Shaoting Zhang

Ziyan Huang, Haoyu Wang, Zhongying Deng et al.

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.

Kexin Ding, Mu Zhou, Dimitris N. Metaxas et al.

Survival outcome assessment is challenging and inherently associated with multiple clinical factors (e.g., imaging and genomics biomarkers) in cancer. Enabling multimodal analytics promises to reveal novel predictive patterns of patient outcomes. In this study, we propose a multimodal transformer (PathOmics) integrating pathology and genomics insights into colon-related cancer survival prediction. We emphasize the unsupervised pretraining to capture the intrinsic interaction between tissue microenvironments in gigapixel whole slide images (WSIs) and a wide range of genomics data (e.g., mRNA-sequence, copy number variant, and methylation). After the multimodal knowledge aggregation in pretraining, our task-specific model finetuning could expand the scope of data utility applicable to both multi- and single-modal data (e.g., image- or genomics-only). We evaluate our approach on both TCGA colon and rectum cancer cohorts, showing that the proposed approach is competitive and outperforms state-of-the-art studies. Finally, our approach is desirable to utilize the limited number of finetuned samples towards data-efficient analytics for survival outcome prediction. The code is available at https://github.com/Cassie07/PathOmics.

Zhao Wang, Chang Liu, Shaoting Zhang et al.

Foundation models have exhibited remarkable success in various applications, such as disease diagnosis and text report generation. To date, a foundation model for endoscopic video analysis is still lacking. In this paper, we propose Endo-FM, a foundation model specifically developed using massive endoscopic video data. First, we build a video transformer, which captures both local and global long-range dependencies across spatial and temporal dimensions. Second, we pre-train our transformer model using global and local views via a self-supervised manner, aiming to make it robust to spatial-temporal variations and discriminative across different scenes. To develop the foundation model, we construct a large-scale endoscopy video dataset by combining 9 publicly available datasets and a privately collected dataset from Baoshan Branch of Renji Hospital in Shanghai, China. Our dataset overall consists of over 33K video clips with up to 5 million frames, encompassing various protocols, target organs, and disease types. Our pre-trained Endo-FM can be easily adopted for a given downstream task via fine-tuning by serving as the backbone. With experiments on 3 different types of downstream tasks, including classification, segmentation, and detection, our Endo-FM surpasses the current state-of-the-art (SOTA) self-supervised pre-training and adapter-based transfer learning methods by a significant margin, such as VCL (3.1% F1, 4.8% Dice, and 5.5% F1 for classification, segmentation, and detection) and ST-Adapter (5.9% F1, 9.6% Dice, and 9.9% F1 for classification, segmentation, and detection). Code, datasets, and models are released at https://github.com/med-air/Endo-FM.

Yunkun Zhang, Jin Gao, Mu Zhou et al.

The recent surge of foundation models in computer vision and natural language processing opens up perspectives in utilizing multi-modal clinical data to train large models with strong generalizability. Yet pathological image datasets often lack biomedical text annotation and enrichment. Guiding data-efficient image diagnosis from the use of biomedical text knowledge becomes a substantial interest. In this paper, we propose to Connect Image and Text Embeddings (CITE) to enhance pathological image classification. CITE injects text insights gained from language models pre-trained with a broad range of biomedical texts, leading to adapt foundation models towards pathological image understanding. Through extensive experiments on the PatchGastric stomach tumor pathological image dataset, we demonstrate that CITE achieves leading performance compared with various baselines especially when training data is scarce. CITE offers insights into leveraging in-domain text knowledge to reinforce data-efficient pathological image classification. Code is available at https://github.com/Yunkun-Zhang/CITE.

Dequan Wang, Xiaosong Wang, Lilong Wang et al. · berkeley

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

Haoyu Wang, Sizheng Guo, Jin Ye et al.

Existing volumetric medical image segmentation models are typically task-specific, excelling at specific target but struggling to generalize across anatomical structures or modalities. This limitation restricts their broader clinical use. In this paper, we introduce SAM-Med3D for general-purpose segmentation on volumetric medical images. Given only a few 3D prompt points, SAM-Med3D can accurately segment diverse anatomical structures and lesions across various modalities. To achieve this, we gather and process a large-scale 3D medical image dataset, SA-Med3D-140K, from a blend of public sources and licensed private datasets. This dataset includes 22K 3D images and 143K corresponding 3D masks. Then SAM-Med3D, a promptable segmentation model characterized by the fully learnable 3D structure, is trained on this dataset using a two-stage procedure and exhibits impressive performance on both seen and unseen segmentation targets. We comprehensively evaluate SAM-Med3D on 16 datasets covering diverse medical scenarios, including different anatomical structures, modalities, targets, and zero-shot transferability to new/unseen tasks. The evaluation shows the efficiency and efficacy of SAM-Med3D, as well as its promising application to diverse downstream tasks as a pre-trained model. Our approach demonstrates that substantial medical resources can be utilized to develop a general-purpose medical AI for various potential applications. Our dataset, code, and models are available at https://github.com/uni-medical/SAM-Med3D.

Zhuowei Li, Yibo Gao, Zhenzhou Zha et al.

Neural architecture search (NAS) algorithms save tremendous labor from human experts. Recent advancements further reduce the computational overhead to an affordable level. However, it is still cumbersome to deploy the NAS techniques in real-world applications due to the fussy procedures and the supervised learning paradigm. In this work, we propose the self-supervised and weight-preserving neural architecture search (SSWP-NAS) as an extension of the current NAS framework by allowing the self-supervision and retaining the concomitant weights discovered during the search stage. As such, we simplify the workflow of NAS to a one-stage and proxy-free procedure. Experiments show that the architectures searched by the proposed framework achieve state-of-the-art accuracy on CIFAR-10, CIFAR-100, and ImageNet datasets without using manual labels. Moreover, we show that employing the concomitant weights as initialization consistently outperforms the random initialization and the two-stage weight pre-training method by a clear margin under semi-supervised learning scenarios. Codes are publicly available at https://github.com/LzVv123456/SSWP-NAS.

Guotai Wang, Xiangde Luo, Ran Gu et al.

Background and Objective: Open-source deep learning toolkits are one of the driving forces for developing medical image segmentation models. Existing toolkits mainly focus on fully supervised segmentation and require full and accurate pixel-level annotations that are time-consuming and difficult to acquire for segmentation tasks, which makes learning from imperfect labels highly desired for reducing the annotation cost. We aim to develop a new deep learning toolkit to support annotation-efficient learning for medical image segmentation. Methods: Our proposed toolkit named PyMIC is a modular deep learning library for medical image segmentation tasks. In addition to basic components that support development of high-performance models for fully supervised segmentation, it contains several advanced components tailored for learning from imperfect annotations, such as loading annotated and unannounced images, loss functions for unannotated, partially or inaccurately annotated images, and training procedures for co-learning between multiple networks, etc. PyMIC supports development of semi-supervised, weakly supervised and noise-robust learning methods for medical image segmentation. Results: We present several illustrative medical image segmentation tasks based on PyMIC: (1) Achieving competitive performance on fully supervised learning; (2) Semi-supervised cardiac structure segmentation with only 10% training images annotated; (3) Weakly supervised segmentation using scribble annotations; and (4) Learning from noisy labels for chest radiograph segmentation. Conclusions: The PyMIC toolkit is easy to use and facilitates efficient development of medical image segmentation models with imperfect annotations. It is modular and flexible, which enables researchers to develop high-performance models with low annotation cost. The source code is available at: https://github.com/HiLab-git/PyMIC.

Guotai Wang, Jianghao Wu, Xiangde Luo et al.

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

Shaoting Zhang, Dimitris Metaxas

This article discusses the opportunities, applications and future directions of large-scale pre-trained models, i.e., foundation models, for analyzing medical images. Medical foundation models have immense potential in solving a wide range of downstream tasks, as they can help to accelerate the development of accurate and robust models, reduce the large amounts of required labeled data, preserve the privacy and confidentiality of patient data. Specifically, we illustrate the "spectrum" of medical foundation models, ranging from general vision models, modality-specific models, to organ/task-specific models, highlighting their challenges, opportunities and applications. We also discuss how foundation models can be leveraged in downstream medical tasks to enhance the accuracy and efficiency of medical image analysis, leading to more precise diagnosis and treatment decisions.

Jin Ye, Junlong Cheng, Jianpin Chen et al.

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

Ziyan Huang, Zhongying Deng, Jin Ye et al.

Although deep learning have revolutionized abdominal multi-organ segmentation, models often struggle with generalization due to training on small, specific datasets. With the recent emergence of large-scale datasets, some important questions arise: \textbf{Can models trained on these datasets generalize well on different ones? If yes/no, how to further improve their generalizability?} To address these questions, we introduce A-Eval, a benchmark for the cross-dataset Evaluation ('Eval') of Abdominal ('A') multi-organ segmentation. We employ training sets from four large-scale public datasets: FLARE22, AMOS, WORD, and TotalSegmentator, each providing extensive labels for abdominal multi-organ segmentation. For evaluation, we incorporate the validation sets from these datasets along with the training set from the BTCV dataset, forming a robust benchmark comprising five distinct datasets. We evaluate the generalizability of various models using the A-Eval benchmark, with a focus on diverse data usage scenarios: training on individual datasets independently, utilizing unlabeled data via pseudo-labeling, mixing different modalities, and joint training across all available datasets. Additionally, we explore the impact of model sizes on cross-dataset generalizability. Through these analyses, we underline the importance of effective data usage in enhancing models' generalization capabilities, offering valuable insights for assembling large-scale datasets and improving training strategies. The code and pre-trained models are available at \href{https://github.com/uni-medical/A-Eval}{https://github.com/uni-medical/A-Eval}.

Junlong Cheng, Jin Ye, Zhongying Deng et al.

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.

Pengcheng Chen, Jin Ye, Guoan Wang et al. · pku

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 284 datasets across 38 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 53.96%, 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.

Ran Gu, Guotai Wang, Jiangshan Lu et al.

Generalization to previously unseen images with potential domain shifts and different styles is essential for clinically applicable medical image segmentation, and the ability to disentangle domain-specific and domain-invariant features is key for achieving Domain Generalization (DG). However, existing DG methods can hardly achieve effective disentanglement to get high generalizability. To deal with this problem, we propose an efficient Contrastive Domain Disentanglement and Style Augmentation (CDDSA) framework for generalizable medical image segmentation. First, a disentangle network is proposed to decompose an image into a domain-invariant anatomical representation and a domain-specific style code, where the former is sent to a segmentation model that is not affected by the domain shift, and the disentangle network is regularized by a decoder that combines the anatomical and style codes to reconstruct the input image. Second, to achieve better disentanglement, a contrastive loss is proposed to encourage the style codes from the same domain and different domains to be compact and divergent, respectively. Thirdly, to further improve generalizability, we propose a style augmentation method based on the disentanglement representation to synthesize images in various unseen styles with shared anatomical structures. Our method was validated on a public multi-site fundus image dataset for optic cup and disc segmentation and an in-house multi-site Nasopharyngeal Carcinoma Magnetic Resonance Image (NPC-MRI) dataset for nasopharynx Gross Tumor Volume (GTVnx) segmentation. Experimental results showed that the proposed CDDSA achieved remarkable generalizability across different domains, and it outperformed several state-of-the-art methods in domain-generalizable segmentation.

Yunhe Gao, Zhuowei Li, Di Liu et al.

A major focus of clinical imaging workflow is disease diagnosis and management, leading to medical imaging datasets strongly tied to specific clinical objectives. This scenario has led to the prevailing practice of developing task-specific segmentation models, without gaining insights from widespread imaging cohorts. Inspired by the training program of medical radiology residents, we propose a shift towards universal medical image segmentation, a paradigm aiming to build medical image understanding foundation models by leveraging the diversity and commonality across clinical targets, body regions, and imaging modalities. Towards this goal, we develop Hermes, a novel context-prior learning approach to address the challenges of data heterogeneity and annotation differences in medical image segmentation. In a large collection of eleven diverse datasets (2,438 3D images) across five modalities (CT, PET, T1, T2 and cine MRI) and multiple body regions, we demonstrate the merit of the universal paradigm over the traditional paradigm on addressing multiple tasks within a single model. By exploiting the synergy across tasks, Hermes achieves state-of-the-art performance on all testing datasets and shows superior model scalability. Results on two additional datasets reveals Hermes' strong performance for transfer learning, incremental learning, and generalization to downstream tasks. Hermes's learned priors demonstrate an appealing trait to reflect the intricate relations among tasks and modalities, which aligns with the established anatomical and imaging principles in radiology. The code is available: https://github.com/yhygao/universal-medical-image-segmentation.

Zhenyu Tang, Shaoting Zhang, Xiaosong Wang

Deep learning models often require large amounts of data for training, leading to increased costs. It is particularly challenging in medical imaging, i.e., gathering distributed data for centralized training, and meanwhile, obtaining quality labels remains a tedious job. Many methods have been proposed to address this issue in various training paradigms, e.g., continual learning, active learning, and federated learning, which indeed demonstrate certain forms of the data valuation process. However, existing methods are either overly intuitive or limited to common clean/toy datasets in the experiments. In this work, we present two data valuation metrics based on Synaptic Intelligence and gradient norms, respectively, to study the redundancy in real-world image data. Novel online and offline data selection algorithms are then proposed via clustering and grouping based on the examined data values. Our online approach effectively evaluates data utilizing layerwise model parameter updates and gradients in each epoch and can accelerate model training with fewer epochs and a subset (e.g., 19%-59%) of data while maintaining equivalent levels of accuracy in a variety of datasets. It also extends to the offline coreset construction, producing subsets of only 18%-30% of the original. The codes for the proposed adaptive data selection and coreset computation are available (https://github.com/ZhenyuTANG2023/data_selection).

Dongjie Cheng, Ziyuan Qin, Zekun Jiang et al.

The Segment Anything Model (SAM) made an eye-catching debut recently and inspired many researchers to explore its potential and limitation in terms of zero-shot generalization capability. As the first promptable foundation model for segmentation tasks, it was trained on a large dataset with an unprecedented number of images and annotations. This large-scale dataset and its promptable nature endow the model with strong zero-shot generalization. Although the SAM has shown competitive performance on several datasets, we still want to investigate its zero-shot generalization on medical images. As we know, the acquisition of medical image annotation usually requires a lot of effort from professional practitioners. Therefore, if there exists a foundation model that can give high-quality mask prediction simply based on a few point prompts, this model will undoubtedly become the game changer for medical image analysis. To evaluate whether SAM has the potential to become the foundation model for medical image segmentation tasks, we collected more than 12 public medical image datasets that cover various organs and modalities. We also explore what kind of prompt can lead to the best zero-shot performance with different modalities. Furthermore, we find that a pattern shows that the perturbation of the box size will significantly change the prediction accuracy. Finally, Extensive experiments show that the predicted mask quality varied a lot among different datasets. And providing proper prompts, such as bounding boxes, to the SAM will significantly increase its performance.

Xiangde Luo, Minhao Hu, Wenjun Liao et al.

Medical image segmentation plays an irreplaceable role in computer-assisted diagnosis, treatment planning, and following-up. Collecting and annotating a large-scale dataset is crucial to training a powerful segmentation model, but producing high-quality segmentation masks is an expensive and time-consuming procedure. Recently, weakly-supervised learning that uses sparse annotations (points, scribbles, bounding boxes) for network training has achieved encouraging performance and shown the potential for annotation cost reduction. However, due to the limited supervision signal of sparse annotations, it is still challenging to employ them for networks training directly. In this work, we propose a simple yet efficient scribble-supervised image segmentation method and apply it to cardiac MRI segmentation. Specifically, we employ a dual-branch network with one encoder and two slightly different decoders for image segmentation and dynamically mix the two decoders' predictions to generate pseudo labels for auxiliary supervision. By combining the scribble supervision and auxiliary pseudo labels supervision, the dual-branch network can efficiently learn from scribble annotations end-to-end. Experiments on the public ACDC dataset show that our method performs better than current scribble-supervised segmentation methods and also outperforms several semi-supervised segmentation methods.

Wentao Zhu, Yuan Jin, Gege Ma et al.

The accurate diagnosis on pathological subtypes for lung cancer is of significant importance for the follow-up treatments and prognosis managements. In this paper, we propose self-generating hybrid feature network (SGHF-Net) for accurately classifying lung cancer subtypes on computed tomography (CT) images. Inspired by studies stating that cross-scale associations exist in the image patterns between the same case's CT images and its pathological images, we innovatively developed a pathological feature synthetic module (PFSM), which quantitatively maps cross-modality associations through deep neural networks, to derive the "gold standard" information contained in the corresponding pathological images from CT images. Additionally, we designed a radiological feature extraction module (RFEM) to directly acquire CT image information and integrated it with the pathological priors under an effective feature fusion framework, enabling the entire classification model to generate more indicative and specific pathologically related features and eventually output more accurate predictions. The superiority of the proposed model lies in its ability to self-generate hybrid features that contain multi-modality image information based on a single-modality input. To evaluate the effectiveness, adaptability, and generalization ability of our model, we performed extensive experiments on a large-scale multi-center dataset (i.e., 829 cases from three hospitals) to compare our model and a series of state-of-the-art (SOTA) classification models. The experimental results demonstrated the superiority of our model for lung cancer subtypes classification with significant accuracy improvements in terms of accuracy (ACC), area under the curve (AUC), and F1 score.

Zhongzhen Huang, Xiaofan Zhang, Shaoting Zhang

Radiology report generation aims to automatically generate a clinically accurate and coherent paragraph from the X-ray image, which could relieve radiologists from the heavy burden of report writing. Although various image caption methods have shown remarkable performance in the natural image field, generating accurate reports for medical images requires knowledge of multiple modalities, including vision, language, and medical terminology. We propose a Knowledge-injected U-Transformer (KiUT) to learn multi-level visual representation and adaptively distill the information with contextual and clinical knowledge for word prediction. In detail, a U-connection schema between the encoder and decoder is designed to model interactions between different modalities. And a symptom graph and an injected knowledge distiller are developed to assist the report generation. Experimentally, we outperform state-of-the-art methods on two widely used benchmark datasets: IU-Xray and MIMIC-CXR. Further experimental results prove the advantages of our architecture and the complementary benefits of the injected knowledge.

Ran Gu, Jingyang Zhang, Guotai Wang et al.

Convolutional Neural Networks (CNNs) have achieved state-of-the-art performance for medical image segmentation, yet need plenty of manual annotations for training. Semi-Supervised Learning (SSL) methods are promising to reduce the requirement of annotations, but their performance is still limited when the dataset size and the number of annotated images are small. Leveraging existing annotated datasets with similar anatomical structures to assist training has a potential for improving the model's performance. However, it is further challenged by the cross-anatomy domain shift due to the different appearance and even imaging modalities from the target structure. To solve this problem, we propose Contrastive Semi-supervised learning for Cross Anatomy Domain Adaptation (CS-CADA) that adapts a model to segment similar structures in a target domain, which requires only limited annotations in the target domain by leveraging a set of existing annotated images of similar structures in a source domain. We use Domain-Specific Batch Normalization (DSBN) to individually normalize feature maps for the two anatomical domains, and propose a cross-domain contrastive learning strategy to encourage extracting domain invariant features. They are integrated into a Self-Ensembling Mean-Teacher (SE-MT) framework to exploit unlabeled target domain images with a prediction consistency constraint. Extensive experiments show that our CS-CADA is able to solve the challenging cross-anatomy domain shift problem, achieving accurate segmentation of coronary arteries in X-ray images with the help of retinal vessel images and cardiac MR images with the help of fundus images, respectively, given only a small number of annotations in the target domain.

Shuwei Zhai, Guotai Wang, Xiangde Luo et al.

The success of Convolutional Neural Networks (CNNs) in 3D medical image segmentation relies on massive fully annotated 3D volumes for training that are time-consuming and labor-intensive to acquire. In this paper, we propose to annotate a segmentation target with only seven points in 3D medical images, and design a two-stage weakly supervised learning framework PA-Seg. In the first stage, we employ geodesic distance transform to expand the seed points to provide more supervision signal. To further deal with unannotated image regions during training, we propose two contextual regularization strategies, i.e., multi-view Conditional Random Field (mCRF) loss and Variance Minimization (VM) loss, where the first one encourages pixels with similar features to have consistent labels, and the second one minimizes the intensity variance for the segmented foreground and background, respectively. In the second stage, we use predictions obtained by the model pre-trained in the first stage as pseudo labels. To overcome noises in the pseudo labels, we introduce a Self and Cross Monitoring (SCM) strategy, which combines self-training with Cross Knowledge Distillation (CKD) between a primary model and an auxiliary model that learn from soft labels generated by each other. Experiments on public datasets for Vestibular Schwannoma (VS) segmentation and Brain Tumor Segmentation (BraTS) demonstrated that our model trained in the first stage outperformed existing state-of-the-art weakly supervised approaches by a large margin, and after using SCM for additional training, the model's performance was close to its fully supervised counterpart on the BraTS dataset.

Xiaoming Shi, Jie Xu, Jinru Ding et al.

There is an increasing interest in developing LLMs for medical diagnosis to improve diagnosis efficiency. Despite their alluring technological potential, there is no unified and comprehensive evaluation criterion, leading to the inability to evaluate the quality and potential risks of medical LLMs, further hindering the application of LLMs in medical treatment scenarios. Besides, current evaluations heavily rely on labor-intensive interactions with LLMs to obtain diagnostic dialogues and human evaluation on the quality of diagnosis dialogue. To tackle the lack of unified and comprehensive evaluation criterion, we first initially establish an evaluation criterion, termed LLM-specific Mini-CEX to assess the diagnostic capabilities of LLMs effectively, based on original Mini-CEX. To address the labor-intensive interaction problem, we develop a patient simulator to engage in automatic conversations with LLMs, and utilize ChatGPT for evaluating diagnosis dialogues automatically. Experimental results show that the LLM-specific Mini-CEX is adequate and necessary to evaluate medical diagnosis dialogue. Besides, ChatGPT can replace manual evaluation on the metrics of humanistic qualities and provides reproducible and automated comparisons between different LLMs.

Linda Wei, Shengyi Hua, Shaoting Zhang et al.

Breast cancer is a highly fatal disease among cancers in women, and early detection is crucial for treatment. HER2 status, a valuable diagnostic marker based on Immunohistochemistry (IHC) staining, is instrumental in determining breast cancer status. The high cost of IHC staining and the ubiquity of Hematoxylin and Eosin (H&E) staining make the conversion from H&E to IHC staining essential. In this article, we propose a destain-restain framework for converting H&E staining to IHC staining, leveraging the characteristic that H&E staining and IHC staining of the same tissue sections share the Hematoxylin channel. We further design loss functions specifically for Hematoxylin and Diaminobenzidin (DAB) channels to generate IHC images exploiting insights from separated staining channels. Beyond the benchmark metrics on BCI contest, we have developed semantic information metrics for the HER2 level. The experimental results demonstrated that our method outperforms previous open-sourced methods in terms of image intrinsic property and semantic information.

Hao Fu, Guotai Wang, Wenhui Lei et al.

Accurate segmentation of Anatomical brain Barriers to Cancer spread (ABCs) plays an important role for automatic delineation of Clinical Target Volume (CTV) of brain tumors in radiotherapy. Despite that variants of U-Net are state-of-the-art segmentation models, they have limited performance when dealing with ABCs structures with various shapes and sizes, especially thin structures (e.g., the falx cerebri) that span only few slices. To deal with this problem, we propose a High and Multi-Resolution Network (HMRNet) that consists of a multi-scale feature learning branch and a high-resolution branch, which can maintain the high-resolution contextual information and extract more robust representations of anatomical structures with various scales. We further design a Bidirectional Feature Calibration (BFC) block to enable the two branches to generate spatial attention maps for mutual feature calibration. Considering the different sizes and positions of ABCs structures, our network was applied after a rough localization of each structure to obtain fine segmentation results. Experiments on the MICCAI 2020 ABCs challenge dataset showed that: 1) Our proposed two-stage segmentation strategy largely outperformed methods segmenting all the structures in just one stage; 2) The proposed HMRNet with two branches can maintain high-resolution representations and is effective to improve the performance on thin structures; 3) The proposed BFC block outperformed existing attention methods using monodirectional feature calibration. Our method won the second place of ABCs 2020 challenge and has a potential for more accurate and reasonable delineation of CTV of brain tumors.

Meng Han, Xiangde Luo, Wenjun Liao et al.

Multi-organ segmentation in abdominal Computed Tomography (CT) images is of great importance for diagnosis of abdominal lesions and subsequent treatment planning. Though deep learning based methods have attained high performance, they rely heavily on large-scale pixel-level annotations that are time-consuming and labor-intensive to obtain. Due to its low dependency on annotation, weakly supervised segmentation has attracted great attention. However, there is still a large performance gap between current weakly-supervised methods and fully supervised learning, leaving room for exploration. In this work, we propose a novel 3D framework with two consistency constraints for scribble-supervised multiple abdominal organ segmentation from CT. Specifically, we employ a Triple-branch multi-Dilated network (TDNet) with one encoder and three decoders using different dilation rates to capture features from different receptive fields that are complementary to each other to generate high-quality soft pseudo labels. For more stable unsupervised learning, we use voxel-wise uncertainty to rectify the soft pseudo labels and then supervise the outputs of each decoder. To further regularize the network, class relationship information is exploited by encouraging the generated class affinity matrices to be consistent across different decoders under multi-view projection. Experiments on the public WORD dataset show that our method outperforms five existing scribble-supervised methods.

Huahui Yi, Ziyuan Qin, Qicheng Lao et al.

Inevitable domain and task discrepancies in real-world scenarios can impair the generalization performance of the pre-trained deep models for medical data. Therefore, we audaciously propose that we should build a general-purpose medical AI system that can be seamlessly adapted to downstream domains/tasks. Since the domain/task adaption procedures usually involve additional labeling work for the target data, designing a data-efficient adaption algorithm is desired to save the cost of transferring the learned knowledge. Our recent work found that vision-language models (VLMs) are efficient learners with extraordinary cross-domain ability. Therefore, in this work, we further explore the possibility of leveraging pre-trained VLMs as medical foundation models for building general-purpose medical AI, where we thoroughly investigate three machine-learning paradigms, i.e., domain/task-specialized learning, joint learning, and continual learning, for training the VLMs and evaluate their generalization performance on cross-domain and cross-task test sets. To alleviate the catastrophic forgetting during sequential training, we employ rehearsal learning and receive a sharp boost in terms of generalization capability. In a nutshell, our empirical evidence suggests that continual learning may be a practical and efficient learning paradigm for the medical foundation model. And we hope researchers can use our empirical evidence as basement to further explore the path toward medical foundation model.

Xiaoyu Yang, Lijian Xu, Hao Sun et al.

Visual grounding (VG) occupies a pivotal position in multi-modality vision-language models. In this study, we propose ViLaM, a large multi-modality model, that supports multi-tasks of VG using the cycle training strategy, with abundant interaction instructions. The cycle training between referring expression generation (REG) and referring expression comprehension (REC) is introduced. It enhances the consistency between visual location and referring expressions, and addresses the need for high-quality, multi-tasks VG datasets. Moreover, multi-tasks of VG are promoted in our model, contributed by the cycle training strategy. The multi-tasks in REC encompass a range of granularities, from region-level to pixel-level, which include referring bbox detection, referring keypoints detection, and referring image segmentation. In REG, referring region classification determines the fine-grained category of the target, while referring region captioning generates a comprehensive description. Meanwhile, all tasks participate in the joint training, synergistically enhancing one another and collectively improving the overall performance of the model. Furthermore, leveraging the capabilities of large language models, ViLaM extends a wide range of instructions, thereby significantly enhancing its generalization and interaction potentials. Extensive public datasets corroborate the superior capabilities of our model in VG with muti-tasks. Additionally, validating its robust generalization, ViLaM is validated under open-set and few-shot scenarios. Especially in the medical field, our model demonstrates cross-domain robust generalization capabilities. Furthermore, we contribute a VG dataset, especially with multi-tasks. To support and encourage the community focused on VG, we have made both the dataset and our code public: https://github.com/AnonymGiant/ViLaM.

Xiaoming Shi, Zeming Liu, Chuan Wang et al.

Most medical dialogue systems assume that patients have clear goals (medicine querying, surgical operation querying, etc.) before medical consultation. However, in many real scenarios, due to the lack of medical knowledge, it is usually difficult for patients to determine clear goals with all necessary slots. In this paper, we identify this challenge as how to construct medical consultation dialogue systems to help patients clarify their goals. To mitigate this challenge, we propose a novel task and create a human-to-human mixed-type medical consultation dialogue corpus, termed MidMed, covering five dialogue types: task-oriented dialogue for diagnosis, recommendation, knowledge-grounded dialogue, QA, and chitchat. MidMed covers four departments (otorhinolaryngology, ophthalmology, skin, and digestive system), with 8,175 dialogues. Furthermore, we build baselines on MidMed and propose an instruction-guiding medical dialogue generation framework, termed InsMed, to address this task. Experimental results show the effectiveness of InsMed.

Linhao Qu, Dingkang Yang, Dan Huang et al.

Current multi-instance learning algorithms for pathology image analysis often require a substantial number of Whole Slide Images for effective training but exhibit suboptimal performance in scenarios with limited learning data. In clinical settings, restricted access to pathology slides is inevitable due to patient privacy concerns and the prevalence of rare or emerging diseases. The emergence of the Few-shot Weakly Supervised WSI Classification accommodates the significant challenge of the limited slide data and sparse slide-level labels for diagnosis. Prompt learning based on the pre-trained models (\eg, CLIP) appears to be a promising scheme for this setting; however, current research in this area is limited, and existing algorithms often focus solely on patch-level prompts or confine themselves to language prompts. This paper proposes a multi-instance prompt learning framework enhanced with pathology knowledge, \ie, integrating visual and textual prior knowledge into prompts at both patch and slide levels. The training process employs a combination of static and learnable prompts, effectively guiding the activation of pre-trained models and further facilitating the diagnosis of key pathology patterns. Lightweight Messenger (self-attention) and Summary (attention-pooling) layers are introduced to model relationships between patches and slides within the same patient data. Additionally, alignment-wise contrastive losses ensure the feature-level alignment between visual and textual learnable prompts for both patches and slides. Our method demonstrates superior performance in three challenging clinical tasks, significantly outperforming comparative few-shot methods.

Jia Fu, Tao Lu, Shaoting Zhang et al.

Accurate segmentation of the fetal brain from Magnetic Resonance Image (MRI) is important for prenatal assessment of fetal development. Although deep learning has shown the potential to achieve this task, it requires a large fine annotated dataset that is difficult to collect. To address this issue, weakly-supervised segmentation methods with image-level labels have gained attention, which are commonly based on class activation maps from a classification network trained with image tags. However, most of these methods suffer from incomplete activation regions, due to the low-resolution localization without detailed boundary cues. To this end, we propose a novel weakly-supervised method with image-level labels based on semantic features and context information exploration. We first propose an Uncertainty-weighted Multi-resolution Class Activation Map (UM-CAM) to generate high-quality pixel-level supervision. Then, we design a Geodesic distance-based Seed Expansion (GSE) method to provide context information for rectifying the ambiguous boundaries of UM-CAM. Extensive experiments on a fetal brain dataset show that our UM-CAM can provide more accurate activation regions with fewer false positive regions than existing CAM variants, and our proposed method outperforms state-of-the-art weakly-supervised methods with image-level labels.

Linjie Mu, Yannian Gu, Zhongzhen Huang et al.

Large language models with reasoning capabilities have demonstrated impressive performance across a wide range of domains. In clinical applications, a transparent, step-by-step reasoning process provides physicians with strong evidence to support decision-making. While reinforcement learning has effectively enhanced reasoning performance in medical contexts, the clinical reliability of these reasoning processes remains limited because their accuracy and validity are often overlooked during training. To address this gap, we propose MedCEG, a framework that augments medical language models with clinically valid reasoning pathways by explicitly supervising the reasoning process through a Critical Evidence Graph (CEG). We curate a dataset of challenging clinical cases and algorithmically construct a CEG for each sample to represent a high-quality verifiable reasoning pathway. To guide the reasoning process, we introduce a Clinical Reasoning Procedure Reward, which evaluates Node Coverage, Structural Correctness, and Chain Completeness, thereby providing a holistic assessment of reasoning quality. Experimental results show that MedCEG surpasses existing methods in performance while producing clinically valid reasoning chains, representing a solid advancement in reliable medical AI reasoning. The code and models are available at https://github.com/LinjieMu/MedCEG.

Shiyi Du, Xiaosong Wang, Yongyi Lu et al.

Image synthesis approaches, e.g., generative adversarial networks, have been popular as a form of data augmentation in medical image analysis tasks. It is primarily beneficial to overcome the shortage of publicly accessible data and associated quality annotations. However, the current techniques often lack control over the detailed contents in generated images, e.g., the type of disease patterns, the location of lesions, and attributes of the diagnosis. In this work, we adapt the latest advance in the generative model, i.e., the diffusion model, with the added control flow using lesion-specific visual and textual prompts for generating dermatoscopic images. We further demonstrate the advantage of our diffusion model-based framework over the classical generation models in both the image quality and boosting the segmentation performance on skin lesions. It can achieve a 9% increase in the SSIM image quality measure and an over 5% increase in Dice coefficients over the prior arts.

Ran Gu, Jiangshan Lu, Jingyang Zhang et al.

Efficiently utilizing discriminative features is crucial for convolutional neural networks to achieve remarkable performance in medical image segmentation and is also important for model generalization across multiple domains, where letting model recognize domain-specific and domain-invariant information among multi-site datasets is a reasonable strategy for domain generalization. Unfortunately, most of the recent disentangle networks are not directly adaptable to unseen-domain datasets because of the limitations of offered data distribution. To tackle this deficiency, we propose Contrastive Domain Disentangle (CDD) network for generalizable medical image segmentation. We first introduce a disentangle network to decompose medical images into an anatomical representation factor and a modality representation factor. Then, a style contrastive loss is proposed to encourage the modality representations from the same domain to distribute as close as possible while different domains are estranged from each other. Finally, we propose a domain augmentation strategy that can randomly generate new domains for model generalization training. Experimental results on multi-site fundus image datasets for optic cup and disc segmentation show that the CDD has good model generalization. Our proposed CDD outperforms several state-of-the-art methods in domain generalizable segmentation.

Yunkun Zhang, Jin Gao, Zheling Tan et al.

The advent of foundation models (FMs) as an emerging suite of AI techniques has struck a wave of opportunities in computational healthcare. The interactive nature of these models, guided by pre-training data and human instructions, has ignited a data-centric AI paradigm that emphasizes better data characterization, quality, and scale. In healthcare AI, obtaining and processing high-quality clinical data records has been a longstanding challenge, ranging from data quantity, annotation, patient privacy, and ethics. In this survey, we investigate a wide range of data-centric approaches in the FM era (from model pre-training to inference) towards improving the healthcare workflow. We discuss key perspectives in AI security, assessment, and alignment with human values. Finally, we offer a promising outlook of FM-based analytics to enhance the performance of patient outcome and clinical workflow in the evolving landscape of healthcare and medicine. We provide an up-to-date list of healthcare-related foundation models and datasets at https://github.com/Yunkun-Zhang/Data-Centric-FM-Healthcare .

Yuan Jin, Gege Ma, Geng Chen et al.

The accurate diagnosis of pathological subtypes of lung cancer is of paramount importance for follow-up treatments and prognosis managements. Assessment methods utilizing deep learning technologies have introduced novel approaches for clinical diagnosis. However, the majority of existing models rely solely on single-modality image input, leading to limited diagnostic accuracy. To this end, we propose a novel deep learning network designed to accurately classify lung cancer subtype with multi-dimensional and multi-modality images, i.e., CT and pathological images. The strength of the proposed model lies in its ability to dynamically process both paired CT-pathological image sets as well as independent CT image sets, and consequently optimize the pathology-related feature extractions from CT images. This adaptive learning approach enhances the flexibility in processing multi-dimensional and multi-modality datasets and results in performance elevating in the model testing phase. We also develop a contrastive constraint module, which quantitatively maps the cross-modality associations through network training, and thereby helps to explore the "gold standard" pathological information from the corresponding CT scans. To evaluate the effectiveness, adaptability, and generalization ability of our model, we conducted extensive experiments on a large-scale multi-center dataset and compared our model with a series of state-of-the-art classification models. The experimental results demonstrated the superiority of our model for lung cancer subtype classification, showcasing significant improvements in accuracy metrics such as ACC, AUC, and F1-score.

Jiaxuan Lu, Fang Yan, Xiaofan Zhang et al.

As natural image understanding moves towards the pretrain-finetune era, research in pathology imaging is concurrently evolving. Despite the predominant focus on pretraining pathological foundation models, how to adapt foundation models to downstream tasks is little explored. For downstream adaptation, we propose the existence of two domain gaps, i.e., the Foundation-Task Gap and the Task-Instance Gap. To mitigate these gaps, we introduce PathoTune, a framework designed to efficiently adapt pathological or even visual foundation models to pathology-specific tasks via multi-modal prompt tuning. The proposed framework leverages Task-specific Visual Prompts and Task-specific Textual Prompts to identify task-relevant features, along with Instance-specific Visual Prompts for encoding single pathological image features. Results across multiple datasets at both patch-level and WSI-level demonstrate its superior performance over single-modality prompt tuning approaches. Significantly, PathoTune facilitates the direct adaptation of natural visual foundation models to pathological tasks, drastically outperforming pathological foundation models with simple linear probing. The code is available at https://github.com/openmedlab/PathoDuet.

Xiaosong Wang, Xiaofan Zhang, Guotai Wang et al.

The emerging trend of advancing generalist artificial intelligence, such as GPTv4 and Gemini, has reshaped the landscape of research (academia and industry) in machine learning and many other research areas. However, domain-specific applications of such foundation models (e.g., in medicine) remain untouched or often at their very early stages. It will require an individual set of transfer learning and model adaptation techniques by further expanding and injecting these models with domain knowledge and data. The development of such technologies could be largely accelerated if the bundle of data, algorithms, and pre-trained foundation models were gathered together and open-sourced in an organized manner. In this work, we present OpenMEDLab, an open-source platform for multi-modality foundation models. It encapsulates not only solutions of pioneering attempts in prompting and fine-tuning large language and vision models for frontline clinical and bioinformatic applications but also building domain-specific foundation models with large-scale multi-modal medical data. Importantly, it opens access to a group of pre-trained foundation models for various medical image modalities, clinical text, protein engineering, etc. Inspiring and competitive results are also demonstrated for each collected approach and model in a variety of benchmarks for downstream tasks. We welcome researchers in the field of medical artificial intelligence to continuously contribute cutting-edge methods and models to OpenMEDLab, which can be accessed via https://github.com/openmedlab.

Lijian Xu, Hao Sun, Ziyu Ni et al.

Medicine is inherently multimodal and multitask, with diverse data modalities spanning text, imaging. However, most models in medical field are unimodal single tasks and lack good generalizability and explainability. In this study, we introduce MedViLaM, a unified vision-language model towards a generalist model for medical data that can flexibly encode and interpret various forms of medical data, including clinical language and imaging, all using the same set of model weights. To facilitate the creation of such multi-task model, we have curated MultiMedBench, a comprehensive pretaining dataset and benchmark consisting of several distinct tasks, i.e., continuous question-answering, multi-label disease classification, disease localization, generation and summarization of radiology reports. MedViLaM demonstrates strong performance across all MultiMedBench tasks, frequently outpacing other generalist models by a significant margin. Additionally, we present instances of zero-shot generalization to new medical concepts and tasks, effective transfer learning across different tasks, and the emergence of zero-shot medical reasoning.

Kaitao Chen, Mianxin Liu, Fang Yan et al.

The advent of vision-language models fosters the interactive conversations between AI-enabled models and humans. Yet applying these models into clinics must deal with daunting challenges around large-scale training data, financial, and computational resources. Here we propose a cost-effective instruction learning framework for conversational pathology named as CLOVER. CLOVER only trains a lightweight module and uses instruction tuning while freezing the parameters of the large language model. Instead of using costly GPT-4, we propose well-designed prompts on GPT-3.5 for building generation-based instructions, emphasizing the utility of pathological knowledge derived from the Internet source. To augment the use of instructions, we construct a high-quality set of template-based instructions in the context of digital pathology. From two benchmark datasets, our findings reveal the strength of hybrid-form instructions in the visual question-answer in pathology. Extensive results show the cost-effectiveness of CLOVER in answering both open-ended and closed-ended questions, where CLOVER outperforms strong baselines that possess 37 times more training parameters and use instruction data generated from GPT-4. Through the instruction tuning, CLOVER exhibits robustness of few-shot learning in the external clinical dataset. These findings demonstrate that cost-effective modeling of CLOVER could accelerate the adoption of rapid conversational applications in the landscape of digital pathology.

Linhao Qu, Dan Huang, Shaoting Zhang et al.

Survival analysis stands as a pivotal process in cancer treatment research, crucial for predicting patient survival rates accurately. Recent advancements in data collection techniques have paved the way for enhancing survival predictions by integrating information from multiple modalities. However, real-world scenarios often present challenges with incomplete data, particularly when dealing with censored survival labels. Prior works have addressed missing modalities but have overlooked incomplete labels, which can introduce bias and limit model efficacy. To bridge this gap, we introduce a novel framework that simultaneously handles incomplete data across modalities and censored survival labels. Our approach employs advanced foundation models to encode individual modalities and align them into a universal representation space for seamless fusion. By generating pseudo labels and incorporating uncertainty, we significantly enhance predictive accuracy. The proposed method demonstrates outstanding prediction accuracy in two survival analysis tasks on both employed datasets. This innovative approach overcomes limitations associated with disparate modalities and improves the feasibility of comprehensive survival analysis using multiple large foundation models.

Lijian Xu, Ziyu Ni, Xinglong Liu et al.

The emergence of multi-modal deep learning models has made significant impacts on clinical applications in the last decade. However, the majority of models are limited to single-tasking, without considering disease diagnosis is indeed a multi-task procedure. Here, we demonstrate a unified transformer model specifically designed for multi-modal clinical tasks by incorporating customized instruction tuning. We first compose a multi-task training dataset comprising 13.4 million instruction and ground-truth pairs (with approximately one million radiographs) for the customized tuning, involving both image- and pixel-level tasks. Thus, we can unify the various vision-intensive tasks in a single training framework with homogeneous model inputs and outputs to increase clinical interpretability in one reading. Finally, we demonstrate the overall superior performance of our model compared to prior arts on various chest X-ray benchmarks across multi-tasks in both direct inference and finetuning settings. Three radiologists further evaluate the generated reports against the recorded ones, which also exhibit the enhanced explainability of our multi-task model.

Yakun Zhu, Zhongzhen Huang, Linjie Mu et al.

The emergence of groundbreaking large language models capable of performing complex reasoning tasks holds significant promise for addressing various scientific challenges, including those arising in complex clinical scenarios. To enable their safe and effective deployment in real-world healthcare settings, it is urgently necessary to benchmark the diagnostic capabilities of current models systematically. Given the limitations of existing medical benchmarks in evaluating advanced diagnostic reasoning, we present DiagnosisArena, a comprehensive and challenging benchmark designed to rigorously assess professional-level diagnostic competence. DiagnosisArena consists of 1,113 pairs of segmented patient cases and corresponding diagnoses, spanning 28 medical specialties, deriving from clinical case reports published in 10 top-tier medical journals. The benchmark is developed through a meticulous construction pipeline, involving multiple rounds of screening and review by both AI systems and human experts, with thorough checks conducted to prevent data leakage. Our study reveals that even the most advanced reasoning models, o3, o1, and DeepSeek-R1, achieve only 51.12%, 31.09%, and 17.79% accuracy, respectively. This finding highlights a significant generalization bottleneck in current large language models when faced with clinical diagnostic reasoning challenges. Through DiagnosisArena, we aim to drive further advancements in AI's diagnostic reasoning capabilities, enabling more effective solutions for real-world clinical diagnostic challenges. We provide the benchmark and evaluation tools for further research and development https://github.com/SPIRAL-MED/DiagnosisArena.

Yongrui Yu, Zhongzhen Huang, Linjie Mu et al.

Radiology reporting is an essential yet time-consuming and error-prone task for radiologists in clinical examinations, especially for volumetric medical images. Rigorous quality control is also critical but tedious, ensuring that the final report meets clinical standards. Existing automated approaches, including radiology report generation methods and medical vision-language models, focus mainly on the report generation phase and neglect the crucial quality control procedure, limiting their capability to provide comprehensive support to radiologists. We propose Radiologist Copilot, an agentic AI assistant equipped with orchestrated tools designed for automated radiology reporting with quality control. Leveraging large language models as the reasoning backbone, the agentic system autonomously selects tools, plans, and executes actions, emulating the behavior of radiologists throughout the holistic radiology reporting process. The orchestrated tools include region localization, think with image paradigm directed region analysis planning, strategic template selection for report generation, quality assessment and feedback-driven adaptive refinement for quality control. Therefore, Radiologist Copilot facilitates accurate, complete, and efficient radiology reporting, assisting radiologists and improving clinical efficiency. Experimental results demonstrate that Radiologist Copilot significantly surpasses other state-of-the-art methods in radiology reporting. The source code will be released upon acceptance.

Zhengjie Zhang, Xiaoxie Mao, Qihao Guo et al.

Background: Alzheimer's disease (AD) diagnosis heavily relies on amyloid-beta positron emission tomography (Abeta-PET), which is limited by high cost and limited accessibility. This study explores whether Abeta-PET spatial patterns can be predicted from blood-based biomarkers (BBMs) and MRI scans. Methods: We collected Abeta-PET images, T1-weighted MRI scans, and BBMs from 566 participants. A language-enhanced generative model, driven by a large language model (LLM) and multimodal information fusion, was developed to synthesize PET images. Synthesized images were evaluated for image quality, diagnostic consistency, and clinical applicability within a fully automated diagnostic pipeline. Findings: The synthetic PET images closely resemble real PET scans in both structural details (SSIM = 0.920 +/- 0.003) and regional patterns (Pearson's r = 0.955 +/- 0.007). Diagnostic outcomes using synthetic PET show high agreement with real PET-based diagnoses (accuracy = 0.80). Using synthetic PET, we developed a fully automatic AD diagnostic pipeline integrating PET synthesis and classification. The synthetic PET-based model (AUC = 0.78) outperforms T1-based (AUC = 0.68) and BBM-based (AUC = 0.73) models, while combining synthetic PET and BBMs further improved performance (AUC = 0.79). Ablation analysis supports the advantages of LLM integration and prompt engineering. Interpretation: Our language-enhanced generative model synthesizes realistic PET images, enhancing the utility of MRI and BBMs for Abeta spatial pattern assessment and improving the diagnostic workflow for Alzheimer's disease.

Linjie Mu, Zhongzhen Huang, Shengqian Qin et al.

Large vision-language models (LVLMs) have shown great promise in medical applications, particularly in visual question answering (MedVQA) and diagnosis from medical images. However, existing datasets and models often fail to consider critical aspects of medical diagnostics, such as the integration of historical records and the analysis of disease progression over time. In this paper, we introduce MMXU (Multimodal and MultiX-ray Understanding), a novel dataset for MedVQA that focuses on identifying changes in specific regions between two patient visits. Unlike previous datasets that primarily address single-image questions, MMXU enables multi-image questions, incorporating both current and historical patient data. We demonstrate the limitations of current LVLMs in identifying disease progression on MMXU-\textit{test}, even those that perform well on traditional benchmarks. To address this, we propose a MedRecord-Augmented Generation (MAG) approach, incorporating both global and regional historical records. Our experiments show that integrating historical records significantly enhances diagnostic accuracy by at least 20\%, bridging the gap between current LVLMs and human expert performance. Additionally, we fine-tune models with MAG on MMXU-\textit{dev}, which demonstrates notable improvements. We hope this work could illuminate the avenue of advancing the use of LVLMs in medical diagnostics by emphasizing the importance of historical context in interpreting medical images. Our dataset is released at github: https://github.com/linjiemu/MMXU.

Zheling Tan, Kexin Ding, Jin Gao et al.

Foundational models (FMs) have made significant strides in the healthcare domain. Yet the data silo challenge and privacy concern remain in healthcare systems, hindering safe medical data sharing and collaborative model development among institutions. The collection and curation of scalable clinical datasets increasingly become the bottleneck for training strong FMs. In this study, we propose Medical Foundation Models Merging (MedForge), a cooperative framework enabling a community-driven medical foundation model development, meanwhile preventing the information leakage of raw patient data and mitigating synchronization model development issues across clinical institutions. MedForge offers a bottom-up model construction mechanism by flexibly merging task-specific Low-Rank Adaptation (LoRA) modules, which can adapt to downstream tasks while retaining original model parameters. Through an asynchronous LoRA module integration scheme, the resulting composite model can progressively enhance its comprehensive performance on various clinical tasks. MedForge shows strong performance on multiple clinical datasets (e.g., breast cancer, lung cancer, and colon cancer) collected from different institutions. Our major findings highlight the value of collaborative foundation models in advancing multi-center clinical collaboration effectively and cohesively. Our code is publicly available at https://github.com/TanZheling/MedForge.

Jiarun Liu, Hao Yang, Hong-Yu Zhou et al.

Accurate medical image segmentation demands the integration of multi-scale information, spanning from local features to global dependencies. However, it is challenging for existing methods to model long-range global information, where convolutional neural networks (CNNs) are constrained by their local receptive fields, and vision transformers (ViTs) suffer from high quadratic complexity of their attention mechanism. Recently, Mamba-based models have gained great attention for their impressive ability in long sequence modeling. Several studies have demonstrated that these models can outperform popular vision models in various tasks, offering higher accuracy, lower memory consumption, and less computational burden. However, existing Mamba-based models are mostly trained from scratch and do not explore the power of pretraining, which has been proven to be quite effective for data-efficient medical image analysis. This paper introduces a novel Mamba-based model, Swin-UMamba, designed specifically for medical image segmentation tasks, leveraging the advantages of ImageNet-based pretraining. Our experimental results reveal the vital role of ImageNet-based training in enhancing the performance of Mamba-based models. Swin-UMamba demonstrates superior performance with a large margin compared to CNNs, ViTs, and latest Mamba-based models. Notably, on AbdomenMRI, Encoscopy, and Microscopy datasets, Swin-UMamba outperforms its closest counterpart U-Mamba_Enc by an average score of 2.72%.

Chenbin Zhang, Zhiqiang Hu, Chuchu Jiang et al.

Drug-target binding affinity prediction is a fundamental task for drug discovery. It has been extensively explored in literature and promising results are reported. However, in this paper, we demonstrate that the results may be misleading and cannot be well generalized to real practice. The core observation is that the canonical randomized split of a test set in conventional evaluation leaves the test set dominated by samples with high similarity to the training set. The performance of models is severely degraded on samples with lower similarity to the training set but the drawback is highly overlooked in current evaluation. As a result, the performance can hardly be trusted when the model meets low-similarity samples in real practice. To address this problem, we propose a framework of similarity aware evaluation in which a novel split methodology is proposed to adapt to any desired distribution. This is achieved by a formulation of optimization problems which are approximately and efficiently solved by gradient descent. We perform extensive experiments across five representative methods in four datasets for two typical target evaluations and compare them with various counterpart methods. Results demonstrate that the proposed split methodology can significantly better fit desired distributions and guide the development of models. Code is released at https://github.com/Amshoreline/SAE/tree/main.