Yingtai Li

Rongsheng Wang, Fenghe Tang, Zihang Jiang et al.

Learning transferable and interpretable representations from medical volumetric scans remains challenging due to complex anatomical structures and weak, heterogeneous supervision provided by radiology reports. In this paper, we propose Anatomy-aware Semantically-Adaptive Pre-training (ASAP), a principled vision-language pre-training framework for fine-grained medical volumetric representation learning from large-scale chest CT scans and their corresponding radiology reports. ASAP integrates three key components: (1) an anatomy-aware knowledge injection module that incorporates organ-level structural priors via off-the-shelf segmentation tool to encourage anatomically coherent representations; (2) a semantically-adaptive selective alignment mechanism that dynamically associates sentence-level findings with localized volumetric regions; and (3) a semantically-adaptive fusion module for effective interaction between anatomically informed visual features and grounded textual cues under dual-modal masked modeling paradigm. Beyond methodological contributions, we establish a comprehensive benchmark for medical volumetric vision-language pre-training on chest CT, covering 15 datasets and 22 downstream tasks spanning abnormality classification, segmentation, disease prognosis prediction, report generation, vocabulary classification, cross-modal retrieval and visual question answering. This benchmark provides standardized evaluation protocols to systematically assess representation quality under diverse clinical settings and data regimes. Extensive experiments demonstrate that ASAP consistently achieves state-of-the-art performance across tasks and datasets, with particularly pronounced gains under limited supervision and distribution shift, validating its effectiveness in learning transferable and clinically meaningful volumetric representations.

Fenghe Tang, Bingkun Nian, Yingtai Li et al.

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

Yuhe Tian, Kun Zhang, Haoran Ma et al.

While large language models (LLMs) have advanced CT report generation, existing methods typically encode 3D volumes holistically, failing to distinguish informative cues from redundant anatomical background. Inspired by radiological cognitive subtraction, we propose Differential Visual Prompting (DiffVP), which conditions report generation on explicit, high-level semantic scan-to-reference differences rather than solely on absolute visual features. DiffVP employs a hierarchical difference extractor to capture complementary global and local semantic discrepancies into a shared latent space, along with a difference-to-prompt generator that transforms these signals into learnable visual prefix tokens for LLM conditioning. These difference prompts serve as structured conditioning signals that implicitly suppress invariant anatomy while amplifying diagnostically relevant visual evidence, thereby facilitating accurate report generation without explicit lesion localization. On two large-scale benchmarks, DiffVP consistently outperforms prior methods, improving the average BLEU-1-4 by +10.98 and +4.36, respectively, and further boosts clinical efficacy on RadGenome-ChestCT (F1 score 0.421). All codes will be released at https://github.com/ArielTYH/DiffVP/.

Wenxin Ma, Xu Zhang, Qingsong Yao et al.

Anomaly detection (AD) identifies outliers for applications like defect and lesion detection. While CLIP shows promise for zero-shot AD tasks due to its strong generalization capabilities, its inherent Anomaly-Unawareness leads to limited discrimination between normal and abnormal features. To address this problem, we propose Anomaly-Aware CLIP (AA-CLIP), which enhances CLIP's anomaly discrimination ability in both text and visual spaces while preserving its generalization capability. AA-CLIP is achieved through a straightforward yet effective two-stage approach: it first creates anomaly-aware text anchors to differentiate normal and abnormal semantics clearly, then aligns patch-level visual features with these anchors for precise anomaly localization. This two-stage strategy, with the help of residual adapters, gradually adapts CLIP in a controlled manner, achieving effective AD while maintaining CLIP's class knowledge. Extensive experiments validate AA-CLIP as a resource-efficient solution for zero-shot AD tasks, achieving state-of-the-art results in industrial and medical applications. The code is available at https://github.com/Mwxinnn/AA-CLIP.

Xu Zhang, Kun Zhang, Wenxin Ma et al.

ICD Coding aims to assign a wide range of medical codes to a medical text document, which is a popular and challenging task in the healthcare domain. To alleviate the problems of long-tail distribution and the lack of annotations of code-specific evidence, many previous works have proposed incorporating code knowledge to improve coding performance. However, existing methods often focus on a single type of knowledge and design specialized modules that are complex and incompatible with each other, thereby limiting their scalability and effectiveness. To address this issue, we propose GKI-ICD, a novel, general knowledge injection framework that integrates three key types of knowledge, namely ICD Description, ICD Synonym, and ICD Hierarchy, without specialized design of additional modules. The comprehensive utilization of the above knowledge, which exhibits both differences and complementarity, can effectively enhance the ICD coding performance. Extensive experiments on existing popular ICD coding benchmarks demonstrate the effectiveness of GKI-ICD, which achieves the state-of-the-art performance on most evaluation metrics. Code is available at https://github.com/xuzhang0112/GKI-ICD.

Yifan Li, Fenghe Tang, Yingtai Li et al.

General-purpose large Vision-Language Models (VLMs) demonstrate strong capabilities in generating detailed descriptions for natural images. However, their performance in the medical domain remains suboptimal, even for relatively straightforward tasks, primarily due to the lack of large-scale, high-quality, specialized medical imaging datasets and the neglect of the diagnostic process that progresses from coarse to fine-grained. To address the first issue, we construct the CT-RATE-VQA dataset, which has 84K QA pairs. For the second issue, we propose MedReason-R1, a medical VLM with explicit reasoning process for disease diagnosis. MedReason-R1 incorporates a novel strategy that embeds zoom-in disease region-of-interest areas into the image, highlighting the crucial role of both global localization and disease-specific details in enhancing the model's diagnostic performance. Furthermore, we introduce the GRPO reinforcement learning framework to MedReason-R1, which enables effective reasoning without relying on costly manual annotations. Compared to recent general-purpose and medical VLMs, MedReason-R1 achieves state-of-the-art performance in CT disease diagnosis while retaining generalization. The code, checkpoints, and dataset are available at: https://github.com/Leevan001/MedReason-R1

Yingtai Li, Haoran Lai, Xiaoqian Zhou et al.

The emergence of Large Language Models (LLMs) presents unprecedented opportunities to revolutionize medical contrastive vision-language pre-training. In this paper, we show how LLMs can facilitate large-scale supervised pre-training, thereby advancing vision-language alignment. We begin by demonstrate that modern LLMs can automatically extract diagnostic labels from radiology reports with remarkable precision (>96\% AUC in our experiments) without complex prompt engineering, enabling the creation of large-scale "silver-standard" datasets at a minimal cost (~\$3 for 50k CT image-report pairs). Further, we find that vision encoder trained on this "silver-standard" dataset achieves performance comparable to those trained on labels extracted by specialized BERT-based models, thereby democratizing the access to large-scale supervised pre-training. Building on this foundation, we proceed to reveal that supervised pre-training fundamentally improves contrastive vision-language alignment. Our approach achieves state-of-the-art performance using only a 3D ResNet-18 with vanilla CLIP training, including 83.8\% AUC for zero-shot diagnosis on CT-RATE, 77.3\% AUC on RAD-ChestCT, and substantial improvements in cross-modal retrieval (MAP@50=53.7\% for image-image, Recall@100=52.2\% for report-image). These results demonstrate the potential of utilizing LLMs to facilitate {\bf more performant and scalable} medical AI systems. Our code is avaiable at https://github.com/SadVoxel/More-performant-and-scalable.

Xueming Fu, Pei Wu, Yingtai Li et al.

Accurate analysis of cardiac motion is crucial for evaluating cardiac function. While dynamic cardiac magnetic resonance imaging (CMR) can capture detailed tissue motion throughout the cardiac cycle, the fine-grained 4D cardiac motion tracking remains challenging due to the homogeneous nature of myocardial tissue and the lack of distinctive features. Existing approaches can be broadly categorized into image based and representation-based, each with its limitations. Image-based methods, including both raditional and deep learning-based registration approaches, either struggle with topological consistency or rely heavily on extensive training data. Representation-based methods, while promising, often suffer from loss of image-level details. To address these limitations, we propose Dynamic 3D Gaussian Representation (Dyna3DGR), a novel framework that combines explicit 3D Gaussian representation with implicit neural motion field modeling. Our method simultaneously optimizes cardiac structure and motion in a self-supervised manner, eliminating the need for extensive training data or point-to-point correspondences. Through differentiable volumetric rendering, Dyna3DGR efficiently bridges continuous motion representation with image-space alignment while preserving both topological and temporal consistency. Comprehensive evaluations on the ACDC dataset demonstrate that our approach surpasses state-of-the-art deep learning-based diffeomorphic registration methods in tracking accuracy. The code will be available in https://github.com/windrise/Dyna3DGR.

Rundong Wang, Wei Ba, Ying Zhou et al.

Recent methods for pathology report generation from whole-slide image (WSI) are capable of producing slide-level diagnostic descriptions but fail to ground fine-grained statements in localized visual evidence. Furthermore, they lack control over which diagnostic details to include and how to verify them. Inspired by emerging agentic analysis paradigms and the diagnostic workflow of pathologists,who selectively examine multiple fields of view, we propose QCAgent, an agentic framework for quality-controllable WSI report generation. The core innovations of this framework are as follows: (i) it incorporates a customized critique mechanism guided by a user-defined checklist specifying required diagnostic details and constraints; (ii) it re-identifies informative regions in the WSI based on the critique feedback and text-patch semantic retrieval, a process that iteratively enriches and reconciles the report. Experiments demonstrate that by making report requirements explicitly prompt-defined, constraint-aware, and verifiable through evidence-grounded refinement, QCAgent enables controllable generation of clinically meaningful and high-coverage pathology reports from WSI.

Yingtai Li, Xueming Fu, Han Li et al.

Sparse-view computed tomography (CT) reduces radiation exposure by acquiring fewer projections, making it a valuable tool in clinical scenarios where low-dose radiation is essential. However, this often results in increased noise and artifacts due to limited data. In this paper we propose a novel 3D Gaussian representation (3DGR) based method for sparse-view CT reconstruction. Inspired by recent success in novel view synthesis driven by 3D Gaussian splatting, we leverage the efficiency and expressiveness of 3D Gaussian representation as an alternative to implicit neural representation. To unleash the potential of 3DGR for CT imaging scenario, we propose two key innovations: (i) FBP-image-guided Guassian initialization and (ii) efficient integration with a differentiable CT projector. Extensive experiments and ablations on diverse datasets demonstrate the proposed 3DGR-CT consistently outperforms state-of-the-art counterpart methods, achieving higher reconstruction accuracy with faster convergence. Furthermore, we showcase the potential of 3DGR-CT for real-time physical simulation, which holds important clinical applications while challenging for implicit neural representations.

Yingtai Li, Shuai Ming, Mingyue Zhao et al.

The development of radiology foundation models (RFMs) is hindered by a reliance on brute-force scaling. Existing approaches often directly translate methods for natural images, which prioritize scale over precision and hence lead to brittle and expensive models in clinical practice. To address this, we present a resource-efficient pre-training framework, GreenRFM, that achieves state-of-the-art performance. Our framework ensures robust generalization across diverse patient populations and imaging protocols, reducing computational requirements by orders of magnitude while surpassing complex, parameter-heavy models. These capabilities stem from principled supervision design that aims to maximally utilize supervisory signals via More distilled, Ubiquitous, Semantic-enforcing, and Task-aligning (MUST) supervision, rather than simply piling up the quantity of training data. We offer two GreenRFM configurations: (i) a performant model that establishes a new state-of-the-art using a single 24GB GPU within 24 hours, and (ii) a lightweight model that matches existing benchmarks with 6GB VRAM in 4 hours. We conduct extensive experiments using over 200,000 images from four institutions and of two modalities. GreenRFMs achieve superior performances on chest and abdominal CT datasets, regardless of public or private benchmark, surpassing a range of baseline models. In addition, the results on internal musculoskeletal MRI images show that the same supervision principles transfer between different modalities. Our performance and efficiency challenge the ``scale is all you need'' dogma and democratize the equitable development of state-of-the-art RFMs for clinicians even on a laptop.