Daily Papers

Medical imaging analysis faces challenges such as data scarcity, high annotation costs, and privacy concerns. This paper introduces the Medical AI for Synthetic Imaging (MAISI), an innovative approach using the diffusion model to generate synthetic 3D computed tomography (CT) images to address those challenges. MAISI leverages the foundation volume compression network and the latent diffusion model to produce high-resolution CT images (up to a landmark volume dimension of 512 x 512 x 768 ) with flexible volume dimensions and voxel spacing. By incorporating ControlNet, MAISI can process organ segmentation, including 127 anatomical structures, as additional conditions and enables the generation of accurately annotated synthetic images that can be used for various downstream tasks. Our experiment results show that MAISI's capabilities in generating realistic, anatomically accurate images for diverse regions and conditions reveal its promising potential to mitigate challenges using synthetic data.

Medical imaging plays a crucial role in diagnosis, with radiology reports serving as vital documentation. Automating report generation has emerged as a critical need to alleviate the workload of radiologists. While machine learning has facilitated report generation for 2D medical imaging, extending this to 3D has been unexplored due to computational complexity and data scarcity. We introduce the first method to generate radiology reports for 3D medical imaging, specifically targeting chest CT volumes. Given the absence of comparable methods, we establish a baseline using an advanced 3D vision encoder in medical imaging to demonstrate our method's effectiveness, which leverages a novel auto-regressive causal transformer. Furthermore, recognizing the benefits of leveraging information from previous visits, we augment CT2Rep with a cross-attention-based multi-modal fusion module and hierarchical memory, enabling the incorporation of longitudinal multimodal data. Access our code at https://github.com/ibrahimethemhamamci/CT2Rep

Medical imaging papers often focus on methodology, but the quality of the algorithms and the validity of the conclusions are highly dependent on the datasets used. As creating datasets requires a lot of effort, researchers often use publicly available datasets, there is however no adopted standard for citing the datasets used in scientific papers, leading to difficulty in tracking dataset usage. In this work, we present two open-source tools we created that could help with the detection of dataset usage, a pipeline https://github.com/TheoSourget/Public_Medical_Datasets_References using OpenAlex and full-text analysis, and a PDF annotation software https://github.com/TheoSourget/pdf_annotator used in our study to manually label the presence of datasets. We applied both tools on a study of the usage of 20 publicly available medical datasets in papers from MICCAI and MIDL. We compute the proportion and the evolution between 2013 and 2023 of 3 types of presence in a paper: cited, mentioned in the full text, cited and mentioned. Our findings demonstrate the concentration of the usage of a limited set of datasets. We also highlight different citing practices, making the automation of tracking difficult.

Recent work has investigated the distributions of learned convolution filters through a large-scale study containing hundreds of heterogeneous image models. Surprisingly, on average, the distributions only show minor drifts in comparisons of various studied dimensions including the learned task, image domain, or dataset. However, among the studied image domains, medical imaging models appeared to show significant outliers through "spikey" distributions, and, therefore, learn clusters of highly specific filters different from other domains. Following this observation, we study the collected medical imaging models in more detail. We show that instead of fundamental differences, the outliers are due to specific processing in some architectures. Quite the contrary, for standardized architectures, we find that models trained on medical data do not significantly differ in their filter distributions from similar architectures trained on data from other domains. Our conclusions reinforce previous hypotheses stating that pre-training of imaging models can be done with any kind of diverse image data.

Concerns about the reproducibility of deep learning research are more prominent than ever, with no clear solution in sight. The relevance of machine learning research can only be improved if we also employ empirical rigor that incorporates reproducibility guidelines, especially so in the medical imaging field. The Medical Imaging with Deep Learning (MIDL) conference has made advancements in this direction by advocating open access, and recently also recommending authors to make their code public - both aspects being adopted by the majority of the conference submissions. This helps the reproducibility of the methods, however, there is currently little or no support for further evaluation of these supplementary material, making them vulnerable to poor quality, which affects the impact of the entire submission. We have evaluated all accepted full paper submissions to MIDL between 2018 and 2022 using established, but slightly adjusted guidelines on reproducibility and the quality of the public repositories. The evaluations show that publishing repositories and using public datasets are becoming more popular, which helps traceability, but the quality of the repositories has not improved over the years, leaving room for improvement in every aspect of designing repositories. Merely 22% of all submissions contain a repository that were deemed repeatable using our evaluations. From the commonly encountered issues during the evaluations, we propose a set of guidelines for machine learning-related research for medical imaging applications, adjusted specifically for future submissions to MIDL.

Reconstructing medical images from partial measurements is an important inverse problem in Computed Tomography (CT) and Magnetic Resonance Imaging (MRI). Existing solutions based on machine learning typically train a model to directly map measurements to medical images, leveraging a training dataset of paired images and measurements. These measurements are typically synthesized from images using a fixed physical model of the measurement process, which hinders the generalization capability of models to unknown measurement processes. To address this issue, we propose a fully unsupervised technique for inverse problem solving, leveraging the recently introduced score-based generative models. Specifically, we first train a score-based generative model on medical images to capture their prior distribution. Given measurements and a physical model of the measurement process at test time, we introduce a sampling method to reconstruct an image consistent with both the prior and the observed measurements. Our method does not assume a fixed measurement process during training, and can thus be flexibly adapted to different measurement processes at test time. Empirically, we observe comparable or better performance to supervised learning techniques in several medical imaging tasks in CT and MRI, while demonstrating significantly better generalization to unknown measurement processes.

Medical image segmentation is crucial for many healthcare tasks, including disease diagnosis and treatment planning. One key area is the segmentation of skin lesions, which is vital for diagnosing skin cancer and monitoring patients. In this context, this paper introduces SegDT, a new segmentation model based on diffusion transformer (DiT). SegDT is designed to work on low-cost hardware and incorporates Rectified Flow, which improves the generation quality at reduced inference steps and maintains the flexibility of standard diffusion models. Our method is evaluated on three benchmarking datasets and compared against several existing works, achieving state-of-the-art results while maintaining fast inference speeds. This makes the proposed model appealing for real-world medical applications. This work advances the performance and capabilities of deep learning models in medical image analysis, enabling faster, more accurate diagnostic tools for healthcare professionals. The code is made publicly available at https://github.com/Bekhouche/SegDT{GitHub}.

Recent advances in generative AI have brought incredible breakthroughs in several areas, including medical imaging. These generative models have tremendous potential not only to help safely share medical data via synthetic datasets but also to perform an array of diverse applications, such as anomaly detection, image-to-image translation, denoising, and MRI reconstruction. However, due to the complexity of these models, their implementation and reproducibility can be difficult. This complexity can hinder progress, act as a use barrier, and dissuade the comparison of new methods with existing works. In this study, we present MONAI Generative Models, a freely available open-source platform that allows researchers and developers to easily train, evaluate, and deploy generative models and related applications. Our platform reproduces state-of-art studies in a standardised way involving different architectures (such as diffusion models, autoregressive transformers, and GANs), and provides pre-trained models for the community. We have implemented these models in a generalisable fashion, illustrating that their results can be extended to 2D or 3D scenarios, including medical images with different modalities (like CT, MRI, and X-Ray data) and from different anatomical areas. Finally, we adopt a modular and extensible approach, ensuring long-term maintainability and the extension of current applications for future features.

With the rapid advancement of deep learning, particularly in the field of medical image analysis, an increasing number of Vision-Language Models (VLMs) are being widely applied to solve complex health and biomedical challenges. However, existing research has primarily focused on specific tasks or single modalities, which limits their applicability and generalization across diverse medical scenarios. To address this challenge, we propose UMIT, a unified multi-modal, multi-task VLM designed specifically for medical imaging tasks. UMIT is able to solve various tasks, including visual question answering, disease detection, and medical report generation. In addition, it is applicable to multiple imaging modalities (e.g., X-ray, CT and PET), covering a wide range of applications from basic diagnostics to complex lesion analysis. Moreover, UMIT supports both English and Chinese, expanding its applicability globally and ensuring accessibility to healthcare services in different linguistic contexts. To enhance the model's adaptability and task-handling capability, we design a unique two-stage training strategy and fine-tune UMIT with designed instruction templates. Through extensive empirical evaluation, UMIT outperforms previous methods in five tasks across multiple datasets. The performance of UMIT indicates that it can significantly enhance diagnostic accuracy and workflow efficiency, thus providing effective solutions for medical imaging applications.

The progress in generative models, particularly Generative Adversarial Networks (GANs), opened new possibilities for image generation but raised concerns about potential malicious uses, especially in sensitive areas like medical imaging. This study introduces MITS-GAN, a novel approach to prevent tampering in medical images, with a specific focus on CT scans. The approach disrupts the output of the attacker's CT-GAN architecture by introducing finely tuned perturbations that are imperceptible to the human eye. Specifically, the proposed approach involves the introduction of appropriate Gaussian noise to the input as a protective measure against various attacks. Our method aims to enhance tamper resistance, comparing favorably to existing techniques. Experimental results on a CT scan demonstrate MITS-GAN's superior performance, emphasizing its ability to generate tamper-resistant images with negligible artifacts. As image tampering in medical domains poses life-threatening risks, our proactive approach contributes to the responsible and ethical use of generative models. This work provides a foundation for future research in countering cyber threats in medical imaging. Models and codes are publicly available on https://iplab.dmi.unict.it/MITS-GAN-2024/.

Deep learning in medical imaging has the potential to minimize the risk of diagnostic errors, reduce radiologist workload, and accelerate diagnosis. Training such deep learning models requires large and accurate datasets, with annotations for all training samples. However, in the medical imaging domain, annotated datasets for specific tasks are often small due to the high complexity of annotations, limited access, or the rarity of diseases. To address this challenge, deep learning models can be pre-trained on large image datasets without annotations using methods from the field of self-supervised learning. After pre-training, small annotated datasets are sufficient to fine-tune the models for a specific task. The most popular self-supervised pre-training approaches in medical imaging are based on contrastive learning. However, recent studies in natural image processing indicate a strong potential for masked autoencoder approaches. Our work compares state-of-the-art contrastive learning methods with the recently introduced masked autoencoder approach "SparK" for convolutional neural networks (CNNs) on medical images. Therefore we pre-train on a large unannotated CT image dataset and fine-tune on several CT classification tasks. Due to the challenge of obtaining sufficient annotated training data in medical imaging, it is of particular interest to evaluate how the self-supervised pre-training methods perform when fine-tuning on small datasets. By experimenting with gradually reducing the training dataset size for fine-tuning, we find that the reduction has different effects depending on the type of pre-training chosen. The SparK pre-training method is more robust to the training dataset size than the contrastive methods. Based on our results, we propose the SparK pre-training for medical imaging tasks with only small annotated datasets.

Large-scale medical imaging datasets have accelerated development of artificial intelligence tools for clinical decision support. However, the large size of these datasets is a bottleneck for users with limited storage and bandwidth. Many users may not even require such large datasets as AI models are often trained on lower resolution images. If users could directly download at their desired resolution, storage and bandwidth requirements would significantly decrease. However, it is impossible to anticipate every users' requirements and impractical to store the data at multiple resolutions. What if we could store images at a single resolution but send them at different ones? We propose MIST, an open-source framework to operationalize progressive resolution for streaming medical images at multiple resolutions from a single high-resolution copy. We demonstrate that MIST can dramatically reduce imaging infrastructure inefficiencies for hosting and streaming medical images by >90%, while maintaining diagnostic quality for deep learning applications.

In this review, we explore the potential applications of Artificial General Intelligence (AGI) models in healthcare, focusing on foundational Large Language Models (LLMs), Large Vision Models, and Large Multimodal Models. We emphasize the importance of integrating clinical expertise, domain knowledge, and multimodal capabilities into AGI models. In addition, we lay out key roadmaps that guide the development and deployment of healthcare AGI models. Throughout the review, we provide critical perspectives on the potential challenges and pitfalls associated with deploying large-scale AGI models in the medical field. This comprehensive review aims to offer insights into the future implications of AGI in medical imaging, healthcare and beyond.

In some medical imaging tasks and other settings where only small parts of the image are informative for the classification task, traditional CNNs can sometimes struggle to generalise. Manually annotated Regions of Interest (ROI) are sometimes used to isolate the most informative parts of the image. However, these are expensive to collect and may vary significantly across annotators. To overcome these issues, we propose a framework that employs saliency maps to obtain soft spatial attention masks that modulate the image features at different scales. We refer to our method as Adversarial Counterfactual Attention (ACAT). ACAT increases the baseline classification accuracy of lesions in brain CT scans from 71.39% to 72.55% and of COVID-19 related findings in lung CT scans from 67.71% to 70.84% and exceeds the performance of competing methods. We investigate the best way to generate the saliency maps employed in our architecture and propose a way to obtain them from adversarially generated counterfactual images. They are able to isolate the area of interest in brain and lung CT scans without using any manual annotations. In the task of localising the lesion location out of 6 possible regions, they obtain a score of 65.05% on brain CT scans, improving the score of 61.29% obtained with the best competing method.

Multimodal large language models (MLLMs) hold significant potential in the medical field, but their capabilities are often limited by insufficient data in certain medical domains, highlighting the need for understanding what kinds of images can be used by MLLMs for generalization. Current research suggests that multi-task training outperforms single-task as different tasks can benefit each other, but they often overlook the internal relationships within these tasks, providing limited guidance on selecting datasets to enhance specific tasks. To analyze this phenomenon, we attempted to employ compositional generalization (CG)-the ability of models to understand novel combinations by recombining learned elements-as a guiding framework. Since medical images can be precisely defined by Modality, Anatomical area, and Task, naturally providing an environment for exploring CG. Therefore, we assembled 106 medical datasets to create Med-MAT for comprehensive experiments. The experiments confirmed that MLLMs can use CG to understand unseen medical images and identified CG as one of the main drivers of the generalization observed in multi-task training. Additionally, further studies demonstrated that CG effectively supports datasets with limited data and delivers consistent performance across different backbones, highlighting its versatility and broad applicability. Med-MAT is publicly available at https://github.com/FreedomIntelligence/Med-MAT.

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.

Medical Visual Language Models have shown great potential in various healthcare applications, including medical image captioning and diagnostic assistance. However, most existing models rely on text-based instructions, limiting their usability in real-world clinical environments especially in scenarios such as surgery, text-based interaction is often impractical for physicians. In addition, current medical image analysis models typically lack comprehensive reasoning behind their predictions, which reduces their reliability for clinical decision-making. Given that medical diagnosis errors can have life-changing consequences, there is a critical need for interpretable and rational medical assistance. To address these challenges, we introduce an end-to-end speech-driven medical VLM, SilVar-Med, a multimodal medical image assistant that integrates speech interaction with VLMs, pioneering the task of voice-based communication for medical image analysis. In addition, we focus on the interpretation of the reasoning behind each prediction of medical abnormalities with a proposed reasoning dataset. Through extensive experiments, we demonstrate a proof-of-concept study for reasoning-driven medical image interpretation with end-to-end speech interaction. We believe this work will advance the field of medical AI by fostering more transparent, interactive, and clinically viable diagnostic support systems. Our code and dataset are publicly available at SiVar-Med.

The success of automated medical image analysis depends on large-scale and expert-annotated training sets. Unsupervised domain adaptation (UDA) has been raised as a promising approach to alleviate the burden of labeled data collection. However, they generally operate under the closed-set adaptation setting assuming an identical label set between the source and target domains, which is over-restrictive in clinical practice where new classes commonly exist across datasets due to taxonomic inconsistency. While several methods have been presented to tackle both domain shifts and incoherent label sets, none of them take into account the common characteristics of the two issues and consider the learning dynamics along network training. In this work, we propose optimization trajectory distillation, a unified approach to address the two technical challenges from a new perspective. It exploits the low-rank nature of gradient space and devises a dual-stream distillation algorithm to regularize the learning dynamics of insufficiently annotated domain and classes with the external guidance obtained from reliable sources. Our approach resolves the issue of inadequate navigation along network optimization, which is the major obstacle in the taxonomy adaptive cross-domain adaptation scenario. We evaluate the proposed method extensively on several tasks towards various endpoints with clinical and open-world significance. The results demonstrate its effectiveness and improvements over previous methods.

Data augmentation is essential in medical imaging for improving classification accuracy, lesion detection, and organ segmentation under limited data conditions. However, two significant challenges remain. First, a pronounced domain gap between natural photographs and medical images can distort critical disease features. Second, augmentation studies in medical imaging are fragmented and limited to single tasks or architectures, leaving the benefits of advanced mix-based strategies unclear. To address these challenges, we propose a unified evaluation framework with six mix-based augmentation methods integrated with both convolutional and transformer backbones on brain tumour MRI and eye disease fundus datasets. Our contributions are threefold. (1) We introduce MediAug, a comprehensive and reproducible benchmark for advanced data augmentation in medical imaging. (2) We systematically evaluate MixUp, YOCO, CropMix, CutMix, AugMix, and SnapMix with ResNet-50 and ViT-B backbones. (3) We demonstrate through extensive experiments that MixUp yields the greatest improvement on the brain tumor classification task for ResNet-50 with 79.19% accuracy and SnapMix yields the greatest improvement for ViT-B with 99.44% accuracy, and that YOCO yields the greatest improvement on the eye disease classification task for ResNet-50 with 91.60% accuracy and CutMix yields the greatest improvement for ViT-B with 97.94% accuracy. Code will be available at https://github.com/AIGeeksGroup/MediAug.

Segment Anything Model (SAM) has achieved impressive results for natural image segmentation with input prompts such as points and bounding boxes. Its success largely owes to massive labeled training data. However, directly applying SAM to medical image segmentation cannot perform well because SAM lacks medical knowledge -- it does not use medical images for training. To incorporate medical knowledge into SAM, we introduce SA-Med2D-20M, a large-scale segmentation dataset of 2D medical images built upon numerous public and private datasets. It consists of 4.6 million 2D medical images and 19.7 million corresponding masks, covering almost the whole body and showing significant diversity. This paper describes all the datasets collected in SA-Med2D-20M and details how to process these datasets. Furthermore, comprehensive statistics of SA-Med2D-20M are presented to facilitate the better use of our dataset, which can help the researchers build medical vision foundation models or apply their models to downstream medical applications. We hope that the large scale and diversity of SA-Med2D-20M can be leveraged to develop medical artificial intelligence for enhancing diagnosis, medical image analysis, knowledge sharing, and education. The data with the redistribution license is publicly available at https://github.com/OpenGVLab/SAM-Med2D.

This paper presents a comprehensive evaluation of GPT-4V's capabilities across diverse medical imaging tasks, including Radiology Report Generation, Medical Visual Question Answering (VQA), and Visual Grounding. While prior efforts have explored GPT-4V's performance in medical image analysis, to the best of our knowledge, our study represents the first quantitative evaluation on publicly available benchmarks. Our findings highlight GPT-4V's potential in generating descriptive reports for chest X-ray images, particularly when guided by well-structured prompts. Meanwhile, its performance on the MIMIC-CXR dataset benchmark reveals areas for improvement in certain evaluation metrics, such as CIDEr. In the domain of Medical VQA, GPT-4V demonstrates proficiency in distinguishing between question types but falls short of the VQA-RAD benchmark in terms of accuracy. Furthermore, our analysis finds the limitations of conventional evaluation metrics like the BLEU scores, advocating for the development of more semantically robust assessment methods. In the field of Visual Grounding, GPT-4V exhibits preliminary promise in recognizing bounding boxes, but its precision is lacking, especially in identifying specific medical organs and signs. Our evaluation underscores the significant potential of GPT-4V in the medical imaging domain, while also emphasizing the need for targeted refinements to fully unlock its capabilities.

AI is revolutionizing MRI along the acquisition and processing chain. Advanced AI frameworks have been developed to apply AI in various successive tasks, such as image reconstruction, quantitative parameter map estimation, and image segmentation. Existing frameworks are often designed to perform tasks independently or are focused on specific models or datasets, limiting generalization. We introduce ATOMMIC, an open-source toolbox that streamlines AI applications for accelerated MRI reconstruction and analysis. ATOMMIC implements several tasks using DL networks and enables MultiTask Learning (MTL) to perform related tasks integrated, targeting generalization in the MRI domain. We first review the current state of AI frameworks for MRI through a comprehensive literature search and by parsing 12,479 GitHub repositories. We benchmark 25 DL models on eight publicly available datasets to present distinct applications of ATOMMIC on accelerated MRI reconstruction, image segmentation, quantitative parameter map estimation, and joint accelerated MRI reconstruction and image segmentation utilizing MTL. Our findings demonstrate that ATOMMIC is the only MTL framework with harmonized complex-valued and real-valued data support. Evaluations on single tasks show that physics-based models, which enforce data consistency by leveraging the physical properties of MRI, outperform other models in reconstructing highly accelerated acquisitions. Physics-based models that produce high reconstruction quality can accurately estimate quantitative parameter maps. When high-performing reconstruction models are combined with robust segmentation networks utilizing MTL, performance is improved in both tasks. ATOMMIC facilitates MRI reconstruction and analysis by standardizing workflows, enhancing data interoperability, integrating unique features like MTL, and effectively benchmarking DL models.

Self-supervised learning (SSL) has emerged as a promising paradigm in medical imaging, addressing the chronic challenge of limited labeled data in healthcare settings. While SSL has shown impressive results, existing studies in the medical domain are often limited in scope, focusing on specific datasets or modalities, or evaluating only isolated aspects of model performance. This fragmented evaluation approach poses a significant challenge, as models deployed in critical medical settings must not only achieve high accuracy but also demonstrate robust performance and generalizability across diverse datasets and varying conditions. To address this gap, we present a comprehensive evaluation of SSL methods within the medical domain, with a particular focus on robustness and generalizability. Using the MedMNIST dataset collection as a standardized benchmark, we evaluate 8 major SSL methods across 11 different medical datasets. Our study provides an in-depth analysis of model performance in both in-domain scenarios and the detection of out-of-distribution (OOD) samples, while exploring the effect of various initialization strategies, model architectures, and multi-domain pre-training. We further assess the generalizability of SSL methods through cross-dataset evaluations and the in-domain performance with varying label proportions (1%, 10%, and 100%) to simulate real-world scenarios with limited supervision. We hope this comprehensive benchmark helps practitioners and researchers make more informed decisions when applying SSL methods to medical applications.

In this work, we present MedImageInsight, an open-source medical imaging embedding model. MedImageInsight is trained on medical images with associated text and labels across a diverse collection of domains, including X-Ray, CT, MRI, dermoscopy, OCT, fundus photography, ultrasound, histopathology, and mammography. Rigorous evaluations demonstrate MedImageInsight's ability to achieve state-of-the-art (SOTA) or human expert level performance across classification, image-image search, and fine-tuning tasks. Specifically, on public datasets, MedImageInsight achieves SOTA in CT 3D medical image retrieval, as well as SOTA in disease classification and search for chest X-ray, dermatology, and OCT imaging. Furthermore, MedImageInsight achieves human expert performance in bone age estimation (on both public and partner data), as well as AUC above 0.9 in most other domains. When paired with a text decoder, MedImageInsight achieves near SOTA level single image report findings generation with less than 10\% the parameters of other models. Compared to fine-tuning GPT-4o with only MIMIC-CXR data for the same task, MedImageInsight outperforms in clinical metrics, but underperforms on lexical metrics where GPT-4o sets a new SOTA. Importantly for regulatory purposes, MedImageInsight can generate ROC curves, adjust sensitivity and specificity based on clinical need, and provide evidence-based decision support through image-image search (which can also enable retrieval augmented generation). In an independent clinical evaluation of image-image search in chest X-ray, MedImageInsight outperformed every other publicly available foundation model evaluated by large margins (over 6 points AUC), and significantly outperformed other models in terms of AI fairness (across age and gender). We hope releasing MedImageInsight will help enhance collective progress in medical imaging AI research and development.

Foundation models for interactive segmentation in 2D natural images and videos have sparked significant interest in building 3D foundation models for medical imaging. However, the domain gaps and clinical use cases for 3D medical imaging require a dedicated model that diverges from existing 2D solutions. Specifically, such foundation models should support a full workflow that can actually reduce human effort. Treating 3D medical images as sequences of 2D slices and reusing interactive 2D foundation models seems straightforward, but 2D annotation is too time-consuming for 3D tasks. Moreover, for large cohort analysis, it's the highly accurate automatic segmentation models that reduce the most human effort. However, these models lack support for interactive corrections and lack zero-shot ability for novel structures, which is a key feature of "foundation". While reusing pre-trained 2D backbones in 3D enhances zero-shot potential, their performance on complex 3D structures still lags behind leading 3D models. To address these issues, we present VISTA3D, Versatile Imaging SegmenTation and Annotation model, that targets to solve all these challenges and requirements with one unified foundation model. VISTA3D is built on top of the well-established 3D segmentation pipeline, and it is the first model to achieve state-of-the-art performance in both 3D automatic (supporting 127 classes) and 3D interactive segmentation, even when compared with top 3D expert models on large and diverse benchmarks. Additionally, VISTA3D's 3D interactive design allows efficient human correction, and a novel 3D supervoxel method that distills 2D pretrained backbones grants VISTA3D top 3D zero-shot performance. We believe the model, recipe, and insights represent a promising step towards a clinically useful 3D foundation model. Code and weights are publicly available at https://github.com/Project-MONAI/VISTA.

Inpainting has recently been proposed as a successful deep learning technique for unsupervised medical image model discovery. The masks used for inpainting are generally independent of the dataset and are not tailored to perform on different given classes of anatomy. In this work, we introduce a method for generating shape-aware masks for inpainting, which aims at learning the statistical shape prior. We hypothesize that although the variation of masks improves the generalizability of inpainting models, the shape of the masks should follow the topology of the organs of interest. Hence, we propose an unsupervised guided masking approach based on an off-the-shelf inpainting model and a superpixel over-segmentation algorithm to generate a wide range of shape-dependent masks. Experimental results on abdominal MR image reconstruction show the superiority of our proposed masking method over standard methods using square-shaped or dataset of irregular shape masks.

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.

Recent advancements in prompt-based medical image segmentation have enabled clinicians to identify tumors using simple input like bounding boxes or text prompts. However, existing methods face challenges when doctors need to interact through natural language or when position reasoning is required - understanding spatial relationships between anatomical structures and pathologies. We present PRS-Med, a framework that integrates vision-language models with segmentation capabilities to generate both accurate segmentation masks and corresponding spatial reasoning outputs. Additionally, we introduce the MMRS dataset (Multimodal Medical in Positional Reasoning Segmentation), which provides diverse, spatially-grounded question-answer pairs to address the lack of position reasoning data in medical imaging. PRS-Med demonstrates superior performance across six imaging modalities (CT, MRI, X-ray, ultrasound, endoscopy, RGB), significantly outperforming state-of-the-art methods in both segmentation accuracy and position reasoning. Our approach enables intuitive doctor-system interaction through natural language, facilitating more efficient diagnoses. Our dataset pipeline, model, and codebase will be released to foster further research in spatially-aware multimodal reasoning for medical applications.

Obtaining large pre-trained models that can be fine-tuned to new tasks with limited annotated samples has remained an open challenge for medical imaging data. While pre-trained deep networks on ImageNet and vision-language foundation models trained on web-scale data are prevailing approaches, their effectiveness on medical tasks is limited due to the significant domain shift between natural and medical images. To bridge this gap, we introduce LVM-Med, the first family of deep networks trained on large-scale medical datasets. We have collected approximately 1.3 million medical images from 55 publicly available datasets, covering a large number of organs and modalities such as CT, MRI, X-ray, and Ultrasound. We benchmark several state-of-the-art self-supervised algorithms on this dataset and propose a novel self-supervised contrastive learning algorithm using a graph-matching formulation. The proposed approach makes three contributions: (i) it integrates prior pair-wise image similarity metrics based on local and global information; (ii) it captures the structural constraints of feature embeddings through a loss function constructed via a combinatorial graph-matching objective; and (iii) it can be trained efficiently end-to-end using modern gradient-estimation techniques for black-box solvers. We thoroughly evaluate the proposed LVM-Med on 15 downstream medical tasks ranging from segmentation and classification to object detection, and both for the in and out-of-distribution settings. LVM-Med empirically outperforms a number of state-of-the-art supervised, self-supervised, and foundation models. For challenging tasks such as Brain Tumor Classification or Diabetic Retinopathy Grading, LVM-Med improves previous vision-language models trained on 1 billion masks by 6-7% while using only a ResNet-50.

This study presents Latent Diffusion Autoencoder (LDAE), a novel encoder-decoder diffusion-based framework for efficient and meaningful unsupervised learning in medical imaging, focusing on Alzheimer disease (AD) using brain MR from the ADNI database as a case study. Unlike conventional diffusion autoencoders operating in image space, LDAE applies the diffusion process in a compressed latent representation, improving computational efficiency and making 3D medical imaging representation learning tractable. To validate the proposed approach, we explore two key hypotheses: (i) LDAE effectively captures meaningful semantic representations on 3D brain MR associated with AD and ageing, and (ii) LDAE achieves high-quality image generation and reconstruction while being computationally efficient. Experimental results support both hypotheses: (i) linear-probe evaluations demonstrate promising diagnostic performance for AD (ROC-AUC: 90%, ACC: 84%) and age prediction (MAE: 4.1 years, RMSE: 5.2 years); (ii) the learned semantic representations enable attribute manipulation, yielding anatomically plausible modifications; (iii) semantic interpolation experiments show strong reconstruction of missing scans, with SSIM of 0.969 (MSE: 0.0019) for a 6-month gap. Even for longer gaps (24 months), the model maintains robust performance (SSIM > 0.93, MSE < 0.004), indicating an ability to capture temporal progression trends; (iv) compared to conventional diffusion autoencoders, LDAE significantly increases inference throughput (20x faster) while also enhancing reconstruction quality. These findings position LDAE as a promising framework for scalable medical imaging applications, with the potential to serve as a foundation model for medical image analysis. Code available at https://github.com/GabrieleLozupone/LDAE

Language-image pre-training has demonstrated strong performance in 2D medical imaging, but its success in 3D modalities such as CT and MRI remains limited due to the high computational demands of volumetric data, which pose a significant barrier to training on large-scale, uncurated clinical studies. In this study, we introduce Hierarchical attention for Language-Image Pre-training (HLIP), a scalable pre-training framework for 3D medical imaging. HLIP adopts a lightweight hierarchical attention mechanism inspired by the natural hierarchy of radiology data: slice, scan, and study. This mechanism exhibits strong generalizability, e.g., +4.3% macro AUC on the Rad-ChestCT benchmark when pre-trained on CT-RATE. Moreover, the computational efficiency of HLIP enables direct training on uncurated datasets. Trained on 220K patients with 3.13 million scans for brain MRI and 240K patients with 1.44 million scans for head CT, HLIP achieves state-of-the-art performance, e.g., +32.4% balanced ACC on the proposed publicly available brain MRI benchmark Pub-Brain-5; +1.4% and +6.9% macro AUC on head CT benchmarks RSNA and CQ500, respectively. These results demonstrate that, with HLIP, directly pre-training on uncurated clinical datasets is a scalable and effective direction for language-image pre-training in 3D medical imaging. The code is available at https://github.com/Zch0414/hlip

In the era of information explosion, efficiently leveraging large-scale unlabeled data while minimizing the reliance on high-quality pixel-level annotations remains a critical challenge in the field of medical imaging. Semi-supervised learning (SSL) enhances the utilization of unlabeled data by facilitating knowledge transfer, significantly improving the performance of fully supervised models and emerging as a highly promising research direction in medical image analysis. Inspired by the ability of Vision Foundation Models (e.g., SAM-2) to provide rich prior knowledge, we propose SSS (Semi-Supervised SAM-2), a novel approach that leverages SAM-2's robust feature extraction capabilities to uncover latent knowledge in unlabeled medical images, thus effectively enhancing feature support for fully supervised medical image segmentation. Specifically, building upon the single-stream "weak-to-strong" consistency regularization framework, this paper introduces a Discriminative Feature Enhancement (DFE) mechanism to further explore the feature discrepancies introduced by various data augmentation strategies across multiple views. By leveraging feature similarity and dissimilarity across multi-scale augmentation techniques, the method reconstructs and models the features, thereby effectively optimizing the salient regions. Furthermore, a prompt generator is developed that integrates Physical Constraints with a Sliding Window (PCSW) mechanism to generate input prompts for unlabeled data, fulfilling SAM-2's requirement for additional prompts. Extensive experiments demonstrate the superiority of the proposed method for semi-supervised medical image segmentation on two multi-label datasets, i.e., ACDC and BHSD. Notably, SSS achieves an average Dice score of 53.15 on BHSD, surpassing the previous state-of-the-art method by +3.65 Dice. Code will be available at https://github.com/AIGeeksGroup/SSS.

Automated data labeling techniques are crucial for accelerating the development of deep learning models, particularly in complex medical imaging applications. However, ensuring accuracy and efficiency remains challenging. This paper presents iterative refinement strategies for automated data labeling in facial landmark diagnosis to enhance accuracy and efficiency for deep learning models in medical applications, including dermatology, plastic surgery, and ophthalmology. Leveraging feedback mechanisms and advanced algorithms, our approach iteratively refines initial labels, reducing reliance on manual intervention while improving label quality. Through empirical evaluation and case studies, we demonstrate the effectiveness of our proposed strategies in deep learning tasks across medical imaging domains. Our results highlight the importance of iterative refinement in automated data labeling to enhance the capabilities of deep learning systems in medical imaging applications.

Chest X-rays (CXR) are the most common medical imaging study and are used to diagnose multiple medical conditions. This study examines the impact of synthetic data supplementation, using diffusion models, on the performance of deep learning (DL) classifiers for CXR analysis. We employed three datasets: CheXpert, MIMIC-CXR, and Emory Chest X-ray, training conditional denoising diffusion probabilistic models (DDPMs) to generate synthetic frontal radiographs. Our approach ensured that synthetic images mirrored the demographic and pathological traits of the original data. Evaluating the classifiers' performance on internal and external datasets revealed that synthetic data supplementation enhances model accuracy, particularly in detecting less prevalent pathologies. Furthermore, models trained on synthetic data alone approached the performance of those trained on real data. This suggests that synthetic data can potentially compensate for real data shortages in training robust DL models. However, despite promising outcomes, the superiority of real data persists.

In this paper, for the first time, we propose an evaluation method for deep learning models that assesses the performance of a model not only in an unseen test scenario, but also in extreme cases of noise, outliers and ambiguous input data. To this end, we utilize adversarial examples, images that fool machine learning models, while looking imperceptibly different from original data, as a measure to evaluate the robustness of a variety of medical imaging models. Through extensive experiments on skin lesion classification and whole brain segmentation with state-of-the-art networks such as Inception and UNet, we show that models that achieve comparable performance regarding generalizability may have significant variations in their perception of the underlying data manifold, leading to an extensive performance gap in their robustness.

Deep Learning (DL) has the potential to optimize machine learning in both the scientific and clinical communities. However, greater expertise is required to develop DL algorithms, and the variability of implementations hinders their reproducibility, translation, and deployment. Here we present the community-driven Generally Nuanced Deep Learning Framework (GaNDLF), with the goal of lowering these barriers. GaNDLF makes the mechanism of DL development, training, and inference more stable, reproducible, interpretable, and scalable, without requiring an extensive technical background. GaNDLF aims to provide an end-to-end solution for all DL-related tasks in computational precision medicine. We demonstrate the ability of GaNDLF to analyze both radiology and histology images, with built-in support for k-fold cross-validation, data augmentation, multiple modalities and output classes. Our quantitative performance evaluation on numerous use cases, anatomies, and computational tasks supports GaNDLF as a robust application framework for deployment in clinical workflows.

Medical imaging is critical for diagnostics, but clinical adoption of advanced AI-driven imaging faces challenges due to patient variability, image artifacts, and limited model generalization. While deep learning has transformed image analysis, 3D medical imaging still suffers from data scarcity and inconsistencies due to acquisition protocols, scanner differences, and patient motion. Traditional augmentation uses a single pipeline for all transformations, disregarding the unique traits of each augmentation and struggling with large data volumes. To address these challenges, we propose a Multi-encoder Augmentation-Aware Learning (MEAL) framework that leverages four distinct augmentation variants processed through dedicated encoders. Three fusion strategies such as concatenation (CC), fusion layer (FL), and adaptive controller block (BD) are integrated to build multi-encoder models that combine augmentation-specific features before decoding. MEAL-BD uniquely preserves augmentation-aware representations, enabling robust, protocol-invariant feature learning. As demonstrated in a Computed Tomography (CT)-to-T1-weighted Magnetic Resonance Imaging (MRI) translation study, MEAL-BD consistently achieved the best performance on both unseen- and predefined-test data. On both geometric transformations (like rotations and flips) and non-augmented inputs, MEAL-BD outperformed other competing methods, achieving higher mean peak signal-to-noise ratio (PSNR) and structural similarity index measure (SSIM) scores. These results establish MEAL as a reliable framework for preserving structural fidelity and generalizing across clinically relevant variability. By reframing augmentation as a source of diverse, generalizable features, MEAL supports robust, protocol-invariant learning, advancing clinically reliable medical imaging solutions.

Medical imaging plays a crucial role in modern healthcare by providing non-invasive visualisation of internal structures and abnormalities, enabling early disease detection, accurate diagnosis, and treatment planning. This study aims to explore the application of deep learning models, particularly focusing on the UNet architecture and its variants, in medical image segmentation. We seek to evaluate the performance of these models across various challenging medical image segmentation tasks, addressing issues such as image normalization, resizing, architecture choices, loss function design, and hyperparameter tuning. The findings reveal that the standard UNet, when extended with a deep network layer, is a proficient medical image segmentation model, while the Res-UNet and Attention Res-UNet architectures demonstrate smoother convergence and superior performance, particularly when handling fine image details. The study also addresses the challenge of high class imbalance through careful preprocessing and loss function definitions. We anticipate that the results of this study will provide useful insights for researchers seeking to apply these models to new medical imaging problems and offer guidance and best practices for their implementation.

Medical imaging analysis plays a critical role in the diagnosis and treatment of various medical conditions. This paper focuses on chest X-ray images and their corresponding radiological reports. It presents a new model that learns a joint X-ray image & report representation. The model is based on a novel alignment scheme between the visual data and the text, which takes into account both local and global information. Furthermore, the model integrates domain-specific information of two types -- lateral images and the consistent visual structure of chest images. Our representation is shown to benefit three types of retrieval tasks: text-image retrieval, class-based retrieval, and phrase-grounding.

With the rapid development of COVID-19 into a global pandemic, there is an ever more urgent need for cheap, fast and reliable tools that can assist physicians in diagnosing COVID-19. Medical imaging such as CT can take a key role in complementing conventional diagnostic tools from molecular biology, and, using deep learning techniques, several automatic systems were demonstrated promising performances using CT or X-ray data. Here, we advocate a more prominent role of point-of-care ultrasound imaging to guide COVID-19 detection. Ultrasound is non-invasive and ubiquitous in medical facilities around the globe. Our contribution is threefold. First, we gather a lung ultrasound (POCUS) dataset consisting of 1103 images (654 COVID-19, 277 bacterial pneumonia and 172 healthy controls), sampled from 64 videos. This dataset was assembled from various online sources, processed specifically for deep learning models and is intended to serve as a starting point for an open-access initiative. Second, we train a deep convolutional neural network (POCOVID-Net) on this 3-class dataset and achieve an accuracy of 89% and, by a majority vote, a video accuracy of 92% . For detecting COVID-19 in particular, the model performs with a sensitivity of 0.96, a specificity of 0.79 and F1-score of 0.92 in a 5-fold cross validation. Third, we provide an open-access web service (POCOVIDScreen) that is available at: https://pocovidscreen.org. The website deploys the predictive model, allowing to perform predictions on ultrasound lung images. In addition, it grants medical staff the option to (bulk) upload their own screenings in order to contribute to the growing public database of pathological lung ultrasound images. Dataset and code are available from: https://github.com/jannisborn/covid19_pocus_ultrasound. NOTE: This preprint is superseded by our paper in Applied Sciences: https://doi.org/10.3390/app11020672

In medical imaging, the primary challenge is collecting large-scale labeled data due to privacy concerns, logistics, and high labeling costs. In this work, we present the UK Biobank Organs and Bones (UKBOB), the largest labeled dataset of body organs, comprising 51,761 MRI 3D samples (equivalent to 17.9 million 2D images) and more than 1.37 billion 2D segmentation masks of 72 organs, all based on the UK Biobank MRI dataset. We utilize automatic labeling, introduce an automated label cleaning pipeline with organ-specific filters, and manually annotate a subset of 300 MRIs with 11 abdominal classes to validate the quality (referred to as UKBOB-manual). This approach allows for scaling up the dataset collection while maintaining confidence in the labels. We further confirm the validity of the labels by demonstrating zero-shot generalization of trained models on the filtered UKBOB to other small labeled datasets from similar domains (e.g., abdominal MRI). To further mitigate the effect of noisy labels, we propose a novel method called Entropy Test-time Adaptation (ETTA) to refine the segmentation output. We use UKBOB to train a foundation model, Swin-BOB, for 3D medical image segmentation based on the Swin-UNetr architecture, achieving state-of-the-art results in several benchmarks in 3D medical imaging, including the BRATS brain MRI tumor challenge (with a 0.4% improvement) and the BTCV abdominal CT scan benchmark (with a 1.3% improvement). The pre-trained models and the code are available at https://emmanuelleb985.github.io/ukbob , and the filtered labels will be made available with the UK Biobank.

Image translation across domains for unpaired datasets has gained interest and great improvement lately. In medical imaging, there are multiple imaging modalities, with very different characteristics. Our goal is to use cross-modality adaptation between CT and MRI whole cardiac scans for semantic segmentation. We present a segmentation network using synthesised cardiac volumes for extremely limited datasets. Our solution is based on a 3D cross-modality generative adversarial network to share information between modalities and generate synthesized data using unpaired datasets. Our network utilizes semantic segmentation to improve generator shape consistency, thus creating more realistic synthesised volumes to be used when re-training the segmentation network. We show that improved segmentation can be achieved on small datasets when using spatial augmentations to improve a generative adversarial network. These augmentations improve the generator capabilities, thus enhancing the performance of the Segmentor. Using only 16 CT and 16 MRI cardiovascular volumes, improved results are shown over other segmentation methods while using the suggested architecture.

In this paper, we introduce Medical SAM 2 (MedSAM-2), an advanced segmentation model that utilizes the SAM 2 framework to address both 2D and 3D medical image segmentation tasks. By adopting the philosophy of taking medical images as videos, MedSAM-2 not only applies to 3D medical images but also unlocks new One-prompt Segmentation capability. That allows users to provide a prompt for just one or a specific image targeting an object, after which the model can autonomously segment the same type of object in all subsequent images, regardless of temporal relationships between the images. We evaluated MedSAM-2 across a variety of medical imaging modalities, including abdominal organs, optic discs, brain tumors, thyroid nodules, and skin lesions, comparing it against state-of-the-art models in both traditional and interactive segmentation settings. Our findings show that MedSAM-2 not only surpasses existing models in performance but also exhibits superior generalization across a range of medical image segmentation tasks. Our code will be released at: https://github.com/MedicineToken/Medical-SAM2

Developing advanced medical imaging retrieval systems is challenging due to the varying definitions of `similar images' across different medical contexts. This challenge is compounded by the lack of large-scale, high-quality medical imaging retrieval datasets and benchmarks. In this paper, we propose a novel methodology that leverages dense radiology reports to define image-wise similarity ordering at multiple granularities in a scalable and fully automatic manner. Using this approach, we construct two comprehensive medical imaging retrieval datasets: MIMIC-IR for Chest X-rays and CTRATE-IR for CT scans, providing detailed image-image ranking annotations conditioned on diverse anatomical structures. Furthermore, we develop two retrieval systems, RadIR-CXR and model-ChestCT, which demonstrate superior performance in traditional image-image and image-report retrieval tasks. These systems also enable flexible, effective image retrieval conditioned on specific anatomical structures described in text, achieving state-of-the-art results on 77 out of 78 metrics.

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.

Segment Anything Model (SAM) has gained significant attention because of its ability to segment a variety of objects in images given a prompt. The recently developed SAM 2 has extended this ability to video inputs. This opens an opportunity to apply SAM to 3D images, one of the fundamental tasks in the medical imaging field. In this paper, we provide an extensive evaluation of SAM 2's ability to segment both 2D and 3D medical images. We collect 18 medical imaging datasets, including common 3D modalities such as computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET) as well as 2D modalities such as X-ray and ultrasound. We consider two evaluation pipelines of SAM 2: (1) multi-frame 3D segmentation, where prompts are provided to one or multiple slice(s) selected from the volume, and (2) single-frame 2D segmentation, where prompts are provided to each slice. The former is only applicable to 3D modalities, while the latter applies to both 2D and 3D modalities. We learn that SAM 2 exhibits similar performance as SAM under single-frame 2D segmentation, and has variable performance under multi-frame 3D segmentation depending on the choices of slices to annotate, the direction of the propagation, the predictions utilized during the propagation, etc.

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 vision-language models enable co-learning and integrating features from medical imaging and clinical text. However, these models are not easy to train and the latent representation space can be complex. Here we propose a novel way for pre-training and regularising medical vision-language models. The proposed method, named Medical vision-language pre-training with Frozen language models and Latent spAce Geometry optimization (M-FLAG), leverages a frozen language model for training stability and efficiency and introduces a novel orthogonality loss to harmonize the latent space geometry. We demonstrate the potential of the pre-trained model on three downstream tasks: medical image classification, segmentation, and object detection. Extensive experiments across five public datasets demonstrate that M-FLAG significantly outperforms existing medical vision-language pre-training approaches and reduces the number of parameters by 78\%. Notably, M-FLAG achieves outstanding performance on the segmentation task while using only 1\% of the RSNA dataset, even outperforming ImageNet pre-trained models that have been fine-tuned using 100\% of the data.

Deep learning-based point cloud modeling has been widely investigated as an indispensable component of general shape analysis. Recently, transformer and state space model (SSM) have shown promising capacities in point cloud learning. However, limited research has been conducted on medical point clouds, which have great potential in disease diagnosis and treatment. This paper presents an SSM-based hierarchical feature learning framework for medical point cloud understanding. Specifically, we down-sample input into multiple levels through the farthest point sampling. At each level, we perform a series of k-nearest neighbor (KNN) queries to aggregate multi-scale structural information. To assist SSM in processing point clouds, we introduce coordinate-order and inside-out scanning strategies for efficient serialization of irregular points. Point features are calculated progressively from short neighbor sequences and long point sequences through vanilla and group Point SSM blocks, to capture both local patterns and long-range dependencies. To evaluate the proposed method, we build a large-scale medical point cloud dataset named MedPointS for anatomy classification, completion, and segmentation. Extensive experiments conducted on MedPointS demonstrate that our method achieves superior performance across all tasks. The dataset is available at https://flemme-docs.readthedocs.io/en/latest/medpoints.html. Code is merged to a public medical imaging platform: https://github.com/wlsdzyzl/flemme.

Rapid advancements in medical image segmentation performance have been significantly driven by the development of Convolutional Neural Networks (CNNs) and Vision Transformers (ViTs). These models follow the discriminative pixel-wise classification learning paradigm and often have limited ability to generalize across diverse medical imaging datasets. In this manuscript, we introduce Generative Medical Segmentation (GMS), a novel approach leveraging a generative model to perform image segmentation. Concretely, GMS employs a robust pre-trained vision foundation model to extract latent representations for images and corresponding ground truth masks, followed by a model that learns a mapping function from the image to the mask in the latent space. Once trained, the model generates an estimated segmentation mask using the pre-trained vision foundation model to decode the predicted latent representation back into the image space. The design of GMS leads to fewer trainable parameters in the model which reduces the risk of overfitting and enhances its generalization capability. Our experimental analysis across five public datasets in different medical imaging domains demonstrates GMS outperforms existing discriminative and generative segmentation models. Furthermore, GMS is able to generalize well across datasets from different centers within the same imaging modality. Our experiments suggest GMS offers a scalable and effective solution for medical image segmentation. GMS implementation and trained model weights are available at https://github.com/King-HAW/GMS.

We introduce eCLIP, an enhanced version of the CLIP model that integrates expert annotations in the form of radiologist eye-gaze heatmaps. It tackles key challenges in contrastive multi-modal medical imaging analysis, notably data scarcity and the "modality gap" -- a significant disparity between image and text embeddings that diminishes the quality of representations and hampers cross-modal interoperability. eCLIP integrates a heatmap processor and leverages mixup augmentation to efficiently utilize the scarce expert annotations, thus boosting the model's learning effectiveness. eCLIP is designed to be generally applicable to any variant of CLIP without requiring any modifications of the core architecture. Through detailed evaluations across several tasks, including zero-shot inference, linear probing, cross-modal retrieval, and Retrieval Augmented Generation (RAG) of radiology reports using a frozen Large Language Model, eCLIP showcases consistent improvements in embedding quality. The outcomes reveal enhanced alignment and uniformity, affirming eCLIP's capability to harness high-quality annotations for enriched multi-modal analysis in the medical imaging domain.

Language-supervised pre-training has proven to be a valuable method for extracting semantically meaningful features from images, serving as a foundational element in multimodal systems within the computer vision and medical imaging domains. However, resulting features are limited by the information contained within the text. This is particularly problematic in medical imaging, where radiologists' written findings focus on specific observations; a challenge compounded by the scarcity of paired imaging-text data due to concerns over leakage of personal health information. In this work, we fundamentally challenge the prevailing reliance on language supervision for learning general purpose biomedical imaging encoders. We introduce RAD-DINO, a biomedical image encoder pre-trained solely on unimodal biomedical imaging data that obtains similar or greater performance than state-of-the-art biomedical language supervised models on a diverse range of benchmarks. Specifically, the quality of learned representations is evaluated on standard imaging tasks (classification and semantic segmentation), and a vision-language alignment task (text report generation from images). To further demonstrate the drawback of language supervision, we show that features from RAD-DINO correlate with other medical records (e.g., sex or age) better than language-supervised models, which are generally not mentioned in radiology reports. Finally, we conduct a series of ablations determining the factors in RAD-DINO's performance; notably, we observe that RAD-DINO's downstream performance scales well with the quantity and diversity of training data, demonstrating that image-only supervision is a scalable approach for training a foundational biomedical image encoder.

Detecting out-of-distribution (OOD) samples in medical imaging plays an important role for downstream medical diagnosis. However, existing OOD detectors are demonstrated on natural images composed of inter-classes and have difficulty generalizing to medical images. The key issue is the granularity of OOD data in the medical domain, where intra-class OOD samples are predominant. We focus on the generalizability of OOD detection for medical images and propose a self-supervised Cascade Variational autoencoder-based Anomaly Detector (CVAD). We use a variational autoencoders' cascade architecture, which combines latent representation at multiple scales, before being fed to a discriminator to distinguish the OOD data from the in-distribution (ID) data. Finally, both the reconstruction error and the OOD probability predicted by the binary discriminator are used to determine the anomalies. We compare the performance with the state-of-the-art deep learning models to demonstrate our model's efficacy on various open-access medical imaging datasets for both intra- and inter-class OOD. Further extensive results on datasets including common natural datasets show our model's effectiveness and generalizability. The code is available at https://github.com/XiaoyuanGuo/CVAD.

Vision-language models (VLMs) have advanced reasoning in natural scenes, but their role in medical imaging remains underexplored. Medical reasoning tasks demand robust image analysis and well-justified answers, posing challenges due to the complexity of medical images. Transparency and trustworthiness are essential for clinical adoption and regulatory compliance. We introduce Med-R1, a framework exploring reinforcement learning (RL) to enhance VLMs' generalizability and trustworthiness in medical reasoning. Leveraging the DeepSeek strategy, we employ Group Relative Policy Optimization (GRPO) to guide reasoning paths via reward signals. Unlike supervised fine-tuning (SFT), which often overfits and lacks generalization, RL fosters robust and diverse reasoning. Med-R1 is evaluated across eight medical imaging modalities: CT, MRI, Ultrasound, Dermoscopy, Fundus Photography, Optical Coherence Tomography (OCT), Microscopy, and X-ray Imaging. Compared to its base model, Qwen2-VL-2B, Med-R1 achieves a 29.94% accuracy improvement and outperforms Qwen2-VL-72B, which has 36 times more parameters. Testing across five question types-modality recognition, anatomy identification, disease diagnosis, lesion grading, and biological attribute analysis Med-R1 demonstrates superior generalization, exceeding Qwen2-VL-2B by 32.06% and surpassing Qwen2-VL-72B in question-type generalization. These findings show that RL improves medical reasoning and enables parameter-efficient models to outperform significantly larger ones. With interpretable reasoning outputs, Med-R1 represents a promising step toward generalizable, trustworthy, and clinically viable medical VLMs.

Training models with robust group fairness properties is crucial in ethically sensitive application areas such as medical diagnosis. Despite the growing body of work aiming to minimise demographic bias in AI, this problem remains challenging. A key reason for this challenge is the fairness generalisation gap: High-capacity deep learning models can fit all training data nearly perfectly, and thus also exhibit perfect fairness during training. In this case, bias emerges only during testing when generalisation performance differs across subgroups. This motivates us to take a bi-level optimisation perspective on fair learning: Optimising the learning strategy based on validation fairness. Specifically, we consider the highly effective workflow of adapting pre-trained models to downstream medical imaging tasks using parameter-efficient fine-tuning (PEFT) techniques. There is a trade-off between updating more parameters, enabling a better fit to the task of interest vs. fewer parameters, potentially reducing the generalisation gap. To manage this tradeoff, we propose FairTune, a framework to optimise the choice of PEFT parameters with respect to fairness. We demonstrate empirically that FairTune leads to improved fairness on a range of medical imaging datasets. The code is available at https://github.com/Raman1121/FairTune

Image registration is fundamental in medical imaging, enabling precise alignment of anatomical structures for diagnosis, treatment planning, image-guided treatment or longitudinal monitoring. This work introduces IMPACT (Image Metric with Pretrained model-Agnostic Comparison for Transmodality registration), a generic semantic similarity metric designed for seamless integration into diverse image registration frameworks (such as Elastix and Voxelmorph). It compares deep learning-based features extracted from medical images without requiring task-specific training, ensuring broad applicability across various modalities. By leveraging the features of the large-scale pretrained TotalSegmentator models and the ability to integrate Segment Anything Model (SAM) and other large-scale segmentation networks, this approach offers significant advantages. It provides robust, scalable, and efficient solutions for multimodal image registration. The IMPACT loss was evaluated on five challenging registration tasks involving thoracic CT/CBCT, and pelvic MR/CT datasets. Quantitative metrics, such as Target Registration Error and Dice Similarity Coefficient, demonstrated significant improvements in anatomical alignment compared to baseline methods. Qualitative analyses further confirmed the increased robustness of the proposed metric in the face of noise, artifacts, and modality variations. IMPACT's versatility and efficiency make it a valuable tool for advancing registration performance in clinical and research applications, addressing critical challenges in multimodal medical imaging.

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.

In the diverse field of medical imaging, automatic segmentation has numerous applications and must handle a wide variety of input domains, such as different types of Computed Tomography (CT) scans and Magnetic Resonance (MR) images. This heterogeneity challenges automatic segmentation algorithms to maintain consistent performance across different modalities due to the requirement for spatially aligned and paired images. Typically, segmentation models are trained using a single modality, which limits their ability to generalize to other types of input data without employing transfer learning techniques. Additionally, leveraging complementary information from different modalities to enhance segmentation precision often necessitates substantial modifications to popular encoder-decoder designs, such as introducing multiple branched encoding or decoding paths for each modality. In this work, we propose a simple Multi-Modal Segmentation (MulModSeg) strategy to enhance medical image segmentation across multiple modalities, specifically CT and MR. It incorporates two key designs: a modality-conditioned text embedding framework via a frozen text encoder that adds modality awareness to existing segmentation frameworks without significant structural modifications or computational overhead, and an alternating training procedure that facilitates the integration of essential features from unpaired CT and MR inputs. Through extensive experiments with both Fully Convolutional Network and Transformer-based backbones, MulModSeg consistently outperforms previous methods in segmenting abdominal multi-organ and cardiac substructures for both CT and MR modalities. The code is available in this {https://github.com/ChengyinLee/MulModSeg_2024{link}}.

Artificial Intelligence (AI) has the potential to revolutionize diagnosis and segmentation in medical imaging. However, development and clinical implementation face multiple challenges including limited data availability, lack of generalizability, and the necessity to incorporate multi-modal data effectively. A foundation model, which is a large-scale pre-trained AI model, offers a versatile base that can be adapted to a variety of specific tasks and contexts. Here, we present a novel foundation model, VISION-MAE, specifically designed for medical imaging. Specifically, VISION-MAE is trained on a dataset of 2.5 million unlabeled images from various modalities (CT, MR, PET, X-rays, and ultrasound), using self-supervised learning techniques. It is then adapted to classification and segmentation tasks using explicit labels. VISION-MAE has high label efficiency, outperforming several benchmark models in both in-domain and out-of-domain applications, and achieves high performance even with reduced availability of labeled data. This model represents a significant advancement in medical imaging AI, offering a generalizable and robust solution for improving segmentation and classification tasks while reducing the data annotation workload.

Explainable Deep Learning has gained significant attention in the field of artificial intelligence (AI), particularly in domains such as medical imaging, where accurate and interpretable machine learning models are crucial for effective diagnosis and treatment planning. Grad-CAM is a baseline that highlights the most critical regions of an image used in a deep learning model's decision-making process, increasing interpretability and trust in the results. It is applied in many computer vision (CV) tasks such as classification and explanation. This study explores the principles of Explainable Deep Learning and its relevance to medical imaging, discusses various explainability techniques and their limitations, and examines medical imaging applications of Grad-CAM. The findings highlight the potential of Explainable Deep Learning and Grad-CAM in improving the accuracy and interpretability of deep learning models in medical imaging. The code is available in (will be available).

Foundation models, often pre-trained with large-scale data, have achieved paramount success in jump-starting various vision and language applications. Recent advances further enable adapting foundation models in downstream tasks efficiently using only a few training samples, e.g., in-context learning. Yet, the application of such learning paradigms in medical image analysis remains scarce due to the shortage of publicly accessible data and benchmarks. In this paper, we aim at approaches adapting the foundation models for medical image classification and present a novel dataset and benchmark for the evaluation, i.e., examining the overall performance of accommodating the large-scale foundation models downstream on a set of diverse real-world clinical tasks. We collect five sets of medical imaging data from multiple institutes targeting a variety of real-world clinical tasks (22,349 images in total), i.e., thoracic diseases screening in X-rays, pathological lesion tissue screening, lesion detection in endoscopy images, neonatal jaundice evaluation, and diabetic retinopathy grading. Results of multiple baseline methods are demonstrated using the proposed dataset from both accuracy and cost-effective perspectives.

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.

Deep neural networks have brought remarkable breakthroughs in medical image analysis. However, due to their data-hungry nature, the modest dataset sizes in medical imaging projects might be hindering their full potential. Generating synthetic data provides a promising alternative, allowing to complement training datasets and conducting medical image research at a larger scale. Diffusion models recently have caught the attention of the computer vision community by producing photorealistic synthetic images. In this study, we explore using Latent Diffusion Models to generate synthetic images from high-resolution 3D brain images. We used T1w MRI images from the UK Biobank dataset (N=31,740) to train our models to learn about the probabilistic distribution of brain images, conditioned on covariables, such as age, sex, and brain structure volumes. We found that our models created realistic data, and we could use the conditioning variables to control the data generation effectively. Besides that, we created a synthetic dataset with 100,000 brain images and made it openly available to the scientific community.

The accelerating development of general medical artificial intelligence (GMAI), powered by multimodal large language models (MLLMs), offers transformative potential for addressing persistent healthcare challenges, including workforce deficits and escalating costs. The parallel development of systematic evaluation benchmarks emerges as a critical imperative to enable performance assessment and provide technological guidance. Meanwhile, as an invaluable knowledge source, the potential of medical textbooks for benchmark development remains underexploited. Here, we present MedBookVQA, a systematic and comprehensive multimodal benchmark derived from open-access medical textbooks. To curate this benchmark, we propose a standardized pipeline for automated extraction of medical figures while contextually aligning them with corresponding medical narratives. Based on this curated data, we generate 5,000 clinically relevant questions spanning modality recognition, disease classification, anatomical identification, symptom diagnosis, and surgical procedures. A multi-tier annotation system categorizes queries through hierarchical taxonomies encompassing medical imaging modalities (42 categories), body anatomies (125 structures), and clinical specialties (31 departments), enabling nuanced analysis across medical subdomains. We evaluate a wide array of MLLMs, including proprietary, open-sourced, medical, and reasoning models, revealing significant performance disparities across task types and model categories. Our findings highlight critical capability gaps in current GMAI systems while establishing textbook-derived multimodal benchmarks as essential evaluation tools. MedBookVQA establishes textbook-derived benchmarking as a critical paradigm for advancing clinical AI, exposing limitations in GMAI systems while providing anatomically structured performance metrics across specialties.

This paper presents MedSegFactory, a versatile medical synthesis framework that generates high-quality paired medical images and segmentation masks across modalities and tasks. It aims to serve as an unlimited data repository, supplying image-mask pairs to enhance existing segmentation tools. The core of MedSegFactory is a dual-stream diffusion model, where one stream synthesizes medical images and the other generates corresponding segmentation masks. To ensure precise alignment between image-mask pairs, we introduce Joint Cross-Attention (JCA), enabling a collaborative denoising paradigm by dynamic cross-conditioning between streams. This bidirectional interaction allows both representations to guide each other's generation, enhancing consistency between generated pairs. MedSegFactory unlocks on-demand generation of paired medical images and segmentation masks through user-defined prompts that specify the target labels, imaging modalities, anatomical regions, and pathological conditions, facilitating scalable and high-quality data generation. This new paradigm of medical image synthesis enables seamless integration into diverse medical imaging workflows, enhancing both efficiency and accuracy. Extensive experiments show that MedSegFactory generates data of superior quality and usability, achieving competitive or state-of-the-art performance in 2D and 3D segmentation tasks while addressing data scarcity and regulatory constraints.

Synthetic data generation is an important application of machine learning in the field of medical imaging. While existing approaches have successfully applied fine-tuned diffusion models for synthesizing medical images, we explore potential improvements to this pipeline through feature-aligned diffusion. Our approach aligns intermediate features of the diffusion model to the output features of an expert, and our preliminary findings show an improvement of 9% in generation accuracy and ~0.12 in SSIM diversity. Our approach is also synergistic with existing methods, and easily integrated into diffusion training pipelines for improvements. We make our code available at https://github.com/lnairGT/Feature-Aligned-Diffusion.

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.

Trustworthiness is essential for the precise and interpretable application of artificial intelligence (AI) in medical imaging. Traditionally, precision and interpretability have been addressed as separate tasks, namely medical image analysis and explainable AI, each developing its own models independently. In this study, for the first time, we investigate the development of a unified medical vision-language pre-training model that can achieve both accurate analysis and interpretable understanding of medical images across various modalities. To build the model, we construct MedConcept-23M, a large-scale dataset comprising 23 million medical image-text pairs extracted from 6.2 million scientific articles, enriched with concepts from the Unified Medical Language System (UMLS). Based on MedConcept-23M, we introduce ConceptCLIP, a medical AI model utilizing concept-enhanced contrastive language-image pre-training. The pre-training of ConceptCLIP involves two primary components: image-text alignment learning (IT-Align) and patch-concept alignment learning (PC-Align). This dual alignment strategy enhances the model's capability to associate specific image regions with relevant concepts, thereby improving both the precision of analysis and the interpretability of the AI system. We conducted extensive experiments on 5 diverse types of medical image analysis tasks, spanning 51 subtasks across 10 image modalities, with the broadest range of downstream tasks. The results demonstrate the effectiveness of the proposed vision-language pre-training model. Further explainability analysis across 6 modalities reveals that ConceptCLIP achieves superior performance, underscoring its robust ability to advance explainable AI in medical imaging. These findings highlight ConceptCLIP's capability in promoting trustworthy AI in the field of medicine.

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.

We present FOMO60K, a large-scale, heterogeneous dataset of 60,529 brain Magnetic Resonance Imaging (MRI) scans from 13,900 sessions and 11,187 subjects, aggregated from 16 publicly available sources. The dataset includes both clinical- and research-grade images, multiple MRI sequences, and a wide range of anatomical and pathological variability, including scans with large brain anomalies. Minimal preprocessing was applied to preserve the original image characteristics while reducing barriers to entry for new users. Accompanying code for self-supervised pretraining and finetuning is provided. FOMO60K is intended to support the development and benchmarking of self-supervised learning methods in medical imaging at scale.

Advanced autoregressive models have reshaped multimodal AI. However, their transformative potential in medical imaging remains largely untapped due to the absence of a unified visual tokenizer -- one capable of capturing fine-grained visual structures for faithful image reconstruction and realistic image synthesis, as well as rich semantics for accurate diagnosis and image interpretation. To this end, we present MedITok, the first unified tokenizer tailored for medical images, encoding both low-level structural details and high-level clinical semantics within a unified latent space. To balance these competing objectives, we introduce a novel two-stage training framework: a visual representation alignment stage that cold-starts the tokenizer reconstruction learning with a visual semantic constraint, followed by a textual semantic representation alignment stage that infuses detailed clinical semantics into the latent space. Trained on the meticulously collected large-scale dataset with over 30 million medical images and 2 million image-caption pairs, MedITok achieves state-of-the-art performance on more than 30 datasets across 9 imaging modalities and 4 different tasks. By providing a unified token space for autoregressive modeling, MedITok supports a wide range of tasks in clinical diagnostics and generative healthcare applications. Model and code will be made publicly available at: https://github.com/Masaaki-75/meditok.

Medical Vision-Language Models (MVLMs) have achieved par excellence generalization in medical image analysis, yet their performance under noisy, corrupted conditions remains largely untested. Clinical imaging is inherently susceptible to acquisition artifacts and noise; however, existing evaluations predominantly assess generally clean datasets, overlooking robustness -- i.e., the model's ability to perform under real-world distortions. To address this gap, we first introduce MediMeta-C, a corruption benchmark that systematically applies several perturbations across multiple medical imaging datasets. Combined with MedMNIST-C, this establishes a comprehensive robustness evaluation framework for MVLMs. We further propose RobustMedCLIP, a visual encoder adaptation of a pretrained MVLM that incorporates few-shot tuning to enhance resilience against corruptions. Through extensive experiments, we benchmark 5 major MVLMs across 5 medical imaging modalities, revealing that existing models exhibit severe degradation under corruption and struggle with domain-modality tradeoffs. Our findings highlight the necessity of diverse training and robust adaptation strategies, demonstrating that efficient low-rank adaptation when paired with few-shot tuning, improves robustness while preserving generalization across modalities.

Self-supervised learning has emerged as a powerful paradigm for training deep neural networks, particularly in medical imaging where labeled data is scarce. While current approaches typically rely on synthetic augmentations of single images, we propose VET-DINO, a framework that leverages a unique characteristic of medical imaging: the availability of multiple standardized views from the same study. Using a series of clinical veterinary radiographs from the same patient study, we enable models to learn view-invariant anatomical structures and develop an implied 3D understanding from 2D projections. We demonstrate our approach on a dataset of 5 million veterinary radiographs from 668,000 canine studies. Through extensive experimentation, including view synthesis and downstream task performance, we show that learning from real multi-view pairs leads to superior anatomical understanding compared to purely synthetic augmentations. VET-DINO achieves state-of-the-art performance on various veterinary imaging tasks. Our work establishes a new paradigm for self-supervised learning in medical imaging that leverages domain-specific properties rather than merely adapting natural image techniques.

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.

Medical images and radiology reports are crucial for diagnosing medical conditions, highlighting the importance of quantitative analysis for clinical decision-making. However, the diversity and cross-source heterogeneity of these data challenge the generalizability of current data-mining methods. Multimodal large language models (MLLMs) have recently transformed many domains, significantly affecting the medical field. Notably, Gemini-Vision-series (Gemini) and GPT-4-series (GPT-4) models have epitomized a paradigm shift in Artificial General Intelligence (AGI) for computer vision, showcasing their potential in the biomedical domain. In this study, we evaluated the performance of the Gemini, GPT-4, and 4 popular large models for an exhaustive evaluation across 14 medical imaging datasets, including 5 medical imaging categories (dermatology, radiology, dentistry, ophthalmology, and endoscopy), and 3 radiology report datasets. The investigated tasks encompass disease classification, lesion segmentation, anatomical localization, disease diagnosis, report generation, and lesion detection. Our experimental results demonstrated that Gemini-series models excelled in report generation and lesion detection but faces challenges in disease classification and anatomical localization. Conversely, GPT-series models exhibited proficiency in lesion segmentation and anatomical localization but encountered difficulties in disease diagnosis and lesion detection. Additionally, both the Gemini series and GPT series contain models that have demonstrated commendable generation efficiency. While both models hold promise in reducing physician workload, alleviating pressure on limited healthcare resources, and fostering collaboration between clinical practitioners and artificial intelligence technologies, substantial enhancements and comprehensive validations remain imperative before clinical deployment.

Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography (CT), yet they struggle to generalize in uncalibrated modalities -- notably magnetic resonance (MR) imaging, where performance is highly sensitive to the differences in MR contrast, resolution, and orientation. This prevents broad applicability to diverse real-world clinical protocols. We introduce Brain-ID, an anatomical representation learning model for brain imaging. With the proposed "mild-to-severe" intra-subject generation, Brain-ID is robust to the subject-specific brain anatomy regardless of the appearance of acquired images (e.g., contrast, deformation, resolution, artifacts). Trained entirely on synthetic data, Brain-ID readily adapts to various downstream tasks through only one layer. We present new metrics to validate the intra- and inter-subject robustness of Brain-ID features, and evaluate their performance on four downstream applications, covering contrast-independent (anatomy reconstruction/contrast synthesis, brain segmentation), and contrast-dependent (super-resolution, bias field estimation) tasks. Extensive experiments on six public datasets demonstrate that Brain-ID achieves state-of-the-art performance in all tasks on different MRI modalities and CT, and more importantly, preserves its performance on low-resolution and small datasets. Code is available at https://github.com/peirong26/Brain-ID.

Denoising diffusion models, a class of generative models, have garnered immense interest lately in various deep-learning problems. A diffusion probabilistic model defines a forward diffusion stage where the input data is gradually perturbed over several steps by adding Gaussian noise and then learns to reverse the diffusion process to retrieve the desired noise-free data from noisy data samples. Diffusion models are widely appreciated for their strong mode coverage and quality of the generated samples despite their known computational burdens. Capitalizing on the advances in computer vision, the field of medical imaging has also observed a growing interest in diffusion models. To help the researcher navigate this profusion, this survey intends to provide a comprehensive overview of diffusion models in the discipline of medical image analysis. Specifically, we introduce the solid theoretical foundation and fundamental concepts behind diffusion models and the three generic diffusion modelling frameworks: diffusion probabilistic models, noise-conditioned score networks, and stochastic differential equations. Then, we provide a systematic taxonomy of diffusion models in the medical domain and propose a multi-perspective categorization based on their application, imaging modality, organ of interest, and algorithms. To this end, we cover extensive applications of diffusion models in the medical domain. Furthermore, we emphasize the practical use case of some selected approaches, and then we discuss the limitations of the diffusion models in the medical domain and propose several directions to fulfill the demands of this field. Finally, we gather the overviewed studies with their available open-source implementations at https://github.com/amirhossein-kz/Awesome-Diffusion-Models-in-Medical-Imaging.

Computed Tomography (CT) is one of the most popular modalities for medical imaging. By far, CT images have contributed to the largest publicly available datasets for volumetric medical segmentation tasks, covering full-body anatomical structures. Large amounts of full-body CT images provide the opportunity to pre-train powerful models, e.g., STU-Net pre-trained in a supervised fashion, to segment numerous anatomical structures. However, it remains unclear in which conditions these pre-trained models can be transferred to various downstream medical segmentation tasks, particularly segmenting the other modalities and diverse targets. To address this problem, a large-scale benchmark for comprehensive evaluation is crucial for finding these conditions. Thus, we collected 87 public datasets varying in modality, target, and sample size to evaluate the transfer ability of full-body CT pre-trained models. We then employed a representative model, STU-Net with multiple model scales, to conduct transfer learning across modalities and targets. Our experimental results show that (1) there may be a bottleneck effect concerning the dataset size in fine-tuning, with more improvement on both small- and large-scale datasets than medium-size ones. (2) Models pre-trained on full-body CT demonstrate effective modality transfer, adapting well to other modalities such as MRI. (3) Pre-training on the full-body CT not only supports strong performance in structure detection but also shows efficacy in lesion detection, showcasing adaptability across target tasks. We hope that this large-scale open evaluation of transfer learning can direct future research in volumetric medical image segmentation.

Metalens is an emerging optical system with an irreplaceable merit in that it can be manufactured in ultra-thin and compact sizes, which shows great promise of various applications such as medical imaging and augmented/virtual reality (AR/VR). Despite its advantage in miniaturization, its practicality is constrained by severe aberrations and distortions, which significantly degrade the image quality. Several previous arts have attempted to address different types of aberrations, yet most of them are mainly designed for the traditional bulky lens and not convincing enough to remedy harsh aberrations of the metalens. While there have existed aberration correction methods specifically for metalens, they still fall short of restoration quality. In this work, we propose MetaFormer, an aberration correction framework for metalens-captured images, harnessing Vision Transformers (ViT) that has shown remarkable restoration performance in diverse image restoration tasks. Specifically, we devise a Multiple Adaptive Filters Guidance (MAFG), where multiple Wiener filters enrich the degraded input images with various noise-detail balances, enhancing output restoration quality. In addition, we introduce a Spatial and Transposed self-Attention Fusion (STAF) module, which aggregates features from spatial self-attention and transposed self-attention modules to further ameliorate aberration correction. We conduct extensive experiments, including correcting aberrated images and videos, and clean 3D reconstruction from the degraded images. The proposed method outperforms the previous arts by a significant margin. We further fabricate a metalens and verify the practicality of MetaFormer by restoring the images captured with the manufactured metalens in the wild. Code and pre-trained models are available at https://benhenryl.github.io/MetaFormer

The generation of medical images presents significant challenges due to their high-resolution and three-dimensional nature. Existing methods often yield suboptimal performance in generating high-quality 3D medical images, and there is currently no universal generative framework for medical imaging. In this paper, we introduce the 3D Medical Diffusion (3D MedDiffusion) model for controllable, high-quality 3D medical image generation. 3D MedDiffusion incorporates a novel, highly efficient Patch-Volume Autoencoder that compresses medical images into latent space through patch-wise encoding and recovers back into image space through volume-wise decoding. Additionally, we design a new noise estimator to capture both local details and global structure information during diffusion denoising process. 3D MedDiffusion can generate fine-detailed, high-resolution images (up to 512x512x512) and effectively adapt to various downstream tasks as it is trained on large-scale datasets covering CT and MRI modalities and different anatomical regions (from head to leg). Experimental results demonstrate that 3D MedDiffusion surpasses state-of-the-art methods in generative quality and exhibits strong generalizability across tasks such as sparse-view CT reconstruction, fast MRI reconstruction, and data augmentation.

Text-guided image editing has seen rapid progress in natural image domains, but its adaptation to medical imaging remains limited and lacks standardized evaluation. Clinically, such editing holds promise for simulating surgical outcomes, creating personalized teaching materials, and enhancing patient communication. To bridge this gap, we introduce MedEBench, a comprehensive benchmark for evaluating text-guided medical image editing. It consists of 1,182 clinically sourced image-prompt triplets spanning 70 tasks across 13 anatomical regions. MedEBench offers three key contributions: (1) a clinically relevant evaluation framework covering Editing Accuracy, Contextual Preservation, and Visual Quality, supported by detailed descriptions of expected change and ROI (Region of Interest) masks; (2) a systematic comparison of seven state-of-the-art models, revealing common failure patterns; and (3) a failure analysis protocol based on attention grounding, using IoU between attention maps and ROIs to identify mislocalization. MedEBench provides a solid foundation for developing and evaluating reliable, clinically meaningful medical image editing systems.

Sequence modeling plays a vital role across various domains, with recurrent neural networks being historically the predominant method of performing these tasks. However, the emergence of transformers has altered this paradigm due to their superior performance. Built upon these advances, transformers have conjoined CNNs as two leading foundational models for learning visual representations. However, transformers are hindered by the O(N^2) complexity of their attention mechanisms, while CNNs lack global receptive fields and dynamic weight allocation. State Space Models (SSMs), specifically the \textbf{Mamba} model with selection mechanisms and hardware-aware architecture, have garnered immense interest lately in sequential modeling and visual representation learning, challenging the dominance of transformers by providing infinite context lengths and offering substantial efficiency maintaining linear complexity in the input sequence. Capitalizing on the advances in computer vision, medical imaging has heralded a new epoch with Mamba models. Intending to help researchers navigate the surge, this survey seeks to offer an encyclopedic review of Mamba models in medical imaging. Specifically, we start with a comprehensive theoretical review forming the basis of SSMs, including Mamba architecture and its alternatives for sequence modeling paradigms in this context. Next, we offer a structured classification of Mamba models in the medical field and introduce a diverse categorization scheme based on their application, imaging modalities, and targeted organs. Finally, we summarize key challenges, discuss different future research directions of the SSMs in the medical domain, and propose several directions to fulfill the demands of this field. In addition, we have compiled the studies discussed in this paper along with their open-source implementations on our GitHub repository.

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 dataset with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, facial and skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://medshapenet.ikim.nrw/ and https://github.com/Jianningli/medshapenet-feedback

The deep learning field is converging towards the use of general foundation models that can be easily adapted for diverse tasks. While this paradigm shift has become common practice within the field of natural language processing, progress has been slower in computer vision. In this paper we attempt to address this issue by investigating the transferability of various state-of-the-art foundation models to medical image classification tasks. Specifically, we evaluate the performance of five foundation models, namely SAM, SEEM, DINOv2, BLIP, and OpenCLIP across four well-established medical imaging datasets. We explore different training settings to fully harness the potential of these models. Our study shows mixed results. DINOv2 consistently outperforms the standard practice of ImageNet pretraining. However, other foundation models failed to consistently beat this established baseline indicating limitations in their transferability to medical image classification tasks.

Phrase grounding, i.e., mapping natural language phrases to specific image regions, holds significant potential for disease localization in medical imaging through clinical reports. While current state-of-the-art methods rely on discriminative, self-supervised contrastive models, we demonstrate that generative text-to-image diffusion models, leveraging cross-attention maps, can achieve superior zero-shot phrase grounding performance. Contrary to prior assumptions, we show that fine-tuning diffusion models with a frozen, domain-specific language model, such as CXR-BERT, substantially outperforms domain-agnostic counterparts. This setup achieves remarkable improvements, with mIoU scores doubling those of current discriminative methods. These findings highlight the underexplored potential of generative models for phrase grounding tasks. To further enhance performance, we introduce Bimodal Bias Merging (BBM), a novel post-processing technique that aligns text and image biases to identify regions of high certainty. BBM refines cross-attention maps, achieving even greater localization accuracy. Our results establish generative approaches as a more effective paradigm for phrase grounding in the medical imaging domain, paving the way for more robust and interpretable applications in clinical practice. The source code and model weights are available at https://github.com/Felix-012/generate_to_ground.

Most existing learning-based methods for solving imaging inverse problems can be roughly divided into two classes: iterative algorithms, such as plug-and-play and diffusion methods, that leverage pretrained denoisers, and unrolled architectures that are trained end-to-end for specific imaging problems. Iterative methods in the first class are computationally costly and often provide suboptimal reconstruction performance, whereas unrolled architectures are generally specific to a single inverse problem and require expensive training. In this work, we propose a novel non-iterative, lightweight architecture that incorporates knowledge about the forward operator (acquisition physics and noise parameters) without relying on unrolling. Our model is trained to solve a wide range of inverse problems beyond denoising, including deblurring, magnetic resonance imaging, computed tomography, inpainting, and super-resolution. The proposed model can be easily adapted to unseen inverse problems or datasets with a few fine-tuning steps (up to a few images) in a self-supervised way, without ground-truth references. Throughout a series of experiments, we demonstrate state-of-the-art performance from medical imaging to low-photon imaging and microscopy.

Biomedical data is inherently multimodal, consisting of electronic health records, medical imaging, digital pathology, genome sequencing, wearable sensors, and more. The application of artificial intelligence tools to these multifaceted sensing technologies has the potential to revolutionize the prognosis, diagnosis, and management of human health and disease. However, current approaches to biomedical AI typically only train and evaluate with one or a small set of medical modalities and tasks. This limitation hampers the development of comprehensive tools that can leverage the rich interconnected information across many heterogeneous biomedical sensors. To address this challenge, we present MultiMed, a benchmark designed to evaluate and enable large-scale learning across a wide spectrum of medical modalities and tasks. MultiMed consists of 2.56 million samples across ten medical modalities such as medical reports, pathology, genomics, and protein data, and is structured into eleven challenging tasks, including disease prognosis, protein structure prediction, and medical question answering. Using MultiMed, we conduct comprehensive experiments benchmarking state-of-the-art unimodal, multimodal, and multitask models. Our analysis highlights the advantages of training large-scale medical models across many related modalities and tasks. Moreover, MultiMed enables studies of generalization across related medical concepts, robustness to real-world noisy data and distribution shifts, and novel modality combinations to improve prediction performance. MultiMed will be publicly available and regularly updated and welcomes inputs from the community.

This paper presents a proof-of-concept approach for learned synergistic reconstruction of medical images using multi-branch generative models. Leveraging variational autoencoders (VAEs) and generative adversarial networks (GANs), our models learn from pairs of images simultaneously, enabling effective denoising and reconstruction. Synergistic image reconstruction is achieved by incorporating the trained models in a regularizer that evaluates the distance between the images and the model, in a similar fashion to multichannel dictionary learning (DiL). We demonstrate the efficacy of our approach on both Modified National Institute of Standards and Technology (MNIST) and positron emission tomography (PET)/computed tomography (CT) datasets, showcasing improved image quality and information sharing between modalities. Despite challenges such as patch decomposition and model limitations, our results underscore the potential of generative models for enhancing medical imaging reconstruction.

Parameter-efficient fine-tuning (PEFT) that was initially developed for exploiting pre-trained large language models has recently emerged as an effective approach to perform transfer learning on computer vision tasks. However, the effectiveness of PEFT on medical vision foundation models is still unclear and remains to be explored. As a proof of concept, we conducted a detailed empirical study on applying PEFT to chest radiography foundation models. Specifically, we delved into LoRA, a representative PEFT method, and compared it against full-parameter fine-tuning (FFT) on two self-supervised radiography foundation models across three well-established chest radiograph datasets. Our results showed that LoRA outperformed FFT in 13 out of 18 transfer learning tasks by at most 2.9% using fewer than 1% tunable parameters. Combining LoRA with foundation models, we set up new state-of-the-art on a range of data-efficient learning tasks, such as an AUROC score of 80.6% using 1% labeled data on NIH ChestX-ray14. We hope this study can evoke more attention from the community in the use of PEFT for transfer learning on medical imaging tasks. Code and models are available at https://github.com/RL4M/MED-PEFT.

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.

Human organs constantly undergo anatomical changes due to a complex mix of short-term (e.g., heartbeat) and long-term (e.g., aging) factors. Evidently, prior knowledge of these factors will be beneficial when modeling their future state, i.e., via image generation. However, most of the medical image generation tasks only rely on the input from a single image, thus ignoring the sequential dependency even when longitudinal data is available. Sequence-aware deep generative models, where model input is a sequence of ordered and timestamped images, are still underexplored in the medical imaging domain that is featured by several unique challenges: 1) Sequences with various lengths; 2) Missing data or frame, and 3) High dimensionality. To this end, we propose a sequence-aware diffusion model (SADM) for the generation of longitudinal medical images. Recently, diffusion models have shown promising results in high-fidelity image generation. Our method extends this new technique by introducing a sequence-aware transformer as the conditional module in a diffusion model. The novel design enables learning longitudinal dependency even with missing data during training and allows autoregressive generation of a sequence of images during inference. Our extensive experiments on 3D longitudinal medical images demonstrate the effectiveness of SADM compared with baselines and alternative methods. The code is available at https://github.com/ubc-tea/SADM-Longitudinal-Medical-Image-Generation.

The performance on deep learning is significantly affected by volume of training data. Models pre-trained from massive dataset such as ImageNet become a powerful weapon for speeding up training convergence and improving accuracy. Similarly, models based on large dataset are important for the development of deep learning in 3D medical images. However, it is extremely challenging to build a sufficiently large dataset due to difficulty of data acquisition and annotation in 3D medical imaging. We aggregate the dataset from several medical challenges to build 3DSeg-8 dataset with diverse modalities, target organs, and pathologies. To extract general medical three-dimension (3D) features, we design a heterogeneous 3D network called Med3D to co-train multi-domain 3DSeg-8 so as to make a series of pre-trained models. We transfer Med3D pre-trained models to lung segmentation in LIDC dataset, pulmonary nodule classification in LIDC dataset and liver segmentation on LiTS challenge. Experiments show that the Med3D can accelerate the training convergence speed of target 3D medical tasks 2 times compared with model pre-trained on Kinetics dataset, and 10 times compared with training from scratch as well as improve accuracy ranging from 3% to 20%. Transferring our Med3D model on state-the-of-art DenseASPP segmentation network, in case of single model, we achieve 94.6\% Dice coefficient which approaches the result of top-ranged algorithms on the LiTS challenge.

Multimodal Large Language Models (MLLMs) have demonstrated impressive capabilities in understanding common visual elements, largely due to their large-scale datasets and advanced training strategies. However, their effectiveness in medical applications remains limited due to the inherent discrepancies between data and tasks in medical scenarios and those in the general domain. Concretely, existing medical MLLMs face the following critical limitations: (1) limited coverage of medical knowledge beyond imaging, (2) heightened susceptibility to hallucinations due to suboptimal data curation processes, (3) lack of reasoning capabilities tailored for complex medical scenarios. To address these challenges, we first propose a comprehensive data curation procedure that (1) efficiently acquires rich medical knowledge data not only from medical imaging but also from extensive medical texts and general-domain data; and (2) synthesizes accurate medical captions, visual question answering (VQA), and reasoning samples. As a result, we build a multimodal dataset enriched with extensive medical knowledge. Building on the curated data, we introduce our medical-specialized MLLM: Lingshu. Lingshu undergoes multi-stage training to embed medical expertise and enhance its task-solving capabilities progressively. Besides, we preliminarily explore the potential of applying reinforcement learning with verifiable rewards paradigm to enhance Lingshu's medical reasoning ability. Additionally, we develop MedEvalKit, a unified evaluation framework that consolidates leading multimodal and textual medical benchmarks for standardized, fair, and efficient model assessment. We evaluate the performance of Lingshu on three fundamental medical tasks, multimodal QA, text-based QA, and medical report generation. The results show that Lingshu consistently outperforms the existing open-source multimodal models on most tasks ...

Large Language Models (LLMs), known for their versatility in textual data, are increasingly being explored for their potential to enhance medical image segmentation, a crucial task for accurate diagnostic imaging. This study explores enhancing Vision Transformers (ViTs) for medical image segmentation by integrating pre-trained LLM transformer blocks. Our approach, which incorporates a frozen LLM transformer block into the encoder of a ViT-based model, leads to substantial improvements in segmentation performance across various medical imaging modalities. We propose a Hybrid Attention Mechanism that combines global and local feature learning with a Multi-Scale Fusion Block for aggregating features across different scales. The enhanced model shows significant performance gains, including an average Dice score increase from 0.74 to 0.79 and improvements in accuracy, precision, and the Jaccard Index. These results demonstrate the effectiveness of LLM-based transformers in refining medical image segmentation, highlighting their potential to significantly boost model accuracy and robustness. The source code and our implementation are available at: https://bit.ly/3zf2CVs

In the field of medical sciences, reliable detection and classification of brain tumors from images remains a formidable challenge due to the rarity of tumors within the population of patients. Therefore, the ability to detect tumors in anomaly scenarios is paramount for ensuring timely interventions and improved patient outcomes. This study addresses the issue by leveraging deep learning (DL) techniques to detect and classify brain tumors in challenging situations. The curated data set from the National Brain Mapping Lab (NBML) comprises 81 patients, including 30 Tumor cases and 51 Normal cases. The detection and classification pipelines are separated into two consecutive tasks. The detection phase involved comprehensive data analysis and pre-processing to modify the number of image samples and the number of patients of each class to anomaly distribution (9 Normal per 1 Tumor) to comply with real world scenarios. Next, in addition to common evaluation metrics for the testing, we employed a novel performance evaluation method called Patient to Patient (PTP), focusing on the realistic evaluation of the model. In the detection phase, we fine-tuned a YOLOv8n detection model to detect the tumor region. Subsequent testing and evaluation yielded competitive performance both in Common Evaluation Metrics and PTP metrics. Furthermore, using the Data Efficient Image Transformer (DeiT) module, we distilled a Vision Transformer (ViT) model from a fine-tuned ResNet152 as a teacher in the classification phase. This approach demonstrates promising strides in reliable tumor detection and classification, offering potential advancements in tumor diagnosis for real-world medical imaging scenarios.

This paper investigates discrepancies in how neural networks learn from different imaging domains, which are commonly overlooked when adopting computer vision techniques from the domain of natural images to other specialized domains such as medical images. Recent works have found that the generalization error of a trained network typically increases with the intrinsic dimension (d_{data}) of its training set. Yet, the steepness of this relationship varies significantly between medical (radiological) and natural imaging domains, with no existing theoretical explanation. We address this gap in knowledge by establishing and empirically validating a generalization scaling law with respect to d_{data}, and propose that the substantial scaling discrepancy between the two considered domains may be at least partially attributed to the higher intrinsic ``label sharpness'' (K_F) of medical imaging datasets, a metric which we propose. Next, we demonstrate an additional benefit of measuring the label sharpness of a training set: it is negatively correlated with the trained model's adversarial robustness, which notably leads to models for medical images having a substantially higher vulnerability to adversarial attack. Finally, we extend our d_{data} formalism to the related metric of learned representation intrinsic dimension (d_{repr}), derive a generalization scaling law with respect to d_{repr}, and show that d_{data} serves as an upper bound for d_{repr}. Our theoretical results are supported by thorough experiments with six models and eleven natural and medical imaging datasets over a range of training set sizes. Our findings offer insights into the influence of intrinsic dataset properties on generalization, representation learning, and robustness in deep neural networks. Code link: https://github.com/mazurowski-lab/intrinsic-properties

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

After being collected for patient care, Observational Health Data (OHD) can further benefit patient well-being by sustaining the development of health informatics and medical research. Vast potential is unexploited because of the fiercely private nature of patient-related data and regulations to protect it. Generative Adversarial Networks (GANs) have recently emerged as a groundbreaking way to learn generative models that produce realistic synthetic data. They have revolutionized practices in multiple domains such as self-driving cars, fraud detection, digital twin simulations in industrial sectors, and medical imaging. The digital twin concept could readily apply to modelling and quantifying disease progression. In addition, GANs posses many capabilities relevant to common problems in healthcare: lack of data, class imbalance, rare diseases, and preserving privacy. Unlocking open access to privacy-preserving OHD could be transformative for scientific research. In the midst of COVID-19, the healthcare system is facing unprecedented challenges, many of which of are data related for the reasons stated above. Considering these facts, publications concerning GAN applied to OHD seemed to be severely lacking. To uncover the reasons for this slow adoption, we broadly reviewed the published literature on the subject. Our findings show that the properties of OHD were initially challenging for the existing GAN algorithms (unlike medical imaging, for which state-of-the-art model were directly transferable) and the evaluation synthetic data lacked clear metrics. We find more publications on the subject than expected, starting slowly in 2017, and since then at an increasing rate. The difficulties of OHD remain, and we discuss issues relating to evaluation, consistency, benchmarking, data modelling, and reproducibility.

Limitations on bandwidth and power consumption impose strict bounds on data rates of diagnostic imaging systems. Consequently, the design of suitable (i.e. task- and data-aware) compression and reconstruction techniques has attracted considerable attention in recent years. Compressed sensing emerged as a popular framework for sparse signal reconstruction from a small set of compressed measurements. However, typical compressed sensing designs measure a (non)linearly weighted combination of all input signal elements, which poses practical challenges. These designs are also not necessarily task-optimal. In addition, real-time recovery is hampered by the iterative and time-consuming nature of sparse recovery algorithms. Recently, deep learning methods have shown promise for fast recovery from compressed measurements, but the design of adequate and practical sensing strategies remains a challenge. Here, we propose a deep learning solution termed Deep Probabilistic Sub-sampling (DPS), that learns a task-driven sub-sampling pattern, while jointly training a subsequent task model. Once learned, the task-based sub-sampling patterns are fixed and straightforwardly implementable, e.g. by non-uniform analog-to-digital conversion, sparse array design, or slow-time ultrasound pulsing schemes. The effectiveness of our framework is demonstrated in-silico for sparse signal recovery from partial Fourier measurements, and in-vivo for both anatomical image and tissue-motion (Doppler) reconstruction from sub-sampled medical ultrasound imaging data.

Accurately segmenting different organs from medical images is a critical prerequisite for computer-assisted diagnosis and intervention planning. This study proposes a deep learning-based approach for segmenting various organs from CT and MRI scans and classifying diseases. Our study introduces a novel technique integrating momentum within residual blocks for enhanced training dynamics in medical image analysis. We applied our method in two distinct tasks: segmenting liver, lung, & colon data and classifying abdominal pelvic CT and MRI scans. The proposed approach has shown promising results, outperforming state-of-the-art methods on publicly available benchmarking datasets. For instance, in the lung segmentation dataset, our approach yielded significant enhancements over the TransNetR model, including a 5.72% increase in dice score, a 5.04% improvement in mean Intersection over Union (mIoU), an 8.02% improvement in recall, and a 4.42% improvement in precision. Hence, incorporating momentum led to state-of-the-art performance in both segmentation and classification tasks, representing a significant advancement in the field of medical imaging.

Medical image segmentation remains a formidable challenge due to the label scarcity. Pre-training Vision Transformer (ViT) through masked image modeling (MIM) on large-scale unlabeled medical datasets presents a promising solution, providing both computational efficiency and model generalization for various downstream tasks. However, current ViT-based MIM pre-training frameworks predominantly emphasize local aggregation representations in output layers and fail to exploit the rich representations across different ViT layers that better capture fine-grained semantic information needed for more precise medical downstream tasks. To fill the above gap, we hereby present Hierarchical Encoder-driven MAE (Hi-End-MAE), a simple yet effective ViT-based pre-training solution, which centers on two key innovations: (1) Encoder-driven reconstruction, which encourages the encoder to learn more informative features to guide the reconstruction of masked patches; and (2) Hierarchical dense decoding, which implements a hierarchical decoding structure to capture rich representations across different layers. We pre-train Hi-End-MAE on a large-scale dataset of 10K CT scans and evaluated its performance across seven public medical image segmentation benchmarks. Extensive experiments demonstrate that Hi-End-MAE achieves superior transfer learning capabilities across various downstream tasks, revealing the potential of ViT in medical imaging applications. The code is available at: https://github.com/FengheTan9/Hi-End-MAE

Recently, the state space model Mamba has demonstrated efficient long-sequence modeling capabilities, particularly for addressing long-sequence visual tasks in 3D medical imaging. However, existing generative self-supervised learning methods have not yet fully unleashed Mamba's potential for handling long-range dependencies because they overlook the inherent causal properties of state space sequences in masked modeling. To address this challenge, we propose a general-purpose pre-training framework called MambaMIM, a masked image modeling method based on a novel TOKen-Interpolation strategy (TOKI) for the selective structure state space sequence, which learns causal relationships of state space within the masked sequence. Further, MambaMIM introduces a bottom-up 3D hybrid masking strategy to maintain a masking consistency across different architectures and can be used on any single or hybrid Mamba architecture to enhance its multi-scale and long-range representation capability. We pre-train MambaMIM on a large-scale dataset of 6.8K CT scans and evaluate its performance across eight public medical segmentation benchmarks. Extensive downstream experiments reveal the feasibility and advancement of using Mamba for medical image pre-training. In particular, when we apply the MambaMIM to a customized architecture that hybridizes MedNeXt and Vision Mamba, we consistently obtain the state-of-the-art segmentation performance. The code is available at: https://github.com/FengheTan9/MambaMIM.

Large Multimodal Models (LMMs) have shown remarkable progress in the field of medical Visual Question Answering (Med-VQA), achieving high accuracy on existing benchmarks. However, their reliability under robust evaluation is questionable. This study reveals that state-of-the-art models, when subjected to simple probing evaluation, perform worse than random guessing on medical diagnosis questions. To address this critical evaluation problem, we introduce the Probing Evaluation for Medical Diagnosis (ProbMed) dataset to rigorously assess LMM performance in medical imaging through probing evaluation and procedural diagnosis. Particularly, probing evaluation features pairing original questions with negation questions with hallucinated attributes, while procedural diagnosis requires reasoning across various diagnostic dimensions for each image, including modality recognition, organ identification, clinical findings, abnormalities, and positional grounding. Our evaluation reveals that top-performing models like GPT-4V and Gemini Pro perform worse than random guessing on specialized diagnostic questions, indicating significant limitations in handling fine-grained medical inquiries. Besides, models like LLaVA-Med struggle even with more general questions, and results from CheXagent demonstrate the transferability of expertise across different modalities of the same organ, showing that specialized domain knowledge is still crucial for improving performance. This study underscores the urgent need for more robust evaluation to ensure the reliability of LMMs in critical fields like medical diagnosis, and current LMMs are still far from applicable to those fields.

Multimodal models trained on large natural image-text pair datasets have exhibited astounding abilities in generating high-quality images. Medical imaging data is fundamentally different to natural images, and the language used to succinctly capture relevant details in medical data uses a different, narrow but semantically rich, domain-specific vocabulary. Not surprisingly, multi-modal models trained on natural image-text pairs do not tend to generalize well to the medical domain. Developing generative imaging models faithfully representing medical concepts while providing compositional diversity could mitigate the existing paucity of high-quality, annotated medical imaging datasets. In this work, we develop a strategy to overcome the large natural-medical distributional shift by adapting a pre-trained latent diffusion model on a corpus of publicly available chest x-rays (CXR) and their corresponding radiology (text) reports. We investigate the model's ability to generate high-fidelity, diverse synthetic CXR conditioned on text prompts. We assess the model outputs quantitatively using image quality metrics, and evaluate image quality and text-image alignment by human domain experts. We present evidence that the resulting model (RoentGen) is able to create visually convincing, diverse synthetic CXR images, and that the output can be controlled to a new extent by using free-form text prompts including radiology-specific language. Fine-tuning this model on a fixed training set and using it as a data augmentation method, we measure a 5% improvement of a classifier trained jointly on synthetic and real images, and a 3% improvement when trained on a larger but purely synthetic training set. Finally, we observe that this fine-tuning distills in-domain knowledge in the text-encoder and can improve its representation capabilities of certain diseases like pneumothorax by 25%.

Medical imaging often contains critical fine-grained features, such as tumors or hemorrhages, crucial for diagnosis yet potentially too subtle for detection with conventional methods. In this paper, we introduce DIA, dissolving is amplifying. DIA is a fine-grained anomaly detection framework for medical images. First, we introduce dissolving transformations. We employ diffusion with a generative diffusion model as a dedicated feature-aware denoiser. Applying diffusion to medical images in a certain manner can remove or diminish fine-grained discriminative features. Second, we introduce an amplifying framework based on contrastive learning to learn a semantically meaningful representation of medical images in a self-supervised manner, with a focus on fine-grained features. The amplifying framework contrasts additional pairs of images with and without dissolving transformations applied and thereby emphasizes the dissolved fine-grained features. DIA significantly improves the medical anomaly detection performance with around 18.40\% AUC boost against the baseline method and achieves an overall SOTA against other benchmark methods. Our code is available at https://github.com/shijianjian/DIA.git.

Medical imaging plays a significant role in clinical practice of medical diagnosis, where the text reports of the images are essential in understanding them and facilitating later treatments. By generating the reports automatically, it is beneficial to help lighten the burden of radiologists and significantly promote clinical automation, which already attracts much attention in applying artificial intelligence to medical domain. Previous studies mainly follow the encoder-decoder paradigm and focus on the aspect of text generation, with few studies considering the importance of cross-modal mappings and explicitly exploit such mappings to facilitate radiology report generation. In this paper, we propose a cross-modal memory networks (CMN) to enhance the encoder-decoder framework for radiology report generation, where a shared memory is designed to record the alignment between images and texts so as to facilitate the interaction and generation across modalities. Experimental results illustrate the effectiveness of our proposed model, where state-of-the-art performance is achieved on two widely used benchmark datasets, i.e., IU X-Ray and MIMIC-CXR. Further analyses also prove that our model is able to better align information from radiology images and texts so as to help generating more accurate reports in terms of clinical indicators.

Medical imaging is critical to the diagnosis and treatment of numerous medical problems, including many forms of cancer. Medical imaging reports distill the findings and observations of radiologists, creating an unstructured textual representation of unstructured medical images. Large-scale use of this text-encoded information requires converting the unstructured text to a structured, semantic representation. We explore the extraction and normalization of anatomical information in radiology reports that is associated with radiological findings. We investigate this extraction and normalization task using a span-based relation extraction model that jointly extracts entities and relations using BERT. This work examines the factors that influence extraction and normalization performance, including the body part/organ system, frequency of occurrence, span length, and span diversity. It discusses approaches for improving performance and creating high-quality semantic representations of radiological phenomena.

The outbreak of COVID-19 has shocked the entire world with its fairly rapid spread and has challenged different sectors. One of the most effective ways to limit its spread is the early and accurate diagnosing infected patients. Medical imaging, such as X-ray and Computed Tomography (CT), combined with the potential of Artificial Intelligence (AI), plays an essential role in supporting medical personnel in the diagnosis process. Thus, in this article five different deep learning models (ResNet18, ResNet34, InceptionV3, InceptionResNetV2 and DenseNet161) and their ensemble, using majority voting have been used to classify COVID-19, pneumoni{\ae} and healthy subjects using chest X-ray images. Multilabel classification was performed to predict multiple pathologies for each patient, if present. Firstly, the interpretability of each of the networks was thoroughly studied using local interpretability methods - occlusion, saliency, input X gradient, guided backpropagation, integrated gradients, and DeepLIFT, and using a global technique - neuron activation profiles. The mean Micro-F1 score of the models for COVID-19 classifications ranges from 0.66 to 0.875, and is 0.89 for the ensemble of the network models. The qualitative results showed that the ResNets were the most interpretable models. This research demonstrates the importance of using interpretability methods to compare different models before making a decision regarding the best performing model.

We focus on the Source Free Object Detection (SFOD) problem, when source data is unavailable during adaptation, and the model must adapt to the unlabeled target domain. In medical imaging, several approaches have leveraged a semi-supervised student-teacher architecture to bridge domain discrepancy. Context imbalance in labeled training data and significant domain shifts between domains can lead to biased teacher models that produce inaccurate pseudolabels, degrading the student model's performance and causing a mode collapse. Class imbalance, particularly when one class significantly outnumbers another, leads to contextual bias. To tackle the problem of context bias and the significant performance drop of the student model in the SFOD setting, we introduce Grounded Teacher (GT) as a standard framework. In this study, we model contextual relationships using a dedicated relational context module and leverage it to mitigate inherent biases in the model. This approach enables us to apply augmentations to closely related classes, across and within domains, enhancing the performance of underrepresented classes while keeping the effect on dominant classes minimal. We further improve the quality of predictions by implementing an expert foundational branch to supervise the student model. We validate the effectiveness of our approach in mitigating context bias under the SFOD setting through experiments on three medical datasets supported by comprehensive ablation studies. All relevant resources, including preprocessed data, trained model weights, and code, are publicly available at this https://github.com/Tajamul21/Grounded_Teacher.

Deep neural networks (DNNs) offer significant promise for improving breast cancer diagnosis in medical imaging. However, these models are highly susceptible to adversarial attacks--small, imperceptible changes that can mislead classifiers--raising critical concerns about their reliability and security. Traditional attacks rely on fixed-norm perturbations, misaligning with human perception. In contrast, diffusion-based attacks require pre-trained models, demanding substantial data when these models are unavailable, limiting practical use in data-scarce scenarios. In medical imaging, however, this is often unfeasible due to the limited availability of datasets. Building on recent advancements in learnable prompts, we propose Prompt2Perturb (P2P), a novel language-guided attack method capable of generating meaningful attack examples driven by text instructions. During the prompt learning phase, our approach leverages learnable prompts within the text encoder to create subtle, yet impactful, perturbations that remain imperceptible while guiding the model towards targeted outcomes. In contrast to current prompt learning-based approaches, our P2P stands out by directly updating text embeddings, avoiding the need for retraining diffusion models. Further, we leverage the finding that optimizing only the early reverse diffusion steps boosts efficiency while ensuring that the generated adversarial examples incorporate subtle noise, thus preserving ultrasound image quality without introducing noticeable artifacts. We show that our method outperforms state-of-the-art attack techniques across three breast ultrasound datasets in FID and LPIPS. Moreover, the generated images are both more natural in appearance and more effective compared to existing adversarial attacks. Our code will be publicly available https://github.com/yasamin-med/P2P.

In medical imaging, the diffusion models have shown great potential in synthetic image generation tasks. However, these models often struggle with the interpretable connections between the generated and existing images and could create illusions. To address these challenges, our research proposes a novel diffusion-based generative model based on deformation diffusion and recovery. This model, named Deformation-Recovery Diffusion Model (DRDM), diverges from traditional score/intensity and latent feature-based approaches, emphasizing morphological changes through deformation fields rather than direct image synthesis. This is achieved by introducing a topological-preserving deformation field generation method, which randomly samples and integrates a set of multi-scale Deformation Vector Fields (DVF). DRDM is trained to learn to recover unreasonable deformation components, thereby restoring each randomly deformed image to a realistic distribution. These innovations facilitate the generation of diverse and anatomically plausible deformations, enhancing data augmentation and synthesis for further analysis in downstream tasks, such as few-shot learning and image registration. Experimental results in cardiac MRI and pulmonary CT show DRDM is capable of creating diverse, large (over 10\% image size deformation scale), and high-quality (negative rate of the Jacobian matrix's determinant is lower than 1\%) deformation fields. The further experimental results in downstream tasks, 2D image segmentation and 3D image registration, indicate significant improvements resulting from DRDM, showcasing the potential of our model to advance image manipulation and synthesis in medical imaging and beyond. Project page: https://jianqingzheng.github.io/def_diff_rec/

In the field of medical imaging, the scarcity of large-scale datasets due to privacy restrictions stands as a significant barrier to develop large models for medical. To address this issue, we introduce SynFundus-1M, a high-quality synthetic dataset with over 1 million retinal fundus images and extensive disease and pathologies annotations, which is generated by a Denoising Diffusion Probabilistic Model. The SynFundus-Generator and SynFundus-1M achieve superior Frechet Inception Distance (FID) scores compared to existing methods on main-stream public real datasets. Furthermore, the ophthalmologists evaluation validate the difficulty in discerning these synthetic images from real ones, confirming the SynFundus-1M's authenticity. Through extensive experiments, we demonstrate that both CNN and ViT can benifit from SynFundus-1M by pretraining or training directly. Compared to datasets like ImageNet or EyePACS, models train on SynFundus-1M not only achieve better performance but also faster convergence on various downstream tasks.

Multiple Instance learning (MIL) models have been extensively used in pathology to predict biomarkers and risk-stratify patients from gigapixel-sized images. Machine learning problems in medical imaging often deal with rare diseases, making it important for these models to work in a label-imbalanced setting. In pathology images, there is another level of imbalance, where given a positively labeled Whole Slide Image (WSI), only a fraction of pixels within it contribute to the positive label. This compounds the severity of imbalance and makes imbalanced classification in pathology challenging. Furthermore, these imbalances can occur in out-of-distribution (OOD) datasets when the models are deployed in the real-world. We leverage the idea that decoupling feature and classifier learning can lead to improved decision boundaries for label imbalanced datasets. To this end, we investigate the integration of supervised contrastive learning with multiple instance learning (SC-MIL). Specifically, we propose a joint-training MIL framework in the presence of label imbalance that progressively transitions from learning bag-level representations to optimal classifier learning. We perform experiments with different imbalance settings for two well-studied problems in cancer pathology: subtyping of non-small cell lung cancer and subtyping of renal cell carcinoma. SC-MIL provides large and consistent improvements over other techniques on both in-distribution (ID) and OOD held-out sets across multiple imbalanced settings.

Patient data from real-world clinical practice often suffers from data scarcity and long-tail imbalances, leading to biased outcomes or algorithmic unfairness. This study addresses these challenges by generating lesion-containing image-segmentation pairs from lesion-free images. Previous efforts in medical imaging synthesis have struggled with separating lesion information from background, resulting in low-quality backgrounds and limited control over the synthetic output. Inspired by diffusion-based image inpainting, we propose LeFusion, a lesion-focused diffusion model. By redesigning the diffusion learning objectives to focus on lesion areas, we simplify the learning process and improve control over the output while preserving high-fidelity backgrounds by integrating forward-diffused background contexts into the reverse diffusion process. Additionally, we tackle two major challenges in lesion texture synthesis: 1) multi-peak and 2) multi-class lesions. We introduce two effective strategies: histogram-based texture control and multi-channel decomposition, enabling the controlled generation of high-quality lesions in difficult scenarios. Furthermore, we incorporate lesion mask diffusion, allowing control over lesion size, location, and boundary, thus increasing lesion diversity. Validated on 3D cardiac lesion MRI and lung nodule CT datasets, LeFusion-generated data significantly improves the performance of state-of-the-art segmentation models, including nnUNet and SwinUNETR. Code and model are available at https://github.com/M3DV/LeFusion.

In the domain of medical imaging, many supervised learning based methods for segmentation face several challenges such as high variability in annotations from multiple experts, paucity of labelled data and class imbalanced datasets. These issues may result in segmentations that lack the requisite precision for clinical analysis and can be misleadingly overconfident without associated uncertainty quantification. We propose the PULASki for biomedical image segmentation that accurately captures variability in expert annotations, even in small datasets. Our approach makes use of an improved loss function based on statistical distances in a conditional variational autoencoder structure (Probabilistic UNet), which improves learning of the conditional decoder compared to the standard cross-entropy particularly in class imbalanced problems. We analyse our method for two structurally different segmentation tasks (intracranial vessel and multiple sclerosis (MS) lesion) and compare our results to four well-established baselines in terms of quantitative metrics and qualitative output. Empirical results demonstrate the PULASKi method outperforms all baselines at the 5\% significance level. The generated segmentations are shown to be much more anatomically plausible than in the 2D case, particularly for the vessel task. Our method can also be applied to a wide range of multi-label segmentation tasks and and is useful for downstream tasks such as hemodynamic modelling (computational fluid dynamics and data assimilation), clinical decision making, and treatment planning.

Curating a large scale medical imaging dataset for machine learning applications is both time consuming and expensive. Balancing the workload between model development, data collection and annotations is difficult for machine learning practitioners, especially under time constraints. Causal analysis is often used in medicine and economics to gain insights about the effects of actions and policies. In this paper we explore the effect of dataset interventions on the output of image classification models. Through a causal approach we investigate the effects of the quantity and type of data we need to incorporate in a dataset to achieve better performance for specific subtasks. The main goal of this paper is to highlight the potential of causal analysis as a tool for resource optimization for developing medical imaging ML applications. We explore this concept with a synthetic dataset and an exemplary use-case for Diabetic Retinopathy image analysis.

Magnetic resonance imaging (MRI) is a common and life-saving medical imaging technique. However, acquiring high signal-to-noise ratio MRI scans requires long scan times, resulting in increased costs and patient discomfort, and decreased throughput. Thus, there is great interest in denoising MRI scans, especially for the subtype of diffusion MRI scans that are severely SNR-limited. While most prior MRI denoising methods are supervised in nature, acquiring supervised training datasets for the multitude of anatomies, MRI scanners, and scan parameters proves impractical. Here, we propose Denoising Diffusion Models for Denoising Diffusion MRI (DDM^2), a self-supervised denoising method for MRI denoising using diffusion denoising generative models. Our three-stage framework integrates statistic-based denoising theory into diffusion models and performs denoising through conditional generation. During inference, we represent input noisy measurements as a sample from an intermediate posterior distribution within the diffusion Markov chain. We conduct experiments on 4 real-world in-vivo diffusion MRI datasets and show that our DDM^2 demonstrates superior denoising performances ascertained with clinically-relevant visual qualitative and quantitative metrics.

Federated learning (FL) is a distributed learning method that offers medical institutes the prospect of collaboration in a global model while preserving the privacy of their patients. Although most medical centers conduct similar medical imaging tasks, their differences, such as specializations, number of patients, and devices, lead to distinctive data distributions. Data heterogeneity poses a challenge for FL and the personalization of the local models. In this work, we investigate an adaptive hierarchical clustering method for FL to produce intermediate semi-global models, so clients with similar data distribution have the chance of forming a more specialized model. Our method forms several clusters consisting of clients with the most similar data distributions; then, each cluster continues to train separately. Inside the cluster, we use meta-learning to improve the personalization of the participants' models. We compare the clustering approach with classical FedAvg and centralized training by evaluating our proposed methods on the HAM10k dataset for skin lesion classification with extreme heterogeneous data distribution. Our experiments demonstrate significant performance gain in heterogeneous distribution compared to standard FL methods in classification accuracy. Moreover, we show that the models converge faster if applied in clusters and outperform centralized training while using only a small subset of data.

Magnetic resonance imaging (MRI) is a cornerstone of modern medical imaging. However, long image acquisition times, the need for qualitative expert analysis, and the lack of (and difficulty extracting) quantitative indicators that are sensitive to tissue health have curtailed widespread clinical and research studies. While recent machine learning methods for MRI reconstruction and analysis have shown promise for reducing this burden, these techniques are primarily validated with imperfect image quality metrics, which are discordant with clinically-relevant measures that ultimately hamper clinical deployment and clinician trust. To mitigate this challenge, we present the Stanford Knee MRI with Multi-Task Evaluation (SKM-TEA) dataset, a collection of quantitative knee MRI (qMRI) scans that enables end-to-end, clinically-relevant evaluation of MRI reconstruction and analysis tools. This 1.6TB dataset consists of raw-data measurements of ~25,000 slices (155 patients) of anonymized patient MRI scans, the corresponding scanner-generated DICOM images, manual segmentations of four tissues, and bounding box annotations for sixteen clinically relevant pathologies. We provide a framework for using qMRI parameter maps, along with image reconstructions and dense image labels, for measuring the quality of qMRI biomarker estimates extracted from MRI reconstruction, segmentation, and detection techniques. Finally, we use this framework to benchmark state-of-the-art baselines on this dataset. We hope our SKM-TEA dataset and code can enable a broad spectrum of research for modular image reconstruction and image analysis in a clinically informed manner. Dataset access, code, and benchmarks are available at https://github.com/StanfordMIMI/skm-tea.

To generate evidence regarding the safety and efficacy of artificial intelligence (AI) enabled medical devices, AI models need to be evaluated on a diverse population of patient cases, some of which may not be readily available. We propose an evaluation approach for testing medical imaging AI models that relies on in silico imaging pipelines in which stochastic digital models of human anatomy (in object space) with and without pathology are imaged using a digital replica imaging acquisition system to generate realistic synthetic image datasets. Here, we release M-SYNTH, a dataset of cohorts with four breast fibroglandular density distributions imaged at different exposure levels using Monte Carlo x-ray simulations with the publicly available Virtual Imaging Clinical Trial for Regulatory Evaluation (VICTRE) toolkit. We utilize the synthetic dataset to analyze AI model performance and find that model performance decreases with increasing breast density and increases with higher mass density, as expected. As exposure levels decrease, AI model performance drops with the highest performance achieved at exposure levels lower than the nominal recommended dose for the breast type.

Accurate localization and segmentation of intervertebral disc (IVD) is crucial for the assessment of spine disease diagnosis. Despite the technological advances in medical imaging, IVD localization and segmentation are still manually performed, which is time-consuming and prone to errors. If, in addition, multi-modal imaging is considered, the burden imposed on disease assessments increases substantially. In this paper, we propose an architecture for IVD localization and segmentation in multi-modal MRI, which extends the well-known UNet. Compared to single images, multi-modal data brings complementary information, contributing to better data representation and discriminative power. Our contributions are three-fold. First, how to effectively integrate and fully leverage multi-modal data remains almost unexplored. In this work, each MRI modality is processed in a different path to better exploit their unique information. Second, inspired by HyperDenseNet, the network is densely-connected both within each path and across different paths, granting the model the freedom to learn where and how the different modalities should be processed and combined. Third, we improved standard U-Net modules by extending inception modules with two dilated convolutions blocks of different scale, which helps handling multi-scale context. We report experiments over the data set of the public MICCAI 2018 Challenge on Automatic Intervertebral Disc Localization and Segmentation, with 13 multi-modal MRI images used for training and 3 for validation. We trained IVD-Net on an NVidia TITAN XP GPU with 16 GBs RAM, using ADAM as optimizer and a learning rate of 10e-5 during 200 epochs. Training took about 5 hours, and segmentation of a whole volume about 2-3 seconds, on average. Several baselines, with different multi-modal fusion strategies, were used to demonstrate the effectiveness of the proposed architecture.

The burgeoning integration of 3D medical imaging into healthcare has led to a substantial increase in the workload of medical professionals. To assist clinicians in their diagnostic processes and alleviate their workload, the development of a robust system for retrieving similar case studies presents a viable solution. While the concept holds great promise, the field of 3D medical text-image retrieval is currently limited by the absence of robust evaluation benchmarks and curated datasets. To remedy this, our study presents a groundbreaking dataset, BIMCV-R (This dataset will be released upon acceptance.), which includes an extensive collection of 8,069 3D CT volumes, encompassing over 2 million slices, paired with their respective radiological reports. Expanding upon the foundational work of our dataset, we craft a retrieval strategy, MedFinder. This approach employs a dual-stream network architecture, harnessing the potential of large language models to advance the field of medical image retrieval beyond existing text-image retrieval solutions. It marks our preliminary step towards developing a system capable of facilitating text-to-image, image-to-text, and keyword-based retrieval tasks.

Ultrasound (US) is a widely used medical imaging modality due to its real-time capabilities, non-invasive nature, and cost-effectiveness. Robotic ultrasound can further enhance its utility by reducing operator dependence and improving access to complex anatomical regions. For this, while deep reinforcement learning (DRL) and imitation learning (IL) have shown potential for autonomous navigation, their use in complex surgical tasks such as anatomy reconstruction and surgical guidance remains limited -- largely due to the lack of realistic and efficient simulation environments tailored to these tasks. We introduce SonoGym, a scalable simulation platform for complex robotic ultrasound tasks that enables parallel simulation across tens to hundreds of environments. Our framework supports realistic and real-time simulation of US data from CT-derived 3D models of the anatomy through both a physics-based and a generative modeling approach. Sonogym enables the training of DRL and recent IL agents (vision transformers and diffusion policies) for relevant tasks in robotic orthopedic surgery by integrating common robotic platforms and orthopedic end effectors. We further incorporate submodular DRL -- a recent method that handles history-dependent rewards -- for anatomy reconstruction and safe reinforcement learning for surgery. Our results demonstrate successful policy learning across a range of scenarios, while also highlighting the limitations of current methods in clinically relevant environments. We believe our simulation can facilitate research in robot learning approaches for such challenging robotic surgery applications. Dataset, codes, and videos are publicly available at https://sonogym.github.io/.

Deep learning has demonstrated remarkable success in medical image segmentation and computer-aided diagnosis. In particular, numerous advanced methods have achieved state-of-the-art performance in brain tumor segmentation from MRI scans. While recent studies in other medical imaging domains have revealed that integrating textual reports with visual data can enhance segmentation accuracy, the field of brain tumor analysis lacks a comprehensive dataset that combines radiological images with corresponding textual annotations. This limitation has hindered the exploration of multimodal approaches that leverage both imaging and textual data. To bridge this critical gap, we introduce the TextBraTS dataset, the first publicly available volume-level multimodal dataset that contains paired MRI volumes and rich textual annotations, derived from the widely adopted BraTS2020 benchmark. Building upon this novel dataset, we propose a novel baseline framework and sequential cross-attention method for text-guided volumetric medical image segmentation. Through extensive experiments with various text-image fusion strategies and templated text formulations, our approach demonstrates significant improvements in brain tumor segmentation accuracy, offering valuable insights into effective multimodal integration techniques. Our dataset, implementation code, and pre-trained models are publicly available at https://github.com/Jupitern52/TextBraTS.

Multimodal magnetic resonance imaging (MRI) constitutes the first line of investigation for clinicians in the care of brain tumors, providing crucial insights for surgery planning, treatment monitoring, and biomarker identification. Pre-training on large datasets have been shown to help models learn transferable representations and adapt with minimal labeled data. This behavior is especially valuable in medical imaging, where annotations are often scarce. However, applying this paradigm to multimodal medical data introduces a challenge: most existing approaches assume that all imaging modalities are available during both pre-training and fine-tuning. In practice, missing modalities often occur due to acquisition issues, specialist unavailability, or specific experimental designs on small in-house datasets. Consequently, a common approach involves training a separate model for each desired modality combination, making the process both resource-intensive and impractical for clinical use. Therefore, we introduce BM-MAE, a masked image modeling pre-training strategy tailored for multimodal MRI data. The same pre-trained model seamlessly adapts to any combination of available modalities, extracting rich representations that capture both intra- and inter-modal information. This allows fine-tuning on any subset of modalities without requiring architectural changes, while still benefiting from a model pre-trained on the full set of modalities. Extensive experiments show that the proposed pre-training strategy outperforms or remains competitive with baselines that require separate pre-training for each modality subset, while substantially surpassing training from scratch on several downstream tasks. Additionally, it can quickly and efficiently reconstruct missing modalities, highlighting its practical value. Code and trained models are available at: https://github.com/Lucas-rbnt/BM-MAE

The deployment of foundation models for medical imaging has demonstrated considerable success. However, their training overheads associated with downstream tasks remain substantial due to the size of the image encoders employed, and the inference complexity is also significantly high. Although lightweight variants have been obtained for these foundation models, their performance is constrained by their limited model capacity and suboptimal training strategies. In order to achieve an improved tradeoff between complexity and performance, we propose a new framework to improve the performance of low complexity models via knowledge distillation from multiple large medical foundation models (e.g., MedSAM, RAD-DINO, MedCLIP), each specializing in different vision tasks, with the goal to effectively bridge the performance gap for medical image segmentation tasks. The agglomerated model demonstrates superior generalization across 12 segmentation tasks, whereas specialized models require explicit training for each task. Our approach achieved an average performance gain of 2\% in Dice coefficient compared to simple distillation.

In this study, we introduce the Multi-Head Explainer (MHEX), a versatile and modular framework that enhances both the explainability and accuracy of Convolutional Neural Networks (CNNs) and Transformer-based models. MHEX consists of three core components: an Attention Gate that dynamically highlights task-relevant features, Deep Supervision that guides early layers to capture fine-grained details pertinent to the target class, and an Equivalent Matrix that unifies refined local and global representations to generate comprehensive saliency maps. Our approach demonstrates superior compatibility, enabling effortless integration into existing residual networks like ResNet and Transformer architectures such as BERT with minimal modifications. Extensive experiments on benchmark datasets in medical imaging and text classification show that MHEX not only improves classification accuracy but also produces highly interpretable and detailed saliency scores.

Cervical disc herniation (CDH) is a prevalent musculoskeletal disorder that significantly impacts health and requires labor-intensive analysis from experts. Despite advancements in automated detection of medical imaging, two significant challenges hinder the real-world application of these methods. First, the computational complexity and resource demands present a significant gap for real-time application. Second, noise in MRI reduces the effectiveness of existing methods by distorting feature extraction. To address these challenges, we propose three key contributions: Firstly, we introduced MedDet, which leverages the multi-teacher single-student knowledge distillation for model compression and efficiency, meanwhile integrating generative adversarial training to enhance performance. Additionally, we customize the second-order nmODE to improve the model's resistance to noise in MRI. Lastly, we conducted comprehensive experiments on the CDH-1848 dataset, achieving up to a 5% improvement in mAP compared to previous methods. Our approach also delivers over 5 times faster inference speed, with approximately 67.8% reduction in parameters and 36.9% reduction in FLOPs compared to the teacher model. These advancements significantly enhance the performance and efficiency of automated CDH detection, demonstrating promising potential for future application in clinical practice. See project website https://steve-zeyu-zhang.github.io/MedDet

Development of artificial intelligence (AI) techniques in medical imaging requires access to large-scale and diverse datasets for training and evaluation. In dermatology, obtaining such datasets remains challenging due to significant variations in patient populations, illumination conditions, and acquisition system characteristics. In this work, we propose S-SYNTH, the first knowledge-based, adaptable open-source skin simulation framework to rapidly generate synthetic skin, 3D models and digitally rendered images, using an anatomically inspired multi-layer, multi-component skin and growing lesion model. The skin model allows for controlled variation in skin appearance, such as skin color, presence of hair, lesion shape, and blood fraction among other parameters. We use this framework to study the effect of possible variations on the development and evaluation of AI models for skin lesion segmentation, and show that results obtained using synthetic data follow similar comparative trends as real dermatologic images, while mitigating biases and limitations from existing datasets including small dataset size, lack of diversity, and underrepresentation.

The integration of neural-network-based systems into clinical practice is limited by challenges related to domain generalization and robustness. The computer vision community established benchmarks such as ImageNet-C as a fundamental prerequisite to measure progress towards those challenges. Similar datasets are largely absent in the medical imaging community which lacks a comprehensive benchmark that spans across imaging modalities and applications. To address this gap, we create and open-source MedMNIST-C, a benchmark dataset based on the MedMNIST+ collection covering 12 datasets and 9 imaging modalities. We simulate task and modality-specific image corruptions of varying severity to comprehensively evaluate the robustness of established algorithms against real-world artifacts and distribution shifts. We further provide quantitative evidence that our simple-to-use artificial corruptions allow for highly performant, lightweight data augmentation to enhance model robustness. Unlike traditional, generic augmentation strategies, our approach leverages domain knowledge, exhibiting significantly higher robustness when compared to widely adopted methods. By introducing MedMNIST-C and open-sourcing the corresponding library allowing for targeted data augmentations, we contribute to the development of increasingly robust methods tailored to the challenges of medical imaging. The code is available at https://github.com/francescodisalvo05/medmnistc-api .

Humans effortlessly interpret images by parsing them into part-whole hierarchies; deep learning excels in learning multi-level feature spaces, but they often lack explicit coding of part-whole relations, a prominent property of medical imaging. To overcome this limitation, we introduce Adam-v2, a new self-supervised learning framework extending Adam [79] by explicitly incorporating part-whole hierarchies into its learning objectives through three key branches: (1) Localizability, acquiring discriminative representations to distinguish different anatomical patterns; (2) Composability, learning each anatomical structure in a parts-to-whole manner; and (3) Decomposability, comprehending each anatomical structure in a whole-to-parts manner. Experimental results across 10 tasks, compared to 11 baselines in zero-shot, few-shot transfer, and full fine-tuning settings, showcase Adam-v2's superior performance over large-scale medical models and existing SSL methods across diverse downstream tasks. The higher generality and robustness of Adam-v2's representations originate from its explicit construction of hierarchies for distinct anatomical structures from unlabeled medical images. Adam-v2 preserves a semantic balance of anatomical diversity and harmony in its embedding, yielding representations that are both generic and semantically meaningful, yet overlooked in existing SSL methods. All code and pretrained models are available at https://github.com/JLiangLab/Eden.

Despite the ever-increasing interest in applying deep learning (DL) models to medical imaging, the typical scarcity and imbalance of medical datasets can severely impact the performance of DL models. The generation of synthetic data that might be freely shared without compromising patient privacy is a well-known technique for addressing these difficulties. Inpainting algorithms are a subset of DL generative models that can alter one or more regions of an input image while matching its surrounding context and, in certain cases, non-imaging input conditions. Although the majority of inpainting techniques for medical imaging data use generative adversarial networks (GANs), the performance of these algorithms is frequently suboptimal due to their limited output variety, a problem that is already well-known for GANs. Denoising diffusion probabilistic models (DDPMs) are a recently introduced family of generative networks that can generate results of comparable quality to GANs, but with diverse outputs. In this paper, we describe a DDPM to execute multiple inpainting tasks on 2D axial slices of brain MRI with various sequences, and present proof-of-concept examples of its performance in a variety of evaluation scenarios. Our model and a public online interface to try our tool are available at: https://github.com/Mayo-Radiology-Informatics-Lab/MBTI

In clinical radiology reports, doctors capture important information about the patient's health status. They convey their observations from raw medical imaging data about the inner structures of a patient. As such, formulating reports requires medical experts to possess wide-ranging knowledge about anatomical regions with their normal, healthy appearance as well as the ability to recognize abnormalities. This explicit grasp on both the patient's anatomy and their appearance is missing in current medical image-processing systems as annotations are especially difficult to gather. This renders the models to be narrow experts e.g. for identifying specific diseases. In this work, we recover this missing link by adding human anatomy into the mix and enable the association of content in medical reports to their occurrence in associated imagery (medical phrase grounding). To exploit anatomical structures in this scenario, we present a sophisticated automatic pipeline to gather and integrate human bodily structures from computed tomography datasets, which we incorporate in our PAXRay: A Projected dataset for the segmentation of Anatomical structures in X-Ray data. Our evaluation shows that methods that take advantage of anatomical information benefit heavily in visually grounding radiologists' findings, as our anatomical segmentations allow for up to absolute 50% better grounding results on the OpenI dataset as compared to commonly used region proposals. The PAXRay dataset is available at https://constantinseibold.github.io/paxray/.

Image registration is important for medical imaging, the estimation of the spatial transformation between different images. Many previous studies have used learning-based methods for coarse-to-fine registration to efficiently perform 3D image registration. The coarse-to-fine approach, however, is limited when dealing with the different motions of nearby objects. Here we propose a novel Motion-Aware (MA) structure that captures the different motions in a region. The MA structure incorporates a novel Residual Aligner (RA) module which predicts the multi-head displacement field used to disentangle the different motions of multiple neighbouring objects. Compared with other deep learning methods, the network based on the MA structure and RA module achieve one of the most accurate unsupervised inter-subject registration on the 9 organs of assorted sizes in abdominal CT scans, with the highest-ranked registration of the veins (Dice Similarity Coefficient / Average surface distance: 62\%/4.9mm for the vena cava and 34\%/7.9mm for the portal and splenic vein), with a half-sized structure and more efficient computation. Applied to the segmentation of lungs in chest CT scans, the new network achieves results which were indistinguishable from the best-ranked networks (94\%/3.0mm). Additionally, the theorem on predicted motion pattern and the design of MA structure are validated by further analysis.

Deep learning in the presence of noisy annotations has been studied extensively in classification, but much less in segmentation tasks. In this work, we study the learning dynamics of deep segmentation networks trained on inaccurately-annotated data. We discover a phenomenon that has been previously reported in the context of classification: the networks tend to first fit the clean pixel-level labels during an "early-learning" phase, before eventually memorizing the false annotations. However, in contrast to classification, memorization in segmentation does not arise simultaneously for all semantic categories. Inspired by these findings, we propose a new method for segmentation from noisy annotations with two key elements. First, we detect the beginning of the memorization phase separately for each category during training. This allows us to adaptively correct the noisy annotations in order to exploit early learning. Second, we incorporate a regularization term that enforces consistency across scales to boost robustness against annotation noise. Our method outperforms standard approaches on a medical-imaging segmentation task where noises are synthesized to mimic human annotation errors. It also provides robustness to realistic noisy annotations present in weakly-supervised semantic segmentation, achieving state-of-the-art results on PASCAL VOC 2012. Code is available at https://github.com/Kangningthu/ADELE

We propose a novel attention gate (AG) model for medical imaging that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules of cascaded convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN architectures such as the U-Net model with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed Attention U-Net architecture is evaluated on two large CT abdominal datasets for multi-class image segmentation. Experimental results show that AGs consistently improve the prediction performance of U-Net across different datasets and training sizes while preserving computational efficiency. The code for the proposed architecture is publicly available.

Recent advances in artificial intelligence (AI), specifically in computer vision (CV) and deep learning (DL), have created opportunities for novel systems in many fields. In the last few years, deep learning applications have demonstrated impressive results not only in fields such as autonomous driving and robotics, but also in the field of medicine, where they have, in some cases, even exceeded human-level performance. However, despite the huge potential, adoption of deep learning-based methods is still slow in many areas, especially in veterinary medicine, where we haven't been able to find any research papers using modern convolutional neural networks (CNNs) in medical image processing. We believe that using deep learning-based medical imaging can enable more accurate, faster and less expensive diagnoses in veterinary medicine. In order to do so, however, these methods have to be accessible to everyone in this field, not just to computer scientists. To show the potential of this technology, we present results on a real-world task in veterinary medicine that is usually done manually: feline reticulocyte percentage. Using an open source Keras implementation of the Single-Shot MultiBox Detector (SSD) model architecture and training it on only 800 labeled images, we achieve an accuracy of 98.7% at predicting the correct number of aggregate reticulocytes in microscope images of cat blood smears. The main motivation behind this paper is to show not only that deep learning can approach or even exceed human-level performance on a task like this, but also that anyone in the field can implement it, even without a background in computer science.

Disease progression simulation is a crucial area of research that has significant implications for clinical diagnosis, prognosis, and treatment. One major challenge in this field is the lack of continuous medical imaging monitoring of individual patients over time. To address this issue, we develop a novel framework termed Progressive Image Editing (PIE) that enables controlled manipulation of disease-related image features, facilitating precise and realistic disease progression simulation. Specifically, we leverage recent advancements in text-to-image generative models to simulate disease progression accurately and personalize it for each patient. We theoretically analyze the iterative refining process in our framework as a gradient descent with an exponentially decayed learning rate. To validate our framework, we conduct experiments in three medical imaging domains. Our results demonstrate the superiority of PIE over existing methods such as Stable Diffusion Walk and Style-Based Manifold Extrapolation based on CLIP score (Realism) and Disease Classification Confidence (Alignment). Our user study collected feedback from 35 veteran physicians to assess the generated progressions. Remarkably, 76.2% of the feedback agrees with the fidelity of the generated progressions. To our best knowledge, PIE is the first of its kind to generate disease progression images meeting real-world standards. It is a promising tool for medical research and clinical practice, potentially allowing healthcare providers to model disease trajectories over time, predict future treatment responses, and improve patient outcomes.

A major challenge in computational research in 3D medical imaging is the lack of comprehensive datasets. Addressing this issue, our study introduces CT-RATE, the first 3D medical imaging dataset that pairs images with textual reports. CT-RATE consists of 25,692 non-contrast chest CT volumes, expanded to 50,188 through various reconstructions, from 21,304 unique patients, along with corresponding radiology text reports. Leveraging CT-RATE, we developed CT-CLIP, a CT-focused contrastive language-image pre-training framework. As a versatile, self-supervised model, CT-CLIP is designed for broad application and does not require task-specific training. Remarkably, CT-CLIP outperforms state-of-the-art, fully supervised methods in multi-abnormality detection across all key metrics, thus eliminating the need for manual annotation. We also demonstrate its utility in case retrieval, whether using imagery or textual queries, thereby advancing knowledge dissemination. The open-source release of CT-RATE and CT-CLIP marks a significant advancement in medical AI, enhancing 3D imaging analysis and fostering innovation in healthcare.

Active learning promises to improve annotation efficiency by iteratively selecting the most important data to be annotated first. However, we uncover a striking contradiction to this promise: active learning fails to select data as efficiently as random selection at the first few choices. We identify this as the cold start problem in vision active learning, caused by a biased and outlier initial query. This paper seeks to address the cold start problem by exploiting the three advantages of contrastive learning: (1) no annotation is required; (2) label diversity is ensured by pseudo-labels to mitigate bias; (3) typical data is determined by contrastive features to reduce outliers. Experiments are conducted on CIFAR-10-LT and three medical imaging datasets (i.e. Colon Pathology, Abdominal CT, and Blood Cell Microscope). Our initial query not only significantly outperforms existing active querying strategies but also surpasses random selection by a large margin. We foresee our solution to the cold start problem as a simple yet strong baseline to choose the initial query for vision active learning. Code is available: https://github.com/c-liangyu/CSVAL

Sparse autoencoders (SAEs) emerged as a promising tool for mechanistic interpretability of transformer-based foundation models. Very recently, SAEs were also adopted for the visual domain, enabling the discovery of visual concepts and their patch-wise attribution to tokens in the transformer model. While a growing number of foundation models emerged for medical imaging, tools for explaining their inferences are still lacking. In this work, we show the applicability of SAEs for hematology. We propose CytoSAE, a sparse autoencoder which is trained on over 40,000 peripheral blood single-cell images. CytoSAE generalizes to diverse and out-of-domain datasets, including bone marrow cytology, where it identifies morphologically relevant concepts which we validated with medical experts. Furthermore, we demonstrate scenarios in which CytoSAE can generate patient-specific and disease-specific concepts, enabling the detection of pathognomonic cells and localized cellular abnormalities at the patch level. We quantified the effect of concepts on a patient-level AML subtype classification task and show that CytoSAE concepts reach performance comparable to the state-of-the-art, while offering explainability on the sub-cellular level. Source code and model weights are available at https://github.com/dynamical-inference/cytosae.

One of the key impediments for developing and assessing robust medical imaging algorithms is limited access to large-scale datasets with suitable annotations. Synthetic data generated with plausible physical and biological constraints may address some of these data limitations. We propose the use of physics simulations to generate synthetic images with pixel-level segmentation annotations, which are notoriously difficult to obtain. Specifically, we apply this approach to breast imaging analysis and release T-SYNTH, a large-scale open-source dataset of paired 2D digital mammography (DM) and 3D digital breast tomosynthesis (DBT) images. Our initial experimental results indicate that T-SYNTH images show promise for augmenting limited real patient datasets for detection tasks in DM and DBT. Our data and code are publicly available at https://github.com/DIDSR/tsynth-release.

Existing adaptation techniques typically require architectural modifications or added parameters, leading to high computational costs and complexity. We introduce Attention Projection Layer Adaptation (APLA), a simple approach to adapt vision transformers (ViTs) without altering the architecture or adding parameters. Through a systematic analysis, we find that the layer immediately after the attention mechanism is crucial for adaptation. By updating only this projection layer, or even just a random subset of this layer's weights, APLA achieves state-of-the-art performance while reducing GPU memory usage by up to 52.63% and training time by up to 43.0%, with no extra cost at inference. Across 46 datasets covering a variety of tasks including scene classification, medical imaging, satellite imaging, and fine-grained classification, APLA consistently outperforms 17 other leading adaptation methods, including full fine-tuning, on classification, segmentation, and detection tasks. The code is available at https://github.com/MoeinSorkhei/APLA.

Foundation models (FMs) have shown transformative potential in radiology by performing diverse, complex tasks across imaging modalities. Here, we developed CT-FM, a large-scale 3D image-based pre-trained model designed explicitly for various radiological tasks. CT-FM was pre-trained using 148,000 computed tomography (CT) scans from the Imaging Data Commons through label-agnostic contrastive learning. We evaluated CT-FM across four categories of tasks, namely, whole-body and tumor segmentation, head CT triage, medical image retrieval, and semantic understanding, showing superior performance against state-of-the-art models. Beyond quantitative success, CT-FM demonstrated the ability to cluster regions anatomically and identify similar anatomical and structural concepts across scans. Furthermore, it remained robust across test-retest settings and indicated reasonable salient regions attached to its embeddings. This study demonstrates the value of large-scale medical imaging foundation models and by open-sourcing the model weights, code, and data, aims to support more adaptable, reliable, and interpretable AI solutions in radiology.

Self-supervised learning (SSL) has potential for effective representation learning in medical imaging, but the choice of data augmentation is critical and domain-specific. It remains uncertain if general augmentation policies suit surgical applications. In this work, we automate the search for suitable augmentation policies through a new method called Dimensionality Driven Augmentation Search (DDA). DDA leverages the local dimensionality of deep representations as a proxy target, and differentiably searches for suitable data augmentation policies in contrastive learning. We demonstrate the effectiveness and efficiency of DDA in navigating a large search space and successfully identifying an appropriate data augmentation policy for laparoscopic surgery. We systematically evaluate DDA across three laparoscopic image classification and segmentation tasks, where it significantly improves over existing baselines. Furthermore, DDA's optimised set of augmentations provides insight into domain-specific dependencies when applying contrastive learning in medical applications. For example, while hue is an effective augmentation for natural images, it is not advantageous for laparoscopic images.

This paper introduces an innovative methodology for producing high-quality 3D lung CT images guided by textual information. While diffusion-based generative models are increasingly used in medical imaging, current state-of-the-art approaches are limited to low-resolution outputs and underutilize radiology reports' abundant information. The radiology reports can enhance the generation process by providing additional guidance and offering fine-grained control over the synthesis of images. Nevertheless, expanding text-guided generation to high-resolution 3D images poses significant memory and anatomical detail-preserving challenges. Addressing the memory issue, we introduce a hierarchical scheme that uses a modified UNet architecture. We start by synthesizing low-resolution images conditioned on the text, serving as a foundation for subsequent generators for complete volumetric data. To ensure the anatomical plausibility of the generated samples, we provide further guidance by generating vascular, airway, and lobular segmentation masks in conjunction with the CT images. The model demonstrates the capability to use textual input and segmentation tasks to generate synthesized images. The results of comparative assessments indicate that our approach exhibits superior performance compared to the most advanced models based on GAN and diffusion techniques, especially in accurately retaining crucial anatomical features such as fissure lines, airways, and vascular structures. This innovation introduces novel possibilities. This study focuses on two main objectives: (1) the development of a method for creating images based on textual prompts and anatomical components, and (2) the capability to generate new images conditioning on anatomical elements. The advancements in image generation can be applied to enhance numerous downstream tasks.

Whole slide image (WSI) analysis has become increasingly important in the medical imaging community, enabling automated and objective diagnosis, prognosis, and therapeutic-response prediction. However, in clinical practice, the ever-evolving environment hamper the utility of WSI analysis models. In this paper, we propose the FIRST continual learning framework for WSI analysis, named ConSlide, to tackle the challenges of enormous image size, utilization of hierarchical structure, and catastrophic forgetting by progressive model updating on multiple sequential datasets. Our framework contains three key components. The Hierarchical Interaction Transformer (HIT) is proposed to model and utilize the hierarchical structural knowledge of WSI. The Breakup-Reorganize (BuRo) rehearsal method is developed for WSI data replay with efficient region storing buffer and WSI reorganizing operation. The asynchronous updating mechanism is devised to encourage the network to learn generic and specific knowledge respectively during the replay stage, based on a nested cross-scale similarity learning (CSSL) module. We evaluated the proposed ConSlide on four public WSI datasets from TCGA projects. It performs best over other state-of-the-art methods with a fair WSI-based continual learning setting and achieves a better trade-off of the overall performance and forgetting on previous task

Following the impressive development of LLMs, vision-language alignment in LLMs is actively being researched to enable multimodal reasoning and visual IO. This direction of research is particularly relevant to medical imaging because medical image analysis and generation consist of reasoning based on a combination of visual features and prior knowledge. Many recent works have focused on training adapter networks that serve as an information bridge between image processing networks and LLMs; but presumably, in order to achieve maximum reasoning potential of LLMs on visual information as well, visual and language features should be allowed to interact more freely. This is especially important in the medical domain because understanding and generating medical images such as chest X-rays (CXR) require not only accurate visual and language-based reasoning but also a more intimate mapping between the two modalities. Thus, taking inspiration from previous work on the transformer and VQ-GAN combination for bidirectional image and text generation, we build upon this approach and develop a method for instruction-tuning an LLM pre-trained only on text to gain vision-language capabilities for medical images. Specifically, we leverage a pretrained LLM's existing question-answering and instruction-following abilities to teach it to understand visual inputs by instructing it to answer questions about image inputs and, symmetrically, output both text and image responses appropriate to a given query by tuning the LLM with diverse tasks that encompass image-based text-generation and text-based image-generation. We show that our model, LLM-CXR, trained in this approach shows better image-text alignment in both CXR understanding and generation tasks while being smaller in size compared to previously developed models that perform a narrower range of tasks. The code is at https://github.com/hyn2028/llm-cxr.

Deep learning methods have shown outstanding classification accuracy in medical imaging problems, which is largely attributed to the availability of large-scale datasets manually annotated with clean labels. However, given the high cost of such manual annotation, new medical imaging classification problems may need to rely on machine-generated noisy labels extracted from radiology reports. Indeed, many Chest X-ray (CXR) classifiers have already been modelled from datasets with noisy labels, but their training procedure is in general not robust to noisy-label samples, leading to sub-optimal models. Furthermore, CXR datasets are mostly multi-label, so current noisy-label learning methods designed for multi-class problems cannot be easily adapted. In this paper, we propose a new method designed for the noisy multi-label CXR learning, which detects and smoothly re-labels samples from the dataset, which is then used to train common multi-label classifiers. The proposed method optimises a bag of multi-label descriptors (BoMD) to promote their similarity with the semantic descriptors produced by BERT models from the multi-label image annotation. Our experiments on diverse noisy multi-label training sets and clean testing sets show that our model has state-of-the-art accuracy and robustness in many CXR multi-label classification benchmarks.

Domain adaptation (DA) has drawn high interest for its capacity to adapt a model trained on labeled source data to perform well on unlabeled or weakly labeled target data from a different domain. Most common DA techniques require concurrent access to the input images of both the source and target domains. However, in practice, privacy concerns often impede the availability of source images in the adaptation phase. This is a very frequent DA scenario in medical imaging, where, for instance, the source and target images could come from different clinical sites. We introduce a source-free domain adaptation for image segmentation. Our formulation is based on minimizing a label-free entropy loss defined over target-domain data, which we further guide with a domain-invariant prior on the segmentation regions. Many priors can be derived from anatomical information. Here, a class ratio prior is estimated from anatomical knowledge and integrated in the form of a Kullback Leibler (KL) divergence in our overall loss function. Furthermore, we motivate our overall loss with an interesting link to maximizing the mutual information between the target images and their label predictions. We show the effectiveness of our prior aware entropy minimization in a variety of domain-adaptation scenarios, with different modalities and applications, including spine, prostate, and cardiac segmentation. Our method yields comparable results to several state of the art adaptation techniques, despite having access to much less information, as the source images are entirely absent in our adaptation phase. Our straightforward adaptation strategy uses only one network, contrary to popular adversarial techniques, which are not applicable to a source-free DA setting. Our framework can be readily used in a breadth of segmentation problems, and our code is publicly available: https://github.com/mathilde-b/SFDA

Federated learning (FL) has been a promising approach in the field of medical imaging in recent years. A critical problem in FL, specifically in medical scenarios is to have a more accurate shared model which is robust to noisy and out-of distribution clients. In this work, we tackle the problem of statistical heterogeneity in data for FL which is highly plausible in medical data where for example the data comes from different sites with different scanner settings. We propose IDA (Inverse Distance Aggregation), a novel adaptive weighting approach for clients based on meta-information which handles unbalanced and non-iid data. We extensively analyze and evaluate our method against the well-known FL approach, Federated Averaging as a baseline.

Self-supervised pre-training of deep learning models with contrastive learning is a widely used technique in image analysis. Current findings indicate a strong potential for contrastive pre-training on medical images. However, further research is necessary to incorporate the particular characteristics of these images. We hypothesize that the similarity of medical images hinders the success of contrastive learning in the medical imaging domain. To this end, we investigate different strategies based on deep embedding, information theory, and hashing in order to identify and reduce redundancy in medical pre-training datasets. The effect of these different reduction strategies on contrastive learning is evaluated on two pre-training datasets and several downstream classification tasks. In all of our experiments, dataset reduction leads to a considerable performance gain in downstream tasks, e.g., an AUC score improvement from 0.78 to 0.83 for the COVID CT Classification Grand Challenge, 0.97 to 0.98 for the OrganSMNIST Classification Challenge and 0.73 to 0.83 for a brain hemorrhage classification task. Furthermore, pre-training is up to nine times faster due to the dataset reduction. In conclusion, the proposed approach highlights the importance of dataset quality and provides a transferable approach to improve contrastive pre-training for classification downstream tasks on medical images.

This paper introduces a novel one-stage end-to-end detector specifically designed to detect small lesions in medical images. Precise localization of small lesions presents challenges due to their appearance and the diverse contextual backgrounds in which they are found. To address this, our approach introduces a new type of pixel-based anchor that dynamically moves towards the targeted lesion for detection. We refer to this new architecture as GravityNet, and the novel anchors as gravity points since they appear to be "attracted" by the lesions. We conducted experiments on two well-established medical problems involving small lesions to evaluate the performance of the proposed approach: microcalcifications detection in digital mammograms and microaneurysms detection in digital fundus images. Our method demonstrates promising results in effectively detecting small lesions in these medical imaging tasks.

In semantic segmentation, the accuracy of models heavily depends on the high-quality annotations. However, in many practical scenarios such as medical imaging and remote sensing, obtaining true annotations is not straightforward and usually requires significant human labor. Relying on human labor often introduces annotation errors, including mislabeling, omissions, and inconsistency between annotators. In the case of remote sensing, differences in procurement time can lead to misaligned ground truth annotations. These label errors are not independently distributed, and instead usually appear in spatially connected regions where adjacent pixels are more likely to share the same errors. To address these issues, we propose an approximate Bayesian estimation based on a probabilistic model that assumes training data includes label errors, incorporating the tendency for these errors to occur with spatial correlations between adjacent pixels. Bayesian inference requires computing the posterior distribution of label errors, which becomes intractable when spatial correlations are present. We represent the correlation of label errors between adjacent pixels through a Gaussian distribution whose covariance is structured by a Kac-Murdock-Szeg\"{o} (KMS) matrix, solving the computational challenges. Through experiments on multiple segmentation tasks, we confirm that leveraging the spatial correlation of label errors significantly improves performance. Notably, in specific tasks such as lung segmentation, the proposed method achieves performance comparable to training with clean labels under moderate noise levels. Code is available at https://github.com/pfnet-research/Bayesian_SpatialCorr.

A major challenge of the long measurement times in magnetic resonance imaging (MRI), an important medical imaging technology, is that patients may move during data acquisition. This leads to severe motion artifacts in the reconstructed images and volumes. In this paper, we propose a deep learning-based test-time-training method for accurate motion estimation. The key idea is that a neural network trained for motion-free reconstruction has a small loss if there is no motion, thus optimizing over motion parameters passed through the reconstruction network enables accurate estimation of motion. The estimated motion parameters enable to correct for the motion and to reconstruct accurate motion-corrected images. Our method uses 2D reconstruction networks to estimate rigid motion in 3D, and constitutes the first deep learning based method for 3D rigid motion estimation towards 3D-motion-corrected MRI. We show that our method can provably reconstruct motion parameters for a simple signal and neural network model. We demonstrate the effectiveness of our method for both retrospectively simulated motion and prospectively collected real motion-corrupted data.

The Segment Anything Model (SAM) has achieved remarkable successes in the realm of natural image segmentation, but its deployment in the medical imaging sphere has encountered challenges. Specifically, the model struggles with medical images that feature low contrast, faint boundaries, intricate morphologies, and small-sized objects. To address these challenges and enhance SAM's performance in the medical domain, we introduce a comprehensive modification. Firstly, we incorporate a frozen Convolutional Neural Network (CNN) branch as an image encoder, which synergizes with SAM's original Vision Transformer (ViT) encoder through a novel variational attention fusion module. This integration bolsters the model's capability to capture local spatial information, which is often paramount in medical imagery. Moreover, to further optimize SAM for medical imaging, we introduce feature and position adapters within the ViT branch, refining the encoder's representations. We see that compared to current prompting strategies to fine-tune SAM for ultrasound medical segmentation, the use of text descriptions that serve as text prompts for SAM helps significantly improve the performance. Leveraging ChatGPT's natural language understanding capabilities, we generate prompts that offer contextual information and guidance to SAM, enabling it to better understand the nuances of ultrasound medical images and improve its segmentation accuracy. Our method, in its entirety, represents a significant stride towards making universal image segmentation models more adaptable and efficient in the medical domain.

The Segment Anything Model (SAM) has demonstrated outstanding adaptation to medical image segmentation but still faces three major challenges. Firstly, the huge computational costs of SAM limit its real-world applicability. Secondly, SAM depends on manual annotations (e.g., points, boxes) as prompts, which are laborious and impractical in clinical scenarios. Thirdly, SAM handles all segmentation targets equally, which is suboptimal for diverse medical modalities with inherent heterogeneity. To address these issues, we propose an Efficient Self-Prompting SAM for universal medical image segmentation, named ESP-MedSAM. We devise a Multi-Modal Decoupled Knowledge Distillation (MMDKD) strategy to distil common image knowledge and domain-specific medical knowledge from the foundation model to train a lightweight image encoder and a modality controller. Further, they combine with the additionally introduced Self-Patch Prompt Generator (SPPG) and Query-Decoupled Modality Decoder (QDMD) to construct ESP-MedSAM. Specifically, SPPG aims to generate a set of patch prompts automatically and QDMD leverages a one-to-one strategy to provide an independent decoding channel for every modality. Extensive experiments indicate that ESP-MedSAM outperforms state-of-the-arts in diverse medical imaging segmentation takes, displaying superior zero-shot learning and modality transfer ability. Especially, our framework uses only 31.4% parameters compared to SAM-Base.

Coronary artery disease (CAD) remains the leading cause of death globally and invasive coronary angiography (ICA) is considered the gold standard of anatomical imaging evaluation when CAD is suspected. However, risk evaluation based on ICA has several limitations, such as visual assessment of stenosis severity, which has significant interobserver variability. This motivates to development of a lesion classification system that can support specialists in their clinical procedures. Although deep learning classification methods are well-developed in other areas of medical imaging, ICA image classification is still at an early stage. One of the most important reasons is the lack of available and high-quality open-access datasets. In this paper, we reported a new annotated ICA images dataset, CADICA, to provide the research community with a comprehensive and rigorous dataset of coronary angiography consisting of a set of acquired patient videos and associated disease-related metadata. This dataset can be used by clinicians to train their skills in angiographic assessment of CAD severity and by computer scientists to create computer-aided diagnostic systems to help in such assessment. In addition, baseline classification methods are proposed and analyzed, validating the functionality of CADICA and giving the scientific community a starting point to improve CAD detection.

Multi-modal (vision-language) models, such as CLIP, are replacing traditional supervised pre-training models (e.g., ImageNet-based pre-training) as the new generation of visual foundation models. These models with robust and aligned semantic representations learned from billions of internet image-text pairs and can be applied to various downstream tasks in a zero-shot manner. However, in some fine-grained domains like medical imaging and remote sensing, the performance of multi-modal foundation models often leaves much to be desired. Consequently, many researchers have begun to explore few-shot adaptation methods for these models, gradually deriving three main technical approaches: 1) prompt-based methods, 2) adapter-based methods, and 3) external knowledge-based methods. Nevertheless, this rapidly developing field has produced numerous results without a comprehensive survey to systematically organize the research progress. Therefore, in this survey, we introduce and analyze the research advancements in few-shot adaptation methods for multi-modal models, summarizing commonly used datasets and experimental setups, and comparing the results of different methods. In addition, due to the lack of reliable theoretical support for existing methods, we derive the few-shot adaptation generalization error bound for multi-modal models. The theorem reveals that the generalization error of multi-modal foundation models is constrained by three factors: domain gap, model capacity, and sample size. Based on this, we propose three possible solutions from the following aspects: 1) adaptive domain generalization, 2) adaptive model selection, and 3) adaptive knowledge utilization.

Longitudinal analysis has great potential to reveal developmental trajectories and monitor disease progression in medical imaging. This process relies on consistent and robust joint 4D segmentation. Traditional techniques are dependent on the similarity of images over time and the use of subject-specific priors to reduce random variation and improve the robustness and sensitivity of the overall longitudinal analysis. This is however slow and computationally intensive as subject-specific templates need to be rebuilt every time. The focus of this work to accelerate this analysis with the use of deep learning. The proposed approach is based on deep CNNs and incorporates semantic segmentation and provides a longitudinal relationship for the same subject. The proposed approach is based on deep CNNs and incorporates semantic segmentation and provides a longitudinal relationship for the same subject. The state of art using 3D patches as inputs to modified Unet provides results around {0.91 pm 0.5} Dice and using multi-view atlas in CNNs provide around the same results. In this work, different models are explored, each offers better accuracy and fast results while increasing the segmentation quality. These methods are evaluated on 135 scans from the EADC-ADNI Harmonized Hippocampus Protocol. Proposed CNN based segmentation approaches demonstrate how 2D segmentation using prior slices can provide similar results to 3D segmentation while maintaining good continuity in the 3D dimension and improved speed. Just using 2D modified sagittal slices provide us a better Dice and longitudinal analysis for a given subject. For the ADNI dataset, using the simple UNet CNN technique gives us {0.84 pm 0.5} and while using modified CNN techniques on the same input yields {0.89 pm 0.5}. Rate of atrophy and RMS error are calculated for several test cases using various methods and analyzed.

Image Super-Resolution is a fundamental problem in computer vision with broad applications spacing from medical imaging to satellite analysis. The ability to reconstruct high-resolution images from low-resolution inputs is crucial for enhancing downstream tasks such as object detection and segmentation. While deep learning has significantly advanced SR, achieving high-quality reconstructions with fine-grained details and realistic textures remains challenging, particularly at high upscaling factors. Recent approaches leveraging diffusion models have demonstrated promising results, yet they often struggle to balance perceptual quality with structural fidelity. In this work, we introduce ResQu a novel SR framework that integrates a quaternion wavelet preprocessing framework with latent diffusion models, incorporating a new quaternion wavelet- and time-aware encoder. Unlike prior methods that simply apply wavelet transforms within diffusion models, our approach enhances the conditioning process by exploiting quaternion wavelet embeddings, which are dynamically integrated at different stages of denoising. Furthermore, we also leverage the generative priors of foundation models such as Stable Diffusion. Extensive experiments on domain-specific datasets demonstrate that our method achieves outstanding SR results, outperforming in many cases existing approaches in perceptual quality and standard evaluation metrics. The code will be available after the revision process.

Contrastive Language-Image Pre-training (CLIP) demonstrates strong potential in medical image analysis but requires substantial data and computational resources. Due to these restrictions, existing CLIP applications in medical imaging focus mainly on modalities like chest X-rays that have abundant image-report data available, leaving many other important modalities underexplored. Here, we propose one of the first adaptations of the full CLIP model to mammography, which presents significant challenges due to labeled data scarcity, high-resolution images with small regions of interest, and class-wise imbalance. We first develop a specialized supervision framework for mammography that leverages its multi-view nature. Furthermore, we design a symmetric local alignment module to better focus on detailed features in high-resolution images. Lastly, we incorporate a parameter-efficient fine-tuning approach for large language models pre-trained with medical knowledge to address data limitations. Our multi-view and multi-scale alignment (MaMA) method outperforms state-of-the-art baselines for three different tasks on two large real-world mammography datasets, EMBED and RSNA-Mammo, with only 52% model size compared with the largest baseline. The code is available at https://github.com/XYPB/MaMA

Foundation vision-language models are currently transforming computer vision, and are on the rise in medical imaging fueled by their very promising generalization capabilities. However, the initial attempts to transfer this new paradigm to medical imaging have shown less impressive performances than those observed in other domains, due to the significant domain shift and the complex, expert domain knowledge inherent to medical-imaging tasks. Motivated by the need for domain-expert foundation models, we present FLAIR, a pre-trained vision-language model for universal retinal fundus image understanding. To this end, we compiled 37 open-access, mostly categorical fundus imaging datasets from various sources, with up to 97 different target conditions and 284,660 images. We integrate the expert's domain knowledge in the form of descriptive textual prompts, during both pre-training and zero-shot inference, enhancing the less-informative categorical supervision of the data. Such a textual expert's knowledge, which we compiled from the relevant clinical literature and community standards, describes the fine-grained features of the pathologies as well as the hierarchies and dependencies between them. We report comprehensive evaluations, which illustrate the benefit of integrating expert knowledge and the strong generalization capabilities of FLAIR under difficult scenarios with domain shifts or unseen categories. When adapted with a lightweight linear probe, FLAIR outperforms fully-trained, dataset-focused models, more so in the few-shot regimes. Interestingly, FLAIR outperforms by a large margin more generalist, larger-scale image-language models, which emphasizes the potential of embedding experts' domain knowledge and the limitations of generalist models in medical imaging.

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.

Reconstructing 3D shapes from planar cross-sections is a challenge inspired by downstream applications like medical imaging and geographic informatics. The input is an in/out indicator function fully defined on a sparse collection of planes in space, and the output is an interpolation of the indicator function to the entire volume. Previous works addressing this sparse and ill-posed problem either produce low quality results, or rely on additional priors such as target topology, appearance information, or input normal directions. In this paper, we present OReX, a method for 3D shape reconstruction from slices alone, featuring a Neural Field as the interpolation prior. A modest neural network is trained on the input planes to return an inside/outside estimate for a given 3D coordinate, yielding a powerful prior that induces smoothness and self-similarities. The main challenge for this approach is high-frequency details, as the neural prior is overly smoothing. To alleviate this, we offer an iterative estimation architecture and a hierarchical input sampling scheme that encourage coarse-to-fine training, allowing the training process to focus on high frequencies at later stages. In addition, we identify and analyze a ripple-like effect stemming from the mesh extraction step. We mitigate it by regularizing the spatial gradients of the indicator function around input in/out boundaries during network training, tackling the problem at the root. Through extensive qualitative and quantitative experimentation, we demonstrate our method is robust, accurate, and scales well with the size of the input. We report state-of-the-art results compared to previous approaches and recent potential solutions, and demonstrate the benefit of our individual contributions through analysis and ablation studies.

Building AI models with trustworthiness is important especially in regulated areas such as healthcare. In tackling COVID-19, previous work uses convolutional neural networks as the backbone architecture, which has shown to be prone to over-caution and overconfidence in making decisions, rendering them less trustworthy -- a crucial flaw in the context of medical imaging. In this study, we propose a feature learning approach using Vision Transformers, which use an attention-based mechanism, and examine the representation learning capability of Transformers as a new backbone architecture for medical imaging. Through the task of classifying COVID-19 chest radiographs, we investigate into whether generalization capabilities benefit solely from Vision Transformers' architectural advances. Quantitative and qualitative evaluations are conducted on the trustworthiness of the models, through the use of "trust score" computation and a visual explainability technique. We conclude that the attention-based feature learning approach is promising in building trustworthy deep learning models for healthcare.

In biomedical imaging analysis, the dichotomy between 2D and 3D data presents a significant challenge. While 3D volumes offer superior real-world applicability, they are less available for each modality and not easy to train in large scale, whereas 2D samples are abundant but less comprehensive. This paper introduces the Cross-D Conv operation, a novel approach that bridges the dimensional gap by learning the phase shifting in the Fourier domain. Our method enables seamless weight transfer between 2D and 3D convolution operations, effectively facilitating cross-dimensional learning. The proposed architecture leverages the abundance of 2D training data to enhance 3D model performance, offering a practical solution to the multimodal data scarcity challenge in 3D medical model pretraining. Experimental validation on the RadImagenet (2D) and multimodal (3D) sets demonstrates that our approach achieves comparable or superior performance in feature quality assessment comparable to conventional methods. The enhanced convolution operation presents new opportunities for developing efficient classification and segmentation models in medical imaging. This work represents an advancement in cross-dimensional and multi-modal medical image analysis, offering a robust framework for utilizing 2D priors in 3D model pretraining or vice versa while maintaining computational efficiency.

Generative modeling has experienced substantial progress in recent years, particularly in text-to-image and text-to-video synthesis. However, the medical field has not yet fully exploited the potential of large-scale foundational models for synthetic data generation. In this paper, we introduce GenerateCT, the first method for text-conditional computed tomography (CT) generation, addressing the limitations in 3D medical imaging research and making our entire framework open-source. GenerateCT consists of a pre-trained large language model, a transformer-based text-conditional 3D chest CT generation architecture, and a text-conditional spatial super-resolution diffusion model. We also propose CT-ViT, which efficiently compresses CT volumes while preserving auto-regressiveness in-depth, enabling the generation of 3D CT volumes with variable numbers of axial slices. Our experiments demonstrate that GenerateCT can produce realistic, high-resolution, and high-fidelity 3D chest CT volumes consistent with medical language text prompts. We further investigate the potential of GenerateCT by training a model using generated CT volumes for multi-abnormality classification of chest CT volumes. Our contributions provide a valuable foundation for future research in text-conditional 3D medical image generation and have the potential to accelerate advancements in medical imaging research. Our code, pre-trained models, and generated data are available at https://github.com/ibrahimethemhamamci/GenerateCT.

Advances in deep learning and transfer learning have paved the way for various automation classification tasks in agriculture, including plant diseases, pests, weeds, and plant species detection. However, agriculture automation still faces various challenges, such as the limited size of datasets and the absence of plant-domain-specific pretrained models. Domain specific pretrained models have shown state of art performance in various computer vision tasks including face recognition and medical imaging diagnosis. In this paper, we propose AgriNet dataset, a collection of 160k agricultural images from more than 19 geographical locations, several images captioning devices, and more than 423 classes of plant species and diseases. We also introduce AgriNet models, a set of pretrained models on five ImageNet architectures: VGG16, VGG19, Inception-v3, InceptionResNet-v2, and Xception. AgriNet-VGG19 achieved the highest classification accuracy of 94 % and the highest F1-score of 92%. Additionally, all proposed models were found to accurately classify the 423 classes of plant species, diseases, pests, and weeds with a minimum accuracy of 87% for the Inception-v3 model.Finally, experiments to evaluate of superiority of AgriNet models compared to ImageNet models were conducted on two external datasets: pest and plant diseases dataset from Bangladesh and a plant diseases dataset from Kashmir.

We present ReXGradient-160K, representing the largest publicly available chest X-ray dataset to date in terms of the number of patients. This dataset contains 160,000 chest X-ray studies with paired radiological reports from 109,487 unique patients across 3 U.S. health systems (79 medical sites). This comprehensive dataset includes multiple images per study and detailed radiology reports, making it particularly valuable for the development and evaluation of AI systems for medical imaging and automated report generation models. The dataset is divided into training (140,000 studies), validation (10,000 studies), and public test (10,000 studies) sets, with an additional private test set (10,000 studies) reserved for model evaluation on the ReXrank benchmark. By providing this extensive dataset, we aim to accelerate research in medical imaging AI and advance the state-of-the-art in automated radiological analysis. Our dataset will be open-sourced at https://huggingface.co/datasets/rajpurkarlab/ReXGradient-160K.

Analysis of 3D segmentation models, especially in the context of medical imaging, is often limited to segmentation performance metrics that overlook the crucial aspect of explainability and bias. Currently, effectively explaining these models with saliency maps is challenging due to the high dimensions of input images multiplied by the ever-growing number of segmented class labels. To this end, we introduce Agg^2Exp, a methodology for aggregating fine-grained voxel attributions of the segmentation model's predictions. Unlike classical explanation methods that primarily focus on the local feature attribution, Agg^2Exp enables a more comprehensive global view on the importance of predicted segments in 3D images. Our benchmarking experiments show that gradient-based voxel attributions are more faithful to the model's predictions than perturbation-based explanations. As a concrete use-case, we apply Agg^2Exp to discover knowledge acquired by the Swin UNEt TRansformer model trained on the TotalSegmentator v2 dataset for segmenting anatomical structures in computed tomography medical images. Agg^2Exp facilitates the explanatory analysis of large segmentation models beyond their predictive performance.

Label noise is prevalent in machine learning datasets. It is crucial to identify and remove label noise because models trained on noisy data can have substantially reduced accuracy and generalizability. Most existing label noise detection approaches are designed for classification tasks, and data cleaning for outcome prediction analysis is relatively unexplored. Inspired by the fluctuations in performance across different folds in cross-validation, we propose Repeated Cross-Validations for label noise estimation (ReCoV) to address this gap. ReCoV constructs a noise histogram that ranks the noise level of samples based on a large number of cross-validations by recording sample IDs in each worst-performing fold. We further propose three approaches for identifying noisy samples based on noise histograms to address increasingly complex noise distributions. We show that ReCoV outperforms state-of-the-art algorithms for label cleaning in a classification task benchmark. More importantly, we show that removing ReCoV-identified noisy samples in two medical imaging outcome prediction datasets significantly improves model performance on test sets. As a statistical approach that does not rely on hyperparameters, noise distributions, or model structures, ReCoV is compatible with any machine learning analysis.

Conformal prediction is emerging as a popular paradigm for providing rigorous uncertainty quantification in machine learning since it can be easily applied as a post-processing step to already trained models. In this paper, we extend conformal prediction to the federated learning setting. The main challenge we face is data heterogeneity across the clients - this violates the fundamental tenet of exchangeability required for conformal prediction. We propose a weaker notion of partial exchangeability, better suited to the FL setting, and use it to develop the Federated Conformal Prediction (FCP) framework. We show FCP enjoys rigorous theoretical guarantees and excellent empirical performance on several computer vision and medical imaging datasets. Our results demonstrate a practical approach to incorporating meaningful uncertainty quantification in distributed and heterogeneous environments. We provide code used in our experiments https://github.com/clu5/federated-conformal.

The soft Dice loss (SDL) has taken a pivotal role in numerous automated segmentation pipelines in the medical imaging community. Over the last years, some reasons behind its superior functioning have been uncovered and further optimizations have been explored. However, there is currently no implementation that supports its direct utilization in scenarios involving soft labels. Hence, a synergy between the use of SDL and research leveraging the use of soft labels, also in the context of model calibration, is still missing. In this work, we introduce Dice semimetric losses (DMLs), which (i) are by design identical to SDL in a standard setting with hard labels, but (ii) can be employed in settings with soft labels. Our experiments on the public QUBIQ, LiTS and KiTS benchmarks confirm the potential synergy of DMLs with soft labels (e.g.\ averaging, label smoothing, and knowledge distillation) over hard labels (e.g.\ majority voting and random selection). As a result, we obtain superior Dice scores and model calibration, which supports the wider adoption of DMLs in practice. The code is available at https://github.com/zifuwanggg/JDTLosses{https://github.com/zifuwanggg/JDTLosses}.

We explore the problem of generating minority samples using diffusion models. The minority samples are instances that lie on low-density regions of a data manifold. Generating a sufficient number of such minority instances is important, since they often contain some unique attributes of the data. However, the conventional generation process of the diffusion models mostly yields majority samples (that lie on high-density regions of the manifold) due to their high likelihoods, making themselves ineffective and time-consuming for the minority generating task. In this work, we present a novel framework that can make the generation process of the diffusion models focus on the minority samples. We first highlight that Tweedie's denoising formula yields favorable results for majority samples. The observation motivates us to introduce a metric that describes the uniqueness of a given sample. To address the inherent preference of the diffusion models w.r.t. the majority samples, we further develop minority guidance, a sampling technique that can guide the generation process toward regions with desired likelihood levels. Experiments on benchmark real datasets demonstrate that our minority guidance can greatly improve the capability of generating high-quality minority samples over existing generative samplers. We showcase that the performance benefit of our framework persists even in demanding real-world scenarios such as medical imaging, further underscoring the practical significance of our work. Code is available at https://github.com/soobin-um/minority-guidance.

The success of Deep Neural Network (DNN) models significantly depends on the quality of provided annotations. In medical image segmentation, for example, having multiple expert annotations for each data point is common to minimize subjective annotation bias. Then, the goal of estimation is to filter out the label noise and recover the ground-truth masks, which are not explicitly given. This paper proposes a probabilistic model for noisy observations that allows us to build a confident classification and segmentation models. To accomplish it, we explicitly model label noise and introduce a new information-based regularization that pushes the network to recover the ground-truth labels. In addition, for segmentation task we adjust the loss function by prioritizing learning in high-confidence regions where all the annotators agree on labeling. We evaluate the proposed method on a series of classification tasks such as noisy versions of MNIST, CIFAR-10, Fashion-MNIST datasets as well as CIFAR-10N, which is real-world dataset with noisy human annotations. Additionally, for segmentation task, we consider several medical imaging datasets, such as, LIDC and RIGA that reflect real-world inter-variability among multiple annotators. Our experiments show that our algorithm outperforms state-of-the-art solutions for the considered classification and segmentation problems.

Vision Transformer (ViT) has become one of the most popular neural architectures due to its great scalability, computational efficiency, and compelling performance in many vision tasks. However, ViT has shown inferior performance to Convolutional Neural Network (CNN) on medical tasks due to its data-hungry nature and the lack of annotated medical data. In this paper, we pre-train ViTs on 266,340 chest X-rays using Masked Autoencoders (MAE) which reconstruct missing pixels from a small part of each image. For comparison, CNNs are also pre-trained on the same 266,340 X-rays using advanced self-supervised methods (e.g., MoCo v2). The results show that our pre-trained ViT performs comparably (sometimes better) to the state-of-the-art CNN (DenseNet-121) for multi-label thorax disease classification. This performance is attributed to the strong recipes extracted from our empirical studies for pre-training and fine-tuning ViT. The pre-training recipe signifies that medical reconstruction requires a much smaller proportion of an image (10% vs. 25%) and a more moderate random resized crop range (0.5~1.0 vs. 0.2~1.0) compared with natural imaging. Furthermore, we remark that in-domain transfer learning is preferred whenever possible. The fine-tuning recipe discloses that layer-wise LR decay, RandAug magnitude, and DropPath rate are significant factors to consider. We hope that this study can direct future research on the application of Transformers to a larger variety of medical imaging tasks.

While making a tremendous impact in various fields, deep neural networks usually require large amounts of labeled data for training which are expensive to collect in many applications, especially in the medical domain. Unlabeled data, on the other hand, is much more abundant. Semi-supervised learning techniques, such as co-training, could provide a powerful tool to leverage unlabeled data. In this paper, we propose a novel framework, uncertainty-aware multi-view co-training (UMCT), to address semi-supervised learning on 3D data, such as volumetric data from medical imaging. In our work, co-training is achieved by exploiting multi-viewpoint consistency of 3D data. We generate different views by rotating or permuting the 3D data and utilize asymmetrical 3D kernels to encourage diversified features in different sub-networks. In addition, we propose an uncertainty-weighted label fusion mechanism to estimate the reliability of each view's prediction with Bayesian deep learning. As one view requires the supervision from other views in co-training, our self-adaptive approach computes a confidence score for the prediction of each unlabeled sample in order to assign a reliable pseudo label. Thus, our approach can take advantage of unlabeled data during training. We show the effectiveness of our proposed semi-supervised method on several public datasets from medical image segmentation tasks (NIH pancreas & LiTS liver tumor dataset). Meanwhile, a fully-supervised method based on our approach achieved state-of-the-art performances on both the LiTS liver tumor segmentation and the Medical Segmentation Decathlon (MSD) challenge, demonstrating the robustness and value of our framework, even when fully supervised training is feasible.

Poisson noise suppression is an important preprocessing step in several applications, such as medical imaging, microscopy, and astronomical imaging. In this work, we propose a novel patch-wise Poisson noise removal strategy, in which the MMSE estimator is utilized in order to produce the denoising result for each image patch. Fast and accurate computation of the MMSE estimator is carried out using k-d tree search followed by search in the K-nearest neighbor graph. Our experiments show that the proposed method is the preferable choice for low signal-to-noise ratios.

Multiparametric magnetic resonance imaging (mpMRI) has demonstrated promising results in prostate cancer (PCa) detection using deep convolutional neural networks (CNNs). Recently, transformers have achieved competitive performance compared to CNNs in computer vision. Large-scale transformers need abundant annotated data for training, which are difficult to obtain in medical imaging. Self-supervised learning can effectively leverage unlabeled data to extract useful semantic representations without annotation and its associated costs. This can improve model performance on downstream tasks with limited labelled data and increase generalizability. We introduce a novel end-to-end Cross-Shaped windows (CSwin) transformer UNet model, CSwin UNet, to detect clinically significant prostate cancer (csPCa) in prostate bi-parametric MR imaging (bpMRI) and demonstrate the effectiveness of our proposed self-supervised pre-training framework. Using a large prostate bpMRI dataset with 1500 patients, we first pre-train CSwin transformer using multi-task self-supervised learning to improve data-efficiency and network generalizability. We then finetuned using lesion annotations to perform csPCa detection. Five-fold cross validation shows that self-supervised CSwin UNet achieves 0.888 AUC and 0.545 Average Precision (AP), significantly outperforming four state-of-the-art models (Swin UNETR, DynUNet, Attention UNet, UNet). Using a separate bpMRI dataset with 158 patients, we evaluated our model robustness to external hold-out data. Self-supervised CSwin UNet achieves 0.79 AUC and 0.45 AP, still outperforming all other comparable methods and demonstrating generalization to a dataset shift.

Recent 3D face editing methods using masks have produced high-quality edited images by leveraging Neural Radiance Fields (NeRF). Despite their impressive performance, existing methods often provide limited user control due to the use of pre-trained segmentation masks. To utilize masks with a desired layout, an extensive training dataset is required, which is challenging to gather. We present FFaceNeRF, a NeRF-based face editing technique that can overcome the challenge of limited user control due to the use of fixed mask layouts. Our method employs a geometry adapter with feature injection, allowing for effective manipulation of geometry attributes. Additionally, we adopt latent mixing for tri-plane augmentation, which enables training with a few samples. This facilitates rapid model adaptation to desired mask layouts, crucial for applications in fields like personalized medical imaging or creative face editing. Our comparative evaluations demonstrate that FFaceNeRF surpasses existing mask based face editing methods in terms of flexibility, control, and generated image quality, paving the way for future advancements in customized and high-fidelity 3D face editing. The code is available on the {https://kwanyun.github.io/FFaceNeRF_page/{project-page}}.

Deep learning-based super-resolution (SR) methods often perform pixel-wise computations uniformly across entire images, even in homogeneous regions where high-resolution refinement is redundant. We propose the Quadtree Diffusion Model (QDM), a region-adaptive diffusion framework that leverages a quadtree structure to selectively enhance detail-rich regions while reducing computations in homogeneous areas. By guiding the diffusion with a quadtree derived from the low-quality input, QDM identifies key regions-represented by leaf nodes-where fine detail is essential and applies minimal refinement elsewhere. This mask-guided, two-stream architecture adaptively balances quality and efficiency, producing high-fidelity outputs with low computational redundancy. Experiments demonstrate QDM's effectiveness in high-resolution SR tasks across diverse image types, particularly in medical imaging (e.g., CT scans), where large homogeneous regions are prevalent. Furthermore, QDM outperforms or is comparable to state-of-the-art SR methods on standard benchmarks while significantly reducing computational costs, highlighting its efficiency and suitability for resource-limited environments. Our code is available at https://github.com/linYDTHU/QDM.

Brain extraction and removal of skull artifacts from magnetic resonance images (MRI) is an important preprocessing step in neuroimaging analysis. There are many tools developed to handle human fMRI images, which could involve manual steps for verifying results from brain segmentation that makes it time consuming and inefficient. In this study, we will use the segment anything model (SAM), a freely available neural network released by Meta[4], which has shown promising results in many generic segmentation applications. We will analyze the efficiency of SAM for neuroimaging brain segmentation by removing skull artifacts. The results of the experiments showed promising results that explore using automated segmentation algorithms for neuroimaging without the need to train on custom medical imaging dataset.

Ultrasound Localization Microscopy (ULM) enables imaging of vascular structures in the micrometer range by accumulating contrast agent particle locations over time. Precise and efficient target localization accuracy remains an active research topic in the ULM field to further push the boundaries of this promising medical imaging technology. Existing work incorporates Delay-And-Sum (DAS) beamforming into particle localization pipelines, which ultimately determines the ULM image resolution capability. In this paper we propose to feed unprocessed Radio-Frequency (RF) data into a super-resolution network while bypassing DAS beamforming and its limitations. To facilitate this, we demonstrate label projection and inverse point transformation between B-mode and RF coordinate space as required by our approach. We assess our method against state-of-the-art techniques based on a public dataset featuring in silico and in vivo data. Results from our RF-trained network suggest that excluding DAS beamforming offers a great potential to optimize on the ULM resolution performance.

In recent years, Multimodal Large Language Models (MLLM) have achieved notable advancements, demonstrating the feasibility of developing an intelligent biomedical assistant. However, current biomedical MLLMs predominantly focus on image-level understanding and restrict interactions to textual commands, thus limiting their capability boundaries and the flexibility of usage. In this paper, we introduce a novel end-to-end multimodal large language model for the biomedical domain, named MedPLIB, which possesses pixel-level understanding. Excitingly, it supports visual question answering (VQA), arbitrary pixel-level prompts (points, bounding boxes, and free-form shapes), and pixel-level grounding. We propose a novel Mixture-of-Experts (MoE) multi-stage training strategy, which divides MoE into separate training phases for a visual-language expert model and a pixel-grounding expert model, followed by fine-tuning using MoE. This strategy effectively coordinates multitask learning while maintaining the computational cost at inference equivalent to that of a single expert model. To advance the research of biomedical MLLMs, we introduce the Medical Complex Vision Question Answering Dataset (MeCoVQA), which comprises an array of 8 modalities for complex medical imaging question answering and image region understanding. Experimental results indicate that MedPLIB has achieved state-of-the-art outcomes across multiple medical visual language tasks. More importantly, in zero-shot evaluations for the pixel grounding task, MedPLIB leads the best small and large models by margins of 19.7 and 15.6 respectively on the mDice metric. The codes, data, and model checkpoints will be made publicly available at https://github.com/ShawnHuang497/MedPLIB.

We present 4KAgent, a unified agentic super-resolution generalist system designed to universally upscale any image to 4K resolution (and even higher, if applied iteratively). Our system can transform images from extremely low resolutions with severe degradations, for example, highly distorted inputs at 256x256, into crystal-clear, photorealistic 4K outputs. 4KAgent comprises three core components: (1) Profiling, a module that customizes the 4KAgent pipeline based on bespoke use cases; (2) A Perception Agent, which leverages vision-language models alongside image quality assessment experts to analyze the input image and make a tailored restoration plan; and (3) A Restoration Agent, which executes the plan, following a recursive execution-reflection paradigm, guided by a quality-driven mixture-of-expert policy to select the optimal output for each step. Additionally, 4KAgent embeds a specialized face restoration pipeline, significantly enhancing facial details in portrait and selfie photos. We rigorously evaluate our 4KAgent across 11 distinct task categories encompassing a total of 26 diverse benchmarks, setting new state-of-the-art on a broad spectrum of imaging domains. Our evaluations cover natural images, portrait photos, AI-generated content, satellite imagery, fluorescence microscopy, and medical imaging like fundoscopy, ultrasound, and X-ray, demonstrating superior performance in terms of both perceptual (e.g., NIQE, MUSIQ) and fidelity (e.g., PSNR) metrics. By establishing a novel agentic paradigm for low-level vision tasks, we aim to catalyze broader interest and innovation within vision-centric autonomous agents across diverse research communities. We will release all the code, models, and results at: https://4kagent.github.io.

Amid the swift progress of large language models (LLMs) and their evolution into large multimodal models (LMMs), significant strides have been made in high-resource languages such as English and Chinese. While Arabic LLMs have seen notable progress, Arabic LMMs remain largely unexplored, often narrowly focusing on a few specific aspects of the language and visual understanding. To bridge this gap, we introduce AIN-the Arabic Inclusive Multimodal Model-designed to excel across diverse domains. AIN is an English-Arabic bilingual LMM designed to excel in English and Arabic, leveraging carefully constructed 3.6 million high-quality Arabic-English multimodal data samples. AIN demonstrates state-of-the-art Arabic performance, while also possessing strong English-language visual capabilities. On the recent CAMEL-Bench benchmark comprising 38 sub-domains including, multi-image understanding, complex visual perception, handwritten document understanding, video understanding, medical imaging, plant diseases, and remote sensing-based land use understanding, our AIN demonstrates strong performance with the 7B model outperforming GPT-4o by an absolute gain of 3.4% averaged over eight domains and 38 sub-domains. AIN's superior capabilities position it as a significant step toward empowering Arabic speakers with advanced multimodal generative AI tools across diverse applications.

We present Autoregressive Representation Alignment (ARRA), a new training framework that unlocks global-coherent text-to-image generation in autoregressive LLMs without architectural changes. Unlike prior work that requires complex architectural redesigns, ARRA aligns LLM hidden states with visual representations from external visual foundational models via a global visual alignment loss and a hybrid token, <HYBNEXT>. This token enforces dual constraints: local next-token prediction and global semantic distillation, enabling LLMs to implicitly learn spatial and contextual coherence while retaining their original autoregressive paradigm. Extensive experiments validate ARRA's plug-and-play versatility. When training from text-generation-only LLMs or random initialization, ARRA reduces FID by 25.5% (MIMIC-CXR), 8.8% (DeepEyeNet), and 7.5% (ImageNet) for advanced autoregressive LLMs like Chameleon and LlamaGen, all without framework modifications. For domain adaption, ARRA aligns general-purpose LLMs with specialized models (e.g., BioMedCLIP), achieving an 18.6% FID reduction over direct fine-tuning on medical imaging (MIMIC-CXR). By demonstrating that training objective redesign -- not just architectural innovation -- can resolve cross-modal global coherence challenges, ARRA offers a complementary paradigm for advancing autoregressive models. Code and models will be released to advance autoregressive image generation.

Recent advancements in diffusion probabilistic models (DPMs) have revolutionized image processing, demonstrating significant potential in medical applications. Accurate segmentation of the left ventricle (LV) in echocardiograms is crucial for diagnostic procedures and necessary treatments. However, ultrasound images are notoriously noisy with low contrast and ambiguous LV boundaries, thereby complicating the segmentation process. To address these challenges, this paper introduces Echo-DND, a novel dual-noise diffusion model specifically designed for this task. Echo-DND leverages a unique combination of Gaussian and Bernoulli noises. It also incorporates a multi-scale fusion conditioning module to improve segmentation precision. Furthermore, it utilizes spatial coherence calibration to maintain spatial integrity in segmentation masks. The model's performance was rigorously validated on the CAMUS and EchoNet-Dynamic datasets. Extensive evaluations demonstrate that the proposed framework outperforms existing SOTA models. It achieves high Dice scores of 0.962 and 0.939 on these datasets, respectively. The proposed Echo-DND model establishes a new standard in echocardiogram segmentation, and its architecture holds promise for broader applicability in other medical imaging tasks, potentially improving diagnostic accuracy across various medical domains. Project page: https://abdur75648.github.io/Echo-DND

Multi-organ medical segmentation is a crucial component of medical image processing, essential for doctors to make accurate diagnoses and develop effective treatment plans. Despite significant progress in this field, current multi-organ segmentation models often suffer from inaccurate details, dependence on geometric prompts and loss of spatial information. Addressing these challenges, we introduce a novel model named CRISP-SAM2 with CRoss-modal Interaction and Semantic Prompting based on SAM2. This model represents a promising approach to multi-organ medical segmentation guided by textual descriptions of organs. Our method begins by converting visual and textual inputs into cross-modal contextualized semantics using a progressive cross-attention interaction mechanism. These semantics are then injected into the image encoder to enhance the detailed understanding of visual information. To eliminate reliance on geometric prompts, we use a semantic prompting strategy, replacing the original prompt encoder to sharpen the perception of challenging targets. In addition, a similarity-sorting self-updating strategy for memory and a mask-refining process is applied to further adapt to medical imaging and enhance localized details. Comparative experiments conducted on seven public datasets indicate that CRISP-SAM2 outperforms existing models. Extensive analysis also demonstrates the effectiveness of our method, thereby confirming its superior performance, especially in addressing the limitations mentioned earlier. Our code is available at: https://github.com/YU-deep/CRISP\_SAM2.git.

With Artificial Intelligence (AI) increasingly permeating various aspects of society, including healthcare, the adoption of the Transformers neural network architecture is rapidly changing many applications. Transformer is a type of deep learning architecture initially developed to solve general-purpose Natural Language Processing (NLP) tasks and has subsequently been adapted in many fields, including healthcare. In this survey paper, we provide an overview of how this architecture has been adopted to analyze various forms of data, including medical imaging, structured and unstructured Electronic Health Records (EHR), social media, physiological signals, and biomolecular sequences. Those models could help in clinical diagnosis, report generation, data reconstruction, and drug/protein synthesis. We identified relevant studies using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We also discuss the benefits and limitations of using transformers in healthcare and examine issues such as computational cost, model interpretability, fairness, alignment with human values, ethical implications, and environmental impact.

The rise of deep learning has marked significant progress in fields such as computer vision, natural language processing, and medical imaging, primarily through the adaptation of pre-trained models for specific tasks. Traditional fine-tuning methods, involving adjustments to all parameters, face challenges due to high computational and memory demands. This has led to the development of Parameter Efficient Fine-Tuning (PEFT) techniques, which selectively update parameters to balance computational efficiency with performance. This review examines PEFT approaches, offering a detailed comparison of various strategies highlighting applications across different domains, including text generation, medical imaging, protein modeling, and speech synthesis. By assessing the effectiveness of PEFT methods in reducing computational load, speeding up training, and lowering memory usage, this paper contributes to making deep learning more accessible and adaptable, facilitating its wider application and encouraging innovation in model optimization. Ultimately, the paper aims to contribute towards insights into PEFT's evolving landscape, guiding researchers and practitioners in overcoming the limitations of conventional fine-tuning approaches.

Precise camera tracking, high-fidelity 3D tissue reconstruction, and real-time online visualization are critical for intrabody medical imaging devices such as endoscopes and capsule robots. However, existing SLAM (Simultaneous Localization and Mapping) methods often struggle to achieve both complete high-quality surgical field reconstruction and efficient computation, restricting their intraoperative applications among endoscopic surgeries. In this paper, we introduce EndoGSLAM, an efficient SLAM approach for endoscopic surgeries, which integrates streamlined Gaussian representation and differentiable rasterization to facilitate over 100 fps rendering speed during online camera tracking and tissue reconstructing. Extensive experiments show that EndoGSLAM achieves a better trade-off between intraoperative availability and reconstruction quality than traditional or neural SLAM approaches, showing tremendous potential for endoscopic surgeries. The project page is at https://EndoGSLAM.loping151.com

Zero-shot anomaly detection (ZSAD) requires detection models trained using auxiliary data to detect anomalies without any training sample in a target dataset. It is a crucial task when training data is not accessible due to various concerns, eg, data privacy, yet it is challenging since the models need to generalize to anomalies across different domains where the appearance of foreground objects, abnormal regions, and background features, such as defects/tumors on different products/organs, can vary significantly. Recently large pre-trained vision-language models (VLMs), such as CLIP, have demonstrated strong zero-shot recognition ability in various vision tasks, including anomaly detection. However, their ZSAD performance is weak since the VLMs focus more on modeling the class semantics of the foreground objects rather than the abnormality/normality in the images. In this paper we introduce a novel approach, namely AnomalyCLIP, to adapt CLIP for accurate ZSAD across different domains. The key insight of AnomalyCLIP is to learn object-agnostic text prompts that capture generic normality and abnormality in an image regardless of its foreground objects. This allows our model to focus on the abnormal image regions rather than the object semantics, enabling generalized normality and abnormality recognition on diverse types of objects. Large-scale experiments on 17 real-world anomaly detection datasets show that AnomalyCLIP achieves superior zero-shot performance of detecting and segmenting anomalies in datasets of highly diverse class semantics from various defect inspection and medical imaging domains. Code will be made available at https://github.com/zqhang/AnomalyCLIP.

A major problem with Active Learning (AL) is high training costs since models are typically retrained from scratch after every query round. We start by demonstrating that standard AL on neural networks with warm starting fails, both to accelerate training and to avoid catastrophic forgetting when using fine-tuning over AL query rounds. We then develop a new class of techniques, circumventing this problem, by biasing further training towards previously labeled sets. We accomplish this by employing existing, and developing novel, replay-based Continual Learning (CL) algorithms that are effective at quickly learning the new without forgetting the old, especially when data comes from an evolving distribution. We call this paradigm Continual Active Learning (CAL). We show CAL achieves significant speedups using a plethora of replay schemes that use model distillation and that select diverse, uncertain points from the history. We conduct experiments across many data domains, including natural language, vision, medical imaging, and computational biology, each with different neural architectures and dataset sizes. CAL consistently provides a 3x reduction in training time, while retaining performance.

Accurate and efficient 3D segmentation is essential for both clinical and research applications. While foundation models like SAM have revolutionized interactive segmentation, their 2D design and domain shift limitations make them ill-suited for 3D medical images. Current adaptations address some of these challenges but remain limited, either lacking volumetric awareness, offering restricted interactivity, or supporting only a small set of structures and modalities. Usability also remains a challenge, as current tools are rarely integrated into established imaging platforms and often rely on cumbersome web-based interfaces with restricted functionality. We introduce nnInteractive, the first comprehensive 3D interactive open-set segmentation method. It supports diverse prompts-including points, scribbles, boxes, and a novel lasso prompt-while leveraging intuitive 2D interactions to generate full 3D segmentations. Trained on 120+ diverse volumetric 3D datasets (CT, MRI, PET, 3D Microscopy, etc.), nnInteractive sets a new state-of-the-art in accuracy, adaptability, and usability. Crucially, it is the first method integrated into widely used image viewers (e.g., Napari, MITK), ensuring broad accessibility for real-world clinical and research applications. Extensive benchmarking demonstrates that nnInteractive far surpasses existing methods, setting a new standard for AI-driven interactive 3D segmentation. nnInteractive is publicly available: https://github.com/MIC-DKFZ/napari-nninteractive (Napari plugin), https://www.mitk.org/MITK-nnInteractive (MITK integration), https://github.com/MIC-DKFZ/nnInteractive (Python backend).

As deep learning models gain attraction in medical data, ensuring transparent and trustworthy decision-making is essential. In skin cancer diagnosis, while advancements in lesion detection and classification have improved accuracy, the black-box nature of these methods poses challenges in understanding their decision processes, leading to trust issues among physicians. This study leverages the CLIP (Contrastive Language-Image Pretraining) model, trained on different skin lesion datasets, to capture meaningful relationships between visual features and diagnostic criteria terms. To further enhance transparency, we propose a method called MedGrad E-CLIP, which builds on gradient-based E-CLIP by incorporating a weighted entropy mechanism designed for complex medical imaging like skin lesions. This approach highlights critical image regions linked to specific diagnostic descriptions. The developed integrated pipeline not only classifies skin lesions by matching corresponding descriptions but also adds an essential layer of explainability developed especially for medical data. By visually explaining how different features in an image relates to diagnostic criteria, this approach demonstrates the potential of advanced vision-language models in medical image analysis, ultimately improving transparency, robustness, and trust in AI-driven diagnostic systems.

Prostate cancer, a growing global health concern, necessitates precise diagnostic tools, with Magnetic Resonance Imaging (MRI) offering high-resolution soft tissue imaging that significantly enhances diagnostic accuracy. Recent advancements in explainable AI and representation learning have significantly improved prostate cancer diagnosis by enabling automated and precise lesion classification. However, existing explainable AI methods, particularly those based on frameworks like generative adversarial networks (GANs), are predominantly developed for natural image generation, and their application to medical imaging often leads to suboptimal performance due to the unique characteristics and complexity of medical image. To address these challenges, our paper introduces three key contributions. First, we propose ProjectedEx, a generative framework that provides interpretable, multi-attribute explanations, effectively linking medical image features to classifier decisions. Second, we enhance the encoder module by incorporating feature pyramids, which enables multiscale feedback to refine the latent space and improves the quality of generated explanations. Additionally, we conduct comprehensive experiments on both the generator and classifier, demonstrating the clinical relevance and effectiveness of ProjectedEx in enhancing interpretability and supporting the adoption of AI in medical settings. Code will be released at https://github.com/Richardqiyi/ProjectedEx

Background: Recent advances in large language models highlight the need for high-quality multilingual medical datasets. While Japan leads globally in CT scanner deployment and utilization, the lack of large-scale Japanese radiology datasets has hindered the development of specialized language models for medical imaging analysis. Objective: To develop a comprehensive Japanese CT report dataset through machine translation and establish a specialized language model for structured finding classification. Additionally, to create a rigorously validated evaluation dataset through expert radiologist review. Methods: We translated the CT-RATE dataset (24,283 CT reports from 21,304 patients) into Japanese using GPT-4o mini. The training dataset consisted of 22,778 machine-translated reports, while the validation dataset included 150 radiologist-revised reports. We developed CT-BERT-JPN based on "tohoku-nlp/bert-base-japanese-v3" architecture for extracting 18 structured findings from Japanese radiology reports. Results: Translation metrics showed strong performance with BLEU scores of 0.731 and 0.690, and ROUGE scores ranging from 0.770 to 0.876 for Findings and from 0.748 to 0.857 for Impression sections. CT-BERT-JPN demonstrated superior performance compared to GPT-4o in 11 out of 18 conditions, including lymphadenopathy (+14.2%), interlobular septal thickening (+10.9%), and atelectasis (+7.4%). The model maintained F1 scores exceeding 0.95 in 14 out of 18 conditions and achieved perfect scores in four conditions. Conclusions: Our study establishes a robust Japanese CT report dataset and demonstrates the effectiveness of a specialized language model for structured finding classification. The hybrid approach of machine translation and expert validation enables the creation of large-scale medical datasets while maintaining high quality.

Medical eye-tracking data is an important information source for understanding how radiologists visually interpret medical images. This information not only improves the accuracy of deep learning models for X-ray analysis but also their interpretability, enhancing transparency in decision-making. However, the current eye-tracking data is dispersed, unprocessed, and ambiguous, making it difficult to derive meaningful insights. Therefore, there is a need to create a new dataset with more focus and purposeful eyetracking data, improving its utility for diagnostic applications. In this work, we propose a refinement method inspired by the target-present visual search challenge: there is a specific finding and fixations are guided to locate it. After refining the existing eye-tracking datasets, we transform them into a curated visual search dataset, called GazeSearch, specifically for radiology findings, where each fixation sequence is purposefully aligned to the task of locating a particular finding. Subsequently, we introduce a scan path prediction baseline, called ChestSearch, specifically tailored to GazeSearch. Finally, we employ the newly introduced GazeSearch as a benchmark to evaluate the performance of current state-of-the-art methods, offering a comprehensive assessment for visual search in the medical imaging domain. Code is available at https://github.com/UARK-AICV/GazeSearch.

Recent advancements in artificial intelligence (AI) have precipitated significant breakthroughs in healthcare, particularly in refining diagnostic procedures. However, previous studies have often been constrained to limited functionalities. This study introduces MiniGPT-Med, a vision-language model derived from large-scale language models and tailored for medical applications. MiniGPT-Med demonstrates remarkable versatility across various imaging modalities, including X-rays, CT scans, and MRIs, enhancing its utility. The model is capable of performing tasks such as medical report generation, visual question answering (VQA), and disease identification within medical imagery. Its integrated processing of both image and textual clinical data markedly improves diagnostic accuracy. Our empirical assessments confirm MiniGPT-Med's superior performance in disease grounding, medical report generation, and VQA benchmarks, representing a significant step towards reducing the gap in assisting radiology practice. Furthermore, it achieves state-of-the-art performance on medical report generation, higher than the previous best model by 19\% accuracy. MiniGPT-Med promises to become a general interface for radiology diagnoses, enhancing diagnostic efficiency across a wide range of medical imaging applications.

As Neural Processing Units (NPU) or accelerators are increasingly deployed in a variety of applications including safety critical applications such as autonomous vehicle, and medical imaging, it is critical to understand the fault-tolerance nature of the NPUs. We present a reliability study of Arm's Ethos-U55, an important industrial-scale NPU being utilised in embedded and IoT applications. We perform large scale RTL-level fault injections to characterize Ethos-U55 against the Automotive Safety Integrity Level D (ASIL-D) resiliency standard commonly used for safety-critical applications such as autonomous vehicles. We show that, under soft errors, all four configurations of the NPU fall short of the required level of resiliency for a variety of neural networks running on the NPU. We show that it is possible to meet the ASIL-D level resiliency without resorting to conventional strategies like Dual Core Lock Step (DCLS) that has an area overhead of 100%. We achieve so through selective protection, where hardware structures are selectively protected (e.g., duplicated, hardened) based on their sensitivity to soft errors and their silicon areas. To identify the optimal configuration that minimizes the area overhead while meeting the ASIL-D standard, the main challenge is the large search space associated with the time-consuming RTL simulation. To address this challenge, we present a statistical analysis tool that is validated against Arm silicon and that allows us to quickly navigate hundreds of billions of fault sites without exhaustive RTL fault injections. We show that by carefully duplicating a small fraction of the functional blocks and hardening the Flops in other blocks meets the ASIL-D safety standard while introducing an area overhead of only 38%.

With the rapid development of artificial intelligence, large language models (LLMs) have shown promising capabilities in mimicking human-level language comprehension and reasoning. This has sparked significant interest in applying LLMs to enhance various aspects of healthcare, ranging from medical education to clinical decision support. However, medicine involves multifaceted data modalities and nuanced reasoning skills, presenting challenges for integrating LLMs. This paper provides a comprehensive review on the applications and implications of LLMs in medicine. It begins by examining the fundamental applications of general-purpose and specialized LLMs, demonstrating their utilities in knowledge retrieval, research support, clinical workflow automation, and diagnostic assistance. Recognizing the inherent multimodality of medicine, the review then focuses on multimodal LLMs, investigating their ability to process diverse data types like medical imaging and EHRs to augment diagnostic accuracy. To address LLMs' limitations regarding personalization and complex clinical reasoning, the paper explores the emerging development of LLM-powered autonomous agents for healthcare. Furthermore, it summarizes the evaluation methodologies for assessing LLMs' reliability and safety in medical contexts. Overall, this review offers an extensive analysis on the transformative potential of LLMs in modern medicine. It also highlights the pivotal need for continuous optimizations and ethical oversight before these models can be effectively integrated into clinical practice. Visit https://github.com/mingze-yuan/Awesome-LLM-Healthcare for an accompanying GitHub repository containing latest papers.

Generalizing to unseen image domains is a challenging problem primarily due to the lack of diverse training data, inaccessible target data, and the large domain shift that may exist in many real-world settings. As such data augmentation is a critical component of domain generalization methods that seek to address this problem. We present Adversarial Bayesian Augmentation (ABA), a novel algorithm that learns to generate image augmentations in the challenging single-source domain generalization setting. ABA draws on the strengths of adversarial learning and Bayesian neural networks to guide the generation of diverse data augmentations -- these synthesized image domains aid the classifier in generalizing to unseen domains. We demonstrate the strength of ABA on several types of domain shift including style shift, subpopulation shift, and shift in the medical imaging setting. ABA outperforms all previous state-of-the-art methods, including pre-specified augmentations, pixel-based and convolutional-based augmentations.

This report presents a framework called Segment And Track Anything (SAMTrack) that allows users to precisely and effectively segment and track any object in a video. Additionally, SAM-Track employs multimodal interaction methods that enable users to select multiple objects in videos for tracking, corresponding to their specific requirements. These interaction methods comprise click, stroke, and text, each possessing unique benefits and capable of being employed in combination. As a result, SAM-Track can be used across an array of fields, ranging from drone technology, autonomous driving, medical imaging, augmented reality, to biological analysis. SAM-Track amalgamates Segment Anything Model (SAM), an interactive key-frame segmentation model, with our proposed AOT-based tracking model (DeAOT), which secured 1st place in four tracks of the VOT 2022 challenge, to facilitate object tracking in video. In addition, SAM-Track incorporates Grounding-DINO, which enables the framework to support text-based interaction. We have demonstrated the remarkable capabilities of SAM-Track on DAVIS-2016 Val (92.0%), DAVIS-2017 Test (79.2%)and its practicability in diverse applications. The project page is available at: https://github.com/z-x-yang/Segment-and-Track-Anything.

Convolutional neural networks are now seeing widespread use in a variety of fields, including image classification, facial and object recognition, medical imaging analysis, and many more. In addition, there are applications such as physics-informed simulators in which accurate forecasts in real time with a minimal lag are required. The present neural network designs include millions of parameters, which makes it difficult to install such complex models on devices that have limited memory. Compression techniques might be able to resolve these issues by decreasing the size of CNN models that are created by reducing the number of parameters that contribute to the complexity of the models. We propose a compressed tensor format of convolutional layer, a priori, before the training of the neural network. 3-way kernels or 2-way kernels in convolutional layers are replaced by one-way fiters. The overfitting phenomena will be reduced also. The time needed to make predictions or time required for training using the original Convolutional Neural Networks model would be cut significantly if there were fewer parameters to deal with. In this paper we present a method of a priori compressing convolutional neural networks for finite element (FE) predictions of physical data. Afterwards we validate our a priori compressed models on physical data from a FE model solving a 2D wave equation. We show that the proposed convolutinal compression technique achieves equivalent performance as classical convolutional layers with fewer trainable parameters and lower memory footprint.

Pretraining a deep learning model on large image datasets is a standard step before fine-tuning the model on small targeted datasets. The large dataset is usually general images (e.g. imagenet2012) while the small dataset can be specialized datasets that have different distributions from the large dataset. However, this 'large-to-small' strategy is not well-validated when the large dataset is specialized and has a similar distribution to small datasets. We newly compiled three hematoxylin and eosin-stained image datasets, one large (PTCGA200) and two magnification-adjusted small datasets (PCam200 and segPANDA200). Major deep learning models were trained with supervised and self-supervised learning methods and fine-tuned on the small datasets for tumor classification and tissue segmentation benchmarks. ResNet50 pretrained with MoCov2, SimCLR, and BYOL on PTCGA200 was better than imagenet2012 pretraining when fine-tuned on PTCGA200 (accuracy of 83.94%, 86.41%, 84.91%, and 82.72%, respectively). ResNet50 pre-trained on PTCGA200 with MoCov2 exceeded the COCOtrain2017-pretrained baseline and was the best in ResNet50 for the tissue segmentation benchmark (mIoU of 63.53% and 63.22%). We found re-training imagenet-pretrained models (ResNet50, BiT-M-R50x1, and ViT-S/16) on PTCGA200 improved downstream benchmarks.

Data diversity and volume are crucial to the success of training deep learning models, while in the medical imaging field, the difficulty and cost of data collection and annotation are especially huge. Specifically in robotic surgery, data scarcity and imbalance have heavily affected the model accuracy and limited the design and deployment of deep learning-based surgical applications such as surgical instrument segmentation. Considering this, we rethink the surgical instrument segmentation task and propose a one-to-many data generation solution that gets rid of the complicated and expensive process of data collection and annotation from robotic surgery. In our method, we only utilize a single surgical background tissue image and a few open-source instrument images as the seed images and apply multiple augmentations and blending techniques to synthesize amounts of image variations. In addition, we also introduce the chained augmentation mixing during training to further enhance the data diversities. The proposed approach is evaluated on the real datasets of the EndoVis-2018 and EndoVis-2017 surgical scene segmentation. Our empirical analysis suggests that without the high cost of data collection and annotation, we can achieve decent surgical instrument segmentation performance. Moreover, we also observe that our method can deal with novel instrument prediction in the deployment domain. We hope our inspiring results will encourage researchers to emphasize data-centric methods to overcome demanding deep learning limitations besides data shortage, such as class imbalance, domain adaptation, and incremental learning. Our code is available at https://github.com/lofrienger/Single_SurgicalScene_For_Segmentation.

ML models often exhibit unexpectedly poor behavior when they are deployed in real-world domains. We identify underspecification as a key reason for these failures. An ML pipeline is underspecified when it can return many predictors with equivalently strong held-out performance in the training domain. Underspecification is common in modern ML pipelines, such as those based on deep learning. Predictors returned by underspecified pipelines are often treated as equivalent based on their training domain performance, but we show here that such predictors can behave very differently in deployment domains. This ambiguity can lead to instability and poor model behavior in practice, and is a distinct failure mode from previously identified issues arising from structural mismatch between training and deployment domains. We show that this problem appears in a wide variety of practical ML pipelines, using examples from computer vision, medical imaging, natural language processing, clinical risk prediction based on electronic health records, and medical genomics. Our results show the need to explicitly account for underspecification in modeling pipelines that are intended for real-world deployment in any domain.

A common practice in unsupervised representation learning is to use labeled data to evaluate the quality of the learned representations. This supervised evaluation is then used to guide critical aspects of the training process such as selecting the data augmentation policy. However, guiding an unsupervised training process through supervised evaluations is not possible for real-world data that does not actually contain labels (which may be the case, for example, in privacy sensitive fields such as medical imaging). Therefore, in this work we show that evaluating the learned representations with a self-supervised image rotation task is highly correlated with a standard set of supervised evaluations (rank correlation > 0.94). We establish this correlation across hundreds of augmentation policies, training settings, and network architectures and provide an algorithm (SelfAugment) to automatically and efficiently select augmentation policies without using supervised evaluations. Despite not using any labeled data, the learned augmentation policies perform comparably with augmentation policies that were determined using exhaustive supervised evaluations.

Large, fine-grained image segmentation datasets, annotated at pixel-level, are difficult to obtain, particularly in medical imaging, where annotations also require expert knowledge. Weakly-supervised learning can train models by relying on weaker forms of annotation, such as scribbles. Here, we learn to segment using scribble annotations in an adversarial game. With unpaired segmentation masks, we train a multi-scale GAN to generate realistic segmentation masks at multiple resolutions, while we use scribbles to learn their correct position in the image. Central to the model's success is a novel attention gating mechanism, which we condition with adversarial signals to act as a shape prior, resulting in better object localization at multiple scales. Subject to adversarial conditioning, the segmentor learns attention maps that are semantic, suppress the noisy activations outside the objects, and reduce the vanishing gradient problem in the deeper layers of the segmentor. We evaluated our model on several medical (ACDC, LVSC, CHAOS) and non-medical (PPSS) datasets, and we report performance levels matching those achieved by models trained with fully annotated segmentation masks. We also demonstrate extensions in a variety of settings: semi-supervised learning; combining multiple scribble sources (a crowdsourcing scenario) and multi-task learning (combining scribble and mask supervision). We release expert-made scribble annotations for the ACDC dataset, and the code used for the experiments, at https://vios-s.github.io/multiscale-adversarial-attention-gates

Object segmentation is an important step in the workflow of computational pathology. Deep learning based models generally require large amount of labeled data for precise and reliable prediction. However, collecting labeled data is expensive because it often requires expert knowledge, particularly in medical imaging domain where labels are the result of a time-consuming analysis made by one or more human experts. As nuclei, cells and glands are fundamental objects for downstream analysis in computational pathology/cytology, in this paper we propose a simple CNN-based approach to speed up collecting annotations for these objects which requires minimum interaction from the annotator. We show that for nuclei and cells in histology and cytology images, one click inside each object is enough for NuClick to yield a precise annotation. For multicellular structures such as glands, we propose a novel approach to provide the NuClick with a squiggle as a guiding signal, enabling it to segment the glandular boundaries. These supervisory signals are fed to the network as auxiliary inputs along with RGB channels. With detailed experiments, we show that NuClick is adaptable to the object scale, robust against variations in the user input, adaptable to new domains, and delivers reliable annotations. An instance segmentation model trained on masks generated by NuClick achieved the first rank in LYON19 challenge. As exemplar outputs of our framework, we are releasing two datasets: 1) a dataset of lymphocyte annotations within IHC images, and 2) a dataset of segmented WBCs in blood smear images.

With the goal of recovering high-quality image content from its degraded version, image restoration enjoys numerous applications, such as in surveillance, computational photography, medical imaging, and remote sensing. Recently, convolutional neural networks (CNNs) have achieved dramatic improvements over conventional approaches for image restoration task. Existing CNN-based methods typically operate either on full-resolution or on progressively low-resolution representations. In the former case, spatially precise but contextually less robust results are achieved, while in the latter case, semantically reliable but spatially less accurate outputs are generated. In this paper, we present a novel architecture with the collective goals of maintaining spatially-precise high-resolution representations through the entire network and receiving strong contextual information from the low-resolution representations. The core of our approach is a multi-scale residual block containing several key elements: (a) parallel multi-resolution convolution streams for extracting multi-scale features, (b) information exchange across the multi-resolution streams, (c) spatial and channel attention mechanisms for capturing contextual information, and (d) attention based multi-scale feature aggregation. In a nutshell, our approach learns an enriched set of features that combines contextual information from multiple scales, while simultaneously preserving the high-resolution spatial details. Extensive experiments on five real image benchmark datasets demonstrate that our method, named as MIRNet, achieves state-of-the-art results for a variety of image processing tasks, including image denoising, super-resolution, and image enhancement. The source code and pre-trained models are available at https://github.com/swz30/MIRNet.

Deep learning has solved a problem that as little as five years ago was thought by many to be intractable - the automatic recognition of patterns in data; and it can do so with accuracy that often surpasses human beings. It has solved problems beyond the realm of traditional, hand-crafted machine learning algorithms and captured the imagination of practitioners trying to make sense out of the flood of data that now inundates our society. As public awareness of the efficacy of DL increases so does the desire to make use of it. But even for highly trained professionals it can be daunting to approach the rapidly increasing body of knowledge produced by experts in the field. Where does one start? How does one determine if a particular model is applicable to their problem? How does one train and deploy such a network? A primer on the subject can be a good place to start. With that in mind, we present an overview of some of the key multilayer ANNs that comprise DL. We also discuss some new automatic architecture optimization protocols that use multi-agent approaches. Further, since guaranteeing system uptime is becoming critical to many computer applications, we include a section on using neural networks for fault detection and subsequent mitigation. This is followed by an exploratory survey of several application areas where DL has emerged as a game-changing technology: anomalous behavior detection in financial applications or in financial time-series forecasting, predictive and prescriptive analytics, medical image processing and analysis and power systems research. The thrust of this review is to outline emerging areas of application-oriented research within the DL community as well as to provide a reference to researchers seeking to use it in their work for what it does best: statistical pattern recognition with unparalleled learning capacity with the ability to scale with information.

Deep learning has demonstrated tremendous success in variety of application domains in the past few years. This new field of machine learning has been growing rapidly and applied in most of the application domains with some new modalities of applications, which helps to open new opportunity. There are different methods have been proposed on different category of learning approaches, which includes supervised, semi-supervised and un-supervised learning. The experimental results show state-of-the-art performance of deep learning over traditional machine learning approaches in the field of Image Processing, Computer Vision, Speech Recognition, Machine Translation, Art, Medical imaging, Medical information processing, Robotics and control, Bio-informatics, Natural Language Processing (NLP), Cyber security, and many more. This report presents a brief survey on development of DL approaches, including Deep Neural Network (DNN), Convolutional Neural Network (CNN), Recurrent Neural Network (RNN) including Long Short Term Memory (LSTM) and Gated Recurrent Units (GRU), Auto-Encoder (AE), Deep Belief Network (DBN), Generative Adversarial Network (GAN), and Deep Reinforcement Learning (DRL). In addition, we have included recent development of proposed advanced variant DL techniques based on the mentioned DL approaches. Furthermore, DL approaches have explored and evaluated in different application domains are also included in this survey. We have also comprised recently developed frameworks, SDKs, and benchmark datasets that are used for implementing and evaluating deep learning approaches. There are some surveys have published on Deep Learning in Neural Networks [1, 38] and a survey on RL [234]. However, those papers have not discussed the individual advanced techniques for training large scale deep learning models and the recently developed method of generative models [1].

In many real-world applications, deployed models encounter inputs that differ from the data seen during training. Out-of-distribution detection identifies whether an input stems from an unseen distribution, while open-world recognition flags such inputs to ensure the system remains robust as ever-emerging, previously unknown categories appear and must be addressed without retraining. Foundation and vision-language models are pre-trained on large and diverse datasets with the expectation of broad generalization across domains, including medical imaging. However, benchmarking these models on test sets with only a few common outlier types silently collapses the evaluation back to a closed-set problem, masking failures on rare or truly novel conditions encountered in clinical use. We therefore present NOVA, a challenging, real-life evaluation-only benchmark of sim900 brain MRI scans that span 281 rare pathologies and heterogeneous acquisition protocols. Each case includes rich clinical narratives and double-blinded expert bounding-box annotations. Together, these enable joint assessment of anomaly localisation, visual captioning, and diagnostic reasoning. Because NOVA is never used for training, it serves as an extreme stress-test of out-of-distribution generalisation: models must bridge a distribution gap both in sample appearance and in semantic space. Baseline results with leading vision-language models (GPT-4o, Gemini 2.0 Flash, and Qwen2.5-VL-72B) reveal substantial performance drops across all tasks, establishing NOVA as a rigorous testbed for advancing models that can detect, localize, and reason about truly unknown anomalies.

Understanding radiologists' eye movement during Computed Tomography (CT) reading is crucial for developing effective interpretable computer-aided diagnosis systems. However, CT research in this area has been limited by the lack of publicly available eye-tracking datasets and the three-dimensional complexity of CT volumes. To address these challenges, we present the first publicly available eye gaze dataset on CT, called CT-ScanGaze. Then, we introduce CT-Searcher, a novel 3D scanpath predictor designed specifically to process CT volumes and generate radiologist-like 3D fixation sequences, overcoming the limitations of current scanpath predictors that only handle 2D inputs. Since deep learning models benefit from a pretraining step, we develop a pipeline that converts existing 2D gaze datasets into 3D gaze data to pretrain CT-Searcher. Through both qualitative and quantitative evaluations on CT-ScanGaze, we demonstrate the effectiveness of our approach and provide a comprehensive assessment framework for 3D scanpath prediction in medical imaging.

Camouflaged object segmentation presents unique challenges compared to traditional segmentation tasks, primarily due to the high similarity in patterns and colors between camouflaged objects and their backgrounds. Effective solutions to this problem have significant implications in critical areas such as pest control, defect detection, and lesion segmentation in medical imaging. Prior research has predominantly emphasized supervised or unsupervised pre-training methods, leaving zero-shot approaches significantly underdeveloped. Existing zero-shot techniques commonly utilize the Segment Anything Model (SAM) in automatic mode or rely on vision-language models to generate cues for segmentation; however, their performances remain unsatisfactory, due to the similarity of the camouflaged object and the background. This work studies how to avoid training by integrating large pre-trained models like SAM-2 and Owl-v2 with temporal information into a modular pipeline. Evaluated on the MoCA-Mask dataset, our approach achieves outstanding performance improvements, significantly outperforming existing zero-shot methods by raising the F-measure (F_beta^w) from 0.296 to 0.628. Our approach also surpasses supervised methods, increasing the F-measure from 0.476 to 0.628. Additionally, evaluation on the MoCA-Filter dataset demonstrates an increase in the success rate from 0.628 to 0.697 when compared with FlowSAM, a supervised transfer method. A thorough ablation study further validates the individual contributions of each component. Besides our main contributions, we also highlight inconsistencies in previous work regarding metrics and settings. Code can be found in https://github.com/weathon/vcos.

Generative models, particularly text-to-image (T2I) diffusion models, play a crucial role in medical image analysis. However, these models are prone to training data memorization, posing significant risks to patient privacy. Synthetic chest X-ray generation is one of the most common applications in medical image analysis with the MIMIC-CXR dataset serving as the primary data repository for this task. This study adopts a data-driven approach and presents the first systematic attempt to identify prompts and text tokens in MIMIC-CXR that contribute the most to training data memorization. Our analysis reveals an unexpected finding: prompts containing traces of de-identification procedures are among the most memorized, with de-identification markers contributing the most. Furthermore, we also find existing inference-time memorization mitigation strategies are ineffective and fail to sufficiently reduce the model's reliance on memorized text tokens highlighting a broader issue in T2I synthesis with MIMIC-CXR. On this front, we propose actionable strategies to enhance privacy and improve the reliability of generative models in medical imaging. Finally, our results provide a foundation for future work on developing and benchmarking memorization mitigation techniques for synthetic chest X-ray generation using the MIMIC-CXR dataset.

Reconstructing meshes from point clouds is an important task in fields such as robotics, autonomous systems, and medical imaging. This survey examines state-of-the-art learning-based approaches to mesh reconstruction, categorizing them into five paradigms: PointNet family, autoencoder architectures, deformation-based methods, point-move techniques, and primitive-based approaches. Each paradigm is explored in depth, detailing the primary approaches and their underlying methodologies. By comparing these techniques, our study serves as a comprehensive guide, and equips researchers and practitioners with the knowledge to navigate the landscape of learning-based mesh reconstruction techniques. The findings underscore the transformative potential of these methods, which often surpass traditional techniques in allowing detailed and efficient reconstructions.

Recent advancements in multi-modal models have significantly improved vision-language alignment in radiology. However, existing approaches struggle to effectively utilize complex radiology reports for learning, rely on low-resolution images, and offer limited interpretability in attention mechanisms. To address these challenges, we introduce RadZero, a novel similarity-based cross-attention framework for vision-language alignment in radiology with zero-shot multi-task capability. RadZero leverages large language models to extract minimal semantic sentences from radiology reports and employs a multi-positive contrastive learning strategy to effectively capture relationships between images and multiple relevant textual descriptions. It also utilizes a pre-trained vision encoder with additional trainable Transformer layers, allowing efficient high-resolution image processing. By computing similarity between text embeddings and local image patch features, RadZero enables zero-shot inference with similarity probability for classification and pixel-level cross-modal similarity maps for grounding and segmentation. Experimental results on public chest radiograph benchmarks show that RadZero outperforms state-of-the-art methods in zero-shot classification, grounding, and segmentation. Furthermore, cross-modal similarity map analysis highlights its potential for improving explainability in vision-language alignment. Additionally, qualitative evaluation demonstrates RadZero's capability for open-vocabulary semantic segmentation, further validating its effectiveness in medical imaging.

Image classification is a fundamental task in computer vision with diverse applications, ranging from autonomous systems to medical imaging. The CIFAR-10 dataset is a widely used benchmark to evaluate the performance of classification models on small-scale, multi-class datasets. Convolutional Neural Networks (CNNs) have demonstrated state-of-the-art results; however, they often suffer from overfitting and suboptimal feature representation when applied to challenging datasets like CIFAR-10. In this paper, we propose an enhanced CNN architecture that integrates deeper convolutional blocks, batch normalization, and dropout regularization to achieve superior performance. The proposed model achieves a test accuracy of 84.95%, outperforming baseline CNN architectures. Through detailed ablation studies, we demonstrate the effectiveness of the enhancements and analyze the hierarchical feature representations. This work highlights the potential of refined CNN architectures for tackling small-scale image classification problems effectively.

Diffusion models excel in generating images that closely resemble their training data but are also susceptible to data memorization, raising privacy, ethical, and legal concerns, particularly in sensitive domains such as medical imaging. We hypothesize that this memorization stems from the overparameterization of deep models and propose that regularizing model capacity during fine-tuning can mitigate this issue. Firstly, we empirically show that regulating the model capacity via Parameter-efficient fine-tuning (PEFT) mitigates memorization to some extent, however, it further requires the identification of the exact parameter subsets to be fine-tuned for high-quality generation. To identify these subsets, we introduce a bi-level optimization framework, MemControl, that automates parameter selection using memorization and generation quality metrics as rewards during fine-tuning. The parameter subsets discovered through MemControl achieve a superior tradeoff between generation quality and memorization. For the task of medical image generation, our approach outperforms existing state-of-the-art memorization mitigation strategies by fine-tuning as few as 0.019% of model parameters. Moreover, we demonstrate that the discovered parameter subsets are transferable to non-medical domains. Our framework is scalable to large datasets, agnostic to reward functions, and can be integrated with existing approaches for further memorization mitigation. To the best of our knowledge, this is the first study to empirically evaluate memorization in medical images and propose a targeted yet universal mitigation strategy. The code is available at https://github.com/Raman1121/Diffusion_Memorization_HPO.

Segment Anything Model (SAM) is a foundation model for interactive segmentation, and it has catalyzed major advances in generative AI, computational photography, and medical imaging. This model takes in an arbitrary user input and provides segmentation masks of the corresponding objects. It is our goal to develop a version of SAM that is appropriate for use in a photography app. The original SAM model has a few challenges in this setting. First, original SAM a 600 million parameter based on ViT-H, and its high computational cost and large model size that are not suitable for todays mobile hardware. We address this by proposing the SqueezeSAM model architecture, which is 50x faster and 100x smaller than SAM. Next, when a user takes a photo on their phone, it might not occur to them to click on the image and get a mask. Our solution is to use salient object detection to generate the first few clicks. This produces an initial segmentation mask that the user can interactively edit. Finally, when a user clicks on an object, they typically expect all related pieces of the object to be segmented. For instance, if a user clicks on a person t-shirt in a photo, they expect the whole person to be segmented, but SAM typically segments just the t-shirt. We address this with a new data augmentation scheme, and the end result is that if the user clicks on a person holding a basketball, the person and the basketball are all segmented together.

With recent advances in computing hardware and surges of deep-learning architectures, learning-based deep image registration methods have surpassed their traditional counterparts, in terms of metric performance and inference time. However, these methods focus on improving performance measurements such as Dice, resulting in less attention given to model behaviors that are equally desirable for registrations, especially for medical imaging. This paper investigates these behaviors for popular learning-based deep registrations under a sanity-checking microscope. We find that most existing registrations suffer from low inverse consistency and nondiscrimination of identical pairs due to overly optimized image similarities. To rectify these behaviors, we propose a novel regularization-based sanity-enforcer method that imposes two sanity checks on the deep model to reduce its inverse consistency errors and increase its discriminative power simultaneously. Moreover, we derive a set of theoretical guarantees for our sanity-checked image registration method, with experimental results supporting our theoretical findings and their effectiveness in increasing the sanity of models without sacrificing any performance. Our code and models are available at https://github.com/tuffr5/Saner-deep-registration.

Machine learning is a general-purpose technology holding promises for many interdisciplinary research problems. However, significant barriers exist in crossing disciplinary boundaries when most machine learning tools are developed in different areas separately. We present Pykale - a Python library for knowledge-aware machine learning on graphs, images, texts, and videos to enable and accelerate interdisciplinary research. We formulate new green machine learning guidelines based on standard software engineering practices and propose a novel pipeline-based application programming interface (API). PyKale focuses on leveraging knowledge from multiple sources for accurate and interpretable prediction, thus supporting multimodal learning and transfer learning (particularly domain adaptation) with latest deep learning and dimensionality reduction models. We build PyKale on PyTorch and leverage the rich PyTorch ecosystem. Our pipeline-based API design enforces standardization and minimalism, embracing green machine learning concepts via reducing repetitions and redundancy, reusing existing resources, and recycling learning models across areas. We demonstrate its interdisciplinary nature via examples in bioinformatics, knowledge graph, image/video recognition, and medical imaging.

Deep learning expresses a category of machine learning algorithms that have the capability to combine raw inputs into intermediate features layers. These deep learning algorithms have demonstrated great results in different fields. Deep learning has particularly witnessed for a great achievement of human level performance across a number of domains in computer vision and pattern recognition. For the achievement of state-of-the-art performances in diverse domains, the deep learning used different architectures and these architectures used activation functions to perform various computations between hidden and output layers of any architecture. This paper presents a survey on the existing studies of deep learning in handwriting recognition field. Even though the recent progress indicates that the deep learning methods has provided valuable means for speeding up or proving accurate results in handwriting recognition, but following from the extensive literature survey, the present study finds that the deep learning has yet to revolutionize more and has to resolve many of the most pressing challenges in this field, but promising advances have been made on the prior state of the art. Additionally, an inadequate availability of labelled data to train presents problems in this domain. Nevertheless, the present handwriting recognition survey foresees deep learning enabling changes at both bench and bedside with the potential to transform several domains as image processing, speech recognition, computer vision, machine translation, robotics and control, medical imaging, medical information processing, bio-informatics, natural language processing, cyber security, and many others.