Weakly Supervised Image Segmentation

Medical experts often manually segment images to obtain diagnostic statistics and discard the resulting annotations. We aim to train segmentation models to alleviate this burden, but constrained to the retained summary statistics (e.g., the area of the annotated region). Empirical results suggest that statistics alone are insufficient for this task, but adding weak information in the form of a few pixels within the area of interest significantly improves performance. We use a novel loss function that combines terms for image reconstruction quality, matching to summary statistics, and overlap between the predicted foreground and the weak supervisory signal. Experiments on standard image, ultrasound (breast cancer), and Computed Tomography (CT) scan (kidney tumors) data demonstrate the utility and potential of the approach.

In pathology, the spatial distribution and proportions of tissue types are key indicators of disease progression, and are more readily available than fine-grained annotations. However, these assessments are rarely mapped to pixel-wise segmentation. The task is fundamentally underdetermined, as many spatially distinct segmentations can satisfy the same global proportions in the absence of pixel-wise constraints. To address this, we introduce Variational Segmentation from Label Proportions (VSLP), a two-stage framework that infers dense segmentations from global label proportions, without any pixel-level annotations. This framework first leverages a pre-trained transformer model with test-time augmentation to produce a pixel-wise confidence estimate. In the second stage, these estimates are fused by solving a variational optimization problem that incorporates a Wasserstein data fidelity term alongside a learned regularizer. Unlike end-to-end networks, our variational method can visualize the fidelity-regularization energy, resulting in more interpretable segmentation. We validate our approach on two public datasets, achieving superior performance over existing weakly supervised and unsupervised methods. For one of these datasets, proportions have been estimated by an experienced pathologist to provide a realistic benchmark to the community. Furthermore, the method scales to an in-house dataset with noisy pathologist labels, severely outperforming state-of-the-art methods, thereby demonstrating practical applicability. The code and data will be made publicly available upon acceptance at https://github.com/xiaoliangpi/VSLP.

Accurate defect segmentation is critical for industrial inspection, yet dense pixel-level annotations are rarely available. A common workaround is to convert inexpensive bounding boxes into pseudo-masks using foundation segmentation models such as the Segment Anything Model (SAM). However, these pseudo-labels are systematically noisy on industrial surfaces, often hallucinating background structure while missing sparse defects. To address this limitation, a noise-robust box-to-pixel distillation framework, Boxes2Pixels, is proposed that treats SAM as a noisy teacher rather than a source of ground-truth supervision. Bounding boxes are converted into pseudo-masks offline by SAM, and a compact student is trained with (i) a hierarchical decoder over frozen DINOv2 features for semantic stability, (ii) an auxiliary binary localization head to decouple sparse foreground discovery from class prediction, and (iii) a one-sided online self-correction mechanism that relaxes background supervision when the student is confident, targeting teacher false negatives. On a manually annotated wind turbine inspection benchmark, the proposed Boxes2Pixels improves anomaly mIoU by +6.97 and binary IoU by +9.71 over the strongest baseline trained under identical weak supervision. Moreover, online self-correction increases the binary recall by +18.56, while the model employs 80% fewer trainable parameters. Code is available at https://github.com/CLendering/Boxes2Pixels.

Dense annotations, such as segmentation masks, are expensive and time-consuming to obtain, especially for 3D medical images where expert voxel-wise labeling is required. Weakly supervised approaches aim to address this limitation, but often rely on attribution-based methods that struggle to accurately capture small structures such as lung nodules. In this paper, we propose a weakly-supervised segmentation method for lung nodules by combining pretrained state-of-the-art rectified flow and predictor models in a plug-and-play manner. Our approach uses training-free guidance of a 3D rectified flow model, requiring only fine-tuning of the predictor using image-level labels and no retraining of the generative model. The proposed method produces improved-quality segmentations for two separate predictors, consistently detecting lung nodules of varying size and shapes. Experiments on LUNA16 demonstrate improvements over baseline methods, highlighting the potential of generative foundation models as tools for weakly supervised 3D medical image segmentation.

Weakly supervised semantic segmentation aims to achieve pixel-level predictions using image-level labels. Existing methods typically entangle semantic recognition and object localization, which often leads models to focus exclusively on sparse discriminative regions. Although foundation models show immense potential, many approaches still follow the tightly coupled optimization paradigm, struggling to effectively alleviate pseudo-label noise and often relying on time-consuming multi-stage retraining or unstable end-to-end joint optimization. To address the above challenges, we present ModuSeg, a training-free weakly supervised semantic segmentation framework centered on explicitly decoupling object discovery and semantic assignment. Specifically, we integrate a general mask proposer to extract geometric proposals with reliable boundaries, while leveraging semantic foundation models to construct an offline feature bank, transforming segmentation into a non-parametric feature retrieval process. Furthermore, we propose semantic boundary purification and soft-masked feature aggregation strategies to effectively mitigate boundary ambiguity and quantization errors, thereby extracting high-quality category prototypes. Extensive experiments demonstrate that the proposed decoupled architecture better preserves fine boundaries without parameter fine-tuning and achieves highly competitive performance on standard benchmark datasets. Code is available at https://github.com/Autumnair007/ModuSeg.

Detecting unseen anomalies in unstructured environments presents a critical challenge for industrial and agricultural applications such as material recycling and weeding. Existing perception systems frequently fail to satisfy the strict operational requirements of these domains, specifically real-time processing, pixel-level segmentation precision, and robust accuracy, due to their reliance on exhaustively annotated datasets. To address these limitations, we propose a weakly supervised pipeline for object segmentation and classification using weak image-level supervision called 'Patch Aggregation for Segmentation of Targets and Anomalies' (PASTA). By comparing an observed scene with a nominal reference, PASTA identifies Target and Anomaly objects through distribution analysis in self-supervised Vision Transformer (ViT) feature spaces. Our pipeline utilizes semantic text-prompts via the Segment Anything Model 3 to guide zero-shot object segmentation. Evaluations on a custom steel scrap recycling dataset and a plant dataset demonstrate a 75.8% training time reduction of our approach to domain-specific baselines. While being domain-agnostic, our method achieves superior Target (up to 88.3% IoU) and Anomaly (up to 63.5% IoU) segmentation performance in the industrial and agricultural domain.

Acoustic borehole images provide high-resolution borehole-wall structure, but large-scale interpretation remains difficult because dense expert annotations are rarely available and subsurface information is intrinsically multimodal. The challenge is developing weakly supervised methods combining two-dimensional image texture with depth-aligned one-dimensional well-logs. Here, we introduce a weakly supervised multimodal segmentation framework that refines threshold-guided pseudo-labels through learned models. This preserves the annotation-free character of classical thresholding and clustering workflows while extending them with denoising, confidence-aware pseudo-supervision, and physically structured fusion. We establish that threshold-guided learned refinement provides the most robust improvement over raw thresholding, denoised thresholding, and latent clustering baselines. Multimodal performance depends strongly on fusion strategy: direct concatenation provides limited gains, whereas depth-aware cross-attention, gated fusion, and confidence-aware modulation substantially improve agreement with the weak supervisory reference. The strongest model, confidence-gated depth-aware cross-attention (CG-DCA), consistently outperforms threshold-based, image-only, and earlier multimodal baselines. Targeted ablations show its advantage depends specifically on confidence-aware fusion and structured local depth interaction rather than model complexity alone. Cross-well analyses confirm this performance is broadly stable. These results establish a practical, scalable framework for annotation-free segmentation, showing multimodal improvement is maximized when auxiliary logs are incorporated selectively and depth-aware.

Infrared small target detection (IRSTD) methods predominantly formulate the task as pixel-level segmentation, which requires costly dense annotations and is not well suited to tiny targets with weak texture and ambiguous boundaries. To address this issue, we propose Point-to-Mask, a framework that bridges low-cost point supervision and mask-level detection through two components: a Physics-driven Adaptive Mask Generation (PAMG) module that converts point annotations into compact target masks and geometric cues, and a lightweight Radius-aware Point Regression Network (RPR-Net) that reformulates IRSTD as target center localization and effective radius regression using spatiotemporal motion cues. The two modules form a closed loop: PAMG generates pseudo masks and geometric supervision during training, while the geometric predictions of RPR-Net are fed back to PAMG for pixel-level mask recovery during inference. To facilitate systematic evaluation, we further construct SIRSTD-Pixel, a sequential dataset with refined pixel-level annotations. Experiments show that the proposed framework achieves strong pseudo-label quality, high detection accuracy, and efficient inference, approaching full-supervision performance under point-supervised settings with substantially lower annotation cost. Code and datasets will be available at: https://github.com/GaoScience/point-to-mask.

High-resolution sea ice mapping using Synthetic Aperture Radar (SAR) is crucial for Arctic navigation and climate monitoring. However, operational ice charts provide only coarse, region-level polygons (weak labels), forcing automated segmentation models to struggle with pixel-level accuracy and often yielding under-confident, blurred concentration maps. In this paper, we propose a weakly supervised deep learning pipeline that fuses Sentinel-1 SAR and AMSR-2 radiometry data using a U-Net architecture trained with a region-based loss. To overcome the severe under-confidence caused by weak labels, we introduce an Analytical Logit Scaling method applied post-inference. By dynamically calculating the temperature and bias based on the latent space percentiles (2% and 98%) of each scene, we force a physical binarization of the predictions. This adaptive scaling acts as a topological extractor, successfully revealing fine-grained sea ice fractures (leads) at a 40-meter resolution without requiring any manual pixel-level annotations. Our approach not only resolves local topology but also perfectly preserves regional macroscopic concentrations, achieving a 78% accuracy on highly fragmented summer scenes, thereby bridging the gap between weakly supervised learning and high-resolution physical segmentation.

Single-point annotation is increasingly prominent in visual tasks for labeling cost reduction. However, it challenges tasks requiring high precision, such as the point-prompted instance segmentation (PPIS) task, which aims to estimate precise masks using single-point prompts to train a segmentation network. Due to the constraints of point annotations, granularity ambiguity and boundary uncertainty arise the difficulty distinguishing between different levels of detail (eg. whole object vs. parts) and the challenge of precisely delineating object boundaries. Previous works have usually inherited the paradigm of mask generation along with proposal selection to achieve PPIS. However, proposal selection relies solely on category information, failing to resolve the ambiguity of different granularity. Furthermore, mask generators offer only finite discrete solutions that often deviate from actual masks, particularly at boundaries. To address these issues, we propose the Semantic-Aware Point-Prompted Instance Segmentation Network (SAPNet). It integrates Point Distance Guidance and Box Mining Strategy to tackle group and local issues caused by the point's granularity ambiguity. Additionally, we incorporate completeness scores within proposals to add spatial granularity awareness, enhancing multiple instance learning (MIL) in proposal selection termed S-MIL. The Multi-level Affinity Refinement conveys pixel and semantic clues, narrowing boundary uncertainty during mask refinement. These modules culminate in SAPNet++, mitigating point prompt's granularity ambiguity and boundary uncertainty and significantly improving segmentation performance. Extensive experiments on four challenging datasets validate the effectiveness of our methods, highlighting the potential to advance PPIS.

Report-supervised (RSuper) learning seeks to alleviate the need for dense tumor voxel labels with constraints derived from radiology reports (e.g., volumes, counts, sizes, locations). In MRI studies of brain tumors, however, we often involve multi-parametric scans and substructures. Here, fine-grained modality/parameter-wise reports are usually provided along with global findings and are correlated with different substructures. Moreover, the reports often describe only the largest lesion and provide qualitative or uncertain cues (mild,'' possible''). Classical RSuper losses (e.g., sum volume consistency) can over-constrain or hallucinate unreported findings under such incompleteness, and are unable to utilize these hierarchical findings or exploit the priors of varied lesion types in a merged dataset. We explicitly parse the global quantitative and modality-wise qualitative findings and introduce a unified, one-sided, uncertainty-aware formulation (MS-RSuper) that: (i) aligns modality-specific qualitative cues (e.g., T1c enhancement, FLAIR edema) with their corresponding substructures using existence and absence losses; (ii) enforces one-sided lower-bounds for partial quantitative cues (e.g., largest lesion size, minimal multiplicity); and (iii) adds extra- vs. intra-axial anatomical priors to respect cohort differences. Certainty tokens scale penalties; missing cues are down-weighted. On 1238 report-labeled BraTS-MET/MEN scans, our MS-RSuper largely outperforms both a sparsely-supervised baseline and a naive RSuper method.

Domain adaptive segmentation (DAS) is a promising paradigm for delineating intracellular structures from various large-scale electron microscopy (EM) without incurring extensive annotated data in each domain. However, the prevalent unsupervised domain adaptation (UDA) strategies often demonstrate limited and biased performance, which hinders their practical applications. In this study, we explore sparse points and local human preferences as weak labels in the target domain, thereby presenting a more realistic yet annotation-efficient setting. Specifically, we develop Prefer-DAS, which pioneers sparse promptable learning and local preference alignment. The Prefer-DAS is a promptable multitask model that integrates self-training and prompt-guided contrastive learning. Unlike SAM-like methods, the Prefer-DAS allows for the use of full, partial, and even no point prompts during both training and inference stages and thus enables interactive segmentation. Instead of using image-level human preference alignment for segmentation, we introduce Local direct Preference Optimization (LPO), plug-and-play solutions for alignment with spatially varying human feedback. To address potential missing feedback, we also introduce Unsupervised Preference Optimization (UPO), which leverages self-learned preferences. As a result, the Prefer-DAS model can effectively perform both weakly-supervised and unsupervised DAS, depending on the availability of points and human preferences. Comprehensive experiments on four challenging DAS tasks demonstrate that our model outperforms SAM-like methods as well as unsupervised and weakly-supervised DAS methods in both automatic and interactive segmentation modes, highlighting strong generalizability and flexibility. Additionally, the performance of our model is very close to or even exceeds that of supervised models.

Robust anatomical segmentation of chest X-rays (CXRs) remains challenging due to the scarcity of comprehensive annotations and the substantial variability of real-world acquisition conditions. We propose AnyCXR, a unified framework that enables generalizable multi-organ segmentation across arbitrary CXR projection angles using only synthetic supervision. The method combines a Multi-stage Domain Randomization (MSDR) engine, which generates over 100,000 anatomically faithful and highly diverse synthetic radiographs from 3D CT volumes, with a Conditional Joint Annotation Regularization (CAR) learning strategy that leverages partial and imperfect labels by enforcing anatomical consistency in a latent space. Trained entirely on synthetic data, AnyCXR achieves strong zero-shot generalization on multiple real-world datasets, providing accurate delineation of 54 anatomical structures in PA, lateral, and oblique views. The resulting segmentation maps support downstream clinical tasks, including automated cardiothoracic ratio estimation, spine curvature assessment, and disease classification, where the incorporation of anatomical priors improves diagnostic performance. These results demonstrate that AnyCXR establishes a scalable and reliable foundation for anatomy-aware CXR analysis and offers a practical pathway toward reducing annotation burdens while improving robustness across diverse imaging conditions.

Meta-learning aims to uniformly sample homogeneous support-query pairs, characterized by the same categories and similar attributes, and extract useful inductive biases through identical network architectures. However, this identical network design results in over-semantic homogenization. To address this, we propose a novel homologous but heterogeneous network. By treating support-query pairs as dual perspectives, we introduce heterogeneous visual aggregation (HA) modules to enhance complementarity while preserving semantic commonality. To further reduce semantic noise and amplify the uniqueness of heterogeneous semantics, we design a heterogeneous transfer (HT) module. Finally, we propose heterogeneous CLIP (HC) textual information to enhance the generalization capability of multimodal models. In the weakly-supervised few-shot semantic segmentation (WFSS) task, with only 1/24 of the parameters of existing state-of-the-art models, TLG achieves a 13.2% improvement on Pascal-5\textsuperscript{i} and a 9.7% improvement on COCO-20\textsuperscript{i}. To the best of our knowledge, TLG is also the first weakly supervised (image-level) model that outperforms fully supervised (pixel-level) models under the same backbone architectures. The code is available at https://github.com/jarch-ma/TLG.

Semantic segmentation in open-vocabulary scenarios presents significant challenges due to the wide range and granularity of semantic categories. Existing weakly-supervised methods often rely on category-specific supervision and ill-suited feature construction methods for contrastive learning, leading to semantic misalignment and poor performance. In this work, we introduce a novel weakly-supervised approach, SynSeg, to address the challenges. SynSeg performs Multi-Category Contrastive Learning (MCCL) as a stronger training signal which robustly injecting intra- and inter-category knowledge during training. We also propose a new feature reconstruction framework named Feature Synergy Structure (FSS). FSS reconstructs discriminative features for contrastive learning through prior fusion and semantic-activation-map enhancement, effectively avoiding the foreground bias introduced by the visual encoder. Furthermore, SynSeg is a lightweight end-to-end solution capable for real-time inference. In general, SynSeg effectively improves the abilities in semantic localization and discrimination under weak supervision in an efficient manner. Extensive experiments on benchmarks demonstrate that our method outperforms state-of-the-art (SOTA) performance, with mIoU score gains ranging from 0.6% up to 8.9% across all reported benchmarks.

We propose a vision transformer (ViT)-based deep learning framework to refine disaster-affected area segmentation from remote sensing imagery, aiming to support and enhance the Emergent Value Added Product (EVAP) developed by the Taiwan Space Agency (TASA). The process starts with a small set of manually annotated regions. We then apply principal component analysis (PCA)-based feature space analysis and construct a confidence index (CI) to expand these labels, producing a weakly supervised training set. These expanded labels are then used to train ViT-based encoder-decoder models with multi-band inputs from Sentinel-2 and Formosat-5 imagery. Our architecture supports multiple decoder variants and multi-stage loss strategies to improve performance under limited supervision. During the evaluation, model predictions are compared with higher-resolution EVAP output to assess spatial coherence and segmentation consistency. Case studies on the 2022 Poyang Lake drought and the 2023 Rhodes wildfire demonstrate that our framework improves the smoothness and reliability of segmentation results, offering a scalable approach for disaster mapping when accurate ground truth is unavailable.