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arXiv2025

UP2D: Uncertainty-aware Progressive Pseudo-label Denoising for Source-Free Domain Adaptive Medical Image Segmentation

Medical image segmentation models face severe performance drops under domain shifts, especially when data sharing constraints prevent access to source images. We present a novel Uncertainty-aware Progressive Pseudo-label Denoising (UP2D) framework for source-free domain adaptation (SFDA), designed to mitigate noisy pseudo-labels and class imbalance during adaptation. UP2D integrates three key components: (i) a Refined Prototype Filtering module that suppresses uninformative regions and constructs reliable class prototypes to denoise pseudo-labels, (ii) an Uncertainty-Guided EMA (UG-EMA) strategy that selectively updates the teacher model based on spatially weighted boundary uncertainty, and (iii) a quantile-based entropy minimization scheme that focuses learning on ambiguous regions while avoiding overconfidence on easy pixels. This single-stage student-teacher framework progressively improves pseudo-label quality and reduces confirmation bias. Extensive experiments on three challenging retinal fundus benchmarks demonstrate that UP2D achieves state-of-the-art performance across both standard and open-domain settings, outperforming prior UDA and SFDA approaches while maintaining superior boundary precision.

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arXiv2026

SpectraFlow: Unifying Structural Pretraining and Frequency Adaptation for Medical Image Segmentation

Medical image segmentation remains challenging in low-data regimes, where scarce annotations often yield poor generalization and ambiguous boundaries with missing fine structures. Recent self-supervised pretraining has improved transferability, but it often exhibits a texture bias. In contrast, accurate segmentation is inherently geometry-aware and depends on both topological consistency and precise boundary preservation. To address this problem, we propose a two-stage framework that couples structure-aware encoder pretraining with boundary-oriented decoding. In Stage-1, we aim to learn structure-aware representations for downstream segmentation in low-data regimes. To this end, we propose Mixed-Domain MeanFlow Pretraining, which aligns images and binary masks in a shared latent space through latent transport regression, where masks act as conditional structural guidance rather than prediction targets, making the pretraining task-agnostic. To further improve training stability under scarce supervision, we incorporate a lightweight Dispersive Loss to prevent representation collapse. In Stage-2, we fine-tune the pretrained encoder with a lightweight decoder that combines Direct Attentional Fusion for adaptive cross-scale gating and Frequency-Directional Dynamic Convolution for high-frequency boundary refinement under appearance variation. Experiments on ISIC-2016, Kvasir-SEG, and GlaS demonstrate consistent gains over state-of-the-art methods, with improved robustness in low-data settings and sharper boundary delineation.

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arXiv2025

Learning from Disagreement: A Group Decision Simulation Framework for Robust Medical Image Segmentation

Medical image segmentation annotation suffers from inter-rater variability (IRV) due to differences in annotators' expertise and the inherent blurriness of medical images. Standard approaches that simply average expert labels are flawed, as they discard the valuable clinical uncertainty revealed in disagreements. We introduce a fundamentally new approach with our group decision simulation framework, which works by mimicking the collaborative decision-making process of a clinical panel. Under this framework, an Expert Signature Generator (ESG) learns to represent individual annotator styles in a unique latent space. A Simulated Consultation Module (SCM) then intelligently generates the final segmentation by sampling from this space. This method achieved state-of-the-art results on challenging CBCT and MRI datasets (92.11% and 90.72% Dice scores). By treating expert disagreement as a useful signal instead of noise, our work provides a clear path toward more robust and trustworthy AI systems for healthcare.

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arXiv2020

SoftSeg: Advantages of soft versus binary training for image segmentation

Most image segmentation algorithms are trained on binary masks formulated as a classification task per pixel. However, in applications such as medical imaging, this "black-and-white" approach is too constraining because the contrast between two tissues is often ill-defined, i.e., the voxels located on objects' edges contain a mixture of tissues. Consequently, assigning a single "hard" label can result in a detrimental approximation. Instead, a soft prediction containing non-binary values would overcome that limitation. We introduce SoftSeg, a deep learning training approach that takes advantage of soft ground truth labels, and is not bound to binary predictions. SoftSeg aims at solving a regression instead of a classification problem. This is achieved by using (i) no binarization after preprocessing and data augmentation, (ii) a normalized ReLU final activation layer (instead of sigmoid), and (iii) a regression loss function (instead of the traditional Dice loss). We assess the impact of these three features on three open-source MRI segmentation datasets from the spinal cord gray matter, the multiple sclerosis brain lesion, and the multimodal brain tumor segmentation challenges. Across multiple cross-validation iterations, SoftSeg outperformed the conventional approach, leading to an increase in Dice score of 2.0% on the gray matter dataset (p=0.001), 3.3% for the MS lesions, and 6.5% for the brain tumors. SoftSeg produces consistent soft predictions at tissues' interfaces and shows an increased sensitivity for small objects. The richness of soft labels could represent the inter-expert variability, the partial volume effect, and complement the model uncertainty estimation. The developed training pipeline can easily be incorporated into most of the existing deep learning architectures. It is already implemented in the freely-available deep learning toolbox ivadomed (https://ivadomed.org).

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arXiv2024

SAM2-UNet: Segment Anything 2 Makes Strong Encoder for Natural and Medical Image Segmentation

Image segmentation plays an important role in vision understanding. Recently, the emerging vision foundation models continuously achieved superior performance on various tasks. Following such success, in this paper, we prove that the Segment Anything Model 2 (SAM2) can be a strong encoder for U-shaped segmentation models. We propose a simple but effective framework, termed SAM2-UNet, for versatile image segmentation. Specifically, SAM2-UNet adopts the Hiera backbone of SAM2 as the encoder, while the decoder uses the classic U-shaped design. Additionally, adapters are inserted into the encoder to allow parameter-efficient fine-tuning. Preliminary experiments on various downstream tasks, such as camouflaged object detection, salient object detection, marine animal segmentation, mirror detection, and polyp segmentation, demonstrate that our SAM2-UNet can simply beat existing specialized state-of-the-art methods without bells and whistles. Project page: \url{https://github.com/WZH0120/SAM2-UNet}.

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arXiv2023

InterFormer: Real-time Interactive Image Segmentation

Interactive image segmentation enables annotators to efficiently perform pixel-level annotation for segmentation tasks. However, the existing interactive segmentation pipeline suffers from inefficient computations of interactive models because of the following two issues. First, annotators' later click is based on models' feedback of annotators' former click. This serial interaction is unable to utilize model's parallelism capabilities. Second, in each interaction step, the model handles the invariant image along with the sparse variable clicks, resulting in a process that's highly repetitive and redundant. For efficient computations, we propose a method named InterFormer that follows a new pipeline to address these issues. InterFormer extracts and preprocesses the computationally time-consuming part i.e. image processing from the existing process. Specifically, InterFormer employs a large vision transformer (ViT) on high-performance devices to preprocess images in parallel, and then uses a lightweight module called interactive multi-head self attention (I-MSA) for interactive segmentation. Furthermore, the I-MSA module's deployment on low-power devices extends the practical application of interactive segmentation. The I-MSA module utilizes the preprocessed features to efficiently response to the annotator inputs in real-time. The experiments on several datasets demonstrate the effectiveness of InterFormer, which outperforms previous interactive segmentation models in terms of computational efficiency and segmentation quality, achieve real-time high-quality interactive segmentation on CPU-only devices. The code is available at https://github.com/YouHuang67/InterFormer.

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arXiv2026

CANAL: Channel-Aware Noise Allocation for Differentially Private Feature Distillation in Medical Image Segmentation

Medical image segmentation needs diverse training data, but hospitals hold complementary scans they cannot share for privacy and regulatory reasons. Knowledge distillation can bridge this gap by exporting learned feature representations instead of images, but those representations still encode patient-specific anatomy and remain vulnerable to membership-inference and feature-inversion attacks. Adding calibrated Gaussian noise restores a differential-privacy guarantee, yet three issues have been overlooked. First, prior DP feature-distillation pipelines re-sample noise at every student iteration, so each patient image is released many times and the privacy cost composes over those releases, growing by orders of magnitude. We present a sample-once-per-image release, realized by a single precomputation pass, under which each patient contributes one release. Second, uniform noise is wasteful because channels differ in task importance. Using task-gradient energy as the importance measure, we derive CANAL, a closed-form water-filling allocation that gives important channels proportionally less noise, and prove it strictly minimizes importance-weighted distortion at a fixed budget. Third, the clipping caps and importance scores that drive the allocation are themselves data-dependent, so releasing them in the clear silently breaks the guarantee. We give a DP-honest budget split that charges each to the privacy budget, so the reported epsilon is the true epsilon. Across three medical segmentation benchmarks spanning dermoscopy, colonoscopy, and ultrasound, CANAL retains more task-relevant signal than uniform noise at the same privacy budget.

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arXiv2024

AdaptiveClick: Clicks-aware Transformer with Adaptive Focal Loss for Interactive Image Segmentation

Interactive Image Segmentation (IIS) has emerged as a promising technique for decreasing annotation time. Substantial progress has been made in pre- and post-processing for IIS, but the critical issue of interaction ambiguity, notably hindering segmentation quality, has been under-researched. To address this, we introduce AdaptiveClick -- a click-aware transformer incorporating an adaptive focal loss that tackles annotation inconsistencies with tools for mask- and pixel-level ambiguity resolution. To the best of our knowledge, AdaptiveClick is the first transformer-based, mask-adaptive segmentation framework for IIS. The key ingredient of our method is the Click-Aware Mask-adaptive transformer Decoder (CAMD), which enhances the interaction between click and image features. Additionally, AdaptiveClick enables pixel-adaptive differentiation of hard and easy samples in the decision space, independent of their varying distributions. This is primarily achieved by optimizing a generalized Adaptive Focal Loss (AFL) with a theoretical guarantee, where two adaptive coefficients control the ratio of gradient values for hard and easy pixels. Our analysis reveals that the commonly used Focal and BCE losses can be considered special cases of the proposed AFL. With a plain ViT backbone, extensive experimental results on nine datasets demonstrate the superiority of AdaptiveClick compared to state-of-the-art methods. The source code is publicly available at https://github.com/lab206/AdaptiveClick.

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arXiv2024

SegForestNet: Spatial-Partitioning-Based Aerial Image Segmentation

Aerial image segmentation is the basis for applications such as automatically creating maps or tracking deforestation. In true orthophotos, which are often used in these applications, many objects and regions can be approximated well by polygons. However, this fact is rarely exploited by state-of-the-art semantic segmentation models. Instead, most models allow unnecessary degrees of freedom in their predictions by allowing arbitrary region shapes. We therefore present a refinement of our deep learning model which predicts binary space partitioning trees, an efficient polygon representation. The refinements include a new feature decoder architecture and a new differentiable BSP tree renderer which both avoid vanishing gradients. Additionally, we designed a novel loss function specifically designed to improve the spatial partitioning defined by the predicted trees. Furthermore, our expanded model can predict multiple trees at once and thus can predict class-specific segmentations. As an additional contribution, we investigate the impact of a non-optimal training process in comparison to an optimized training process. While model architectures optimized for aerial images, such as PFNet or our own model, show an advantage under non-optimal conditions, this advantage disappears under optimal training conditions. Despite this observation, our model still makes better predictions for small rectangular objects, e.g., cars.

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arXiv2024

Mask Grounding for Referring Image Segmentation

Referring Image Segmentation (RIS) is a challenging task that requires an algorithm to segment objects referred by free-form language expressions. Despite significant progress in recent years, most state-of-the-art (SOTA) methods still suffer from considerable language-image modality gap at the pixel and word level. These methods generally 1) rely on sentence-level language features for language-image alignment and 2) lack explicit training supervision for fine-grained visual grounding. Consequently, they exhibit weak object-level correspondence between visual and language features. Without well-grounded features, prior methods struggle to understand complex expressions that require strong reasoning over relationships among multiple objects, especially when dealing with rarely used or ambiguous clauses. To tackle this challenge, we introduce a novel Mask Grounding auxiliary task that significantly improves visual grounding within language features, by explicitly teaching the model to learn fine-grained correspondence between masked textual tokens and their matching visual objects. Mask Grounding can be directly used on prior RIS methods and consistently bring improvements. Furthermore, to holistically address the modality gap, we also design a cross-modal alignment loss and an accompanying alignment module. These additions work synergistically with Mask Grounding. With all these techniques, our comprehensive approach culminates in MagNet (Mask-grounded Network), an architecture that significantly outperforms prior arts on three key benchmarks (RefCOCO, RefCOCO+ and G-Ref), demonstrating our method's effectiveness in addressing current limitations of RIS algorithms. Our code and pre-trained weights will be released.

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arXiv2024

Learning from Exemplars for Interactive Image Segmentation

Interactive image segmentation enables users to interact minimally with a machine, facilitating the gradual refinement of the segmentation mask for a target of interest. Previous studies have demonstrated impressive performance in extracting a single target mask through interactive segmentation. However, the information cues of previously interacted objects have been overlooked in the existing methods, which can be further explored to speed up interactive segmentation for multiple targets in the same category. To this end, we introduce novel interactive segmentation frameworks for both a single object and multiple objects in the same category. Specifically, our model leverages transformer backbones to extract interaction-focused visual features from the image and the interactions to obtain a satisfactory mask of a target as an exemplar. For multiple objects, we propose an exemplar-informed module to enhance the learning of similarities among the objects of the target category. To combine attended features from different modules, we incorporate cross-attention blocks followed by a feature fusion module. Experiments conducted on mainstream benchmarks demonstrate that our models achieve superior performance compared to previous methods. Particularly, our model reduces users' labor by around 15\%, requiring two fewer clicks to achieve target IoUs 85\% and 90\%. The results highlight our models' potential as a flexible and practical annotation tool. The source code will be released after publication.

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arXiv2022

Position-Aware Contrastive Alignment for Referring Image Segmentation

Referring image segmentation aims to segment the target object described by a given natural language expression. Typically, referring expressions contain complex relationships between the target and its surrounding objects. The main challenge of this task is to understand the visual and linguistic content simultaneously and to find the referred object accurately among all instances in the image. Currently, the most effective way to solve the above problem is to obtain aligned multi-modal features by computing the correlation between visual and linguistic feature modalities under the supervision of the ground-truth mask. However, existing paradigms have difficulty in thoroughly understanding visual and linguistic content due to the inability to perceive information directly about surrounding objects that refer to the target. This prevents them from learning aligned multi-modal features, which leads to inaccurate segmentation. To address this issue, we present a position-aware contrastive alignment network (PCAN) to enhance the alignment of multi-modal features by guiding the interaction between vision and language through prior position information. Our PCAN consists of two modules: 1) Position Aware Module (PAM), which provides position information of all objects related to natural language descriptions, and 2) Contrastive Language Understanding Module (CLUM), which enhances multi-modal alignment by comparing the features of the referred object with those of related objects. Extensive experiments on three benchmarks demonstrate our PCAN performs favorably against the state-of-the-art methods. Our code will be made publicly available.

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arXiv2023

Beyond Self-Attention: Deformable Large Kernel Attention for Medical Image Segmentation

Medical image segmentation has seen significant improvements with transformer models, which excel in grasping far-reaching contexts and global contextual information. However, the increasing computational demands of these models, proportional to the squared token count, limit their depth and resolution capabilities. Most current methods process D volumetric image data slice-by-slice (called pseudo 3D), missing crucial inter-slice information and thus reducing the model's overall performance. To address these challenges, we introduce the concept of \textbf{Deformable Large Kernel Attention (D-LKA Attention)}, a streamlined attention mechanism employing large convolution kernels to fully appreciate volumetric context. This mechanism operates within a receptive field akin to self-attention while sidestepping the computational overhead. Additionally, our proposed attention mechanism benefits from deformable convolutions to flexibly warp the sampling grid, enabling the model to adapt appropriately to diverse data patterns. We designed both 2D and 3D adaptations of the D-LKA Attention, with the latter excelling in cross-depth data understanding. Together, these components shape our novel hierarchical Vision Transformer architecture, the \textit{D-LKA Net}. Evaluations of our model against leading methods on popular medical segmentation datasets (Synapse, NIH Pancreas, and Skin lesion) demonstrate its superior performance. Our code implementation is publicly available at the: https://github.com/mindflow-institue/deformableLKA

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arXiv2024

Demystifying the Effect of Receptive Field Size in U-Net Models for Medical Image Segmentation

Medical image segmentation is a critical task in healthcare applications, and U-Nets have demonstrated promising results. This work delves into the understudied aspect of receptive field (RF) size and its impact on the U-Net and Attention U-Net architectures. This work explores several critical elements including the relationship between RF size, characteristics of the region of interest, and model performance, as well as the balance between RF size and computational costs for U-Net and Attention U-Net methods for different datasets. This work also proposes a mathematical notation for representing the theoretical receptive field (TRF) of a given layer in a network and proposes two new metrics - effective receptive field (ERF) rate and the Object rate to quantify the fraction of significantly contributing pixels within the ERF against the TRF area and assessing the relative size of the segmentation object compared to the TRF size respectively. The results demonstrate that there exists an optimal TRF size that successfully strikes a balance between capturing a wider global context and maintaining computational efficiency, thereby optimizing model performance. Interestingly, a distinct correlation is observed between the data complexity and the required TRF size; segmentation based solely on contrast achieved peak performance even with smaller TRF sizes, whereas more complex segmentation tasks necessitated larger TRFs. Attention U-Net models consistently outperformed their U-Net counterparts, highlighting the value of attention mechanisms regardless of TRF size. These novel insights present an invaluable resource for developing more efficient U-Net-based architectures for medical imaging and pave the way for future exploration. A tool is also developed that calculates the TRF for a U-Net (and Attention U-Net) model, and also suggest an appropriate TRF size for a given model and dataset.

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arXiv2023

Synchronizing Vision and Language: Bidirectional Token-Masking AutoEncoder for Referring Image Segmentation

Referring Image Segmentation (RIS) aims to segment target objects expressed in natural language within a scene at the pixel level. Various recent RIS models have achieved state-of-the-art performance by generating contextual tokens to model multimodal features from pretrained encoders and effectively fusing them using transformer-based cross-modal attention. While these methods match language features with image features to effectively identify likely target objects, they often struggle to correctly understand contextual information in complex and ambiguous sentences and scenes. To address this issue, we propose a novel bidirectional token-masking autoencoder (BTMAE) inspired by the masked autoencoder (MAE). The proposed model learns the context of image-to-language and language-to-image by reconstructing missing features in both image and language features at the token level. In other words, this approach involves mutually complementing across the features of images and language, with a focus on enabling the network to understand interconnected deep contextual information between the two modalities. This learning method enhances the robustness of RIS performance in complex sentences and scenes. Our BTMAE achieves state-of-the-art performance on three popular datasets, and we demonstrate the effectiveness of the proposed method through various ablation studies.

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arXiv2024

Extending CLIP's Image-Text Alignment to Referring Image Segmentation

Referring Image Segmentation (RIS) is a cross-modal task that aims to segment an instance described by a natural language expression. Recent methods leverage large-scale pretrained unimodal models as backbones along with fusion techniques for joint reasoning across modalities. However, the inherent cross-modal nature of RIS raises questions about the effectiveness of unimodal backbones. We propose RISCLIP, a novel framework that effectively leverages the cross-modal nature of CLIP for RIS. Observing CLIP's inherent alignment between image and text features, we capitalize on this starting point and introduce simple but strong modules that enhance unimodal feature extraction and leverage rich alignment knowledge in CLIP's image-text shared-embedding space. RISCLIP exhibits outstanding results on all three major RIS benchmarks and also outperforms previous CLIP-based methods, demonstrating the efficacy of our strategy in extending CLIP's image-text alignment to RIS.

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arXiv2025

RIS-LAD: A Benchmark and Model for Referring Low-Altitude Drone Image Segmentation

Referring Image Segmentation (RIS), which aims to segment specific objects based on natural language descriptions, plays an essential role in vision-language understanding. Despite its progress in remote sensing applications, RIS in Low-Altitude Drone (LAD) scenarios remains underexplored. Existing datasets and methods are typically designed for high-altitude and static-view imagery. They struggle to handle the unique characteristics of LAD views, such as diverse viewpoints and high object density. To fill this gap, we present RIS-LAD, the first fine-grained RIS benchmark tailored for LAD scenarios. This dataset comprises 13,871 carefully annotated image-text-mask triplets collected from realistic drone footage, with a focus on small, cluttered, and multi-viewpoint scenes. It highlights new challenges absent in previous benchmarks, such as category drift caused by tiny objects and object drift under crowded same-class objects. To tackle these issues, we propose the Semantic-Aware Adaptive Reasoning Network (SAARN). Rather than uniformly injecting all linguistic features, SAARN decomposes and routes semantic information to different stages of the network. Specifically, the Category-Dominated Linguistic Enhancement (CDLE) aligns visual features with object categories during early encoding, while the Adaptive Reasoning Fusion Module (ARFM) dynamically selects semantic cues across scales to improve reasoning in complex scenes. The experimental evaluation reveals that RIS-LAD presents substantial challenges to state-of-the-art RIS algorithms, and also demonstrates the effectiveness of our proposed model in addressing these challenges. The dataset and code will be publicly released soon at: https://github.com/AHideoKuzeA/RIS-LAD/.

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arXiv2026

When Online Adaptation Hurts: Parameter-Frozen Test-Time Ensembling for Continual Medical Image Segmentation

Medical image segmenters often get worse when sites, scanner vendors, or protocols change. Continual test-time adaptation (CTTA) addresses this problem without target labels, but it can be impossible to update a model on a non-stationary stream and can lead to a lot of errors. We examine a more reasonable and meaningful alternative: parameter-frozen inference enhancement(PIE). We use a source-trained segmenter that learns about anatomy-preserving scale and flip views, maps their predictions back to the native location, and averages the probabilities. We do not modify the weights of the model or the normalization statistics. On a cardiac MRI stream from M\&Ms, which is trained on vendor A and evaluated sequentially on vendors B, C, and D, PIE has 0.7786 mean Dice, compared to 0.7680 for source-only inference and 0.7388--0.7416 for five other online-adaptation baselines. The controlled ablations show that performance saturates at 28 views, and confidence weighting, class-prior correction, connected-component filtering, morphological refinement, and inter-slice smoothing have no effect or cause negative transfer. Qualitative results on cardiac MRI and fundus images are also consistent with the frozen ensemble keeping thinner and nested anatomical structures. These results provide a strong, stable baseline for medical CTTA and expose an important failure mode: adaptation and handcrafted refinement can be less reliable than carefully designed inference.

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