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Mar 14

RoentGen: Vision-Language Foundation Model for Chest X-ray Generation

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%.

LVM-Med: Learning Large-Scale Self-Supervised Vision Models for Medical Imaging via Second-order Graph Matching

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.

Generative AI for Medical Imaging: extending the MONAI Framework

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.

ATOMMIC: An Advanced Toolbox for Multitask Medical Imaging Consistency to facilitate Artificial Intelligence applications from acquisition to analysis in Magnetic Resonance Imaging

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.

UniMed-CLIP: Towards a Unified Image-Text Pretraining Paradigm for Diverse Medical Imaging Modalities

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.

On the Compositional Generalization of Multimodal LLMs for Medical Imaging

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.

VISTA3D: A Unified Segmentation Foundation Model For 3D Medical Imaging

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.

Diffusion Models for Medical Image Analysis: A Comprehensive Survey

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.

Towards General Purpose Vision Foundation Models for Medical Image Analysis: An Experimental Study of DINOv2 on Radiology Benchmarks

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.

Computation-Efficient Era: A Comprehensive Survey of State Space Models in Medical Image Analysis

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.

Potential of Multimodal Large Language Models for Data Mining of Medical Images and Free-text Reports

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.

Self-Supervised Pre-Training with Contrastive and Masked Autoencoder Methods for Dealing with Small Datasets in Deep Learning for Medical Imaging

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.

MedImageInsight: An Open-Source Embedding Model for General Domain Medical Imaging

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.

Worse than Random? An Embarrassingly Simple Probing Evaluation of Large Multimodal Models in Medical VQA

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.

LeFusion: Controllable Pathology Synthesis via Lesion-Focused Diffusion Models

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.

Generative Medical Segmentation

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.

Coupling AI and Citizen Science in Creation of Enhanced Training Dataset for Medical Image Segmentation

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.

SADM: Sequence-Aware Diffusion Model for Longitudinal Medical Image Generation

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.

Few-shot Adaptation of Multi-modal Foundation Models: A Survey

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.

Large Language Models Illuminate a Progressive Pathway to Artificial Healthcare Assistant: A Review

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.

Less is More: Selective Reduction of CT Data for Self-Supervised Pre-Training of Deep Learning Models with Contrastive Learning Improves Downstream Classification Performance

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.

The Effect of Intrinsic Dataset Properties on Generalization: Unraveling Learning Differences Between Natural and Medical Images

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

Don't Play Favorites: Minority Guidance for Diffusion Models

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.

Unleashing the Potential of Large Language Models for Text-to-Image Generation through Autoregressive Representation Alignment

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.

MedShapeNet -- A Large-Scale Dataset of 3D Medical Shapes for Computer Vision

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

Deformation-Recovery Diffusion Model (DRDM): Instance Deformation for Image Manipulation and Synthesis

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/

SC-MIL: Supervised Contrastive Multiple Instance Learning for Imbalanced Classification in Pathology

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.

MedSyn: Text-guided Anatomy-aware Synthesis of High-Fidelity 3D CT 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.

A Foundation LAnguage-Image model of the Retina (FLAIR): Encoding expert knowledge in text supervision

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.

Rethinking Surgical Instrument Segmentation: A Background Image Can Be All You Need

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.

Development of a Large-scale Dataset of Chest Computed Tomography Reports in Japanese and a High-performance Finding Classification Model

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.

cWDM: Conditional Wavelet Diffusion Models for Cross-Modality 3D Medical Image Synthesis

This paper contributes to the "BraTS 2024 Brain MR Image Synthesis Challenge" and presents a conditional Wavelet Diffusion Model (cWDM) for directly solving a paired image-to-image translation task on high-resolution volumes. While deep learning-based brain tumor segmentation models have demonstrated clear clinical utility, they typically require MR scans from various modalities (T1, T1ce, T2, FLAIR) as input. However, due to time constraints or imaging artifacts, some of these modalities may be missing, hindering the application of well-performing segmentation algorithms in clinical routine. To address this issue, we propose a method that synthesizes one missing modality image conditioned on three available images, enabling the application of downstream segmentation models. We treat this paired image-to-image translation task as a conditional generation problem and solve it by combining a Wavelet Diffusion Model for high-resolution 3D image synthesis with a simple conditioning strategy. This approach allows us to directly apply our model to full-resolution volumes, avoiding artifacts caused by slice- or patch-wise data processing. While this work focuses on a specific application, the presented method can be applied to all kinds of paired image-to-image translation problems, such as CT leftrightarrow MR and MR leftrightarrow PET translation, or mask-conditioned anatomically guided image generation.

From Generalist to Specialist: Adapting Vision Language Models via Task-Specific Visual Instruction Tuning

Large vision language models (VLMs) combine large language models with vision encoders, demonstrating promise across various tasks. However, they often underperform in task-specific applications due to domain gaps between pre-training and fine-tuning. We introduce VITask, a novel framework that enhances task-specific adaptability of VLMs by integrating task-specific models (TSMs). VITask employs three key strategies: exemplar prompting (EP), response distribution alignment (RDA), and contrastive response tuning (CRT) to improve the task-specific performance of VLMs by adjusting their response distributions. EP allows TSM features to guide VLMs, while RDA enables VLMs to adapt without TSMs during inference by learning from exemplar-prompted models. CRT further optimizes the ranking of correct image-response pairs, thereby reducing the risk of generating undesired responses. Experiments on 12 medical diagnosis datasets across 9 imaging modalities show that VITask outperforms both vanilla instruction-tuned VLMs and TSMs, showcasing its ability to integrate complementary features from both models effectively. Additionally, VITask offers practical advantages such as flexible TSM integration and robustness to incomplete instructions, making it a versatile and efficient solution for task-specific VLM tuning. Our code are available at https://github.com/baiyang4/VITask.

GMAI-MMBench: A Comprehensive Multimodal Evaluation Benchmark Towards General Medical AI

Large Vision-Language Models (LVLMs) are capable of handling diverse data types such as imaging, text, and physiological signals, and can be applied in various fields. In the medical field, LVLMs have a high potential to offer substantial assistance for diagnosis and treatment. Before that, it is crucial to develop benchmarks to evaluate LVLMs' effectiveness in various medical applications. Current benchmarks are often built upon specific academic literature, mainly focusing on a single domain, and lacking varying perceptual granularities. Thus, they face specific challenges, including limited clinical relevance, incomplete evaluations, and insufficient guidance for interactive LVLMs. To address these limitations, we developed the GMAI-MMBench, the most comprehensive general medical AI benchmark with well-categorized data structure and multi-perceptual granularity to date. It is constructed from 285 datasets across 39 medical image modalities, 18 clinical-related tasks, 18 departments, and 4 perceptual granularities in a Visual Question Answering (VQA) format. Additionally, we implemented a lexical tree structure that allows users to customize evaluation tasks, accommodating various assessment needs and substantially supporting medical AI research and applications. We evaluated 50 LVLMs, and the results show that even the advanced GPT-4o only achieves an accuracy of 52%, indicating significant room for improvement. Moreover, we identified five key insufficiencies in current cutting-edge LVLMs that need to be addressed to advance the development of better medical applications. We believe that GMAI-MMBench will stimulate the community to build the next generation of LVLMs toward GMAI. Project Page: https://uni-medical.github.io/GMAI-MMBench.github.io/

A Textbook Remedy for Domain Shifts: Knowledge Priors for Medical Image Analysis

While deep networks have achieved broad success in analyzing natural images, when applied to medical scans, they often fail in unexcepted situations. We investigate this challenge and focus on model sensitivity to domain shifts, such as data sampled from different hospitals or data confounded by demographic variables such as sex, race, etc, in the context of chest X-rays and skin lesion images. A key finding we show empirically is that existing visual backbones lack an appropriate prior from the architecture for reliable generalization in these settings. Taking inspiration from medical training, we propose giving deep networks a prior grounded in explicit medical knowledge communicated in natural language. To this end, we introduce Knowledge-enhanced Bottlenecks (KnoBo), a class of concept bottleneck models that incorporates knowledge priors that constrain it to reason with clinically relevant factors found in medical textbooks or PubMed. KnoBo uses retrieval-augmented language models to design an appropriate concept space paired with an automatic training procedure for recognizing the concept. We evaluate different resources of knowledge and recognition architectures on a broad range of domain shifts across 20 datasets. In our comprehensive evaluation with two imaging modalities, KnoBo outperforms fine-tuned models on confounded datasets by 32.4% on average. Finally, evaluations reveal that PubMed is a promising resource for making medical models less sensitive to domain shift, outperforming other resources on both diversity of information and final prediction performance.

RAD-DINO: Exploring Scalable Medical Image Encoders Beyond Text Supervision

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.

RadGenome-Chest CT: A Grounded Vision-Language Dataset for Chest CT Analysis

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

Towards a Multimodal Large Language Model with Pixel-Level Insight for Biomedicine

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.

MemControl: Mitigating Memorization in Diffusion Models via Automated Parameter Selection

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.

Representing Part-Whole Hierarchies in Foundation Models by Learning Localizability, Composability, and Decomposability from Anatomy via Self-Supervision

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.

Synthetic Observational Health Data with GANs: from slow adoption to a boom in medical research and ultimately digital twins?

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.

A for-loop is all you need. For solving the inverse problem in the case of personalized tumor growth modeling

Solving the inverse problem is the key step in evaluating the capacity of a physical model to describe real phenomena. In medical image computing, it aligns with the classical theme of image-based model personalization. Traditionally, a solution to the problem is obtained by performing either sampling or variational inference based methods. Both approaches aim to identify a set of free physical model parameters that results in a simulation best matching an empirical observation. When applied to brain tumor modeling, one of the instances of image-based model personalization in medical image computing, the overarching drawback of the methods is the time complexity for finding such a set. In a clinical setting with limited time between imaging and diagnosis or even intervention, this time complexity may prove critical. As the history of quantitative science is the history of compression, we align in this paper with the historical tendency and propose a method compressing complex traditional strategies for solving an inverse problem into a simple database query task. We evaluated different ways of performing the database query task assessing the trade-off between accuracy and execution time. On the exemplary task of brain tumor growth modeling, we prove that the proposed method achieves one order speed-up compared to existing approaches for solving the inverse problem. The resulting compute time offers critical means for relying on more complex and, hence, realistic models, for integrating image preprocessing and inverse modeling even deeper, or for implementing the current model into a clinical workflow.

Cross-D Conv: Cross-Dimensional Transferable Knowledge Base via Fourier Shifting Operation

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.

CC-SAM: SAM with Cross-feature Attention and Context for Ultrasound Image Segmentation

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.

Imaging foundation model for universal enhancement of non-ideal measurement CT

Non-ideal measurement computed tomography (NICT), which sacrifices optimal imaging standards for new advantages in CT imaging, is expanding the clinical application scope of CT images. However, with the reduction of imaging standards, the image quality has also been reduced, extremely limiting the clinical acceptability. Although numerous studies have demonstrated the feasibility of deep learning for the NICT enhancement in specific scenarios, their high data cost and limited generalizability have become large obstacles. The recent research on the foundation model has brought new opportunities for building a universal NICT enhancement model - bridging the image quality degradation with minimal data cost. However, owing to the challenges in the collection of large pre-training datasets and the compatibility of data variation, no success has been reported. In this paper, we propose a multi-scale integrated Transformer AMPlifier (TAMP), the first imaging foundation model for universal NICT enhancement. It has been pre-trained on a large-scale physical-driven simulation dataset with 3.6 million NICT-ICT image pairs, and is able to directly generalize to the NICT enhancement tasks with various non-ideal settings and body regions. Via the adaptation with few data, it can further achieve professional performance in real-world specific scenarios. Our extensive experiments have demonstrated that the proposed TAMP has significant potential for promoting the exploration and application of NICT and serving a wider range of medical scenarios.

Towards a clinically accessible radiology foundation model: open-access and lightweight, with automated evaluation

The scaling laws and extraordinary performance of large foundation models motivate the development and utilization of such models in biomedicine. However, despite early promising results on some biomedical benchmarks, there are still major challenges that need to be addressed before these models can be used in real-world clinics. Frontier general-domain models such as GPT-4V still have significant performance gaps in multimodal biomedical applications. More importantly, less-acknowledged pragmatic issues, including accessibility, model cost, and tedious manual evaluation make it hard for clinicians to use state-of-the-art large models directly on private patient data. Here, we explore training open-source small multimodal models (SMMs) to bridge competency gaps for unmet clinical needs in radiology. To maximize data efficiency, we adopt a modular approach by incorporating state-of-the-art pre-trained models for image and text modalities, and focusing on training a lightweight adapter to ground each modality to the text embedding space, as exemplified by LLaVA-Med. For training, we assemble a large dataset of over 697 thousand radiology image-text pairs. For evaluation, we propose CheXprompt, a GPT-4-based metric for factuality evaluation, and demonstrate its parity with expert evaluation. For best practice, we conduct a systematic ablation study on various choices in data engineering and multimodal training. The resulting LlaVA-Rad (7B) model attains state-of-the-art results on standard radiology tasks such as report generation and cross-modal retrieval, even outperforming much larger models such as GPT-4V and Med-PaLM M (84B). The inference of LlaVA-Rad is fast and can be performed on a single V100 GPU in private settings, offering a promising state-of-the-art tool for real-world clinical applications.

SegBook: A Simple Baseline and Cookbook for Volumetric Medical Image Segmentation

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.

RadRotator: 3D Rotation of Radiographs with Diffusion Models

Transforming two-dimensional (2D) images into three-dimensional (3D) volumes is a well-known yet challenging problem for the computer vision community. In the medical domain, a few previous studies attempted to convert two or more input radiographs into computed tomography (CT) volumes. Following their effort, we introduce a diffusion model-based technology that can rotate the anatomical content of any input radiograph in 3D space, potentially enabling the visualization of the entire anatomical content of the radiograph from any viewpoint in 3D. Similar to previous studies, we used CT volumes to create Digitally Reconstructed Radiographs (DRRs) as the training data for our model. However, we addressed two significant limitations encountered in previous studies: 1. We utilized conditional diffusion models with classifier-free guidance instead of Generative Adversarial Networks (GANs) to achieve higher mode coverage and improved output image quality, with the only trade-off being slower inference time, which is often less critical in medical applications; and 2. We demonstrated that the unreliable output of style transfer deep learning (DL) models, such as Cycle-GAN, to transfer the style of actual radiographs to DRRs could be replaced with a simple yet effective training transformation that randomly changes the pixel intensity histograms of the input and ground-truth imaging data during training. This transformation makes the diffusion model agnostic to any distribution variations of the input data pixel intensity, enabling the reliable training of a DL model on input DRRs and applying the exact same model to conventional radiographs (or DRRs) during inference.

A Comprehensive Survey of Mamba Architectures for Medical Image Analysis: Classification, Segmentation, Restoration and Beyond

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.

Classification of Brain Tumours in MR Images using Deep Spatiospatial Models

A brain tumour is a mass or cluster of abnormal cells in the brain, which has the possibility of becoming life-threatening because of its ability to invade neighbouring tissues and also form metastases. An accurate diagnosis is essential for successful treatment planning and magnetic resonance imaging is the principal imaging modality for diagnostic of brain tumours and their extent. Deep Learning methods in computer vision applications have shown significant improvement in recent years, most of which can be credited to the fact that a sizeable amount of data is available to train models on, and the improvements in the model architectures yielding better approximations in a supervised setting. Classifying tumours using such deep learning methods has made significant progress with the availability of open datasets with reliable annotations. Typically those methods are either 3D models, which use 3D volumetric MRIs or even 2D models considering each slice separately. However, by treating the slice spatial dimension separately, spatiotemporal models can be employed as spatiospatial models for this task. These models have the capabilities of learning specific spatial and temporal relationship, while reducing computational costs. This paper uses two spatiotemporal models, ResNet (2+1)D and ResNet Mixed Convolution, to classify different types of brain tumours. It was observed that both these models performed superior to the pure 3D convolutional model, ResNet18. Furthermore, it was also observed that pre-training the models on a different, even unrelated dataset before training them for the task of tumour classification improves the performance. Finally, Pre-trained ResNet Mixed Convolution was observed to be the best model in these experiments, achieving a macro F1-score of 0.93 and a test accuracy of 96.98\%, while at the same time being the model with the least computational cost.

Head and Neck Tumor Segmentation from [18F]F-FDG PET/CT Images Based on 3D Diffusion Model

Head and neck (H&N) cancers are among the most prevalent types of cancer worldwide, and [18F]F-FDG PET/CT is widely used for H&N cancer management. Recently, the diffusion model has demonstrated remarkable performance in various image-generation tasks. In this work, we proposed a 3D diffusion model to accurately perform H&N tumor segmentation from 3D PET and CT volumes. The 3D diffusion model was developed considering the 3D nature of PET and CT images acquired. During the reverse process, the model utilized a 3D UNet structure and took the concatenation of PET, CT, and Gaussian noise volumes as the network input to generate the tumor mask. Experiments based on the HECKTOR challenge dataset were conducted to evaluate the effectiveness of the proposed diffusion model. Several state-of-the-art techniques based on U-Net and Transformer structures were adopted as the reference methods. Benefits of employing both PET and CT as the network input as well as further extending the diffusion model from 2D to 3D were investigated based on various quantitative metrics and the uncertainty maps generated. Results showed that the proposed 3D diffusion model could generate more accurate segmentation results compared with other methods. Compared to the diffusion model in 2D format, the proposed 3D model yielded superior results. Our experiments also highlighted the advantage of utilizing dual-modality PET and CT data over only single-modality data for H&N tumor segmentation.

Exploring Multimodal Large Language Models for Radiology Report Error-checking

This paper proposes one of the first clinical applications of multimodal large language models (LLMs) as an assistant for radiologists to check errors in their reports. We created an evaluation dataset from two real-world radiology datasets (MIMIC-CXR and IU-Xray), with 1,000 subsampled reports each. A subset of original reports was modified to contain synthetic errors by introducing various type of mistakes. The evaluation contained two difficulty levels: SIMPLE for binary error-checking and COMPLEX for identifying error types. LLaVA (Large Language and Visual Assistant) variant models, including our instruction-tuned model, were used for the evaluation. Additionally, a domain expert evaluation was conducted on a small test set. At the SIMPLE level, the LLaVA v1.5 model outperformed other publicly available models. Instruction tuning significantly enhanced performance by 47.4% and 25.4% on MIMIC-CXR and IU-Xray data, respectively. The model also surpassed the domain experts accuracy in the MIMIC-CXR dataset by 1.67%. Notably, among the subsets (N=21) of the test set where a clinician did not achieve the correct conclusion, the LLaVA ensemble mode correctly identified 71.4% of these cases. This study marks a promising step toward utilizing multi-modal LLMs to enhance diagnostic accuracy in radiology. The ensemble model demonstrated comparable performance to clinicians, even capturing errors overlooked by humans. Nevertheless, future work is needed to improve the model ability to identify the types of inconsistency.

Detailed Annotations of Chest X-Rays via CT Projection for Report Understanding

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/.

Towards a Single Unified Model for Effective Detection, Segmentation, and Diagnosis of Eight Major Cancers Using a Large Collection of CT Scans

Human readers or radiologists routinely perform full-body multi-organ multi-disease detection and diagnosis in clinical practice, while most medical AI systems are built to focus on single organs with a narrow list of a few diseases. This might severely limit AI's clinical adoption. A certain number of AI models need to be assembled non-trivially to match the diagnostic process of a human reading a CT scan. In this paper, we construct a Unified Tumor Transformer (UniT) model to detect (tumor existence and location) and diagnose (tumor characteristics) eight major cancer-prevalent organs in CT scans. UniT is a query-based Mask Transformer model with the output of multi-organ and multi-tumor semantic segmentation. We decouple the object queries into organ queries, detection queries and diagnosis queries, and further establish hierarchical relationships among the three groups. This clinically-inspired architecture effectively assists inter- and intra-organ representation learning of tumors and facilitates the resolution of these complex, anatomically related multi-organ cancer image reading tasks. UniT is trained end-to-end using a curated large-scale CT images of 10,042 patients including eight major types of cancers and occurring non-cancer tumors (all are pathology-confirmed with 3D tumor masks annotated by radiologists). On the test set of 631 patients, UniT has demonstrated strong performance under a set of clinically relevant evaluation metrics, substantially outperforming both multi-organ segmentation methods and an assembly of eight single-organ expert models in tumor detection, segmentation, and diagnosis. Such a unified multi-cancer image reading model (UniT) can significantly reduce the number of false positives produced by combined multi-system models. This moves one step closer towards a universal high-performance cancer screening tool.

Bora: Biomedical Generalist Video Generation Model

Generative models hold promise for revolutionizing medical education, robot-assisted surgery, and data augmentation for medical AI development. Diffusion models can now generate realistic images from text prompts, while recent advancements have demonstrated their ability to create diverse, high-quality videos. However, these models often struggle with generating accurate representations of medical procedures and detailed anatomical structures. This paper introduces Bora, the first spatio-temporal diffusion probabilistic model designed for text-guided biomedical video generation. Bora leverages Transformer architecture and is pre-trained on general-purpose video generation tasks. It is fine-tuned through model alignment and instruction tuning using a newly established medical video corpus, which includes paired text-video data from various biomedical fields. To the best of our knowledge, this is the first attempt to establish such a comprehensive annotated biomedical video dataset. Bora is capable of generating high-quality video data across four distinct biomedical domains, adhering to medical expert standards and demonstrating consistency and diversity. This generalist video generative model holds significant potential for enhancing medical consultation and decision-making, particularly in resource-limited settings. Additionally, Bora could pave the way for immersive medical training and procedure planning. Extensive experiments on distinct medical modalities such as endoscopy, ultrasound, MRI, and cell tracking validate the effectiveness of our model in understanding biomedical instructions and its superior performance across subjects compared to state-of-the-art generation models.

MRSegmentator: Robust Multi-Modality Segmentation of 40 Classes in MRI and CT Sequences

Purpose: To introduce a deep learning model capable of multi-organ segmentation in MRI scans, offering a solution to the current limitations in MRI analysis due to challenges in resolution, standardized intensity values, and variability in sequences. Materials and Methods: he model was trained on 1,200 manually annotated MRI scans from the UK Biobank, 221 in-house MRI scans and 1228 CT scans, leveraging cross-modality transfer learning from CT segmentation models. A human-in-the-loop annotation workflow was employed to efficiently create high-quality segmentations. The model's performance was evaluated on NAKO and the AMOS22 dataset containing 600 and 60 MRI examinations. Dice Similarity Coefficient (DSC) and Hausdorff Distance (HD) was used to assess segmentation accuracy. The model will be open sourced. Results: The model showcased high accuracy in segmenting well-defined organs, achieving Dice Similarity Coefficient (DSC) scores of 0.97 for the right and left lungs, and 0.95 for the heart. It also demonstrated robustness in organs like the liver (DSC: 0.96) and kidneys (DSC: 0.95 left, 0.95 right), which present more variability. However, segmentation of smaller and complex structures such as the portal and splenic veins (DSC: 0.54) and adrenal glands (DSC: 0.65 left, 0.61 right) revealed the need for further model optimization. Conclusion: The proposed model is a robust, tool for accurate segmentation of 40 anatomical structures in MRI and CT images. By leveraging cross-modality learning and interactive annotation, the model achieves strong performance and generalizability across diverse datasets, making it a valuable resource for researchers and clinicians. It is open source and can be downloaded from https://github.com/hhaentze/MRSegmentator.

STU-Net: Scalable and Transferable Medical Image Segmentation Models Empowered by Large-Scale Supervised Pre-training

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

Vision-Language Generative Model for View-Specific Chest X-ray Generation

Synthetic medical data generation has opened up new possibilities in the healthcare domain, offering a powerful tool for simulating clinical scenarios, enhancing diagnostic and treatment quality, gaining granular medical knowledge, and accelerating the development of unbiased algorithms. In this context, we present a novel approach called ViewXGen, designed to overcome the limitations of existing methods that rely on general domain pipelines using only radiology reports to generate frontal-view chest X-rays. Our approach takes into consideration the diverse view positions found in the dataset, enabling the generation of chest X-rays with specific views, which marks a significant advancement in the field. To achieve this, we introduce a set of specially designed tokens for each view position, tailoring the generation process to the user's preferences. Furthermore, we leverage multi-view chest X-rays as input, incorporating valuable information from different views within the same study. This integration rectifies potential errors and contributes to faithfully capturing abnormal findings in chest X-ray generation. To validate the effectiveness of our approach, we conducted statistical analyses, evaluating its performance in a clinical efficacy metric on the MIMIC-CXR dataset. Also, human evaluation demonstrates the remarkable capabilities of ViewXGen, particularly in producing realistic view-specific X-rays that closely resemble the original images.

Latent Diffusion Model for Medical Image Standardization and Enhancement

Computed tomography (CT) serves as an effective tool for lung cancer screening, diagnosis, treatment, and prognosis, providing a rich source of features to quantify temporal and spatial tumor changes. Nonetheless, the diversity of CT scanners and customized acquisition protocols can introduce significant inconsistencies in texture features, even when assessing the same patient. This variability poses a fundamental challenge for subsequent research that relies on consistent image features. Existing CT image standardization models predominantly utilize GAN-based supervised or semi-supervised learning, but their performance remains limited. We present DiffusionCT, an innovative score-based DDPM model that operates in the latent space to transform disparate non-standard distributions into a standardized form. The architecture comprises a U-Net-based encoder-decoder, augmented by a DDPM model integrated at the bottleneck position. First, the encoder-decoder is trained independently, without embedding DDPM, to capture the latent representation of the input data. Second, the latent DDPM model is trained while keeping the encoder-decoder parameters fixed. Finally, the decoder uses the transformed latent representation to generate a standardized CT image, providing a more consistent basis for downstream analysis. Empirical tests on patient CT images indicate notable improvements in image standardization using DiffusionCT. Additionally, the model significantly reduces image noise in SPAD images, further validating the effectiveness of DiffusionCT for advanced imaging tasks.

ChatCAD: Interactive Computer-Aided Diagnosis on Medical Image using Large Language Models

Large language models (LLMs) have recently demonstrated their potential in clinical applications, providing valuable medical knowledge and advice. For example, a large dialog LLM like ChatGPT has successfully passed part of the US medical licensing exam. However, LLMs currently have difficulty processing images, making it challenging to interpret information from medical images, which are rich in information that supports clinical decisions. On the other hand, computer-aided diagnosis (CAD) networks for medical images have seen significant success in the medical field by using advanced deep-learning algorithms to support clinical decision-making. This paper presents a method for integrating LLMs into medical-image CAD networks. The proposed framework uses LLMs to enhance the output of multiple CAD networks, such as diagnosis networks, lesion segmentation networks, and report generation networks, by summarizing and reorganizing the information presented in natural language text format. The goal is to merge the strengths of LLMs' medical domain knowledge and logical reasoning with the vision understanding capability of existing medical-image CAD models to create a more user-friendly and understandable system for patients compared to conventional CAD systems. In the future, LLM's medical knowledge can be also used to improve the performance of vision-based medical-image CAD models.

Advancing Multimodal Medical Capabilities of Gemini

Many clinical tasks require an understanding of specialized data, such as medical images and genomics, which is not typically found in general-purpose large multimodal models. Building upon Gemini's multimodal models, we develop several models within the new Med-Gemini family that inherit core capabilities of Gemini and are optimized for medical use via fine-tuning with 2D and 3D radiology, histopathology, ophthalmology, dermatology and genomic data. Med-Gemini-2D sets a new standard for AI-based chest X-ray (CXR) report generation based on expert evaluation, exceeding previous best results across two separate datasets by an absolute margin of 1% and 12%, where 57% and 96% of AI reports on normal cases, and 43% and 65% on abnormal cases, are evaluated as "equivalent or better" than the original radiologists' reports. We demonstrate the first ever large multimodal model-based report generation for 3D computed tomography (CT) volumes using Med-Gemini-3D, with 53% of AI reports considered clinically acceptable, although additional research is needed to meet expert radiologist reporting quality. Beyond report generation, Med-Gemini-2D surpasses the previous best performance in CXR visual question answering (VQA) and performs well in CXR classification and radiology VQA, exceeding SoTA or baselines on 17 of 20 tasks. In histopathology, ophthalmology, and dermatology image classification, Med-Gemini-2D surpasses baselines across 18 out of 20 tasks and approaches task-specific model performance. Beyond imaging, Med-Gemini-Polygenic outperforms the standard linear polygenic risk score-based approach for disease risk prediction and generalizes to genetically correlated diseases for which it has never been trained. Although further development and evaluation are necessary in the safety-critical medical domain, our results highlight the potential of Med-Gemini across a wide range of medical tasks.

Towards Generalist Biomedical AI

Medicine is inherently multimodal, with rich data modalities spanning text, imaging, genomics, and more. Generalist biomedical artificial intelligence (AI) systems that flexibly encode, integrate, and interpret this data at scale can potentially enable impactful applications ranging from scientific discovery to care delivery. To enable the development of these models, we first curate MultiMedBench, a new multimodal biomedical benchmark. MultiMedBench encompasses 14 diverse tasks such as medical question answering, mammography and dermatology image interpretation, radiology report generation and summarization, and genomic variant calling. We then introduce Med-PaLM Multimodal (Med-PaLM M), our proof of concept for a generalist biomedical AI system. Med-PaLM M is a large multimodal generative model that flexibly encodes and interprets biomedical data including clinical language, imaging, and genomics with the same set of model weights. Med-PaLM M reaches performance competitive with or exceeding the state of the art on all MultiMedBench tasks, often surpassing specialist models by a wide margin. We also report examples of zero-shot generalization to novel medical concepts and tasks, positive transfer learning across tasks, and emergent zero-shot medical reasoning. To further probe the capabilities and limitations of Med-PaLM M, we conduct a radiologist evaluation of model-generated (and human) chest X-ray reports and observe encouraging performance across model scales. In a side-by-side ranking on 246 retrospective chest X-rays, clinicians express a pairwise preference for Med-PaLM M reports over those produced by radiologists in up to 40.50% of cases, suggesting potential clinical utility. While considerable work is needed to validate these models in real-world use cases, our results represent a milestone towards the development of generalist biomedical AI systems.

Merlin: A Vision Language Foundation Model for 3D Computed Tomography

Over 85 million computed tomography (CT) scans are performed annually in the US, of which approximately one quarter focus on the abdomen. Given the current radiologist shortage, there is a large impetus to use artificial intelligence to alleviate the burden of interpreting these complex imaging studies. Prior state-of-the-art approaches for automated medical image interpretation leverage vision language models (VLMs). However, current medical VLMs are generally limited to 2D images and short reports, and do not leverage electronic health record (EHR) data for supervision. We introduce Merlin - a 3D VLM that we train using paired CT scans (6+ million images from 15,331 CTs), EHR diagnosis codes (1.8+ million codes), and radiology reports (6+ million tokens). We evaluate Merlin on 6 task types and 752 individual tasks. The non-adapted (off-the-shelf) tasks include zero-shot findings classification (31 findings), phenotype classification (692 phenotypes), and zero-shot cross-modal retrieval (image to findings and image to impressions), while model adapted tasks include 5-year disease prediction (6 diseases), radiology report generation, and 3D semantic segmentation (20 organs). We perform internal validation on a test set of 5,137 CTs, and external validation on 7,000 clinical CTs and on two public CT datasets (VerSe, TotalSegmentator). Beyond these clinically-relevant evaluations, we assess the efficacy of various network architectures and training strategies to depict that Merlin has favorable performance to existing task-specific baselines. We derive data scaling laws to empirically assess training data needs for requisite downstream task performance. Furthermore, unlike conventional VLMs that require hundreds of GPUs for training, we perform all training on a single GPU.

Solving 3D Inverse Problems using Pre-trained 2D Diffusion Models

Diffusion models have emerged as the new state-of-the-art generative model with high quality samples, with intriguing properties such as mode coverage and high flexibility. They have also been shown to be effective inverse problem solvers, acting as the prior of the distribution, while the information of the forward model can be granted at the sampling stage. Nonetheless, as the generative process remains in the same high dimensional (i.e. identical to data dimension) space, the models have not been extended to 3D inverse problems due to the extremely high memory and computational cost. In this paper, we combine the ideas from the conventional model-based iterative reconstruction with the modern diffusion models, which leads to a highly effective method for solving 3D medical image reconstruction tasks such as sparse-view tomography, limited angle tomography, compressed sensing MRI from pre-trained 2D diffusion models. In essence, we propose to augment the 2D diffusion prior with a model-based prior in the remaining direction at test time, such that one can achieve coherent reconstructions across all dimensions. Our method can be run in a single commodity GPU, and establishes the new state-of-the-art, showing that the proposed method can perform reconstructions of high fidelity and accuracy even in the most extreme cases (e.g. 2-view 3D tomography). We further reveal that the generalization capacity of the proposed method is surprisingly high, and can be used to reconstruct volumes that are entirely different from the training dataset.

Intensive Vision-guided Network for Radiology Report Generation

Automatic radiology report generation is booming due to its huge application potential for the healthcare industry. However, existing computer vision and natural language processing approaches to tackle this problem are limited in two aspects. First, when extracting image features, most of them neglect multi-view reasoning in vision and model single-view structure of medical images, such as space-view or channel-view. However, clinicians rely on multi-view imaging information for comprehensive judgment in daily clinical diagnosis. Second, when generating reports, they overlook context reasoning with multi-modal information and focus on pure textual optimization utilizing retrieval-based methods. We aim to address these two issues by proposing a model that better simulates clinicians' perspectives and generates more accurate reports. Given the above limitation in feature extraction, we propose a Globally-intensive Attention (GIA) module in the medical image encoder to simulate and integrate multi-view vision perception. GIA aims to learn three types of vision perception: depth view, space view, and pixel view. On the other hand, to address the above problem in report generation, we explore how to involve multi-modal signals to generate precisely matched reports, i.e., how to integrate previously predicted words with region-aware visual content in next word prediction. Specifically, we design a Visual Knowledge-guided Decoder (VKGD), which can adaptively consider how much the model needs to rely on visual information and previously predicted text to assist next word prediction. Hence, our final Intensive Vision-guided Network (IVGN) framework includes a GIA-guided Visual Encoder and the VKGD. Experiments on two commonly-used datasets IU X-Ray and MIMIC-CXR demonstrate the superior ability of our method compared with other state-of-the-art approaches.

Med3D: Transfer Learning for 3D Medical Image Analysis

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.

Eye Fairness: A Large-Scale 3D Imaging Dataset for Equitable Eye Diseases Screening and Fair Identity Scaling

Fairness or equity in machine learning is profoundly important for societal well-being, but limited public datasets hinder its progress, especially in the area of medicine. It is undeniable that fairness in medicine is one of the most important areas for fairness learning's applications. Currently, no large-scale public medical datasets with 3D imaging data for fairness learning are available, while 3D imaging data in modern clinics are standard tests for disease diagnosis. In addition, existing medical fairness datasets are actually repurposed datasets, and therefore they typically have limited demographic identity attributes with at most three identity attributes of age, gender, and race for fairness modeling. To address this gap, we introduce our Eye Fairness dataset with 30,000 subjects (Harvard-EF) covering three major eye diseases including age-related macular degeneration, diabetic retinopathy, and glaucoma affecting 380 million patients globally. Our Harvard-EF dataset includes both 2D fundus photos and 3D optical coherence tomography scans with six demographic identity attributes including age, gender, race, ethnicity, preferred language, and marital status. We also propose a fair identity scaling (FIS) approach combining group and individual scaling together to improve model fairness. Our FIS approach is compared with various state-of-the-art fairness learning methods with superior performance in the racial, gender, and ethnicity fairness tasks with 2D and 3D imaging data, which demonstrate the utilities of our Harvard-EF dataset for fairness learning. To facilitate fairness comparisons between different models, we propose performance-scaled disparity measures, which can be used to compare model fairness accounting for overall performance levels. The dataset and code are publicly accessible via https://ophai.hms.harvard.edu/datasets/harvard-ef30k.

A Survey of Medical Vision-and-Language Applications and Their Techniques

Medical vision-and-language models (MVLMs) have attracted substantial interest due to their capability to offer a natural language interface for interpreting complex medical data. Their applications are versatile and have the potential to improve diagnostic accuracy and decision-making for individual patients while also contributing to enhanced public health monitoring, disease surveillance, and policy-making through more efficient analysis of large data sets. MVLMS integrate natural language processing with medical images to enable a more comprehensive and contextual understanding of medical images alongside their corresponding textual information. Unlike general vision-and-language models trained on diverse, non-specialized datasets, MVLMs are purpose-built for the medical domain, automatically extracting and interpreting critical information from medical images and textual reports to support clinical decision-making. Popular clinical applications of MVLMs include automated medical report generation, medical visual question answering, medical multimodal segmentation, diagnosis and prognosis and medical image-text retrieval. Here, we provide a comprehensive overview of MVLMs and the various medical tasks to which they have been applied. We conduct a detailed analysis of various vision-and-language model architectures, focusing on their distinct strategies for cross-modal integration/exploitation of medical visual and textual features. We also examine the datasets used for these tasks and compare the performance of different models based on standardized evaluation metrics. Furthermore, we highlight potential challenges and summarize future research trends and directions. The full collection of papers and codes is available at: https://github.com/YtongXie/Medical-Vision-and-Language-Tasks-and-Methodologies-A-Survey.

MedMax: Mixed-Modal Instruction Tuning for Training Biomedical Assistants

Recent advancements in mixed-modal generative models have enabled flexible integration of information across image-text content. These models have opened new avenues for developing unified biomedical assistants capable of analyzing biomedical images, answering complex questions about them, and predicting the impact of medical procedures on a patient's health. However, existing resources face challenges such as limited data availability, narrow domain coverage, and restricted sources (e.g., medical papers). To address these gaps, we present MedMax, the first large-scale multimodal biomedical instruction-tuning dataset for mixed-modal foundation models. With 1.47 million instances, MedMax encompasses a diverse range of tasks, including multimodal content generation (interleaved image-text data), biomedical image captioning and generation, visual chatting, and report understanding. These tasks span diverse medical domains such as radiology and histopathology. Subsequently, we fine-tune a mixed-modal foundation model on the MedMax dataset, achieving significant performance improvements: a 26% gain over the Chameleon model and an 18.3% improvement over GPT-4o across 12 downstream biomedical visual question-answering tasks. Additionally, we introduce a unified evaluation suite for biomedical tasks, providing a robust framework to guide the development of next-generation mixed-modal biomedical AI assistants.

LLM-CXR: Instruction-Finetuned LLM for CXR Image Understanding and Generation

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.

MulModSeg: Enhancing Unpaired Multi-Modal Medical Image Segmentation with Modality-Conditioned Text Embedding and Alternating Training

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}}.

Cross-modality (CT-MRI) prior augmented deep learning for robust lung tumor segmentation from small MR datasets

Lack of large expert annotated MR datasets makes training deep learning models difficult. Therefore, a cross-modality (MR-CT) deep learning segmentation approach that augments training data using pseudo MR images produced by transforming expert-segmented CT images was developed. Eighty-One T2-weighted MRI scans from 28 patients with non-small cell lung cancers were analyzed. Cross-modality prior encoding the transformation of CT to pseudo MR images resembling T2w MRI was learned as a generative adversarial deep learning model. This model augmented training data arising from 6 expert-segmented T2w MR patient scans with 377 pseudo MRI from non-small cell lung cancer CT patient scans with obtained from the Cancer Imaging Archive. A two-dimensional Unet implemented with batch normalization was trained to segment the tumors from T2w MRI. This method was benchmarked against (a) standard data augmentation and two state-of-the art cross-modality pseudo MR-based augmentation and (b) two segmentation networks. Segmentation accuracy was computed using Dice similarity coefficient (DSC), Hausdroff distance metrics, and volume ratio. The proposed approach produced the lowest statistical variability in the intensity distribution between pseudo and T2w MR images measured as Kullback-Leibler divergence of 0.069. This method produced the highest segmentation accuracy with a DSC of 0.75 and the lowest Hausdroff distance on the test dataset. This approach produced highly similar estimations of tumor growth as an expert (P = 0.37). A novel deep learning MR segmentation was developed that overcomes the limitation of learning robust models from small datasets by leveraging learned cross-modality priors to augment training. The results show the feasibility of the approach and the corresponding improvement over the state-of-the-art methods.

OrthoDoc: Multimodal Large Language Model for Assisting Diagnosis in Computed Tomography

Multimodal large language models (MLLMs) have achieved significant success in the general field of image processing. Their emerging task generalization and freeform conversational capabilities can greatly facilitate medical diagnostic assistance, helping patients better understand their conditions and enhancing doctor-patient trust. Computed Tomography (CT) is a non-invasive imaging technique used to capture the internal mechanisms of a patient's condition and is widely utilized. However, in past research, the complex textural features of this imaging data have made accurate interpretation by algorithms challenging, impeding the performance of general LLMs in diagnostic assistance. To address this, we developed OrthoDoc, a MLLM designed for CT diagnostics. OrthoDoc is trained on 120,000 CT images and diagnostic reports and includes a Retrieval-Augmented Generation (RAG) module capable of effectively mitigating model hallucinations. This module is informed by extensive medical literature, textbooks, and explanatory data. Thus, OrthoDoc not only processes complex CT images but also stores, understands, and reasons over medical knowledge and language. In extensive experiments, OrthoDoc outperforms commercial models led by GPT-4, demonstrating superior diagnostic capabilities and accuracy. Specifically, OrthoDoc significantly surpasses existing models in the diagnosis of common orthopedic conditions such as fractures, arthritis, and tumors. Additionally, OrthoDoc exhibits robust generalization and stability when handling rare and complex cases.

PIE: Simulating Disease Progression via Progressive Image Editing

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.

TotalSegmentator: robust segmentation of 104 anatomical structures in CT images

We present a deep learning segmentation model that can automatically and robustly segment all major anatomical structures in body CT images. In this retrospective study, 1204 CT examinations (from the years 2012, 2016, and 2020) were used to segment 104 anatomical structures (27 organs, 59 bones, 10 muscles, 8 vessels) relevant for use cases such as organ volumetry, disease characterization, and surgical or radiotherapy planning. The CT images were randomly sampled from routine clinical studies and thus represent a real-world dataset (different ages, pathologies, scanners, body parts, sequences, and sites). The authors trained an nnU-Net segmentation algorithm on this dataset and calculated Dice similarity coefficients (Dice) to evaluate the model's performance. The trained algorithm was applied to a second dataset of 4004 whole-body CT examinations to investigate age dependent volume and attenuation changes. The proposed model showed a high Dice score (0.943) on the test set, which included a wide range of clinical data with major pathologies. The model significantly outperformed another publicly available segmentation model on a separate dataset (Dice score, 0.932 versus 0.871, respectively). The aging study demonstrated significant correlations between age and volume and mean attenuation for a variety of organ groups (e.g., age and aortic volume; age and mean attenuation of the autochthonous dorsal musculature). The developed model enables robust and accurate segmentation of 104 anatomical structures. The annotated dataset (https://doi.org/10.5281/zenodo.6802613) and toolkit (https://www.github.com/wasserth/TotalSegmentator) are publicly available.

Large-Scale 3D Medical Image Pre-training with Geometric Context Priors

The scarcity of annotations poses a significant challenge in medical image analysis. Large-scale pre-training has emerged as a promising label-efficient solution, owing to the utilization of large-scale data, large models, and advanced pre-training techniques. However, its development in medical images remains underexplored. The primary challenge lies in harnessing large-scale unlabeled data and learning high-level semantics without annotations. We observe that 3D medical images exhibit consistent geometric context, i.e., consistent geometric relations between different organs, which leads to a promising way for learning consistent representations. Motivated by this, we introduce a simple-yet-effective Volume Contrast (VoCo) framework to leverage geometric context priors for self-supervision. Given an input volume, we extract base crops from different regions to construct positive and negative pairs for contrastive learning. Then we predict the contextual position of a random crop by contrasting its similarity to the base crops. In this way, VoCo encodes the inherent geometric context into model representations, facilitating high-level semantic learning without annotations. Specifically, we (1) introduce the largest medical pre-training dataset PreCT-160K; (2) investigate scaling laws and propose guidelines for tailoring different model sizes to various medical tasks; (3) build a benchmark encompassing 48 medical tasks. Extensive experiments highlight the superiority of VoCo. Codes at https://github.com/Luffy03/Large-Scale-Medical.

MMed-RAG: Versatile Multimodal RAG System for Medical Vision Language Models

Artificial Intelligence (AI) has demonstrated significant potential in healthcare, particularly in disease diagnosis and treatment planning. Recent progress in Medical Large Vision-Language Models (Med-LVLMs) has opened up new possibilities for interactive diagnostic tools. However, these models often suffer from factual hallucination, which can lead to incorrect diagnoses. Fine-tuning and retrieval-augmented generation (RAG) have emerged as methods to address these issues. However, the amount of high-quality data and distribution shifts between training data and deployment data limit the application of fine-tuning methods. Although RAG is lightweight and effective, existing RAG-based approaches are not sufficiently general to different medical domains and can potentially cause misalignment issues, both between modalities and between the model and the ground truth. In this paper, we propose a versatile multimodal RAG system, MMed-RAG, designed to enhance the factuality of Med-LVLMs. Our approach introduces a domain-aware retrieval mechanism, an adaptive retrieved contexts selection method, and a provable RAG-based preference fine-tuning strategy. These innovations make the RAG process sufficiently general and reliable, significantly improving alignment when introducing retrieved contexts. Experimental results across five medical datasets (involving radiology, ophthalmology, pathology) on medical VQA and report generation demonstrate that MMed-RAG can achieve an average improvement of 43.8% in the factual accuracy of Med-LVLMs. Our data and code are available in https://github.com/richard-peng-xia/MMed-RAG.

LLaVA Needs More Knowledge: Retrieval Augmented Natural Language Generation with Knowledge Graph for Explaining Thoracic Pathologies

Generating Natural Language Explanations (NLEs) for model predictions on medical images, particularly those depicting thoracic pathologies, remains a critical and challenging task. Existing methodologies often struggle due to general models' insufficient domain-specific medical knowledge and privacy concerns associated with retrieval-based augmentation techniques. To address these issues, we propose a novel Vision-Language framework augmented with a Knowledge Graph (KG)-based datastore, which enhances the model's understanding by incorporating additional domain-specific medical knowledge essential for generating accurate and informative NLEs. Our framework employs a KG-based retrieval mechanism that not only improves the precision of the generated explanations but also preserves data privacy by avoiding direct data retrieval. The KG datastore is designed as a plug-and-play module, allowing for seamless integration with various model architectures. We introduce and evaluate three distinct frameworks within this paradigm: KG-LLaVA, which integrates the pre-trained LLaVA model with KG-RAG; Med-XPT, a custom framework combining MedCLIP, a transformer-based projector, and GPT-2; and Bio-LLaVA, which adapts LLaVA by incorporating the Bio-ViT-L vision model. These frameworks are validated on the MIMIC-NLE dataset, where they achieve state-of-the-art results, underscoring the effectiveness of KG augmentation in generating high-quality NLEs for thoracic pathologies.

Preserving Tumor Volumes for Unsupervised Medical Image Registration

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

Vision-Language Modeling in PET/CT for Visual Grounding of Positive Findings

Vision-language models can connect the text description of an object to its specific location in an image through visual grounding. This has potential applications in enhanced radiology reporting. However, these models require large annotated image-text datasets, which are lacking for PET/CT. We developed an automated pipeline to generate weak labels linking PET/CT report descriptions to their image locations and used it to train a 3D vision-language visual grounding model. Our pipeline finds positive findings in PET/CT reports by identifying mentions of SUVmax and axial slice numbers. From 25,578 PET/CT exams, we extracted 11,356 sentence-label pairs. Using this data, we trained ConTEXTual Net 3D, which integrates text embeddings from a large language model with a 3D nnU-Net via token-level cross-attention. The model's performance was compared against LLMSeg, a 2.5D version of ConTEXTual Net, and two nuclear medicine physicians. The weak-labeling pipeline accurately identified lesion locations in 98% of cases (246/251), with 7.5% requiring boundary adjustments. ConTEXTual Net 3D achieved an F1 score of 0.80, outperforming LLMSeg (F1=0.22) and the 2.5D model (F1=0.53), though it underperformed both physicians (F1=0.94 and 0.91). The model achieved better performance on FDG (F1=0.78) and DCFPyL (F1=0.75) exams, while performance dropped on DOTATE (F1=0.58) and Fluciclovine (F1=0.66). The model performed consistently across lesion sizes but showed reduced accuracy on lesions with low uptake. Our novel weak labeling pipeline accurately produced an annotated dataset of PET/CT image-text pairs, facilitating the development of 3D visual grounding models. ConTEXTual Net 3D significantly outperformed other models but fell short of the performance of nuclear medicine physicians. Our study suggests that even larger datasets may be needed to close this performance gap.

Automated Chest X-Ray Report Generator Using Multi-Model Deep Learning Approach

Reading and interpreting chest X-ray images is one of the most radiologist's routines. However, it still can be challenging, even for the most experienced ones. Therefore, we proposed a multi-model deep learning-based automated chest X-ray report generator system designed to assist radiologists in their work. The basic idea of the proposed system is by utilizing multi binary-classification models for detecting multi abnormalities, with each model responsible for detecting one abnormality, in a single image. In this study, we limited the radiology abnormalities detection to only cardiomegaly, lung effusion, and consolidation. The system generates a radiology report by performing the following three steps: image pre-processing, utilizing deep learning models to detect abnormalities, and producing a report. The aim of the image pre-processing step is to standardize the input by scaling it to 128x128 pixels and slicing it into three segments, which covers the upper, lower, and middle parts of the lung. After pre-processing, each corresponding model classifies the image, resulting in a 0 (zero) for no abnormality detected and a 1 (one) for the presence of an abnormality. The prediction outputs of each model are then concatenated to form a 'result code'. The 'result code' is used to construct a report by selecting the appropriate pre-determined sentence for each detected abnormality in the report generation step. The proposed system is expected to reduce the workload of radiologists and increase the accuracy of chest X-ray diagnosis.

Brain-ID: Learning Contrast-agnostic Anatomical Representations for Brain Imaging

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.

MoRE: Multi-Modal Contrastive Pre-training with Transformers on X-Rays, ECGs, and Diagnostic Report

In this paper, we introduce a novel Multi-Modal Contrastive Pre-training Framework that synergistically combines X-rays, electrocardiograms (ECGs), and radiology/cardiology reports. Our approach leverages transformers to encode these diverse modalities into a unified representation space, aiming to enhance diagnostic accuracy and facilitate comprehensive patient assessments. We utilize LoRA-Peft to significantly reduce trainable parameters in the LLM and incorporate recent linear attention dropping strategy in the Vision Transformer(ViT) for smoother attention. Furthermore, we provide novel multimodal attention explanations and retrieval for our model. To the best of our knowledge, we are the first to propose an integrated model that combines X-ray, ECG, and Radiology/Cardiology Report with this approach. By utilizing contrastive loss, MoRE effectively aligns modality-specific features into a coherent embedding, which supports various downstream tasks such as zero-shot classification and multimodal retrieval. Employing our proposed methodology, we achieve state-of-the-art (SOTA) on the Mimic-IV, CheXpert, Edema Severity, and PtbXl downstream datasets, surpassing existing multimodal approaches. Our proposed framework shows significant improvements in capturing intricate inter-modal relationships and its robustness in medical diagnosis that establishes a framework for future research in multimodal learning in the healthcare sector.

Multi-view X-ray Image Synthesis with Multiple Domain Disentanglement from CT Scans

X-ray images play a vital role in the intraoperative processes due to their high resolution and fast imaging speed and greatly promote the subsequent segmentation, registration and reconstruction. However, over-dosed X-rays superimpose potential risks to human health to some extent. Data-driven algorithms from volume scans to X-ray images are restricted by the scarcity of paired X-ray and volume data. Existing methods are mainly realized by modelling the whole X-ray imaging procedure. In this study, we propose a learning-based approach termed CT2X-GAN to synthesize the X-ray images in an end-to-end manner using the content and style disentanglement from three different image domains. Our method decouples the anatomical structure information from CT scans and style information from unpaired real X-ray images/ digital reconstructed radiography (DRR) images via a series of decoupling encoders. Additionally, we introduce a novel consistency regularization term to improve the stylistic resemblance between synthesized X-ray images and real X-ray images. Meanwhile, we also impose a supervised process by computing the similarity of computed real DRR and synthesized DRR images. We further develop a pose attention module to fully strengthen the comprehensive information in the decoupled content code from CT scans, facilitating high-quality multi-view image synthesis in the lower 2D space. Extensive experiments were conducted on the publicly available CTSpine1K dataset and achieved 97.8350, 0.0842 and 3.0938 in terms of FID, KID and defined user-scored X-ray similarity, respectively. In comparison with 3D-aware methods (pi-GAN, EG3D), CT2X-GAN is superior in improving the synthesis quality and realistic to the real X-ray images.

I-MedSAM: Implicit Medical Image Segmentation with Segment Anything

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

GenerateCT: Text-Guided 3D Chest CT Generation

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.

MedTrinity-25M: A Large-scale Multimodal Dataset with Multigranular Annotations for Medicine

This paper introduces MedTrinity-25M, a comprehensive, large-scale multimodal dataset for medicine, covering over 25 million images across 10 modalities, with multigranular annotations for more than 65 diseases. These enriched annotations encompass both global textual information, such as disease/lesion type, modality, region-specific descriptions, and inter-regional relationships, as well as detailed local annotations for regions of interest (ROIs), including bounding boxes, segmentation masks. Unlike existing approach which is limited by the availability of image-text pairs, we have developed the first automated pipeline that scales up multimodal data by generating multigranular visual and texual annotations (in the form of image-ROI-description triplets) without the need for any paired text descriptions. Specifically, data from over 90 different sources have been collected, preprocessed, and grounded using domain-specific expert models to identify ROIs related to abnormal regions. We then build a comprehensive knowledge base and prompt multimodal large language models to perform retrieval-augmented generation with the identified ROIs as guidance, resulting in multigranular texual descriptions. Compared to existing datasets, MedTrinity-25M provides the most enriched annotations, supporting a comprehensive range of multimodal tasks such as captioning and report generation, as well as vision-centric tasks like classification and segmentation. Pretraining on MedTrinity-25M, our model achieves state-of-the-art performance on VQA-RAD and PathVQA, surpassing both multimodal large language models and other representative SoTA approaches. This dataset can also be utilized to support large-scale pre-training of multimodal medical AI models, contributing to the development of future foundation models in the medical domain.

SKM-TEA: A Dataset for Accelerated MRI Reconstruction with Dense Image Labels for Quantitative Clinical Evaluation

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.

CXR-LLaVA: Multimodal Large Language Model for Interpreting Chest X-ray Images

Purpose: Recent advancements in large language models (LLMs) have expanded their capabilities in a multimodal fashion, potentially replicating the image interpretation of human radiologists. This study aimed to develop open-source multimodal large language model for interpreting chest X-ray images (CXR-LLaVA). We also examined the effect of prompt engineering and model parameters such as temperature and nucleus sampling. Materials and Methods: For training, we collected 659,287 publicly available CXRs: 417,336 CXRs had labels for certain radiographic abnormalities (dataset 1); 241,951 CXRs provided free-text radiology reports (dataset 2). After pre-training the Resnet50 as an image encoder, the contrastive language-image pre-training was used to align CXRs and corresponding radiographic abnormalities. Then, the Large Language Model Meta AI-2 was fine-tuned using dataset 2, which were refined using GPT-4, with generating various question answering scenarios. The code can be found at https://github.com/ECOFRI/CXR_LLaVA. Results: In the test set, we observed that the model's performance fluctuated based on its parameters. On average, it achieved F1 score of 0.34 for five pathologic findings (atelectasis, cardiomegaly, consolidation, edema, and pleural effusion), which was improved to 0.46 through prompt engineering. In the independent set, the model achieved an average F1 score of 0.30 for the same pathologic findings. Notably, for the pediatric chest radiograph dataset, which was unseen during training, the model differentiated abnormal radiographs with an F1 score ranging from 0.84 to 0.85. Conclusion: CXR-LLaVA demonstrates promising potential in CXR interpretation. Both prompt engineering and model parameter adjustments can play pivotal roles in interpreting CXRs.

3D Medical Image Segmentation based on multi-scale MPU-Net

The high cure rate of cancer is inextricably linked to physicians' accuracy in diagnosis and treatment, therefore a model that can accomplish high-precision tumor segmentation has become a necessity in many applications of the medical industry. It can effectively lower the rate of misdiagnosis while considerably lessening the burden on clinicians. However, fully automated target organ segmentation is problematic due to the irregular stereo structure of 3D volume organs. As a basic model for this class of real applications, U-Net excels. It can learn certain global and local features, but still lacks the capacity to grasp spatial long-range relationships and contextual information at multiple scales. This paper proposes a tumor segmentation model MPU-Net for patient volume CT images, which is inspired by Transformer with a global attention mechanism. By combining image serialization with the Position Attention Module, the model attempts to comprehend deeper contextual dependencies and accomplish precise positioning. Each layer of the decoder is also equipped with a multi-scale module and a cross-attention mechanism. The capability of feature extraction and integration at different levels has been enhanced, and the hybrid loss function developed in this study can better exploit high-resolution characteristic information. Moreover, the suggested architecture is tested and evaluated on the Liver Tumor Segmentation Challenge 2017 (LiTS 2017) dataset. Compared with the benchmark model U-Net, MPU-Net shows excellent segmentation results. The dice, accuracy, precision, specificity, IOU, and MCC metrics for the best model segmentation results are 92.17%, 99.08%, 91.91%, 99.52%, 85.91%, and 91.74%, respectively. Outstanding indicators in various aspects illustrate the exceptional performance of this framework in automatic medical image segmentation.

SAM-Med2D

The Segment Anything Model (SAM) represents a state-of-the-art research advancement in natural image segmentation, achieving impressive results with input prompts such as points and bounding boxes. However, our evaluation and recent research indicate that directly applying the pretrained SAM to medical image segmentation does not yield satisfactory performance. This limitation primarily arises from significant domain gap between natural images and medical images. To bridge this gap, we introduce SAM-Med2D, the most comprehensive studies on applying SAM to medical 2D images. Specifically, we first collect and curate approximately 4.6M images and 19.7M masks from public and private datasets, constructing a large-scale medical image segmentation dataset encompassing various modalities and objects. Then, we comprehensively fine-tune SAM on this dataset and turn it into SAM-Med2D. Unlike previous methods that only adopt bounding box or point prompts as interactive segmentation approach, we adapt SAM to medical image segmentation through more comprehensive prompts involving bounding boxes, points, and masks. We additionally fine-tune the encoder and decoder of the original SAM to obtain a well-performed SAM-Med2D, leading to the most comprehensive fine-tuning strategies to date. Finally, we conducted a comprehensive evaluation and analysis to investigate the performance of SAM-Med2D in medical image segmentation across various modalities, anatomical structures, and organs. Concurrently, we validated the generalization capability of SAM-Med2D on 9 datasets from MICCAI 2023 challenge. Overall, our approach demonstrated significantly superior performance and generalization capability compared to SAM.

Medical Image Classification with KAN-Integrated Transformers and Dilated Neighborhood Attention

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

VILA-M3: Enhancing Vision-Language Models with Medical Expert Knowledge

Generalist vision language models (VLMs) have made significant strides in computer vision, but they fall short in specialized fields like healthcare, where expert knowledge is essential. In traditional computer vision tasks, creative or approximate answers may be acceptable, but in healthcare, precision is paramount.Current large multimodal models like Gemini and GPT-4o are insufficient for medical tasks due to their reliance on memorized internet knowledge rather than the nuanced expertise required in healthcare. VLMs are usually trained in three stages: vision pre-training, vision-language pre-training, and instruction fine-tuning (IFT). IFT has been typically applied using a mixture of generic and healthcare data. In contrast, we propose that for medical VLMs, a fourth stage of specialized IFT is necessary, which focuses on medical data and includes information from domain expert models. Domain expert models developed for medical use are crucial because they are specifically trained for certain clinical tasks, e.g. to detect tumors and classify abnormalities through segmentation and classification, which learn fine-grained features of medical data-features that are often too intricate for a VLM to capture effectively especially in radiology. This paper introduces a new framework, VILA-M3, for medical VLMs that utilizes domain knowledge via expert models. Through our experiments, we show an improved state-of-the-art (SOTA) performance with an average improvement of ~9% over the prior SOTA model Med-Gemini and ~6% over models trained on the specific tasks. Our approach emphasizes the importance of domain expertise in creating precise, reliable VLMs for medical applications.

Cascaded Multi-Modal Mixing Transformers for Alzheimer's Disease Classification with Incomplete Data

Accurate medical classification requires a large number of multi-modal data, and in many cases, different feature types. Previous studies have shown promising results when using multi-modal data, outperforming single-modality models when classifying diseases such as Alzheimer's Disease (AD). However, those models are usually not flexible enough to handle missing modalities. Currently, the most common workaround is discarding samples with missing modalities which leads to considerable data under-utilization. Adding to the fact that labeled medical images are already scarce, the performance of data-driven methods like deep learning can be severely hampered. Therefore, a multi-modal method that can handle missing data in various clinical settings is highly desirable. In this paper, we present Multi-Modal Mixing Transformer (3MAT), a disease classification transformer that not only leverages multi-modal data but also handles missing data scenarios. In this work, we test 3MT for AD and Cognitively normal (CN) classification and mild cognitive impairment (MCI) conversion prediction to progressive MCI (pMCI) or stable MCI (sMCI) using clinical and neuroimaging data. The model uses a novel Cascaded Modality Transformer architecture with cross-attention to incorporate multi-modal information for more informed predictions. We propose a novel modality dropout mechanism to ensure an unprecedented level of modality independence and robustness to handle missing data scenarios. The result is a versatile network that enables the mixing of arbitrary numbers of modalities with different feature types and also ensures full data utilization missing data scenarios. The model is trained and evaluated on the ADNI dataset with the SOTRA performance and further evaluated with the AIBL dataset with missing data.

CuNeRF: Cube-Based Neural Radiance Field for Zero-Shot Medical Image Arbitrary-Scale Super Resolution

Medical image arbitrary-scale super-resolution (MIASSR) has recently gained widespread attention, aiming to super sample medical volumes at arbitrary scales via a single model. However, existing MIASSR methods face two major limitations: (i) reliance on high-resolution (HR) volumes and (ii) limited generalization ability, which restricts their application in various scenarios. To overcome these limitations, we propose Cube-based Neural Radiance Field (CuNeRF), a zero-shot MIASSR framework that can yield medical images at arbitrary scales and viewpoints in a continuous domain. Unlike existing MIASSR methods that fit the mapping between low-resolution (LR) and HR volumes, CuNeRF focuses on building a coordinate-intensity continuous representation from LR volumes without the need for HR references. This is achieved by the proposed differentiable modules: including cube-based sampling, isotropic volume rendering, and cube-based hierarchical rendering. Through extensive experiments on magnetic resource imaging (MRI) and computed tomography (CT) modalities, we demonstrate that CuNeRF outperforms state-of-the-art MIASSR methods. CuNeRF yields better visual verisimilitude and reduces aliasing artifacts at various upsampling factors. Moreover, our CuNeRF does not need any LR-HR training pairs, which is more flexible and easier to be used than others. Our code will be publicly available soon.

Optimized Conformal Selection: Powerful Selective Inference After Conformity Score Optimization

Model selection/optimization in conformal inference is challenging, since it may break the exchangeability between labeled and unlabeled data. We study this problem in the context of conformal selection, which uses conformal p-values to select ``interesting'' instances with large unobserved labels from a pool of unlabeled data, while controlling the FDR in finite sample. For validity, existing solutions require the model choice to be independent of the data used to construct the p-values and calibrate the selection set. However, when presented with many model choices and limited labeled data, it is desirable to (i) select the best model in a data-driven manner, and (ii) mitigate power loss due to sample splitting. This paper presents OptCS, a general framework that allows valid statistical testing (selection) after flexible data-driven model optimization. We introduce general conditions under which OptCS constructs valid conformal p-values despite substantial data reuse and handles complex p-value dependencies to maintain finite-sample FDR control via a novel multiple testing procedure. We instantiate this general recipe to propose three FDR-controlling procedures, each optimizing the models differently: (i) selecting the most powerful one among multiple pre-trained candidate models, (ii) using all data for model fitting without sample splitting, and (iii) combining full-sample model fitting and selection. We demonstrate the efficacy of our methods via simulation studies and real applications in drug discovery and alignment of large language models in radiology report generation.

Assessment of Data Consistency through Cascades of Independently Recurrent Inference Machines for fast and robust accelerated MRI reconstruction

Machine Learning methods can learn how to reconstruct Magnetic Resonance Images and thereby accelerate acquisition, which is of paramount importance to the clinical workflow. Physics-informed networks incorporate the forward model of accelerated MRI reconstruction in the learning process. With increasing network complexity, robustness is not ensured when reconstructing data unseen during training. We aim to embed data consistency (DC) in deep networks while balancing the degree of network complexity. While doing so, we will assess whether either explicit or implicit enforcement of DC in varying network architectures is preferred to optimize performance. We propose a scheme called Cascades of Independently Recurrent Inference Machines (CIRIM) to assess DC through unrolled optimization. Herein we assess DC both implicitly by gradient descent and explicitly by a designed term. Extensive comparison of the CIRIM to CS as well as to other methods is performed: the E2EVN, CascadeNet, KIKINet, LPDNet, RIM, IRIM, and UNet. Models were trained and evaluated on T1-weighted and FLAIR contrast brain data, and T2-weighted knee data. Both 1D and 2D undersampling patterns were evaluated. Robustness was tested by reconstructing 7.5x prospectively undersampled 3D FLAIR MRI data of Multiple Sclerosis (MS) patients with white matter lesions. The CIRIM performed best when implicitly enforcing DC, while the E2EVN required an explicit DC formulation. In reconstructing MS patient data, prospectively acquired with a sampling pattern unseen during model training, the CIRIM maintained lesion contrast while efficiently denoising the images. The CIRIM showed highly promising generalization capabilities maintaining a very fair trade-off between reconstructed image quality and fast reconstruction times, which is crucial in the clinical workflow.

LSMS: Language-guided Scale-aware MedSegmentor for Medical Image Referring Segmentation

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