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arXiv2022

TranSiam: Fusing Multimodal Visual Features Using Transformer for Medical Image Segmentation

Automatic segmentation of medical images based on multi-modality is an important topic for disease diagnosis. Although the convolutional neural network (CNN) has been proven to have excellent performance in image segmentation tasks, it is difficult to obtain global information. The lack of global information will seriously affect the accuracy of the segmentation results of the lesion area. In addition, there are visual representation differences between multimodal data of the same patient. These differences will affect the results of the automatic segmentation methods. To solve these problems, we propose a segmentation method suitable for multimodal medical images that can capture global information, named TranSiam. TranSiam is a 2D dual path network that extracts features of different modalities. In each path, we utilize convolution to extract detailed information in low level stage, and design a ICMT block to extract global information in high level stage. ICMT block embeds convolution in the transformer, which can extract global information while retaining spatial and detailed information. Furthermore, we design a novel fusion mechanism based on cross attention and selfattention, called TMM block, which can effectively fuse features between different modalities. On the BraTS 2019 and BraTS 2020 multimodal datasets, we have a significant improvement in accuracy over other popular methods.

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arXiv2023

The Fully Convolutional Transformer for Medical Image Segmentation

We propose a novel transformer model, capable of segmenting medical images of varying modalities. Challenges posed by the fine grained nature of medical image analysis mean that the adaptation of the transformer for their analysis is still at nascent stages. The overwhelming success of the UNet lay in its ability to appreciate the fine-grained nature of the segmentation task, an ability which existing transformer based models do not currently posses. To address this shortcoming, we propose The Fully Convolutional Transformer (FCT), which builds on the proven ability of Convolutional Neural Networks to learn effective image representations, and combines them with the ability of Transformers to effectively capture long-term dependencies in its inputs. The FCT is the first fully convolutional Transformer model in medical imaging literature. It processes its input in two stages, where first, it learns to extract long range semantic dependencies from the input image, and then learns to capture hierarchical global attributes from the features. FCT is compact, accurate and robust. Our results show that it outperforms all existing transformer architectures by large margins across multiple medical image segmentation datasets of varying data modalities without the need for any pre-training. FCT outperforms its immediate competitor on the ACDC dataset by 1.3%, on the Synapse dataset by 4.4%, on the Spleen dataset by 1.2% and on ISIC 2017 dataset by 1.1% on the dice metric, with up to five times fewer parameters. Our code, environments and models will be available via GitHub.

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arXiv2020

DA-RefineNet:A Dual Input Whole Slide Image Segmentation Algorithm Based on Attention

Automatic medical image segmentation has wide applications for disease diagnosing. However, it is much more challenging than natural optical image segmentation due to the high-resolution of medical images and the corresponding huge computation cost. The sliding window is a commonly used technique for whole slide image (WSI) segmentation, however, for these methods based on the sliding window, the main drawback is lacking global contextual information for supervision. In this paper, we propose a dual-inputs attention network (denoted as DA-RefineNet) for WSI segmentation, where both local fine-grained information and global coarse information can be efficiently utilized. Sufficient comparative experiments are conducted to evaluate the effectiveness of the proposed method, the results prove that the proposed method can achieve better performance on WSI segmentation compared to methods relying on single-input.

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arXiv2013

Hybrid Image Segmentation using Discerner Cluster in FCM and Histogram Thresholding

Image thresholding has played an important role in image segmentation. This paper presents a hybrid approach for image segmentation based on the thresholding by fuzzy c-means (THFCM) algorithm for image segmentation. The goal of the proposed approach is to find a discerner cluster able to find an automatic threshold. The algorithm is formulated by applying the standard FCM clustering algorithm to the frequencies (y-values) on the smoothed histogram. Hence, the frequencies of an image can be used instead of the conventional whole data of image. The cluster that has the highest peak which represents the maximum frequency in the image histogram will play as an excellent role in determining a discerner cluster to the grey level image. Then, the pixels belong to the discerner cluster represent an object in the gray level histogram while the other clusters represent a background. Experimental results with standard test images have been obtained through the proposed approach (THFCM).

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arXiv2016

Convex Histogram-Based Joint Image Segmentation with Regularized Optimal Transport Cost

We investigate in this work a versatile convex framework for multiple image segmentation, relying on the regularized optimal mass transport theory. In this setting, several transport cost functions are considered and used to match statistical distributions of features. In practice, global multidimensional histograms are estimated from the segmented image regions, and are compared to referring models that are either fixed histograms given a priori, or directly inferred in the non-supervised case. The different convex problems studied are solved efficiently using primal-dual algorithms. The proposed approach is generic and enables multi-phase segmentation as well as co-segmentation of multiple images.

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arXiv2019

Non-Local Context Encoder: Robust Biomedical Image Segmentation against Adversarial Attacks

Recent progress in biomedical image segmentation based on deep convolutional neural networks (CNNs) has drawn much attention. However, its vulnerability towards adversarial samples cannot be overlooked. This paper is the first one that discovers that all the CNN-based state-of-the-art biomedical image segmentation models are sensitive to adversarial perturbations. This limits the deployment of these methods in safety-critical biomedical fields. In this paper, we discover that global spatial dependencies and global contextual information in a biomedical image can be exploited to defend against adversarial attacks. To this end, non-local context encoder (NLCE) is proposed to model short- and long range spatial dependencies and encode global contexts for strengthening feature activations by channel-wise attention. The NLCE modules enhance the robustness and accuracy of the non-local context encoding network (NLCEN), which learns robust enhanced pyramid feature representations with NLCE modules, and then integrates the information across different levels. Experiments on both lung and skin lesion segmentation datasets have demonstrated that NLCEN outperforms any other state-of-the-art biomedical image segmentation methods against adversarial attacks. In addition, NLCE modules can be applied to improve the robustness of other CNN-based biomedical image segmentation methods.

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arXiv2026

Semantic-Driven Scale and Spatial Selection for Efficient Cross-Modal Alignment in Referring Remote Sensing Image Segmentation

Referring Remote Sensing Image Segmentation (RRSIS) seeks to localize and segment the target object or region specified by a natural language expression in a remote sensing image. While existing RRSIS models have benefited from large-scale foundation models, they predominantly rely on full fine-tuning. These approaches are computationally intensive and may weaken the generalization ability of pre-trained models, as extensive fine-tuning on significantly smaller downstream datasets can distort the well-structured feature representations learned during large-scale pre-training. Although Parameter-Efficient Tuning (PET) offers a potential alternative, existing PET frameworks primarily focus on single-modal optimization, failing to capture the complex cross-modal dependencies required for multimodal reasoning, while simultaneously struggling to bridge the substantial domain gap between natural scenes and aerial imagery. To address these limitations, we propose a novel framework, Semantic-driven Scale and Spatial Selection for Efficient Cross-modal Alignment (S4ECA), which enables effective and efficient cross-modal interaction through parameter-efficient adaptation. Specifically, we design a dual-encoder adapter architecture. The textual adapter employs learnable queries to distill highly semantic language proxies from word-level embeddings, facilitating early grounding. Simultaneously, the visual adapter refines hierarchical feature representations through a multi-scale dense extractor, followed by a language-guided scale and spatial selection mechanism that dynamically emphasizes relevant visual contexts, ensuring precise cross-modal alignment. By updating only 2.4% of the backbone parameters, our proposed model achieves state-of-the-art performance on the RRSIS-D and RefSegRS datasets, demonstrating superior efficiency and precision in complex aerial scenarios.

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arXiv2024

FDiff-Fusion:Denoising diffusion fusion network based on fuzzy learning for 3D medical image segmentation

In recent years, the denoising diffusion model has achieved remarkable success in image segmentation modeling. With its powerful nonlinear modeling capabilities and superior generalization performance, denoising diffusion models have gradually been applied to medical image segmentation tasks, bringing new perspectives and methods to this field. However, existing methods overlook the uncertainty of segmentation boundaries and the fuzziness of regions, resulting in the instability and inaccuracy of the segmentation results. To solve this problem, a denoising diffusion fusion network based on fuzzy learning for 3D medical image segmentation (FDiff-Fusion) is proposed in this paper. By integrating the denoising diffusion model into the classical U-Net network, this model can effectively extract rich semantic information from input medical images, thus providing excellent pixel-level representation for medical image segmentation. ... Finally, to validate the effectiveness of FDiff-Fusion, we compare it with existing advanced segmentation networks on the BRATS 2020 brain tumor dataset and the BTCV abdominal multi-organ dataset. The results show that FDiff-Fusion significantly improves the Dice scores and HD95 distance on these two datasets, demonstrating its superiority in medical image segmentation tasks.

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arXiv2014

Particle methods enable fast and simple approximation of Sobolev gradients in image segmentation

Bio-image analysis is challenging due to inhomogeneous intensity distributions and high levels of noise in the images. Bayesian inference provides a principled way for regularizing the problem using prior knowledge. A fundamental choice is how one measures "distances" between shapes in an image. It has been shown that the straightforward geometric L2 distance is degenerate and leads to pathological situations. This is avoided when using Sobolev gradients, rendering the segmentation problem less ill-posed. The high computational cost and implementation overhead of Sobolev gradients, however, have hampered practical applications. We show how particle methods as applied to image segmentation allow for a simple and computationally efficient implementation of Sobolev gradients. We show that the evaluation of Sobolev gradients amounts to particle-particle interactions along the contour in an image. We extend an existing particle-based segmentation algorithm to using Sobolev gradients. Using synthetic and real-world images, we benchmark the results for both 2D and 3D images using piecewise smooth and piecewise constant region models. The present particle approximation of Sobolev gradients is 2.8 to 10 times faster than the previous reference implementation, but retains the known favorable properties of Sobolev gradients. This speedup is achieved by using local particle-particle interactions instead of solving a global Poisson equation at each iteration. The computational time per iteration is higher for Sobolev gradients than for L2 gradients. Since Sobolev gradients precondition the optimization problem, however, a smaller number of overall iterations may be necessary for the algorithm to converge, which can in some cases amortize the higher per-iteration cost.

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arXiv2022

UNeXt: MLP-based Rapid Medical Image Segmentation Network

UNet and its latest extensions like TransUNet have been the leading medical image segmentation methods in recent years. However, these networks cannot be effectively adopted for rapid image segmentation in point-of-care applications as they are parameter-heavy, computationally complex and slow to use. To this end, we propose UNeXt which is a Convolutional multilayer perceptron (MLP) based network for image segmentation. We design UNeXt in an effective way with an early convolutional stage and a MLP stage in the latent stage. We propose a tokenized MLP block where we efficiently tokenize and project the convolutional features and use MLPs to model the representation. To further boost the performance, we propose shifting the channels of the inputs while feeding in to MLPs so as to focus on learning local dependencies. Using tokenized MLPs in latent space reduces the number of parameters and computational complexity while being able to result in a better representation to help segmentation. The network also consists of skip connections between various levels of encoder and decoder. We test UNeXt on multiple medical image segmentation datasets and show that we reduce the number of parameters by 72x, decrease the computational complexity by 68x, and improve the inference speed by 10x while also obtaining better segmentation performance over the state-of-the-art medical image segmentation architectures. Code is available at https://github.com/jeya-maria-jose/UNeXt-pytorch

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arXiv2025

MaskAttn-UNet: A Mask Attention-Driven Framework for Universal Low-Resolution Image Segmentation

Low-resolution image segmentation is crucial in real-world applications such as robotics, augmented reality, and large-scale scene understanding, where high-resolution data is often unavailable due to computational constraints. To address this challenge, we propose MaskAttn-UNet, a novel segmentation framework that enhances the traditional U-Net architecture via a mask attention mechanism. Our model selectively emphasizes important regions while suppressing irrelevant backgrounds, thereby improving segmentation accuracy in cluttered and complex scenes. Unlike conventional U-Net variants, MaskAttn-UNet effectively balances local feature extraction with broader contextual awareness, making it particularly well-suited for low-resolution inputs. We evaluate our approach on three benchmark datasets with input images rescaled to 128x128 and demonstrate competitive performance across semantic, instance, and panoptic segmentation tasks. Our results show that MaskAttn-UNet achieves accuracy comparable to state-of-the-art methods at significantly lower computational cost than transformer-based models, making it an efficient and scalable solution for low-resolution segmentation in resource-constrained scenarios.

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arXiv2022

HyperSegNAS: Bridging One-Shot Neural Architecture Search with 3D Medical Image Segmentation using HyperNet

Semantic segmentation of 3D medical images is a challenging task due to the high variability of the shape and pattern of objects (such as organs or tumors). Given the recent success of deep learning in medical image segmentation, Neural Architecture Search (NAS) has been introduced to find high-performance 3D segmentation network architectures. However, because of the massive computational requirements of 3D data and the discrete optimization nature of architecture search, previous NAS methods require a long search time or necessary continuous relaxation, and commonly lead to sub-optimal network architectures. While one-shot NAS can potentially address these disadvantages, its application in the segmentation domain has not been well studied in the expansive multi-scale multi-path search space. To enable one-shot NAS for medical image segmentation, our method, named HyperSegNAS, introduces a HyperNet to assist super-net training by incorporating architecture topology information. Such a HyperNet can be removed once the super-net is trained and introduces no overhead during architecture search. We show that HyperSegNAS yields better performing and more intuitive architectures compared to the previous state-of-the-art (SOTA) segmentation networks; furthermore, it can quickly and accurately find good architecture candidates under different computing constraints. Our method is evaluated on public datasets from the Medical Segmentation Decathlon (MSD) challenge, and achieves SOTA performances.

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arXiv2026

MID: Mask-Image Distributional Divergence for Evaluating Medical Image Segmentation

Current evaluation protocols for medical image segmentation remain largely anchored in sample-wise comparisons, e.g., Dice and Hausdorff distance, which require each prediction to be paired with a ground-truth mask. Yet two limitations arise in practice: they are inapplicable when predictions are made on unlabeled data; and even when annotations are available, they cannot assess whether a collection of predictions matches the distributional structure of the ground-truth population. We introduce MID (Mask-Image Distributional Divergence), a distribution-level evaluation metric for medical image segmentation. MID builds upon the observation that segmentation quality is a property of the joint image-mask distribution: a mask may be anatomically plausible in isolation yet incorrect for the image it accompanies. MID compares the joint distribution of images and masks between a reference set and a set of predictions, without requiring sample-wise correspondence. This captures both mask realism and image-mask consistency. We evaluate MID across 13 publicly available datasets spanning CT, MRI, and MRA. Under anatomically realistic corruptions across 56 organ groups, MID tracks mean Dice and Hausdorff distance without per-sample ground-truth pairing. MID also detects distributional shifts across modalities and anatomies, identifies image-mask misalignment through controlled shuffling experiments, and produces reliable model rankings across real segmentation models. Official implementation available at github.com/erc-caravel/pytorch-mid

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arXiv2025

FlowSDF: Flow Matching for Medical Image Segmentation Using Distance Transforms

Medical image segmentation plays an important role in accurately identifying and isolating regions of interest within medical images. Generative approaches are particularly effective in modeling the statistical properties of segmentation masks that are closely related to the respective structures. In this work we introduce FlowSDF, an image-guided conditional flow matching framework, designed to represent the signed distance function (SDF), and, in turn, to represent an implicit distribution of segmentation masks. The advantage of leveraging the SDF is a more natural distortion when compared to that of binary masks. Through the learning of a vector field associated with the probability path of conditional SDF distributions, our framework enables accurate sampling of segmentation masks and the computation of relevant statistical measures. This probabilistic approach also facilitates the generation of uncertainty maps represented by the variance, thereby supporting enhanced robustness in prediction and further analysis. We qualitatively and quantitatively illustrate competitive performance of the proposed method on a public nuclei and gland segmentation data set, highlighting its utility in medical image segmentation applications.

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arXiv2025

DeRIS: Decoupling Perception and Cognition for Enhanced Referring Image Segmentation through Loopback Synergy

Referring Image Segmentation (RIS) is a challenging task that aims to segment objects in an image based on natural language expressions. While prior studies have predominantly concentrated on improving vision-language interactions and achieving fine-grained localization, a systematic analysis of the fundamental bottlenecks in existing RIS frameworks remains underexplored. To bridge this gap, we propose DeRIS, a novel framework that decomposes RIS into two key components: perception and cognition. This modular decomposition facilitates a systematic analysis of the primary bottlenecks impeding RIS performance. Our findings reveal that the predominant limitation lies not in perceptual deficiencies, but in the insufficient multi-modal cognitive capacity of current models. To mitigate this, we propose a Loopback Synergy mechanism, which enhances the synergy between the perception and cognition modules, thereby enabling precise segmentation while simultaneously improving robust image-text comprehension. Additionally, we analyze and introduce a simple non-referent sample conversion data augmentation to address the long-tail distribution issue related to target existence judgement in general scenarios. Notably, DeRIS demonstrates inherent adaptability to both non- and multi-referents scenarios without requiring specialized architectural modifications, enhancing its general applicability. The codes and models are available at https://github.com/Dmmm1997/DeRIS.

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arXiv2023

PyMIC: A deep learning toolkit for annotation-efficient medical image segmentation

Background and Objective: Open-source deep learning toolkits are one of the driving forces for developing medical image segmentation models. Existing toolkits mainly focus on fully supervised segmentation and require full and accurate pixel-level annotations that are time-consuming and difficult to acquire for segmentation tasks, which makes learning from imperfect labels highly desired for reducing the annotation cost. We aim to develop a new deep learning toolkit to support annotation-efficient learning for medical image segmentation. Methods: Our proposed toolkit named PyMIC is a modular deep learning library for medical image segmentation tasks. In addition to basic components that support development of high-performance models for fully supervised segmentation, it contains several advanced components tailored for learning from imperfect annotations, such as loading annotated and unannounced images, loss functions for unannotated, partially or inaccurately annotated images, and training procedures for co-learning between multiple networks, etc. PyMIC supports development of semi-supervised, weakly supervised and noise-robust learning methods for medical image segmentation. Results: We present several illustrative medical image segmentation tasks based on PyMIC: (1) Achieving competitive performance on fully supervised learning; (2) Semi-supervised cardiac structure segmentation with only 10% training images annotated; (3) Weakly supervised segmentation using scribble annotations; and (4) Learning from noisy labels for chest radiograph segmentation. Conclusions: The PyMIC toolkit is easy to use and facilitates efficient development of medical image segmentation models with imperfect annotations. It is modular and flexible, which enables researchers to develop high-performance models with low annotation cost. The source code is available at: https://github.com/HiLab-git/PyMIC.

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arXiv2016

Mixed Robust/Average Submodular Partitioning: Fast Algorithms, Guarantees, and Applications to Parallel Machine Learning and Multi-Label Image Segmentation

We study two mixed robust/average-case submodular partitioning problems that we collectively call Submodular Partitioning. These problems generalize both purely robust instances of the problem (namely max-min submodular fair allocation (SFA) and min-max submodular load balancing (SLB) and also generalize average-case instances (that is the submodular welfare problem (SWP) and submodular multiway partition (SMP). While the robust versions have been studied in the theory community, existing work has focused on tight approximation guarantees, and the resultant algorithms are not, in general, scalable to very large real-world applications. This is in contrast to the average case, where most of the algorithms are scalable. In the present paper, we bridge this gap, by proposing several new algorithms (including those based on greedy, majorization-minimization, minorization-maximization, and relaxation algorithms) that not only scale to large sizes but that also achieve theoretical approximation guarantees close to the state-of-the-art, and in some cases achieve new tight bounds. We also provide new scalable algorithms that apply to additive combinations of the robust and average-case extreme objectives. We show that these problems have many applications in machine learning (ML). This includes: 1) data partitioning and load balancing for distributed machine algorithms on parallel machines; 2) data clustering; and 3) multi-label image segmentation with (only) Boolean submodular functions via pixel partitioning. We empirically demonstrate the efficacy of our algorithms on real-world problems involving data partitioning for distributed optimization of standard machine learning objectives (including both convex and deep neural network objectives), and also on purely unsupervised (i.e., no supervised or semi-supervised learning, and no interactive segmentation) image segmentation.

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arXiv2025

Contextual Peano Scan and Fast Image Segmentation Using Hidden and Evidential Markov Chains

Transforming bi-dimensional sets of image pixels into mono-dimensional sequences with a Peano scan (PS) is an established technique enabling the use of hidden Markov chains (HMCs) for unsupervised image segmentation. Related Bayesian segmentation methods can compete with hidden Markov fields (HMFs)-based ones and are much faster. PS has recently been extended to the contextual PS, and some initial experiments have shown the value of the associated HMC model, denoted as HMC-CPS, in image segmentation. Moreover, HMCs have been extended to hidden evidential Markov chains (HEMCs), which are capable of improving HMC-based Bayesian segmentation. In this study, we introduce a new HEMC-CPS model by simultaneously considering contextual PS and evidential HMC. We show its effectiveness for Bayesian maximum posterior mode (MPM) segmentation using synthetic and real images. Segmentation is performed in an unsupervised manner, with parameters being estimated using the stochastic expectation--maximization (SEM) method. The new HEMC-CPS model presents potential for the modeling and segmentation of more complex images, such as three-dimensional or multi-sensor multi-resolution images. Finally, the HMC-CPS and HEMC-CPS models are not limited to image segmentation and could be used for any kind of spatially correlated data.

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