# MSE-Nets: Multi-annotated Semi-supervised Ensemble Networks for Improving Segmentation of Medical Image with Ambiguous Boundaries

arXiv: https://arxiv.org/abs/2311.10380 · HTML: https://mlsanity.com/paper/2311.10380/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 24 of its 41 references that are in the map.
- First posted on arXiv 17 Nov 2023.

## Builds on (most cited first, 24 of 24)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Fully Convolutional Networks for Semantic Segmentation](https://mlsanity.com/paper/1411.4038/) (2014)
- [DeepLab: Semantic Image Segmentation with Deep Convolutional Nets, Atrous Convolution, and Fully Connected CRFs](https://mlsanity.com/paper/1606.00915/) (2016)
- [CutMix: Regularization Strategy to Train Strong Classifiers with Localizable Features](https://mlsanity.com/paper/1905.04899/) (2019)
- [SegNet: A Deep Convolutional Encoder-Decoder Architecture for Image Segmentation](https://mlsanity.com/paper/1511.00561/) (2015)
- [Co-teaching: Robust Training of Deep Neural Networks with Extremely Noisy Labels](https://mlsanity.com/paper/1804.06872/) (2018)
- [Skin Lesion Analysis Toward Melanoma Detection: A Challenge at the 2017 International Symposium on Biomedical Imaging (ISBI), Hosted by the International Skin Imaging Collaboration (ISIC)](https://mlsanity.com/paper/1710.05006/) (2017)
- [Semi-Supervised Semantic Segmentation with Cross Pseudo Supervision](https://mlsanity.com/paper/2106.01226/) (2021)
- [Uncertainty-aware Self-ensembling Model for Semi-supervised 3D Left Atrium Segmentation](https://mlsanity.com/paper/1907.07034/) (2019)
- [Semi-Supervised Semantic Segmentation with Cross-Consistency Training](https://mlsanity.com/paper/2003.09005/) (2020)
- [Interpolation Consistency Training for Semi-Supervised Learning](https://mlsanity.com/paper/1903.03825/) (2019)
- [REFUGE Challenge: A Unified Framework for Evaluating Automated Methods for Glaucoma Assessment from Fundus Photographs](https://mlsanity.com/paper/1910.03667/) (2019)
- [Semi-supervised Medical Image Segmentation through Dual-task Consistency](https://mlsanity.com/paper/2009.04448/) (2020)
- [LinkNet: Exploiting Encoder Representations for Efficient Semantic Segmentation](https://mlsanity.com/paper/1707.03718/) (2017)
- [Shape-aware Semi-supervised 3D Semantic Segmentation for Medical Images](https://mlsanity.com/paper/2007.10732/) (2020)
- [Dual Student: Breaking the Limits of the Teacher in Semi-supervised Learning](https://mlsanity.com/paper/1909.01804/) (2019)
- [Semi-Supervised Brain Lesion Segmentation with an Adapted Mean Teacher Model](https://mlsanity.com/paper/1903.01248/) (2019)
- [Structured Consistency Loss for semi-supervised semantic segmentation](https://mlsanity.com/paper/2001.04647/) (2020)
- [Pick-and-Learn: Automatic Quality Evaluation for Noisy-Labeled Image Segmentation](https://mlsanity.com/paper/1907.11835/) (2019)
- [D-LEMA: Deep Learning Ensembles from Multiple Annotations -- Application to Skin Lesion Segmentation](https://mlsanity.com/paper/2012.07206/) (2020)
- [Distilling effective supervision for robust medical image segmentation with noisy labels](https://mlsanity.com/paper/2106.11099/) (2021)
- [Label noise in segmentation networks : mitigation must deal with bias](https://mlsanity.com/paper/2107.02189/) (2021)
- [Handling Inter-Annotator Agreement for Automated Skin Lesion Segmentation](https://mlsanity.com/paper/1906.02415/) (2019)
- [Less is More: Sample Selection and Label Conditioning Improve Skin Lesion Segmentation](https://mlsanity.com/paper/2004.13856/) (2020)

## Built on by (most cited first, 1 of 1)

- [What Can We Learn from Inter-Annotator Variability in Skin Lesion Segmentation?](https://mlsanity.com/paper/2508.09381/) (2025)

## Abstract (arXiv)

Medical image segmentation annotations exhibit variations among experts due to the ambiguous boundaries of segmented objects and backgrounds in medical images. Although using multiple annotations for each image in the fully-supervised has been extensively studied for training deep models, obtaining a large amount of multi-annotated data is challenging due to the substantial time and manpower costs required for segmentation annotations, resulting in most images lacking any annotations. To address this, we propose Multi-annotated Semi-supervised Ensemble Networks (MSE-Nets) for learning segmentation from limited multi-annotated and abundant unannotated data. Specifically, we introduce the Network Pairwise Consistency Enhancement (NPCE) module and Multi-Network Pseudo Supervised (MNPS) module to enhance MSE-Nets for the segmentation task by considering two major factors: (1) to optimize the utilization of all accessible multi-annotated data, the NPCE separates (dis)agreement annotations of multi-annotated data at the pixel level and handles agreement and disagreement annotations in different ways, (2) to mitigate the introduction of imprecise pseudo-labels, the MNPS extends the training data by leveraging consistent pseudo-labels from unannotated data. Finally, we improve confidence calibration by averaging the predictions of base networks. Experiments on the ISIC dataset show that we reduced the demand for multi-annotated data by 97.75% and narrowed the gap with the best fully-supervised baseline to just a Jaccard index of 4%. Furthermore, compared to other semi-supervised methods that rely only on a single annotation or a combined fusion approach, the comprehensive experimental results on ISIC and RIGA datasets demonstrate the superior performance of our proposed method in medical image segmentation with ambiguous boundaries.