Junde Wu

Junde Wu, Wei Ji, Yuanpei Liu et al.

The Segment Anything Model (SAM) has recently gained popularity in the field of image segmentation due to its impressive capabilities in various segmentation tasks and its prompt-based interface. However, recent studies and individual experiments have shown that SAM underperforms in medical image segmentation, since the lack of the medical specific knowledge. This raises the question of how to enhance SAM's segmentation capability for medical images. In this paper, instead of fine-tuning the SAM model, we propose the Medical SAM Adapter (Med-SA), which incorporates domain-specific medical knowledge into the segmentation model using a light yet effective adaptation technique. In Med-SA, we propose Space-Depth Transpose (SD-Trans) to adapt 2D SAM to 3D medical images and Hyper-Prompting Adapter (HyP-Adpt) to achieve prompt-conditioned adaptation. We conduct comprehensive evaluation experiments on 17 medical image segmentation tasks across various image modalities. Med-SA outperforms several state-of-the-art (SOTA) medical image segmentation methods, while updating only 2\% of the parameters. Our code is released at https://github.com/KidsWithTokens/Medical-SAM-Adapter.

Junde Wu, Rao Fu, Huihui Fang et al.

Diffusion probabilistic model (DPM) recently becomes one of the hottest topic in computer vision. Its image generation application such as Imagen, Latent Diffusion Models and Stable Diffusion have shown impressive generation capabilities, which aroused extensive discussion in the community. Many recent studies also found it is useful in many other vision tasks, like image deblurring, super-resolution and anomaly detection. Inspired by the success of DPM, we propose the first DPM based model toward general medical image segmentation tasks, which we named MedSegDiff. In order to enhance the step-wise regional attention in DPM for the medical image segmentation, we propose dynamic conditional encoding, which establishes the state-adaptive conditions for each sampling step. We further propose Feature Frequency Parser (FF-Parser), to eliminate the negative effect of high-frequency noise component in this process. We verify MedSegDiff on three medical segmentation tasks with different image modalities, which are optic cup segmentation over fundus images, brain tumor segmentation over MRI images and thyroid nodule segmentation over ultrasound images. The experimental results show that MedSegDiff outperforms state-of-the-art (SOTA) methods with considerable performance gap, indicating the generalization and effectiveness of the proposed model. Our code is released at https://github.com/WuJunde/MedSegDiff.

Junde Wu, Wei Ji, Huazhu Fu et al.

The Diffusion Probabilistic Model (DPM) has recently gained popularity in the field of computer vision, thanks to its image generation applications, such as Imagen, Latent Diffusion Models, and Stable Diffusion, which have demonstrated impressive capabilities and sparked much discussion within the community. Recent investigations have further unveiled the utility of DPM in the domain of medical image analysis, as underscored by the commendable performance exhibited by the medical image segmentation model across various tasks. Although these models were originally underpinned by a UNet architecture, there exists a potential avenue for enhancing their performance through the integration of vision transformer mechanisms. However, we discovered that simply combining these two models resulted in subpar performance. To effectively integrate these two cutting-edge techniques for the Medical image segmentation, we propose a novel Transformer-based Diffusion framework, called MedSegDiff-V2. We verify its effectiveness on 20 medical image segmentation tasks with different image modalities. Through comprehensive evaluation, our approach demonstrates superiority over prior state-of-the-art (SOTA) methodologies. Code is released at https://github.com/KidsWithTokens/MedSegDiff

Junde Wu, Jiayuan Zhu, Yunli Qi et al.

We introduce a novel graph-based Retrieval-Augmented Generation (RAG) framework specifically designed for the medical domain, called \textbf{MedGraphRAG}, aimed at enhancing Large Language Model (LLM) capabilities for generating evidence-based medical responses, thereby improving safety and reliability when handling private medical data. Graph-based RAG (GraphRAG) leverages LLMs to organize RAG data into graphs, showing strong potential for gaining holistic insights from long-form documents. However, its standard implementation is overly complex for general use and lacks the ability to generate evidence-based responses, limiting its effectiveness in the medical field. To extend the capabilities of GraphRAG to the medical domain, we propose unique Triple Graph Construction and U-Retrieval techniques over it. In our graph construction, we create a triple-linked structure that connects user documents to credible medical sources and controlled vocabularies. In the retrieval process, we propose U-Retrieval which combines Top-down Precise Retrieval with Bottom-up Response Refinement to balance global context awareness with precise indexing. These effort enable both source information retrieval and comprehensive response generation. Our approach is validated on 9 medical Q\&A benchmarks, 2 health fact-checking benchmarks, and one collected dataset testing long-form generation. The results show that MedGraphRAG consistently outperforms state-of-the-art models across all benchmarks, while also ensuring that responses include credible source documentation and definitions. Our code is released at: https://github.com/MedicineToken/Medical-Graph-RAG.

Yu Zhang, Xiaoguang Di, Junde Wu et al.

Image enhancement is a common technique used to mitigate issues such as severe noise, low brightness, low contrast, and color deviation in low-light images. However, providing an optimal high-light image as a reference for low-light image enhancement tasks is impossible, which makes the learning process more difficult than other image processing tasks. As a result, although several low-light image enhancement methods have been proposed, most of them are either too complex or insufficient in addressing all the issues in low-light images. In this paper, to make the learning easier in low-light image enhancement, we introduce FLW-Net (Fast and LightWeight Network) and two relative loss functions. Specifically, we first recognize the challenges of the need for a large receptive field to obtain global contrast and the lack of an absolute reference, which limits the simplification of network structures in this task. Then, we propose an efficient global feature information extraction component and two loss functions based on relative information to overcome these challenges. Finally, we conducted comparative experiments to demonstrate the effectiveness of the proposed method, and the results confirm that the proposed method can significantly reduce the complexity of supervised low-light image enhancement networks while improving processing effect. The code is available at \url{https://github.com/hitzhangyu/FLW-Net}.

Haofeng Liu, Erli Zhang, Junde Wu et al.

Surgical video segmentation is a critical task in computer-assisted surgery and is vital for enhancing surgical quality and patient outcomes. Recently, the Segment Anything Model 2 (SAM2) framework has shown superior advancements in image and video segmentation. However, SAM2 struggles with efficiency due to the high computational demands of processing high-resolution images and complex and long-range temporal dynamics in surgical videos. To address these challenges, we introduce Surgical SAM 2 (SurgSAM2), an advanced model to utilize SAM2 with an Efficient Frame Pruning (EFP) mechanism, to facilitate real-time surgical video segmentation. The EFP mechanism dynamically manages the memory bank by selectively retaining only the most informative frames, reducing memory usage and computational cost while maintaining high segmentation accuracy. Our extensive experiments demonstrate that SurgSAM2 significantly improves both efficiency and segmentation accuracy compared to the vanilla SAM2. Remarkably, SurgSAM2 achieves a 3$\times$ FPS compared with SAM2, while also delivering state-of-the-art performance after fine-tuning with lower-resolution data. These advancements establish SurgSAM2 as a leading model for surgical video analysis, making real-time surgical video segmentation in resource-constrained environments a reality. Our source code is available at https://github.com/jinlab-imvr/Surgical-SAM-2.

Huihui Fang, Fei Li, Huazhu Fu et al.

Glaucoma causes irreversible vision loss due to damage to the optic nerve, and there is no cure for glaucoma.OCT imaging modality is an essential technique for assessing glaucomatous damage since it aids in quantifying fundus structures. To promote the research of AI technology in the field of OCT-assisted diagnosis of glaucoma, we held a Glaucoma OCT Analysis and Layer Segmentation (GOALS) Challenge in conjunction with the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) 2022 to provide data and corresponding annotations for researchers studying layer segmentation from OCT images and the classification of glaucoma. This paper describes the released 300 circumpapillary OCT images, the baselines of the two sub-tasks, and the evaluation methodology. The GOALS Challenge is accessible at https://aistudio.baidu.com/aistudio/competition/detail/230.

Junde Wu, Huihui Fang, Fei Li et al.

GAMMA Challenge is organized to encourage the AI models to screen the glaucoma from a combination of 2D fundus image and 3D optical coherence tomography volume, like the ophthalmologists.

Junde Wu, Huihui Fang, Yehui Yang et al.

Different from the general visual classification, some classification tasks are more challenging as they need the professional categories of the images. In the paper, we call them expert-level classification. Previous fine-grained vision classification (FGVC) has made many efforts on some of its specific sub-tasks. However, they are difficult to expand to the general cases which rely on the comprehensive analysis of part-global correlation and the hierarchical features interaction. In this paper, we propose Expert Network (ExpNet) to address the unique challenges of expert-level classification through a unified network. In ExpNet, we hierarchically decouple the part and context features and individually process them using a novel attentive mechanism, called Gaze-Shift. In each stage, Gaze-Shift produces a focal-part feature for the subsequent abstraction and memorizes a context-related embedding. Then we fuse the final focal embedding with all memorized context-related embedding to make the prediction. Such an architecture realizes the dual-track processing of partial and global information and hierarchical feature interactions. We conduct the experiments over three representative expert-level classification tasks: FGVC, disease classification, and artwork attributes classification. In these experiments, superior performance of our ExpNet is observed comparing to the state-of-the-arts in a wide range of fields, indicating the effectiveness and generalization of our ExpNet. The code will be made publicly available.

Junde Wu, Huihui Fang, Hoayi Xiong et al.

On the medical images, many of the tissues/lesions may be ambiguous. That is why the medical segmentation is typically annotated by a group of clinical experts to mitigate the personal bias. However, this clinical routine also brings new challenges to the application of machine learning algorithms. Without a definite ground-truth, it will be difficult to train and evaluate the deep learning models. When the annotations are collected from different graders, a common choice is majority vote. However such a strategy ignores the difference between the grader expertness. In this paper, we consider the task of predicting the segmentation with the calibrated inter-observer uncertainty. We note that in clinical practice, the medical image segmentation is usually used to assist the disease diagnosis. Inspired by this observation, we propose diagnosis-first principle, which is to take disease diagnosis as the criterion to calibrate the inter-observer segmentation uncertainty. Following this idea, a framework named Diagnosis First segmentation Framework (DiFF) is proposed to estimate diagnosis-first segmentation from the raw images.Specifically, DiFF will first learn to fuse the multi-rater segmentation labels to a single ground-truth which could maximize the disease diagnosis performance. We dubbed the fused ground-truth as Diagnosis First Ground-truth (DF-GT).Then, we further propose Take and Give Modelto segment DF-GT from the raw image. We verify the effectiveness of DiFF on three different medical segmentation tasks: OD/OC segmentation on fundus images, thyroid nodule segmentation on ultrasound images, and skin lesion segmentation on dermoscopic images. Experimental results show that the proposed DiFF is able to significantly facilitate the corresponding disease diagnosis, which outperforms previous state-of-the-art multi-rater learning methods.

Junde Wu, Huihui Fang, Yehui Yang et al.

In medical image segmentation, it is often necessary to collect opinions from multiple experts to make the final decision. This clinical routine helps to mitigate individual bias. But when data is multiply annotated, standard deep learning models are often not applicable. In this paper, we propose a novel neural network framework, called Multi-Rater Prism (MrPrism) to learn the medical image segmentation from multiple labels. Inspired by the iterative half-quadratic optimization, the proposed MrPrism will combine the multi-rater confidences assignment task and calibrated segmentation task in a recurrent manner. In this recurrent process, MrPrism can learn inter-observer variability taking into account the image semantic properties, and finally converges to a self-calibrated segmentation result reflecting the inter-observer agreement. Specifically, we propose Converging Prism (ConP) and Diverging Prism (DivP) to process the two tasks iteratively. ConP learns calibrated segmentation based on the multi-rater confidence maps estimated by DivP. DivP generates multi-rater confidence maps based on the segmentation masks estimated by ConP. The experimental results show that by recurrently running ConP and DivP, the two tasks can achieve mutual improvement. The final converged segmentation result of MrPrism outperforms state-of-the-art (SOTA) strategies on a wide range of medical image segmentation tasks.

Jiayuan Zhu, Abdullah Hamdi, Yunli Qi et al.

Medical image segmentation plays a pivotal role in clinical diagnostics and treatment planning, yet existing models often face challenges in generalization and in handling both 2D and 3D data uniformly. In this paper, we introduce Medical SAM 2 (MedSAM-2), a generalized auto-tracking model for universal 2D and 3D medical image segmentation. The core concept is to leverage the Segment Anything Model 2 (SAM2) pipeline to treat all 2D and 3D medical segmentation tasks as a video object tracking problem. To put it into practice, we propose a novel \emph{self-sorting memory bank} mechanism that dynamically selects informative embeddings based on confidence and dissimilarity, regardless of temporal order. This mechanism not only significantly improves performance in 3D medical image segmentation but also unlocks a \emph{One-Prompt Segmentation} capability for 2D images, allowing segmentation across multiple images from a single prompt without temporal relationships. We evaluated MedSAM-2 on five 2D tasks and nine 3D tasks, including white blood cells, optic cups, retinal vessels, mandibles, coronary arteries, kidney tumors, liver tumors, breast cancer, nasopharynx cancer, vestibular schwannoma, mediastinal lymph nodules, cerebral artery, inferior alveolar nerve, and abdominal organs, comparing it against state-of-the-art (SOTA) models in task-tailored, general and interactive segmentation settings. Our findings demonstrate that MedSAM-2 surpasses a wide range of existing models and updates new SOTA on several benchmarks. The code is released on the project page: https://supermedintel.github.io/Medical-SAM2/.

Weixiang Shen, Yanzhu Hu, Che Liu et al.

Currently, evaluating vision-language models (VLMs) in medical imaging tasks oversimplifies clinical reality by relying on pre-selected 2D images that demand significant manual labor to curate. This setup misses the core challenge of realworld diagnostics: a true clinical agent must actively navigate full 3D volumes across multiple sequences or modalities to gather evidence and ultimately support a final decision. To address this, we propose MEDOPENCLAW, an auditable runtime designed to let VLMs operate dynamically within standard medical tools or viewers (e.g., 3D Slicer). On top of this runtime, we introduce MEDFLOWBENCH, a full-study medical imaging benchmark covering multi-sequence brain MRI and lung CT/PET. It systematically evaluates medical agentic capabilities across viewer-only, tool-use, and open-method tracks. Initial results reveal a critical insight: while state-of-the-art LLMs/VLMs (e.g., Gemini 3.1 Pro and GPT-5.4) can successfully navigate the viewer to solve basic study-level tasks, their performance paradoxically degrades when given access to professional support tools due to a lack of precise spatial grounding. By bridging the gap between static-image perception and interactive clinical workflows, MEDOPENCLAW and MEDFLOWBENCH establish a reproducible foundation for developing auditable, full-study medical imaging agents.

Yuyuan Liu, Yiping Ji, Anjie Le et al.

Finetuning Large Vision-Language Models with reinforcement learning has emerged as a promising approach to enhance their capability in object-level grounding. However, existing methods, mainly based on GRPO, assign rewards at the response level. Such sparse reward, often criterion-induced, leads to minimal learning signals when all candidate responses fail in challenging scenarios. In this work, we propose a group-revision optimisation paradigm that enhances learning on hard cases. It begins with a sampled initial response and generates a set of revised candidates to explore improved grounding outcomes. Inspired by reward shaping, we introduce a consolidation process that quantifies each candidate's improvement over the initial attempt and converts it into informative shaping signals. These signals are used to both refine the reward and modulate the advantage, amplifying the influence of high-quality revisions. Our method achieves consistent gains across referring and reasoning segmentation, REC, and counting benchmarks compared with prior GRPO-based models. Our code is available at https://github.com/yyliu01/GroupRevision.

Junde Wu, Huihui Fang, Fangxin Shang et al.

Clinically, the accurate annotation of lesions/tissues can significantly facilitate the disease diagnosis. For example, the segmentation of optic disc/cup (OD/OC) on fundus image would facilitate the glaucoma diagnosis, the segmentation of skin lesions on dermoscopic images is helpful to the melanoma diagnosis, etc. With the advancement of deep learning techniques, a wide range of methods proved the lesions/tissues segmentation can also facilitate the automated disease diagnosis models. However, existing methods are limited in the sense that they can only capture static regional correlations in the images. Inspired by the global and dynamic nature of Vision Transformer, in this paper, we propose Segmentation-Assisted diagnosis Transformer (SeATrans) to transfer the segmentation knowledge to the disease diagnosis network. Specifically, we first propose an asymmetric multi-scale interaction strategy to correlate each single low-level diagnosis feature with multi-scale segmentation features. Then, an effective strategy called SeA-block is adopted to vitalize diagnosis feature via correlated segmentation features. To model the segmentation-diagnosis interaction, SeA-block first embeds the diagnosis feature based on the segmentation information via the encoder, and then transfers the embedding back to the diagnosis feature space by a decoder. Experimental results demonstrate that SeATrans surpasses a wide range of state-of-the-art (SOTA) segmentation-assisted diagnosis methods on several disease diagnosis tasks.

Junde Wu, Huihui Fang, Fangxin Shang et al.

The segmentation of optic disc(OD) and optic cup(OC) from fundus images is an important fundamental task for glaucoma diagnosis. In the clinical practice, it is often necessary to collect opinions from multiple experts to obtain the final OD/OC annotation. This clinical routine helps to mitigate the individual bias. But when data is multiply annotated, standard deep learning models will be inapplicable. In this paper, we propose a novel neural network framework to learn OD/OC segmentation from multi-rater annotations. The segmentation results are self-calibrated through the iterative optimization of multi-rater expertness estimation and calibrated OD/OC segmentation. In this way, the proposed method can realize a mutual improvement of both tasks and finally obtain a refined segmentation result. Specifically, we propose Diverging Model(DivM) and Converging Model(ConM) to process the two tasks respectively. ConM segments the raw image based on the multi-rater expertness map provided by DivM. DivM generates multi-rater expertness map from the segmentation mask provided by ConM. The experiment results show that by recurrently running ConM and DivM, the results can be self-calibrated so as to outperform a range of state-of-the-art(SOTA) multi-rater segmentation methods.

Jiazhen Pan, Che Liu, Junde Wu et al.

Reasoning is a critical frontier for advancing medical image analysis, where transparency and trustworthiness play a central role in both clinician trust and regulatory approval. Although Medical Visual Language Models (VLMs) show promise for radiological tasks, most existing VLMs merely produce final answers without revealing the underlying reasoning. To address this gap, we introduce MedVLM-R1, a medical VLM that explicitly generates natural language reasoning to enhance transparency and trustworthiness. Instead of relying on supervised fine-tuning (SFT), which often suffers from overfitting to training distributions and fails to foster genuine reasoning, MedVLM-R1 employs a reinforcement learning framework that incentivizes the model to discover human-interpretable reasoning paths without using any reasoning references. Despite limited training data (600 visual question answering samples) and model parameters (2B), MedVLM-R1 boosts accuracy from 55.11% to 78.22% across MRI, CT, and X-ray benchmarks, outperforming larger models trained on over a million samples. It also demonstrates robust domain generalization under out-of-distribution tasks. By unifying medical image analysis with explicit reasoning, MedVLM-R1 marks a pivotal step toward trustworthy and interpretable AI in clinical practice. Inference model is available at: https://huggingface.co/JZPeterPan/MedVLM-R1.

Fangxin Shang, Yehui Yang, Dalu Yang et al.

Pre-training is essential to deep learning model performance, especially in medical image analysis tasks where limited training data are available. However, existing pre-training methods are inflexible as the pre-trained weights of one model cannot be reused by other network architectures. In this paper, we propose an architecture-irrelevant hyper-initializer, which can initialize any given network architecture well after being pre-trained for only once. The proposed initializer is a hypernetwork which takes a downstream architecture as input graphs and outputs the initialization parameters of the respective architecture. We show the effectiveness and efficiency of the hyper-initializer through extensive experimental results on multiple medical imaging modalities, especially in data-limited fields. Moreover, we prove that the proposed algorithm can be reused as a favorable plug-and-play initializer for any downstream architecture and task (both classification and segmentation) of the same modality.

Jinge Wu, Hongjian Zhou, Mingde Zeng et al.

Building a deep research agent today is an exercise in glue code: the same backbone evaluated on the same benchmark can report different accuracies in different papers because harness and tool registry all differ, and integrating a new foundation model into a comparable evaluation surface costs weeks of model-specific engineering. We call this the per-paper engineering tax and release BioMedArena, an open-source toolkit that not only alleviates it but also provides an arena for fair comparison of different foundation models when evaluating them as deep-research agents. BioMedArena decouples six layers of biomedical agent evaluation -- benchmark loading, tool exposure, tool selection, execution mode, context management, and scoring -- and exposes 147 biomedical benchmarks and 75 biomedical tools across 9 functional families. Adding a new model, benchmark, or tool reduces to registering a few-line provider adapter. We further provide 6 agent harnesses with 6 context-management strategies, which provide 12 backbones with competitive research capabilities and significantly improved performance, achieving state-of-the-art (SOTA) results on 8 representative biomedical benchmarks, with an average lift of +15.03 percentage points over prior SOTA. The toolkit, configurations, and per-task traces are available at https://github.com/AI-in-Health/BioMedArena

Wenshuo Zhou, Dalu Yang, Binghong Wu et al.

Deep learning based medical imaging classification models usually suffer from the domain shift problem, where the classification performance drops when training data and real-world data differ in imaging equipment manufacturer, image acquisition protocol, patient populations, etc. We propose Feature Centroid Contrast Learning (FCCL), which can improve target domain classification performance by extra supervision during training with contrastive loss between instance and class centroid. Compared with current unsupervised domain adaptation and domain generalization methods, FCCL performs better while only requires labeled image data from a single source domain and no target domain. We verify through extensive experiments that FCCL can achieve superior performance on at least three imaging modalities, i.e. fundus photographs, dermatoscopic images, and H & E tissue images.

Junde Wu, Jiayuan Zhu, Yuyuan Liu et al.

We introduce Agentic Reasoning, a framework that enhances large language model (LLM) reasoning by integrating external tool-using agents. Agentic Reasoning dynamically leverages web search, code execution, and structured memory to address complex problems requiring deep research. A key innovation in our framework is the Mind-Map agent, which constructs a structured knowledge graph to store reasoning context and track logical relationships, ensuring coherence in long reasoning chains with extensive tool usage. Additionally, we conduct a comprehensive exploration of the Web-Search agent, leading to a highly effective search mechanism that surpasses all prior approaches. When deployed on DeepSeek-R1, our method achieves a new state-of-the-art (SOTA) among public models and delivers performance comparable to OpenAI Deep Research, the leading proprietary model in this domain. Extensive ablation studies validate the optimal selection of agentic tools and confirm the effectiveness of our Mind-Map and Web-Search agents in enhancing LLM reasoning. The code is at: https://github.com/theworldofagents/Agentic-Reasoning

Junde Wu, Yu Zhang, Rao Fu et al.

Open checkout-free grocery is the grocery store where the customers never have to wait in line to check out. Developing a system like this is not trivial since it faces challenges of recognizing the dynamic and massive flow of people. In particular, a clustering method that can efficiently assign each snapshot to the corresponding customer is essential for the system. In order to address the unique challenges in the open checkout-free grocery, we propose an efficient and effective person clustering method. Specifically, we first propose a Crowded Sub-Graph (CSG) to localize the relationship among massive and continuous data streams. CSG is constructed by the proposed Pick-Link-Weight (PLW) strategy, which \textbf{picks} the nodes based on time-space information, \textbf{links} the nodes via trajectory information, and \textbf{weighs} the links by the proposed von Mises-Fisher (vMF) similarity metric. Then, to ensure that the method adapts to the dynamic and unseen person flow, we propose Graph Convolutional Network (GCN) with a simple Nearest Neighbor (NN) strategy to accurately cluster the instances of CSG. GCN is adopted to project the features into low-dimensional separable space, and NN is able to quickly produce a result in this space upon dynamic person flow. The experimental results show that the proposed method outperforms other alternative algorithms in this scenario. In practice, the whole system has been implemented and deployed in several real-world open checkout-free groceries.

Jiayuan Zhu, Junde Wu

Although segmenting natural images has shown impressive performance, these techniques cannot be directly applied to medical image segmentation. Medical image segmentation is particularly complicated by inherent uncertainties. For instance, the ambiguous boundaries of tissues can lead to diverse but plausible annotations from different clinicians. These uncertainties cause significant discrepancies in clinical interpretations and impact subsequent medical interventions. Therefore, achieving quantitative segmentations from uncertain medical images becomes crucial in clinical practice. To address this, we propose a novel approach that integrates an \textbf{uncertainty-aware model} with \textbf{human-in-the-loop interaction}. The uncertainty-aware model proposes several plausible segmentations to address the uncertainties inherent in medical images, while the human-in-the-loop interaction iteratively modifies the segmentation under clinician supervision. This collaborative model ensures that segmentation is not solely dependent on automated techniques but is also refined through clinician expertise. As a result, our approach represents a significant advancement in the field which enhances the safety of medical image segmentation. It not only offers a comprehensive solution to produce quantitative segmentation from inherent uncertain medical images, but also establishes a synergistic balance between algorithmic precision and clincian knowledge. We evaluated our method on various publicly available multi-clinician annotated datasets: REFUGE2, LIDC-IDRI and QUBIQ. Our method showcases superior segmentation capabilities, outperforming a wide range of deterministic and uncertainty-aware models. We also demonstrated that our model produced significantly better results with fewer interactions compared to previous interactive models. We will release the code to foster further research in this area.

Ziyue Wang, Junde Wu, Linghan Cai et al.

In modern medicine, clinical diagnosis relies on the comprehensive analysis of primarily textual and visual data, drawing on medical expertise to ensure systematic and rigorous reasoning. Recent advances in large Vision-Language Models (VLMs) and agent-based methods hold great potential for medical diagnosis, thanks to the ability to effectively integrate multi-modal patient data. However, they often provide direct answers and draw empirical-driven conclusions without quantitative analysis, which reduces their reliability and clinical usability. We propose MedAgent-Pro, a new agentic reasoning paradigm that follows the diagnosis principle in modern medicine, to decouple the process into sequential components for step-by-step, evidence-based reasoning. Our MedAgent-Pro workflow presents a hierarchical diagnostic structure to mirror this principle, consisting of disease-level standardized plan generation and patient-level personalized step-by-step reasoning. To support disease-level planning, an RAG-based agent is designed to retrieve medical guidelines to ensure alignment with clinical standards. For patient-level reasoning, we propose to integrate professional tools such as visual models to enable quantitative assessments. Meanwhile, we propose to verify the reliability of each step to achieve evidence-based diagnosis, enforcing rigorous logical reasoning and a well-founded conclusion. Extensive experiments across a wide range of anatomical regions, imaging modalities, and diseases demonstrate the superiority of MedAgent-Pro to mainstream VLMs, agentic systems and state-of-the-art expert models. Ablation studies and human evaluation by clinical experts further validate its robustness and clinical relevance. Code is available at https://github.com/jinlab-imvr/MedAgent-Pro.

Haofeng Liu, Mingqi Gao, Xuxiao Luo et al.

Surgical scene segmentation is critical in computer-assisted surgery and is vital for enhancing surgical quality and patient outcomes. Recently, referring surgical segmentation is emerging, given its advantage of providing surgeons with an interactive experience to segment the target object. However, existing methods are limited by low efficiency and short-term tracking, hindering their applicability in complex real-world surgical scenarios. In this paper, we introduce ReSurgSAM2, a two-stage surgical referring segmentation framework that leverages Segment Anything Model 2 to perform text-referred target detection, followed by tracking with reliable initial frame identification and diversity-driven long-term memory. For the detection stage, we propose a cross-modal spatial-temporal Mamba to generate precise detection and segmentation results. Based on these results, our credible initial frame selection strategy identifies the reliable frame for the subsequent tracking. Upon selecting the initial frame, our method transitions to the tracking stage, where it incorporates a diversity-driven memory mechanism that maintains a credible and diverse memory bank, ensuring consistent long-term tracking. Extensive experiments demonstrate that ReSurgSAM2 achieves substantial improvements in accuracy and efficiency compared to existing methods, operating in real-time at 61.2 FPS. Our code and datasets will be available at https://github.com/jinlab-imvr/ReSurgSAM2.

Jiazhen Pan, Bailiang Jian, Paul Hager et al.

Ensuring the safety and reliability of large language models (LLMs) in clinical practice is critical to prevent patient harm and promote trustworthy healthcare applications of AI. However, LLMs are advancing so rapidly that static safety benchmarks often become obsolete upon publication, yielding only an incomplete and sometimes misleading picture of model trustworthiness. We demonstrate that a Dynamic, Automatic, and Systematic (DAS) red-teaming framework that continuously stress-tests LLMs can reveal significant weaknesses of current LLMs across four safety-critical domains: robustness, privacy, bias/fairness, and hallucination. A suite of adversarial agents is applied to autonomously mutate test cases, identify/evolve unsafe-triggering strategies, and evaluate responses, uncovering vulnerabilities in real time without human intervention. Applying DAS to 15 proprietary and open-source LLMs revealed a stark contrast between static benchmark performance and vulnerability under adversarial pressure. Despite a median MedQA accuracy exceeding 80\%, 94\% of previously correct answers failed our dynamic robustness tests. We observed similarly high failure rates across other domains: privacy leaks were elicited in 86\% of scenarios, cognitive-bias priming altered clinical recommendations in 81\% of fairness tests, and we identified hallucination rates exceeding 66\% in widely used models. Such profound residual risks are incompatible with routine clinical practice. By converting red-teaming from a static checklist into a dynamic stress-test audit, DAS red-teaming offers the surveillance that hospitals/regulators/technology vendors require as LLMs become embedded in patient chatbots, decision-support dashboards, and broader healthcare workflows. Our framework delivers an evolvable, scalable, and reliable safeguard for the next generation of medical AI.

Zhicheng He, Yunpeng Zhao, Junde Wu et al.

Medical image generation is pivotal in applications like data augmentation for low-resource clinical tasks and privacy-preserving data sharing. However, developing a scalable generative backbone for medical imaging requires architectural efficiency, sufficient multi-organ data, and principled evaluation, yet current approaches leave these aspects unresolved. Therefore, we introduce MedVAR, the first autoregressive-based foundation model that adopts the next-scale prediction paradigm to enable fast and scale-up-friendly medical image synthesis. MedVAR generates images in a coarse-to-fine manner and produces structured multi-scale representations suitable for downstream use. To support hierarchical generation, we curate a harmonized dataset of around 440,000 CT and MRI images spanning six anatomical regions. Comprehensive experiments across fidelity, diversity, and scalability show that MedVAR achieves state-of-the-art generative performance and offers a promising architectural direction for future medical generative foundation models.

Ziyue Wang, Linghan Cai, Chang Han Low et al.

3D CT analysis spans a continuum from low-level perception to high-level clinical understanding. Existing 3D-oriented analysis methods adopt either isolated task-specific modeling or task-agnostic end-to-end paradigms to produce one-hop outputs, impeding the systematic accumulation of perceptual evidence for downstream reasoning. In parallel, recent multimodal large language models (MLLMs) exhibit improved visual perception and can integrate visual and textual information effectively, yet their predominantly 2D-oriented designs fundamentally limit their ability to perceive and analyze volumetric medical data. To bridge this gap, we propose 3DMedAgent, a unified agent that enables 2D MLLMs to perform general 3D CT analysis without 3D-specific fine-tuning. 3DMedAgent coordinates heterogeneous visual and textual tools through a flexible MLLM agent, progressively decomposing complex 3D analysis into tractable subtasks that transition from global to regional views, from 3D volumes to informative 2D slices, and from visual evidence to structured textual representations. Central to this design, 3DMedAgent maintains a long-term structured memory that aggregates intermediate tool outputs and supports query-adaptive, evidence-driven multi-step reasoning. We further introduce the DeepChestVQA benchmark for evaluating unified perception-to-understanding capabilities in 3D thoracic imaging. Experiments across over 40 tasks demonstrate that 3DMedAgent consistently outperforms general, medical, and 3D-specific MLLMs, highlighting a scalable path toward general-purpose 3D clinical assistants.Code and data are available at \href{https://github.com/jinlab-imvr/3DMedAgent}{https://github.com/jinlab-imvr/3DMedAgent}.

Zeyu Chen, Junde Wu

Affine automata provide a finite-state computational model that preserves the linear-algebraic structure of quantum computation while operating entirely over the reals. Recent work has shown that affine automata can far surpass classical probabilistic finite-state verifiers. However, prior constructions relied on arbitrary real-valued transition matrices, leaving open whether the observed power stems from the affine mechanism itself or from computational resources implicitly encoded in irrational or infinite-precision parameters. This paper studies one-way and two-way automata with deterministic and affine states as verifiers in Arthur--Merlin proof systems under the restriction that every affine transition matrix has rational entries, and shows that the resulting rational model still supports the main verification advantages of affine finite-state verification. At the one-way level, we verify benchmark nonregular languages that are provably hard or impossible for classical two-way probabilistic verifiers. At the two-way level, we achieve weak verification of every Turing-recognizable language, strong bounded-error verification for every language in $\mathbf{ATIME}(2^{O(n)})$, and perfect-completeness strong verification for every language in $\mathbf{PSPACE}$. These results establish that the remarkable verification power of affine finite-state automata is structural.

Zeyu Chen, Junde Wu

This paper identifies exact probabilistic simulation cost as the natural quantitative measure of quantum advantage for finite automata under strict cutpoints. It gives sharp simulation laws for two representative models. A one-way finite automaton with $c$ classical states and a $q$-dimensional quantum register has exact probabilistic simulation cost $Θ(cq^2)$, while an $n$-dimensional measure-once one-way quantum finite automaton has worst-case cost $Θ(n^2)$. The proofs develop a prepare--test framework, in which prefixes generate the relevant real operator degrees of freedom and suffixes convert them into strict-cutpoint tests. The same obstruction is recast through finite sign-rank matrices, clarifying the role of Forster's spectral method. Placed beside the surrounding two-way separations, these results give a clean hierarchy of finite-automata quantum advantage.

Yuyuan Liu, Yuanhong Chen, Chong Wang et al.

Segment Anything Model 2 (SAM2) exhibits strong generalisation for promptable segmentation in video clips; however, its integration with the audio modality remains underexplored. Existing approaches mainly follow two directions: (1) injecting adapters into the image encoder to receive audio signals, which incurs efficiency costs during prompt engineering, and (2) leveraging additional foundation models to generate visual prompts for the sounding objects, which are often imprecisely localised, leading to misguidance in SAM2. Moreover, these methods overlook the rich semantic interplay between hierarchical visual features and other modalities, resulting in suboptimal cross-modal fusion. In this work, we propose AuralSAM2, comprising the novel AuralFuser module, which externally attaches to SAM2 to integrate features from different modalities and generate feature-level prompts, guiding SAM2's decoder in segmenting sounding targets. Such integration is facilitated by a feature pyramid, further refining semantic understanding and enhancing object awareness in multimodal scenarios. Additionally, the audio-guided contrastive learning is introduced to explicitly align audio and visual representations and to also mitigate biases caused by dominant visual patterns. Results on public benchmarks show that our approach achieves remarkable improvements over the previous methods in the field. Code is available at https://github.com/yyliu01/AuralSAM2.

Junde Wu, Jiayuan Zhu, Yueming Jin et al.

Large foundation models, known for their strong zero-shot generalization, have excelled in visual and language applications. However, applying them to medical image segmentation, a domain with diverse imaging types and target labels, remains an open challenge. Current approaches, such as adapting interactive segmentation models like Segment Anything Model (SAM), require user prompts for each sample during inference. Alternatively, transfer learning methods like few/one-shot models demand labeled samples, leading to high costs. This paper introduces a new paradigm toward the universal medical image segmentation, termed 'One-Prompt Segmentation.' One-Prompt Segmentation combines the strengths of one-shot and interactive methods. In the inference stage, with just \textbf{one prompted sample}, it can adeptly handle the unseen task in a single forward pass. We train One-Prompt Model on 64 open-source medical datasets, accompanied by the collection of over 3,000 clinician-labeled prompts. Tested on 14 previously unseen datasets, the One-Prompt Model showcases superior zero-shot segmentation capabilities, outperforming a wide range of related methods. The code and data is released as https://github.com/KidsWithTokens/one-prompt.

Huihui Fang, Fei Li, Junde Wu et al.

With the rapid development of artificial intelligence (AI) in medical image processing, deep learning in color fundus photography (CFP) analysis is also evolving. Although there are some open-source, labeled datasets of CFPs in the ophthalmology community, large-scale datasets for screening only have labels of disease categories, and datasets with annotations of fundus structures are usually small in size. In addition, labeling standards are not uniform across datasets, and there is no clear information on the acquisition device. Here we release a multi-annotation, multi-quality, and multi-device color fundus image dataset for glaucoma analysis on an original challenge -- Retinal Fundus Glaucoma Challenge 2nd Edition (REFUGE2). The REFUGE2 dataset contains 2000 color fundus images with annotations of glaucoma classification, optic disc/cup segmentation, as well as fovea localization. Meanwhile, the REFUGE2 challenge sets three sub-tasks of automatic glaucoma diagnosis and fundus structure analysis and provides an online evaluation framework. Based on the characteristics of multi-device and multi-quality data, some methods with strong generalizations are provided in the challenge to make the predictions more robust. This shows that REFUGE2 brings attention to the characteristics of real-world multi-domain data, bridging the gap between scientific research and clinical application.

Zeyu Chen, Junde Wu

A basic question in the theory of two-state measure-once quantum finite automata (MO-QFAs) is whether two distinct input words can be separated with certainty. In the setting considered here, this exact separation problem reduces to a trace-vanishing question in \(SU(2)\): given distinct positive words \(u\) and \(v\), find matrices \(A,B\in SU(2)\) such that the evaluated trace of \(u^{-1}v\) is zero. The central difficulty lies in the genuinely nonabelian regime where \(u\) and \(v\) have the same abelianization, so the obvious commutative information disappears and the fine structure of the word must be connected to the geometry of representations. This paper develops a slice-driven framework for that task and proves exact separation for every hard positive-word difference covered by four explicit certified conditions, thereby reducing the problem to a sharply delimited residual super-degenerate class. The method extracts algebraic data from the positive-word difference and uses them to select explicit low-dimensional families in \(SU(2)^2\) on which the trace becomes computable. On the algebraic side, the metabelian polynomial is decomposed into explicit interval blocks determined by prefix statistics, and a suitable slope specialization preserves nontrivial information. On the analytic side, the paper derives a computable quadratic trace identity on a visible one-parameter family and complements it with a Laurent-matrix sum-of-squares identity in a parallel algebraic model. These certified criteria are already strong in numerical experiments. This paper also shows that no method based only on finitely many finite-image tests can be universal.

Jiayuan Zhu, Jiazhen Pan, Yuyuan Liu et al.

The severe shortage of medical doctors limits access to timely and reliable healthcare, leaving millions underserved. Large language models (LLMs) offer a potential solution but struggle in real-world clinical interactions. Many LLMs are not grounded in authoritative medical guidelines and fail to transparently manage diagnostic uncertainty. Their language is often rigid and mechanical, lacking the human-like qualities essential for patient trust. To address these challenges, we propose Ask Patients with Patience (APP), a multi-turn LLM-based medical assistant designed for grounded reasoning, transparent diagnoses, and human-centric interaction. APP enhances communication by eliciting user symptoms through empathetic dialogue, significantly improving accessibility and user engagement. It also incorporates Bayesian active learning to support transparent and adaptive diagnoses. The framework is built on verified medical guidelines, ensuring clinically grounded and evidence-based reasoning. To evaluate its performance, we develop a new benchmark that simulates realistic medical conversations using patient agents driven by profiles extracted from real-world consultation cases. We compare APP against SOTA one-shot and multi-turn LLM baselines. The results show that APP improves diagnostic accuracy, reduces uncertainty, and enhances user experience. By integrating medical expertise with transparent, human-like interaction, APP bridges the gap between AI-driven medical assistance and real-world clinical practice.

Zhitao Zeng, Zhu Zhuo, Xiaojun Jia et al. · pku

Foundation models have achieved transformative success across biomedical domains by enabling holistic understanding of multimodal data. However, their application in surgery remains underexplored. Surgical intelligence presents unique challenges - requiring surgical visual perception, temporal analysis, and reasoning. Existing general-purpose vision-language models fail to address these needs due to insufficient domain-specific supervision and the lack of a large-scale high-quality surgical database. To bridge this gap, we propose SurgVLM, one of the first large vision-language foundation models for surgical intelligence, where this single universal model can tackle versatile surgical tasks. To enable this, we construct a large-scale multimodal surgical database, SurgVLM-DB, comprising over 1.81 million frames with 7.79 million conversations, spanning more than 16 surgical types and 18 anatomical structures. We unify and reorganize 23 public datasets across 10 surgical tasks, followed by standardizing labels and doing hierarchical vision-language alignment to facilitate comprehensive coverage of gradually finer-grained surgical tasks, from visual perception, temporal analysis, to high-level reasoning. Building upon this comprehensive dataset, we propose SurgVLM, which is built upon Qwen2.5-VL, and undergoes instruction tuning to 10+ surgical tasks. We further construct a surgical multimodal benchmark, SurgVLM-Bench, for method evaluation. SurgVLM-Bench consists of 6 popular and widely-used datasets in surgical domain, covering several crucial downstream tasks. Based on SurgVLM-Bench, we evaluate the performance of our SurgVLM (3 SurgVLM variants: SurgVLM-7B, SurgVLM-32B, and SurgVLM-72B), and conduct comprehensive comparisons with 14 mainstream commercial VLMs (e.g., GPT-4o, Gemini 2.0 Flash, Qwen2.5-Max).

Mingzhou Jiang, Jiaying Zhou, Junde Wu et al.

Collective intelligence from multiple medical experts consistently surpasses individual expertise in clinical diagnosis, particularly for ambiguous medical image segmentation tasks involving unclear tissue boundaries or pathological variations. The Segment Anything Model (SAM), a powerful vision foundation model originally designed for natural image segmentation, has shown remarkable potential when adapted to medical image segmentation tasks. However, existing SAM adaptation methods follow a single-expert paradigm, developing models based on individual expert annotations to predict deterministic masks. These methods systematically ignore the inherent uncertainty and variability in expert annotations, which fundamentally contradicts clinical practice, where multiple specialists provide different yet equally valid interpretations that collectively enhance diagnostic confidence. We propose an Uncertainty-aware Adapter, the first SAM adaptation framework designed to transition from single expert mindset to collective intelligence representation. Our approach integrates stochastic uncertainty sampling from a Conditional Variational Autoencoder into the adapters, enabling diverse prediction generation that captures expert knowledge distributions rather than individual expert annotations. We employ a novel position-conditioned control mechanism to integrate multi-expert knowledge, ensuring that the output distribution closely aligns with the multi-annotation distribution. Comprehensive evaluations across seven medical segmentation benchmarks have demonstrated that our collective intelligence-based adaptation achieves superior performance while maintaining computational efficiency, establishing a new adaptation framework for reliable clinical implementation.

Zeyu Chen, Junde Wu

Generalized finite automata (GFAs), probabilistic finite automata (PFAs), and one-way general quantum finite automata (1gQFA) recognize the same strict-cutpoint languages, but the state complexity of exact probabilistic simulation has remained unclear. This paper determines that worst-case cost exactly: every \(n\)-state 1gQFA admits exact strict-cutpoint simulation by a one-way PFA with \(O(n^2)\) states, via the standard \(n^2\)-dimensional mixed-state linearization together with an explicit alphabet-preserving construction that converts each \(k\)-state GFA into a one-way PFA with at most \(2k+6\) states; conversely, for every \(n\ge 2\), there exists an \(n\)-state 1gQFA for which every equivalent one-way PFA requires at least \(n^2-1\) states, obtained from a prepare--test construction and a Vapnik--Chervonenkis dimension argument. Hence the worst-case probabilistic state cost of exact strict-cutpoint simulation is \(Θ(n^2)\).

Jared Zhu, Minhao Hu, Junde Wu

Large language models are increasingly used as programming agents for repository level software engineering tasks. While recent benchmarks evaluate correctness in realistic codebases, they largely treat tasks as independent and do not assess whether agents can reuse experience across related problems. As a result, the ability of agents to accumulate, retrieve, and apply prior experience, as well as the efficiency gains from such reuse, remains difficult to measure. We introduce SWE-ContextBench, a benchmark designed to explicitly evaluate experience reuse in programming agents. Built on SWE-Bench Lite, SWE-ContextBench augments 300 base tasks with 99 related tasks derived from real dependency and reference relationships among GitHub issues and pull requests, forming task sequences with shared context. The benchmark evaluates agents along three complementary dimensions: prediction accuracy, time efficiency, and cost efficiency. Using SWE-ContextBench, we study multiple experience reuse settings, including oracle guided and autonomous retrieval, as well as full execution trajectories and compact summaries. Our results show that correctly selected summarized experience improves resolution accuracy and substantially reduces runtime and token cost, particularly on harder tasks. In contrast, unfiltered or incorrectly selected experience provides limited or negative benefits. These findings highlight the importance of experience representation and retrieval quality, and position SWE-ContextBench as a principled benchmark for studying experience reuse in programming agents.

Guanyi Qin, Ziyue Wang, Daiyun Shen et al.

Given an object mask, Semi-supervised Video Object Segmentation (SVOS) technique aims to track and segment the object across video frames, serving as a fundamental task in computer vision. Although recent memory-based methods demonstrate potential, they often struggle with scenes involving occlusion, particularly in handling object interactions and high feature similarity. To address these issues and meet the real-time processing requirements of downstream applications, in this paper, we propose a novel bOundary Amendment video object Segmentation method with Inherent Structure refinement, hereby named OASIS. Specifically, a lightweight structure refinement module is proposed to enhance segmentation accuracy. With the fusion of rough edge priors captured by the Canny filter and stored object features, the module can generate an object-level structure map and refine the representations by highlighting boundary features. Evidential learning for uncertainty estimation is introduced to further address challenges in occluded regions. The proposed method, OASIS, maintains an efficient design, yet extensive experiments on challenging benchmarks demonstrate its superior performance and competitive inference speed compared to other state-of-the-art methods, i.e., achieving the F values of 91.6 (vs. 89.7 on DAVIS-17 validation set) and G values of 86.6 (vs. 86.2 on YouTubeVOS 2019 validation set) while maintaining a competitive speed of 48 FPS on DAVIS.

Jiayuan Zhu, Junde Wu, Cheng Ouyang et al.

Medical image segmentation data inherently contain uncertainty. This can stem from both imperfect image quality and variability in labeling preferences on ambiguous pixels, which depend on annotator expertise and the clinical context of the annotations. For instance, a boundary pixel might be labeled as tumor in diagnosis to avoid under-estimation of severity, but as normal tissue in radiotherapy to prevent damage to sensitive structures. As segmentation preferences vary across downstream applications, it is often desirable for an image segmentation model to offer user-adaptable predictions rather than a fixed output. While prior uncertainty-aware and interactive methods offer adaptability, they are inefficient at test time: uncertainty-aware models require users to choose from numerous similar outputs, while interactive models demand significant user input through click or box prompts to refine segmentation. To address these challenges, we propose \textbf{SPA}, a new \textbf{S}egmentation \textbf{P}reference \textbf{A}lignment framework that efficiently adapts to diverse test-time preferences with minimal human interaction. By presenting users with a select few, distinct segmentation candidates that best capture uncertainties, it reduces the user workload to reach the preferred segmentation. To accommodate user preference, we introduce a probabilistic mechanism that leverages user feedback to adapt a model's segmentation preference. The proposed framework is evaluated on several medical image segmentation tasks: color fundus images, lung lesion and kidney CT scans, MRI scans of brain and prostate. SPA shows 1) a significant reduction in user time and effort compared to existing interactive segmentation approaches, 2) strong adaptability based on human feedback, and 3) state-of-the-art image segmentation performance across different imaging modalities and semantic labels.

Jared Zhu, Junde Wu

Decades' advances in digital health technologies, such as electronic health records, have largely streamlined routine clinical processes. Yet, most these systems are still hard to learn and use: Clinicians often face the burden of managing multiple tools, repeating manual actions for each patient, navigating complicated UI trees to locate functions, and spending significant time on administration instead of caring for patients. The recent rise of large language model (LLM) based agents demonstrates exceptional capability in coding and computer operation, revealing the potential for humans to interact with operating systems and software not by direct manipulation, but by instructing agents through natural language. This shift highlights the need for an abstraction layer, an agent-computer interface, that translates human language into machine-executable commands. In digital healthcare, however, requires a more domain-specific abstractions that strictly follow trusted clinical guidelines and procedural standards to ensure safety, transparency, and compliance. To address this need, we present \textbf{MedicalOS}, a unified agent-based operational system designed as such a domain-specific abstract layer for healthcare. It translates human instructions into pre-defined digital healthcare commands, such as patient inquiry, history retrieval, exam management, report generation, referrals, treatment planning, that we wrapped as off-the-shelf tools using machine languages (e.g., Python, APIs, MCP, Linux). We empirically validate MedicalOS on 214 patient cases across 22 specialties, demonstrating high diagnostic accuracy and confidence, clinically sound examination requests, and consistent generation of structured reports and medication recommendations. These results highlight MedicalOS as a trustworthy and scalable foundation for advancing workflow automation in clinical practice.

Jiaying Zhou, Mingzhou Jiang, Junde Wu et al.

Medicine is inherently a multimodal discipline. Medical images can reflect the pathological changes of cancer and tumors, while the expression of specific genes can influence their morphological characteristics. However, most deep learning models employed for these medical tasks are unimodal, making predictions using either image data or genomic data exclusively. In this paper, we propose a multimodal pre-training framework that jointly incorporates genomics and medical images for downstream tasks. To address the issues of high computational complexity and difficulty in capturing long-range dependencies in genes sequence modeling with MLP or Transformer architectures, we utilize Mamba to model these long genomic sequences. We aligns medical images and genes using a self-supervised contrastive learning approach which combines the Mamba as a genetic encoder and the Vision Transformer (ViT) as a medical image encoder. We pre-trained on the TCGA dataset using paired gene expression data and imaging data, and fine-tuned it for downstream tumor segmentation tasks. The results show that our model outperformed a wide range of related methods.

Junde Wu, Jiayuan Zhu, Min Xu et al.

Some visual recognition tasks are more challenging then the general ones as they require professional categories of images. The previous efforts, like fine-grained vision classification, primarily introduced models tailored to specific tasks, like identifying bird species or car brands with limited scalability and generalizability. This paper aims to design a scalable and explainable model to solve Professional Visual Recognition tasks from a generic standpoint. We introduce a biologically-inspired structure named Pro-NeXt and reveal that Pro-NeXt exhibits substantial generalizability across diverse professional fields such as fashion, medicine, and art-areas previously considered disparate. Our basic-sized Pro-NeXt-B surpasses all preceding task-specific models across 12 distinct datasets within 5 diverse domains. Furthermore, we find its good scaling property that scaling up Pro-NeXt in depth and width with increasing GFlops can consistently enhances its accuracy. Beyond scalability and adaptability, the intermediate features of Pro-NeXt achieve reliable object detection and segmentation performance without extra training, highlighting its solid explainability. We will release the code to foster further research in this area.

Huihui Fang, Fei Li, Junde Wu et al.

Pathologic myopia (PM) is a common blinding retinal degeneration suffered by highly myopic population. Early screening of this condition can reduce the damage caused by the associated fundus lesions and therefore prevent vision loss. Automated diagnostic tools based on artificial intelligence methods can benefit this process by aiding clinicians to identify disease signs or to screen mass populations using color fundus photographs as inputs. This paper provides insights about PALM, our open fundus imaging dataset for pathological myopia recognition and anatomical structure annotation. Our databases comprises 1200 images with associated labels for the pathologic myopia category and manual annotations of the optic disc, the position of the fovea and delineations of lesions such as patchy retinal atrophy (including peripapillary atrophy) and retinal detachment. In addition, this paper elaborates on other details such as the labeling process used to construct the database, the quality and characteristics of the samples and provides other relevant usage notes.

Junde Wu, Huihui Fang, Fei Li et al.

Color fundus photography and Optical Coherence Tomography (OCT) are the two most cost-effective tools for glaucoma screening. Both two modalities of images have prominent biomarkers to indicate glaucoma suspected. Clinically, it is often recommended to take both of the screenings for a more accurate and reliable diagnosis. However, although numerous algorithms are proposed based on fundus images or OCT volumes in computer-aided diagnosis, there are still few methods leveraging both of the modalities for the glaucoma assessment. Inspired by the success of Retinal Fundus Glaucoma Challenge (REFUGE) we held previously, we set up the Glaucoma grAding from Multi-Modality imAges (GAMMA) Challenge to encourage the development of fundus \& OCT-based glaucoma grading. The primary task of the challenge is to grade glaucoma from both the 2D fundus images and 3D OCT scanning volumes. As part of GAMMA, we have publicly released a glaucoma annotated dataset with both 2D fundus color photography and 3D OCT volumes, which is the first multi-modality dataset for glaucoma grading. In addition, an evaluation framework is also established to evaluate the performance of the submitted methods. During the challenge, 1272 results were submitted, and finally, top-10 teams were selected to the final stage. We analysis their results and summarize their methods in the paper. Since all these teams submitted their source code in the challenge, a detailed ablation study is also conducted to verify the effectiveness of the particular modules proposed. We find many of the proposed techniques are practical for the clinical diagnosis of glaucoma. As the first in-depth study of fundus \& OCT multi-modality glaucoma grading, we believe the GAMMA Challenge will be an essential starting point for future research.

Junde Wu, Huihui Fang, Dalu Yang et al.

With the advancement of deep learning techniques, an increasing number of methods have been proposed for optic disc and cup (OD/OC) segmentation from the fundus images. Clinically, OD/OC segmentation is often annotated by multiple clinical experts to mitigate the personal bias. However, it is hard to train the automated deep learning models on multiple labels. A common practice to tackle the issue is majority vote, e.g., taking the average of multiple labels. However such a strategy ignores the different expertness of medical experts. Motivated by the observation that OD/OC segmentation is often used for the glaucoma diagnosis clinically, in this paper, we propose a novel strategy to fuse the multi-rater OD/OC segmentation labels via the glaucoma diagnosis performance. Specifically, we assess the expertness of each rater through an attentive glaucoma diagnosis network. For each rater, its contribution for the diagnosis will be reflected as an expertness map. To ensure the expertness maps are general for different glaucoma diagnosis models, we further propose an Expertness Generator (ExpG) to eliminate the high-frequency components in the optimization process. Based on the obtained expertness maps, the multi-rater labels can be fused as a single ground-truth which we dubbed as Diagnosis First Ground-truth (DiagFirstGT). Experimental results show that by using DiagFirstGT as ground-truth, OD/OC segmentation networks will predict the masks with superior glaucoma diagnosis performance.

Binghong Wu, Yehui Yang, Dalu Yang et al.

In object detection, multi-level prediction (e.g., FPN) and reweighting skills (e.g., focal loss) have drastically improved one-stage detector performance. However, the synergy between these two techniques is not fully explored in a unified framework. We find that, during training, the one-stage detector's optimization is not only restricted to the static hard-case mining loss (gradient drift) but also suffered from the diverse positive samples' proportions split by different pyramid levels (level discrepancy). Under this concern, we propose Hierarchical Progressive Focus (HPF) consisting of two key designs: 1) progressive focus, a more flexible hard-case mining setting calculated adaptive to the convergence progress, 2) hierarchical sampling, automatically generating a set of progressive focus for level-specific target optimization. Based on focal loss with ATSS-R50, our approach achieves 40.5 AP, surpassing the state-of-the-art QFL (Quality Focal Loss, 39.9 AP) and VFL (Varifocal Loss, 40.1 AP). Our best model achieves 55.1 AP on COCO test-dev, obtaining excellent results with only a typical training setting. Moreover, as a plug-and-play scheme, HPF can cooperate well with recent advances, providing a stable performance improvement on nine mainstream detectors.

Wenting Chen, Shuang Yu, Junde Wu et al.

Retinal artery/vein (A/V) classification lays the foundation for the quantitative analysis of retinal vessels, which is associated with potential risks of various cardiovascular and cerebral diseases. The topological connection relationship, which has been proved effective in improving the A/V classification performance for the conventional graph based method, has not been exploited by the deep learning based method. In this paper, we propose a Topology Ranking Generative Adversarial Network (TR-GAN) to improve the topology connectivity of the segmented arteries and veins, and further to boost the A/V classification performance. A topology ranking discriminator based on ordinal regression is proposed to rank the topological connectivity level of the ground-truth, the generated A/V mask and the intentionally shuffled mask. The ranking loss is further back-propagated to the generator to generate better connected A/V masks. In addition, a topology preserving module with triplet loss is also proposed to extract the high-level topological features and further to narrow the feature distance between the predicted A/V mask and the ground-truth. The proposed framework effectively increases the topological connectivity of the predicted A/V masks and achieves state-of-the-art A/V classification performance on the publicly available AV-DRIVE dataset.

Junde Wu, Shuang Yu, Wenting Chen et al.

Recently, deep learning has been adopted to the glaucoma classification task with performance comparable to that of human experts. However, a well trained deep learning model demands a large quantity of properly labeled data, which is relatively expensive since the accurate labeling of glaucoma requires years of specialist training. In order to alleviate this problem, we propose a glaucoma classification framework which takes advantage of not only the properly labeled images, but also undiagnosed images without glaucoma labels. To be more specific, the proposed framework is adapted from the teacher-student-learning paradigm. The teacher model encodes the wrapped information of undiagnosed images to a latent feature space, meanwhile the student model learns from the teacher through knowledge transfer to improve the glaucoma classification. For the model training procedure, we propose a novel training strategy that simulates the real-world teaching practice named as 'Learning To Teach with Knowledge Transfer (L2T-KT)', and establish a 'Quiz Pool' as the teacher's optimization target. Experiments show that the proposed framework is able to utilize the undiagnosed data effectively to improve the glaucoma prediction performance.