# Beyond Pixel-Wise Supervision for Medical Image Segmentation: From Traditional Models to Foundation Models

arXiv: https://arxiv.org/abs/2404.13239 · HTML: https://mlsanity.com/paper/2404.13239/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Builds on 96 of its 144 references that are in the map.
- First posted on arXiv 20 Apr 2024.

## Builds on (most cited first, 30 of 96)

- [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)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [Segment Anything](https://mlsanity.com/paper/2304.02643/) (2023)
- [Grad-CAM: Visual Explanations from Deep Networks via Gradient-based Localization](https://mlsanity.com/paper/1610.02391/) (2016)
- [On the Opportunities and Risks of Foundation Models](https://mlsanity.com/paper/2108.07258/) (2021)
- [Grounding DINO: Marrying DINO with Grounded Pre-Training for Open-Set Object Detection](https://mlsanity.com/paper/2303.05499/) (2023)
- [Learning Deep Features for Discriminative Localization](https://mlsanity.com/paper/1512.04150/) (2015)
- [Fourier Features Let Networks Learn High Frequency Functions in Low Dimensional Domains](https://mlsanity.com/paper/2006.10739/) (2020)
- [TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation](https://mlsanity.com/paper/2102.04306/) (2021)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Deep High-Resolution Representation Learning for Visual Recognition](https://mlsanity.com/paper/1908.07919/) (2019)
- [A Survey on Deep Learning in Medical Image Analysis](https://mlsanity.com/paper/1702.05747/) (2017)
- [Grad-CAM++: Improved Visual Explanations for Deep Convolutional Networks](https://mlsanity.com/paper/1710.11063/) (2017)
- [The Medical Segmentation Decathlon](https://mlsanity.com/paper/2106.05735/) (2021)
- [UNet++: Redesigning Skip Connections to Exploit Multiscale Features in Image Segmentation](https://mlsanity.com/paper/1912.05074/) (2019)
- [Score-CAM: Score-Weighted Visual Explanations for Convolutional Neural Networks](https://mlsanity.com/paper/1910.01279/) (2019)
- [The Liver Tumor Segmentation Benchmark (LiTS)](https://mlsanity.com/paper/1901.04056/) (2019)
- [Medical SAM Adapter: Adapting Segment Anything Model for Medical Image Segmentation](https://mlsanity.com/paper/2304.12620/) (2023)
- [ScribbleSup: Scribble-Supervised Convolutional Networks for Semantic Segmentation](https://mlsanity.com/paper/1604.05144/) (2016)
- [CHAOS Challenge -- Combined (CT-MR) Healthy Abdominal Organ Segmentation](https://mlsanity.com/paper/2001.06535/) (2020)
- [Recognize Anything: A Strong Image Tagging Model](https://mlsanity.com/paper/2306.03514/) (2023)
- [Track Anything: Segment Anything Meets Videos](https://mlsanity.com/paper/2304.11968/) (2023)
- [CoTr: Efficiently Bridging CNN and Transformer for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.03024/) (2021)
- [AbdomenCT-1K: Is Abdominal Organ Segmentation A Solved Problem?](https://mlsanity.com/paper/2010.14808/) (2020)
- [SegGPT: Segmenting Everything In Context](https://mlsanity.com/paper/2304.03284/) (2023)
- [The state of the art in kidney and kidney tumor segmentation in contrast-enhanced CT imaging: Results of the KiTS19 Challenge](https://mlsanity.com/paper/1912.01054/) (2019)
- [Semantic-SAM: Segment and Recognize Anything at Any Granularity](https://mlsanity.com/paper/2307.04767/) (2023)
- [nnFormer: Interleaved Transformer for Volumetric Segmentation](https://mlsanity.com/paper/2109.03201/) (2021)
- [Segment Anything Model (SAM) for Digital Pathology: Assess Zero-shot Segmentation on Whole Slide Imaging](https://mlsanity.com/paper/2304.04155/) (2023)

## Built on by (most cited first, 4 of 4)

- [SegAnyPET: Universal Promptable Segmentation from Positron Emission Tomography Images](https://mlsanity.com/paper/2502.14351/) (2025)
- [Finally Outshining the Random Baseline: A Simple and Effective Solution for Active Learning in 3D Biomedical Imaging](https://mlsanity.com/paper/2601.13677/) (2026)
- [When Adaptation Hurts: Connecting Representational Drift to OOD Failures in MedSAM Fine-Tuning](https://mlsanity.com/paper/2608.21300/) (2026)
- [A Comprehensive Survey of Medical Image Segmentation: Challenges, Benchmarks, and Beyond](https://mlsanity.com/paper/2606.16153/) (2026)

## Abstract (arXiv)

Medical image segmentation plays an important role in many image-guided clinical approaches. However, existing segmentation algorithms mostly rely on the availability of fully annotated images with pixel-wise annotations for training, which can be both labor-intensive and expertise-demanding, especially in the medical imaging domain where only experts can provide reliable and accurate annotations. To alleviate this challenge, there has been a growing focus on developing segmentation methods that can train deep models with weak annotations, such as image-level, bounding boxes, scribbles, and points. The emergence of vision foundation models, notably the Segment Anything Model (SAM), has introduced innovative capabilities for segmentation tasks using weak annotations for promptable segmentation enabled by large-scale pre-training. Adopting foundation models together with traditional learning methods has increasingly gained recent interest research community and shown potential for real-world applications. In this paper, we present a comprehensive survey of recent progress on annotation-efficient learning for medical image segmentation utilizing weak annotations before and in the era of foundation models. Furthermore, we analyze and discuss several challenges of existing approaches, which we believe will provide valuable guidance for shaping the trajectory of foundational models to further advance the field of medical image segmentation.