Breast cancer remains the leading cause of cancer-related mortality among women worldwide, necessitating the meticulous examination of mammograms by radiologists to characterize abnormal lesions. This manual process demands high accuracy and is often time-consuming, costly, and error-prone. Automated image segmentation using artificial intelligence offers a promising alternative to streamline this workflow. However, most existing methods are supervised, requiring large, expertly annotated datasets that are not always available, and they experience significant generalization issues. Thus, unsupervised learning models can be leveraged for image segmentation, but they come at a cost of reduced accuracy, or require extensive computational resourcess. In this paper, we propose the first end-to-end quantum-enhanced framework for unsupervised mammography medical images segmentation that balances between performance accuracy and computational requirements. We first introduce a quantum-inspired image representation that serves as an initial approximation of the segmentation mask. The segmentation task is then formulated as a QUBO problem, aiming to maximize the contrast between the background and the tumor region while ensuring a cohesive segmentation mask with minimal connected components. We conduct an extensive evaluation of quantum and quantum-inspired methods for image segmentation, demonstrating that quantum annealing and variational quantum circuits achieve performance comparable to classical optimization techniques. Notably, quantum annealing is shown to be an order of magnitude faster than the classical optimization method in our experiments. Our findings demonstrate that this framework achieves performance comparable to state-of-the-art supervised methods, including UNet-based architectures, offering a viable unsupervised alternative for breast cancer image segmentation.
Domain-invariant representation learning is a powerful method for domain generalization. Previous approaches face challenges such as high computational demands, training instability, and limited effectiveness with high-dimensional data, potentially leading to the loss of valuable features. To address these issues, we hypothesize that an ideal generalized representation should exhibit similar pattern responses within the same channel across cross-domain images. Based on this hypothesis, we use deep features from the source domain as queries, and deep features from the generated domain as keys and values. Through a cross-channel attention mechanism, the original deep features are reconstructed into robust regularization representations, forming an explicit constraint that guides the model to learn domain-invariant representations. Additionally, style augmentation is another common method. However, existing methods typically generate new styles through convex combinations of source domains, which limits the diversity of training samples by confining the generated styles to the original distribution. To overcome this limitation, we propose an Adaptive Feature Blending (AFB) method that generates out-of-distribution samples while exploring the in-distribution space, significantly expanding the domain range. Extensive experimental results demonstrate that our proposed methods achieve superior performance on two standard domain generalization benchmarks for medical image segmentation.
Medical image segmentation is crucial for accurate clinical diagnoses, yet it faces challenges such as low contrast between lesions and normal tissues, unclear boundaries, and high variability across patients. Deep learning has improved segmentation accuracy and efficiency, but it still relies heavily on expert annotations and struggles with the complexities of medical images. The small size of medical image datasets and the high cost of data acquisition further limit the performance of segmentation networks. Diffusion models, with their iterative denoising process, offer a promising alternative for better detail capture in segmentation. However, they face difficulties in accurately segmenting small targets and maintaining the precision of boundary details. This article discusses the importance of medical image segmentation, the limitations of current deep learning approaches, and the potential of diffusion models to address these challenges.
Deep learning (DL) methods have shown remarkable successes in medical image segmentation, often using large amounts of annotated data for model training. However, acquiring a large number of diverse labeled 3D medical image datasets is highly difficult and expensive. Recently, mask propagation DL methods were developed to reduce the annotation burden on 3D medical images. For example, Sli2Vol~\cite{yeung2021sli2vol} proposed a self-supervised framework (SSF) to learn correspondences by matching neighboring slices via slice reconstruction in the training stage; the learned correspondences were then used to propagate a labeled slice to other slices in the test stage. But, these methods are still prone to error accumulation due to the inter-slice propagation of reconstruction errors. Also, they do not handle discontinuities well, which can occur between consecutive slices in 3D images, as they emphasize exploiting object continuity. To address these challenges, in this work, we propose a new SSF, called \proposed, {for segmenting any anatomical structures in 3D medical images using only a single annotated slice per training and testing volume.} Specifically, in the training stage, we first propagate an annotated 2D slice of a training volume to the other slices, generating pseudo-labels (PLs). Then, we develop a novel Object Estimation Guided Correspondence Flow Network to learn reliable correspondences between consecutive slices and corresponding PLs in a self-supervised manner. In the test stage, such correspondences are utilized to propagate a single annotated slice to the other slices of a test volume. We demonstrate the effectiveness of our method on various medical image segmentation tasks with different datasets, showing better generalizability across different organs, modalities, and modals. Code is available at \url{https://github.com/adlsn/Sli2Volplus}
Interactive Medical Image Segmentation (IMIS) has long been constrained by the limited availability of large-scale, diverse, and densely annotated datasets, which hinders model generalization and consistent evaluation across different models. In this paper, we introduce the IMed-361M benchmark dataset, a significant advancement in general IMIS research. First, we collect and standardize over 6.4 million medical images and their corresponding ground truth masks from multiple data sources. Then, leveraging the strong object recognition capabilities of a vision foundational model, we automatically generated dense interactive masks for each image and ensured their quality through rigorous quality control and granularity management. Unlike previous datasets, which are limited by specific modalities or sparse annotations, IMed-361M spans 14 modalities and 204 segmentation targets, totaling 361 million masks-an average of 56 masks per image. Finally, we developed an IMIS baseline network on this dataset that supports high-quality mask generation through interactive inputs, including clicks, bounding boxes, text prompts, and their combinations. We evaluate its performance on medical image segmentation tasks from multiple perspectives, demonstrating superior accuracy and scalability compared to existing interactive segmentation models. To facilitate research on foundational models in medical computer vision, we release the IMed-361M and model at https://github.com/uni-medical/IMIS-Bench.
In the field of medical image segmentation, challenges such as indistinct lesion features, ambiguous boundaries,and multi-scale characteristics have long revailed. This paper proposes an improved method named Intensity-Spatial Dual Masked AutoEncoder (ISD-MAE). Based on the tissue-contrast semi-masked autoencoder, a Masked AutoEncoder (MAE) branch is introduced to perform intensity masking and spatial masking operations on chest CT images for multi-scale feature learning and segmentation tasks. The model utilizes a dual-branch structure and contrastive learning to enhance the ability to learn tissue features and boundary details. Experiments are conducted on multiple 2D and 3D datasets. The results show that ISD-MAE significantly outperforms other methods in 2D pneumonia and mediastinal tumor segmentation tasks. For example, the Dice score reaches 90.10% on the COVID19 LESION dataset, and the performance is relatively stable. However, there is still room for improvement on 3D datasets. In response to this, improvement directions are proposed, including optimizing the loss function, using enhanced 3D convolution blocks, and processing datasets from multiple perspectives.Our code is available at:https://github.com/prowontheus/ISD-MAE.
Semi-supervised learning (SSL) has made notable advancements in medical image segmentation (MIS), particularly in scenarios with limited labeled data and significantly enhancing data utilization efficiency. Previous methods primarily focus on complex training strategies to utilize unlabeled data but neglect the importance of graph structural information. Different from existing methods, we propose a graph-based clustering for semi-supervised medical image segmentation (GraphCL) by jointly modeling graph data structure in a unified deep model. The proposed GraphCL model enjoys several advantages. Firstly, to the best of our knowledge, this is the first work to model the data structure information for semi-supervised medical image segmentation (SSMIS). Secondly, to get the clustered features across different graphs, we integrate both pairwise affinities between local image features and raw features as inputs. Extensive experimental results on three standard benchmarks show that the proposed GraphCL algorithm outperforms state-of-the-art semi-supervised medical image segmentation methods.
Semantic segmentation is a crucial task in medical imaging. Although supervised learning techniques have proven to be effective in performing this task, they heavily depend on large amounts of annotated training data. The recently introduced Segment Anything Model (SAM) enables prompt-based segmentation and offers zero-shot generalization to unfamiliar objects. In our work, we leverage SAM's abstract object understanding for medical image segmentation to provide pseudo labels for semi-supervised learning, thereby mitigating the need for extensive annotated training data. Our approach refines initial segmentations that are derived from a limited amount of annotated data (comprising up to 43 cases) by extracting bounding boxes and seed points as prompts forwarded to SAM. Thus, it enables the generation of dense segmentation masks as pseudo labels for unlabelled data. The results show that training with our pseudo labels yields an improvement in Dice score from $74.29\,\%$ to $84.17\,\%$ and from $66.63\,\%$ to $74.87\,\%$ for the segmentation of bones of the paediatric wrist and teeth in dental radiographs, respectively. As a result, our method outperforms intensity-based post-processing methods, state-of-the-art supervised learning for segmentation (nnU-Net), and the semi-supervised mean teacher approach. Our Code is available on GitHub.
Medical image segmentation is crucial in robotic surgeries, disease diagnosis, and treatment plans. This research presents an innovative methodology that combines Kolmogorov-Arnold Networks (KAN) with an adapted Mamba layer for medical image segmentation. The proposed KAN-Mamba FusionNet framework improves image segmentation by integrating attention-driven mechanisms with convolutional parallel training and autoregressive deployment, while preserving interpretability, in contrast to the state-of-the-art techniques that depend exclusively on Mamba for ailment localization and accurate diagnosis. We evaluated our proposed KAN-Mamba FusionNet model on three distinct medical image segmentation datasets, BUSI, Kvasir-Seg and GlaS. The results indicated that the KAN-Mamba FusionNet consistently yields better IoU and F1 scores in comparison to the state-of-the-art methods. Further, we offer insights into the model's behavior via ablation studies, examining the effects of various components and assessing their contributions to the overall performance of the proposed model. The findings illustrate the strength and effectiveness of this methodology for dependable medical image segmentation, providing a unique approach to address intricate visual data issues in healthcare.
As a technique to alleviate the pressure of data annotation, semi-supervised learning (SSL) has attracted widespread attention. In the specific domain of medical image segmentation, semi-supervised methods (SSMIS) have become a research hotspot due to their ability to reduce the need for large amounts of precisely annotated data. SSMIS focuses on enhancing the model's generalization performance by leveraging a small number of labeled samples and a large number of unlabeled samples. The latest sharpness-aware optimization (SAM) technique, which optimizes the model by reducing the sharpness of the loss function, has shown significant success in SSMIS. However, SAM and its variants may not fully account for the distribution differences between different datasets. To address this issue, we propose a sharpness-aware optimization method based on $f$-divergence minimization (DiM) for semi-supervised medical image segmentation. This method enhances the model's stability by fine-tuning the sensitivity of model parameters and improves the model's adaptability to different datasets through the introduction of $f$-divergence. By reducing $f$-divergence, the DiM method not only improves the performance balance between the source and target datasets but also prevents performance degradation due to overfitting on the source dataset.
In machine learning, a loss function measures the difference between model predictions and ground-truth (or target) values. For neural network models, visualizing how this loss changes as model parameters are varied can provide insights into the local structure of the so-called loss landscape (e.g., smoothness) as well as global properties of the underlying model (e.g., generalization performance). While various methods for visualizing the loss landscape have been proposed, many approaches limit sampling to just one or two directions, ignoring potentially relevant information in this extremely high-dimensional space. This paper introduces a new representation based on topological data analysis that enables the visualization of higher-dimensional loss landscapes. After describing this new topological landscape profile representation, we show how the shape of loss landscapes can reveal new details about model performance and learning dynamics, highlighting several use cases, including image segmentation (e.g., UNet) and scientific machine learning (e.g., physics-informed neural networks). Through these examples, we provide new insights into how loss landscapes vary across distinct hyperparameter spaces: we find that the topology of the loss landscape is simpler for better-performing models; and we observe greater variation in the shape of loss landscapes near transitions from low to high model performance.
Accurately segmenting lesions in ultrasound images is challenging due to the difficulty in distinguishing boundaries between lesions and surrounding tissues. While deep learning has improved segmentation accuracy, there is limited focus on boundary quality and its relationship with body structures. To address this, we introduce UBBS-Net, a dual-branch deep neural network that learns the relationship between body and boundary for improved segmentation. We also propose a feature fusion module to integrate body and boundary information. Evaluated on three public datasets, UBBS-Net outperforms existing methods, achieving Dice Similarity Coefficients of 81.05% for breast cancer, 76.41% for brachial plexus nerves, and 87.75% for infantile hemangioma segmentation. Our results demonstrate the effectiveness of UBBS-Net for ultrasound image segmentation. The code is available at https://github.com/apple1986/DBF-Net.
With the growing application of transformer in computer vision, hybrid architecture that combine convolutional neural networks (CNNs) and transformers demonstrates competitive ability in medical image segmentation. However, direct fusion of features from CNNs and transformers often leads to feature imbalance and redundant information. To address these issues, we propose a Feaure Imbalance-Aware Segmentation (FIAS) network, which incorporates a dual-path encoder and a novel Mixing Attention (MixAtt) decoder. The dual-branches encoder integrates a DilateFormer for long-range global feature extraction and a Depthwise Multi-Kernel (DMK) convolution for capturing fine-grained local details. A Context-Aware Fusion (CAF) block dynamically balances the contribution of these global and local features, preventing feature imbalance. The MixAtt decoder further enhances segmentation accuracy by combining self-attention and Monte Carlo attention, enabling the model to capture both small details and large-scale dependencies. Experimental results on the Synapse multi-organ and ACDC datasets demonstrate the strong competitiveness of our approach in medical image segmentation tasks.
The advancement of medical image segmentation techniques has been propelled by the adoption of deep learning techniques, particularly UNet-based approaches, which exploit semantic information to improve the accuracy of segmentations. However, the order of organs in scanned images has been disregarded by current medical image segmentation approaches based on UNet. Furthermore, the inherent network structure of UNet does not provide direct capabilities for integrating temporal information. To efficiently integrate temporal information, we propose TP-UNet that utilizes temporal prompts, encompassing organ-construction relationships, to guide the segmentation UNet model. Specifically, our framework is featured with cross-attention and semantic alignment based on unsupervised contrastive learning to combine temporal prompts and image features effectively. Extensive evaluations on two medical image segmentation datasets demonstrate the state-of-the-art performance of TP-UNet. Our implementation will be open-sourced after acceptance.
In a setting where segmentation models have to be built for multiple datasets, each with its own corresponding label set, a straightforward way is to learn one model for every dataset and its labels. Alternatively, multi-task architectures with shared encoders and multiple segmentation heads or shared weights with compound labels can also be made use of. This work proposes a novel label sharing framework where a shared common label space is constructed and each of the individual label sets are systematically mapped to the common labels. This transforms multiple datasets with disparate label sets into a single large dataset with shared labels, and therefore all the segmentation tasks can be addressed by learning a single model. This eliminates the need for task specific adaptations in network architectures and also results in parameter and data efficient models. Furthermore, label sharing framework is naturally amenable for incremental learning where segmentations for new datasets can be easily learnt. We experimentally validate our method on various medical image segmentation datasets, each involving multi-label segmentation. Furthermore, we demonstrate the efficacy of the proposed method in terms of performance and incremental learning ability vis-a-vis alternative methods.
Deep learning-based medical image segmentation helps assist diagnosis and accelerate the treatment process while the model training usually requires large-scale dense annotation datasets. Weakly semi-supervised medical image segmentation is an essential application because it only requires a small amount of scribbles and a large number of unlabeled data to train the model, which greatly reduces the clinician's effort to fully annotate images. To handle the inadequate supervisory information challenge in weakly semi-supervised segmentation (WSSS), a SuperPixel-Propagated Pseudo-label (SP${}^3$) learning method is proposed, using the structural information contained in superpixel for supplemental information. Specifically, the annotation of scribbles is propagated to superpixels and thus obtains a dense annotation for supervised training. Since the quality of pseudo-labels is limited by the low-quality annotation, the beneficial superpixels selected by dynamic thresholding are used to refine pseudo-labels. Furthermore, aiming to alleviate the negative impact of noise in pseudo-label, superpixel-level uncertainty is incorporated to guide the pseudo-label supervision for stable learning. Our method achieves state-of-the-art performance on both tumor and organ segmentation datasets under the WSSS setting, using only 3\% of the annotation workload compared to fully supervised methods and attaining approximately 80\% Dice score. Additionally, our method outperforms eight weakly and semi-supervised methods under both weakly supervised and semi-supervised settings. Results of extensive experiments validate the effectiveness and annotation efficiency of our weakly semi-supervised segmentation, which can assist clinicians in achieving automated segmentation for organs or tumors quickly and ultimately benefit patients.
Many state-of-the-art computer vision architectures leverage U-Net for its adaptability and efficient feature extraction. However, the multi-resolution convolutional design often leads to significant computational demands, limiting deployment on edge devices. We present a streamlined alternative: a 1D convolutional encoder that retains accuracy while enhancing its suitability for edge applications. Our novel encoder architecture achieves semantic segmentation through channel-wise 1D convolutions combined with pixel-unshuffle operations. By incorporating PixelShuffle, known for improving accuracy in super-resolution tasks while reducing computational load, OneNet captures spatial relationships without requiring 2D convolutions, reducing parameters by up to 47%. Additionally, we explore a fully 1D encoder-decoder that achieves a 71% reduction in size, albeit with some accuracy loss. We benchmark our approach against U-Net variants across diverse mask-generation tasks, demonstrating that it preserves accuracy effectively. Although focused on image segmentation, this architecture is adaptable to other convolutional applications. Code for the project is available at https://github.com/shbyun080/OneNet .
In clinical medicine, precise image segmentation can provide substantial support to clinicians. However, achieving such precision often requires a large amount of finely annotated data, which can be costly. Scribble annotation presents a more efficient alternative, boosting labeling efficiency. However, utilizing such minimal supervision for medical image segmentation training, especially with scribble annotations, poses significant challenges. To address these challenges, we introduce ScribbleVS, a novel framework that leverages scribble annotations. We introduce a Regional Pseudo Labels Diffusion Module to expand the scope of supervision and reduce the impact of noise present in pseudo labels. Additionally, we propose a Dynamic Competitive Selection module for enhanced refinement in selecting pseudo labels. Experiments conducted on the ACDC and MSCMRseg datasets have demonstrated promising results, achieving performance levels that even exceed those of fully supervised methodologies. The codes of this study are available at https://github.com/ortonwang/ScribbleVS.
Medical images often exhibit distribution shifts due to variations in imaging protocols and scanners across different medical centers. Domain Generalization (DG) methods aim to train models on source domains that can generalize to unseen target domains. Recently, the segment anything model (SAM) has demonstrated strong generalization capabilities due to its prompt-based design, and has gained significant attention in image segmentation tasks. Existing SAM-based approaches attempt to address the need for manual prompts by introducing prompt generators that automatically generate these prompts. However, we argue that auto-generated prompts may not be sufficiently accurate under distribution shifts, potentially leading to incorrect predictions that still require manual verification and correction by clinicians. To address this challenge, we propose a method for 2D medical image segmentation called Self-Correcting SAM (CoSAM). Our approach begins by generating coarse masks using SAM in a prompt-free manner, providing prior prompts for the subsequent stages, and eliminating the need for prompt generators. To automatically refine these coarse masks, we introduce a generalized error decoder that simulates the correction process typically performed by clinicians. Furthermore, we generate diverse prompts as feedback based on the corrected masks, which are used to iteratively refine the predictions within a self-correcting loop, enhancing the generalization performance of our model. Extensive experiments on two medical image segmentation benchmarks across multiple scenarios demonstrate the superiority of CoSAM over state-of-the-art SAM-based methods.
Recent progress in interactive point prompt based Image Segmentation allows to significantly reduce the manual effort to obtain high quality semantic labels. State-of-the-art unsupervised methods use self-supervised pre-trained models to obtain pseudo-labels which are used in training a prompt-based segmentation model. In this paper, we propose a novel unsupervised and training-free approach based solely on the self-attention of Stable Diffusion. We interpret the self-attention tensor as a Markov transition operator, which enables us to iteratively construct a Markov chain. Pixel-wise counting of the required number of iterations along the Markov-chain to reach a relative probability threshold yields a Markov-iteration-map, which we simply call a Markov-map. Compared to the raw attention maps, we show that our proposed Markov-map has less noise, sharper semantic boundaries and more uniform values within semantically similar regions. We integrate the Markov-map in a simple yet effective truncated nearest neighbor framework to obtain interactive point prompt based segmentation. Despite being training-free, we experimentally show that our approach yields excellent results in terms of Number of Clicks (NoC), even outperforming state-of-the-art training based unsupervised methods in most of the datasets.