Daily Papers

Driven by advancements in deep learning, computer-aided diagnoses have made remarkable progress. However, outside controlled laboratory settings, algorithms may encounter several challenges. In the medical domain, these difficulties often stem from limited data availability due to ethical and legal restrictions, as well as the high cost and time required for expert annotations-especially in the face of emerging or rare diseases. In this context, open-set recognition plays a vital role by identifying whether a sample belongs to one of the known classes seen during training or should be rejected as an unknown. Recent studies have shown that features learned in the later stages of deep neural networks are observed to cluster around their class means, which themselves are arranged as individual vertices of a regular simplex [32]. The proposed method introduces a loss function designed to reject samples of unknown classes effectively by penalizing open space regions using auxiliary datasets. This approach achieves significant performance gain across four MedMNIST datasets-BloodMNIST, OCTMNIST, DermaMNIST, TissueMNIST and a publicly available skin dataset [29] outperforming state-of-the-art techniques.

Convolutional networks, transformers, hybrid models, and Mamba-based architectures have demonstrated strong performance across various medical image classification tasks. However, these methods were primarily designed to classify clean images using labeled data. In contrast, real-world clinical data often involve image corruptions that are unique to multi-center studies and stem from variations in imaging equipment across manufacturers. In this paper, we introduce the Medical Vision Transformer (MedViTV2), a novel architecture incorporating Kolmogorov-Arnold Network (KAN) layers into the transformer architecture for the first time, aiming for generalized medical image classification. We have developed an efficient KAN block to reduce computational load while enhancing the accuracy of the original MedViT. Additionally, to counteract the fragility of our MedViT when scaled up, we propose an enhanced Dilated Neighborhood Attention (DiNA), an adaptation of the efficient fused dot-product attention kernel capable of capturing global context and expanding receptive fields to scale the model effectively and addressing feature collapse issues. Moreover, a hierarchical hybrid strategy is introduced to stack our Local Feature Perception and Global Feature Perception blocks in an efficient manner, which balances local and global feature perceptions to boost performance. Extensive experiments on 17 medical image classification datasets and 12 corrupted medical image datasets demonstrate that MedViTV2 achieved state-of-the-art results in 27 out of 29 experiments with reduced computational complexity. MedViTV2 is 44\% more computationally efficient than the previous version and significantly enhances accuracy, achieving improvements of 4.6\% on MedMNIST, 5.8\% on NonMNIST, and 13.4\% on the MedMNIST-C benchmark.

Conventional few-shot medical image segmentation (FSMIS) approaches face performance bottlenecks that hinder broader clinical applicability. Although the Segment Anything Model (SAM) exhibits strong category-agnostic segmentation capabilities, its direct application to medical images often leads to over-segmentation due to ambiguous anatomical boundaries. In this paper, we reformulate SAM-based FSMIS as a prompt localization task and propose FoB (Focus on Background), a background-centric prompt generator that provides accurate background prompts to constrain SAM's over-segmentation. Specifically, FoB bridges the gap between segmentation and prompt localization by category-agnostic generation of support background prompts and localizing them directly in the query image. To address the challenge of prompt localization for novel categories, FoB models rich contextual information to capture foreground-background spatial dependencies. Moreover, inspired by the inherent structural patterns of background prompts in medical images, FoB models this structure as a constraint to progressively refine background prompt predictions. Experiments on three diverse medical image datasets demonstrate that FoB outperforms other baselines by large margins, achieving state-of-the-art performance on FSMIS, and exhibiting strong cross-domain generalization. Our code is available at https://github.com/primebo1/FoB_SAM.

This work introduces a new framework, ProtoSAM, for one-shot medical image segmentation. It combines the use of prototypical networks, known for few-shot segmentation, with SAM - a natural image foundation model. The method proposed creates an initial coarse segmentation mask using the ALPnet prototypical network, augmented with a DINOv2 encoder. Following the extraction of an initial mask, prompts are extracted, such as points and bounding boxes, which are then input into the Segment Anything Model (SAM). State-of-the-art results are shown on several medical image datasets and demonstrate automated segmentation capabilities using a single image example (one shot) with no need for fine-tuning of the foundation model. Our code is available at: https://github.com/levayz/ProtoSAM

Advances in medical imaging technologies have enabled the collection of longitudinal images, which involve repeated scanning of the same patients over time, to monitor disease progression. However, predictive modeling of such data remains challenging due to high dimensionality, irregular sampling, and data sparsity. To address these issues, we propose ImageFlowNet, a novel model designed to forecast disease trajectories from initial images while preserving spatial details. ImageFlowNet first learns multiscale joint representation spaces across patients and time points, then optimizes deterministic or stochastic flow fields within these spaces using a position-parameterized neural ODE/SDE framework. The model leverages a UNet architecture to create robust multiscale representations and mitigates data scarcity by combining knowledge from all patients. We provide theoretical insights that support our formulation of ODEs, and motivate our regularizations involving high-level visual features, latent space organization, and trajectory smoothness. We validate ImageFlowNet on three longitudinal medical image datasets depicting progression in geographic atrophy, multiple sclerosis, and glioblastoma, demonstrating its ability to effectively forecast disease progression and outperform existing methods. Our contributions include the development of ImageFlowNet, its theoretical underpinnings, and empirical validation on real-world datasets. The official implementation is available at https://github.com/KrishnaswamyLab/ImageFlowNet.

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.

Semantic segmentation of medical images aims to associate a pixel with a label in a medical image without human initialization. The success of semantic segmentation algorithms is contingent on the availability of high-quality imaging data with corresponding labels provided by experts. We sought to create a large collection of annotated medical image datasets of various clinically relevant anatomies available under open source license to facilitate the development of semantic segmentation algorithms. Such a resource would allow: 1) objective assessment of general-purpose segmentation methods through comprehensive benchmarking and 2) open and free access to medical image data for any researcher interested in the problem domain. Through a multi-institutional effort, we generated a large, curated dataset representative of several highly variable segmentation tasks that was used in a crowd-sourced challenge - the Medical Segmentation Decathlon held during the 2018 Medical Image Computing and Computer Aided Interventions Conference in Granada, Spain. Here, we describe these ten labeled image datasets so that these data may be effectively reused by the research community.

The remarkable success of deep learning in recent years has prompted applications in medical image classification and diagnosis tasks. While classification models have demonstrated robustness in classifying simpler datasets like MNIST or natural images such as ImageNet, this resilience is not consistently observed in complex medical image datasets where data is more scarce and lacks diversity. Moreover, previous findings on natural image datasets have indicated a potential trade-off between data likelihood and classification accuracy. In this study, we explore the use of score-based generative models as classifiers for medical images, specifically mammographic images. Our findings suggest that our proposed generative classifier model not only achieves superior classification results on CBIS-DDSM, INbreast and Vin-Dr Mammo datasets, but also introduces a novel approach to image classification in a broader context. Our code is publicly available at https://github.com/sushmitasarker/sgc_for_medical_image_classification

Medical image segmentation allows quantifying target structure size and shape, aiding in disease diagnosis, prognosis, surgery planning, and comprehension.Building upon recent advancements in foundation Vision-Language Models (VLMs) from natural image-text pairs, several studies have proposed adapting them to Vision-Language Segmentation Models (VLSMs) that allow using language text as an additional input to segmentation models. Introducing auxiliary information via text with human-in-the-loop prompting during inference opens up unique opportunities, such as open vocabulary segmentation and potentially more robust segmentation models against out-of-distribution data. Although transfer learning from natural to medical images has been explored for image-only segmentation models, the joint representation of vision-language in segmentation problems remains underexplored. This study introduces the first systematic study on transferring VLSMs to 2D medical images, using carefully curated 11 datasets encompassing diverse modalities and insightful language prompts and experiments. Our findings demonstrate that although VLSMs show competitive performance compared to image-only models for segmentation after finetuning in limited medical image datasets, not all VLSMs utilize the additional information from language prompts, with image features playing a dominant role. While VLSMs exhibit enhanced performance in handling pooled datasets with diverse modalities and show potential robustness to domain shifts compared to conventional segmentation models, our results suggest that novel approaches are required to enable VLSMs to leverage the various auxiliary information available through language prompts. The code and datasets are available at https://github.com/naamiinepal/medvlsm.

Foundation models pre-trained on large-scale natural image datasets offer a powerful paradigm for medical image segmentation. However, effectively transferring their learned representations for precise clinical applications remains a challenge. In this work, we propose Dino U-Net, a novel encoder-decoder architecture designed to exploit the high-fidelity dense features of the DINOv3 vision foundation model. Our architecture introduces an encoder built upon a frozen DINOv3 backbone, which employs a specialized adapter to fuse the model's rich semantic features with low-level spatial details. To preserve the quality of these representations during dimensionality reduction, we design a new fidelity-aware projection module (FAPM) that effectively refines and projects the features for the decoder. We conducted extensive experiments on seven diverse public medical image segmentation datasets. Our results show that Dino U-Net achieves state-of-the-art performance, consistently outperforming previous methods across various imaging modalities. Our framework proves to be highly scalable, with segmentation accuracy consistently improving as the backbone model size increases up to the 7-billion-parameter variant. The findings demonstrate that leveraging the superior, dense-pretrained features from a general-purpose foundation model provides a highly effective and parameter-efficient approach to advance the accuracy of medical image segmentation. The code is available at https://github.com/yifangao112/DinoUNet.

We propose an adaptive training scheme for unsupervised medical image registration. Existing methods rely on image reconstruction as the primary supervision signal. However, nuisance variables (e.g. noise and covisibility), violation of the Lambertian assumption in physical waves (e.g. ultrasound), and inconsistent image acquisition can all cause a loss of correspondence between medical images. As the unsupervised learning scheme relies on intensity constancy between images to establish correspondence for reconstruction, this introduces spurious error residuals that are not modeled by the typical training objective. To mitigate this, we propose an adaptive framework that re-weights the error residuals with a correspondence scoring map during training, preventing the parametric displacement estimator from drifting away due to noisy gradients, which leads to performance degradation. To illustrate the versatility and effectiveness of our method, we tested our framework on three representative registration architectures across three medical image datasets along with other baselines. Our adaptive framework consistently outperforms other methods both quantitatively and qualitatively. Paired t-tests show that our improvements are statistically significant. Code available at: https://voldemort108x.github.io/AdaCS/.

Foundation models have demonstrated remarkable success across diverse domains and tasks, primarily due to the thrive of large-scale, diverse, and high-quality datasets. However, in the field of medical imaging, the curation and assembling of such medical datasets are highly challenging due to the reliance on clinical expertise and strict ethical and privacy constraints, resulting in a scarcity of large-scale unified medical datasets and hindering the development of powerful medical foundation models. In this work, we present the largest survey to date of medical image datasets, covering over 1,000 open-access datasets with a systematic catalog of their modalities, tasks, anatomies, annotations, limitations, and potential for integration. Our analysis exposes a landscape that is modest in scale, fragmented across narrowly scoped tasks, and unevenly distributed across organs and modalities, which in turn limits the utility of existing medical image datasets for developing versatile and robust medical foundation models. To turn fragmentation into scale, we propose a metadata-driven fusion paradigm (MDFP) that integrates public datasets with shared modalities or tasks, thereby transforming multiple small data silos into larger, more coherent resources. Building on MDFP, we release an interactive discovery portal that enables end-to-end, automated medical image dataset integration, and compile all surveyed datasets into a unified, structured table that clearly summarizes their key characteristics and provides reference links, offering the community an accessible and comprehensive repository. By charting the current terrain and offering a principled path to dataset consolidation, our survey provides a practical roadmap for scaling medical imaging corpora, supporting faster data discovery, more principled dataset creation, and more capable medical foundation models.

Deep learning-based automatic medical image segmentation plays a critical role in clinical diagnosis and treatment planning but remains challenging in few-shot scenarios due to the scarcity of annotated training data. Recently, self-supervised foundation models such as DINOv3, which were trained on large natural image datasets, have shown strong potential for dense feature extraction that can help with the few-shot learning challenge. Yet, their direct application to medical images is hindered by domain differences. In this work, we propose DINO-AugSeg, a novel framework that leverages DINOv3 features to address the few-shot medical image segmentation challenge. Specifically, we introduce WT-Aug, a wavelet-based feature-level augmentation module that enriches the diversity of DINOv3-extracted features by perturbing frequency components, and CG-Fuse, a contextual information-guided fusion module that exploits cross-attention to integrate semantic-rich low-resolution features with spatially detailed high-resolution features. Extensive experiments on six public benchmarks spanning five imaging modalities, including MRI, CT, ultrasound, endoscopy, and dermoscopy, demonstrate that DINO-AugSeg consistently outperforms existing methods under limited-sample conditions. The results highlight the effectiveness of incorporating wavelet-domain augmentation and contextual fusion for robust feature representation, suggesting DINO-AugSeg as a promising direction for advancing few-shot medical image segmentation. Code and data will be made available on https://github.com/apple1986/DINO-AugSeg.

Recent advancements in medical imaging and artificial intelligence (AI) have greatly enhanced diagnostic capabilities, but the development of effective deep learning (DL) models is still constrained by the lack of high-quality annotated datasets. The traditional manual annotation process by medical experts is time- and resource-intensive, limiting the scalability of these datasets. In this work, we introduce a robust and versatile framework that combines AI and crowdsourcing to improve both the quality and quantity of medical image datasets across different modalities. Our approach utilises a user-friendly online platform that enables a diverse group of crowd annotators to label medical images efficiently. By integrating the MedSAM segmentation AI with this platform, we accelerate the annotation process while maintaining expert-level quality through an algorithm that merges crowd-labelled images. Additionally, we employ pix2pixGAN, a generative AI model, to expand the training dataset with synthetic images that capture realistic morphological features. These methods are combined into a cohesive framework designed to produce an enhanced dataset, which can serve as a universal pre-processing pipeline to boost the training of any medical deep learning segmentation model. Our results demonstrate that this framework significantly improves model performance, especially when training data is limited.

Deep AUC Maximization (DAM) is a new paradigm for learning a deep neural network by maximizing the AUC score of the model on a dataset. Most previous works of AUC maximization focus on the perspective of optimization by designing efficient stochastic algorithms, and studies on generalization performance of large-scale DAM on difficult tasks are missing. In this work, we aim to make DAM more practical for interesting real-world applications (e.g., medical image classification). First, we propose a new margin-based min-max surrogate loss function for the AUC score (named as AUC min-max-margin loss or simply AUC margin loss for short). It is more robust than the commonly used AUC square loss, while enjoying the same advantage in terms of large-scale stochastic optimization. Second, we conduct extensive empirical studies of our DAM method on four difficult medical image classification tasks, namely (i) classification of chest x-ray images for identifying many threatening diseases, (ii) classification of images of skin lesions for identifying melanoma, (iii) classification of mammogram for breast cancer screening, and (iv) classification of microscopic images for identifying tumor tissue. Our studies demonstrate that the proposed DAM method improves the performance of optimizing cross-entropy loss by a large margin, and also achieves better performance than optimizing the existing AUC square loss on these medical image classification tasks. Specifically, our DAM method has achieved the 1st place on Stanford CheXpert competition on Aug. 31, 2020. To the best of our knowledge, this is the first work that makes DAM succeed on large-scale medical image datasets. We also conduct extensive ablation studies to demonstrate the advantages of the new AUC margin loss over the AUC square loss on benchmark datasets. The proposed method is implemented in our open-sourced library LibAUC (www.libauc.org).

The field of Machine Learning, a subset of Artificial Intelligence, has led to remarkable advancements in many areas, including medicine. Machine Learning algorithms require large datasets to train computer models successfully. Although there are medical image datasets available, more image datasets are needed from a variety of medical entities, especially cancer pathology. Even more scarce are ML-ready image datasets. To address this need, we created an image dataset (LC25000) with 25,000 color images in 5 classes. Each class contains 5,000 images of the following histologic entities: colon adenocarcinoma, benign colonic tissue, lung adenocarcinoma, lung squamous cell carcinoma, and benign lung tissue. All images are de-identified, HIPAA compliant, validated, and freely available for download to AI researchers.

The limited availability of 3D medical image datasets, due to privacy concerns and high collection or annotation costs, poses significant challenges in the field of medical imaging. While a promising alternative is the use of synthesized medical data, there are few solutions for realistic 3D medical image synthesis due to difficulties in backbone design and fewer 3D training samples compared to 2D counterparts. In this paper, we propose GEM-3D, a novel generative approach to the synthesis of 3D medical images and the enhancement of existing datasets using conditional diffusion models. Our method begins with a 2D slice, noted as the informed slice to serve the patient prior, and propagates the generation process using a 3D segmentation mask. By decomposing the 3D medical images into masks and patient prior information, GEM-3D offers a flexible yet effective solution for generating versatile 3D images from existing datasets. GEM-3D can enable dataset enhancement by combining informed slice selection and generation at random positions, along with editable mask volumes to introduce large variations in diffusion sampling. Moreover, as the informed slice contains patient-wise information, GEM-3D can also facilitate counterfactual image synthesis and dataset-level de-enhancement with desired control. Experiments on brain MRI and abdomen CT images demonstrate that GEM-3D is capable of synthesizing high-quality 3D medical images with volumetric consistency, offering a straightforward solution for dataset enhancement during inference. The code is available at https://github.com/HKU-MedAI/GEM-3D.

Medical images are acquired at high resolutions with large fields of view in order to capture fine-grained features necessary for clinical decision-making. Consequently, training deep learning models on medical images can incur large computational costs. In this work, we address the challenge of downsizing medical images in order to improve downstream computational efficiency while preserving clinically-relevant features. We introduce MedVAE, a family of six large-scale 2D and 3D autoencoders capable of encoding medical images as downsized latent representations and decoding latent representations back to high-resolution images. We train MedVAE autoencoders using a novel two-stage training approach with 1,052,730 medical images. Across diverse tasks obtained from 20 medical image datasets, we demonstrate that (1) utilizing MedVAE latent representations in place of high-resolution images when training downstream models can lead to efficiency benefits (up to 70x improvement in throughput) while simultaneously preserving clinically-relevant features and (2) MedVAE can decode latent representations back to high-resolution images with high fidelity. Our work demonstrates that large-scale, generalizable autoencoders can help address critical efficiency challenges in the medical domain. Our code is available at https://github.com/StanfordMIMI/MedVAE.

In this paper, we address a key scientific problem in machine learning: Given a training set for an image classification task, can we train a generative model on this dataset to enhance the classification performance? (i.e., closed-set generative data augmentation). We start by exploring the distinctions and similarities between real images and closed-set synthetic images generated by advanced generative models. Through extensive experiments, we offer systematic insights into the effective use of closed-set synthetic data for augmentation. Notably, we empirically determine the equivalent scale of synthetic images needed for augmentation. In addition, we also show quantitative equivalence between the real data augmentation and open-set generative augmentation (generative models trained using data beyond the given training set). While it aligns with the common intuition that real images are generally preferred, our empirical formulation also offers a guideline to quantify the increased scale of synthetic data augmentation required to achieve comparable image classification performance. Our results on natural and medical image datasets further illustrate how this effect varies with the baseline training set size and the amount of synthetic data incorporated.

Image segmentation remains a pivotal component in medical image analysis, aiding in the extraction of critical information for precise diagnostic practices. With the advent of deep learning, automated image segmentation methods have risen to prominence, showcasing exceptional proficiency in processing medical imagery. Motivated by the Segment Anything Model (SAM)-a foundational model renowned for its remarkable precision and robust generalization capabilities in segmenting 2D natural images-we introduce SAM3D, an innovative adaptation tailored for 3D volumetric medical image analysis. Unlike current SAM-based methods that segment volumetric data by converting the volume into separate 2D slices for individual analysis, our SAM3D model processes the entire 3D volume image in a unified approach. Extensive experiments are conducted on multiple medical image datasets to demonstrate that our network attains competitive results compared with other state-of-the-art methods in 3D medical segmentation tasks while being significantly efficient in terms of parameters. Code and checkpoints are available at https://github.com/UARK-AICV/SAM3D.

Learning medical visual representations directly from paired radiology reports has become an emerging topic in representation learning. However, existing medical image-text joint learning methods are limited by instance or local supervision analysis, ignoring disease-level semantic correspondences. In this paper, we present a novel Multi-Granularity Cross-modal Alignment (MGCA) framework for generalized medical visual representation learning by harnessing the naturally exhibited semantic correspondences between medical image and radiology reports at three different levels, i.e., pathological region-level, instance-level, and disease-level. Specifically, we first incorporate the instance-wise alignment module by maximizing the agreement between image-report pairs. Further, for token-wise alignment, we introduce a bidirectional cross-attention strategy to explicitly learn the matching between fine-grained visual tokens and text tokens, followed by contrastive learning to align them. More important, to leverage the high-level inter-subject relationship semantic (e.g., disease) correspondences, we design a novel cross-modal disease-level alignment paradigm to enforce the cross-modal cluster assignment consistency. Extensive experimental results on seven downstream medical image datasets covering image classification, object detection, and semantic segmentation tasks demonstrate the stable and superior performance of our framework.

Machine learning models for medical image analysis often suffer from poor performance on important subsets of a population that are not identified during training or testing. For example, overall performance of a cancer detection model may be high, but the model still consistently misses a rare but aggressive cancer subtype. We refer to this problem as hidden stratification, and observe that it results from incompletely describing the meaningful variation in a dataset. While hidden stratification can substantially reduce the clinical efficacy of machine learning models, its effects remain difficult to measure. In this work, we assess the utility of several possible techniques for measuring and describing hidden stratification effects, and characterize these effects on multiple medical imaging datasets. We find evidence that hidden stratification can occur in unidentified imaging subsets with low prevalence, low label quality, subtle distinguishing features, or spurious correlates, and that it can result in relative performance differences of over 20% on clinically important subsets. Finally, we explore the clinical implications of our findings, and suggest that evaluation of hidden stratification should be a critical component of any machine learning deployment in medical imaging.

Due to the rapid advancements in recent years, medical image analysis is largely dominated by deep learning (DL). However, building powerful and robust DL models requires training with large multi-party datasets. While multiple stakeholders have provided publicly available datasets, the ways in which these data are labeled vary widely. For Instance, an institution might provide a dataset of chest radiographs containing labels denoting the presence of pneumonia, while another institution might have a focus on determining the presence of metastases in the lung. Training a single AI model utilizing all these data is not feasible with conventional federated learning (FL). This prompts us to propose an extension to the widespread FL process, namely flexible federated learning (FFL) for collaborative training on such data. Using 695,000 chest radiographs from five institutions from across the globe - each with differing labels - we demonstrate that having heterogeneously labeled datasets, FFL-based training leads to significant performance increase compared to conventional FL training, where only the uniformly annotated images are utilized. We believe that our proposed algorithm could accelerate the process of bringing collaborative training methods from research and simulation phase to the real-world applications in healthcare.

Images and structured tables are essential parts of real-world databases. Though tabular-image representation learning is promising to create new insights, it remains a challenging task, as tabular data is typically heterogeneous and incomplete, presenting significant modality disparities with images. Earlier works have mainly focused on simple modality fusion strategies in complete data scenarios, without considering the missing data issue, and thus are limited in practice. In this paper, we propose TIP, a novel tabular-image pre-training framework for learning multimodal representations robust to incomplete tabular data. Specifically, TIP investigates a novel self-supervised learning (SSL) strategy, including a masked tabular reconstruction task for tackling data missingness, and image-tabular matching and contrastive learning objectives to capture multimodal information. Moreover, TIP proposes a versatile tabular encoder tailored for incomplete, heterogeneous tabular data and a multimodal interaction module for inter-modality representation learning. Experiments are performed on downstream multimodal classification tasks using both natural and medical image datasets. The results show that TIP outperforms state-of-the-art supervised/SSL image/multimodal algorithms in both complete and incomplete data scenarios. Our code is available at https://github.com/siyi-wind/TIP.

In recent advancements, multimodal large language models (MLLMs) have been fine-tuned on specific medical image datasets to address medical visual question answering (Med-VQA) tasks. However, this common approach of task-specific fine-tuning is costly and necessitates separate models for each downstream task, limiting the exploration of zero-shot capabilities. In this paper, we introduce MC-CoT, a modular cross-modal collaboration Chain-of-Thought (CoT) framework designed to enhance the zero-shot performance of MLLMs in Med-VQA by leveraging large language models (LLMs). MC-CoT improves reasoning and information extraction by integrating medical knowledge and task-specific guidance, where LLM provides various complex medical reasoning chains and MLLM provides various observations of medical images based on instructions of the LLM. Our experiments on datasets such as SLAKE, VQA-RAD, and PATH-VQA show that MC-CoT surpasses standalone MLLMs and various multimodality CoT frameworks in recall rate and accuracy. These findings highlight the importance of incorporating background information and detailed guidance in addressing complex zero-shot Med-VQA tasks.

The success of Deep Learning applications critically depends on the quality and scale of the underlying training data. Generative adversarial networks (GANs) can generate arbitrary large datasets, but diversity and fidelity are limited, which has recently been addressed by denoising diffusion probabilistic models (DDPMs) whose superiority has been demonstrated on natural images. In this study, we propose Medfusion, a conditional latent DDPM for medical images. We compare our DDPM-based model against GAN-based models, which constitute the current state-of-the-art in the medical domain. Medfusion was trained and compared with (i) StyleGan-3 on n=101,442 images from the AIROGS challenge dataset to generate fundoscopies with and without glaucoma, (ii) ProGAN on n=191,027 from the CheXpert dataset to generate radiographs with and without cardiomegaly and (iii) wGAN on n=19,557 images from the CRCMS dataset to generate histopathological images with and without microsatellite stability. In the AIROGS, CRMCS, and CheXpert datasets, Medfusion achieved lower (=better) FID than the GANs (11.63 versus 20.43, 30.03 versus 49.26, and 17.28 versus 84.31). Also, fidelity (precision) and diversity (recall) were higher (=better) for Medfusion in all three datasets. Our study shows that DDPM are a superior alternative to GANs for image synthesis in the medical domain.

Prenatal ultrasound imaging is the first-choice modality to assess fetal health. Medical image datasets for AI and ML methods must be diverse (i.e. diagnoses, diseases, pathologies, scanners, demographics, etc), however there are few public ultrasound fetal imaging datasets due to insufficient amounts of clinical data, patient privacy, rare occurrence of abnormalities in general practice, and limited experts for data collection and validation. To address such data scarcity, we proposed generative adversarial networks (GAN)-based models, diffusion-super-resolution-GAN and transformer-based-GAN, to synthesise images of fetal ultrasound brain planes from one public dataset. We reported that GAN-based methods can generate 256x256 pixel size of fetal ultrasound trans-cerebellum brain image plane with stable training losses, resulting in lower FID values for diffusion-super-resolution-GAN (average 7.04 and lower FID 5.09 at epoch 10) than the FID values of transformer-based-GAN (average 36.02 and lower 28.93 at epoch 60). The results of this work illustrate the potential of GAN-based methods to synthesise realistic high-resolution ultrasound images, leading to future work with other fetal brain planes, anatomies, devices and the need of a pool of experts to evaluate synthesised images. Code, data and other resources to reproduce this work are available at https://github.com/budai4medtech/midl2023.

Multimodal deep learning (MDL) has achieved remarkable success across various domains, yet its practical deployment is often hindered by incomplete multimodal data. Existing incomplete MDL methods either discard missing modalities, risking the loss of valuable task-relevant information, or recover them, potentially introducing irrelevant noise, leading to the discarding-imputation dilemma. To address this dilemma, in this paper, we propose DyMo, a new inference-time dynamic modality selection framework that adaptively identifies and integrates reliable recovered modalities, fully exploring task-relevant information beyond the conventional discard-or-impute paradigm. Central to DyMo is a novel selection algorithm that maximizes multimodal task-relevant information for each test sample. Since direct estimation of such information at test time is intractable due to the unknown data distribution, we theoretically establish a connection between information and the task loss, which we compute at inference time as a tractable proxy. Building on this, a novel principled reward function is proposed to guide modality selection. In addition, we design a flexible multimodal network architecture compatible with arbitrary modality combinations, alongside a tailored training strategy for robust representation learning. Extensive experiments on diverse natural and medical image datasets show that DyMo significantly outperforms state-of-the-art incomplete/dynamic MDL methods across various missing-data scenarios. Our code is available at https://github.com//siyi-wind/DyMo.

Convolutional Neural Networks (CNNs) have demonstrated outstanding performance in computer vision tasks such as image classification, detection, segmentation, and medical image analysis. In general, an arbitrary number of epochs is used to train such neural networks. In a single epoch, the entire training data -- divided by batch size -- are fed to the network. In practice, validation error with training loss is used to estimate the neural network's generalization, which indicates the optimal learning capacity of the network. Current practice is to stop training when the training loss decreases and the gap between training and validation error increases (i.e., the generalization gap) to avoid overfitting. However, this is a trial-and-error-based approach which raises a critical question: Is it possible to estimate when neural networks stop learning based on training data? This research work introduces a hypothesis that analyzes the data variation across all the layers of a CNN variant to anticipate its near-optimal learning capacity. In the training phase, we use our hypothesis to anticipate the near-optimal learning capacity of a CNN variant without using any validation data. Our hypothesis can be deployed as a plug-and-play to any existing CNN variant without introducing additional trainable parameters to the network. We test our hypothesis on six different CNN variants and three different general image datasets (CIFAR10, CIFAR100, and SVHN). The result based on these CNN variants and datasets shows that our hypothesis saves 58.49\% of computational time (on average) in training. We further conduct our hypothesis on ten medical image datasets and compared with the MedMNIST-V2 benchmark. Based on our experimental result, we save approx 44.1\% of computational time without losing accuracy against the MedMNIST-V2 benchmark.

Medical images often contain artificial markers added by doctors, which can negatively affect the accuracy of AI-based diagnosis. To address this issue and recover the missing visual contents, inpainting techniques are highly needed. However, existing inpainting methods require manual mask input, limiting their application scenarios. In this paper, we introduce a novel blind inpainting method that automatically completes visual contents without specifying masks for target areas in an image. Our proposed model includes a mask-free reconstruction network and an object-aware discriminator. The reconstruction network consists of two branches that predict the corrupted regions with artificial markers and simultaneously recover the missing visual contents. The object-aware discriminator relies on the powerful recognition capabilities of the dense object detector to ensure that the markers of reconstructed images cannot be detected in any local regions. As a result, the reconstructed image can be close to the clean one as much as possible. Our proposed method is evaluated on different medical image datasets, covering multiple imaging modalities such as ultrasound (US), magnetic resonance imaging (MRI), and electron microscopy (EM), demonstrating that our method is effective and robust against various unknown missing region patterns.

Precise breast cancer classification on histopathological images has the potential to greatly improve the diagnosis and patient outcome in oncology. The data imbalance problem largely stems from the inherent imbalance within medical image datasets, where certain tumor subtypes may appear much less frequently. This constitutes a considerable limitation in biased model predictions that can overlook critical but rare classes. In this work, we adopted EfficientNet, a state-of-the-art convolutional neural network (CNN) model that balances high accuracy with computational cost efficiency. To address data imbalance, we introduce an intensive data augmentation pipeline and cost-sensitive learning, improving representation and ensuring that the model does not overly favor majority classes. This approach provides the ability to learn effectively from rare tumor types, improving its robustness. Additionally, we fine-tuned the model using transfer learning, where weights in the beginning trained on a binary classification task were adopted to multi-class classification, improving the capability to detect complex patterns within the BreakHis dataset. Our results underscore significant improvements in the binary classification performance, achieving an exceptional recall increase for benign cases from 0.92 to 0.95, alongside an accuracy enhancement from 97.35 % to 98.23%. Our approach improved the performance of multi-class tasks from 91.27% with regular augmentation to 94.54% with intensive augmentation, reaching 95.04% with transfer learning. This framework demonstrated substantial gains in precision in the minority classes, such as Mucinous carcinoma and Papillary carcinoma, while maintaining high recall consistently across these critical subtypes, as further confirmed by confusion matrix analysis.

Foundation Vision-Language Models (VLMs) trained using large-scale open-domain images and text pairs have recently been adapted to develop Vision-Language Segmentation Models (VLSMs) that allow providing text prompts during inference to guide image segmentation. If robust and powerful VLSMs can be built for medical images, it could aid medical professionals in many clinical tasks where they must spend substantial time delineating the target structure of interest. VLSMs for medical images resort to fine-tuning base VLM or VLSM pretrained on open-domain natural image datasets due to fewer annotated medical image datasets; this fine-tuning is resource-consuming and expensive as it usually requires updating all or a significant fraction of the pretrained parameters. Recently, lightweight blocks called adapters have been proposed in VLMs that keep the pretrained model frozen and only train adapters during fine-tuning, substantially reducing the computing resources required. We introduce a novel adapter, VLSM-Adapter, that can fine-tune pretrained vision-language segmentation models using transformer encoders. Our experiments in widely used CLIP-based segmentation models show that with only 3 million trainable parameters, the VLSM-Adapter outperforms state-of-the-art and is comparable to the upper bound end-to-end fine-tuning. The source code is available at: https://github.com/naamiinepal/vlsm-adapter.

Developing generalist foundation model has recently attracted tremendous attention among researchers in the field of AI for Medicine (AI4Medicine). A pivotal insight in developing these models is their reliance on dataset scaling, which emphasizes the requirements on developing open-source medical image datasets that incorporate diverse supervision signals across various imaging modalities. In this paper, we introduce RadGenome-Chest CT, a comprehensive, large-scale, region-guided 3D chest CT interpretation dataset based on CT-RATE. Specifically, we leverage the latest powerful universal segmentation and large language models, to extend the original datasets (over 25,692 non-contrast 3D chest CT volume and reports from 20,000 patients) from the following aspects: (i) organ-level segmentation masks covering 197 categories, which provide intermediate reasoning visual clues for interpretation; (ii) 665 K multi-granularity grounded reports, where each sentence of the report is linked to the corresponding anatomical region of CT volume in the form of a segmentation mask; (iii) 1.3 M grounded VQA pairs, where questions and answers are all linked with reference segmentation masks, enabling models to associate visual evidence with textual explanations. All grounded reports and VQA pairs in the validation set have gone through manual verification to ensure dataset quality. We believe that RadGenome-Chest CT can significantly advance the development of multimodal medical foundation models, by training to generate texts based on given segmentation regions, which is unattainable with previous relevant datasets. We will release all segmentation masks, grounded reports, and VQA pairs to facilitate further research and development in this field.

Deep learning methods for unsupervised registration often rely on objectives that assume a uniform noise level across the spatial domain (e.g. mean-squared error loss), but noise distributions are often heteroscedastic and input-dependent in real-world medical images. Thus, this assumption often leads to degradation in registration performance, mainly due to the undesired influence of noise-induced outliers. To mitigate this, we propose a framework for heteroscedastic image uncertainty estimation that can adaptively reduce the influence of regions with high uncertainty during unsupervised registration. The framework consists of a collaborative training strategy for the displacement and variance estimators, and a novel image fidelity weighting scheme utilizing signal-to-noise ratios. Our approach prevents the model from being driven away by spurious gradients caused by the simplified homoscedastic assumption, leading to more accurate displacement estimation. To illustrate its versatility and effectiveness, we tested our framework on two representative registration architectures across three medical image datasets. Our method consistently outperforms baselines and produces sensible uncertainty estimates. The code is publicly available at https://voldemort108x.github.io/hetero_uncertainty/.

The scarcity of high-quality data remains a primary bottleneck in adapting multimodal generative models for medical image editing. Existing medical image editing datasets often suffer from limited diversity, neglect of medical image understanding and inability to balance quality with scalability. To address these gaps, we propose MieDB-100k, a large-scale, high-quality and diverse dataset for text-guided medical image editing. It categorizes editing tasks into perspectives of Perception, Modification and Transformation, considering both understanding and generation abilities. We construct MieDB-100k via a data curation pipeline leveraging both modality-specific expert models and rule-based data synthetic methods, followed by rigorous manual inspection to ensure clinical fidelity. Extensive experiments demonstrate that model trained with MieDB-100k consistently outperform both open-source and proprietary models while exhibiting strong generalization ability. We anticipate that this dataset will serve as a cornerstone for future advancements in specialized medical image editing.

Convolutional neural networks (CNNs) have been the consensus for medical image segmentation tasks. However, they suffer from the limitation in modeling long-range dependencies and spatial correlations due to the nature of convolution operation. Although transformers were first developed to address this issue, they fail to capture low-level features. In contrast, it is demonstrated that both local and global features are crucial for dense prediction, such as segmenting in challenging contexts. In this paper, we propose HiFormer, a novel method that efficiently bridges a CNN and a transformer for medical image segmentation. Specifically, we design two multi-scale feature representations using the seminal Swin Transformer module and a CNN-based encoder. To secure a fine fusion of global and local features obtained from the two aforementioned representations, we propose a Double-Level Fusion (DLF) module in the skip connection of the encoder-decoder structure. Extensive experiments on various medical image segmentation datasets demonstrate the effectiveness of HiFormer over other CNN-based, transformer-based, and hybrid methods in terms of computational complexity, and quantitative and qualitative results. Our code is publicly available at: https://github.com/amirhossein-kz/HiFormer

Medical image classification is a critical problem for healthcare, with the potential to alleviate the workload of doctors and facilitate diagnoses of patients. However, two challenges arise when deploying deep learning models to real-world healthcare applications. First, neural models tend to learn spurious correlations instead of desired features, which could fall short when generalizing to new domains (e.g., patients with different ages). Second, these black-box models lack interpretability. When making diagnostic predictions, it is important to understand why a model makes a decision for trustworthy and safety considerations. In this paper, to address these two limitations, we propose a new paradigm to build robust and interpretable medical image classifiers with natural language concepts. Specifically, we first query clinical concepts from GPT-4, then transform latent image features into explicit concepts with a vision-language model. We systematically evaluate our method on eight medical image classification datasets to verify its effectiveness. On challenging datasets with strong confounding factors, our method can mitigate spurious correlations thus substantially outperform standard visual encoders and other baselines. Finally, we show how classification with a small number of concepts brings a level of interpretability for understanding model decisions through case studies in real medical data.

U-shaped networks and its variants have demonstrated exceptional results for medical image segmentation. In this paper, we propose a novel dual self-distillation (DSD) framework in U-shaped networks for volumetric medical image segmentation. DSD distills knowledge from the ground-truth segmentation labels to the decoder layers. Additionally, DSD also distills knowledge from the deepest decoder and encoder layer to the shallower decoder and encoder layers respectively of a single U-shaped network. DSD is a general training strategy that could be attached to the backbone architecture of any U-shaped network to further improve its segmentation performance. We attached DSD on several state-of-the-art U-shaped backbones, and extensive experiments on various public 3D medical image segmentation datasets (cardiac substructure, brain tumor and Hippocampus) demonstrated significant improvement over the same backbones without DSD. On average, after attaching DSD to the U-shaped backbones, we observed an increase of 2.82\%, 4.53\% and 1.3\% in Dice similarity score, a decrease of 7.15 mm, 6.48 mm and 0.76 mm in the Hausdorff distance, for cardiac substructure, brain tumor and Hippocampus segmentation, respectively. These improvements were achieved with negligible increase in the number of trainable parameters and training time. Our proposed DSD framework also led to significant qualitative improvements for cardiac substructure, brain tumor and Hippocampus segmentation over the U-shaped backbones. The source code is publicly available at https://github.com/soumbane/DualSelfDistillation.

This short technical report demonstrates a simple technique that yields state of the art results in medical image-text matching tasks. We analyze the use of OpenAI's CLIP, a general image-text matching model, and observe that CLIP's limited textual input size has negative impact on downstream performance in the medical domain where encoding longer textual contexts is often required. We thus train and release ClipMD, which is trained with a simple sliding window technique to encode textual captions. ClipMD was tested on two medical image-text datasets and compared with other image-text matching models. The results show that ClipMD outperforms other models on both datasets by a large margin. We make our code and pretrained model publicly available.

Vision-language pre-training, i.e., aligning images with paired text, is a powerful paradigm to create encoders that can be directly used for tasks such as classification and retrieval, and for downstream tasks such as segmentation and report generation. In the 3D medical image domain, these capabilities allow vision-language encoders (VLEs) to support radiologists by retrieving patients with similar abnormalities or predicting likelihoods of abnormality. While the methodology holds promise, data availability limits the capabilities of current 3D VLEs. In this paper, we alleviate the lack of data by injecting additional inductive biases: introducing a report generation objective and pairing vision-language pre-training with vision-only pre-training. This allows us to leverage both image-only and paired image-text 3D datasets, increasing the total amount of data to which our model is exposed. Through these additional inductive biases, paired with best practices of the 3D medical imaging domain, we develop the Comprehensive Language-image Pre-training (COLIPRI) encoder family. Our COLIPRI encoders achieve state-of-the-art performance in report generation, classification probing, and zero-shot classification, and remain competitive for semantic segmentation.

Diffusion models have been used extensively for high quality image and video generation tasks. In this paper, we propose a novel conditional diffusion model with spatial attention and latent embedding (cDAL) for medical image segmentation. In cDAL, a convolutional neural network (CNN) based discriminator is used at every time-step of the diffusion process to distinguish between the generated labels and the real ones. A spatial attention map is computed based on the features learned by the discriminator to help cDAL generate more accurate segmentation of discriminative regions in an input image. Additionally, we incorporated a random latent embedding into each layer of our model to significantly reduce the number of training and sampling time-steps, thereby making it much faster than other diffusion models for image segmentation. We applied cDAL on 3 publicly available medical image segmentation datasets (MoNuSeg, Chest X-ray and Hippocampus) and observed significant qualitative and quantitative improvements with higher Dice scores and mIoU over the state-of-the-art algorithms. The source code is publicly available at https://github.com/Hejrati/cDAL/.

Recent advances in deep learning-based medical image segmentation studies achieve nearly human-level performance in fully supervised manner. However, acquiring pixel-level expert annotations is extremely expensive and laborious in medical imaging fields. Unsupervised domain adaptation (UDA) can alleviate this problem, which makes it possible to use annotated data in one imaging modality to train a network that can successfully perform segmentation on target imaging modality with no labels. In this work, we propose SDC-UDA, a simple yet effective volumetric UDA framework for slice-direction continuous cross-modality medical image segmentation which combines intra- and inter-slice self-attentive image translation, uncertainty-constrained pseudo-label refinement, and volumetric self-training. Our method is distinguished from previous methods on UDA for medical image segmentation in that it can obtain continuous segmentation in the slice direction, thereby ensuring higher accuracy and potential in clinical practice. We validate SDC-UDA with multiple publicly available cross-modality medical image segmentation datasets and achieve state-of-the-art segmentation performance, not to mention the superior slice-direction continuity of prediction compared to previous studies.

Vision-Language Models (VLMs) trained via contrastive learning have achieved notable success in natural image tasks. However, their application in the medical domain remains limited due to the scarcity of openly accessible, large-scale medical image-text datasets. Existing medical VLMs either train on closed-source proprietary or relatively small open-source datasets that do not generalize well. Similarly, most models remain specific to a single or limited number of medical imaging domains, again restricting their applicability to other modalities. To address this gap, we introduce UniMed, a large-scale, open-source multi-modal medical dataset comprising over 5.3 million image-text pairs across six diverse imaging modalities: X-ray, CT, MRI, Ultrasound, Pathology, and Fundus. UniMed is developed using a data-collection framework that leverages Large Language Models (LLMs) to transform modality-specific classification datasets into image-text formats while incorporating existing image-text data from the medical domain, facilitating scalable VLM pretraining. Using UniMed, we trained UniMed-CLIP, a unified VLM for six modalities that significantly outperforms existing generalist VLMs and matches modality-specific medical VLMs, achieving notable gains in zero-shot evaluations. For instance, UniMed-CLIP improves over BiomedCLIP (trained on proprietary data) by an absolute gain of +12.61, averaged over 21 datasets, while using 3x less training data. To facilitate future research, we release UniMed dataset, training codes, and models at https://github.com/mbzuai-oryx/UniMed-CLIP.

In semi-supervised medical image segmentation, there exist empirical mismatch problems between labeled and unlabeled data distribution. The knowledge learned from the labeled data may be largely discarded if treating labeled and unlabeled data separately or in an inconsistent manner. We propose a straightforward method for alleviating the problem - copy-pasting labeled and unlabeled data bidirectionally, in a simple Mean Teacher architecture. The method encourages unlabeled data to learn comprehensive common semantics from the labeled data in both inward and outward directions. More importantly, the consistent learning procedure for labeled and unlabeled data can largely reduce the empirical distribution gap. In detail, we copy-paste a random crop from a labeled image (foreground) onto an unlabeled image (background) and an unlabeled image (foreground) onto a labeled image (background), respectively. The two mixed images are fed into a Student network and supervised by the mixed supervisory signals of pseudo-labels and ground-truth. We reveal that the simple mechanism of copy-pasting bidirectionally between labeled and unlabeled data is good enough and the experiments show solid gains (e.g., over 21% Dice improvement on ACDC dataset with 5% labeled data) compared with other state-of-the-arts on various semi-supervised medical image segmentation datasets. Code is available at https://github.com/DeepMed-Lab-ECNU/BCP}.

Collecting pixel-level labels for medical datasets can be a laborious and expensive process, and enhancing segmentation performance with a scarcity of labeled data is a crucial challenge. This work introduces AugPaint, a data augmentation framework that utilizes inpainting to generate image-label pairs from limited labeled data. AugPaint leverages latent diffusion models, known for their ability to generate high-quality in-domain images with low overhead, and adapts the sampling process for the inpainting task without need for retraining. Specifically, given a pair of image and label mask, we crop the area labeled with the foreground and condition on it during reversed denoising process for every noise level. Masked background area would gradually be filled in, and all generated images are paired with the label mask. This approach ensures the accuracy of match between synthetic images and label masks, setting it apart from existing dataset generation methods. The generated images serve as valuable supervision for training downstream segmentation models, effectively addressing the challenge of limited annotations. We conducted extensive evaluations of our data augmentation method on four public medical image segmentation datasets, including CT, MRI, and skin imaging. Results across all datasets demonstrate that AugPaint outperforms state-of-the-art label-efficient methodologies, significantly improving segmentation performance.

Existing vision-text contrastive learning like CLIP aims to match the paired image and caption embeddings while pushing others apart, which improves representation transferability and supports zero-shot prediction. However, medical image-text datasets are orders of magnitude below the general images and captions from the internet. Moreover, previous methods encounter many false negatives, i.e., images and reports from separate patients probably carry the same semantics but are wrongly treated as negatives. In this paper, we decouple images and texts for multimodal contrastive learning thus scaling the usable training data in a combinatorial magnitude with low cost. We also propose to replace the InfoNCE loss with semantic matching loss based on medical knowledge to eliminate false negatives in contrastive learning. We prove that MedCLIP is a simple yet effective framework: it outperforms state-of-the-art methods on zero-shot prediction, supervised classification, and image-text retrieval. Surprisingly, we observe that with only 20K pre-training data, MedCLIP wins over the state-of-the-art method (using around 200K data). Our code is available at https://github.com/RyanWangZf/MedCLIP.

The state-of-the-art models for medical image segmentation are variants of U-Net and fully convolutional networks (FCN). Despite their success, these models have two limitations: (1) their optimal depth is apriori unknown, requiring extensive architecture search or inefficient ensemble of models of varying depths; and (2) their skip connections impose an unnecessarily restrictive fusion scheme, forcing aggregation only at the same-scale feature maps of the encoder and decoder sub-networks. To overcome these two limitations, we propose UNet++, a new neural architecture for semantic and instance segmentation, by (1) alleviating the unknown network depth with an efficient ensemble of U-Nets of varying depths, which partially share an encoder and co-learn simultaneously using deep supervision; (2) redesigning skip connections to aggregate features of varying semantic scales at the decoder sub-networks, leading to a highly flexible feature fusion scheme; and (3) devising a pruning scheme to accelerate the inference speed of UNet++. We have evaluated UNet++ using six different medical image segmentation datasets, covering multiple imaging modalities such as computed tomography (CT), magnetic resonance imaging (MRI), and electron microscopy (EM), and demonstrating that (1) UNet++ consistently outperforms the baseline models for the task of semantic segmentation across different datasets and backbone architectures; (2) UNet++ enhances segmentation quality of varying-size objects -- an improvement over the fixed-depth U-Net; (3) Mask RCNN++ (Mask R-CNN with UNet++ design) outperforms the original Mask R-CNN for the task of instance segmentation; and (4) pruned UNet++ models achieve significant speedup while showing only modest performance degradation. Our implementation and pre-trained models are available at https://github.com/MrGiovanni/UNetPlusPlus.

Recent advances in multi-modal algorithms have driven and been driven by the increasing availability of large image-text datasets, leading to significant strides in various fields, including computational pathology. However, in most existing medical image-text datasets, the text typically provides high-level summaries that may not sufficiently describe sub-tile regions within a large pathology image. For example, an image might cover an extensive tissue area containing cancerous and healthy regions, but the accompanying text might only specify that this image is a cancer slide, lacking the nuanced details needed for in-depth analysis. In this study, we introduce STimage-1K4M, a novel dataset designed to bridge this gap by providing genomic features for sub-tile images. STimage-1K4M contains 1,149 images derived from spatial transcriptomics data, which captures gene expression information at the level of individual spatial spots within a pathology image. Specifically, each image in the dataset is broken down into smaller sub-image tiles, with each tile paired with 15,000-30,000 dimensional gene expressions. With 4,293,195 pairs of sub-tile images and gene expressions, STimage-1K4M offers unprecedented granularity, paving the way for a wide range of advanced research in multi-modal data analysis an innovative applications in computational pathology, and beyond.

Medical image segmentation is a cornerstone of modern clinical diagnostics. While Vision Transformers that leverage shifted window-based self-attention have established new benchmarks in this field, they are often hampered by a critical limitation: their localized attention mechanism struggles to effectively fuse local details with global context. This deficiency is particularly detrimental to challenging tasks such as the segmentation of microtumors and miniature organs, where both fine-grained boundary definition and broad contextual understanding are paramount. To address this gap, we propose HBFormer, a novel Hybrid-Bridge Transformer architecture. The 'Hybrid' design of HBFormer synergizes a classic U-shaped encoder-decoder framework with a powerful Swin Transformer backbone for robust hierarchical feature extraction. The core innovation lies in its 'Bridge' mechanism, a sophisticated nexus for multi-scale feature integration. This bridge is architecturally embodied by our novel Multi-Scale Feature Fusion (MFF) decoder. Departing from conventional symmetric designs, the MFF decoder is engineered to fuse multi-scale features from the encoder with global contextual information. It achieves this through a synergistic combination of channel and spatial attention modules, which are constructed from a series of dilated and depth-wise convolutions. These components work in concert to create a powerful feature bridge that explicitly captures long-range dependencies and refines object boundaries with exceptional precision. Comprehensive experiments on challenging medical image segmentation datasets, including multi-organ, liver tumor, and bladder tumor benchmarks, demonstrate that HBFormer achieves state-of-the-art results, showcasing its outstanding capabilities in microtumor and miniature organ segmentation. Code and models are available at: https://github.com/lzeeorno/HBFormer.

While leveraging additional training data is well established to improve adversarial robustness, it incurs the unavoidable cost of data collection and the heavy computation to train models. To mitigate the costs, we propose Guided Adversarial Training (GAT), a novel adversarial training technique that exploits auxiliary tasks under a limited set of training data. Our approach extends single-task models into multi-task models during the min-max optimization of adversarial training, and drives the loss optimization with a regularization of the gradient curvature across multiple tasks. GAT leverages two types of auxiliary tasks: self-supervised tasks, where the labels are generated automatically, and domain-knowledge tasks, where human experts provide additional labels. Experimentally, GAT increases the robust AUC of CheXpert medical imaging dataset from 50% to 83% and On CIFAR-10, GAT outperforms eight state-of-the-art adversarial training and achieves 56.21% robust accuracy with Resnet-50. Overall, we demonstrate that guided multi-task learning is an actionable and promising avenue to push further the boundaries of model robustness.

High-quality preference data is essential for aligning foundation models with human values through preference learning. However, manual annotation of such data is often time-consuming and costly. Recent methods often adopt a self-rewarding approach, where the target model generates and annotates its own preference data, but this can lead to inaccuracies since the reward model shares weights with the target model, thereby amplifying inherent biases. To address these issues, we propose Anyprefer, a framework designed to synthesize high-quality preference data for aligning the target model. Anyprefer frames the data synthesis process as a cooperative two-player Markov Game, where the target model and the judge model collaborate together. Here, a series of external tools are introduced to assist the judge model in accurately rewarding the target model's responses, mitigating biases in the rewarding process. In addition, a feedback mechanism is introduced to optimize prompts for both models, enhancing collaboration and improving data quality. The synthesized data is compiled into a new preference dataset, Anyprefer-V1, consisting of 58K high-quality preference pairs. Extensive experiments show that Anyprefer significantly improves model alignment performance across four main applications, covering 21 datasets, achieving average improvements of 18.55% in five natural language generation datasets, 3.66% in nine vision-language understanding datasets, 30.05% in three medical image analysis datasets, and 16.00% in four visuo-motor control tasks.

Medical visual question answering (VQA) is a challenging multimodal task, where Vision-Language Pre-training (VLP) models can effectively improve the generalization performance. However, most methods in the medical field treat VQA as an answer classification task which is difficult to transfer to practical application scenarios. Additionally, due to the privacy of medical images and the expensive annotation process, large-scale medical image-text pairs datasets for pretraining are severely lacking. In this paper, we propose a large-scale MultI-task Self-Supervised learning based framework (MISS) for medical VQA tasks. Unlike existing methods, we treat medical VQA as a generative task. We unify the text encoder and multimodal encoder and align image-text features through multi-task learning. Furthermore, we propose a Transfer-and-Caption method that extends the feature space of single-modal image datasets using large language models (LLMs), enabling those traditional medical vision field task data to be applied to VLP. Experiments show that our method achieves excellent results with fewer multimodal datasets and demonstrates the advantages of generative VQA models. The code and model weights will be released upon the paper's acceptance.

Semantic image segmentation, the process of classifying each pixel in an image into a particular class, plays an important role in many visual understanding systems. As the predominant criterion for evaluating the performance of statistical models, loss functions are crucial for shaping the development of deep learning-based segmentation algorithms and improving their overall performance. To aid researchers in identifying the optimal loss function for their particular application, this survey provides a comprehensive and unified review of 25 loss functions utilized in image segmentation. We provide a novel taxonomy and thorough review of how these loss functions are customized and leveraged in image segmentation, with a systematic categorization emphasizing their significant features and applications. Furthermore, to evaluate the efficacy of these methods in real-world scenarios, we propose unbiased evaluations of some distinct and renowned loss functions on established medical and natural image datasets. We conclude this review by identifying current challenges and unveiling future research opportunities. Finally, we have compiled the reviewed studies that have open-source implementations on our GitHub page.

The field of medical image segmentation is hindered by the scarcity of large, publicly available annotated datasets. Not all datasets are made public for privacy reasons, and creating annotations for a large dataset is time-consuming and expensive, as it requires specialized expertise to accurately identify regions of interest (ROIs) within the images. To address these challenges, we evaluate the performance of the Segment Anything Model (SAM) as an annotation tool for medical data by using it to produce so-called "pseudo labels" on the Medical Segmentation Decathlon (MSD) computed tomography (CT) tasks. The pseudo labels are then used in place of ground truth labels to train a UNet model in a weakly-supervised manner. We experiment with different prompt types on SAM and find that the bounding box prompt is a simple yet effective method for generating pseudo labels. This method allows us to develop a weakly-supervised model that performs comparably to a fully supervised model.

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.

Image registration is an essential step in many medical image analysis tasks. Traditional methods for image registration are primarily optimization-driven, finding the optimal deformations that maximize the similarity between two images. Recent learning-based methods, trained to directly predict transformations between two images, run much faster, but suffer from performance deficiencies due to model generalization and the inefficiency in handling individual image specific deformations. Here we present a new neural net based image registration framework, called NIR (Neural Image Registration), which is based on optimization but utilizes deep neural nets to model deformations between image pairs. NIR represents the transformation between two images with a continuous function implemented via neural fields, receiving a 3D coordinate as input and outputting the corresponding deformation vector. NIR provides two ways of generating deformation field: directly output a displacement vector field for general deformable registration, or output a velocity vector field and integrate the velocity field to derive the deformation field for diffeomorphic image registration. The optimal registration is discovered by updating the parameters of the neural field via stochastic gradient descent. We describe several design choices that facilitate model optimization, including coordinate encoding, sinusoidal activation, coordinate sampling, and intensity sampling. Experiments on two 3D MR brain scan datasets demonstrate that NIR yields state-of-the-art performance in terms of both registration accuracy and regularity, while running significantly faster than traditional optimization-based methods.

Unified Medical Image Segmentation (UMIS) is critical for comprehensive anatomical assessment but faces challenges due to multi-scale structural heterogeneity. Conventional pixel-based approaches, lacking object-level anatomical insight and inter-organ relational modeling, struggle with morphological complexity and feature conflicts, limiting their efficacy in UMIS. We propose Mamba Snake, a novel deep snake framework enhanced by state space modeling for UMIS. Mamba Snake frames multi-contour evolution as a hierarchical state space atlas, effectively modeling macroscopic inter-organ topological relationships and microscopic contour refinements. We introduce a snake-specific vision state space module, the Mamba Evolution Block (MEB), which leverages effective spatiotemporal information aggregation for adaptive refinement of complex morphologies. Energy map shape priors further ensure robust long-range contour evolution in heterogeneous data. Additionally, a dual-classification synergy mechanism is incorporated to concurrently optimize detection and segmentation, mitigating under-segmentation of microstructures in UMIS. Extensive evaluations across five clinical datasets reveal Mamba Snake's superior performance, with an average Dice improvement of 3\% over state-of-the-art methods.

Fairness in artificial intelligence models has gained significantly more attention in recent years, especially in the area of medicine, as fairness in medical models is critical to people's well-being and lives. High-quality medical fairness datasets are needed to promote fairness learning research. Existing medical fairness datasets are all for classification tasks, and no fairness datasets are available for medical segmentation, while medical segmentation is an equally important clinical task as classifications, which can provide detailed spatial information on organ abnormalities ready to be assessed by clinicians. In this paper, we propose the first fairness dataset for medical segmentation named Harvard-FairSeg with 10,000 subject samples. In addition, we propose a fair error-bound scaling approach to reweight the loss function with the upper error-bound in each identity group, using the segment anything model (SAM). We anticipate that the segmentation performance equity can be improved by explicitly tackling the hard cases with high training errors in each identity group. To facilitate fair comparisons, we utilize a novel equity-scaled segmentation performance metric to compare segmentation metrics in the context of fairness, such as the equity-scaled Dice coefficient. Through comprehensive experiments, we demonstrate that our fair error-bound scaling approach either has superior or comparable fairness performance to the state-of-the-art fairness learning models. The dataset and code are publicly accessible via https://ophai.hms.harvard.edu/datasets/harvard-fairseg10k.

Imputation of missing images via source-to-target modality translation can improve diversity in medical imaging protocols. A pervasive approach for synthesizing target images involves one-shot mapping through generative adversarial networks (GAN). Yet, GAN models that implicitly characterize the image distribution can suffer from limited sample fidelity. Here, we propose a novel method based on adversarial diffusion modeling, SynDiff, for improved performance in medical image translation. To capture a direct correlate of the image distribution, SynDiff leverages a conditional diffusion process that progressively maps noise and source images onto the target image. For fast and accurate image sampling during inference, large diffusion steps are taken with adversarial projections in the reverse diffusion direction. To enable training on unpaired datasets, a cycle-consistent architecture is devised with coupled diffusive and non-diffusive modules that bilaterally translate between two modalities. Extensive assessments are reported on the utility of SynDiff against competing GAN and diffusion models in multi-contrast MRI and MRI-CT translation. Our demonstrations indicate that SynDiff offers quantitatively and qualitatively superior performance against competing baselines.

In this paper, we present the VMSE U-Net and VM-Unet CBAM+ model, two cutting-edge deep learning architectures designed to enhance medical image segmentation. Our approach integrates Squeeze-and-Excitation (SE) and Convolutional Block Attention Module (CBAM) techniques into the traditional VM U-Net framework, significantly improving segmentation accuracy, feature localization, and computational efficiency. Both models show superior performance compared to the baseline VM-Unet across multiple datasets. Notably, VMSEUnet achieves the highest accuracy, IoU, precision, and recall while maintaining low loss values. It also exhibits exceptional computational efficiency with faster inference times and lower memory usage on both GPU and CPU. Overall, the study suggests that the enhanced architecture VMSE-Unet is a valuable tool for medical image analysis. These findings highlight its potential for real-world clinical applications, emphasizing the importance of further research to optimize accuracy, robustness, and computational efficiency.

Medical Image Analysis (MedIA) has become an essential tool in medicine and healthcare, aiding in disease diagnosis, prognosis, and treatment planning, and recent successes in deep learning (DL) have made significant contributions to its advances. However, DL models for MedIA remain challenging to deploy in real-world situations, failing for generalization under the distributional gap between training and testing samples, known as a distribution shift problem. Researchers have dedicated their efforts to developing various DL methods to adapt and perform robustly on unknown and out-of-distribution data distributions. This paper comprehensively reviews domain generalization studies specifically tailored for MedIA. We provide a holistic view of how domain generalization techniques interact within the broader MedIA system, going beyond methodologies to consider the operational implications on the entire MedIA workflow. Specifically, we categorize domain generalization methods into data-level, feature-level, model-level, and analysis-level methods. We show how those methods can be used in various stages of the MedIA workflow with DL equipped from data acquisition to model prediction and analysis. Furthermore, we include benchmark datasets and applications used to evaluate these approaches and analyze the strengths and weaknesses of various methods, unveiling future research opportunities.

Promptable segmentation foundation models such as SAM3 have demonstrated strong generalization capabilities through interactive and concept-based prompting. However, their direct applicability to medical image segmentation remains limited by severe domain shifts, the absence of privileged spatial prompts, and the need to reason over complex anatomical and volumetric structures. Here we present Medical SAM3, a foundation model for universal prompt-driven medical image segmentation, obtained by fully fine-tuning SAM3 on large-scale, heterogeneous 2D and 3D medical imaging datasets with paired segmentation masks and text prompts. Through a systematic analysis of vanilla SAM3, we observe that its performance degrades substantially on medical data, with its apparent competitiveness largely relying on strong geometric priors such as ground-truth-derived bounding boxes. These findings motivate full model adaptation beyond prompt engineering alone. By fine-tuning SAM3's model parameters on 33 datasets spanning 10 medical imaging modalities, Medical SAM3 acquires robust domain-specific representations while preserving prompt-driven flexibility. Extensive experiments across organs, imaging modalities, and dimensionalities demonstrate consistent and significant performance gains, particularly in challenging scenarios characterized by semantic ambiguity, complex morphology, and long-range 3D context. Our results establish Medical SAM3 as a universal, text-guided segmentation foundation model for medical imaging and highlight the importance of holistic model adaptation for achieving robust prompt-driven segmentation under severe domain shift. Code and model will be made available at https://github.com/AIM-Research-Lab/Medical-SAM3.

Medical image segmentation is evolving from task-specific models toward generalizable frameworks. Recent research leverages Multi-modal Large Language Models (MLLMs) as autonomous agents, employing reinforcement learning with verifiable reward (RLVR) to orchestrate specialized tools like the Segment Anything Model (SAM). However, these approaches often rely on single-turn, rigid interaction strategies and lack process-level supervision during training, which hinders their ability to fully exploit the dynamic potential of interactive tools and leads to redundant actions. To bridge this gap, we propose MedSAM-Agent, a framework that reformulates interactive segmentation as a multi-step autonomous decision-making process. First, we introduce a hybrid prompting strategy for expert-curated trajectory generation, enabling the model to internalize human-like decision heuristics and adaptive refinement strategies. Furthermore, we develop a two-stage training pipeline that integrates multi-turn, end-to-end outcome verification with a clinical-fidelity process reward design to promote interaction parsimony and decision efficiency. Extensive experiments across 6 medical modalities and 21 datasets demonstrate that MedSAM-Agent achieves state-of-the-art performance, effectively unifying autonomous medical reasoning with robust, iterative optimization. Code is available https://github.com/CUHK-AIM-Group/MedSAM-Agent{here}.

Conventional medical image segmentation methods have been found inadequate in facilitating physicians with the identification of specific lesions for diagnosis and treatment. Given the utility of text as an instructional format, we introduce a novel task termed Medical Image Referring Segmentation (MIRS), which requires segmenting specified lesions in images based on the given language expressions. Due to the varying object scales in medical images, MIRS demands robust vision-language modeling and comprehensive multi-scale interaction for precise localization and segmentation under linguistic guidance. However, existing medical image segmentation methods fall short in meeting these demands, resulting in insufficient segmentation accuracy. In response, we propose an approach named Language-guided Scale-aware MedSegmentor (LSMS), incorporating two appealing designs: (1)~a Scale-aware Vision-Language Attention module that leverages diverse convolutional kernels to acquire rich visual knowledge and interact closely with linguistic features, thereby enhancing lesion localization capability; (2)~a Full-Scale Decoder that globally models multi-modal features across various scales, capturing complementary information between scales to accurately outline lesion boundaries. Addressing the lack of suitable datasets for MIRS, we constructed a vision-language medical dataset called Reference Hepatic Lesion Segmentation (RefHL-Seg). This dataset comprises 2,283 abdominal CT slices from 231 cases, with corresponding textual annotations and segmentation masks for various liver lesions in images. We validated the performance of LSMS for MIRS and conventional medical image segmentation tasks across various datasets. Our LSMS consistently outperforms on all datasets with lower computational costs. The code and datasets will be released.

Medical image foundation models (MIFMs) have demonstrated remarkable potential for a wide range of clinical tasks, yet their development is constrained by the scarcity, heterogeneity, and high cost of large-scale annotated datasets. Here, we propose RaSD (Randomized Synthesis and Disentanglement), a scalable framework for pre-training MIFMs entirely on synthetic data. By modeling anatomical structures and appearance variations with randomized Gaussian distributions, RaSD exposes models to sufficient multi-scale structural and appearance perturbations, forcing them to rely on invariant and task-relevant anatomical cues rather than dataset-specific textures, thereby enabling robust and transferable representation learning. We pre-trained RaSD on 1.2 million 3D volumes and 9.6 million 2D images, and extensively evaluated the resulting models across 6 imaging modalities, 48 datasets, and 56 downstream tasks. Across all evaluated downstream tasks, RaSD consistently outperforms training-from-scratch models, achieves the best performance on 17 tasks, and remains comparable to models pre-trained on large real datasets in most others. These results demonstrate that the capacity of synthetic data alone to drive robust representation learning. Our findings establish a paradigm shift in medical AI, demonstrating that synthetic data can serve as a "free lunch" for scalable, privacy-preserving, and clinically generalizable foundation models.

Automatic medical image segmentation is a crucial topic in the medical domain and successively a critical counterpart in the computer-aided diagnosis paradigm. U-Net is the most widespread image segmentation architecture due to its flexibility, optimized modular design, and success in all medical image modalities. Over the years, the U-Net model achieved tremendous attention from academic and industrial researchers. Several extensions of this network have been proposed to address the scale and complexity created by medical tasks. Addressing the deficiency of the naive U-Net model is the foremost step for vendors to utilize the proper U-Net variant model for their business. Having a compendium of different variants in one place makes it easier for builders to identify the relevant research. Also, for ML researchers it will help them understand the challenges of the biological tasks that challenge the model. To address this, we discuss the practical aspects of the U-Net model and suggest a taxonomy to categorize each network variant. Moreover, to measure the performance of these strategies in a clinical application, we propose fair evaluations of some unique and famous designs on well-known datasets. We provide a comprehensive implementation library with trained models for future research. In addition, for ease of future studies, we created an online list of U-Net papers with their possible official implementation. All information is gathered in https://github.com/NITR098/Awesome-U-Net repository.

Recent reasoning based medical MLLMs have made progress in generating step by step textual reasoning chains. However, they still struggle with complex tasks that necessitate dynamic and iterative focusing on fine-grained visual regions to achieve precise grounding and diagnosis. We introduce Ophiuchus, a versatile, tool-augmented framework that equips an MLLM to (i) decide when additional visual evidence is needed, (ii) determine where to probe and ground within the medical image, and (iii) seamlessly weave the relevant sub-image content back into an interleaved, multimodal chain of thought. In contrast to prior approaches limited by the performance ceiling of specialized tools, Ophiuchus integrates the model's inherent grounding and perception capabilities with external tools, thereby fostering higher-level reasoning. The core of our method is a three-stage training strategy: cold-start training with tool-integrated reasoning data to achieve basic tool selection and adaptation for inspecting key regions; self-reflection fine-tuning to strengthen reflective reasoning and encourage revisiting tool outputs; and Agentic Tool Reinforcement Learning to directly optimize task-specific rewards and emulate expert-like diagnostic behavior. Extensive experiments show that Ophiuchus consistently outperforms both closed-source and open-source SOTA methods across diverse medical benchmarks, including VQA, detection, and reasoning-based segmentation. Our approach illuminates a path toward medical AI agents that can genuinely "think with images" through tool-integrated reasoning. Datasets, codes, and trained models will be released publicly.

Compared to single view medical image classification, using multiple views can significantly enhance predictive accuracy as it can account for the complementarity of each view while leveraging correlations between views. Existing multi-view approaches typically employ separate convolutional or transformer branches combined with simplistic feature fusion strategies. However, these approaches inadvertently disregard essential cross-view correlations, leading to suboptimal classification performance, and suffer from challenges with limited receptive field (CNNs) or quadratic computational complexity (transformers). Inspired by state space sequence models, we propose XFMamba, a pure Mamba-based cross-fusion architecture to address the challenge of multi-view medical image classification. XFMamba introduces a novel two-stage fusion strategy, facilitating the learning of single-view features and their cross-view disparity. This mechanism captures spatially long-range dependencies in each view while enhancing seamless information transfer between views. Results on three public datasets, MURA, CheXpert and DDSM, illustrate the effectiveness of our approach across diverse multi-view medical image classification tasks, showing that it outperforms existing convolution-based and transformer-based multi-view methods. Code is available at https://github.com/XZheng0427/XFMamba.

The Segment Anything Model (SAM) has set a new standard in interactive image segmentation, offering robust performance across various tasks. However, its significant computational requirements limit its deployment in real-time or resource-constrained environments. To address these challenges, we propose a novel knowledge distillation approach, KD SAM, which incorporates both encoder and decoder optimization through a combination of Mean Squared Error (MSE) and Perceptual Loss. This dual-loss framework captures structural and semantic features, enabling the student model to maintain high segmentation accuracy while reducing computational complexity. Based on the model evaluation on datasets, including Kvasir-SEG, ISIC 2017, Fetal Head Ultrasound, and Breast Ultrasound, we demonstrate that KD SAM achieves comparable or superior performance to the baseline models, with significantly fewer parameters. KD SAM effectively balances segmentation accuracy and computational efficiency, making it well-suited for real-time medical image segmentation applications in resource-constrained environments.

Current vision-language models (VLMs) in medicine are primarily designed for categorical question answering (e.g., "Is this normal or abnormal?") or qualitative descriptive tasks. However, clinical decision-making often relies on quantitative assessments, such as measuring the size of a tumor or the angle of a joint, from which physicians draw their own diagnostic conclusions. This quantitative reasoning capability remains underexplored and poorly supported in existing VLMs. In this work, we introduce MedVision, a large-scale dataset and benchmark specifically designed to evaluate and improve VLMs on quantitative medical image analysis. MedVision spans 22 public datasets covering diverse anatomies and modalities, with 30.8 million image-annotation pairs. We focus on three representative quantitative tasks: (1) detection of anatomical structures and abnormalities, (2) tumor/lesion (T/L) size estimation, and (3) angle/distance (A/D) measurement. Our benchmarks show that current off-the-shelf VLMs perform poorly on these tasks. However, with supervised fine-tuning on MedVision, we significantly enhance their performance across detection, T/L estimation, and A/D measurement, demonstrating reduced error rates and improved precision. This work provides a foundation for developing VLMs with robust quantitative reasoning capabilities in medical imaging. Code and data are available at https://medvision-vlm.github.io.

Convolutional neural networks (CNNs) are widely used for high-stakes applications like medicine, often surpassing human performance. However, most explanation methods rely on post-hoc attribution, approximating the decision-making process of already trained black-box models. These methods are often sensitive, unreliable, and fail to reflect true model reasoning, limiting their trustworthiness in critical applications. In this work, we introduce SoftCAM, a straightforward yet effective approach that makes standard CNN architectures inherently interpretable. By removing the global average pooling layer and replacing the fully connected classification layer with a convolution-based class evidence layer, SoftCAM preserves spatial information and produces explicit class activation maps that form the basis of the model's predictions. Evaluated on three medical datasets, SoftCAM maintains classification performance while significantly improving both the qualitative and quantitative explanation compared to existing post-hoc methods. Our results demonstrate that CNNs can be inherently interpretable without compromising performance, advancing the development of self-explainable deep learning for high-stakes decision-making. The code is available at https://github.com/kdjoumessi/SoftCAM

Visual grounding is essential for precise perception and reasoning in multimodal large language models (MLLMs), especially in medical imaging domains. While existing medical visual grounding benchmarks primarily focus on single-image scenarios, real-world clinical applications often involve sequential images, where accurate lesion localization across different modalities and temporal tracking of disease progression (e.g., pre- vs. post-treatment comparison) require fine-grained cross-image semantic alignment and context-aware reasoning. To remedy the underrepresentation of image sequences in existing medical visual grounding benchmarks, we propose MedSG-Bench, the first benchmark tailored for Medical Image Sequences Grounding. It comprises eight VQA-style tasks, formulated into two paradigms of the grounding tasks, including 1) Image Difference Grounding, which focuses on detecting change regions across images, and 2) Image Consistency Grounding, which emphasizes detection of consistent or shared semantics across sequential images. MedSG-Bench covers 76 public datasets, 10 medical imaging modalities, and a wide spectrum of anatomical structures and diseases, totaling 9,630 question-answer pairs. We benchmark both general-purpose MLLMs (e.g., Qwen2.5-VL) and medical-domain specialized MLLMs (e.g., HuatuoGPT-vision), observing that even the advanced models exhibit substantial limitations in medical sequential grounding tasks. To advance this field, we construct MedSG-188K, a large-scale instruction-tuning dataset tailored for sequential visual grounding, and further develop MedSeq-Grounder, an MLLM designed to facilitate future research on fine-grained understanding across medical sequential images. The benchmark, dataset, and model are available at https://huggingface.co/MedSG-Bench

Ensuring equitable Artificial Intelligence (AI) in healthcare demands systems that make unbiased decisions across all demographic groups, bridging technical innovation with ethical principles. Foundation Models (FMs), trained on vast datasets through self-supervised learning, enable efficient adaptation across medical imaging tasks while reducing dependency on labeled data. These models demonstrate potential for enhancing fairness, though significant challenges remain in achieving consistent performance across demographic groups. Our review indicates that effective bias mitigation in FMs requires systematic interventions throughout all stages of development. While previous approaches focused primarily on model-level bias mitigation, our analysis reveals that fairness in FMs requires integrated interventions throughout the development pipeline, from data documentation to deployment protocols. This comprehensive framework advances current knowledge by demonstrating how systematic bias mitigation, combined with policy engagement, can effectively address both technical and institutional barriers to equitable AI in healthcare. The development of equitable FMs represents a critical step toward democratizing advanced healthcare technologies, particularly for underserved populations and regions with limited medical infrastructure and computational resources.

Semi-supervised image segmentation has attracted great attention recently. The key is how to leverage unlabeled images in the training process. Most methods maintain consistent predictions of the unlabeled images under variations (e.g., adding noise/perturbations, or creating alternative versions) in the image and/or model level. In most image-level variation, medical images often have prior structure information, which has not been well explored. In this paper, we propose novel dual structure-aware image filterings (DSAIF) as the image-level variations for semi-supervised medical image segmentation. Motivated by connected filtering that simplifies image via filtering in structure-aware tree-based image representation, we resort to the dual contrast invariant Max-tree and Min-tree representation. Specifically, we propose a novel connected filtering that removes topologically equivalent nodes (i.e. connected components) having no siblings in the Max/Min-tree. This results in two filtered images preserving topologically critical structure. Applying the proposed DSAIF to mutually supervised networks decreases the consensus of their erroneous predictions on unlabeled images. This helps to alleviate the confirmation bias issue of overfitting to noisy pseudo labels of unlabeled images, and thus effectively improves the segmentation performance. Extensive experimental results on three benchmark datasets demonstrate that the proposed method significantly/consistently outperforms some state-of-the-art methods. The source codes will be publicly available.

Although purely transformer-based architectures showed promising performance in many computer vision tasks, many hybrid models consisting of CNN and transformer blocks are introduced to fit more specialized tasks. Nevertheless, despite the performance gain of both pure and hybrid transformer-based architectures compared to CNNs in medical imaging segmentation, their high training cost and complexity make it challenging to use them in real scenarios. In this work, we propose simple architectures based on purely convolutional layers, and show that by just taking advantage of the attention map visualizations obtained from a self-supervised pretrained vision transformer network (e.g., DINO) one can outperform complex transformer-based networks with much less computation costs. The proposed architecture is composed of two encoder branches with the original image as input in one branch and the attention map visualizations of the same image from multiple self-attention heads from a pre-trained DINO model (as multiple channels) in the other branch. The results of our experiments on two publicly available medical imaging datasets show that the proposed pipeline outperforms U-Net and the state-of-the-art medical image segmentation models.

Recent trends in semi-supervised learning have significantly boosted the performance of 3D semi-supervised medical image segmentation. Compared with 2D images, 3D medical volumes involve information from different directions, e.g., transverse, sagittal, and coronal planes, so as to naturally provide complementary views. These complementary views and the intrinsic similarity among adjacent 3D slices inspire us to develop a novel annotation way and its corresponding semi-supervised model for effective segmentation. Specifically, we firstly propose the orthogonal annotation by only labeling two orthogonal slices in a labeled volume, which significantly relieves the burden of annotation. Then, we perform registration to obtain the initial pseudo labels for sparsely labeled volumes. Subsequently, by introducing unlabeled volumes, we propose a dual-network paradigm named Dense-Sparse Co-training (DeSCO) that exploits dense pseudo labels in early stage and sparse labels in later stage and meanwhile forces consistent output of two networks. Experimental results on three benchmark datasets validated our effectiveness in performance and efficiency in annotation. For example, with only 10 annotated slices, our method reaches a Dice up to 86.93% on KiTS19 dataset.

Transformer-based models have been widely demonstrated to be successful in computer vision tasks by modelling long-range dependencies and capturing global representations. However, they are often dominated by features of large patterns leading to the loss of local details (e.g., boundaries and small objects), which are critical in medical image segmentation. To alleviate this problem, we propose a Dual-Aggregation Transformer Network called DuAT, which is characterized by two innovative designs, namely, the Global-to-Local Spatial Aggregation (GLSA) and Selective Boundary Aggregation (SBA) modules. The GLSA has the ability to aggregate and represent both global and local spatial features, which are beneficial for locating large and small objects, respectively. The SBA module is used to aggregate the boundary characteristic from low-level features and semantic information from high-level features for better preserving boundary details and locating the re-calibration objects. Extensive experiments in six benchmark datasets demonstrate that our proposed model outperforms state-of-the-art methods in the segmentation of skin lesion images, and polyps in colonoscopy images. In addition, our approach is more robust than existing methods in various challenging situations such as small object segmentation and ambiguous object boundaries.

The ability to interpret and intervene model decisions is important for the adoption of computer-aided diagnosis methods in clinical workflows. Recent concept-based methods link the model predictions with interpretable concepts and modify their activation scores to interact with the model. However, these concepts are at the image level, which hinders the model from pinpointing the exact patches the concepts are activated. Alternatively, prototype-based methods learn representations from training image patches and compare these with test image patches, using the similarity scores for final class prediction. However, interpreting the underlying concepts of these patches can be challenging and often necessitates post-hoc guesswork. To address this issue, this paper introduces the novel Concept-based Similarity Reasoning network (CSR), which offers (i) patch-level prototype with intrinsic concept interpretation, and (ii) spatial interactivity. First, the proposed CSR provides localized explanation by grounding prototypes of each concept on image regions. Second, our model introduces novel spatial-level interaction, allowing doctors to engage directly with specific image areas, making it an intuitive and transparent tool for medical imaging. CSR improves upon prior state-of-the-art interpretable methods by up to 4.5\% across three biomedical datasets. Our code is released at https://github.com/tadeephuy/InteractCSR.

With the development of Deep Neural Networks (DNNs), many efforts have been made to handle medical image segmentation. Traditional methods such as nnUNet train specific segmentation models on the individual datasets. Plenty of recent methods have been proposed to adapt the foundational Segment Anything Model (SAM) to medical image segmentation. However, they still focus on discrete representations to generate pixel-wise predictions, which are spatially inflexible and scale poorly to higher resolution. In contrast, implicit methods learn continuous representations for segmentation, which is crucial for medical image segmentation. In this paper, we propose I-MedSAM, which leverages the benefits of both continuous representations and SAM, to obtain better cross-domain ability and accurate boundary delineation. Since medical image segmentation needs to predict detailed segmentation boundaries, we designed a novel adapter to enhance the SAM features with high-frequency information during Parameter-Efficient Fine-Tuning (PEFT). To convert the SAM features and coordinates into continuous segmentation output, we utilize Implicit Neural Representation (INR) to learn an implicit segmentation decoder. We also propose an uncertainty-guided sampling strategy for efficient learning of INR. Extensive evaluations on 2D medical image segmentation tasks have shown that our proposed method with only 1.6M trainable parameters outperforms existing methods including discrete and implicit methods. The code will be available at: https://github.com/ucwxb/I-MedSAM.

Mamba, a special case of the State Space Model, is gaining popularity as an alternative to template-based deep learning approaches in medical image analysis. While transformers are powerful architectures, they have drawbacks, including quadratic computational complexity and an inability to address long-range dependencies efficiently. This limitation affects the analysis of large and complex datasets in medical imaging, where there are many spatial and temporal relationships. In contrast, Mamba offers benefits that make it well-suited for medical image analysis. It has linear time complexity, which is a significant improvement over transformers. Mamba processes longer sequences without attention mechanisms, enabling faster inference and requiring less memory. Mamba also demonstrates strong performance in merging multimodal data, improving diagnosis accuracy and patient outcomes. The organization of this paper allows readers to appreciate the capabilities of Mamba in medical imaging step by step. We begin by defining core concepts of SSMs and models, including S4, S5, and S6, followed by an exploration of Mamba architectures such as pure Mamba, U-Net variants, and hybrid models with convolutional neural networks, transformers, and Graph Neural Networks. We also cover Mamba optimizations, techniques and adaptations, scanning, datasets, applications, experimental results, and conclude with its challenges and future directions in medical imaging. This review aims to demonstrate the transformative potential of Mamba in overcoming existing barriers within medical imaging while paving the way for innovative advancements in the field. A comprehensive list of Mamba architectures applied in the medical field, reviewed in this work, is available at Github.

Generally, the small size of public medical imaging datasets coupled with stringent privacy concerns, hampers the advancement of data-hungry deep learning models in medical imaging. This study addresses these challenges for 3D cardiac MRI images in the short-axis view. We propose Latent Diffusion Models that generate synthetic images conditioned on medical attributes, while ensuring patient privacy through differentially private model training. To our knowledge, this is the first work to apply and quantify differential privacy in 3D medical image generation. We pre-train our models on public data and finetune them with differential privacy on the UK Biobank dataset. Our experiments reveal that pre-training significantly improves model performance, achieving a Fréchet Inception Distance (FID) of 26.77 at ε=10, compared to 92.52 for models without pre-training. Additionally, we explore the trade-off between privacy constraints and image quality, investigating how tighter privacy budgets affect output controllability and may lead to degraded performance. Our results demonstrate that proper consideration during training with differential privacy can substantially improve the quality of synthetic cardiac MRI images, but there are still notable challenges in achieving consistent medical realism.

Medical image registration is a critical task that estimates the spatial correspondence between pairs of images. However, current traditional and deep-learning-based methods rely on similarity measures to generate a deforming field, which often results in disproportionate volume changes in dissimilar regions, especially in tumor regions. These changes can significantly alter the tumor size and underlying anatomy, which limits the practical use of image registration in clinical diagnosis. To address this issue, we have formulated image registration with tumors as a constraint problem that preserves tumor volumes while maximizing image similarity in other normal regions. Our proposed strategy involves a two-stage process. In the first stage, we use similarity-based registration to identify potential tumor regions by their volume change, generating a soft tumor mask accordingly. In the second stage, we propose a volume-preserving registration with a novel adaptive volume-preserving loss that penalizes the change in size adaptively based on the masks calculated from the previous stage. Our approach balances image similarity and volume preservation in different regions, i.e., normal and tumor regions, by using soft tumor masks to adjust the imposition of volume-preserving loss on each one. This ensures that the tumor volume is preserved during the registration process. We have evaluated our strategy on various datasets and network architectures, demonstrating that our method successfully preserves the tumor volume while achieving comparable registration results with state-of-the-art methods. Our codes is available at: https://dddraxxx.github.io/Volume-Preserving-Registration/.

This study introduces a novel On-the-Fly Guidance (OFG) training framework for enhancing existing learning-based image registration models, addressing the limitations of weakly-supervised and unsupervised methods. Weakly-supervised methods struggle due to the scarcity of labeled data, and unsupervised methods directly depend on image similarity metrics for accuracy. Our method proposes a supervised fashion for training registration models, without the need for any labeled data. OFG generates pseudo-ground truth during training by refining deformation predictions with a differentiable optimizer, enabling direct supervised learning. OFG optimizes deformation predictions efficiently, improving the performance of registration models without sacrificing inference speed. Our method is tested across several benchmark datasets and leading models, it significantly enhanced performance, providing a plug-and-play solution for training learning-based registration models. Code available at: https://github.com/cilix-ai/on-the-fly-guidance

Large-scale models pre-trained on large-scale datasets have profoundly advanced the development of deep learning. However, the state-of-the-art models for medical image segmentation are still small-scale, with their parameters only in the tens of millions. Further scaling them up to higher orders of magnitude is rarely explored. An overarching goal of exploring large-scale models is to train them on large-scale medical segmentation datasets for better transfer capacities. In this work, we design a series of Scalable and Transferable U-Net (STU-Net) models, with parameter sizes ranging from 14 million to 1.4 billion. Notably, the 1.4B STU-Net is the largest medical image segmentation model to date. Our STU-Net is based on nnU-Net framework due to its popularity and impressive performance. We first refine the default convolutional blocks in nnU-Net to make them scalable. Then, we empirically evaluate different scaling combinations of network depth and width, discovering that it is optimal to scale model depth and width together. We train our scalable STU-Net models on a large-scale TotalSegmentator dataset and find that increasing model size brings a stronger performance gain. This observation reveals that a large model is promising in medical image segmentation. Furthermore, we evaluate the transferability of our model on 14 downstream datasets for direct inference and 3 datasets for further fine-tuning, covering various modalities and segmentation targets. We observe good performance of our pre-trained model in both direct inference and fine-tuning. The code and pre-trained models are available at https://github.com/Ziyan-Huang/STU-Net.

How to ensure fairness is an important topic in federated learning (FL). Recent studies have investigated how to reward clients based on their contribution (collaboration fairness), and how to achieve uniformity of performance across clients (performance fairness). Despite achieving progress on either one, we argue that it is critical to consider them together, in order to engage and motivate more diverse clients joining FL to derive a high-quality global model. In this work, we propose a novel method to optimize both types of fairness simultaneously. Specifically, we propose to estimate client contribution in gradient and data space. In gradient space, we monitor the gradient direction differences of each client with respect to others. And in data space, we measure the prediction error on client data using an auxiliary model. Based on this contribution estimation, we propose a FL method, federated training via contribution estimation (FedCE), i.e., using estimation as global model aggregation weights. We have theoretically analyzed our method and empirically evaluated it on two real-world medical datasets. The effectiveness of our approach has been validated with significant performance improvements, better collaboration fairness, better performance fairness, and comprehensive analytical studies.

Medical image segmentation remains challenging due to limited annotations for training, ambiguous anatomical features, and domain shifts. While vision-language models such as CLIP offer strong cross-modal representations, their potential for dense, text-guided medical image segmentation remains underexplored. We present MedCLIPSeg, a novel framework that adapts CLIP for robust, data-efficient, and uncertainty-aware medical image segmentation. Our approach leverages patch-level CLIP embeddings through probabilistic cross-modal attention, enabling bidirectional interaction between image and text tokens and explicit modeling of predictive uncertainty. Together with a soft patch-level contrastive loss that encourages more nuanced semantic learning across diverse textual prompts, MedCLIPSeg effectively improves data efficiency and domain generalizability. Extensive experiments across 16 datasets spanning five imaging modalities and six organs demonstrate that MedCLIPSeg outperforms prior methods in accuracy, efficiency, and robustness, while providing interpretable uncertainty maps that highlight local reliability of segmentation results. This work demonstrates the potential of probabilistic vision-language modeling for text-driven medical image segmentation.

We introduce VoxTell, a vision-language model for text-prompted volumetric medical image segmentation. It maps free-form descriptions, from single words to full clinical sentences, to 3D masks. Trained on 62K+ CT, MRI, and PET volumes spanning over 1K anatomical and pathological classes, VoxTell uses multi-stage vision-language fusion across decoder layers to align textual and visual features at multiple scales. It achieves state-of-the-art zero-shot performance across modalities on unseen datasets, excelling on familiar concepts while generalizing to related unseen classes. Extensive experiments further demonstrate strong cross-modality transfer, robustness to linguistic variations and clinical language, as well as accurate instance-specific segmentation from real-world text. Code is available at: https://www.github.com/MIC-DKFZ/VoxTell

Deep learning models have emerged as a powerful tool for various medical applications. However, their success depends on large, high-quality datasets that are challenging to obtain due to privacy concerns and costly annotation. Generative models, such as diffusion models, offer a potential solution by synthesizing medical images, but their practical adoption is hindered by long inference times. In this paper, we propose the use of an optimal transport flow matching approach to accelerate image generation. By introducing a straighter mapping between the source and target distribution, our method significantly reduces inference time while preserving and further enhancing the quality of the outputs. Furthermore, this approach is highly adaptable, supporting various medical imaging modalities, conditioning mechanisms (such as class labels and masks), and different spatial dimensions, including 2D and 3D. Beyond image generation, it can also be applied to related tasks such as image enhancement. Our results demonstrate the efficiency and versatility of this framework, making it a promising advancement for medical imaging applications. Code with checkpoints and a synthetic dataset (beneficial for classification and segmentation) is now available on: https://github.com/milad1378yz/MOTFM.

Differential privacy (DP)'s effect in medical imaging is typically evaluated only through end-to-end performance, leaving the mechanism of privacy-induced utility loss unclear. We introduce Differential Privacy Representation Geometry for Medical Imaging (DP-RGMI), a framework that interprets DP as a structured transformation of representation space and decomposes performance degradation into encoder geometry and task-head utilization. Geometry is quantified by representation displacement from initialization and spectral effective dimension, while utilization is measured as the gap between linear-probe and end-to-end utility. Across over 594,000 images from four chest X-ray datasets and multiple pretrained initializations, we show that DP is consistently associated with a utilization gap even when linear separability is largely preserved. At the same time, displacement and spectral dimension exhibit non-monotonic, initialization- and dataset-dependent reshaping, indicating that DP alters representation anisotropy rather than uniformly collapsing features. Correlation analysis reveals that the association between end-to-end performance and utilization is robust across datasets but can vary by initialization, while geometric quantities capture additional prior- and dataset-conditioned variation. These findings position DP-RGMI as a reproducible framework for diagnosing privacy-induced failure modes and informing privacy model selection.

Medical image segmentation plays a vital role in clinical decision-making, enabling precise localization of lesions and guiding interventions. Despite significant advances in segmentation accuracy, the black-box nature of most deep models has raised growing concerns about their trustworthiness in high-stakes medical scenarios. Current explanation techniques have primarily focused on classification tasks, leaving the segmentation domain relatively underexplored. We introduced an explanation model for segmentation task which employs the causal inference framework and backpropagates the average treatment effect (ATE) into a quantification metric to determine the influence of input regions, as well as network components, on target segmentation areas. Through comparison with recent segmentation explainability techniques on two representative medical imaging datasets, we demonstrated that our approach provides more faithful explanations than existing approaches. Furthermore, we carried out a systematic causal analysis of multiple foundational segmentation models using our method, which reveals significant heterogeneity in perceptual strategies across different models, and even between different inputs for the same model. Suggesting the potential of our method to provide notable insights for optimizing segmentation models. Our code can be found at https://github.com/lcmmai/PdCR.

Differential privacy (DP) provides formal protection for sensitive data but typically incurs substantial losses in diagnostic performance. Model initialization has emerged as a critical factor in mitigating this degradation, yet the role of modern self-supervised learning under full-model DP remains poorly understood. Here, we present a large-scale evaluation of initialization strategies for differentially private medical image analysis, using chest radiograph classification as a representative benchmark with more than 800,000 images. Using state-of-the-art ConvNeXt models trained with DP-SGD across realistic privacy regimes, we compare non-domain-specific supervised ImageNet initialization, non-domain-specific self-supervised DINOv3 initialization, and domain-specific supervised pretraining on MIMIC-CXR, the largest publicly available chest radiograph dataset. Evaluations are conducted across five external datasets spanning diverse institutions and acquisition settings. We show that DINOv3 initialization consistently improves diagnostic utility relative to ImageNet initialization under DP, but remains inferior to domain-specific supervised pretraining, which achieves performance closest to non-private baselines. We further demonstrate that initialization choice strongly influences demographic fairness, cross-dataset generalization, and robustness to data scale and model capacity under privacy constraints. The results establish initialization strategy as a central determinant of utility, fairness, and generalization in differentially private medical imaging.

Semi-supervised learning (SSL) has emerged as an effective paradigm for medical image segmentation, reducing the reliance on extensive expert annotations. Meanwhile, vision-language models (VLMs) have demonstrated strong generalization and few-shot capabilities across diverse visual domains. In this work, we integrate VLM-based segmentation into semi-supervised medical image segmentation by introducing a Vision-Language Enhanced Semi-supervised Segmentation Assistant (VESSA) that incorporates foundation-level visual-semantic understanding into SSL frameworks. Our approach consists of two stages. In Stage 1, the VLM-enhanced segmentation foundation model VESSA is trained as a reference-guided segmentation assistant using a template bank containing gold-standard exemplars, simulating learning from limited labeled data. Given an input-template pair, VESSA performs visual feature matching to extract representative semantic and spatial cues from exemplar segmentations, generating structured prompts for a SAM2-inspired mask decoder to produce segmentation masks. In Stage 2, VESSA is integrated into a state-of-the-art SSL framework, enabling dynamic interaction with the student model: as student predictions become more refined, they are fed back to VESSA as prompts, allowing it to generate higher-quality pseudo-labels and stronger guidance. Extensive experiments across multiple segmentation datasets and domains show that VESSA-augmented SSL significantly enhances segmentation accuracy, outperforming state-of-the-art baselines under extremely limited annotation conditions.

Although new vision foundation models such as Segment Anything Model 2 (SAM2) have significantly enhanced zero-shot image segmentation capabilities, reliance on human-provided prompts poses significant challenges in adapting SAM2 to medical image segmentation tasks. Moreover, SAM2's performance in medical image segmentation was limited by the domain shift issue, since it was originally trained on natural images and videos. To address these challenges, we proposed SAM2 with support-set guided prompting (SAM2-SGP), a framework that eliminated the need for manual prompts. The proposed model leveraged the memory mechanism of SAM2 to generate pseudo-masks using image-mask pairs from a support set via a Pseudo-mask Generation (PMG) module. We further introduced a novel Pseudo-mask Attention (PMA) module, which used these pseudo-masks to automatically generate bounding boxes and enhance localized feature extraction by guiding attention to relevant areas. Furthermore, a low-rank adaptation (LoRA) strategy was adopted to mitigate the domain shift issue. The proposed framework was evaluated on both 2D and 3D datasets across multiple medical imaging modalities, including fundus photography, X-ray, computed tomography (CT), magnetic resonance imaging (MRI), positron emission tomography (PET), and ultrasound. The results demonstrated a significant performance improvement over state-of-the-art models, such as nnUNet and SwinUNet, as well as foundation models, such as SAM2 and MedSAM2, underscoring the effectiveness of the proposed approach. Our code is publicly available at https://github.com/astlian9/SAM_Support.

In this study, we present seg2med, an advanced medical image synthesis framework that uses Denoising Diffusion Probabilistic Models (DDPM) to generate high-quality synthetic medical images conditioned on anatomical masks from TotalSegmentator. The framework synthesizes CT and MR images from segmentation masks derived from real patient data and XCAT digital phantoms, achieving a Structural Similarity Index Measure (SSIM) of 0.94 +/- 0.02 for CT and 0.89 +/- 0.04 for MR images compared to ground-truth images of real patients. It also achieves a Feature Similarity Index Measure (FSIM) of 0.78 +/- 0.04 for CT images from XCAT. The generative quality is further supported by a Fr\'echet Inception Distance (FID) of 3.62 for CT image generation. Additionally, seg2med can generate paired CT and MR images with consistent anatomical structures and convert images between CT and MR modalities, achieving SSIM values of 0.91 +/- 0.03 for MR-to-CT and 0.77 +/- 0.04 for CT-to-MR conversion. Despite the limitations of incomplete anatomical details in segmentation masks, the framework shows strong performance in cross-modality synthesis and multimodal imaging. seg2med also demonstrates high anatomical fidelity in CT synthesis, achieving a mean Dice coefficient greater than 0.90 for 11 abdominal organs and greater than 0.80 for 34 organs out of 59 in 58 test cases. The highest Dice of 0.96 +/- 0.01 was recorded for the right scapula. Leveraging the TotalSegmentator toolkit, seg2med enables segmentation mask generation across diverse datasets, supporting applications in clinical imaging, data augmentation, multimodal synthesis, and diagnostic algorithm development.

Few-shot semantic segmentation (FSS) methods have shown great promise in handling data-scarce scenarios, particularly in medical image segmentation tasks. However, most existing FSS architectures lack sufficient interpretability and fail to fully incorporate the underlying physical structures of semantic regions. To address these issues, in this paper, we propose a novel deep unfolding network, called the Learned Mumford-Shah Network (LMS-Net), for the FSS task. Specifically, motivated by the effectiveness of pixel-to-prototype comparison in prototypical FSS methods and the capability of deep priors to model complex spatial structures, we leverage our learned Mumford-Shah model (LMS model) as a mathematical foundation to integrate these insights into a unified framework. By reformulating the LMS model into prototype update and mask update tasks, we propose an alternating optimization algorithm to solve it efficiently. Further, the iterative steps of this algorithm are unfolded into corresponding network modules, resulting in LMS-Net with clear interpretability. Comprehensive experiments on three publicly available medical segmentation datasets verify the effectiveness of our method, demonstrating superior accuracy and robustness in handling complex structures and adapting to challenging segmentation scenarios. These results highlight the potential of LMS-Net to advance FSS in medical imaging applications. Our code will be available at: https://github.com/SDZhang01/LMSNet

Dense contrastive representation learning (DCRL) has greatly improved the learning efficiency for image-dense prediction tasks, showing its great potential to reduce the large costs of medical image collection and dense annotation. However, the properties of medical images make unreliable correspondence discovery, bringing an open problem of large-scale false positive and negative (FP&N) pairs in DCRL. In this paper, we propose GEoMetric vIsual deNse sImilarity (GEMINI) learning which embeds the homeomorphism prior to DCRL and enables a reliable correspondence discovery for effective dense contrast. We propose a deformable homeomorphism learning (DHL) which models the homeomorphism of medical images and learns to estimate a deformable mapping to predict the pixels' correspondence under topological preservation. It effectively reduces the searching space of pairing and drives an implicit and soft learning of negative pairs via a gradient. We also propose a geometric semantic similarity (GSS) which extracts semantic information in features to measure the alignment degree for the correspondence learning. It will promote the learning efficiency and performance of deformation, constructing positive pairs reliably. We implement two practical variants on two typical representation learning tasks in our experiments. Our promising results on seven datasets which outperform the existing methods show our great superiority. We will release our code on a companion link: https://github.com/YutingHe-list/GEMINI.

In recent years, significant advancements have been made in deep learning for medical image segmentation, particularly with convolutional neural networks (CNNs) and transformer models. However, CNNs face limitations in capturing long-range dependencies, while transformers suffer from high computational complexity. To address this, we propose RWKV-UNet, a novel model that integrates the RWKV (Receptance Weighted Key Value) structure into the U-Net architecture. This integration enhances the model's ability to capture long-range dependencies and to improve contextual understanding, which is crucial for accurate medical image segmentation. We build a strong encoder with developed Global-Local Spatial Perception (GLSP) blocks combining CNNs and RWKVs. We also propose a Cross-Channel Mix (CCM) module to improve skip connections with multi-scale feature fusion, achieving global channel information integration. Experiments on 11 benchmark datasets show that the RWKV-UNet achieves state-of-the-art performance on various types of medical image segmentation tasks. Additionally, smaller variants, RWKV-UNet-S and RWKV-UNet-T, balance accuracy and computational efficiency, making them suitable for broader clinical applications.

Addressing fairness in artificial intelligence (AI), particularly in medical AI, is crucial for ensuring equitable healthcare outcomes. Recent efforts to enhance fairness have introduced new methodologies and datasets in medical AI. However, the fairness issue under the setting of domain transfer is almost unexplored, while it is common that clinics rely on different imaging technologies (e.g., different retinal imaging modalities) for patient diagnosis. This paper presents FairDomain, a pioneering systemic study into algorithmic fairness under domain shifts, employing state-of-the-art domain adaptation (DA) and generalization (DG) algorithms for both medical segmentation and classification tasks to understand how biases are transferred between different domains. We also introduce a novel plug-and-play fair identity attention (FIA) module that adapts to various DA and DG algorithms to improve fairness by using self-attention to adjust feature importance based on demographic attributes. Additionally, we curate the first fairness-focused dataset with two paired imaging modalities for the same patient cohort on medical segmentation and classification tasks, to rigorously assess fairness in domain-shift scenarios. Excluding the confounding impact of demographic distribution variation between source and target domains will allow clearer quantification of the performance of domain transfer models. Our extensive evaluations reveal that the proposed FIA significantly enhances both model performance accounted for fairness across all domain shift settings (i.e., DA and DG) with respect to different demographics, which outperforms existing methods on both segmentation and classification. The code and data can be accessed at https://ophai.hms.harvard.edu/datasets/harvard-fairdomain20k.

An efficient and effective decoding mechanism is crucial in medical image segmentation, especially in scenarios with limited computational resources. However, these decoding mechanisms usually come with high computational costs. To address this concern, we introduce EMCAD, a new efficient multi-scale convolutional attention decoder, designed to optimize both performance and computational efficiency. EMCAD leverages a unique multi-scale depth-wise convolution block, significantly enhancing feature maps through multi-scale convolutions. EMCAD also employs channel, spatial, and grouped (large-kernel) gated attention mechanisms, which are highly effective at capturing intricate spatial relationships while focusing on salient regions. By employing group and depth-wise convolution, EMCAD is very efficient and scales well (e.g., only 1.91M parameters and 0.381G FLOPs are needed when using a standard encoder). Our rigorous evaluations across 12 datasets that belong to six medical image segmentation tasks reveal that EMCAD achieves state-of-the-art (SOTA) performance with 79.4% and 80.3% reduction in #Params and #FLOPs, respectively. Moreover, EMCAD's adaptability to different encoders and versatility across segmentation tasks further establish EMCAD as a promising tool, advancing the field towards more efficient and accurate medical image analysis. Our implementation is available at https://github.com/SLDGroup/EMCAD.

The adoption of Vision Transformers (ViTs) based architectures represents a significant advancement in 3D Medical Image (MI) segmentation, surpassing traditional Convolutional Neural Network (CNN) models by enhancing global contextual understanding. While this paradigm shift has significantly enhanced 3D segmentation performance, state-of-the-art architectures require extremely large and complex architectures with large scale computing resources for training and deployment. Furthermore, in the context of limited datasets, often encountered in medical imaging, larger models can present hurdles in both model generalization and convergence. In response to these challenges and to demonstrate that lightweight models are a valuable area of research in 3D medical imaging, we present SegFormer3D, a hierarchical Transformer that calculates attention across multiscale volumetric features. Additionally, SegFormer3D avoids complex decoders and uses an all-MLP decoder to aggregate local and global attention features to produce highly accurate segmentation masks. The proposed memory efficient Transformer preserves the performance characteristics of a significantly larger model in a compact design. SegFormer3D democratizes deep learning for 3D medical image segmentation by offering a model with 33x less parameters and a 13x reduction in GFLOPS compared to the current state-of-the-art (SOTA). We benchmark SegFormer3D against the current SOTA models on three widely used datasets Synapse, BRaTs, and ACDC, achieving competitive results. Code: https://github.com/OSUPCVLab/SegFormer3D.git

Due to the inherent flexibility of prompting, foundation models have emerged as the predominant force in the fields of natural language processing and computer vision. The recent introduction of the Segment Anything Model (SAM) signifies a noteworthy expansion of the prompt-driven paradigm into the domain of image segmentation, thereby introducing a plethora of previously unexplored capabilities. However, the viability of its application to medical image segmentation remains uncertain, given the substantial distinctions between natural and medical images. In this work, we provide a comprehensive overview of recent endeavors aimed at extending the efficacy of SAM to medical image segmentation tasks, encompassing both empirical benchmarking and methodological adaptations. Additionally, we explore potential avenues for future research directions in SAM's role within medical image segmentation. While direct application of SAM to medical image segmentation does not yield satisfactory performance on multi-modal and multi-target medical datasets so far, numerous insights gleaned from these efforts serve as valuable guidance for shaping the trajectory of foundational models in the realm of medical image analysis. To support ongoing research endeavors, we maintain an active repository that contains an up-to-date paper list and a succinct summary of open-source projects at https://github.com/YichiZhang98/SAM4MIS.

Precise image segmentation provides clinical study with meaningful and well-structured information. Despite the remarkable progress achieved in medical image segmentation, there is still an absence of foundation segmentation model that can segment a wide range of anatomical categories with easy user interaction. In this paper, we propose a universal and interactive volumetric medical image segmentation model, named SegVol. By training on 90k unlabeled Computed Tomography (CT) volumes and 6k labeled CTs, this foundation model supports the segmentation of over 200 anatomical categories using semantic and spatial prompts. Extensive experiments verify that SegVol outperforms the state of the art by a large margin on multiple segmentation benchmarks. Notably, on three challenging lesion datasets, our method achieves around 20% higher Dice score than nnU-Net. The model and data are publicly available at: https://github.com/BAAI-DCAI/SegVol.

Once deployed, medical image analysis methods are often faced with unexpected image corruptions and noise perturbations. These unknown covariate shifts present significant challenges to deep learning based methods trained on "clean" images. This often results in unreliable predictions and poorly calibrated confidence, hence hindering clinical applicability. While recent methods have been developed to address specific issues such as confidence calibration or adversarial robustness, no single framework effectively tackles all these challenges simultaneously. To bridge this gap, we propose LaDiNE, a novel ensemble learning method combining the robustness of Vision Transformers with diffusion-based generative models for improved reliability in medical image classification. Specifically, transformer encoder blocks are used as hierarchical feature extractors that learn invariant features from images for each ensemble member, resulting in features that are robust to input perturbations. In addition, diffusion models are used as flexible density estimators to estimate member densities conditioned on the invariant features, leading to improved modeling of complex data distributions while retaining properly calibrated confidence. Extensive experiments on tuberculosis chest X-rays and melanoma skin cancer datasets demonstrate that LaDiNE achieves superior performance compared to a wide range of state-of-the-art methods by simultaneously improving prediction accuracy and confidence calibration under unseen noise, adversarial perturbations, and resolution degradation.

Pretraining with large-scale 3D volumes has a potential for improving the segmentation performance on a target medical image dataset where the training images and annotations are limited. Due to the high cost of acquiring pixel-level segmentation annotations on the large-scale pretraining dataset, pretraining with unannotated images is highly desirable. In this work, we propose a novel self-supervised learning strategy named Volume Fusion (VF) for pretraining 3D segmentation models. It fuses several random patches from a foreground sub-volume to a background sub-volume based on a predefined set of discrete fusion coefficients, and forces the model to predict the fusion coefficient of each voxel, which is formulated as a self-supervised segmentation task without manual annotations. Additionally, we propose a novel network architecture based on parallel convolution and transformer blocks that is suitable to be transferred to different downstream segmentation tasks with various scales of organs and lesions. The proposed model was pretrained with 110k unannotated 3D CT volumes, and experiments with different downstream segmentation targets including head and neck organs, thoracic/abdominal organs showed that our pretrained model largely outperformed training from scratch and several state-of-the-art self-supervised training methods and segmentation models. The code and pretrained model are available at https://github.com/openmedlab/MIS-FM.

Despite the considerable progress in automatic abdominal multi-organ segmentation from CT/MRI scans in recent years, a comprehensive evaluation of the models' capabilities is hampered by the lack of a large-scale benchmark from diverse clinical scenarios. Constraint by the high cost of collecting and labeling 3D medical data, most of the deep learning models to date are driven by datasets with a limited number of organs of interest or samples, which still limits the power of modern deep models and makes it difficult to provide a fully comprehensive and fair estimate of various methods. To mitigate the limitations, we present AMOS, a large-scale, diverse, clinical dataset for abdominal organ segmentation. AMOS provides 500 CT and 100 MRI scans collected from multi-center, multi-vendor, multi-modality, multi-phase, multi-disease patients, each with voxel-level annotations of 15 abdominal organs, providing challenging examples and test-bed for studying robust segmentation algorithms under diverse targets and scenarios. We further benchmark several state-of-the-art medical segmentation models to evaluate the status of the existing methods on this new challenging dataset. We have made our datasets, benchmark servers, and baselines publicly available, and hope to inspire future research. Information can be found at https://amos22.grand-challenge.org.

Computer-aided medical image segmentation has been applied widely in diagnosis and treatment to obtain clinically useful information of shapes and volumes of target organs and tissues. In the past several years, convolutional neural network (CNN) based methods (e.g., U-Net) have dominated this area, but still suffered from inadequate long-range information capturing. Hence, recent work presented computer vision Transformer variants for medical image segmentation tasks and obtained promising performances. Such Transformers model long-range dependency by computing pair-wise patch relations. However, they incur prohibitive computational costs, especially on 3D medical images (e.g., CT and MRI). In this paper, we propose a new method called Dilated Transformer, which conducts self-attention for pair-wise patch relations captured alternately in local and global scopes. Inspired by dilated convolution kernels, we conduct the global self-attention in a dilated manner, enlarging receptive fields without increasing the patches involved and thus reducing computational costs. Based on this design of Dilated Transformer, we construct a U-shaped encoder-decoder hierarchical architecture called D-Former for 3D medical image segmentation. Experiments on the Synapse and ACDC datasets show that our D-Former model, trained from scratch, outperforms various competitive CNN-based or Transformer-based segmentation models at a low computational cost without time-consuming per-training process.

Recent advances in computer vision have shown promising results in image generation. Diffusion probabilistic models in particular have generated realistic images from textual input, as demonstrated by DALL-E 2, Imagen and Stable Diffusion. However, their use in medicine, where image data typically comprises three-dimensional volumes, has not been systematically evaluated. Synthetic images may play a crucial role in privacy preserving artificial intelligence and can also be used to augment small datasets. Here we show that diffusion probabilistic models can synthesize high quality medical imaging data, which we show for Magnetic Resonance Images (MRI) and Computed Tomography (CT) images. We provide quantitative measurements of their performance through a reader study with two medical experts who rated the quality of the synthesized images in three categories: Realistic image appearance, anatomical correctness and consistency between slices. Furthermore, we demonstrate that synthetic images can be used in a self-supervised pre-training and improve the performance of breast segmentation models when data is scarce (dice score 0.91 vs. 0.95 without vs. with synthetic data). The code is publicly available on GitHub: https://github.com/FirasGit/medicaldiffusion.

While deep learning models have become the predominant method for medical image segmentation, they are typically not capable of generalizing to unseen segmentation tasks involving new anatomies, image modalities, or labels. Given a new segmentation task, researchers generally have to train or fine-tune models, which is time-consuming and poses a substantial barrier for clinical researchers, who often lack the resources and expertise to train neural networks. We present UniverSeg, a method for solving unseen medical segmentation tasks without additional training. Given a query image and example set of image-label pairs that define a new segmentation task, UniverSeg employs a new Cross-Block mechanism to produce accurate segmentation maps without the need for additional training. To achieve generalization to new tasks, we have gathered and standardized a collection of 53 open-access medical segmentation datasets with over 22,000 scans, which we refer to as MegaMedical. We used this collection to train UniverSeg on a diverse set of anatomies and imaging modalities. We demonstrate that UniverSeg substantially outperforms several related methods on unseen tasks, and thoroughly analyze and draw insights about important aspects of the proposed system. The UniverSeg source code and model weights are freely available at https://universeg.csail.mit.edu

Accurate medical image segmentation is essential for clinical diagnosis and treatment planning. While recent interactive foundation models (e.g., nnInteractive) enhance generalization through large-scale multimodal pretraining, they still depend on precise prompts and often perform below expectations in contexts that are underrepresented in their training data. We present AtlasSegFM, an atlas-guided framework that customizes available foundation models to clinical contexts with a single annotated example. The core innovations are: 1) a pipeline that provides context-aware prompts for foundation models via registration between a context atlas and query images, and 2) a test-time adapter to fuse predictions from both atlas registration and the foundation model. Extensive experiments across public and in-house datasets spanning multiple modalities and organs demonstrate that AtlasSegFM consistently improves segmentation, particularly for small, delicate structures. AtlasSegFM provides a lightweight, deployable solution one-shot customization of foundation models in real-world clinical workflows. The code will be made publicly available.

Medical image segmentation is a critical component of clinical workflows, enabling accurate diagnosis, treatment planning, and disease monitoring. However, despite the superior performance of transformer-based models over convolutional architectures, their limited interpretability remains a major obstacle to clinical trust and deployment. Existing explainable artificial intelligence (XAI) techniques, including gradient-based saliency methods and perturbation-based approaches, are often computationally expensive, require numerous forward passes, and frequently produce noisy or anatomically irrelevant explanations. To address these limitations, we propose XAI-CLIP, an ROI-guided perturbation framework that leverages multimodal vision-language model embeddings to localize clinically meaningful anatomical regions and guide the explanation process. By integrating language-informed region localization with medical image segmentation and applying targeted, region-aware perturbations, the proposed method generates clearer, boundary-aware saliency maps while substantially reducing computational overhead. Experiments conducted on the FLARE22 and CHAOS datasets demonstrate that XAI-CLIP achieves up to a 60\% reduction in runtime, a 44.6\% improvement in dice score, and a 96.7\% increase in Intersection-over-Union for occlusion-based explanations compared to conventional perturbation methods. Qualitative results further confirm cleaner and more anatomically consistent attribution maps with fewer artifacts, highlighting that the incorporation of multimodal vision-language representations into perturbation-based XAI frameworks significantly enhances both interpretability and efficiency, thereby enabling transparent and clinically deployable medical image segmentation systems.

For equitable deployment of AI tools in hospitals and healthcare facilities, we need Deep Segmentation Networks that offer high performance and can be trained on cost-effective GPUs with limited memory and large batch sizes. In this work, we propose Wave-GMS, a lightweight and efficient multi-scale generative model for medical image segmentation. Wave-GMS has a substantially smaller number of trainable parameters, does not require loading memory-intensive pretrained vision foundation models, and supports training with large batch sizes on GPUs with limited memory. We conducted extensive experiments on four publicly available datasets (BUS, BUSI, Kvasir-Instrument, and HAM10000), demonstrating that Wave-GMS achieves state-of-the-art segmentation performance with superior cross-domain generalizability, while requiring only ~2.6M trainable parameters. Code is available at https://github.com/ATPLab-LUMS/Wave-GMS.

Obtaining pixel-level annotations in the medical domain is both expensive and time-consuming, often requiring close collaboration between clinical experts and developers. Semi-supervised medical image segmentation aims to leverage limited annotated data alongside abundant unlabeled data to achieve accurate segmentation. However, existing semi-supervised methods often struggle to structure semantic distributions in the latent space due to noise introduced by pseudo-labels. In this paper, we propose a novel diffusion-based framework for semi-supervised medical image segmentation. Our method introduces a constraint into the latent structure of semantic labels during the denoising diffusion process by enforcing prototype-based contrastive consistency. Rather than explicitly delineating semantic boundaries, the model leverages class prototypes centralized semantic representations in the latent space as anchors. This strategy improves the robustness of dense predictions, particularly in the presence of noisy pseudo-labels. We also introduce a new publicly available benchmark: Multi-Object Segmentation in X-ray Angiography Videos (MOSXAV), which provides detailed, manually annotated segmentation ground truth for multiple anatomical structures in X-ray angiography videos. Extensive experiments on the EndoScapes2023 and MOSXAV datasets demonstrate that our method outperforms state-of-the-art medical image segmentation approaches under the semi-supervised learning setting. This work presents a robust and data-efficient diffusion model that offers enhanced flexibility and strong potential for a wide range of clinical applications.

State Space Models (SSMs), especially Mamba, have shown great promise in medical image segmentation due to their ability to model long-range dependencies with linear computational complexity. However, accurate medical image segmentation requires the effective learning of both multi-scale detailed feature representations and global contextual dependencies. Although existing works have attempted to address this issue by integrating CNNs and SSMs to leverage their respective strengths, they have not designed specialized modules to effectively capture multi-scale feature representations, nor have they adequately addressed the directional sensitivity problem when applying Mamba to 2D image data. To overcome these limitations, we propose a Multi-Scale Vision Mamba UNet model for medical image segmentation, termed MSVM-UNet. Specifically, by introducing multi-scale convolutions in the VSS blocks, we can more effectively capture and aggregate multi-scale feature representations from the hierarchical features of the VMamba encoder and better handle 2D visual data. Additionally, the large kernel patch expanding (LKPE) layers achieve more efficient upsampling of feature maps by simultaneously integrating spatial and channel information. Extensive experiments on the Synapse and ACDC datasets demonstrate that our approach is more effective than some state-of-the-art methods in capturing and aggregating multi-scale feature representations and modeling long-range dependencies between pixels.

UNet and its variants have been widely used in medical image segmentation. However, these models, especially those based on Transformer architectures, pose challenges due to their large number of parameters and computational loads, making them unsuitable for mobile health applications. Recently, State Space Models (SSMs), exemplified by Mamba, have emerged as competitive alternatives to CNN and Transformer architectures. Building upon this, we employ Mamba as a lightweight substitute for CNN and Transformer within UNet, aiming at tackling challenges stemming from computational resource limitations in real medical settings. To this end, we introduce the Lightweight Mamba UNet (LightM-UNet) that integrates Mamba and UNet in a lightweight framework. Specifically, LightM-UNet leverages the Residual Vision Mamba Layer in a pure Mamba fashion to extract deep semantic features and model long-range spatial dependencies, with linear computational complexity. Extensive experiments conducted on two real-world 2D/3D datasets demonstrate that LightM-UNet surpasses existing state-of-the-art literature. Notably, when compared to the renowned nnU-Net, LightM-UNet achieves superior segmentation performance while drastically reducing parameter and computation costs by 116x and 21x, respectively. This highlights the potential of Mamba in facilitating model lightweighting. Our code implementation is publicly available at https://github.com/MrBlankness/LightM-UNet.

Semantic medical image segmentation is a crucial part of both scientific research and clinical care. With enough labelled data, deep learning models can be trained to accurately automate specific medical image segmentation tasks. However, manually segmenting images to create training data is highly labor intensive. In this paper, we present ScribblePrompt, an interactive segmentation framework for medical imaging that enables human annotators to segment unseen structures using scribbles, clicks, and bounding boxes. Scribbles are an intuitive and effective form of user interaction for complex tasks, however most existing methods focus on click-based interactions. We introduce algorithms for simulating realistic scribbles that enable training models that are amenable to multiple types of interaction. To achieve generalization to new tasks, we train on a diverse collection of 65 open-access biomedical datasets -- using both real and synthetic labels. We test ScribblePrompt on multiple network architectures and unseen datasets, and demonstrate that it can be used in real-time on a single CPU. We evaluate ScribblePrompt using manually-collected scribbles, simulated interactions, and a user study. ScribblePrompt outperforms existing methods in all our evaluations. In the user study, ScribblePrompt reduced annotation time by 28% while improving Dice by 15% compared to existing methods. We showcase ScribblePrompt in an online demo and provide code at https://scribbleprompt.csail.mit.edu

Even though convolutional neural networks (CNNs) are driving progress in medical image segmentation, standard models still have some drawbacks. First, the use of multi-scale approaches, i.e., encoder-decoder architectures, leads to a redundant use of information, where similar low-level features are extracted multiple times at multiple scales. Second, long-range feature dependencies are not efficiently modeled, resulting in non-optimal discriminative feature representations associated with each semantic class. In this paper we attempt to overcome these limitations with the proposed architecture, by capturing richer contextual dependencies based on the use of guided self-attention mechanisms. This approach is able to integrate local features with their corresponding global dependencies, as well as highlight interdependent channel maps in an adaptive manner. Further, the additional loss between different modules guides the attention mechanisms to neglect irrelevant information and focus on more discriminant regions of the image by emphasizing relevant feature associations. We evaluate the proposed model in the context of semantic segmentation on three different datasets: abdominal organs, cardiovascular structures and brain tumors. A series of ablation experiments support the importance of these attention modules in the proposed architecture. In addition, compared to other state-of-the-art segmentation networks our model yields better segmentation performance, increasing the accuracy of the predictions while reducing the standard deviation. This demonstrates the efficiency of our approach to generate precise and reliable automatic segmentations of medical images. Our code is made publicly available at https://github.com/sinAshish/Multi-Scale-Attention

Segment Anything Model (SAM) has demonstrated impressive zero-shot performance and brought a range of unexplored capabilities to natural image segmentation tasks. However, as a very important branch of image segmentation, the performance of SAM remains uncertain when applied to medical image segmentation due to the significant differences between natural images and medical images. Meanwhile, it is harsh to meet the SAM's requirements of extra prompts provided, such as points or boxes to specify medical regions. In this paper, we propose a novel self-prompt SAM adaptation framework for medical image segmentation, named Self-Prompt-SAM. We design a multi-scale prompt generator combined with the image encoder in SAM to generate auxiliary masks. Then, we use the auxiliary masks to generate bounding boxes as box prompts and use Distance Transform to select the most central points as point prompts. Meanwhile, we design a 3D depth-fused adapter (DfusedAdapter) and inject the DFusedAdapter into each transformer in the image encoder and mask decoder to enable pre-trained 2D SAM models to extract 3D information and adapt to 3D medical images. Extensive experiments demonstrate that our method achieves state-of-the-art performance and outperforms nnUNet by 2.3% on AMOS2022, 1.6% on ACDCand 0.5% on Synapse datasets.

Despite that deep learning has achieved state-of-the-art performance for medical image segmentation, its success relies on a large set of manually annotated images for training that are expensive to acquire. In this paper, we propose an annotation-efficient learning framework for segmentation tasks that avoids annotations of training images, where we use an improved Cycle-Consistent Generative Adversarial Network (GAN) to learn from a set of unpaired medical images and auxiliary masks obtained either from a shape model or public datasets. We first use the GAN to generate pseudo labels for our training images under the implicit high-level shape constraint represented by a Variational Auto-encoder (VAE)-based discriminator with the help of the auxiliary masks, and build a Discriminator-guided Generator Channel Calibration (DGCC) module which employs our discriminator's feedback to calibrate the generator for better pseudo labels. To learn from the pseudo labels that are noisy, we further introduce a noise-robust iterative learning method using noise-weighted Dice loss. We validated our framework with two situations: objects with a simple shape model like optic disc in fundus images and fetal head in ultrasound images, and complex structures like lung in X-Ray images and liver in CT images. Experimental results demonstrated that 1) Our VAE-based discriminator and DGCC module help to obtain high-quality pseudo labels. 2) Our proposed noise-robust learning method can effectively overcome the effect of noisy pseudo labels. 3) The segmentation performance of our method without using annotations of training images is close or even comparable to that of learning from human annotations.

Accurate computer-aided polyp detection and segmentation during colonoscopy examinations can help endoscopists resect abnormal tissue and thereby decrease chances of polyps growing into cancer. Towards developing a fully automated model for pixel-wise polyp segmentation, we propose ResUNet++, which is an improved ResUNet architecture for colonoscopic image segmentation. Our experimental evaluations show that the suggested architecture produces good segmentation results on publicly available datasets. Furthermore, ResUNet++ significantly outperforms U-Net and ResUNet, two key state-of-the-art deep learning architectures, by achieving high evaluation scores with a dice coefficient of 81.33%, and a mean Intersection over Union (mIoU) of 79.27% for the Kvasir-SEG dataset and a dice coefficient of 79.55%, and a mIoU of 79.62% with CVC-612 dataset.

The integration of deep learning systems into the medical domain has been hindered by the resource-intensive process of data annotation and the inability of these systems to generalize to different data distributions. Foundation models, which are models pre-trained on large datasets, have emerged as a solution to reduce reliance on annotated data and enhance model generalizability and robustness. DINOv2, an open-source foundation model pre-trained with self-supervised learning on 142 million curated natural images, excels in extracting general-purpose visual representations, exhibiting promising capabilities across various vision tasks. Nevertheless, a critical question remains unanswered regarding DINOv2's adaptability to radiological imaging, and the clarity on whether its features are sufficiently general to benefit radiology image analysis is yet to be established. Therefore, this study comprehensively evaluates DINOv2 for radiology, conducting over 100 experiments across diverse modalities (X-ray, CT, and MRI). Tasks include disease classification and organ segmentation on both 2D and 3D images, evaluated under different settings like kNN, few-shot learning, linear-probing, end-to-end fine-tuning, and parameter-efficient fine-tuning, to measure the effectiveness and generalizability of the DINOv2 feature embeddings. Comparative analyses with established medical image analysis models, U-Net and TransUnet for segmentation, and CNN and ViT models pre-trained via supervised, weakly supervised, and self-supervised learning for classification, reveal DINOv2's superior performance in segmentation tasks and competitive results in disease classification. The findings contribute insights to potential avenues for optimizing pre-training strategies for medical imaging and enhancing the broader understanding of DINOv2's role in bridging the gap between natural and radiological image analysis.