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arXiv2024

Lagrange Duality and Compound Multi-Attention Transformer for Semi-Supervised Medical Image Segmentation

Medical image segmentation, a critical application of semantic segmentation in healthcare, has seen significant advancements through specialized computer vision techniques. While deep learning-based medical image segmentation is essential for assisting in medical diagnosis, the lack of diverse training data causes the long-tail problem. Moreover, most previous hybrid CNN-ViT architectures have limited ability to combine various attentions in different layers of the Convolutional Neural Network. To address these issues, we propose a Lagrange Duality Consistency (LDC) Loss, integrated with Boundary-Aware Contrastive Loss, as the overall training objective for semi-supervised learning to mitigate the long-tail problem. Additionally, we introduce CMAformer, a novel network that synergizes the strengths of ResUNet and Transformer. The cross-attention block in CMAformer effectively integrates spatial attention and channel attention for multi-scale feature fusion. Overall, our results indicate that CMAformer, combined with the feature fusion framework and the new consistency loss, demonstrates strong complementarity in semi-supervised learning ensembles. We achieve state-of-the-art results on multiple public medical image datasets. Example code are available at: \url{https://github.com/lzeeorno/Lagrange-Duality-and-CMAformer}.

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arXiv2022

Active Diffusion and VCA-Assisted Image Segmentation of Hyperspectral Images

Hyperspectral images encode rich structure that can be exploited for material discrimination by machine learning algorithms. This article introduces the Active Diffusion and VCA-Assisted Image Segmentation (ADVIS) for active material discrimination. ADVIS selects high-purity, high-density pixels that are far in diffusion distance (a data-dependent metric) from other high-purity, high-density pixels in the hyperspectral image. The ground truth labels of these pixels are queried and propagated to the rest of the image. The ADVIS active learning algorithm is shown to strongly outperform its fully unsupervised clustering algorithm counterpart, suggesting that the incorporation of a very small number of carefully-selected ground truth labels can result in substantially superior material discrimination in hyperspectral images.

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arXiv2026

From Spatial Semantics to Temporal Context: Leveraging Gaze Trajectory for Weakly Supervised Medical Image Segmentation

Medical image segmentation heavily depends on labor-intensive and time-consuming pixel-level annotations. Eye tracking offers a cost-effective solution that can be naturally integrated into clinical workflows. Recorded by eye trackers, gaze conveys the spatial regions of clinicians' attention through fixations and the temporal context of clinicians' progressive visual perception from trajectories. Nevertheless, effective modeling of temporal trajectories remains challenging, and noise in gaze caused by exploratory fixations greatly limits segmentation performance. To overcome these limitations, we propose the Trajectory-guided Uncertainty-aware Network (TrailNet), which exploits gaze-supervised medical image segmentation from spatial semantics modeling to temporal context by jointly leveraging fixations and trajectories. Specifically, the proposed trajectory-guided spatio-temporal encoder models temporal context and establishes complementary interactions with image spatial semantics to strengthen target perception. Furthermore, the multi-scale uncertainty decoder leverages category mutual-exclusivity constraints to produce deterministic predictions and mitigate supervision uncertainty induced by noise. To enable gaze-free inference, we further introduce a cycle distillation strategy that transfers feature-level knowledge via teacher-student networks. Experimental results on two public datasets demonstrate that TrailNet outperforms state-of-the-art methods, achieving Dice scores of 81.25% and 81.85%, respectively.

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arXiv2024

Fuzzy Rank-based Late Fusion Technique for Cytology image Segmentation

Cytology image segmentation is quite challenging due to its complex cellular structure and multiple overlapping regions. On the other hand, for supervised machine learning techniques, we need a large amount of annotated data, which is costly. In recent years, late fusion techniques have given some promising performances in the field of image classification. In this paper, we have explored a fuzzy-based late fusion techniques for cytology image segmentation. This fusion rule integrates three traditional semantic segmentation models UNet, SegNet, and PSPNet. The technique is applied on two cytology image datasets, i.e., cervical cytology(HErlev) and breast cytology(JUCYT-v1) image datasets. We have achieved maximum MeanIoU score 84.27% and 83.79% on the HErlev dataset and JUCYT-v1 dataset after the proposed late fusion technique, respectively which are better than that of the traditional fusion rules such as average probability, geometric mean, Borda Count, etc. The codes of the proposed model are available on GitHub.

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arXiv2025

Boosting Semi-Supervised Medical Image Segmentation via Masked Image Consistency and Discrepancy Learning

Semi-supervised learning is of great significance in medical image segmentation by exploiting unlabeled data. Among its strategies, the co-training framework is prominent. However, previous co-training studies predominantly concentrate on network initialization variances and pseudo-label generation, while overlooking the equilibrium between information interchange and model diversity preservation. In this paper, we propose the Masked Image Consistency and Discrepancy Learning (MICD) framework with three key modules. The Masked Cross Pseudo Consistency (MCPC) module enriches context perception and small sample learning via pseudo-labeling across masked-input branches. The Cross Feature Consistency (CFC) module fortifies information exchange and model robustness by ensuring decoder feature consistency. The Cross Model Discrepancy (CMD) module utilizes EMA teacher networks to oversee outputs and preserve branch diversity. Together, these modules address existing limitations by focusing on fine-grained local information and maintaining diversity in a heterogeneous framework. Experiments on two public medical image datasets, AMOS and Synapse, demonstrate that our approach outperforms state-of-the-art methods.

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arXiv2022

TFCNs: A CNN-Transformer Hybrid Network for Medical Image Segmentation

Medical image segmentation is one of the most fundamental tasks concerning medical information analysis. Various solutions have been proposed so far, including many deep learning-based techniques, such as U-Net, FC-DenseNet, etc. However, high-precision medical image segmentation remains a highly challenging task due to the existence of inherent magnification and distortion in medical images as well as the presence of lesions with similar density to normal tissues. In this paper, we propose TFCNs (Transformers for Fully Convolutional denseNets) to tackle the problem by introducing ResLinear-Transformer (RL-Transformer) and Convolutional Linear Attention Block (CLAB) to FC-DenseNet. TFCNs is not only able to utilize more latent information from the CT images for feature extraction, but also can capture and disseminate semantic features and filter non-semantic features more effectively through the CLAB module. Our experimental results show that TFCNs can achieve state-of-the-art performance with dice scores of 83.72\% on the Synapse dataset. In addition, we evaluate the robustness of TFCNs for lesion area effects on the COVID-19 public datasets. The Python code will be made publicly available on https://github.com/HUANGLIZI/TFCNs.

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arXiv2021

Using Soft Labels to Model Uncertainty in Medical Image Segmentation

Medical image segmentation is inherently uncertain. For a given image, there may be multiple plausible segmentation hypotheses, and physicians will often disagree on lesion and organ boundaries. To be suited to real-world application, automatic segmentation systems must be able to capture this uncertainty and variability. Thus far, this has been addressed by building deep learning models that, through dropout, multiple heads, or variational inference, can produce a set - infinite, in some cases - of plausible segmentation hypotheses for any given image. However, in clinical practice, it may not be practical to browse all hypotheses. Furthermore, recent work shows that segmentation variability plateaus after a certain number of independent annotations, suggesting that a large enough group of physicians may be able to represent the whole space of possible segmentations. Inspired by this, we propose a simple method to obtain soft labels from the annotations of multiple physicians and train models that, for each image, produce a single well-calibrated output that can be thresholded at multiple confidence levels, according to each application's precision-recall requirements. We evaluated our method on the MICCAI 2021 QUBIQ challenge, showing that it performs well across multiple medical image segmentation tasks, produces well-calibrated predictions, and, on average, performs better at matching physicians' predictions than other physicians.

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arXiv2021

U-Net Transformer: Self and Cross Attention for Medical Image Segmentation

Medical image segmentation remains particularly challenging for complex and low-contrast anatomical structures. In this paper, we introduce the U-Transformer network, which combines a U-shaped architecture for image segmentation with self- and cross-attention from Transformers. U-Transformer overcomes the inability of U-Nets to model long-range contextual interactions and spatial dependencies, which are arguably crucial for accurate segmentation in challenging contexts. To this end, attention mechanisms are incorporated at two main levels: a self-attention module leverages global interactions between encoder features, while cross-attention in the skip connections allows a fine spatial recovery in the U-Net decoder by filtering out non-semantic features. Experiments on two abdominal CT-image datasets show the large performance gain brought out by U-Transformer compared to U-Net and local Attention U-Nets. We also highlight the importance of using both self- and cross-attention, and the nice interpretability features brought out by U-Transformer.

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arXiv2025

Adaptive Noise-Tolerant Network for Image Segmentation

Unlike image classification and annotation, for which deep network models have achieved dominating superior performances compared to traditional computer vision algorithms, deep learning for automatic image segmentation still faces critical challenges. One of such hurdles is to obtain ground-truth segmentations as the training labels for deep network training. Especially when we study biomedical images, such as histopathological images (histo-images), it is unrealistic to ask for manual segmentation labels as the ground truth for training due to the fine image resolution as well as the large image size and complexity. In this paper, instead of relying on clean segmentation labels, we study whether and how integrating imperfect or noisy segmentation results from off-the-shelf segmentation algorithms may help achieve better segmentation results through a new Adaptive Noise-Tolerant Network (ANTN) model. We extend the noisy label deep learning to image segmentation with two novel aspects: (1) multiple noisy labels can be integrated into one deep learning model; (2) noisy segmentation modeling, including probabilistic parameters, is adaptive, depending on the given testing image appearance. Implementation of the new ANTN model on both the synthetic data and real-world histo-images demonstrates its effectiveness and superiority over off-the-shelf and other existing deep-learning-based image segmentation algorithms.

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arXiv2023

Introducing Shape Prior Module in Diffusion Model for Medical Image Segmentation

Medical image segmentation is critical for diagnosing and treating spinal disorders. However, the presence of high noise, ambiguity, and uncertainty makes this task highly challenging. Factors such as unclear anatomical boundaries, inter-class similarities, and irrational annotations contribute to this challenge. Achieving both accurate and diverse segmentation templates is essential to support radiologists in clinical practice. In recent years, denoising diffusion probabilistic modeling (DDPM) has emerged as a prominent research topic in computer vision. It has demonstrated effectiveness in various vision tasks, including image deblurring, super-resolution, anomaly detection, and even semantic representation generation at the pixel level. Despite the robustness of existing diffusion models in visual generation tasks, they still struggle with discrete masks and their various effects. To address the need for accurate and diverse spine medical image segmentation templates, we propose an end-to-end framework called VerseDiff-UNet, which leverages the denoising diffusion probabilistic model (DDPM). Our approach integrates the diffusion model into a standard U-shaped architecture. At each step, we combine the noise-added image with the labeled mask to guide the diffusion direction accurately towards the target region. Furthermore, to capture specific anatomical a priori information in medical images, we incorporate a shape a priori module. This module efficiently extracts structural semantic information from the input spine images. We evaluate our method on a single dataset of spine images acquired through X-ray imaging. Our results demonstrate that VerseDiff-UNet significantly outperforms other state-of-the-art methods in terms of accuracy while preserving the natural features and variations of anatomy.

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arXiv2026

Structure and Progress Aware Diffusion for Medical Image Segmentation

Medical image segmentation is crucial for computer-aided diagnosis, which necessitates understanding both coarse morphological and semantic structures, as well as carving fine boundaries. The morphological and semantic structures in medical images are beneficial and stable clues for target understanding. While the fine boundaries of medical targets (like tumors and lesions) are usually ambiguous and noisy since lesion overlap, annotation uncertainty, and so on, making it not reliable to serve as early supervision. However, existing methods simultaneously learn coarse structures and fine boundaries throughout the training process. In this paper, we propose a structure and progress-aware diffusion (SPAD) for medical image segmentation, which consists of a semantic-concentrated diffusion (ScD) and a boundary-centralized diffusion (BcD) modulated by a progress-aware scheduler (PaS). Specifically, the semantic-concentrated diffusion introduces anchor-preserved target perturbation, which perturbs pixels within a medical target but preserves unaltered areas as semantic anchors, encouraging the model to infer noisy target areas from the surrounding semantic context. The boundary-centralized diffusion introduces progress-aware boundary noise, which blurs unreliable and ambiguous boundaries, thus compelling the model to focus on coarse but stable anatomical morphology and global semantics. Furthermore, the progress-aware scheduler gradually modulates noise intensity of the ScD and BcD forming a coarse-to-fine diffusion paradigm, which encourage focusing on coarse morphological and semantic structures during early target understanding stages and gradually shifting to fine target boundaries during later contour adjusting stages.

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arXiv2024

GenSelfDiff-HIS: Generative Self-Supervision Using Diffusion for Histopathological Image Segmentation

Histopathological image segmentation is a laborious and time-intensive task, often requiring analysis from experienced pathologists for accurate examinations. To reduce this burden, supervised machine-learning approaches have been adopted using large-scale annotated datasets for histopathological image analysis. However, in several scenarios, the availability of large-scale annotated data is a bottleneck while training such models. Self-supervised learning (SSL) is an alternative paradigm that provides some respite by constructing models utilizing only the unannotated data which is often abundant. The basic idea of SSL is to train a network to perform one or many pseudo or pretext tasks on unannotated data and use it subsequently as the basis for a variety of downstream tasks. It is seen that the success of SSL depends critically on the considered pretext task. While there have been many efforts in designing pretext tasks for classification problems, there haven't been many attempts on SSL for histopathological segmentation. Motivated by this, we propose an SSL approach for segmenting histopathological images via generative diffusion models in this paper. Our method is based on the observation that diffusion models effectively solve an image-to-image translation task akin to a segmentation task. Hence, we propose generative diffusion as the pretext task for histopathological image segmentation. We also propose a multi-loss function-based fine-tuning for the downstream task. We validate our method using several metrics on two publically available datasets along with a newly proposed head and neck (HN) cancer dataset containing hematoxylin and eosin (H\&E) stained images along with annotations. Codes will be made public at https://github.com/suhas-srinath/GenSelfDiff-HIS.

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arXiv2024

Diagonal Hierarchical Consistency Learning for Semi-supervised Medical Image Segmentation

Medical image segmentation, which is essential for many clinical applications, has achieved almost human-level performance via data-driven deep learning technologies. Nevertheless, its performance is predicated upon the costly process of manually annotating a vast amount of medical images. To this end, we propose a novel framework for robust semi-supervised medical image segmentation using diagonal hierarchical consistency learning (DiHC-Net). First, it is composed of multiple sub-models with identical multi-scale architecture but with distinct sub-layers, such as up-sampling and normalisation layers. Second, with mutual consistency, a novel consistency regularisation is enforced between one model's intermediate and final prediction and soft pseudo labels from other models in a diagonal hierarchical fashion. A series of experiments verifies the efficacy of our simple framework, outperforming all previous approaches on public benchmark dataset covering organ and tumour.

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arXiv2025

BiPVL-Seg: Bidirectional Progressive Vision-Language Fusion with Global-Local Alignment for Medical Image Segmentation

Medical image segmentation typically relies solely on visual data, overlooking the rich textual information clinicians use for diagnosis. Vision-language models attempt to bridge this gap, but existing approaches often process visual and textual features independently, resulting in weak cross-modal alignment. Simple fusion techniques fail due to the inherent differences between spatial visual features and sequential text embeddings. Additionally, medical terminology deviates from general language, limiting the effectiveness of off-the-shelf text encoders and further hindering vision-language alignment. We propose BiPVL-Seg, an end-to-end framework that integrates vision-language fusion and embedding alignment through architectural and training innovations, where both components reinforce each other to enhance medical image segmentation. BiPVL-Seg introduces bidirectional progressive fusion in the architecture, which facilitates stage-wise information exchange between vision and text encoders. Additionally, it incorporates global-local contrastive alignment, a training objective that enhances the text encoder's comprehension by aligning text and vision embeddings at both class and concept levels. Extensive experiments on diverse medical imaging benchmarks across CT and MR modalities demonstrate BiPVL-Seg's superior performance when compared with state-of-the-art methods in complex multi-class segmentation. Source code is available in this GitHub repository.

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arXiv2025

QTSeg: A Query Token-Based Dual-Mix Attention Framework with Multi-Level Feature Distribution for Medical Image Segmentation

Medical image segmentation plays a crucial role in assisting healthcare professionals with accurate diagnoses and enabling automated diagnostic processes. Traditional convolutional neural networks (CNNs) often struggle with capturing long-range dependencies, while transformer-based architectures, despite their effectiveness, come with increased computational complexity. Recent efforts have focused on combining CNNs and transformers to balance performance and efficiency, but existing approaches still face challenges in achieving high segmentation accuracy while maintaining low computational costs. Furthermore, many methods underutilize the CNN encoder's capability to capture local spatial information, concentrating primarily on mitigating long-range dependency issues. To address these limitations, we propose QTSeg, a novel architecture for medical image segmentation that effectively integrates local and global information. QTSeg features a dual-mix attention decoder designed to enhance segmentation performance through: (1) a cross-attention mechanism for improved feature alignment, (2) a spatial attention module to capture long-range dependencies, and (3) a channel attention block to learn inter-channel relationships. Additionally, we introduce a multi-level feature distribution module, which adaptively balances feature propagation between the encoder and decoder, further boosting performance. Extensive experiments on five publicly available datasets covering diverse segmentation tasks, including lesion, polyp, breast cancer, cell, and retinal vessel segmentation, demonstrate that QTSeg outperforms state-of-the-art methods across multiple evaluation metrics while maintaining lower computational costs. Our implementation can be found at: https://github.com/tpnam0901/QTSeg (v1.0.0)

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arXiv2025

ConStyX: Content Style Augmentation for Generalizable Medical Image Segmentation

Medical images are usually collected from multiple domains, leading to domain shifts that impair the performance of medical image segmentation models. Domain Generalization (DG) aims to address this issue by training a robust model with strong generalizability. Recently, numerous domain randomization-based DG methods have been proposed. However, these methods suffer from the following limitations: 1) constrained efficiency of domain randomization due to their exclusive dependence on image style perturbation, and 2) neglect of the adverse effects of over-augmented images on model training. To address these issues, we propose a novel domain randomization-based DG method, called content style augmentation (ConStyX), for generalizable medical image segmentation. Specifically, ConStyX 1) augments the content and style of training data, allowing the augmented training data to better cover a wider range of data domains, and 2) leverages well-augmented features while mitigating the negative effects of over-augmented features during model training. Extensive experiments across multiple domains demonstrate that our ConStyX achieves superior generalization performance. The code is available at https://github.com/jwxsp1/ConStyX.

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arXiv2023

Towards Robust Referring Image Segmentation

Referring Image Segmentation (RIS) is a fundamental vision-language task that outputs object masks based on text descriptions. Many works have achieved considerable progress for RIS, including different fusion method designs. In this work, we explore an essential question, ``What if the text description is wrong or misleading?'' For example, the described objects are not in the image. We term such a sentence as a negative sentence. However, existing solutions for RIS cannot handle such a setting. To this end, we propose a new formulation of RIS, named Robust Referring Image Segmentation (R-RIS). It considers the negative sentence inputs besides the regular positive text inputs. To facilitate this new task, we create three R-RIS datasets by augmenting existing RIS datasets with negative sentences and propose new metrics to evaluate both types of inputs in a unified manner. Furthermore, we propose a new transformer-based model, called RefSegformer, with a token-based vision and language fusion module. Our design can be easily extended to our R-RIS setting by adding extra blank tokens. Our proposed RefSegformer achieves state-of-the-art results on both RIS and R-RIS datasets, establishing a solid baseline for both settings. Our project page is at \url{https://github.com/jianzongwu/robust-ref-seg}.

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arXiv2024

Weak-Mamba-UNet: Visual Mamba Makes CNN and ViT Work Better for Scribble-based Medical Image Segmentation

Medical image segmentation is increasingly reliant on deep learning techniques, yet the promising performance often come with high annotation costs. This paper introduces Weak-Mamba-UNet, an innovative weakly-supervised learning (WSL) framework that leverages the capabilities of Convolutional Neural Network (CNN), Vision Transformer (ViT), and the cutting-edge Visual Mamba (VMamba) architecture for medical image segmentation, especially when dealing with scribble-based annotations. The proposed WSL strategy incorporates three distinct architecture but same symmetrical encoder-decoder networks: a CNN-based UNet for detailed local feature extraction, a Swin Transformer-based SwinUNet for comprehensive global context understanding, and a VMamba-based Mamba-UNet for efficient long-range dependency modeling. The key concept of this framework is a collaborative and cross-supervisory mechanism that employs pseudo labels to facilitate iterative learning and refinement across the networks. The effectiveness of Weak-Mamba-UNet is validated on a publicly available MRI cardiac segmentation dataset with processed scribble annotations, where it surpasses the performance of a similar WSL framework utilizing only UNet or SwinUNet. This highlights its potential in scenarios with sparse or imprecise annotations. The source code is made publicly accessible.

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