# Prompt Tuning for Parameter-efficient Medical Image Segmentation

arXiv: https://arxiv.org/abs/2211.09233 · HTML: https://mlsanity.com/paper/2211.09233/

## Key facts

- Cited by 22 papers in the map (data through 14 Oct 2026).
- Builds on 69 of its 86 references that are in the map.
- First posted on arXiv 16 Nov 2022.

## Builds on (most cited first, 30 of 69)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [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)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Representation Learning with Contrastive Predictive Coding](https://mlsanity.com/paper/1807.03748/) (2018)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [PaLM: Scaling Language Modeling with Pathways](https://mlsanity.com/paper/2204.02311/) (2022)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [Parameter-Efficient Transfer Learning for NLP](https://mlsanity.com/paper/1902.00751/) (2019)
- [On the Opportunities and Risks of Foundation Models](https://mlsanity.com/paper/2108.07258/) (2021)
- [Prefix-Tuning: Optimizing Continuous Prompts for Generation](https://mlsanity.com/paper/2101.00190/) (2021)
- [The Power of Scale for Parameter-Efficient Prompt Tuning](https://mlsanity.com/paper/2104.08691/) (2021)
- [Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation](https://mlsanity.com/paper/1802.02611/) (2018)
- [Prototypical Networks for Few-shot Learning](https://mlsanity.com/paper/1703.05175/) (2017)
- [Unsupervised Learning of Visual Features by Contrasting Cluster Assignments](https://mlsanity.com/paper/2006.09882/) (2020)
- [BEiT: BERT Pre-Training of Image Transformers](https://mlsanity.com/paper/2106.08254/) (2021)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [Pre-train, Prompt, and Predict: A Systematic Survey of Prompting Methods in Natural Language Processing](https://mlsanity.com/paper/2107.13586/) (2021)
- [Visual Prompt Tuning](https://mlsanity.com/paper/2203.12119/) (2022)
- [An Empirical Study of Training Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.02057/) (2021)
- [Unsupervised Representation Learning by Predicting Image Rotations](https://mlsanity.com/paper/1803.07728/) (2018)
- [TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation](https://mlsanity.com/paper/2102.04306/) (2021)
- [Context Encoders: Feature Learning by Inpainting](https://mlsanity.com/paper/1604.07379/) (2016)
- [Unsupervised Learning of Visual Representations by Solving Jigsaw Puzzles](https://mlsanity.com/paper/1603.09246/) (2016)
- [Rethinking Semantic Segmentation from a Sequence-to-Sequence Perspective with Transformers](https://mlsanity.com/paper/2012.15840/) (2020)

## Built on by (most cited first, 22 of 22)

- [Foundation Model for Advancing Healthcare: Challenges, Opportunities, and Future Directions](https://mlsanity.com/paper/2404.03264/) (2024)
- [Parameter-Efficient Fine-Tuning for Medical Image Analysis: The Missed Opportunity](https://mlsanity.com/paper/2305.08252/) (2023)
- [Artificial General Intelligence for Medical Imaging Analysis](https://mlsanity.com/paper/2306.05480/) (2023)
- [Facing the Elephant in the Room: Visual Prompt Tuning or Full Finetuning?](https://mlsanity.com/paper/2401.12902/) (2024)
- [Few-shot Adaptation of Medical Vision-Language Models](https://mlsanity.com/paper/2409.03868/) (2024)
- [See Further for Parameter Efficient Fine-tuning by Standing on the Shoulders of Decomposition](https://mlsanity.com/paper/2407.05417/) (2024)
- [EigenLoRAx: Recycling Adapters to Find Principal Subspaces for Resource-Efficient Adaptation and Inference](https://mlsanity.com/paper/2502.04700/) (2025)
- [Contrastive Learning with Counterfactual Explanations for Radiology Report Generation](https://mlsanity.com/paper/2407.14474/) (2024)
- [Surgical Scene Understanding in the Era of Foundation AI Models: A Comprehensive Review](https://mlsanity.com/paper/2502.14886/) (2025)
- [Maintaining Structural Integrity in Parameter Spaces for Parameter Efficient Fine-tuning](https://mlsanity.com/paper/2405.14739/) (2024)
- [Efficient Medical Vision-Language Alignment Through Adapting Masked Vision Models](https://mlsanity.com/paper/2506.08990/) (2025)
- [ProstNFound+: A Prospective Study using Medical Foundation Models for Prostate Cancer Detection](https://mlsanity.com/paper/2510.26703/) (2025)
- [FlexLoRA: Entropy-Guided Flexible Low-Rank Adaptation](https://mlsanity.com/paper/2601.22905/) (2026)
- [Task-Specific Directions: Definition, Exploration, and Utilization in Parameter Efficient Fine-Tuning](https://mlsanity.com/paper/2409.01035/) (2024)
- [Med-Tuning: A New Parameter-Efficient Tuning Framework for Medical Volumetric Segmentation](https://mlsanity.com/paper/2304.10880/) (2023)
- [Adaptation of Foundation Models for Medical Image Analysis: Strategies, Challenges, and Future Directions](https://mlsanity.com/paper/2511.01284/) (2025)
- [Generalist Models in Medical Image Segmentation: A Survey and Performance Comparison with Task-Specific Approaches](https://mlsanity.com/paper/2506.10825/) (2025)
- [Unlocking Positive Transfer in Incrementally Learning Surgical Instruments: A Self-reflection Hierarchical Prompt Framework](https://mlsanity.com/paper/2604.02877/) (2026)
- [Prompt Mechanisms in Medical Imaging: A Comprehensive Survey](https://mlsanity.com/paper/2507.01055/) (2025)
- [Vision-Language Semantic Aggregation Leveraging Foundation Model for Generalizable Medical Image Segmentation](https://mlsanity.com/paper/2509.08570/) (2025)
- [DINO-MVR: Multi-View Readout of Frozen DINOv3 for Annotation-Efficient Medical Segmentation](https://mlsanity.com/paper/2605.07221/) (2026)
- [PGSB: Pretrained-Guided Shared Basis for LoRA Model Merging](https://mlsanity.com/paper/2610.14558/) (2026)

## Abstract (arXiv)

Neural networks pre-trained on a self-supervision scheme have become the standard when operating in data rich environments with scarce annotations. As such, fine-tuning a model to a downstream task in a parameter-efficient but effective way, e.g. for a new set of classes in the case of semantic segmentation, is of increasing importance. In this work, we propose and investigate several contributions to achieve a parameter-efficient but effective adaptation for semantic segmentation on two medical imaging datasets. Relying on the recently popularized prompt tuning approach, we provide a prompt-able UNet (PUNet) architecture, that is frozen after pre-training, but adaptable throughout the network by class-dependent learnable prompt tokens. We pre-train this architecture with a dedicated dense self-supervision scheme based on assignments to online generated prototypes (contrastive prototype assignment, CPA) of a student teacher combination alongside a concurrent segmentation loss on a subset of classes. We demonstrate that the resulting neural network model is able to attenuate the gap between fully fine-tuned and parameter-efficiently adapted models on CT imaging datasets. As such, the difference between fully fine-tuned and prompt-tuned variants amounts to only 3.83 pp for the TCIA/BTCV dataset and 2.67 pp for the CT-ORG dataset in the mean Dice Similarity Coefficient (DSC, in %) while only prompt tokens, corresponding to 0.85% of the pre-trained backbone model with 6.8M frozen parameters, are adjusted. The code for this work is available on https://github.com/marcdcfischer/PUNet .