# Semi-supervised Segmentation of Histopathology Images with Noise-Aware Topological Consistency

arXiv: https://arxiv.org/abs/2311.16447 · HTML: https://mlsanity.com/paper/2311.16447/

## Key facts

- Cited by 11 papers in the map (data through 14 Oct 2026).
- Builds on 39 of its 65 references that are in the map.
- First posted on arXiv 28 Nov 2023.

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

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation](https://mlsanity.com/paper/1802.02611/) (2018)
- [Pyramid Scene Parsing Network](https://mlsanity.com/paper/1612.01105/) (2016)
- [FixMatch: Simplifying Semi-Supervised Learning with Consistency and Confidence](https://mlsanity.com/paper/2001.07685/) (2020)
- [UNet++: A Nested U-Net Architecture for Medical Image Segmentation](https://mlsanity.com/paper/1807.10165/) (2018)
- [MixMatch: A Holistic Approach to Semi-Supervised Learning](https://mlsanity.com/paper/1905.02249/) (2019)
- [Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2105.05537/) (2021)
- [ADVENT: Adversarial Entropy Minimization for Domain Adaptation in Semantic Segmentation](https://mlsanity.com/paper/1811.12833/) (2018)
- [Generalised Dice overlap as a deep learning loss function for highly unbalanced segmentations](https://mlsanity.com/paper/1707.03237/) (2017)
- [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)
- [clDice -- A Novel Topology-Preserving Loss Function for Tubular Structure Segmentation](https://mlsanity.com/paper/2003.07311/) (2020)
- [Gland Segmentation in Colon Histology Images: The GlaS Challenge Contest](https://mlsanity.com/paper/1603.00275/) (2016)
- [Topology-Preserving Deep Image Segmentation](https://mlsanity.com/paper/1906.05404/) (2019)
- [UCTransNet: Rethinking the Skip Connections in U-Net from a Channel-wise Perspective with Transformer](https://mlsanity.com/paper/2109.04335/) (2021)
- [Transformation Consistent Self-ensembling Model for Semi-supervised Medical Image Segmentation](https://mlsanity.com/paper/1903.00348/) (2019)
- [A Topological Loss Function for Deep-Learning based Image Segmentation using Persistent Homology](https://mlsanity.com/paper/1910.01877/) (2019)
- [Mutual Consistency Learning for Semi-supervised Medical Image Segmentation](https://mlsanity.com/paper/2109.09960/) (2021)
- [MILD-Net: Minimal Information Loss Dilated Network for Gland Instance Segmentation in Colon Histology Images](https://mlsanity.com/paper/1806.01963/) (2018)
- [SimCVD: Simple Contrastive Voxel-Wise Representation Distillation for Semi-Supervised Medical Image Segmentation](https://mlsanity.com/paper/2108.06227/) (2021)
- [Learning with Limited Annotations: A Survey on Deep Semi-Supervised Learning for Medical Image Segmentation](https://mlsanity.com/paper/2207.14191/) (2022)
- [Topology-Aware Segmentation Using Discrete Morse Theory](https://mlsanity.com/paper/2103.09992/) (2021)
- [Inconsistency-aware Uncertainty Estimation for Semi-supervised Medical Image Segmentation](https://mlsanity.com/paper/2110.08762/) (2021)
- [BoostMIS: Boosting Medical Image Semi-supervised Learning with Adaptive Pseudo Labeling and Informative Active Annotation](https://mlsanity.com/paper/2203.02533/) (2022)
- [Enhancing Pseudo Label Quality for Semi-Supervised Domain-Generalized Medical Image Segmentation](https://mlsanity.com/paper/2201.08657/) (2022)
- [Topologically faithful image segmentation via induced matching of persistence barcodes](https://mlsanity.com/paper/2211.15272/) (2022)
- [Rethinking Semi-Supervised Medical Image Segmentation: A Variance-Reduction Perspective](https://mlsanity.com/paper/2302.01735/) (2023)
- [Geometry Helps to Compare Persistence Diagrams](https://mlsanity.com/paper/1606.03357/) (2016)
- [Semi-Supervised Semantic Segmentation via Gentle Teaching Assistant](https://mlsanity.com/paper/2301.07340/) (2023)
- [Reference-guided Pseudo-Label Generation for Medical Semantic Segmentation](https://mlsanity.com/paper/2112.00735/) (2021)

## Built on by (most cited first, 11 of 11)

- [Model Extraction Attacks Revisited](https://mlsanity.com/paper/2312.05386/) (2023)
- [TopoCellGen: Generating Histopathology Cell Topology with a Diffusion Model](https://mlsanity.com/paper/2412.06011/) (2024)
- [TopoDiffusionNet: A Topology-aware Diffusion Model](https://mlsanity.com/paper/2410.16646/) (2024)
- [Act Like a Pathologist: Tissue-Aware Whole Slide Image Reasoning](https://mlsanity.com/paper/2603.00667/) (2026)
- [RankByGene: Gene-Guided Histopathology Representation Learning Through Cross-Modal Ranking Consistency](https://mlsanity.com/paper/2411.15076/) (2024)
- [MATCH: Multi-faceted Adaptive Topo-Consistency for Semi-Supervised Histopathology Segmentation](https://mlsanity.com/paper/2510.01532/) (2025)
- [UniSemAlign: Text-Prototype Alignment with a Foundation Encoder for Semi-Supervised Histopathology Segmentation](https://mlsanity.com/paper/2604.09169/) (2026)
- [MorphoSeg: An Uncertainty-Aware Deep Learning Method for Biomedical Segmentation of Complex Cellular Morphologies](https://mlsanity.com/paper/2409.17110/) (2024)
- [Topo-R1: Detecting Topological Anomalies via Vision-Language Models](https://mlsanity.com/paper/2603.13054/) (2026)
- [Towards High-Quality Image Segmentation: Improving Topology Accuracy by Penalizing Neighbor Pixels](https://mlsanity.com/paper/2603.18671/) (2026)
- [Widest-Path Reachability Fields for Connectivity-Preserving Slender Structure Segmentation](https://mlsanity.com/paper/2607.07123/) (2026)

## Abstract (arXiv)

In digital pathology, segmenting densely distributed objects like glands and nuclei is crucial for downstream analysis. Since detailed pixel-wise annotations are very time-consuming, we need semi-supervised segmentation methods that can learn from unlabeled images. Existing semi-supervised methods are often prone to topological errors, e.g., missing or incorrectly merged/separated glands or nuclei. To address this issue, we propose TopoSemiSeg, the first semi-supervised method that learns the topological representation from unlabeled histopathology images. The major challenge is for unlabeled images; we only have predictions carrying noisy topology. To this end, we introduce a noise-aware topological consistency loss to align the representations of a teacher and a student model. By decomposing the topology of the prediction into signal topology and noisy topology, we ensure that the models learn the true topological signals and become robust to noise. Extensive experiments on public histopathology image datasets show the superiority of our method, especially on topology-aware evaluation metrics. Code is available at https://github.com/Melon-Xu/TopoSemiSeg.