# Foundation Model-guided Iteratively Prompting and Pseudo-Labeling for Partially Labeled Medical Image Segmentation

arXiv: https://arxiv.org/abs/2604.01038 · HTML: https://mlsanity.com/paper/2604.01038/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 9 of its 15 references that are in the map.
- First posted on arXiv 1 Apr 2026.

## Builds on (most cited first, 9 of 9)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [UNet++: A Nested U-Net Architecture for Medical Image Segmentation](https://mlsanity.com/paper/1807.10165/) (2018)
- [Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2105.05537/) (2021)
- [AMOS: A Large-Scale Abdominal Multi-Organ Benchmark for Versatile Medical Image Segmentation](https://mlsanity.com/paper/2206.08023/) (2022)
- [SAM-Med3D: Towards General-purpose Segmentation Models for Volumetric Medical Images](https://mlsanity.com/paper/2310.15161/) (2023)
- [MedSAM2: Segment Anything in 3D Medical Images and Videos](https://mlsanity.com/paper/2504.03600/) (2025)
- [Multi-organ Segmentation over Partially Labeled Datasets with Multi-scale Feature Abstraction](https://mlsanity.com/paper/2001.00208/) (2020)
- [nnInteractive: Redefining 3D Promptable Segmentation](https://mlsanity.com/paper/2503.08373/) (2025)
- [Learning from partially labeled data for multi-organ and tumor segmentation](https://mlsanity.com/paper/2211.06894/) (2022)

## Abstract (arXiv)

Automated medical image segmentation has achieved remarkable progress with fully labeled data. However, site-specific clinical priorities and the high cost of manual annotation often yield scans with only a subset of organs labeled, leading to the partially labeled problem that degrades performance. To address this issue, we propose IPnP, an Iteratively Prompting and Pseudo-labeling framework, for partially labeled medical image segmentation. IPnP iteratively generates and refines pseudo-labels for unlabeled organs through collaboration between a trainable segmentation network (specialist) and a frozen foundation model (generalist), progressively recovering full-organ supervision. On the public dataset AMOS with the simulated partial-label setting, IPnP consistently improves segmentation performance over prior methods and approaches the performance of the fully labeled reference. We further evaluate on a private, partially labeled dataset of 210 head-and-neck cancer patients and demonstrate our effectiveness in real-world clinical settings.