042/) (2024)
- [Enhancing SAM with Efficient Prompting and Preference Optimization for Semi-supervised Medical Image Segmentation](https://mlsanity.com/paper/2503.04639/) (2025)
- [S-SAM: SVD-based Fine-Tuning of Segment Anything Model for Medical Image Segmentation](https://mlsanity.com/paper/2408.06447/) (2024)
- [Generalizable Disaster Damage Assessment via Change Detection with Vision Foundation Model](https://mlsanity.com/paper/2406.08020/) (2024)
- [Enhancing the Reliability of Segment Anything Model for Auto-Prompting Medical Image Segmentation with Uncertainty Rectification](https://mlsanity.com/paper/2311.10529/) (2023)
- [Recent Advances in Medical Imaging Segmentation: A Survey](https://mlsanity.com/paper/2505.09274/) (2025)
- [Sam2Rad: A Segmentation Model for Medical Images with Learnable Prompts](https://mlsanity.com/paper/2409.06821/) (2024)
- [Diff-VPS: Video Polyp Segmentation via a Multi-task Diffusion Network with Adversarial Temporal Reasoning](https://mlsanity.com/paper/2409.07238/) (2024)
- [AdapterShadow: Adapting Segment Anything Model for Shadow Detection](https://mlsanity.com/paper/2311.08891/) (2023)
- [SAMCT: Segment Any CT Allowing Labor-Free Task-Indicator Prompts](https://mlsanity.com/paper/2403.13258/) (2024)
- [Automating MedSAM by Learning Prompts with Weak Few-Shot Supervision](https://mlsanity.com/paper/2409.20293/) (2024)
- [TextSAM-EUS: Text Prompt Learning for SAM to Accurately Segment Pancreatic Tumor in Endoscopic Ultrasound](https://mlsanity.com/paper/2507.18082/) (2025)
- [MedVL-SAM2: A unified 3D medical vision-language model for multimodal reasoning and prompt-driven segmentation](https://mlsanity.com/paper/2601.09879/) (2026)
- [Industrial Segment Anything -- a Case Study in Aircraft Manufacturing, Intralogistics, Maintenance, Repair, and Overhaul](https://mlsanity.com/paper/2307.12674/) (2023)
- [Exploring SAM Ablations for Enhancing Medical Segmentation in Radiology and Pathology](https://mlsanity.com/paper/2310.00504/) (2023)
- [MaskSAM: Towards Auto-prompt SAM with Mask Classification for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/2403.14103/) (2024)
- [Beyond Pixel-Wise Supervision for Medical Image Segmentation: From Traditional Models to Foundation Models](https://mlsanity.com/paper/2404.13239/) (2024)
- [Ultrasound SAM Adapter: Adapting SAM for Breast Lesion Segmentation in Ultrasound Images](https://mlsanity.com/paper/2404.14837/) (2024)

## Abstract (arXiv)

The recently introduced Segment Anything Model (SAM) combines a clever architecture and large quantities of training data to obtain remarkable image segmentation capabilities. However, it fails to reproduce such results for Out-Of-Distribution (OOD) domains such as medical images. Moreover, while SAM is conditioned on either a mask or a set of points, it may be desirable to have a fully automatic solution. In this work, we replace SAM's conditioning with an encoder that operates on the same input image. By adding this encoder and without further fine-tuning SAM, we obtain state-of-the-art results on multiple medical images and video benchmarks. This new encoder is trained via gradients provided by a frozen SAM. For inspecting the knowledge within it, and providing a lightweight segmentation solution, we also learn to decode it into a mask by a shallow deconvolution network.