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arXiv2024

S-SAM: SVD-based Fine-Tuning of Segment Anything Model for Medical Image Segmentation

Medical image segmentation has been traditionally approached by training or fine-tuning the entire model to cater to any new modality or dataset. However, this approach often requires tuning a large number of parameters during training. With the introduction of the Segment Anything Model (SAM) for prompted segmentation of natural images, many efforts have been made towards adapting it efficiently for medical imaging, thus reducing the training time and resources. However, these methods still require expert annotations for every image in the form of point prompts or bounding box prompts during training and inference, making it tedious to employ them in practice. In this paper, we propose an adaptation technique, called S-SAM, that only trains parameters equal to 0.4% of SAM's parameters and at the same time uses simply the label names as prompts for producing precise masks. This not only makes tuning SAM more efficient than the existing adaptation methods but also removes the burden of providing expert prompts. We call this modified version S-SAM and evaluate it on five different modalities including endoscopic images, x-ray, ultrasound, CT, and histology images. Our experiments show that S-SAM outperforms state-of-the-art methods as well as existing SAM adaptation methods while tuning a significantly less number of parameters. We release the code for S-SAM at https://github.com/JayParanjape/SVDSAM.

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arXiv2020

Linguistic Structure Guided Context Modeling for Referring Image Segmentation

Referring image segmentation aims to predict the foreground mask of the object referred by a natural language sentence. Multimodal context of the sentence is crucial to distinguish the referent from the background. Existing methods either insufficiently or redundantly model the multimodal context. To tackle this problem, we propose a "gather-propagate-distribute" scheme to model multimodal context by cross-modal interaction and implement this scheme as a novel Linguistic Structure guided Context Modeling (LSCM) module. Our LSCM module builds a Dependency Parsing Tree suppressed Word Graph (DPT-WG) which guides all the words to include valid multimodal context of the sentence while excluding disturbing ones through three steps over the multimodal feature, i.e., gathering, constrained propagation and distributing. Extensive experiments on four benchmarks demonstrate that our method outperforms all the previous state-of-the-arts.

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arXiv2021

PointFlow: Flowing Semantics Through Points for Aerial Image Segmentation

Aerial Image Segmentation is a particular semantic segmentation problem and has several challenging characteristics that general semantic segmentation does not have. There are two critical issues: The one is an extremely foreground-background imbalanced distribution, and the other is multiple small objects along with the complex background. Such problems make the recent dense affinity context modeling perform poorly even compared with baselines due to over-introduced background context. To handle these problems, we propose a point-wise affinity propagation module based on the Feature Pyramid Network (FPN) framework, named PointFlow. Rather than dense affinity learning, a sparse affinity map is generated upon selected points between the adjacent features, which reduces the noise introduced by the background while keeping efficiency. In particular, we design a dual point matcher to select points from the salient area and object boundaries, respectively. Experimental results on three different aerial segmentation datasets suggest that the proposed method is more effective and efficient than state-of-the-art general semantic segmentation methods. Especially, our methods achieve the best speed and accuracy trade-off on three aerial benchmarks. Further experiments on three general semantic segmentation datasets prove the generality of our method. Code will be provided in (https: //github.com/lxtGH/PFSegNets).

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arXiv2022

Contrastive and Selective Hidden Embeddings for Medical Image Segmentation

Medical image segmentation has been widely recognized as a pivot procedure for clinical diagnosis, analysis, and treatment planning. However, the laborious and expensive annotation process lags down the speed of further advances. Contrastive learning-based weight pre-training provides an alternative by leveraging unlabeled data to learn a good representation. In this paper, we investigate how contrastive learning benefits the general supervised medical segmentation tasks. To this end, patch-dragsaw contrastive regularization (PDCR) is proposed to perform patch-level tugging and repulsing with the extent controlled by a continuous affinity score. And a new structure dubbed uncertainty-aware feature selection block (UAFS) is designed to perform the feature selection process, which can handle the learning target shift caused by minority features with high uncertainty. By plugging the proposed 2 modules into the existing segmentation architecture, we achieve state-of-the-art results across 8 public datasets from 6 domains. Newly designed modules further decrease the amount of training data to a quarter while achieving comparable, if not better, performances. From this perspective, we take the opposite direction of the original self/un-supervised contrastive learning by further excavating information contained within the label.

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arXiv2022

CoupAlign: Coupling Word-Pixel with Sentence-Mask Alignments for Referring Image Segmentation

Referring image segmentation aims at localizing all pixels of the visual objects described by a natural language sentence. Previous works learn to straightforwardly align the sentence embedding and pixel-level embedding for highlighting the referred objects, but ignore the semantic consistency of pixels within the same object, leading to incomplete masks and localization errors in predictions. To tackle this problem, we propose CoupAlign, a simple yet effective multi-level visual-semantic alignment method, to couple sentence-mask alignment with word-pixel alignment to enforce object mask constraint for achieving more accurate localization and segmentation. Specifically, the Word-Pixel Alignment (WPA) module performs early fusion of linguistic and pixel-level features in intermediate layers of the vision and language encoders. Based on the word-pixel aligned embedding, a set of mask proposals are generated to hypothesize possible objects. Then in the Sentence-Mask Alignment (SMA) module, the masks are weighted by the sentence embedding to localize the referred object, and finally projected back to aggregate the pixels for the target. To further enhance the learning of the two alignment modules, an auxiliary loss is designed to contrast the foreground and background pixels. By hierarchically aligning pixels and masks with linguistic features, our CoupAlign captures the pixel coherence at both visual and semantic levels, thus generating more accurate predictions. Extensive experiments on popular datasets (e.g., RefCOCO and G-Ref) show that our method achieves consistent improvements over state-of-the-art methods, e.g., about 2% oIoU increase on the validation and testing set of RefCOCO. Especially, CoupAlign has remarkable ability in distinguishing the target from multiple objects of the same class.

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arXiv2023

AerialFormer: Multi-resolution Transformer for Aerial Image Segmentation

Aerial Image Segmentation is a top-down perspective semantic segmentation and has several challenging characteristics such as strong imbalance in the foreground-background distribution, complex background, intra-class heterogeneity, inter-class homogeneity, and tiny objects. To handle these problems, we inherit the advantages of Transformers and propose AerialFormer, which unifies Transformers at the contracting path with lightweight Multi-Dilated Convolutional Neural Networks (MD-CNNs) at the expanding path. Our AerialFormer is designed as a hierarchical structure, in which Transformer encoder outputs multi-scale features and MD-CNNs decoder aggregates information from the multi-scales. Thus, it takes both local and global contexts into consideration to render powerful representations and high-resolution segmentation. We have benchmarked AerialFormer on three common datasets including iSAID, LoveDA, and Potsdam. Comprehensive experiments and extensive ablation studies show that our proposed AerialFormer outperforms previous state-of-the-art methods with remarkable performance. Our source code will be publicly available upon acceptance.

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arXiv2024

Densely Decoded Networks with Adaptive Deep Supervision for Medical Image Segmentation

Medical image segmentation using deep neural networks has been highly successful. However, the effectiveness of these networks is often limited by inadequate dense prediction and inability to extract robust features. To achieve refined dense prediction, we propose densely decoded networks (ddn), by selectively introducing 'crutch' network connections. Such 'crutch' connections in each upsampling stage of the network decoder (1) enhance target localization by incorporating high resolution features from the encoder, and (2) improve segmentation by facilitating multi-stage contextual information flow. Further, we present a training strategy based on adaptive deep supervision (ads), which exploits and adapts specific attributes of input dataset, for robust feature extraction. In particular, ads strategically locates and deploys auxiliary supervision, by matching the average input object size with the layer-wise effective receptive fields (lerf) of a network, resulting in a class of ddns. Such inclusion of 'companion objective' from a specific hidden layer, helps the model pay close attention to some distinct input-dependent features, which the network might otherwise 'ignore' during training. Our new networks and training strategy are validated on 4 diverse datasets of different modalities, demonstrating their effectiveness.

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arXiv2024

Two-Stage Multi-task Self-Supervised Learning for Medical Image Segmentation

Medical image segmentation has been significantly advanced by deep learning (DL) techniques, though the data scarcity inherent in medical applications poses a great challenge to DL-based segmentation methods. Self-supervised learning offers a solution by creating auxiliary learning tasks from the available dataset and then leveraging the knowledge acquired from solving auxiliary tasks to help better solve the target segmentation task. Different auxiliary tasks may have different properties and thus can help the target task to different extents. It is desired to leverage their complementary advantages to enhance the overall assistance to the target task. To achieve this, existing methods often adopt a joint training paradigm, which co-solves segmentation and auxiliary tasks by integrating their losses or intermediate gradients. However, direct coupling of losses or intermediate gradients risks undesirable interference because the knowledge acquired from solving each auxiliary task at every training step may not always benefit the target task. To address this issue, we propose a two-stage training approach. In the first stage, the target segmentation task will be independently co-solved with each auxiliary task in both joint training and pre-training modes, with the better model selected via validation performance. In the second stage, the models obtained with respect to each auxiliary task are converted into a single model using an ensemble knowledge distillation method. Our approach allows for making best use of each auxiliary task to create multiple elite segmentation models and then combine them into an even more powerful model. We employed five auxiliary tasks of different proprieties in our approach and applied it to train the U-Net model on an X-ray pneumothorax segmentation dataset. Experimental results demonstrate the superiority of our approach over several existing methods.

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arXiv2024

Spatial Semantic Recurrent Mining for Referring Image Segmentation

Referring Image Segmentation (RIS) consistently requires language and appearance semantics to more understand each other. The need becomes acute especially under hard situations. To achieve, existing works tend to resort to various trans-representing mechanisms to directly feed forward language semantic along main RGB branch, which however will result in referent distribution weakly-mined in space and non-referent semantic contaminated along channel. In this paper, we propose Spatial Semantic Recurrent Mining (S\textsuperscript{2}RM) to achieve high-quality cross-modality fusion. It follows a working strategy of trilogy: distributing language feature, spatial semantic recurrent coparsing, and parsed-semantic balancing. During fusion, S\textsuperscript{2}RM will first generate a constraint-weak yet distribution-aware language feature, then bundle features of each row and column from rotated features of one modality context to recurrently correlate relevant semantic contained in feature from other modality context, and finally resort to self-distilled weights to weigh on the contributions of different parsed semantics. Via coparsing, S\textsuperscript{2}RM transports information from the near and remote slice layers of generator context to the current slice layer of parsed context, capable of better modeling global relationship bidirectional and structured. Besides, we also propose a Cross-scale Abstract Semantic Guided Decoder (CASG) to emphasize the foreground of the referent, finally integrating different grained features at a comparatively low cost. Extensive experimental results on four current challenging datasets show that our proposed method performs favorably against other state-of-the-art algorithms.

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arXiv2024

SegStitch: Multidimensional Transformer for Robust and Efficient Medical Imaging Segmentation

Medical imaging segmentation plays a significant role in the automatic recognition and analysis of lesions. State-of-the-art methods, particularly those utilizing transformers, have been prominently adopted in 3D semantic segmentation due to their superior performance in scalability and generalizability. However, plain vision transformers encounter challenges due to their neglect of local features and their high computational complexity. To address these challenges, we introduce three key contributions: Firstly, we proposed SegStitch, an innovative architecture that integrates transformers with denoising ODE blocks. Instead of taking whole 3D volumes as inputs, we adapt axial patches and customize patch-wise queries to ensure semantic consistency. Additionally, we conducted extensive experiments on the BTCV and ACDC datasets, achieving improvements up to 11.48% and 6.71% respectively in mDSC, compared to state-of-the-art methods. Lastly, our proposed method demonstrates outstanding efficiency, reducing the number of parameters by 36.7% and the number of FLOPS by 10.7% compared to UNETR. This advancement holds promising potential for adapting our method to real-world clinical practice. The code will be available at https://github.com/goblin327/SegStitch

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arXiv2025

A Simple Baseline with Single-encoder for Referring Image Segmentation

Referring image segmentation (RIS) requires dense vision-language interactions between visual pixels and textual words to segment objects based on a given description. However, commonly adapted dual-encoders in RIS, e.g., Swin transformer and BERT (uni-modal encoders) or CLIP (a multi-modal dual-encoder), lack dense multi-modal interactions during pre-training, leading to a gap with a pixel-level RIS task. To bridge this gap, existing RIS methods often rely on multi-modal fusion modules that interact two encoders, but this approach leads to high computational costs. In this paper, we present a novel RIS method with a single-encoder, i.e., BEiT-3, maximizing the potential of shared self-attention across all framework components. This enables seamless interactions of two modalities from input to final prediction, producing granularly aligned multi-modal features. Furthermore, we propose lightweight yet effective decoder modules, a Shared FPN and a Shared Mask Decoder, which contribute to the high efficiency of our model. Our simple baseline with a single encoder achieves outstanding performances on the RIS benchmark datasets while maintaining computational efficiency, compared to the most recent SoTA methods based on dual-encoders.

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arXiv2025

From Gaze to Insight: Bridging Human Visual Attention and Vision Language Model Explanation for Weakly-Supervised Medical Image Segmentation

Medical image segmentation remains challenging due to the high cost of pixel-level annotations for training. In the context of weak supervision, clinician gaze data captures regions of diagnostic interest; however, its sparsity limits its use for segmentation. In contrast, vision-language models (VLMs) provide semantic context through textual descriptions but lack the explanation precision required. Recognizing that neither source alone suffices, we propose a teacher-student framework that integrates both gaze and language supervision, leveraging their complementary strengths. Our key insight is that gaze data indicates where clinicians focus during diagnosis, while VLMs explain why those regions are significant. To implement this, the teacher model first learns from gaze points enhanced by VLM-generated descriptions of lesion morphology, establishing a foundation for guiding the student model. The teacher then directs the student through three strategies: (1) Multi-scale feature alignment to fuse visual cues with textual semantics; (2) Confidence-weighted consistency constraints to focus on reliable predictions; (3) Adaptive masking to limit error propagation in uncertain areas. Experiments on the Kvasir-SEG, NCI-ISBI, and ISIC datasets show that our method achieves Dice scores of 80.78%, 80.53%, and 84.22%, respectively-improving 3-5% over gaze baselines without increasing the annotation burden. By preserving correlations among predictions, gaze data, and lesion descriptions, our framework also maintains clinical interpretability. This work illustrates how integrating human visual attention with AI-generated semantic context can effectively overcome the limitations of individual weak supervision signals, thereby advancing the development of deployable, annotation-efficient medical AI systems. Code is available at: https://github.com/jingkunchen/FGI.

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arXiv2025

Auto-nnU-Net: Towards Automated Medical Image Segmentation

Medical Image Segmentation (MIS) includes diverse tasks, from bone to organ segmentation, each with its own challenges in finding the best segmentation model. The state-of-the-art AutoML-related MIS-framework nnU-Net automates many aspects of model configuration but remains constrained by fixed hyperparameters and heuristic design choices. As a full-AutoML framework for MIS, we propose Auto-nnU-Net, a novel nnU-Net variant enabling hyperparameter optimization (HPO), neural architecture search (NAS), and hierarchical NAS (HNAS). Additionally, we propose Regularized PriorBand to balance model accuracy with the computational resources required for training, addressing the resource constraints often faced in real-world medical settings that limit the feasibility of extensive training procedures. We evaluate our approach across diverse MIS datasets from the well-established Medical Segmentation Decathlon, analyzing the impact of AutoML techniques on segmentation performance, computational efficiency, and model design choices. The results demonstrate that our AutoML approach substantially improves the segmentation performance of nnU-Net on 6 out of 10 datasets and is on par on the other datasets while maintaining practical resource requirements. Our code is available at https://github.com/automl/AutoNNUnet.

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arXiv2025

FreqU-FNet: Frequency-Aware U-Net for Imbalanced Medical Image Segmentation

Medical image segmentation faces persistent challenges due to severe class imbalance and the frequency-specific distribution of anatomical structures. Most conventional CNN-based methods operate in the spatial domain and struggle to capture minority class signals, often affected by frequency aliasing and limited spectral selectivity. Transformer-based models, while powerful in modeling global dependencies, tend to overlook critical local details necessary for fine-grained segmentation. To overcome these limitations, we propose FreqU-FNet, a novel U-shaped segmentation architecture operating in the frequency domain. Our framework incorporates a Frequency Encoder that leverages Low-Pass Frequency Convolution and Daubechies wavelet-based downsampling to extract multi-scale spectral features. To reconstruct fine spatial details, we introduce a Spatial Learnable Decoder (SLD) equipped with an adaptive multi-branch upsampling strategy. Furthermore, we design a frequency-aware loss (FAL) function to enhance minority class learning. Extensive experiments on multiple medical segmentation benchmarks demonstrate that FreqU-FNet consistently outperforms both CNN and Transformer baselines, particularly in handling under-represented classes, by effectively exploiting discriminative frequency bands.

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arXiv2025

Text-guided multi-stage cross-perception network for medical image segmentation

Medical image segmentation plays a crucial role in clinical medicine, serving as a key tool for auxiliary diagnosis, treatment planning, and disease monitoring. However, traditional segmentation methods such as U-Net are often limited by weak semantic expression of target regions, which stems from insufficient generalization and a lack of interactivity. Incorporating text prompts offers a promising avenue to more accurately pinpoint lesion locations, yet existing text-guided methods are still hindered by insufficient cross-modal interaction and inadequate cross-modal feature representation. To address these challenges, we propose the Text-guided Multi-stage Cross-perception network (TMC). TMC incorporates a Multi-stage Cross-attention Module (MCM) to enhance the model's understanding of fine-grained semantic details and a Multi-stage Alignment Loss (MA Loss) to improve the consistency of cross-modal semantics across different feature levels. Experimental results on three public datasets (QaTa-COV19, MosMedData, and Duke-Breast-Cancer-MRI) demonstrate the superior performance of TMC, achieving Dice scores of 84.65\%, 78.39\%, and 88.09\%, respectively, and consistently outperforming both U-Net-based networks and existing text-guided methods.

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arXiv2025

DCFFSNet: Deep Connectivity Feature Fusion Separation Network for Medical Image Segmentation

Medical image segmentation leverages topological connectivity theory to enhance edge precision and regional consistency. However, existing deep networks integrating connectivity often forcibly inject it as an additional feature module, resulting in coupled feature spaces with no standardized mechanism to quantify different feature strengths. To address these issues, we propose DCFFSNet (Dual-Connectivity Feature Fusion-Separation Network). It introduces an innovative feature space decoupling strategy. This strategy quantifies the relative strength between connectivity features and other features. It then builds a deep connectivity feature fusion-separation architecture. This architecture dynamically balances multi-scale feature expression. Experiments were conducted on the ISIC2018, DSB2018, and MoNuSeg datasets. On ISIC2018, DCFFSNet outperformed the next best model (CMUNet) by 1.3% (Dice) and 1.2% (IoU). On DSB2018, it surpassed TransUNet by 0.7% (Dice) and 0.9% (IoU). On MoNuSeg, it exceeded CSCAUNet by 0.8% (Dice) and 0.9% (IoU). The results demonstrate that DCFFSNet exceeds existing mainstream methods across all metrics. It effectively resolves segmentation fragmentation and achieves smooth edge transitions. This significantly enhances clinical usability.

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arXiv2025

USEANet: Ultrasound-Specific Edge-Aware Multi-Branch Network for Lightweight Medical Image Segmentation

Ultrasound image segmentation faces unique challenges including speckle noise, low contrast, and ambiguous boundaries, while clinical deployment demands computationally efficient models. We propose USEANet, an ultrasound-specific edge-aware multi-branch network that achieves optimal performance-efficiency balance through four key innovations: (1) ultrasound-specific multi-branch processing with specialized modules for noise reduction, edge enhancement, and contrast improvement; (2) edge-aware attention mechanisms that focus on boundary information with minimal computational overhead; (3) hierarchical feature aggregation with adaptive weight learning; and (4) ultrasound-aware decoder enhancement for optimal segmentation refinement. Built on an ultra-lightweight PVT-B0 backbone, USEANet significantly outperforms existing methods across five ultrasound datasets while using only 3.64M parameters and 0.79G FLOPs. Experimental results demonstrate superior segmentation accuracy with 67.01 IoU on BUSI dataset, representing substantial improvements over traditional approaches while maintaining exceptional computational efficiency suitable for real-time clinical applications. Code is available at https://github.com/chouheiwa/USEANet.

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arXiv2025

U-MAN: U-Net with Multi-scale Adaptive KAN Network for Medical Image Segmentation

Medical image segmentation faces significant challenges in preserving fine-grained details and precise boundaries due to complex anatomical structures and pathological regions. These challenges primarily stem from two key limitations of conventional U-Net architectures: (1) their simple skip connections ignore the encoder-decoder semantic gap between various features, and (2) they lack the capability for multi-scale feature extraction in deep layers. To address these challenges, we propose the U-Net with Multi-scale Adaptive KAN (U-MAN), a novel architecture that enhances the emerging Kolmogorov-Arnold Network (KAN) with two specialized modules: Progressive Attention-Guided Feature Fusion (PAGF) and the Multi-scale Adaptive KAN (MAN). Our PAGF module replaces the simple skip connection, using attention to fuse features from the encoder and decoder. The MAN module enables the network to adaptively process features at multiple scales, improving its ability to segment objects of various sizes. Experiments on three public datasets (BUSI, GLAS, and CVC) show that U-MAN outperforms state-of-the-art methods, particularly in defining accurate boundaries and preserving fine details.

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