Numerous studies have recently focused on incorporating different variations of equivariance in Convolutional Neural Networks (CNNs). In particular, rotation-equivariance has gathered significant attention due to its relevance in many applications related to medical imaging, microscopic imaging, satellite imaging, industrial tasks, etc. While prior research has primarily focused on enhancing classification tasks with rotation equivariant CNNs, their impact on more complex architectures, such as U-Net for image segmentation, remains scarcely explored. Indeed, previous work interested in integrating rotation-equivariance into U-Net architecture have focused on solving specific applications with a limited scope. In contrast, this paper aims to provide a more exhaustive evaluation of rotation equivariant U-Net for image segmentation across a broader range of tasks. We benchmark their effectiveness against standard U-Net architectures, assessing improvements in terms of performance and sustainability (i.e., computational cost). Our evaluation focuses on datasets whose orientation of objects of interest is arbitrary in the image (e.g., Kvasir-SEG), but also on more standard segmentation datasets (such as COCO-Stuff) as to explore the wider applicability of rotation equivariance beyond tasks undoubtedly concerned by rotation equivariance. The main contribution of this work is to provide insights into the trade-offs and advantages of integrating rotation equivariance for segmentation tasks.
Developing artificial intelligence (AI) and machine learning (ML) models for medical imaging typically involves extensive training and testing on large datasets, consuming significant computational time, energy, and resources. There is a need for more efficient methods that can achieve comparable or superior diagnostic performance without the associated resource burden. We investigated the feasibility of replacing conventional training procedures with an embedding-based approach that leverages concise and semantically meaningful representations of medical images. Using pre-trained foundational models-specifically, convolutional neural networks (CNN) like ResNet and multimodal models like Contrastive Language-Image Pre-training (CLIP)-we generated image embeddings for multi-class classification tasks. Simple linear classifiers were then applied to these embeddings. The approach was evaluated across diverse medical imaging modalities, including retinal images, mammography, dermatoscopic images, and chest radiographs. Performance was compared to benchmark models trained and tested using traditional methods. The embedding-based models surpassed the benchmark area under the receiver operating characteristic curve (AUC-ROC) scores by up to 87 percentage in multi-class classification tasks across the various medical imaging modalities. Notably, CLIP embedding models achieved the highest AUC-ROC scores, demonstrating superior classification performance while significantly reducing computational demands. Our study indicates that leveraging embeddings from pre-trained foundational models can effectively replace conventional, resource-intensive training and testing procedures in medical image analysis. This embedding-based approach offers a more efficient alternative for image segmentation, classification, and prediction, potentially accelerating AI technology integration into clinical practice.
A tumor is an abnormal growth of cells, either cancerous or benign, that develops in an organ. Early detection and segmentation of brain tumors are crucial for effective treatment, but manual analysis by experts is a labor-intensive and time-consuming process. The proposed solution is a deep learning framework called RobU-Net, a modified U-Net, to improve the accuracy and robustness of MRI image segmentation, specifically designed to handle Rician noise in MRI scans. The study uses various encoder-decoder architectures to segment MRI scans, achieving optimal results that match the ground truth. The approach also employs discrete wavelet transforms for contrast enhancement and tests the framework's robustness. This study used the MRI brain tumor dataset with 3064 slices. The space and time analysis have been carried out using sensitivity (Sn), dice loss (DL), dice coefficient (DC), and Jaccard index (JI). A comprehensive assessment of our proposed framework depicted that it is better than recently existing frameworks. We have found the so far highest Sn, DC, and JI values for noise-impregnated and original MRI datasets using two novice architectures (overall best for A1-E2 and optimum or noisy dataset for A2-E1) as (0.9831, 0.9726, and 0.9468) and (0.9199, 0.9781, and 0.9571).
Existing few-shot medical image segmentation (FSMIS) models fail to address a practical issue in medical imaging: the domain shift caused by different imaging techniques, which limits the applicability to current FSMIS tasks. To overcome this limitation, we focus on the cross-domain few-shot medical image segmentation (CD-FSMIS) task, aiming to develop a generalized model capable of adapting to a broader range of medical image segmentation scenarios with limited labeled data from the novel target domain. Inspired by the characteristics of frequency domain similarity across different domains, we propose a Frequency-aware Matching Network (FAMNet), which includes two key components: a Frequency-aware Matching (FAM) module and a Multi-Spectral Fusion (MSF) module. The FAM module tackles two problems during the meta-learning phase: 1) intra-domain variance caused by the inherent support-query bias, due to the different appearances of organs and lesions, and 2) inter-domain variance caused by different medical imaging techniques. Additionally, we design an MSF module to integrate the different frequency features decoupled by the FAM module, and further mitigate the impact of inter-domain variance on the model's segmentation performance. Combining these two modules, our FAMNet surpasses existing FSMIS models and Cross-domain Few-shot Semantic Segmentation models on three cross-domain datasets, achieving state-of-the-art performance in the CD-FSMIS task.
The Information Bottleneck (IB) principle has emerged as a promising approach for enhancing the generalization, robustness, and interpretability of deep neural networks, demonstrating efficacy across image segmentation, document clustering, and semantic communication. Among IB implementations, the IB Lagrangian method, employing Lagrangian multipliers, is widely adopted. While numerous methods for the optimizations of IB Lagrangian based on variational bounds and neural estimators are feasible, their performance is highly dependent on the quality of their design, which is inherently prone to errors. To address this limitation, we introduce Structured IB, a framework for investigating potential structured features. By incorporating auxiliary encoders to extract missing informative features, we generate more informative representations. Our experiments demonstrate superior prediction accuracy and task-relevant information preservation compared to the original IB Lagrangian method, even with reduced network size.
Image reflection removal is crucial for restoring image quality. Distorted images can negatively impact tasks like object detection and image segmentation. In this paper, we present a novel approach for image reflection removal using a single image. Instead of focusing on model architecture, we introduce a new training technique that can be generalized to image-to-image problems, with input and output being similar in nature. This technique is embodied in our multi-step loss mechanism, which has proven effective in the reflection removal task. Additionally, we address the scarcity of reflection removal training data by synthesizing a high-quality, non-linear synthetic dataset called RefGAN using Pix2Pix GAN. This dataset significantly enhances the model's ability to learn better patterns for reflection removal. We also utilize a ranged depth map, extracted from the depth estimation of the ambient image, as an auxiliary feature, leveraging its property of lacking depth estimations for reflections. Our approach demonstrates superior performance on the SIR^2 benchmark and other real-world datasets, proving its effectiveness by outperforming other state-of-the-art models.
Medical image segmentation is a key task in the imaging workflow, influencing many image-based decisions. Traditional, fully-supervised segmentation models rely on large amounts of labeled training data, typically obtained through manual annotation, which can be an expensive, time-consuming, and error-prone process. This signals a need for accurate, automatic, and annotation-efficient methods of training these models. We propose SAM-Mix, a novel multitask learning framework for medical image segmentation that uses class activation maps produced by an auxiliary classifier to guide the predictions of the semi-supervised segmentation branch, which is based on the SAM framework. Experimental evaluations on the public LiTS dataset confirm the effectiveness of SAM-Mix for simultaneous classification and segmentation of the liver from abdominal computed tomography (CT) scans. When trained for 90% fewer epochs on only 50 labeled 2D slices, representing just 0.04% of the available labeled training data, SAM-Mix achieves a Dice improvement of 5.1% over the best baseline model. The generalization results for SAM-Mix are even more impressive, with the same model configuration yielding a 25.4% Dice improvement on a cross-domain segmentation task. Our code is available at https://github.com/tbwa233/SAM-Mix.
Medical image segmentation plays an important role in clinical decision making, treatment planning, and disease tracking. However, it still faces two major challenges. On the one hand, there is often a ``soft boundary'' between foreground and background in medical images, with poor illumination and low contrast further reducing the distinguishability of foreground and background within the image. On the other hand, co-occurrence phenomena are widespread in medical images, and learning these features is misleading to the model's judgment. To address these challenges, we propose a general framework called Contrast-Driven Medical Image Segmentation (ConDSeg). First, we develop a contrastive training strategy called Consistency Reinforcement. It is designed to improve the encoder's robustness in various illumination and contrast scenarios, enabling the model to extract high-quality features even in adverse environments. Second, we introduce a Semantic Information Decoupling module, which is able to decouple features from the encoder into foreground, background, and uncertainty regions, gradually acquiring the ability to reduce uncertainty during training. The Contrast-Driven Feature Aggregation module then contrasts the foreground and background features to guide multi-level feature fusion and key feature enhancement, further distinguishing the entities to be segmented. We also propose a Size-Aware Decoder to solve the scale singularity of the decoder. It accurately locate entities of different sizes in the image, thus avoiding erroneous learning of co-occurrence features. Extensive experiments on five medical image datasets across three scenarios demonstrate the state-of-the-art performance of our method, proving its advanced nature and general applicability to various medical image segmentation scenarios. Our released code is available at \url{https://github.com/Mengqi-Lei/ConDSeg}.
In medical imaging, precise annotation of lesions or organs is often required. However, 3D volumetric images typically consist of hundreds or thousands of slices, making the annotation process extremely time-consuming and laborious. Recently, the Segment Anything Model (SAM) has drawn widespread attention due to its remarkable zero-shot generalization capabilities in interactive segmentation. While researchers have explored adapting SAM for medical applications, such as using SAM adapters or constructing 3D SAM models, a key question remains: Can traditional CNN networks achieve the same strong zero-shot generalization in this task? In this paper, we propose the Lightweight Interactive Network for 3D Medical Image Segmentation (LIM-Net), a novel approach demonstrating the potential of compact CNN-based models. Built upon a 2D CNN backbone, LIM-Net initiates segmentation by generating a 2D prompt mask from user hints. This mask is then propagated through the 3D sequence via the Memory Module. To refine and stabilize results during interaction, the Multi-Round Result Fusion (MRF) Module selects and merges optimal masks from multiple rounds. Our extensive experiments across multiple datasets and modalities demonstrate LIM-Net's competitive performance. It exhibits stronger generalization to unseen data compared to SAM-based models, with competitive accuracy while requiring fewer interactions. Notably, LIM-Net's lightweight design offers significant advantages in deployment and inference efficiency, with low GPU memory consumption suitable for resource-constrained environments. These promising results demonstrate LIM-Net can serve as a strong baseline, complementing and contrasting with popular SAM models to further boost effective interactive medical image segmentation. The code will be released at \url{https://github.com/goodtime-123/LIM-Net}.
Accurate segmentation of brain tumors from 3D multimodal MRI is vital for diagnosis and treatment planning across diverse brain tumors. This paper addresses the challenges posed by the BraTS 2023, presenting a unified transfer learning approach that applies to a broader spectrum of brain tumors. We introduce HT-CNNs, an ensemble of Hybrid Transformers and Convolutional Neural Networks optimized through transfer learning for varied brain tumor segmentation. This method captures spatial and contextual details from MRI data, fine-tuned on diverse datasets representing common tumor types. Through transfer learning, HT-CNNs utilize the learned representations from one task to improve generalization in another, harnessing the power of pre-trained models on large datasets and fine-tuning them on specific tumor types. We preprocess diverse datasets from multiple international distributions, ensuring representativeness for the most common brain tumors. Our rigorous evaluation employs standardized quantitative metrics across all tumor types, ensuring robustness and generalizability. The proposed ensemble model achieves superior segmentation results across the BraTS validation datasets over the previous winning methods. Comprehensive quantitative evaluations using the DSC and HD95 demonstrate the effectiveness of our approach. Qualitative segmentation predictions further validate the high-quality outputs produced by our model. Our findings underscore the potential of transfer learning and ensemble approaches in medical image segmentation, indicating a substantial enhancement in clinical decision-making and patient care. Despite facing challenges related to post-processing and domain gaps, our study sets a new precedent for future research for brain tumor segmentation. The docker image for the code and models has been made publicly available, https://hub.docker.com/r/razeineldin/ht-cnns.
Natural language offers a convenient, flexible interface for controlling robotic C-arm X-ray systems, making advanced functionality and controls accessible. However, enabling language interfaces requires specialized AI models that interpret X-ray images to create a semantic representation for reasoning. The fixed outputs of such AI models limit the functionality of language controls. Incorporating flexible, language-aligned AI models prompted through language enables more versatile interfaces for diverse tasks and procedures. Using a language-aligned foundation model for X-ray image segmentation, our system continually updates a patient digital twin based on sparse reconstructions of desired anatomical structures. This supports autonomous capabilities such as visualization, patient-specific viewfinding, and automatic collimation from novel viewpoints, enabling commands 'Focus in on the lower lumbar vertebrae.' In a cadaver study, users visualized, localized, and collimated structures across the torso using verbal commands, achieving 84% end-to-end success. Post hoc analysis of randomly oriented images showed our patient digital twin could localize 35 commonly requested structures to within 51.68 mm, enabling localization and isolation from arbitrary orientations. Our results demonstrate how intelligent robotic X-ray systems can incorporate physicians' expressed intent directly. While existing foundation models for intra-operative X-ray analysis exhibit failure modes, as they improve, they can facilitate highly flexible, intelligent robotic C-arms.
We find that the well-trained victim models (VMs), against which the attacks are generated, serve as fundamental prerequisites for adversarial attacks, i.e. a segmentation VM is needed to generate attacks for segmentation. In this context, the victim model is assumed to be robust to achieve effective adversarial perturbation generation. Instead of focusing on improving the robustness of the task-specific victim models, we shift our attention to image generation. From an image generation perspective, we derive a novel VM for segmentation, aiming to generate adversarial perturbations for segmentation tasks without requiring models explicitly designed for image segmentation. Our approach to adversarial attack generation diverges from conventional white-box or black-box attacks, offering a fresh outlook on adversarial attack strategies. Experiments show that our attack method is able to generate effective adversarial attacks with good transferability.
The Segment Anything Model (SAM), originally built on a 2D Vision Transformer (ViT), excels at capturing global patterns in 2D natural images but struggles with 3D medical imaging modalities like CT and MRI. These modalities require capturing spatial information in volumetric space for tasks such as organ segmentation and tumor quantification. To address this challenge, we introduce RefSAM3D, which adapts SAM for 3D medical imaging by incorporating a 3D image adapter and cross-modal reference prompt generation. Our approach modifies the visual encoder to handle 3D inputs and enhances the mask decoder for direct 3D mask generation. We also integrate textual prompts to improve segmentation accuracy and consistency in complex anatomical scenarios. By employing a hierarchical attention mechanism, our model effectively captures and integrates information across different scales. Extensive evaluations on multiple medical imaging datasets demonstrate the superior performance of RefSAM3D over state-of-the-art methods. Our contributions advance the application of SAM in accurately segmenting complex anatomical structures in medical imaging.
Traditional domain generalization methods often rely on domain alignment to reduce inter-domain distribution differences and learn domain-invariant representations. However, domain shifts are inherently difficult to eliminate, which limits model generalization. To address this, we propose an innovative framework that enhances data representation quality through probabilistic modeling and contrastive learning, reducing dependence on domain alignment and improving robustness under domain variations. Specifically, we combine deterministic features with uncertainty modeling to capture comprehensive feature distributions. Contrastive learning enforces distribution-level alignment by aligning the mean and covariance of feature distributions, enabling the model to dynamically adapt to domain variations and mitigate distribution shifts. Additionally, we design a frequency-domain-based structural enhancement strategy using discrete wavelet transforms to preserve critical structural details and reduce visual distortions caused by style variations. Experimental results demonstrate that the proposed framework significantly improves segmentation performance, providing a robust solution to domain generalization challenges in medical image segmentation.
Osteoporosis is a widespread and chronic metabolic bone disease that often remains undiagnosed and untreated due to limited access to bone mineral density (BMD) tests like Dual-energy X-ray absorptiometry (DXA). In response to this challenge, current advancements are pivoting towards detecting osteoporosis by examining alternative indicators from peripheral bone areas, with the goal of increasing screening rates without added expenses or time. In this paper, we present a method to predict osteoporosis using hand and wrist X-ray images, which are both widely accessible and affordable, though their link to DXA-based data is not thoroughly explored. We employ a sophisticated image segmentation model that utilizes a mixture of probabilistic U-Net decoders, specifically designed to capture predictive uncertainty in the segmentation of the ulna, radius, and metacarpal bones. This model is formulated as an optimal transport (OT) problem, enabling it to handle the inherent uncertainties in image segmentation more effectively. Further, we adopt a self-supervised learning (SSL) approach to extract meaningful representations without the need for explicit labels, and move on to classify osteoporosis in a supervised manner. Our method is evaluated on a dataset with 192 individuals, cross-referencing their verified osteoporosis conditions against the standard DXA test. With a notable classification score, this integration of uncertainty-aware segmentation and self-supervised learning represents a pioneering effort in leveraging vision-based techniques for the early detection of osteoporosis from peripheral skeletal sites.
Spinal cord tumors significantly contribute to neurological morbidity and mortality. Precise morphometric quantification, encompassing the size, location, and type of such tumors, holds promise for optimizing treatment planning strategies. Although recent methods have demonstrated excellent performance in medical image segmentation, they primarily focus on discerning shapes with relatively large morphology such as brain tumors, ignoring the challenging problem of identifying spinal cord tumors which tend to have tiny sizes, diverse locations, and shapes. To tackle this hard problem of multiclass spinal cord tumor segmentation, we propose a new method, called BATseg, to learn a tumor surface distance field by applying our new multiclass boundary-aware loss function. To verify the effectiveness of our approach, we also introduce the first and large-scale spinal cord tumor dataset. It comprises gadolinium-enhanced T1-weighted 3D MRI scans from 653 patients and contains the four most common spinal cord tumor types: astrocytomas, ependymomas, hemangioblastomas, and spinal meningiomas. Extensive experiments on our dataset and another public kidney tumor segmentation dataset show that our proposed method achieves superior performance for multiclass tumor segmentation.
Pre-trained vision-language models (VLMs), such as CLIP, have demonstrated impressive zero-shot recognition capability, but still underperform in dense prediction tasks. Self-distillation recently is emerging as a promising approach for fine-tuning VLMs to better adapt to local regions without requiring extensive annotations. However, previous state-of-the-art approaches often suffer from significant `foreground bias', where models tend to wrongly identify background regions as foreground objects. To alleviate this issue, we propose DenseVLM, a framework designed to learn unbiased region-language alignment from powerful pre-trained VLM representations. By leveraging the pre-trained VLM to retrieve categories for unlabeled regions, DenseVLM effectively decouples the interference between foreground and background region features, ensuring that each region is accurately aligned with its corresponding category. We show that DenseVLM can be seamlessly integrated into open-vocabulary object detection and image segmentation tasks, leading to notable performance improvements. Furthermore, it exhibits promising zero-shot scalability when training on more extensive and diverse datasets.
A novel method for tackling the problem of imbalanced data in medical image segmentation is proposed in this work. In balanced cross entropy (CE) loss, which is a type of weighted CE loss, the weight assigned to each class is the in-verse of the class frequency. These balancing weights are expected to equalize the effect of each class on the overall loss and prevent the model from being biased towards the majority class. But, as it has been shown in previous studies, this method degrades the performance by a large margin. Therefore, balanced CE is not a popular loss in medical segmentation tasks, and usually a region-based loss, like the Dice loss, is used to address the class imbalance problem. In the pro-posed method, the weighting of cross entropy loss for each class is based on a dilated area of each class mask, and balancing weights are assigned to each class together with its surrounding pixels. The goal of this study is to show that the performance of balanced CE loss can be greatly improved my modifying its weighting strategy. Experiments on different datasets show that the proposed dilated balanced CE (DBCE) loss outperforms the balanced CE loss by a large margin and produces superior results compared to CE loss, and its performance is similar to the performance of the combination of Dice and CE loss. This means that a weighted cross entropy loss with the right weighing strategy can be as effective as a region-based loss in handling the problem of class imbalance in medical segmentation tasks.
Medical image segmentation involves partitioning medical images into meaningful regions, with a focus on identifying anatomical structures and lesions. It has broad applications in healthcare, and deep learning methods have enabled significant advancements in automating this process. Recently, the introduction of the Segmentation Anything Model (SAM), the first foundation model for segmentation task, has prompted researchers to adapt it for the medical domain to improve performance across various tasks. However, SAM's large model size and high GPU requirements hinder its scalability and development in the medical domain. In this work, we propose MCP-MedSAM, a powerful and lightweight medical SAM model designed to be trainable on a single A100 GPU with 40GB of memory within one day while delivering superior segmentation performance. Recognizing the significant internal differences between modalities and the need for direct segmentation target information within bounding boxes, we introduce two kinds of prompts: the modality prompt and the content prompt. After passing through the prompt encoder, their embedding representations can further improve the segmentation performance by incorporating more relevant information without adding significant training overhead. Additionally, we adopt an effective modality-based data sampling strategy to address data imbalance between modalities, ensuring more balanced performance across all modalities. Our method was trained and evaluated using a large-scale challenge dataset, compared to top-ranking methods on the challenge leaderboard, MCP-MedSAM achieved superior performance while requiring only one day of training on a single GPU. The code is publicly available at \textcolor{blue}{https://github.com/dong845/MCP-MedSAM}.}
Fine-grained remote sensing image segmentation is essential for accurately identifying detailed objects in remote sensing images. Recently, vision transformer models (VTMs) pre-trained on large-scale datasets have demonstrated strong zero-shot generalization. However, directly applying them to specific tasks may lead to domain shift. We introduce a novel end-to-end learning paradigm combining knowledge guidance with domain refinement to enhance performance. We present two key components: the Feature Alignment Module (FAM) and the Feature Modulation Module (FMM). FAM aligns features from a CNN-based backbone with those from the pretrained VTM's encoder using channel transformation and spatial interpolation, and transfers knowledge via KL divergence and L2 normalization constraint. FMM further adapts the knowledge to the specific domain to address domain shift. We also introduce a fine-grained grass segmentation dataset and demonstrate, through experiments on two datasets, that our method achieves a significant improvement of 2.57 mIoU on the grass dataset and 3.73 mIoU on the cloud dataset. The results highlight the potential of combining knowledge transfer and domain adaptation to overcome domain-related challenges and data limitations. The project page is available at https://xavierjiezou.github.io/KTDA/.