Daily Papers

Multi-modal interpretation of biomedical images opens up novel opportunities in biomedical image analysis. Conventional AI approaches typically rely on disjointed training, i.e., Large Language Models (LLMs) for clinical text generation and segmentation models for target extraction, which results in inflexible real-world deployment and a failure to leverage holistic biomedical information. To this end, we introduce UniBiomed, the first universal foundation model for grounded biomedical image interpretation. UniBiomed is based on a novel integration of Multi-modal Large Language Model (MLLM) and Segment Anything Model (SAM), which effectively unifies the generation of clinical texts and the segmentation of corresponding biomedical objects for grounded interpretation. In this way, UniBiomed is capable of tackling a wide range of biomedical tasks across ten diverse biomedical imaging modalities. To develop UniBiomed, we curate a large-scale dataset comprising over 27 million triplets of images, annotations, and text descriptions across ten imaging modalities. Extensive validation on 84 internal and external datasets demonstrated that UniBiomed achieves state-of-the-art performance in segmentation, disease recognition, region-aware diagnosis, visual question answering, and report generation. Moreover, unlike previous models that rely on clinical experts to pre-diagnose images and manually craft precise textual or visual prompts, UniBiomed can provide automated and end-to-end grounded interpretation for biomedical image analysis. This represents a novel paradigm shift in clinical workflows, which will significantly improve diagnostic efficiency. In summary, UniBiomed represents a novel breakthrough in biomedical AI, unlocking powerful grounded interpretation capabilities for more accurate and efficient biomedical image analysis.

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

Radiology reporting generative AI holds significant potential to alleviate clinical workloads and streamline medical care. However, achieving high clinical accuracy is challenging, as radiological images often feature subtle lesions and intricate structures. Existing systems often fall short, largely due to their reliance on fixed size, patch-level image features and insufficient incorporation of pathological information. This can result in the neglect of such subtle patterns and inconsistent descriptions of crucial pathologies. To address these challenges, we propose an innovative approach that leverages pathology-aware regional prompts to explicitly integrate anatomical and pathological information of various scales, significantly enhancing the precision and clinical relevance of generated reports. We develop an anatomical region detector that extracts features from distinct anatomical areas, coupled with a novel multi-label lesion detector that identifies global pathologies. Our approach emulates the diagnostic process of radiologists, producing clinically accurate reports with comprehensive diagnostic capabilities. Experimental results show that our model outperforms previous state-of-the-art methods on most natural language generation and clinical efficacy metrics, with formal expert evaluations affirming its potential to enhance radiology practice.

Medical imaging is widely used in clinical practice for diagnosis and treatment. Report-writing can be error-prone for unexperienced physicians, and time- consuming and tedious for experienced physicians. To address these issues, we study the automatic generation of medical imaging reports. This task presents several challenges. First, a complete report contains multiple heterogeneous forms of information, including findings and tags. Second, abnormal regions in medical images are difficult to identify. Third, the re- ports are typically long, containing multiple sentences. To cope with these challenges, we (1) build a multi-task learning framework which jointly performs the pre- diction of tags and the generation of para- graphs, (2) propose a co-attention mechanism to localize regions containing abnormalities and generate narrations for them, (3) develop a hierarchical LSTM model to generate long paragraphs. We demonstrate the effectiveness of the proposed methods on two publicly available datasets.

Automatic medical report generation (MRG) is of great research value as it has the potential to relieve radiologists from the heavy burden of report writing. Despite recent advancements, accurate MRG remains challenging due to the need for precise clinical understanding and the identification of clinical findings. Moreover, the imbalanced distribution of diseases makes the challenge even more pronounced, as rare diseases are underrepresented in training data, making their diagnostic performance unreliable. To address these challenges, we propose diagnosis-driven prompts for medical report generation (PromptMRG), a novel framework that aims to improve the diagnostic accuracy of MRG with the guidance of diagnosis-aware prompts. Specifically, PromptMRG is based on encoder-decoder architecture with an extra disease classification branch. When generating reports, the diagnostic results from the classification branch are converted into token prompts to explicitly guide the generation process. To further improve the diagnostic accuracy, we design cross-modal feature enhancement, which retrieves similar reports from the database to assist the diagnosis of a query image by leveraging the knowledge from a pre-trained CLIP. Moreover, the disease imbalanced issue is addressed by applying an adaptive logit-adjusted loss to the classification branch based on the individual learning status of each disease, which overcomes the barrier of text decoder's inability to manipulate disease distributions. Experiments on two MRG benchmarks show the effectiveness of the proposed method, where it obtains state-of-the-art clinical efficacy performance on both datasets.

Clinical diagnosis is a highly specialized discipline requiring both domain expertise and strict adherence to rigorous guidelines. While current AI-driven medical research predominantly focuses on knowledge graphs or natural text pretraining paradigms to incorporate medical knowledge, these approaches primarily rely on implicitly encoded knowledge within model parameters, neglecting task-specific knowledge required by diverse downstream tasks. To address this limitation, we propose Retrieval-Augmented Diagnosis (RAD), a novel framework that explicitly injects external knowledge into multimodal models directly on downstream tasks. Specifically, RAD operates through three key mechanisms: retrieval and refinement of disease-centered knowledge from multiple medical sources, a guideline-enhanced contrastive loss that constrains the latent distance between multi-modal features and guideline knowledge, and the dual transformer decoder that employs guidelines as queries to steer cross-modal fusion, aligning the models with clinical diagnostic workflows from guideline acquisition to feature extraction and decision-making. Moreover, recognizing the lack of quantitative evaluation of interpretability for multimodal diagnostic models, we introduce a set of criteria to assess the interpretability from both image and text perspectives. Extensive evaluations across four datasets with different anatomies demonstrate RAD's generalizability, achieving state-of-the-art performance. Furthermore, RAD enables the model to concentrate more precisely on abnormal regions and critical indicators, ensuring evidence-based, trustworthy diagnosis. Our code is available at https://github.com/tdlhl/RAD.

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

Deep learning based automated pathological diagnosis has markedly improved diagnostic efficiency and reduced variability between observers, yet its clinical adoption remains limited by opaque model decisions and a lack of traceable rationale. To address this, recent multimodal visual reasoning architectures provide a unified framework that generates segmentation masks at the pixel level alongside semantically aligned textual explanations. By localizing lesion regions and producing expert style diagnostic narratives, these models deliver the transparent and interpretable insights necessary for dependable AI assisted pathology. Building on these advancements, we propose PathMR, a cell-level Multimodal visual Reasoning framework for Pathological image analysis. Given a pathological image and a textual query, PathMR generates expert-level diagnostic explanations while simultaneously predicting cell distribution patterns. To benchmark its performance, we evaluated our approach on the publicly available PathGen dataset as well as on our newly developed GADVR dataset. Extensive experiments on these two datasets demonstrate that PathMR consistently outperforms state-of-the-art visual reasoning methods in text generation quality, segmentation accuracy, and cross-modal alignment. These results highlight the potential of PathMR for improving interpretability in AI-driven pathological diagnosis. The code will be publicly available in https://github.com/zhangye-zoe/PathMR.

Accurate disease interpretation from radiology remains challenging due to imaging heterogeneity. Achieving expert-level diagnostic decisions requires integration of subtle image features with clinical knowledge. Yet major vision-language models (VLMs) treat images as holistic entities and overlook fine-grained image details that are vital for disease diagnosis. Clinicians analyze images by utilizing their prior medical knowledge and identify anatomical structures as important region of interests (ROIs). Inspired from this human-centric workflow, we introduce Anatomy-VLM, a fine-grained, vision-language model that incorporates multi-scale information. First, we design a model encoder to localize key anatomical features from entire medical images. Second, these regions are enriched with structured knowledge for contextually-aware interpretation. Finally, the model encoder aligns multi-scale medical information to generate clinically-interpretable disease prediction. Anatomy-VLM achieves outstanding performance on both in- and out-of-distribution datasets. We also validate the performance of Anatomy-VLM on downstream image segmentation tasks, suggesting that its fine-grained alignment captures anatomical and pathology-related knowledge. Furthermore, the Anatomy-VLM's encoder facilitates zero-shot anatomy-wise interpretation, providing its strong expert-level clinical interpretation capabilities.

Medical image segmentation poses challenges due to domain gaps, data modality variations, and dependency on domain knowledge or experts, especially for low- and middle-income countries (LMICs). Whereas for humans, given a few exemplars (with corresponding labels), we are able to segment different medical images even without exten-sive domain-specific clinical training. In addition, current SAM-based medical segmentation models use fine-grained visual prompts, such as the bounding rectangle generated from manually annotated target segmentation mask, as the bounding box (bbox) prompt during the testing phase. However, in actual clinical scenarios, no such precise prior knowledge is available. Our experimental results also reveal that previous models nearly fail to predict when given coarser bbox prompts. Considering these issues, in this paper, we introduce a domain-aware selective adaptation approach to adapt the general knowledge learned from a large model trained with natural images to the corresponding medical domains/modalities, with access to only a few (e.g. less than 5) exemplars. Our method mitigates the aforementioned limitations, providing an efficient and LMICs-friendly solution. Extensive experimental analysis showcases the effectiveness of our approach, offering potential advancements in healthcare diagnostics and clinical applications in LMICs.

Several medical Multimodal Large Languange Models (MLLMs) have been developed to address tasks involving visual images with textual instructions across various medical modalities, achieving impressive results. Most current medical generalist models are region-agnostic, treating the entire image as a holistic representation. However, they struggle to identify which specific regions they are focusing on when generating a sentence. To mimic the behavior of doctors, who typically begin by reviewing the entire image before concentrating on specific regions for a thorough evaluation, we aim to enhance the capability of medical MLLMs in understanding anatomical regions within entire medical scans. To achieve it, we first formulate Region-Centric tasks and construct a large-scale dataset, MedRegInstruct, to incorporate regional information into training. Combining our collected dataset with other medical multimodal corpora for training, we propose a Region-Aware medical MLLM, MedRegA, which is the first bilingual generalist medical AI system to simultaneously handle image-level and region-level medical vision-language tasks across a broad range of modalities. Our MedRegA not only enables three region-centric tasks, but also achieves the best performance for visual question answering, report generation and medical image classification over 8 modalities, showcasing significant versatility. Experiments demonstrate that our model can not only accomplish powerful performance across various medical vision-language tasks in bilingual settings, but also recognize and detect structures in multimodal medical scans, boosting the interpretability and user interactivity of medical MLLMs. Our project page is https://medrega.github.io.

Medical phrase grounding is crucial for identifying relevant regions in medical images based on phrase queries, facilitating accurate image analysis and diagnosis. However, current methods rely on manual extraction of key phrases from medical reports, reducing efficiency and increasing the workload for clinicians. Additionally, the lack of model confidence estimation limits clinical trust and usability. In this paper, we introduce a novel task called Medical Report Grounding (MRG), which aims to directly identify diagnostic phrases and their corresponding grounding boxes from medical reports in an end-to-end manner. To address this challenge, we propose uMedGround, a robust and reliable framework that leverages a multimodal large language model to predict diagnostic phrases by embedding a unique token, <BOX>, into the vocabulary to enhance detection capabilities. A vision encoder-decoder processes the embedded token and input image to generate grounding boxes. Critically, uMedGround incorporates an uncertainty-aware prediction model, significantly improving the robustness and reliability of grounding predictions. Experimental results demonstrate that uMedGround outperforms state-of-the-art medical phrase grounding methods and fine-tuned large visual-language models, validating its effectiveness and reliability. This study represents a pioneering exploration of the MRG task, marking the first-ever endeavor in this domain. Additionally, we demonstrate the applicability of uMedGround in medical visual question answering and class-based localization tasks, where it highlights visual evidence aligned with key diagnostic phrases, supporting clinicians in interpreting various types of textual inputs, including free-text reports, visual question answering queries, and class labels.

The objective of Radiology Report Generation (RRG) is to automatically generate coherent textual analyses of diseases based on radiological images, thereby alleviating the workload of radiologists. Current AI-based methods for RRG primarily focus on modifications to the encoder-decoder model architecture. To advance these approaches, this paper introduces an Organ-Regional Information Driven (ORID) framework which can effectively integrate multi-modal information and reduce the influence of noise from unrelated organs. Specifically, based on the LLaVA-Med, we first construct an RRG-related instruction dataset to improve organ-regional diagnosis description ability and get the LLaVA-Med-RRG. After that, we propose an organ-based cross-modal fusion module to effectively combine the information from the organ-regional diagnosis description and radiology image. To further reduce the influence of noise from unrelated organs on the radiology report generation, we introduce an organ importance coefficient analysis module, which leverages Graph Neural Network (GNN) to examine the interconnections of the cross-modal information of each organ region. Extensive experiments an1d comparisons with state-of-the-art methods across various evaluation metrics demonstrate the superior performance of our proposed method.

The recent release of RadGenome-Chest CT has significantly advanced CT-based report generation. However, existing methods primarily focus on global features, making it challenging to capture region-specific details, which may cause certain abnormalities to go unnoticed. To address this, we propose MedRegion-CT, a region-focused Multi-Modal Large Language Model (MLLM) framework, featuring three key innovations. First, we introduce Region Representative (R^2) Token Pooling, which utilizes a 2D-wise pretrained vision model to efficiently extract 3D CT features. This approach generates global tokens representing overall slice features and region tokens highlighting target areas, enabling the MLLM to process comprehensive information effectively. Second, a universal segmentation model generates pseudo-masks, which are then processed by a mask encoder to extract region-centric features. This allows the MLLM to focus on clinically relevant regions, using six predefined region masks. Third, we leverage segmentation results to extract patient-specific attributions, including organ size, diameter, and locations. These are converted into text prompts, enriching the MLLM's understanding of patient-specific contexts. To ensure rigorous evaluation, we conducted benchmark experiments on report generation using the RadGenome-Chest CT. MedRegion-CT achieved state-of-the-art performance, outperforming existing methods in natural language generation quality and clinical relevance while maintaining interpretability. The code for our framework is publicly available.

Clinical decision-making routinely demands reasoning over heterogeneous data, yet existing multimodal language models (MLLMs) remain largely vision-centric and fail to generalize across clinical specialties. To bridge this gap, we introduce QoQ-Med-7B/32B, the first open generalist clinical foundation model that jointly reasons across medical images, time-series signals, and text reports. QoQ-Med is trained with Domain-aware Relative Policy Optimization (DRPO), a novel reinforcement-learning objective that hierarchically scales normalized rewards according to domain rarity and modality difficulty, mitigating performance imbalance caused by skewed clinical data distributions. Trained on 2.61 million instruction tuning pairs spanning 9 clinical domains, we show that DRPO training boosts diagnostic performance by 43% in macro-F1 on average across all visual domains as compared to other critic-free training methods like GRPO. Furthermore, with QoQ-Med trained on intensive segmentation data, it is able to highlight salient regions related to the diagnosis, with an IoU 10x higher than open models while reaching the performance of OpenAI o4-mini. To foster reproducibility and downstream research, we release (i) the full model weights, (ii) the modular training pipeline, and (iii) all intermediate reasoning traces at https://github.com/DDVD233/QoQ_Med.

Automated interpretation of electrocardiograms (ECG) has garnered significant attention with the advancements in machine learning methodologies. Despite the growing interest, most current studies focus solely on classification or regression tasks, which overlook a crucial aspect of clinical cardio-disease diagnosis: the diagnostic report generated by experienced human clinicians. In this paper, we introduce a novel approach to ECG interpretation, leveraging recent breakthroughs in Large Language Models (LLMs) and Vision-Transformer (ViT) models. Rather than treating ECG diagnosis as a classification or regression task, we propose an alternative method of automatically identifying the most similar clinical cases based on the input ECG data. Also, since interpreting ECG as images is more affordable and accessible, we process ECG as encoded images and adopt a vision-language learning paradigm to jointly learn vision-language alignment between encoded ECG images and ECG diagnosis reports. Encoding ECG into images can result in an efficient ECG retrieval system, which will be highly practical and useful in clinical applications. More importantly, our findings could serve as a crucial resource for providing diagnostic services in underdeveloped regions.

Understanding the semantics of individual regions or patches within unconstrained images, such as in open-world object detection, represents a critical yet challenging task in computer vision. Building on the success of powerful image-level vision-language (ViL) foundation models like CLIP, recent efforts have sought to harness their capabilities by either training a contrastive model from scratch with an extensive collection of region-label pairs or aligning the outputs of a detection model with image-level representations of region proposals. Despite notable progress, these approaches are plagued by computationally intensive training requirements, susceptibility to data noise, and deficiency in contextual information. To address these limitations, we explore the synergistic potential of off-the-shelf foundation models, leveraging their respective strengths in localization and semantics. We introduce a novel, generic, and efficient region recognition architecture, named RegionSpot, designed to integrate position-aware localization knowledge from a localization foundation model (e.g., SAM) with semantic information extracted from a ViL model (e.g., CLIP). To fully exploit pretrained knowledge while minimizing training overhead, we keep both foundation models frozen, focusing optimization efforts solely on a lightweight attention-based knowledge integration module. Through extensive experiments in the context of open-world object recognition, our RegionSpot demonstrates significant performance improvements over prior alternatives, while also providing substantial computational savings. For instance, training our model with 3 million data in a single day using 8 V100 GPUs. Our model outperforms GLIP by 6.5 % in mean average precision (mAP), with an even larger margin by 14.8 % for more challenging and rare categories.

Vision-specific concepts such as "region" have played a key role in extending general machine learning frameworks to tasks like object detection. Given the success of region-based detectors for supervised learning and the progress of intra-image methods for contrastive learning, we explore the use of regions for reconstructive pre-training. Starting from Masked Autoencoding (MAE) both as a baseline and an inspiration, we propose a parallel pre-text task tailored to address the one-to-many mapping between images and regions. Since such regions can be generated in an unsupervised way, our approach (R-MAE) inherits the wide applicability from MAE, while being more "region-aware". We conduct thorough analyses during the development of R-MAE, and converge on a variant that is both effective and efficient (1.3% overhead over MAE). Moreover, it shows consistent quantitative improvements when generalized to various pre-training data and downstream detection and segmentation benchmarks. Finally, we provide extensive qualitative visualizations to enhance the understanding of R-MAE's behaviour and potential. Code will be made available at https://github.com/facebookresearch/r-mae.

The rapid advancement of large-scale vision-language models has showcased remarkable capabilities across various tasks. However, the lack of extensive and high-quality image-text data in medicine has greatly hindered the development of large-scale medical vision-language models. In this work, we present a diagnosis-guided bootstrapping strategy that exploits both image and label information to construct vision-language datasets. Based on the constructed dataset, we developed MedDr, a generalist foundation model for healthcare capable of handling diverse medical data modalities, including radiology, pathology, dermatology, retinography, and endoscopy. Moreover, during inference, we propose a simple but effective retrieval-augmented medical diagnosis strategy, which enhances the model's generalization ability. Extensive experiments on visual question answering, medical report generation, and medical image diagnosis demonstrate the superiority of our method.

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

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

Medical diagnostic applications require models that can process multimodal medical inputs (images, patient histories, lab results) and generate diverse outputs including both textual reports and visual content (annotations, segmentation masks, and images). Despite this need, existing medical AI systems disrupt this unified process: medical image understanding models interpret images but cannot generate visual outputs, while medical image generation models synthesize images but cannot provide textual explanations. This leads to gaps in data representation, feature integration, and task-level multimodal capabilities. To this end, we propose a multi-level framework that draws inspiration from diagnostic workflows through the Observation-Knowledge-Analysis (OKA) paradigm. Specifically, at the observation level, we construct UniMed-5M, a dataset comprising over 5.6M samples that reformat diverse unimodal data into multimodal pairs for foundational observation. At the knowledge level, we propose Progressive Curriculum Learning that systematically introduces medical multimodal knowledge. At the analysis level, we introduce UniMedVL, the first medical unified multimodal model for the simultaneous analysis of image understanding and generation tasks within a single architecture. UniMedVL achieves superior performance on five medical image understanding benchmarks, while matching specialized models in generation quality across eight medical imaging modalities. Crucially, our unified architecture enables bidirectional knowledge sharing: generation tasks enhance visual understanding features, demonstrating that integrating traditionally separate capabilities within a single medical framework unlocks improvements across diverse medical vision-language tasks. Code is available at https://github.com/uni-medical/UniMedVL.

Precision medicine, such as patient-adaptive treatments assisted by medical image analysis, poses new challenges for segmentation algorithms in adapting to new patients, due to the large variability across different patients and the limited availability of annotated data for each patient. In this work, we propose a data-efficient segmentation algorithm, namely Part-aware Prompted Segment Anything Model (P^2SAM). Without any model fine-tuning, P^2SAM enables seamless adaptation to any new patients relying only on one-shot patient-specific data. We introduce a novel part-aware prompt mechanism to select multiple-point prompts based on the part-level features of the one-shot data, which can be extensively integrated into different promptable segmentation models, such as SAM and SAM 2. Moreover, to determine the optimal number of parts for each specific case, we propose a distribution-guided retrieval approach that further enhances the robustness of the part-aware prompt mechanism. P^2SAM improves the performance by +8.0% and +2.0% mean Dice score for two different patient-adaptive segmentation applications, respectively. In addition, P^2SAM also exhibits impressive generalizability in other adaptive segmentation tasks in the natural image domain, e.g., +6.4% mIoU within personalized object segmentation task. The code is available at: https://github.com/Zch0414/p2sam

Learning visual representations is foundational for a broad spectrum of downstream tasks. Although recent vision-language contrastive models, such as CLIP and SigLIP, have achieved impressive zero-shot performance via large-scale vision-language alignment, their reliance on global representations constrains their effectiveness for dense prediction tasks, such as grounding, OCR, and segmentation. To address this gap, we introduce Region-Aware Cluster Discrimination (RICE), a novel method that enhances region-level visual and OCR capabilities. We first construct a billion-scale candidate region dataset and propose a Region Transformer layer to extract rich regional semantics. We further design a unified region cluster discrimination loss that jointly supports object and OCR learning within a single classification framework, enabling efficient and scalable distributed training on large-scale data. Extensive experiments show that RICE consistently outperforms previous methods on tasks, including segmentation, dense detection, and visual perception for Multimodal Large Language Models (MLLMs). The pre-trained models have been released at https://github.com/deepglint/MVT.

Radiologic diagnostic errors-under-reading errors, inattentional blindness, and communication failures-remain prevalent in clinical practice. These issues often stem from missed localized abnormalities, limited global context, and variability in report language. These challenges are amplified in 3D imaging, where clinicians must examine hundreds of slices per scan. Addressing them requires systems with precise localized detection, global volume-level reasoning, and semantically consistent natural language reporting. However, existing 3D vision-language models are unable to meet all three needs jointly, lacking local-global understanding for spatial reasoning and struggling with the variability and noise of uncurated radiology reports. We present MedVista3D, a multi-scale semantic-enriched vision-language pretraining framework for 3D CT analysis. To enable joint disease detection and holistic interpretation, MedVista3D performs local and global image-text alignment for fine-grained representation learning within full-volume context. To address report variability, we apply language model rewrites and introduce a Radiology Semantic Matching Bank for semantics-aware alignment. MedVista3D achieves state-of-the-art performance on zero-shot disease classification, report retrieval, and medical visual question answering, while transferring well to organ segmentation and prognosis prediction. Code and datasets will be released.

Clinical diagnosis is critical in medical practice, typically requiring a continuous and evolving process that includes primary diagnosis, differential diagnosis, and final diagnosis. However, most existing clinical diagnostic tasks are single-step processes, which does not align with the complex multi-step diagnostic procedures found in real-world clinical settings. In this paper, we propose a multi-step diagnostic task and annotate a clinical diagnostic dataset (MSDiagnosis). This dataset includes primary diagnosis, differential diagnosis, and final diagnosis questions. Additionally, we propose a novel and effective framework. This framework combines forward inference, backward inference, reflection, and refinement, enabling the LLM to self-evaluate and adjust its diagnostic results. To assess the effectiveness of our proposed method, we design and conduct extensive experiments. The experimental results demonstrate the effectiveness of the proposed method. We also provide a comprehensive experimental analysis and suggest future research directions for this task.

Most current medical vision language models struggle to jointly generate diagnostic text and pixel-level segmentation masks in response to complex visual questions. This represents a major limitation towards clinical application, as assistive systems that fail to provide both modalities simultaneously offer limited value to medical practitioners. To alleviate this limitation, we first introduce RadDiagSeg-D, a dataset combining abnormality detection, diagnosis, and multi-target segmentation into a unified and hierarchical task. RadDiagSeg-D covers multiple imaging modalities and is precisely designed to support the development of models that produce descriptive text and corresponding segmentation masks in tandem. Subsequently, we leverage the dataset to propose a novel vision-language model, RadDiagSeg-M, capable of joint abnormality detection, diagnosis, and flexible segmentation. RadDiagSeg-M provides highly informative and clinically useful outputs, effectively addressing the need to enrich contextual information for assistive diagnosis. Finally, we benchmark RadDiagSeg-M and showcase its strong performance across all components involved in the task of multi-target text-and-mask generation, establishing a robust and competitive baseline.

Clinical diagnosis prediction models, when provided with a patient's medical history, aim to detect potential diseases early, facilitating timely intervention and improving prognostic outcomes. However, the inherent scarcity of patient data and large disease candidate space often pose challenges in developing satisfactory models for this intricate task. The exploration of leveraging Large Language Models (LLMs) for encapsulating clinical decision processes has been limited. We introduce MERA, a clinical diagnosis prediction model that bridges pertaining natural language knowledge with medical practice. We apply hierarchical contrastive learning on a disease candidate ranking list to alleviate the large decision space issue. With concept memorization through fine-tuning, we bridge the natural language clinical knowledge with medical codes. Experimental results on MIMIC-III and IV datasets show that MERA achieves the state-of-the-art diagnosis prediction performance and dramatically elevates the diagnosis prediction capabilities of generative LMs.

Real-world medical image segmentation has tremendous long-tailed complexity of objects, among which tail conditions correlate with relatively rare diseases and are clinically significant. A trustworthy medical AI algorithm should demonstrate its effectiveness on tail conditions to avoid clinically dangerous damage in these out-of-distribution (OOD) cases. In this paper, we adopt the concept of object queries in Mask Transformers to formulate semantic segmentation as a soft cluster assignment. The queries fit the feature-level cluster centers of inliers during training. Therefore, when performing inference on a medical image in real-world scenarios, the similarity between pixels and the queries detects and localizes OOD regions. We term this OOD localization as MaxQuery. Furthermore, the foregrounds of real-world medical images, whether OOD objects or inliers, are lesions. The difference between them is less than that between the foreground and background, possibly misleading the object queries to focus redundantly on the background. Thus, we propose a query-distribution (QD) loss to enforce clear boundaries between segmentation targets and other regions at the query level, improving the inlier segmentation and OOD indication. Our proposed framework is tested on two real-world segmentation tasks, i.e., segmentation of pancreatic and liver tumors, outperforming previous state-of-the-art algorithms by an average of 7.39% on AUROC, 14.69% on AUPR, and 13.79% on FPR95 for OOD localization. On the other hand, our framework improves the performance of inlier segmentation by an average of 5.27% DSC when compared with the leading baseline nnUNet.

Multimodal large language models (MLLMs) demonstrate significant potential in the field of medical diagnosis. However, they face critical challenges in specialized domains such as ophthalmology, particularly the fragmentation of annotation granularity and inconsistencies in clinical reasoning logic, which hinder precise cross-modal understanding. This paper introduces FundusExpert, an ophthalmology-specific MLLM with integrated positioning-diagnosis reasoning capabilities, along with FundusGen, a dataset constructed through the intelligent Fundus-Engine system. Fundus-Engine automates localization and leverages MLLM-based semantic expansion to integrate global disease classification, local object detection, and fine-grained feature analysis within a single fundus image. Additionally, by constructing a clinically aligned cognitive chain, it guides the model to generate interpretable reasoning paths. FundusExpert, fine-tuned with instruction data from FundusGen, achieves the best performance in ophthalmic question-answering tasks, surpassing the average accuracy of the 40B MedRegA by 26.6%. It also excels in zero-shot report generation tasks, achieving a clinical consistency of 77.0%, significantly outperforming GPT-4o's 47.6%. Furthermore, we reveal a scaling law between data quality and model capability (L propto N^{0.068}), demonstrating that the cognitive alignment annotations in FundusGen enhance data utilization efficiency. By integrating region-level localization with diagnostic reasoning chains, our work develops a scalable, clinically-aligned MLLM and explores a pathway toward bridging the visual-language gap in specific MLLMs. Our project can be found at https://github.com/MeteorElf/FundusExpert.

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

In this work, we address the problem of grounding abnormalities in medical images, where the goal is to localize clinical findings based on textual descriptions. While generalist Vision-Language Models (VLMs) excel in natural grounding tasks, they often struggle in the medical domain due to rare, compositional, and domain-specific terms that are poorly aligned with visual patterns. Specialized medical VLMs address this challenge via large-scale domain pretraining, but at the cost of substantial annotation and computational resources. To overcome these limitations, we propose Knowledge to Sight (K2Sight), a framework that introduces structured semantic supervision by decomposing clinical concepts into interpretable visual attributes, such as shape, density, and anatomical location. These attributes are distilled from domain ontologies and encoded into concise instruction-style prompts, which guide region-text alignment during training. Unlike conventional report-level supervision, our approach explicitly bridges domain knowledge and spatial structure, enabling data-efficient training of compact models. We train compact models with 0.23B and 2B parameters using only 1.5\% of the data required by state-of-the-art medical VLMs. Despite their small size and limited training data, these models achieve performance on par with or better than 7B+ medical VLMs, with up to 9.82\% improvement in mAP_{50}. Code and models: https://lijunrio.github.io/K2Sight/{SOTAPink{https://lijunrio.github.io/K2Sight/}}.

Multi-modal brain tumor segmentation is critical for clinical diagnosis, and it requires accurate identification of distinct internal anatomical subregions. While the recent prompt-based segmentation paradigms enable interactive experiences for clinicians, existing methods ignore cross-modal correlations and rely on labor-intensive category-specific prompts, limiting their applicability in real-world scenarios. To address these issues, we propose a MSM-Seg framework for multi-modal brain tumor segmentation. The MSM-Seg introduces a novel dual-memory segmentation paradigm that synergistically integrates multi-modal and inter-slice information with the efficient category-agnostic prompt for brain tumor understanding. To this end, we first devise a modality-and-slice memory attention (MSMA) to exploit the cross-modal and inter-slice relationships among the input scans. Then, we propose a multi-scale category-agnostic prompt encoder (MCP-Encoder) to provide tumor region guidance for decoding. Moreover, we devise a modality-adaptive fusion decoder (MF-Decoder) that leverages the complementary decoding information across different modalities to improve segmentation accuracy. Extensive experiments on different MRI datasets demonstrate that our MSM-Seg framework outperforms state-of-the-art methods in multi-modal metastases and glioma tumor segmentation. The code is available at https://github.com/xq141839/MSM-Seg.

Although Vision Language Models (VLMs) have shown strong generalization in medical imaging, pathology presents unique challenges due to ultra-high resolution, complex tissue structures, and nuanced clinical semantics. These factors make pathology VLMs prone to hallucinations, i.e., generating outputs inconsistent with visual evidence, which undermines clinical trust. Existing RAG approaches in this domain largely depend on text-based knowledge bases, limiting their ability to leverage diagnostic visual cues. To address this, we propose Patho-AgenticRAG, a multimodal RAG framework with a database built on page-level embeddings from authoritative pathology textbooks. Unlike traditional text-only retrieval systems, it supports joint text-image search, enabling direct retrieval of textbook pages that contain both the queried text and relevant visual cues, thus avoiding the loss of critical image-based information. Patho-AgenticRAG also supports reasoning, task decomposition, and multi-turn search interactions, improving accuracy in complex diagnostic scenarios. Experiments show that Patho-AgenticRAG significantly outperforms existing multimodal models in complex pathology tasks like multiple-choice diagnosis and visual question answering. Our project is available at the Patho-AgenticRAG repository: https://github.com/Wenchuan-Zhang/Patho-AgenticRAG.

Vision language models (VLMs) have experienced rapid advancements through the integration of large language models (LLMs) with image-text pairs, yet they struggle with detailed regional visual understanding due to limited spatial awareness of the vision encoder, and the use of coarse-grained training data that lacks detailed, region-specific captions. To address this, we introduce RegionGPT (short as RGPT), a novel framework designed for complex region-level captioning and understanding. RGPT enhances the spatial awareness of regional representation with simple yet effective modifications to existing visual encoders in VLMs. We further improve performance on tasks requiring a specific output scope by integrating task-guided instruction prompts during both training and inference phases, while maintaining the model's versatility for general-purpose tasks. Additionally, we develop an automated region caption data generation pipeline, enriching the training set with detailed region-level captions. We demonstrate that a universal RGPT model can be effectively applied and significantly enhancing performance across a range of region-level tasks, including but not limited to complex region descriptions, reasoning, object classification, and referring expressions comprehension.

Pancreatic cancer is one of the leading causes of cancer-related death. Accurate detection, segmentation, and differential diagnosis of the full taxonomy of pancreatic lesions, i.e., normal, seven major types of lesions, and other lesions, is critical to aid the clinical decision-making of patient management and treatment. However, existing works focus on segmentation and classification for very specific lesion types (PDAC) or groups. Moreover, none of the previous work considers using lesion prevalence-related non-imaging patient information to assist the differential diagnosis. To this end, we develop a meta-information-aware dual-path transformer and exploit the feasibility of classification and segmentation of the full taxonomy of pancreatic lesions. Specifically, the proposed method consists of a CNN-based segmentation path (S-path) and a transformer-based classification path (C-path). The S-path focuses on initial feature extraction by semantic segmentation using a UNet-based network. The C-path utilizes both the extracted features and meta-information for patient-level classification based on stacks of dual-path transformer blocks that enhance the modeling of global contextual information. A large-scale multi-phase CT dataset of 3,096 patients with pathology-confirmed pancreatic lesion class labels, voxel-wise manual annotations of lesions from radiologists, and patient meta-information, was collected for training and evaluations. Our results show that our method can enable accurate classification and segmentation of the full taxonomy of pancreatic lesions, approaching the accuracy of the radiologist's report and significantly outperforming previous baselines. Results also show that adding the common meta-information, i.e., gender and age, can boost the model's performance, thus demonstrating the importance of meta-information for aiding pancreatic disease diagnosis.

Medical imaging provides critical evidence for clinical diagnosis, treatment planning, and surgical decisions, yet most existing imaging models are narrowly focused and require multiple specialized networks, limiting their generalization. Although large-scale language and multimodal models exhibit strong reasoning and multi-task capabilities, real-world clinical applications demand precise visual grounding, multimodal integration, and chain-of-thought reasoning. We introduce Citrus-V, a multimodal medical foundation model that combines image analysis with textual reasoning. The model integrates detection, segmentation, and multimodal chain-of-thought reasoning, enabling pixel-level lesion localization, structured report generation, and physician-like diagnostic inference in a single framework. We propose a novel multimodal training approach and release a curated open-source data suite covering reasoning, detection, segmentation, and document understanding tasks. Evaluations demonstrate that Citrus-V outperforms existing open-source medical models and expert-level imaging systems across multiple benchmarks, delivering a unified pipeline from visual grounding to clinical reasoning and supporting precise lesion quantification, automated reporting, and reliable second opinions.

Scalp disorders are highly prevalent worldwide, yet remain underdiagnosed due to limited access to expert evaluation and the high cost of annotation. Although AI-based approaches hold great promise, their practical deployment is hindered by challenges such as severe data imbalance and the absence of pixel-level segmentation labels. To address these issues, we propose ScalpVision, an AI-driven system for the holistic diagnosis of scalp diseases. In ScalpVision, effective hair segmentation is achieved using pseudo image-label pairs and an innovative prompting method in the absence of traditional hair masking labels. Additionally, ScalpVision introduces DiffuseIT-M, a generative model adopted for dataset augmentation while maintaining hair information, facilitating improved predictions of scalp disease severity. Our experimental results affirm ScalpVision's efficiency in diagnosing a variety of scalp conditions, showcasing its potential as a valuable tool in dermatological care. Our code is available at https://github.com/winston1214/ScalpVision.

Generalist Large Language Models (LLMs), such as GPT-4, have shown considerable promise in various domains, including medical diagnosis. Rare diseases, affecting approximately 300 million people worldwide, often have unsatisfactory clinical diagnosis rates primarily due to a lack of experienced physicians and the complexity of differentiating among many rare diseases. In this context, recent news such as "ChatGPT correctly diagnosed a 4-year-old's rare disease after 17 doctors failed" underscore LLMs' potential, yet underexplored, role in clinically diagnosing rare diseases. To bridge this research gap, we introduce RareBench, a pioneering benchmark designed to systematically evaluate the capabilities of LLMs on 4 critical dimensions within the realm of rare diseases. Meanwhile, we have compiled the largest open-source dataset on rare disease patients, establishing a benchmark for future studies in this domain. To facilitate differential diagnosis of rare diseases, we develop a dynamic few-shot prompt methodology, leveraging a comprehensive rare disease knowledge graph synthesized from multiple knowledge bases, significantly enhancing LLMs' diagnostic performance. Moreover, we present an exhaustive comparative study of GPT-4's diagnostic capabilities against those of specialist physicians. Our experimental findings underscore the promising potential of integrating LLMs into the clinical diagnostic process for rare diseases. This paves the way for exciting possibilities in future advancements in this field.

Different medical imaging modalities capture diagnostic information at varying spatial resolutions, from coarse global patterns to fine-grained localized structures. However, most existing vision-language frameworks in the medical domain apply a uniform strategy for local feature extraction, overlooking the modality-specific demands. In this work, we present MedMoE, a modular and extensible vision-language processing framework that dynamically adapts visual representation based on the diagnostic context. MedMoE incorporates a Mixture-of-Experts (MoE) module conditioned on the report type, which routes multi-scale image features through specialized expert branches trained to capture modality-specific visual semantics. These experts operate over feature pyramids derived from a Swin Transformer backbone, enabling spatially adaptive attention to clinically relevant regions. This framework produces localized visual representations aligned with textual descriptions, without requiring modality-specific supervision at inference. Empirical results on diverse medical benchmarks demonstrate that MedMoE improves alignment and retrieval performance across imaging modalities, underscoring the value of modality-specialized visual representations in clinical vision-language systems.

The differential diagnosis of neurodegenerative dementias is a challenging clinical task, mainly because of the overlap in symptom presentation and the similarity of patterns observed in structural neuroimaging. To improve diagnostic efficiency and accuracy, deep learning-based methods such as Convolutional Neural Networks and Vision Transformers have been proposed for the automatic classification of brain MRIs. However, despite their strong predictive performance, these models find limited clinical utility due to their opaque decision making. In this work, we propose a framework that integrates two core components to enhance diagnostic transparency. First, we introduce a modular pipeline for converting 3D T1-weighted brain MRIs into textual radiology reports. Second, we explore the potential of modern Large Language Models (LLMs) to assist clinicians in the differential diagnosis between Frontotemporal dementia subtypes, Alzheimer's disease, and normal aging based on the generated reports. To bridge the gap between predictive accuracy and explainability, we employ reinforcement learning to incentivize diagnostic reasoning in LLMs. Without requiring supervised reasoning traces or distillation from larger models, our approach enables the emergence of structured diagnostic rationales grounded in neuroimaging findings. Unlike post-hoc explainability methods that retrospectively justify model decisions, our framework generates diagnostic rationales as part of the inference process-producing causally grounded explanations that inform and guide the model's decision-making process. In doing so, our framework matches the diagnostic performance of existing deep learning methods while offering rationales that support its diagnostic conclusions.

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

In the light of the COVID-19 pandemic, deep learning methods have been widely investigated in detecting COVID-19 from chest X-rays. However, a more pragmatic approach to applying AI methods to a medical diagnosis is designing a framework that facilitates human-machine interaction and expert decision making. Studies have shown that categorization can play an essential rule in accelerating real-world decision making. Inspired by descriptive document clustering, we propose a domain-independent explanatory clustering framework to group contextually related instances and support radiologists' decision making. While most descriptive clustering approaches employ domain-specific characteristics to form meaningful clusters, we focus on model-level explanation as a more general-purpose element of every learning process to achieve cluster homogeneity. We employ DeepSHAP to generate homogeneous clusters in terms of disease severity and describe the clusters using favorable and unfavorable saliency maps, which visualize the class discriminating regions of an image. These human-interpretable maps complement radiologist knowledge to investigate the whole cluster at once. Besides, as part of this study, we evaluate a model based on VGG-19, which can identify COVID and pneumonia cases with a positive predictive value of 95% and 97%, respectively, comparable to the recent explainable approaches for COVID diagnosis.

Recently computer-aided diagnosis has demonstrated promising performance, effectively alleviating the workload of clinicians. However, the inherent sample imbalance among different diseases leads algorithms biased to the majority categories, leading to poor performance for rare categories. Existing works formulated this challenge as a long-tailed problem and attempted to tackle it by decoupling the feature representation and classification. Yet, due to the imbalanced distribution and limited samples from tail classes, these works are prone to biased representation learning and insufficient classifier calibration. To tackle these problems, we propose a new Long-tailed Medical Diagnosis (LMD) framework for balanced medical image classification on long-tailed datasets. In the initial stage, we develop a Relation-aware Representation Learning (RRL) scheme to boost the representation ability by encouraging the encoder to capture intrinsic semantic features through different data augmentations. In the subsequent stage, we propose an Iterative Classifier Calibration (ICC) scheme to calibrate the classifier iteratively. This is achieved by generating a large number of balanced virtual features and fine-tuning the encoder using an Expectation-Maximization manner. The proposed ICC compensates for minority categories to facilitate unbiased classifier optimization while maintaining the diagnostic knowledge in majority classes. Comprehensive experiments on three public long-tailed medical datasets demonstrate that our LMD framework significantly surpasses state-of-the-art approaches. The source code can be accessed at https://github.com/peterlipan/LMD.

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

Visual Language Models (VLMs) have demonstrated impressive capabilities in visual grounding tasks. However, their effectiveness in the medical domain, particularly for abnormality detection and localization within medical images, remains underexplored. A major challenge is the complex and abstract nature of medical terminology, which makes it difficult to directly associate pathological anomaly terms with their corresponding visual features. In this work, we introduce a novel approach to enhance VLM performance in medical abnormality detection and localization by leveraging decomposed medical knowledge. Instead of directly prompting models to recognize specific abnormalities, we focus on breaking down medical concepts into fundamental attributes and common visual patterns. This strategy promotes a stronger alignment between textual descriptions and visual features, improving both the recognition and localization of abnormalities in medical images.We evaluate our method on the 0.23B Florence-2 base model and demonstrate that it achieves comparable performance in abnormality grounding to significantly larger 7B LLaVA-based medical VLMs, despite being trained on only 1.5% of the data used for such models. Experimental results also demonstrate the effectiveness of our approach in both known and previously unseen abnormalities, suggesting its strong generalization capabilities.

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

We introduce Medal S, a medical segmentation foundation model that supports native-resolution spatial and textual prompts within an end-to-end trainable framework. Unlike text-only methods lacking spatial awareness, Medal S achieves channel-wise alignment between volumetric prompts and text embeddings, mitigating inaccuracies from resolution mismatches. By preserving full 3D context, it efficiently processes multiple native-resolution masks in parallel, enhancing multi-class segmentation performance. A lightweight 3D convolutional module enables precise voxel-space refinement guided by both prompt types, supporting up to 243 classes across CT, MRI, PET, ultrasound, and microscopy modalities in the BiomedSegFM dataset. Medal S offers two prompting modes: a text-only mode, where model predictions serve as spatial prompts for self-refinement without human input, and a hybrid mode, incorporating manual annotations for enhanced flexibility. For 24-class segmentation, parallel spatial prompting reduces inference time by more than 90% compared to sequential prompting. We propose dynamic resampling to address target-patch ratio imbalance, extending SAT and nnU-Net for data augmentation. Furthermore, we develop optimized text preprocessing, a two-stage inference strategy, and post-processing techniques to improve memory efficiency, precision, and inference speed. On the five-modality average on the validation set, Medal S outperforms SAT with a DSC of 75.44 (vs. 69.83), NSD of 77.34 (vs. 71.06), F1 of 38.24 (vs. 24.88), and DSC TP of 65.46 (vs. 46.97). Medal S achieves excellent performance by harmonizing spatial precision with semantic textual guidance, demonstrating superior efficiency and accuracy in multi-class medical segmentation tasks compared to sequential prompt-based approaches. Medal S will be publicly available at https://github.com/yinghemedical/Medal-S.

Recently, large pre-trained vision-language models have shown remarkable performance in zero-shot anomaly detection (ZSAD). With fine-tuning on a single auxiliary dataset, the model enables cross-category anomaly detection on diverse datasets covering industrial defects and medical lesions. Compared to manually designed prompts, prompt learning eliminates the need for expert knowledge and trial-and-error. However, it still faces the following challenges: (i) static learnable tokens struggle to capture the continuous and diverse patterns of normal and anomalous states, limiting generalization to unseen categories; (ii) fixed textual labels provide overly sparse category information, making the model prone to overfitting to a specific semantic subspace. To address these issues, we propose Conditional Prompt Synthesis (CoPS), a novel framework that synthesizes dynamic prompts conditioned on visual features to enhance ZSAD performance. Specifically, we extract representative normal and anomaly prototypes from fine-grained patch features and explicitly inject them into prompts, enabling adaptive state modeling. Given the sparsity of class labels, we leverage a variational autoencoder to model semantic image features and implicitly fuse varied class tokens into prompts. Additionally, integrated with our spatially-aware alignment mechanism, extensive experiments demonstrate that CoPS surpasses state-of-the-art methods by 2.5% AUROC in both classification and segmentation across 13 industrial and medical datasets. Code will be available at https://github.com/cqylunlun/CoPS.

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

Accurate segmentation of regions of interest in biomedical images holds substantial value in image analysis. Although several foundation models for biomedical segmentation have currently achieved excellent performance on certain datasets, they typically demonstrate sub-optimal performance on unseen domain data. We owe the deficiency to lack of vision-language knowledge before segmentation. Multimodal Large Language Models (MLLMs) bring outstanding understanding and reasoning capabilities to multimodal tasks, which inspires us to leverage MLLMs to inject Vision-Language Knowledge (VLK), thereby enabling vision models to demonstrate superior generalization capabilities on cross-domain datasets. In this paper, we propose using MLLMs to guide SAM in learning microscopy crose-domain data, unifying Segment Anything in Microscopy, named uLLSAM. Specifically, we propose the Vision-Language Semantic Alignment (VLSA) module, which injects VLK into Segment Anything Model (SAM). We find that after SAM receives global VLK prompts, its performance improves significantly, but there are deficiencies in boundary contour perception. Therefore, we further propose Semantic Boundary Regularization (SBR) to prompt SAM. Our method achieves performance improvements of 7.71% in Dice and 12.10% in SA across 9 in-domain microscopy datasets, achieving state-of-the-art performance. Our method also demonstrates improvements of 6.79% in Dice and 10.08% in SA across 10 out-ofdomain datasets, exhibiting strong generalization capabilities. Code is available at https://github.com/ieellee/uLLSAM.

This paper presents our team's participation in the MEDIQA-ClinicalNLP2024 shared task B. We present a novel approach to diagnosing clinical dermatology cases by integrating large multimodal models, specifically leveraging the capabilities of GPT-4V under a retriever and a re-ranker framework. Our investigation reveals that GPT-4V, when used as a retrieval agent, can accurately retrieve the correct skin condition 85% of the time using dermatological images and brief patient histories. Additionally, we empirically show that Naive Chain-of-Thought (CoT) works well for retrieval while Medical Guidelines Grounded CoT is required for accurate dermatological diagnosis. Further, we introduce a Multi-Agent Conversation (MAC) framework and show its superior performance and potential over the best CoT strategy. The experiments suggest that using naive CoT for retrieval and multi-agent conversation for critique-based diagnosis, GPT-4V can lead to an early and accurate diagnosis of dermatological conditions. The implications of this work extend to improving diagnostic workflows, supporting dermatological education, and enhancing patient care by providing a scalable, accessible, and accurate diagnostic tool.

WHO has declared that more than 2.2 billion people worldwide are suffering from visual disorders, such as media haze, glaucoma, and drusen. At least 1 billion of these cases could have been either prevented or successfully treated, yet they remain unaddressed due to poverty, a lack of specialists, inaccurate ocular fundus diagnoses by ophthalmologists, or the presence of a rare disease. To address this, the research has developed the Hybrid Trio-Network Model Algorithm for accurately diagnosing 12 distinct common and rare eye diseases. This algorithm utilized the RFMiD dataset of 3,200 fundus images and the Binary Relevance Method to detect diseases separately, ensuring expandability and avoiding incorrect correlations. Each detector, incorporating finely tuned hyperparameters to optimize performance, consisted of three feature components: A classical transfer learning CNN model, a two-stage CNN model, and a Siamese Network. The diagnosis was made using features extracted through this Trio-Model with Ensembled Machine Learning algorithms. The proposed model achieved an average accuracy of 97% and an AUC score of 0.96. Compared to past benchmark studies, an increase of over 10% in the F1-score was observed for most diseases. Furthermore, using the Siamese Network, the model successfully made predictions in diseases like optic disc pallor, which past studies failed to predict due to low confidence. This diagnostic tool presents a stable, adaptive, cost-effective, efficient, accessible, and fast solution for globalizing early detection of both common and rare diseases.

Current AI-assisted skin image diagnosis has achieved dermatologist-level performance in classifying skin cancer, driven by rapid advancements in deep learning architectures. However, unlike traditional vision tasks, skin images in general present unique challenges due to the limited availability of well-annotated datasets, complex variations in conditions, and the necessity for detailed interpretations to ensure patient safety. Previous segmentation methods have sought to reduce image noise and enhance diagnostic performance, but these techniques require fine-grained, pixel-level ground truth masks for training. In contrast, with the rise of foundation models, the Segment Anything Model (SAM) has been introduced to facilitate promptable segmentation, enabling the automation of the segmentation process with simple yet effective prompts. Efforts applying SAM predominantly focus on dermatoscopy images, which present more easily identifiable lesion boundaries than clinical photos taken with smartphones. This limitation constrains the practicality of these approaches to real-world applications. To overcome the challenges posed by noisy clinical photos acquired via non-standardized protocols and to improve diagnostic accessibility, we propose a novel Cross-Attentive Fusion framework for interpretable skin lesion diagnosis. Our method leverages SAM to generate visual concepts for skin diseases using prompts, integrating local visual concepts with global image features to enhance model performance. Extensive evaluation on two skin disease datasets demonstrates our proposed method's effectiveness on lesion diagnosis and interpretability.

Recent progress has been made in region-aware vision-language modeling, particularly with the emergence of the Describe Anything Model (DAM). DAM is capable of generating detailed descriptions of any specific image areas or objects without the need for additional localized image-text alignment supervision. We hypothesize that such region-level descriptive capability is beneficial for the task of Visual Question Answering (VQA), especially in challenging scenarios involving images with dense text. In such settings, the fine-grained extraction of textual information is crucial to producing correct answers. Motivated by this, we introduce DAM-QA, a framework with a tailored evaluation protocol, developed to investigate and harness the region-aware capabilities from DAM for the text-rich VQA problem that requires reasoning over text-based information within images. DAM-QA incorporates a mechanism that aggregates answers from multiple regional views of image content, enabling more effective identification of evidence that may be tied to text-related elements. Experiments on six VQA benchmarks show that our approach consistently outperforms the baseline DAM, with a notable 7+ point gain on DocVQA. DAM-QA also achieves the best overall performance among region-aware models with fewer parameters, significantly narrowing the gap with strong generalist VLMs. These results highlight the potential of DAM-like models for text-rich and broader VQA tasks when paired with efficient usage and integration strategies. Our code is publicly available at https://github.com/Linvyl/DAM-QA.git.

Automatic detecting anomalous regions in images of objects or textures without priors of the anomalies is challenging, especially when the anomalies appear in very small areas of the images, making difficult-to-detect visual variations, such as defects on manufacturing products. This paper proposes an effective unsupervised anomaly segmentation approach that can detect and segment out the anomalies in small and confined regions of images. Concretely, we develop a multi-scale regional feature generator that can generate multiple spatial context-aware representations from pre-trained deep convolutional networks for every subregion of an image. The regional representations not only describe the local characteristics of corresponding regions but also encode their multiple spatial context information, making them discriminative and very beneficial for anomaly detection. Leveraging these descriptive regional features, we then design a deep yet efficient convolutional autoencoder and detect anomalous regions within images via fast feature reconstruction. Our method is simple yet effective and efficient. It advances the state-of-the-art performances on several benchmark datasets and shows great potential for real applications.

There has been a rapidly growing interest in Automatic Symptom Detection (ASD) and Automatic Diagnosis (AD) systems in the machine learning research literature, aiming to assist doctors in telemedicine services. These systems are designed to interact with patients, collect evidence about their symptoms and relevant antecedents, and possibly make predictions about the underlying diseases. Doctors would review the interactions, including the evidence and the predictions, collect if necessary additional information from patients, before deciding on next steps. Despite recent progress in this area, an important piece of doctors' interactions with patients is missing in the design of these systems, namely the differential diagnosis. Its absence is largely due to the lack of datasets that include such information for models to train on. In this work, we present a large-scale synthetic dataset of roughly 1.3 million patients that includes a differential diagnosis, along with the ground truth pathology, symptoms and antecedents for each patient. Unlike existing datasets which only contain binary symptoms and antecedents, this dataset also contains categorical and multi-choice symptoms and antecedents useful for efficient data collection. Moreover, some symptoms are organized in a hierarchy, making it possible to design systems able to interact with patients in a logical way. As a proof-of-concept, we extend two existing AD and ASD systems to incorporate the differential diagnosis, and provide empirical evidence that using differentials as training signals is essential for the efficiency of such systems or for helping doctors better understand the reasoning of those systems.

Whole Slide Image (WSI) analysis is a powerful method to facilitate the diagnosis of cancer in tissue samples. Automating this diagnosis poses various issues, most notably caused by the immense image resolution and limited annotations. WSIs commonly exhibit resolutions of 100Kx100K pixels. Annotating cancerous areas in WSIs on the pixel level is prohibitively labor-intensive and requires a high level of expert knowledge. Multiple instance learning (MIL) alleviates the need for expensive pixel-level annotations. In MIL, learning is performed on slide-level labels, in which a pathologist provides information about whether a slide includes cancerous tissue. Here, we propose Self-ViT-MIL, a novel approach for classifying and localizing cancerous areas based on slide-level annotations, eliminating the need for pixel-wise annotated training data. Self-ViT- MIL is pre-trained in a self-supervised setting to learn rich feature representation without relying on any labels. The recent Vision Transformer (ViT) architecture builds the feature extractor of Self-ViT-MIL. For localizing cancerous regions, a MIL aggregator with global attention is utilized. To the best of our knowledge, Self-ViT- MIL is the first approach to introduce self-supervised ViTs in MIL-based WSI analysis tasks. We showcase the effectiveness of our approach on the common Camelyon16 dataset. Self-ViT-MIL surpasses existing state-of-the-art MIL-based approaches in terms of accuracy and area under the curve (AUC).

With the rapid development of computational pathology, many AI-assisted diagnostic tasks have emerged. Cellular nuclei segmentation can segment various types of cells for downstream analysis, but it relies on predefined categories and lacks flexibility. Moreover, pathology visual question answering can perform image-level understanding but lacks region-level detection capability. To address this, we propose a new benchmark called Pathology Visual Grounding (PathVG), which aims to detect regions based on expressions with different attributes. To evaluate PathVG, we create a new dataset named RefPath which contains 27,610 images with 33,500 language-grounded boxes. Compared to visual grounding in other domains, PathVG presents pathological images at multi-scale and contains expressions with pathological knowledge. In the experimental study, we found that the biggest challenge was the implicit information underlying the pathological expressions. Based on this, we proposed Pathology Knowledge-enhanced Network (PKNet) as the baseline model for PathVG. PKNet leverages the knowledge-enhancement capabilities of Large Language Models (LLMs) to convert pathological terms with implicit information into explicit visual features, and fuses knowledge features with expression features through the designed Knowledge Fusion Module (KFM). The proposed method achieves state-of-the-art performance on the PathVG benchmark.

Accurate and interpretable multi-disease diagnosis remains a critical challenge in medical research, particularly when leveraging heterogeneous multimodal medical data. Current approaches often rely on single-modal data, limiting their ability to comprehensively understand complex diseases. To address this, we propose MedTVT-R1, a novel Multimodal Large Language Model (MLLM) framework designed to integrate clinical multimodal data for reasoning and diagnosing multiple diseases. We construct MedTVT-QA, a curated instruction dataset that provides question-answer pairs for physiological-level interpretations and disease-level diagnoses with a Chain of Evidence approach. MedTVT-R1 incorporates a modality perception layer to capture inter-modal dependencies and adaptively weight modality contributions. Additionally, we employ Group Relative Policy Optimization (GRPO)-based Reinforcement Fine-Tuning with a Jaccard Reward function to enhance diagnostic reasoning. Experimental results demonstrate MedTVT-R1's superiority in multimodal feature utilization and multi-disease diagnosis, offering significant potential for clinical applications such as diagnostic report generation and comorbidity reasoning. The dataset and code are available at https://github.com/keke-nice/MedTVT-R1.

Vision-Language Models (VLMs) show promise in medical image analysis, yet their capacity for structured reasoning in complex domains like dermatology is often limited by data scarcity and the high computational cost of advanced training techniques. To address these challenges, we introduce DermIQ-VLM, a VLM developed through a multi-stage, resource-efficient methodology designed to emulate a dermatologist's diagnostic process. Our primary contribution is a modified version of Grouped Relative Policy Optimization (GRPO), called GRPO++, which stabilizes the powerful but data-intensive GRPO framework. Our proposed training pipeline first employs GRPO++ for reasoning-oriented disease recognition, followed by supervised fine-tuning for conversational ability. To mitigate factual errors introduced during this step, we then align the model using Direct Preference Optimization (DPO), leveraging a Knowledge Graph-based system as a scalable proxy for expert preference. A preliminary evaluation on a curated dermatological dataset demonstrates that our proposed methodology yields notable performance gains over standard fine-tuning approaches. These findings validate the potential of our pipeline as a feasible pathway for developing specialized, reliable VLMs in resource-constrained environments.

Accurate classification of computed tomography (CT) images is essential for diagnosis and treatment planning, but existing methods often struggle with the subtle and spatially diverse nature of pathological features. Current approaches typically process images uniformly, limiting their ability to detect localized abnormalities that require focused analysis. We introduce UGPL, an uncertainty-guided progressive learning framework that performs a global-to-local analysis by first identifying regions of diagnostic ambiguity and then conducting detailed examination of these critical areas. Our approach employs evidential deep learning to quantify predictive uncertainty, guiding the extraction of informative patches through a non-maximum suppression mechanism that maintains spatial diversity. This progressive refinement strategy, combined with an adaptive fusion mechanism, enables UGPL to integrate both contextual information and fine-grained details. Experiments across three CT datasets demonstrate that UGPL consistently outperforms state-of-the-art methods, achieving improvements of 3.29%, 2.46%, and 8.08% in accuracy for kidney abnormality, lung cancer, and COVID-19 detection, respectively. Our analysis shows that the uncertainty-guided component provides substantial benefits, with performance dramatically increasing when the full progressive learning pipeline is implemented. Our code is available at: https://github.com/shravan-18/UGPL

Medical image analysis is critical yet challenged by the need of jointly segmenting organs or tissues, and numerous instances for anatomical structures and tumor microenvironment analysis. Existing studies typically formulated different segmentation tasks in isolation, which overlooks the fundamental interdependencies between these tasks, leading to suboptimal segmentation performance and insufficient medical image understanding. To address this issue, we propose a Co-Seg++ framework for versatile medical segmentation. Specifically, we introduce a novel co-segmentation paradigm, allowing semantic and instance segmentation tasks to mutually enhance each other. We first devise a spatio-temporal prompt encoder (STP-Encoder) to capture long-range spatial and temporal relationships between segmentation regions and image embeddings as prior spatial constraints. Moreover, we devise a multi-task collaborative decoder (MTC-Decoder) that leverages cross-guidance to strengthen the contextual consistency of both tasks, jointly computing semantic and instance segmentation masks. Extensive experiments on diverse CT and histopathology datasets demonstrate that the proposed Co-Seg++ outperforms state-of-the-arts in the semantic, instance, and panoptic segmentation of dental anatomical structures, histopathology tissues, and nuclei instances. The source code is available at https://github.com/xq141839/Co-Seg-Plus.

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-mini, o1, and DeepSeek-R1, achieve only 45.82%, 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 AIs 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.

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

Dermatological diagnosis represents a complex multimodal challenge that requires integrating visual features with specialized clinical knowledge. While vision-language pretraining (VLP) has advanced medical AI, its effectiveness in dermatology is limited by text length constraints and the lack of structured texts. In this paper, we introduce MAKE, a Multi-Aspect Knowledge-Enhanced vision-language pretraining framework for zero-shot dermatological tasks. Recognizing that comprehensive dermatological descriptions require multiple knowledge aspects that exceed standard text constraints, our framework introduces: (1) a multi-aspect contrastive learning strategy that decomposes clinical narratives into knowledge-enhanced sub-texts through large language models, (2) a fine-grained alignment mechanism that connects subcaptions with diagnostically relevant image features, and (3) a diagnosis-guided weighting scheme that adaptively prioritizes different sub-captions based on clinical significance prior. Through pretraining on 403,563 dermatological image-text pairs collected from education resources, MAKE significantly outperforms state-of-the-art VLP models on eight datasets across zero-shot skin disease classification, concept annotation, and cross-modal retrieval tasks. Our code will be made publicly available at https: //github.com/SiyuanYan1/MAKE.

Semi-supervised learning has become a compelling approach for 3D tooth segmentation from CBCT scans, where labeled data is minimal. However, existing methods still face two persistent challenges: limited corrective supervision in structurally ambiguous or mislabeled regions during supervised training and performance degradation caused by unreliable pseudo-labels on unlabeled data. To address these problems, we propose Region-Aware Instructive Learning (RAIL), a dual-group dual-student, semi-supervised framework. Each group contains two student models guided by a shared teacher network. By alternating training between the two groups, RAIL promotes intergroup knowledge transfer and collaborative region-aware instruction while reducing overfitting to the characteristics of any single model. Specifically, RAIL introduces two instructive mechanisms. Disagreement-Focused Supervision (DFS) Controller improves supervised learning by instructing predictions only within areas where student outputs diverge from both ground truth and the best student, thereby concentrating supervision on structurally ambiguous or mislabeled areas. In the unsupervised phase, Confidence-Aware Learning (CAL) Modulator reinforces agreement in regions with high model certainty while reducing the effect of low-confidence predictions during training. This helps prevent our model from learning unstable patterns and improves the overall reliability of pseudo-labels. Extensive experiments on four CBCT tooth segmentation datasets show that RAIL surpasses state-of-the-art methods under limited annotation. Our code will be available at https://github.com/Tournesol-Saturday/RAIL.

Medical imaging is crucial for diagnosing a patient's health condition, and accurate segmentation of these images is essential for isolating regions of interest to ensure precise diagnosis and treatment planning. Existing methods primarily rely on bounding boxes or point-based prompts, while few have explored text-related prompts, despite clinicians often describing their observations and instructions in natural language. To address this gap, we first propose a RAG-based free-form text prompt generator, that leverages the domain corpus to generate diverse and realistic descriptions. Then, we introduce FLanS, a novel medical image segmentation model that handles various free-form text prompts, including professional anatomy-informed queries, anatomy-agnostic position-driven queries, and anatomy-agnostic size-driven queries. Additionally, our model also incorporates a symmetry-aware canonicalization module to ensure consistent, accurate segmentations across varying scan orientations and reduce confusion between the anatomical position of an organ and its appearance in the scan. FLanS is trained on a large-scale dataset of over 100k medical images from 7 public datasets. Comprehensive experiments demonstrate the model's superior language understanding and segmentation precision, along with a deep comprehension of the relationship between them, outperforming SOTA baselines on both in-domain and out-of-domain datasets.

Current Vision-Language Models (VLMs) struggle to ground anatomical regions in 3D medical images and reason about them in a step-by-step manner, a key requirement of real-world diagnostic assessment. This ability is essential for aligning model outputs with the diagnostic workflows clinicians use in practice, enabling trustworthy clinician-AI collaboration. Existing 3D datasets provide localization labels, but none support this "grounded reasoning" ability. To address this gap, we introduce 3DReasonKnee, the first 3D grounded reasoning dataset for medical images, which provides 494k high-quality quintuples derived from 7,970 3D knee MRI volumes. Each quintuple includes: (1) the 3D MRI volume, (2) a diagnostic question targeting a specific anatomical region (3) a 3D bounding box localizing the relevant anatomical structures, (4) clinician-generated diagnostic reasoning steps that explicitly detail the 3D reasoning process, and (5) structured severity assessments for the relevant anatomical region. The creation and validation of 3DReasonKnee, involving over 450 hours of expert clinician time for manually segmenting MRIs and generating reasoning chains, ensures its superior quality and clinical relevance. We establish ReasonKnee-Bench to evaluate localization and diagnostic accuracy, providing insight into VLM ability to perform grounding and severity assessment across anatomical regions and diagnostic inquiries. We benchmark five state-of-the-art VLMs, providing baseline performance for ReasonKnee-Bench. By providing this unique resource of expert-annotated 3D reasoning pathways, 3DReasonKnee serves as a repository of orthopedic surgeons' diagnostic expertise and offers a vital testbed for advancing multimodal medical AI systems towards 3D, clinically aligned, localized decision-making capabilities. The dataset can be found in: https://huggingface.co/datasets/rajpurkarlab/3DReasonKnee

Retrieval-augmented generation (RAG) is a well-suited technique for retrieving privacy-sensitive Electronic Health Records (EHR). It can serve as a key module of the healthcare copilot, helping reduce misdiagnosis for healthcare practitioners and patients. However, the diagnostic accuracy and specificity of existing heuristic-based RAG models used in the medical domain are inadequate, particularly for diseases with similar manifestations. This paper proposes MedRAG, a RAG model enhanced by knowledge graph (KG)-elicited reasoning for the medical domain that retrieves diagnosis and treatment recommendations based on manifestations. MedRAG systematically constructs a comprehensive four-tier hierarchical diagnostic KG encompassing critical diagnostic differences of various diseases. These differences are dynamically integrated with similar EHRs retrieved from an EHR database, and reasoned within a large language model. This process enables more accurate and specific decision support, while also proactively providing follow-up questions to enhance personalized medical decision-making. MedRAG is evaluated on both a public dataset DDXPlus and a private chronic pain diagnostic dataset (CPDD) collected from Tan Tock Seng Hospital, and its performance is compared against various existing RAG methods. Experimental results show that, leveraging the information integration and relational abilities of the KG, our MedRAG provides more specific diagnostic insights and outperforms state-of-the-art models in reducing misdiagnosis rates. Our code will be available at https://github.com/SNOWTEAM2023/MedRAG

This study presents a deep learning system for breast cancer detection in mammography, developed using a modified EfficientNetV2 architecture with enhanced attention mechanisms. The model was trained on mammograms from a major Thai medical center and validated on three distinct datasets: an in-domain test set (9,421 cases), a biopsy-confirmed set (883 cases), and an out-of-domain generalizability set (761 cases) collected from two different hospitals. For cancer detection, the model achieved AUROCs of 0.89, 0.96, and 0.94 on the respective datasets. The system's lesion localization capability, evaluated using metrics including Lesion Localization Fraction (LLF) and Non-Lesion Localization Fraction (NLF), demonstrated robust performance in identifying suspicious regions. Clinical validation through concordance tests showed strong agreement with radiologists: 83.5% classification and 84.0% localization concordance for biopsy-confirmed cases, and 78.1% classification and 79.6% localization concordance for out-of-domain cases. Expert radiologists' acceptance rate also averaged 96.7% for biopsy-confirmed cases, and 89.3% for out-of-domain cases. The system achieved a System Usability Scale score of 74.17 for source hospital, and 69.20 for validation hospitals, indicating good clinical acceptance. These results demonstrate the model's effectiveness in assisting mammogram interpretation, with the potential to enhance breast cancer screening workflows in clinical practice.

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

Vision-grounded medical report generation aims to produce clinically accurate descriptions of medical images, anchored in explicit visual evidence to improve interpretability and facilitate integration into clinical workflows. However, existing methods often rely on separately trained detection modules that require extensive expert annotations, introducing high labeling costs and limiting generalizability due to pathology distribution bias across datasets. To address these challenges, we propose Self-Supervised Anatomical Consistency Learning (SS-ACL) -- a novel and annotation-free framework that aligns generated reports with corresponding anatomical regions using simple textual prompts. SS-ACL constructs a hierarchical anatomical graph inspired by the invariant top-down inclusion structure of human anatomy, organizing entities by spatial location. It recursively reconstructs fine-grained anatomical regions to enforce intra-sample spatial alignment, inherently guiding attention maps toward visually relevant areas prompted by text. To further enhance inter-sample semantic alignment for abnormality recognition, SS-ACL introduces a region-level contrastive learning based on anatomical consistency. These aligned embeddings serve as priors for report generation, enabling attention maps to provide interpretable visual evidence. Extensive experiments demonstrate that SS-ACL, without relying on expert annotations, (i) generates accurate and visually grounded reports -- outperforming state-of-the-art methods by 10\% in lexical accuracy and 25\% in clinical efficacy, and (ii) achieves competitive performance on various downstream visual tasks, surpassing current leading visual foundation models by 8\% in zero-shot visual grounding.

Histology review is often used as the `gold standard' for disease diagnosis. Computer aided diagnosis tools can potentially help improve current pathology workflows by reducing examination time and interobserver variability. Previous work in cancer grading has focused mainly on classifying pre-defined regions of interest (ROIs), or relied on large amounts of fine-grained labels. In this paper, we propose a two-stage attention-based multiple instance learning model for slide-level cancer grading and weakly-supervised ROI detection and demonstrate its use in prostate cancer. Compared with existing Gleason classification models, our model goes a step further by utilizing visualized saliency maps to select informative tiles for fine-grained grade classification. The model was primarily developed on a large-scale whole slide dataset consisting of 3,521 prostate biopsy slides with only slide-level labels from 718 patients. The model achieved state-of-the-art performance for prostate cancer grading with an accuracy of 85.11\% for classifying benign, low-grade (Gleason grade 3+3 or 3+4), and high-grade (Gleason grade 4+3 or higher) slides on an independent test set.

Precision agriculture relies heavily on accurate image analysis for crop disease identification and treatment recommendation, yet existing vision-language models (VLMs) often underperform in specialized agricultural domains. This work presents a domain-aware framework for agricultural image processing that combines prompt-based expert evaluation with self-consistency mechanisms to enhance VLM reliability in precision agriculture applications. We introduce two key innovations: (1) a prompt-based evaluation protocol that configures a language model as an expert plant pathologist for scalable assessment of image analysis outputs, and (2) a cosine-consistency self-voting mechanism that generates multiple candidate responses from agricultural images and selects the most semantically coherent diagnosis using domain-adapted embeddings. Applied to maize leaf disease identification from field images using a fine-tuned PaliGemma model, our approach improves diagnostic accuracy from 82.2\% to 87.8\%, symptom analysis from 38.9\% to 52.2\%, and treatment recommendation from 27.8\% to 43.3\% compared to standard greedy decoding. The system remains compact enough for deployment on mobile devices, supporting real-time agricultural decision-making in resource-constrained environments. These results demonstrate significant potential for AI-driven precision agriculture tools that can operate reliably in diverse field conditions.

Medical image segmentation is fundamental for biomedical discovery. Existing methods lack generalizability and demand extensive, time-consuming manual annotation for new clinical application. Here, we propose MedSAM-3, a text promptable medical segmentation model for medical image and video segmentation. By fine-tuning the Segment Anything Model (SAM) 3 architecture on medical images paired with semantic conceptual labels, our MedSAM-3 enables medical Promptable Concept Segmentation (PCS), allowing precise targeting of anatomical structures via open-vocabulary text descriptions rather than solely geometric prompts. We further introduce the MedSAM-3 Agent, a framework that integrates Multimodal Large Language Models (MLLMs) to perform complex reasoning and iterative refinement in an agent-in-the-loop workflow. Comprehensive experiments across diverse medical imaging modalities, including X-ray, MRI, Ultrasound, CT, and video, demonstrate that our approach significantly outperforms existing specialist and foundation models. We will release our code and model at https://github.com/Joey-S-Liu/MedSAM3.

This paper concerns the research problem of point cloud registration to find the rigid transformation to optimally align the source point set with the target one. Learning robust point cloud registration models with deep neural networks has emerged as a powerful paradigm, offering promising performance in predicting the global geometric transformation for a pair of point sets. Existing methods firstly leverage an encoder to regress a latent shape embedding, which is then decoded into a shape-conditioned transformation via concatenation-based conditioning. However, different regions of a 3D shape vary in their geometric structures which makes it more sense that we have a region-conditioned transformation instead of the shape-conditioned one. In this paper we present a Region-Aware point cloud Registration, denoted as RAR, to predict transformation for pairwise point sets in the self-supervised learning fashion. More specifically, we develop a novel region-aware decoder (RAD) module that is formed with an implicit neural region representation parameterized by neural networks. The implicit neural region representation is learned with a self-supervised 3D shape reconstruction loss without the need for region labels. Consequently, the region-aware decoder (RAD) module guides the training of the region-aware transformation (RAT) module and region-aware weight (RAW) module, which predict the transforms and weights for different regions respectively. The global geometric transformation from source point set to target one is then formed by the weighted fusion of region-aware transforms. Compared to the state-of-the-art approaches, our experiments show that our RAR achieves superior registration performance over various benchmark datasets (e.g. ModelNet40).

Automated interpretation of CT images-particularly localizing and describing abnormal findings across multi-plane and whole-body scans-remains a significant challenge in clinical radiology. This work aims to address this challenge through four key contributions: (i) On taxonomy, we collaborate with senior radiologists to propose a comprehensive hierarchical classification system, with 404 representative abnormal findings across all body regions; (ii) On data, we contribute a dataset containing over 14.5K CT images from multiple planes and all human body regions, and meticulously provide grounding annotations for over 19K abnormalities, each linked to the detailed description and cast into the taxonomy; (iii) On model development, we propose OminiAbnorm-CT, which can automatically ground and describe abnormal findings on multi-plane and whole-body CT images based on text queries, while also allowing flexible interaction through visual prompts; (iv) On benchmarks, we establish three representative evaluation tasks based on real clinical scenarios. Through extensive experiments, we show that OminiAbnorm-CT can significantly outperform existing methods on all the tasks and metrics.

Pathology is the study of microscopic inspection of tissue, and a pathology diagnosis is often the medical gold standard to diagnose disease. Pathology images provide a unique challenge for computer-vision-based analysis: a single pathology Whole Slide Image (WSI) is gigapixel-sized and often contains hundreds of thousands to millions of objects of interest across multiple resolutions. In this work, we propose PathoLogy Universal TransfOrmer (PLUTO): a light-weight pathology FM that is pre-trained on a diverse dataset of 195 million image tiles collected from multiple sites and extracts meaningful representations across multiple WSI scales that enable a large variety of downstream pathology tasks. In particular, we design task-specific adaptation heads that utilize PLUTO's output embeddings for tasks which span pathology scales ranging from subcellular to slide-scale, including instance segmentation, tile classification, and slide-level prediction. We compare PLUTO's performance to other state-of-the-art methods on a diverse set of external and internal benchmarks covering multiple biologically relevant tasks, tissue types, resolutions, stains, and scanners. We find that PLUTO matches or outperforms existing task-specific baselines and pathology-specific foundation models, some of which use orders-of-magnitude larger datasets and model sizes when compared to PLUTO. Our findings present a path towards a universal embedding to power pathology image analysis, and motivate further exploration around pathology foundation models in terms of data diversity, architectural improvements, sample efficiency, and practical deployability in real-world applications.

With over 85 million CT scans performed annually in the United States, creating tumor-related reports is a challenging and time-consuming task for radiologists. To address this need, we present RadGPT, an Anatomy-Aware Vision-Language AI Agent for generating detailed reports from CT scans. RadGPT first segments tumors, including benign cysts and malignant tumors, and their surrounding anatomical structures, then transforms this information into both structured reports and narrative reports. These reports provide tumor size, shape, location, attenuation, volume, and interactions with surrounding blood vessels and organs. Extensive evaluation on unseen hospitals shows that RadGPT can produce accurate reports, with high sensitivity/specificity for small tumor (<2 cm) detection: 80/73% for liver tumors, 92/78% for kidney tumors, and 77/77% for pancreatic tumors. For large tumors, sensitivity ranges from 89% to 97%. The results significantly surpass the state-of-the-art in abdominal CT report generation. RadGPT generated reports for 17 public datasets. Through radiologist review and refinement, we have ensured the reports' accuracy, and created the first publicly available image-text 3D medical dataset, comprising over 1.8 million text tokens and 2.7 million images from 9,262 CT scans, including 2,947 tumor scans/reports of 8,562 tumor instances. Our reports can: (1) localize tumors in eight liver sub-segments and three pancreatic sub-segments annotated per-voxel; (2) determine pancreatic tumor stage (T1-T4) in 260 reports; and (3) present individual analyses of multiple tumors--rare in human-made reports. Importantly, 948 of the reports are for early-stage tumors.

Medical imaging plays a pivotal role in modern healthcare, with computed tomography pulmonary angiography (CTPA) being a critical tool for diagnosing pulmonary embolism and other thoracic conditions. However, the complexity of interpreting CTPA scans and generating accurate radiology reports remains a significant challenge. This paper introduces Abn-BLIP (Abnormality-aligned Bootstrapping Language-Image Pretraining), an advanced diagnosis model designed to align abnormal findings to generate the accuracy and comprehensiveness of radiology reports. By leveraging learnable queries and cross-modal attention mechanisms, our model demonstrates superior performance in detecting abnormalities, reducing missed findings, and generating structured reports compared to existing methods. Our experiments show that Abn-BLIP outperforms state-of-the-art medical vision-language models and 3D report generation methods in both accuracy and clinical relevance. These results highlight the potential of integrating multimodal learning strategies for improving radiology reporting. The source code is available at https://github.com/zzs95/abn-blip.

The field of computational pathology has been transformed with recent advances in foundation models that encode histopathology region-of-interests (ROIs) into versatile and transferable feature representations via self-supervised learning (SSL). However, translating these advancements to address complex clinical challenges at the patient and slide level remains constrained by limited clinical data in disease-specific cohorts, especially for rare clinical conditions. We propose TITAN, a multimodal whole slide foundation model pretrained using 335,645 WSIs via visual self-supervised learning and vision-language alignment with corresponding pathology reports and 423,122 synthetic captions generated from a multimodal generative AI copilot for pathology. Without any finetuning or requiring clinical labels, TITAN can extract general-purpose slide representations and generate pathology reports that generalize to resource-limited clinical scenarios such as rare disease retrieval and cancer prognosis. We evaluate TITAN on diverse clinical tasks and find that TITAN outperforms both ROI and slide foundation models across machine learning settings such as linear probing, few-shot and zero-shot classification, rare cancer retrieval and cross-modal retrieval, and pathology report generation.

Medical vision-language models (VLMs) excel at image-text understanding but typically rely on a single-pass reasoning that neglects localized visual cues. In clinical practice, however, human experts iteratively scan, focus, and refine the regions of interest before reaching a final diagnosis. To narrow this machine-human perception gap, we introduce ViTAR, a novel VLM framework that emulates the iterative reasoning process of human experts through a cognitive chain of "think-act-rethink-answer". ViTAR treats medical images as interactive objects, enabling models to engage multi-step visual reasoning. To support this approach, we curate a high-quality instruction dataset comprising 1K interactive examples that encode expert-like diagnostic behaviors. In addition, a 16K visual question answering training data has been curated towards fine-grained visual diagnosis. We introduce a two-stage training strategy that begins with supervised fine-tuning to guide cognitive trajectories, followed by the reinforcement learning to optimize decision-making. Extensive evaluations demonstrate that ViTAR outperforms strong state-of-the-art models. Visual attention analysis reveals that from the "think" to "rethink" rounds, ViTAR increasingly anchors visual grounding to clinically critical regions and maintains high attention allocation to visual tokens during reasoning, providing mechanistic insight into its improved performance. These findings demonstrate that embedding expert-style iterative thinking chains into VLMs enhances both performance and trustworthiness of medical AI.

Transformer-based methods have demonstrated impressive results in medical image restoration, attributed to the multi-head self-attention (MSA) mechanism in the spatial dimension. However, the majority of existing Transformers conduct attention within fixed and coarsely partitioned regions (e.g. the entire image or fixed patches), resulting in interference from irrelevant regions and fragmentation of continuous image content. To overcome these challenges, we introduce a novel Region Attention Transformer (RAT) that utilizes a region-based multi-head self-attention mechanism (R-MSA). The R-MSA dynamically partitions the input image into non-overlapping semantic regions using the robust Segment Anything Model (SAM) and then performs self-attention within these regions. This region partitioning is more flexible and interpretable, ensuring that only pixels from similar semantic regions complement each other, thereby eliminating interference from irrelevant regions. Moreover, we introduce a focal region loss to guide our model to adaptively focus on recovering high-difficulty regions. Extensive experiments demonstrate the effectiveness of RAT in various medical image restoration tasks, including PET image synthesis, CT image denoising, and pathological image super-resolution. Code is available at https://github.com/Yaziwel/Region-Attention-Transformer-for-Medical-Image-Restoration.git{https://github.com/RAT}.

Rare diseases collectively affect over 300 million individuals worldwide, yet timely and accurate diagnosis remains a pervasive challenge. This is largely due to their clinical heterogeneity, low individual prevalence, and the limited familiarity most clinicians have with rare conditions. Here, we introduce DeepRare, the first rare disease diagnosis agentic system powered by a large language model (LLM), capable of processing heterogeneous clinical inputs. The system generates ranked diagnostic hypotheses for rare diseases, each accompanied by a transparent chain of reasoning that links intermediate analytic steps to verifiable medical evidence. DeepRare comprises three key components: a central host with a long-term memory module; specialized agent servers responsible for domain-specific analytical tasks integrating over 40 specialized tools and web-scale, up-to-date medical knowledge sources, ensuring access to the most current clinical information. This modular and scalable design enables complex diagnostic reasoning while maintaining traceability and adaptability. We evaluate DeepRare on eight datasets. The system demonstrates exceptional diagnostic performance among 2,919 diseases, achieving 100% accuracy for 1013 diseases. In HPO-based evaluations, DeepRare significantly outperforms other 15 methods, like traditional bioinformatics diagnostic tools, LLMs, and other agentic systems, achieving an average Recall@1 score of 57.18% and surpassing the second-best method (Reasoning LLM) by a substantial margin of 23.79 percentage points. For multi-modal input scenarios, DeepRare achieves 70.60% at Recall@1 compared to Exomiser's 53.20% in 109 cases. Manual verification of reasoning chains by clinical experts achieves 95.40% agreements. Furthermore, the DeepRare system has been implemented as a user-friendly web application http://raredx.cn/doctor.

Automatic diabetic retinopathy (DR) lesions segmentation makes great sense of assisting ophthalmologists in diagnosis. Although many researches have been conducted on this task, most prior works paid too much attention to the designs of networks instead of considering the pathological association for lesions. Through investigating the pathogenic causes of DR lesions in advance, we found that certain lesions are closed to specific vessels and present relative patterns to each other. Motivated by the observation, we propose a relation transformer block (RTB) to incorporate attention mechanisms at two main levels: a self-attention transformer exploits global dependencies among lesion features, while a cross-attention transformer allows interactions between lesion and vessel features by integrating valuable vascular information to alleviate ambiguity in lesion detection caused by complex fundus structures. In addition, to capture the small lesion patterns first, we propose a global transformer block (GTB) which preserves detailed information in deep network. By integrating the above blocks of dual-branches, our network segments the four kinds of lesions simultaneously. Comprehensive experiments on IDRiD and DDR datasets well demonstrate the superiority of our approach, which achieves competitive performance compared to state-of-the-arts.

We present Perceive Anything Model (PAM), a conceptually straightforward and efficient framework for comprehensive region-level visual understanding in images and videos. Our approach extends the powerful segmentation model SAM 2 by integrating Large Language Models (LLMs), enabling simultaneous object segmentation with the generation of diverse, region-specific semantic outputs, including categories, label definition, functional explanations, and detailed captions. A key component, Semantic Perceiver, is introduced to efficiently transform SAM 2's rich visual features, which inherently carry general vision, localization, and semantic priors into multi-modal tokens for LLM comprehension. To support robust multi-granularity understanding, we also develop a dedicated data refinement and augmentation pipeline, yielding a high-quality dataset of 1.5M image and 0.6M video region-semantic annotations, including novel region-level streaming video caption data. PAM is designed for lightweightness and efficiency, while also demonstrates strong performance across a diverse range of region understanding tasks. It runs 1.2-2.4x faster and consumes less GPU memory than prior approaches, offering a practical solution for real-world applications. We believe that our effective approach will serve as a strong baseline for future research in region-level visual understanding.

Medical image grounding aims to align natural language phrases with specific regions in medical images, serving as a foundational task for intelligent diagnosis, visual question answering (VQA), and automated report generation (MRG). However, existing research is constrained by limited modality coverage, coarse-grained annotations, and the absence of a unified, generalizable grounding framework. To address these challenges, we construct a large-scale medical grounding dataset Med-GLIP-5M comprising over 5.3 million region-level annotations across seven imaging modalities, covering diverse anatomical structures and pathological findings. The dataset supports both segmentation and grounding tasks with hierarchical region labels, ranging from organ-level boundaries to fine-grained lesions. Based on this foundation, we propose Med-GLIP, a modality-aware grounding framework trained on Med-GLIP-5M. Rather than relying on explicitly designed expert modules, Med-GLIP implicitly acquires hierarchical semantic understanding from diverse training data -- enabling it to recognize multi-granularity structures, such as distinguishing lungs from pneumonia lesions. Extensive experiments demonstrate that Med-GLIP consistently outperforms state-of-the-art baselines across multiple grounding benchmarks. Furthermore, integrating its spatial outputs into downstream tasks, including medical VQA and report generation, leads to substantial performance gains. Our dataset will be released soon.

In healthcare, medical image segmentation is crucial for accurate disease diagnosis and the development of effective treatment strategies. Early detection can significantly aid in managing diseases and potentially prevent their progression. Machine learning, particularly deep convolutional neural networks, has emerged as a promising approach to addressing segmentation challenges. Traditional methods like U-Net use encoding blocks for local representation modeling and decoding blocks to uncover semantic relationships. However, these models often struggle with multi-scale objects exhibiting significant variations in texture and shape, and they frequently fail to capture long-range dependencies in the input data. Transformers designed for sequence-to-sequence predictions have been proposed as alternatives, utilizing global self-attention mechanisms. Yet, they can sometimes lack precise localization due to insufficient granular details. To overcome these limitations, we introduce TransDAE: a novel approach that reimagines the self-attention mechanism to include both spatial and channel-wise associations across the entire feature space, while maintaining computational efficiency. Additionally, TransDAE enhances the skip connection pathway with an inter-scale interaction module, promoting feature reuse and improving localization accuracy. Remarkably, TransDAE outperforms existing state-of-the-art methods on the Synaps multi-organ dataset, even without relying on pre-trained weights.

Deep learning has enabled the development of highly robust foundation models for various pathological tasks across diverse diseases and patient cohorts. Among these models, vision-language pre-training, which leverages large-scale paired data to align pathology image and text embedding spaces, and provides a novel zero-shot paradigm for downstream tasks. However, existing models have been primarily data-driven and lack the incorporation of domain-specific knowledge, which limits their performance in cancer diagnosis, especially for rare tumor subtypes. To address this limitation, we establish a Knowledge-enhanced Pathology (KEEP) foundation model that harnesses disease knowledge to facilitate vision-language pre-training. Specifically, we first construct a disease knowledge graph (KG) that covers 11,454 human diseases with 139,143 disease attributes, including synonyms, definitions, and hypernym relations. We then systematically reorganize the millions of publicly available noisy pathology image-text pairs, into 143K well-structured semantic groups linked through the hierarchical relations of the disease KG. To derive more nuanced image and text representations, we propose a novel knowledge-enhanced vision-language pre-training approach that integrates disease knowledge into the alignment within hierarchical semantic groups instead of unstructured image-text pairs. Validated on 18 diverse benchmarks with more than 14,000 whole slide images (WSIs), KEEP achieves state-of-the-art performance in zero-shot cancer diagnostic tasks. Notably, for cancer detection, KEEP demonstrates an average sensitivity of 89.8% at a specificity of 95.0% across 7 cancer types. For cancer subtyping, KEEP achieves a median balanced accuracy of 0.456 in subtyping 30 rare brain cancers, indicating strong generalizability for diagnosing rare tumors.

Bridging clinical diagnostic reasoning with AI remains a central challenge in medical imaging. We introduce MedCLM, an automated pipeline that converts detection datasets into large-scale medical visual question answering (VQA) data with Chain-of-Thought (CoT) reasoning by linking lesion boxes to organ segmentation and structured rationales. These contextual signals enable medical vision-language models to generate question-answer pairs with step-by-step reasoning. To utilize this data effectively, we propose an Integrated CoT-Curriculum Strategy composed of an Easy stage with explicit lesion boxes for visual grounding, a Medium stage that encourages implicit localization, and a Hard stage for weakly supervised reasoning. Experimental results demonstrate that MedCLM attains state-of-the-art performance on several medical VQA benchmarks, providing a scalable framework for developing clinically aligned medical vision-language models.

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-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-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 https://github.com/linjiemu/MMXU{https://github.com/linjiemu/MMXU}.

Automated diagnosis prediction from medical images is a valuable resource to support clinical decision-making. However, such systems usually need to be trained on large amounts of annotated data, which often is scarce in the medical domain. Zero-shot methods address this challenge by allowing a flexible adaption to new settings with different clinical findings without relying on labeled data. Further, to integrate automated diagnosis in the clinical workflow, methods should be transparent and explainable, increasing medical professionals' trust and facilitating correctness verification. In this work, we introduce Xplainer, a novel framework for explainable zero-shot diagnosis in the clinical setting. Xplainer adapts the classification-by-description approach of contrastive vision-language models to the multi-label medical diagnosis task. Specifically, instead of directly predicting a diagnosis, we prompt the model to classify the existence of descriptive observations, which a radiologist would look for on an X-Ray scan, and use the descriptor probabilities to estimate the likelihood of a diagnosis. Our model is explainable by design, as the final diagnosis prediction is directly based on the prediction of the underlying descriptors. We evaluate Xplainer on two chest X-ray datasets, CheXpert and ChestX-ray14, and demonstrate its effectiveness in improving the performance and explainability of zero-shot diagnosis. Our results suggest that Xplainer provides a more detailed understanding of the decision-making process and can be a valuable tool for clinical diagnosis.

LLMs for clinical decision support often fail under small but clinically meaningful input shifts such as masking a symptom or negating a finding, despite high performance on static benchmarks. These reasoning failures frequently go undetected by standard NLP metrics, which are insensitive to latent representation shifts that drive diagnosis instability. We propose a geometry-aware evaluation framework, LAPD (Latent Agentic Perturbation Diagnostics), which systematically probes the latent robustness of clinical LLMs under structured adversarial edits. Within this framework, we introduce Latent Diagnosis Flip Rate (LDFR), a model-agnostic diagnostic signal that captures representational instability when embeddings cross decision boundaries in PCA-reduced latent space. Clinical notes are generated using a structured prompting pipeline grounded in diagnostic reasoning, then perturbed along four axes: masking, negation, synonym replacement, and numeric variation to simulate common ambiguities and omissions. We compute LDFR across both foundation and clinical LLMs, finding that latent fragility emerges even under minimal surface-level changes. Finally, we validate our findings on 90 real clinical notes from the DiReCT benchmark (MIMIC-IV), confirming the generalizability of LDFR beyond synthetic settings. Our results reveal a persistent gap between surface robustness and semantic stability, underscoring the importance of geometry-aware auditing in safety-critical clinical AI.

We investigate fine-tuning Vision-Language Models (VLMs) for multi-task medical image understanding, focusing on detection, localization, and counting of findings in medical images. Our objective is to evaluate whether instruction-tuned VLMs can simultaneously improve these tasks, with the goal of enhancing diagnostic accuracy and efficiency. Using MedMultiPoints, a multimodal dataset with annotations from endoscopy (polyps and instruments) and microscopy (sperm cells), we reformulate each task into instruction-based prompts suitable for vision-language reasoning. We fine-tune Qwen2.5-VL-7B-Instruct using Low-Rank Adaptation (LoRA) across multiple task combinations. Results show that multi-task training improves robustness and accuracy. For example, it reduces the Count Mean Absolute Error (MAE) and increases Matching Accuracy in the Counting + Pointing task. However, trade-offs emerge, such as more zero-case point predictions, indicating reduced reliability in edge cases despite overall performance gains. Our study highlights the potential of adapting general-purpose VLMs to specialized medical tasks via prompt-driven fine-tuning. This approach mirrors clinical workflows, where radiologists simultaneously localize, count, and describe findings - demonstrating how VLMs can learn composite diagnostic reasoning patterns. The model produces interpretable, structured outputs, offering a promising step toward explainable and versatile medical AI. Code, model weights, and scripts will be released for reproducibility at https://github.com/simula/PointDetectCount.

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

Medical image classification in radiology faces significant challenges, particularly in generalizing to unseen pathologies. In contrast, CLIP offers a promising solution by leveraging multimodal learning to improve zero-shot classification performance. However, in the medical domain, lesions can be small and might not be well represented in the embedding space. Therefore, in this paper, we explore the potential of visual prompt engineering to enhance the capabilities of Vision Language Models (VLMs) in radiology. Leveraging BiomedCLIP, trained on extensive biomedical image-text pairs, we investigate the impact of embedding visual markers directly within radiological images to guide the model's attention to critical regions. Our evaluation on the JSRT dataset, focusing on lung nodule malignancy classification, demonstrates that incorporating visual prompts x2013 such as arrows, circles, and contours x2013 significantly improves classification metrics including AUROC, AUPRC, F1 score, and accuracy. Moreover, the study provides attention maps, showcasing enhanced model interpretability and focus on clinically relevant areas. These findings underscore the efficacy of visual prompt engineering as a straightforward yet powerful approach to advance VLM performance in medical image analysis.

The emergence of vision-language models (VLMs) has opened new possibilities for clinical reasoning and has shown promising performance in dermatological diagnosis. However, their trustworthiness and clinical utility are often limited by three major factors: (1) Data heterogeneity, where diverse datasets lack consistent diagnostic labels and clinical concept annotations; (2) Absence of grounded diagnostic rationales, leading to a scarcity of reliable reasoning supervision; and (3) Limited scalability and generalization, as models trained on small, densely annotated datasets struggle to transfer nuanced reasoning to large, sparsely-annotated ones. To address these limitations, we propose SkinR1, a novel dermatological VLM that combines deep, textbook-based reasoning with the broad generalization capabilities of reinforcement learning (RL). SkinR1 systematically resolves the key challenges through a unified, end-to-end framework. First, we design a textbook-based reasoning generator that synthesizes high-fidelity, hierarchy-aware, and differential-diagnosis (DDx)-informed trajectories, providing reliable expert-level supervision. Second, we leverage the constructed trajectories for supervised fine-tuning (SFT) empowering the model with grounded reasoning ability. Third, we develop a novel RL paradigm that, by incorporating the hierarchical structure of diseases, effectively transfers these grounded reasoning patterns to large-scale, sparse data. Extensive experiments on multiple dermatology datasets demonstrate that SkinR1 achieves superior diagnostic accuracy. The ablation study demonstrates the importance of the reasoning foundation instilled by SFT.

Automated structured radiology report generation (SRRG) from chest X-ray images offers significant potential to reduce workload of radiologists by generating reports in structured formats that ensure clarity, consistency, and adherence to clinical reporting standards. While radiologists effectively utilize available clinical contexts in their diagnostic reasoning, existing SRRG systems overlook these essential elements. This fundamental gap leads to critical problems including temporal hallucinations when referencing non-existent clinical contexts. To address these limitations, we propose contextualized SRRG (C-SRRG) that comprehensively incorporates rich clinical context for SRRG. We curate C-SRRG dataset by integrating comprehensive clinical context encompassing 1) multi-view X-ray images, 2) clinical indication, 3) imaging techniques, and 4) prior studies with corresponding comparisons based on patient histories. Through extensive benchmarking with state-of-the-art multimodal large language models, we demonstrate that incorporating clinical context with the proposed C-SRRG significantly improves report generation quality. We publicly release dataset, code, and checkpoints to facilitate future research for clinically-aligned automated RRG at https://github.com/vuno/contextualized-srrg.

The chest X-ray is one of the most commonly accessible radiological examinations for screening and diagnosis of many lung diseases. A tremendous number of X-ray imaging studies accompanied by radiological reports are accumulated and stored in many modern hospitals' Picture Archiving and Communication Systems (PACS). On the other side, it is still an open question how this type of hospital-size knowledge database containing invaluable imaging informatics (i.e., loosely labeled) can be used to facilitate the data-hungry deep learning paradigms in building truly large-scale high precision computer-aided diagnosis (CAD) systems. In this paper, we present a new chest X-ray database, namely "ChestX-ray8", which comprises 108,948 frontal-view X-ray images of 32,717 unique patients with the text-mined eight disease image labels (where each image can have multi-labels), from the associated radiological reports using natural language processing. Importantly, we demonstrate that these commonly occurring thoracic diseases can be detected and even spatially-located via a unified weakly-supervised multi-label image classification and disease localization framework, which is validated using our proposed dataset. Although the initial quantitative results are promising as reported, deep convolutional neural network based "reading chest X-rays" (i.e., recognizing and locating the common disease patterns trained with only image-level labels) remains a strenuous task for fully-automated high precision CAD systems. Data download link: https://nihcc.app.box.com/v/ChestXray-NIHCC

Accurate diagnosis with medical large language models is hindered by knowledge gaps and hallucinations. Retrieval and tool-augmented methods help, but their impact is limited by weak use of external knowledge and poor feedback-reasoning traceability. To address these challenges, We introduce Deep-DxSearch, an agentic RAG system trained end-to-end with reinforcement learning (RL) that enables steer tracebale retrieval-augmented reasoning for medical diagnosis. In Deep-DxSearch, we first construct a large-scale medical retrieval corpus comprising patient records and reliable medical knowledge sources to support retrieval-aware reasoning across diagnostic scenarios. More crutially, we frame the LLM as the core agent and the retrieval corpus as its environment, using tailored rewards on format, retrieval, reasoning structure, and diagnostic accuracy, thereby evolving the agentic RAG policy from large-scale data through RL. Experiments demonstrate that our end-to-end agentic RL training framework consistently outperforms prompt-engineering and training-free RAG approaches across multiple data centers. After training, Deep-DxSearch achieves substantial gains in diagnostic accuracy, surpassing strong diagnostic baselines such as GPT-4o, DeepSeek-R1, and other medical-specific frameworks for both common and rare disease diagnosis under in-distribution and out-of-distribution settings. Moreover, ablation studies on reward design and retrieval corpus components confirm their critical roles, underscoring the uniqueness and effectiveness of our approach compared with traditional implementations. Finally, case studies and interpretability analyses highlight improvements in Deep-DxSearch's diagnostic policy, providing deeper insight into its performance gains and supporting clinicians in delivering more reliable and precise preliminary diagnoses. See https://github.com/MAGIC-AI4Med/Deep-DxSearch.

Pathology diagnosis based on EEG signals and decoding brain activity holds immense importance in understanding neurological disorders. With the advancement of artificial intelligence methods and machine learning techniques, the potential for accurate data-driven diagnoses and effective treatments has grown significantly. However, applying machine learning algorithms to real-world datasets presents diverse challenges at multiple levels. The scarcity of labelled data, especially in low regime scenarios with limited availability of real patient cohorts due to high costs of recruitment, underscores the vital deployment of scaling and transfer learning techniques. In this study, we explore a real-world pathology classification task to highlight the effectiveness of data and model scaling and cross-dataset knowledge transfer. As such, we observe varying performance improvements through data scaling, indicating the need for careful evaluation and labelling. Additionally, we identify the challenges of possible negative transfer and emphasize the significance of some key components to overcome distribution shifts and potential spurious correlations and achieve positive transfer. We see improvement in the performance of the target model on the target (NMT) datasets by using the knowledge from the source dataset (TUAB) when a low amount of labelled data was available. Our findings indicate a small and generic model (e.g. ShallowNet) performs well on a single dataset, however, a larger model (e.g. TCN) performs better on transfer and learning from a larger and diverse dataset.

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.

A pre-trained visual-language model, contrastive language-image pre-training (CLIP), successfully accomplishes various downstream tasks with text prompts, such as finding images or localizing regions within the image. Despite CLIP's strong multi-modal data capabilities, it remains limited in specialized environments, such as medical applications. For this purpose, many CLIP variants-i.e., BioMedCLIP, and MedCLIP-SAMv2-have emerged, but false positives related to normal regions persist. Thus, we aim to present a simple yet important goal of reducing false positives in medical anomaly detection. We introduce a Contrastive LAnguage Prompting (CLAP) method that leverages both positive and negative text prompts. This straightforward approach identifies potential lesion regions by visual attention to the positive prompts in the given image. To reduce false positives, we attenuate attention on normal regions using negative prompts. Extensive experiments with the BMAD dataset, including six biomedical benchmarks, demonstrate that CLAP method enhances anomaly detection performance. Our future plans include developing an automated fine prompting method for more practical usage.

Representation learning of pathology whole-slide images (WSIs) has been has primarily relied on weak supervision with Multiple Instance Learning (MIL). However, the slide representations resulting from this approach are highly tailored to specific clinical tasks, which limits their expressivity and generalization, particularly in scenarios with limited data. Instead, we hypothesize that morphological redundancy in tissue can be leveraged to build a task-agnostic slide representation in an unsupervised fashion. To this end, we introduce PANTHER, a prototype-based approach rooted in the Gaussian mixture model that summarizes the set of WSI patches into a much smaller set of morphological prototypes. Specifically, each patch is assumed to have been generated from a mixture distribution, where each mixture component represents a morphological exemplar. Utilizing the estimated mixture parameters, we then construct a compact slide representation that can be readily used for a wide range of downstream tasks. By performing an extensive evaluation of PANTHER on subtyping and survival tasks using 13 datasets, we show that 1) PANTHER outperforms or is on par with supervised MIL baselines and 2) the analysis of morphological prototypes brings new qualitative and quantitative insights into model interpretability.

Clinical decision-making relies heavily on understanding relative positions of anatomical structures and anomalies. Therefore, for Vision-Language Models (VLMs) to be applicable in clinical practice, the ability to accurately determine relative positions on medical images is a fundamental prerequisite. Despite its importance, this capability remains highly underexplored. To address this gap, we evaluate the ability of state-of-the-art VLMs, GPT-4o, Llama3.2, Pixtral, and JanusPro, and find that all models fail at this fundamental task. Inspired by successful approaches in computer vision, we investigate whether visual prompts, such as alphanumeric or colored markers placed on anatomical structures, can enhance performance. While these markers provide moderate improvements, results remain significantly lower on medical images compared to observations made on natural images. Our evaluations suggest that, in medical imaging, VLMs rely more on prior anatomical knowledge than on actual image content for answering relative position questions, often leading to incorrect conclusions. To facilitate further research in this area, we introduce the MIRP , Medical Imaging Relative Positioning, benchmark dataset, designed to systematically evaluate the capability to identify relative positions in medical images.

Image segmentation plays an essential role in medicine for both diagnostic and interventional tasks. Segmentation approaches are either manual, semi-automated or fully-automated. Manual segmentation offers full control over the quality of the results, but is tedious, time consuming and prone to operator bias. Fully automated methods require no human effort, but often deliver sub-optimal results without providing users with the means to make corrections. Semi-automated approaches keep users in control of the results by providing means for interaction, but the main challenge is to offer a good trade-off between precision and required interaction. In this paper we present a deep learning (DL) based semi-automated segmentation approach that aims to be a "smart" interactive tool for region of interest delineation in medical images. We demonstrate its use for segmenting multiple organs on computed tomography (CT) of the abdomen. Our approach solves some of the most pressing clinical challenges: (i) it requires only one to a few user clicks to deliver excellent 2D segmentations in a fast and reliable fashion; (ii) it can generalize to previously unseen structures and "corner cases"; (iii) it delivers results that can be corrected quickly in a smart and intuitive way up to an arbitrary degree of precision chosen by the user and (iv) ensures high accuracy. We present our approach and compare it to other techniques and previous work to show the advantages brought by our method.

Longitudinal multimodal data, including electronic health records (EHR) and sequential chest X-rays (CXRs), is critical for modeling disease progression, yet remains underutilized due to two key challenges: (1) redundancy in consecutive CXR sequences, where static anatomical regions dominate over clinically-meaningful dynamics, and (2) temporal misalignment between sparse, irregular imaging and continuous EHR data. We introduce DiPro, a novel framework that addresses these challenges through region-aware disentanglement and multi-timescale alignment. First, we disentangle static (anatomy) and dynamic (pathology progression) features in sequential CXRs, prioritizing disease-relevant changes. Second, we hierarchically align these static and dynamic CXR features with asynchronous EHR data via local (pairwise interval-level) and global (full-sequence) synchronization to model coherent progression pathways. Extensive experiments on the MIMIC dataset demonstrate that DiPro could effectively extract temporal clinical dynamics and achieve state-of-the-art performance on both disease progression identification and general ICU prediction tasks.

Efficient vision-language understanding of large Remote Sensing Images (RSIs) is meaningful but challenging. Current Large Vision-Language Models (LVLMs) typically employ limited pre-defined grids to process images, leading to information loss when handling gigapixel RSIs. Conversely, using unlimited grids significantly increases computational costs. To preserve image details while reducing computational complexity, we propose a text-guided token pruning method with Dynamic Image Pyramid (DIP) integration. Our method introduces: (i) a Region Focus Module (RFM) that leverages text-aware region localization capability to identify critical vision tokens, and (ii) a coarse-to-fine image tile selection and vision token pruning strategy based on DIP, which is guided by RFM outputs and avoids directly processing the entire large imagery. Additionally, existing benchmarks for evaluating LVLMs' perception ability on large RSI suffer from limited question diversity and constrained image sizes. We construct a new benchmark named LRS-VQA, which contains 7,333 QA pairs across 8 categories, with image length up to 27,328 pixels. Our method outperforms existing high-resolution strategies on four datasets using the same data. Moreover, compared to existing token reduction methods, our approach demonstrates higher efficiency under high-resolution settings. Dataset and code are in https://github.com/VisionXLab/LRS-VQA.

The rapid increase in the number of Computed Tomography (CT) scan examinations has created an urgent need for automated tools, such as organ segmentation, anomaly classification, and report generation, to assist radiologists with their growing workload. Multi-label classification of Three-Dimensional (3D) CT scans is a challenging task due to the volumetric nature of the data and the variety of anomalies to be detected. Existing deep learning methods based on Convolutional Neural Networks (CNNs) struggle to capture long-range dependencies effectively, while Vision Transformers require extensive pre-training, posing challenges for practical use. Additionally, these existing methods do not explicitly model the radiologist's navigational behavior while scrolling through CT scan slices, which requires both global context understanding and local detail awareness. In this study, we present CT-Scroll, a novel global-local attention model specifically designed to emulate the scrolling behavior of radiologists during the analysis of 3D CT scans. Our approach is evaluated on two public datasets, demonstrating its efficacy through comprehensive experiments and an ablation study that highlights the contribution of each model component.

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

Effectively representing medical images, especially retinal images, presents a considerable challenge due to variations in appearance, size, and contextual information of pathological signs called lesions. Precise discrimination of these lesions is crucial for diagnosing vision-threatening issues such as diabetic retinopathy. While visual attention-based neural networks have been introduced to learn spatial context and channel correlations from retinal images, they often fall short in capturing localized lesion context. Addressing this limitation, we propose a novel attention mechanism called Guided Context Gating, an unique approach that integrates Context Formulation, Channel Correlation, and Guided Gating to learn global context, spatial correlations, and localized lesion context. Our qualitative evaluation against existing attention mechanisms emphasize the superiority of Guided Context Gating in terms of explainability. Notably, experiments on the Zenodo-DR-7 dataset reveal a substantial 2.63% accuracy boost over advanced attention mechanisms & an impressive 6.53% improvement over the state-of-the-art Vision Transformer for assessing the severity grade of retinopathy, even with imbalanced and limited training samples for each class.

Zero-shot medical detection can further improve detection performance without relying on annotated medical images even upon the fine-tuned model, showing great clinical value. Recent studies leverage grounded vision-language models (GLIP) to achieve this by using detailed disease descriptions as prompts for the target disease name during the inference phase. However, these methods typically treat prompts as equivalent context to the target name, making it difficult to assign specific disease knowledge based on visual information, leading to a coarse alignment between images and target descriptions. In this paper, we propose StructuralGLIP, which introduces an auxiliary branch to encode prompts into a latent knowledge bank layer-by-layer, enabling more context-aware and fine-grained alignment. Specifically, in each layer, we select highly similar features from both the image representation and the knowledge bank, forming structural representations that capture nuanced relationships between image patches and target descriptions. These features are then fused across modalities to further enhance detection performance. Extensive experiments demonstrate that StructuralGLIP achieves a +4.1\% AP improvement over prior state-of-the-art methods across seven zero-shot medical detection benchmarks, and consistently improves fine-tuned models by +3.2\% AP on endoscopy image datasets.

Convolutional Neural Networks (CNNs) have advanced existing medical systems for automatic disease diagnosis. However, there are still concerns about the reliability of deep medical diagnosis systems against the potential threats of adversarial attacks since inaccurate diagnosis could lead to disastrous consequences in the safety realm. In this study, we propose a highly robust yet efficient CNN-Transformer hybrid model which is equipped with the locality of CNNs as well as the global connectivity of vision Transformers. To mitigate the high quadratic complexity of the self-attention mechanism while jointly attending to information in various representation subspaces, we construct our attention mechanism by means of an efficient convolution operation. Moreover, to alleviate the fragility of our Transformer model against adversarial attacks, we attempt to learn smoother decision boundaries. To this end, we augment the shape information of an image in the high-level feature space by permuting the feature mean and variance within mini-batches. With less computational complexity, our proposed hybrid model demonstrates its high robustness and generalization ability compared to the state-of-the-art studies on a large-scale collection of standardized MedMNIST-2D datasets.

Pathology plays a critical role in diagnosing a wide range of diseases, yet existing approaches often rely heavily on task-specific models trained on extensive, well-labeled datasets. These methods face sustainability challenges due to the diversity of pathologies and the labor-intensive nature of data collection. To address these limitations, we highlight the need for universal multimodal embeddings that can support multiple downstream tasks. Previous approaches often involve fine-tuning CLIP-based models, which handle images and text separately, limiting their ability to capture complex multimodal relationships. Additionally, these models are evaluated across diverse datasets without a unified benchmark for assessing multimodal embeddings in pathology. To address these challenges, we propose MLLM4PUE, a novel framework that leverages Multimodal Large Language Models (MLLMs) to generate Pathology Universal Embeddings. The MLLM4PUE framework not only facilitates robust integration of images and text but also enhances understanding and fusion capabilities across various tasks. We further introduce the Pathology Multimodal Embedding Benchmark (PMEB), a comprehensive benchmark designed to assess the quality of pathology multimodal embeddings. PMEB comprises 15 original tasks drawn from 14 datasets, organized into three meta-tasks: retrieval, classification, and composed retrieval. Experimental results demonstrate the superiority of MLLM4PUE, illustrating MLLM-based models can effectively support a wide range of downstream tasks and unify the research direction for foundation models in pathology.

Recent accelerations in multi-modal applications have been made possible with the plethora of image and text data available online. However, the scarcity of analogous data in the medical field, specifically in histopathology, has halted comparable progress. To enable similar representation learning for histopathology, we turn to YouTube, an untapped resource of videos, offering 1,087 hours of valuable educational histopathology videos from expert clinicians. From YouTube, we curate Quilt: a large-scale vision-language dataset consisting of 768,826 image and text pairs. Quilt was automatically curated using a mixture of models, including large language models, handcrafted algorithms, human knowledge databases, and automatic speech recognition. In comparison, the most comprehensive datasets curated for histopathology amass only around 200K samples. We combine Quilt with datasets from other sources, including Twitter, research papers, and the internet in general, to create an even larger dataset: Quilt-1M, with 1M paired image-text samples, marking it as the largest vision-language histopathology dataset to date. We demonstrate the value of Quilt-1M by fine-tuning a pre-trained CLIP model. Our model outperforms state-of-the-art models on both zero-shot and linear probing tasks for classifying new histopathology images across 13 diverse patch-level datasets of 8 different sub-pathologies and cross-modal retrieval tasks.

Leveraging pre-trained models with tailored prompts for in-context learning has proven highly effective in NLP tasks. Building on this success, recent studies have applied a similar approach to the Segment Anything Model (SAM) within a ``one-shot" framework, where only a single reference image and its label are employed. However, these methods face limitations in the medical domain, primarily due to SAM's essential requirement for visual prompts and the over-reliance on pixel similarity for generating them. This dependency may lead to (1) inaccurate prompt generation and (2) clustering of point prompts, resulting in suboptimal outcomes. To address these challenges, we introduce Med-PerSAM, a novel and straightforward one-shot framework designed for the medical domain. Med-PerSAM uses only visual prompt engineering and eliminates the need for additional training of the pretrained SAM or human intervention, owing to our novel automated prompt generation process. By integrating our lightweight warping-based prompt tuning model with SAM, we enable the extraction and iterative refinement of visual prompts, enhancing the performance of the pre-trained SAM. This advancement is particularly meaningful in the medical domain, where creating visual prompts poses notable challenges for individuals lacking medical expertise. Our model outperforms various foundational models and previous SAM-based approaches across diverse 2D medical imaging datasets.

Multimodal Large Language Models (MLLMs) have achieved impressive results on vision-language benchmarks, yet it remains unclear whether these benchmarks assess genuine global reasoning or allow success via localized visual cues. Existing evaluation methods do not explicitly measure this distinction, hindering effective dataset curation and real-world focused model development. We introduce Region Comprehension Index (RCI), the first model-based score to directly quantify a dataset's reliance on global versus local visual information. RCI systematically compares reference-model performance on image patches versus full images, revealing if tasks require holistic image understanding or can be solved with partial or localized visual cues. When applying RCI to 13 widely used multimodal benchmarks, we observed that most of them favor localized reasoning and exhibit significant spatial biases, indicating potential risks in real-world applications. RCI equips researchers & practitioners with an actionable tool for diagnosing & mitigating these biases, enabling the construction of datasets and benchmarks to foster the development of robust, enterprise-ready multimodal systems.

Considering the increased workload in pathology laboratories today, automated tools such as artificial intelligence models can help pathologists with their tasks and ease the workload. In this paper, we are proposing a segmentation model (DRU-Net) that can provide a delineation of human non-small cell lung carcinomas and an augmentation method that can improve classification results. The proposed model is a fused combination of truncated pre-trained DenseNet201 and ResNet101V2 as a patch-wise classifier followed by a lightweight U-Net as a refinement model. We have used two datasets (Norwegian Lung Cancer Biobank and Haukeland University Hospital lung cancer cohort) to create our proposed model. The DRU-Net model achieves an average of 0.91 Dice similarity coefficient. The proposed spatial augmentation method (multi-lens distortion) improved the network performance by 3%. Our findings show that choosing image patches that specifically include regions of interest leads to better results for the patch-wise classifier compared to other sampling methods. The qualitative analysis showed that the DRU-Net model is generally successful in detecting the tumor. On the test set, some of the cases showed areas of false positive and false negative segmentation in the periphery, particularly in tumors with inflammatory and reactive changes.

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.