Align and Segment: Unsupervised Learning for Building Segmentation From Misaligned Labels
Authors: Venkanna Babu Guthula, Oswin Krause, Dimitri Gominski, Hui Zhang, Johan Mottelson, Ankit Kariryaa, Nico Lang, Christian Igel
Organizations: University of Copenhagen, Copenhagen, Denmark · Royal Danish Academy, Copenhagen, Denmark
Abstract
Supervised learning for image segmentation typically requires spatially aligned image and label sets. When images and labels originate from different sources, the pairing may be misaligned, which can significantly deteriorate the performance of the learned models. This is especially common in remote sensing, when aerial or satellite images are co-registered with labels from another source (e.g., OpenStreetMap). In this work, we propose a novel approach for training on misaligned labels, where we simultaneously learn the label alignment. Our align and segment (AnS) approach builds on the spatial transformer module to transform the misaligned labels using an affine transformation to provide a better learning target for a canonical semantic segmentation network. We prevent shortcut learning of misaligned labels in these semantic segmentation networks through a self-supervised regularization loss and show that it is complementary to data augmentation, especially for systematically misaligned training data. A decisive characteristic of our AnS approach is that it learns without requiring any golden labels. We experimentally show on both synthetic and real-world data from different cities that our approach enables high-quality building segmentation and precise label-image alignment at the same time. Code and derived datasets are available at https://github.com/venkanna37/align-and-segment
Labeled datasets reflect the biases of their annotation pipelines, which sometimes introduce label bias: group-conditional label errors that cause systematic performance disparities across demographic subgroups. Label bias in image segmentation remains underexplored, as even detecting it typically requires clean, unbiased annotations, which are not readily available. We present a data-centric adaptation of Confident Learning to segmentation, allowing detection of label bias directly in the training data without a clean, unbiased ground truth. By comparing the provided training labels to the model's confident predictions, we isolate directional errors that quantify the presence and nature of bias, where standard overlap metrics like Dice fail. We further show that label bias influences subgroup separability in the encoder's feature space, an artifact we leverage for bias mitigation rather than suppressing it. We evaluate three datasets, spanning from synthetic to real-life bias, showing how our framework reliably detects and mitigates bias without access to clean labels, achieving equitable performance across experimental conditions.
In practical settings, medical image segmentation models are often developed with limited annotated data rather than fully labeled datasets. Training frequently begins in ultra-low labeled regimes where only a small number of volumes are annotated. In such scenarios, practitioners must simultaneously decide which cases to annotate and how to best use the remaining unlabeled data. Although active learning (AL) and semi-supervised learning (SSL) both target annotation scarcity, they are typically designed and optimized independently, resulting in objective mismatch and unstable training during early-stage "cold start" conditions. We propose RegAL, a unified active semi-supervised framework governed by a shared topology-aware Pareto optimization that couples sample acquisition with unlabeled data utilization. RegAL evaluates images along three complementary axes, voxel-wise uncertainty, feature diversity, and a novel topological consistency metric, to select anatomically informative edge cases for annotation. On the other hand, the same criteria are used to identify geometrically stable atlas candidates for diffeomorphic registration-guided augmentation to train a self-supervised Mean Teacher segmentation network. Across BraTS 2021, dHCP, and ProstateX, RegAL remains stable with few labeled volumes and consistently outperforms state-of-the-art AL, SSL, and active semi-supervised baselines across Dice and boundary-distance (ASD, HD95) metrics under extreme annotation scarcity.
Semi-supervised learning addresses label scarcity and high annotation costs in medical image segmentation by exploiting the latent information in unlabeled data to enhance model performance. Traditional discriminative segmentation relies on segmentation masks, neglecting feature-level distribution constraints. This limits robust semantic representation learning and adaptive modeling of unlabeled data in scenarios with few labels. To address these limitations, we propose SemiGDA, a novel Generative Dual-distribution Alignment framework for semi-supervised medical image segmentation. Our SemiGDA overcomes the reliance of discriminative methods on large labeled datasets by aligning feature and semantic distributions to boost semantic learning and scene adaptability. Specifically, we propose a Dual-distribution Alignment Module (DAM), which employs two structurally distinct encoders to model image and mask feature distributions. It enforces their alignment in the latent space via distributional constraints, establishing structured feature consistency. Moreover, we design a Consistency-Driven Skip Adapter (CDSA) strategy, which introduces dual skip adapters (Image and Mask) to fuse multi-scale features via skip connections. Using a consistency loss, CDSA enhances cross-branch semantic alignment and reinforces fine-grained semantic consistency. Experimental results on diverse medical datasets show that our method outperforms other state-of-the-art semi-supervised segmentation methods. Code is released at: https://github.com/taozh2017/SemiGDA.