Qingsong Yao

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.

Heqin Zhu, Quan Quan, Qingsong Yao et al.

One-shot medical landmark detection gains much attention and achieves great success for its label-efficient training process. However, existing one-shot learning methods are highly specialized in a single domain and suffer domain preference heavily in the situation of multi-domain unlabeled data. Moreover, one-shot learning is not robust that it faces performance drop when annotating a sub-optimal image. To tackle these issues, we resort to developing a domain-adaptive one-shot landmark detection framework for handling multi-domain medical images, named Universal One-shot Detection (UOD). UOD consists of two stages and two corresponding universal models which are designed as combinations of domain-specific modules and domain-shared modules. In the first stage, a domain-adaptive convolution model is self-supervised learned to generate pseudo landmark labels. In the second stage, we design a domain-adaptive transformer to eliminate domain preference and build the global context for multi-domain data. Even though only one annotated sample from each domain is available for training, the domain-shared modules help UOD aggregate all one-shot samples to detect more robust and accurate landmarks. We investigated both qualitatively and quantitatively the proposed UOD on three widely-used public X-ray datasets in different anatomical domains (i.e., head, hand, chest) and obtained state-of-the-art performances in each domain. The code is available at https://github.com/heqin-zhu/UOD_universal_oneshot_detection.

Qingsong Yao, Jianji Wang, Yihua Sun et al.

Contrastive learning based methods such as cascade comparing to detect (CC2D) have shown great potential for one-shot medical landmark detection. However, the important cue of relative distance between landmarks is ignored in CC2D. In this paper, we upgrade CC2D to version II by incorporating a simple-yet-effective relative distance bias in the training stage, which is theoretically proved to encourage the encoder to project the relatively distant landmarks to the embeddings with low similarities. As consequence, CC2Dv2 is less possible to detect a wrong point far from the correct landmark. Furthermore, we present an open-source, landmark-labeled dataset for the measurement of biomechanical parameters of the lower extremity to alleviate the burden of orthopedic surgeons. The effectiveness of CC2Dv2 is evaluated on the public dataset from the ISBI 2015 Grand-Challenge of cephalometric radiographs and our new dataset, which greatly outperforms the state-of-the-art one-shot landmark detection approaches.

Fenghe Tang, Ronghao Xu, Qingsong Yao et al.

The generative self-supervised learning strategy exhibits remarkable learning representational capabilities. However, there is limited attention to end-to-end pre-training methods based on a hybrid architecture of CNN and Transformer, which can learn strong local and global representations simultaneously. To address this issue, we propose a generative pre-training strategy called Hybrid Sparse masKing (HySparK) based on masked image modeling and apply it to large-scale pre-training on medical images. First, we perform a bottom-up 3D hybrid masking strategy on the encoder to keep consistency masking. Then we utilize sparse convolution for the top CNNs and encode unmasked patches for the bottom vision Transformers. Second, we employ a simple hierarchical decoder with skip-connections to achieve dense multi-scale feature reconstruction. Third, we implement our pre-training method on a collection of multiple large-scale 3D medical imaging datasets. Extensive experiments indicate that our proposed pre-training strategy demonstrates robust transfer-ability in supervised downstream tasks and sheds light on HySparK's promising prospects. The code is available at https://github.com/FengheTan9/HySparK

Zikang Xu, Jun Li, Qingsong Yao et al.

Deep learning algorithms have demonstrated remarkable efficacy in various medical image analysis (MedIA) applications. However, recent research highlights a performance disparity in these algorithms when applied to specific subgroups, such as exhibiting poorer predictive performance in elderly females. Addressing this fairness issue has become a collaborative effort involving AI scientists and clinicians seeking to understand its origins and develop solutions for mitigation within MedIA. In this survey, we thoroughly examine the current advancements in addressing fairness issues in MedIA, focusing on methodological approaches. We introduce the basics of group fairness and subsequently categorize studies on fair MedIA into fairness evaluation and unfairness mitigation. Detailed methods employed in these studies are presented too. Our survey concludes with a discussion of existing challenges and opportunities in establishing a fair MedIA and healthcare system. By offering this comprehensive review, we aim to foster a shared understanding of fairness among AI researchers and clinicians, enhance the development of unfairness mitigation methods, and contribute to the creation of an equitable MedIA society.

Zikang Xu, Shang Zhao, Quan Quan et al.

Deep learning is becoming increasingly ubiquitous in medical research and applications while involving sensitive information and even critical diagnosis decisions. Researchers observe a significant performance disparity among subgroups with different demographic attributes, which is called model unfairness, and put lots of effort into carefully designing elegant architectures to address unfairness, which poses heavy training burden, brings poor generalization, and reveals the trade-off between model performance and fairness. To tackle these issues, we propose FairAdaBN by making batch normalization adaptive to sensitive attribute. This simple but effective design can be adopted to several classification backbones that are originally unaware of fairness. Additionally, we derive a novel loss function that restrains statistical parity between subgroups on mini-batches, encouraging the model to converge with considerable fairness. In order to evaluate the trade-off between model performance and fairness, we propose a new metric, named Fairness-Accuracy Trade-off Efficiency (FATE), to compute normalized fairness improvement over accuracy drop. Experiments on two dermatological datasets show that our proposed method outperforms other methods on fairness criteria and FATE.

Haoran Lai, Qingsong Yao, Zhiyang He et al.

Chest X-rays (CXR) often reveal rare diseases, demanding precise diagnosis. However, current computer-aided diagnosis (CAD) methods focus on common diseases, leading to inadequate detection of rare conditions due to the absence of comprehensive datasets. To overcome this, we present a novel benchmark for long-tailed multi-label classification in CXRs, encapsulating both common and rare thoracic diseases. Our approach includes developing the "LTML-MIMIC-CXR" dataset, an augmentation of MIMIC-CXR with 26 additional rare diseases. We propose a baseline method for this classification challenge, integrating adaptive negative regularization to address negative logits' over-suppression in tail classes, and a large loss reconsideration strategy for correcting noisy labels from automated annotations. Our evaluation on LTML-MIMIC-CXR demonstrates significant advancements in rare disease detection. This work establishes a foundation for robust CAD methods, achieving a balance in identifying a spectrum of thoracic diseases in CXRs. Access to our code and dataset is provided at:https://github.com/laihaoran/LTML-MIMIC-CXR.

Heqin Zhu, Qingsong Yao, S. Kevin Zhou

Accurate anatomical landmark detection plays an increasingly vital role in medical image analysis. Although existing methods achieve satisfying performance, they are mostly based on CNN and specialized for a single domain say associated with a particular anatomical region. In this work, we propose a universal model for multi-domain landmark detection by taking advantage of transformer for modeling long dependencies and develop a domain-adaptive transformer model, named as DATR, which is trained on multiple mixed datasets from different anatomies and capable of detecting landmarks of any image from those anatomies. The proposed DATR exhibits three primary features: (i) It is the first universal model which introduces transformer as an encoder for multi-anatomy landmark detection; (ii) We design a domain-adaptive transformer for anatomy-aware landmark detection, which can be effectively extended to any other transformer network; (iii) Following previous studies, we employ a light-weighted guidance network, which encourages the transformer network to detect more accurate landmarks. We carry out experiments on three widely used X-ray datasets for landmark detection, which have 1,588 images and 62 landmarks in total, including three different anatomies (head, hand, and chest). Experimental results demonstrate that our proposed DATR achieves state-of-the-art performances by most metrics and behaves much better than any previous convolution-based models. The code will be released publicly.

Yihua Sun, Qingsong Yao, Yuanyuan Lyu et al.

Digital chest tomosynthesis (DCT) is a technique to produce sectional 3D images of a human chest for pulmonary disease screening, with 2D X-ray projections taken within an extremely limited range of angles. However, under the limited angle scenario, DCT contains strong artifacts caused by the presence of ribs, jamming the imaging quality of the lung area. Recently, great progress has been achieved for rib suppression in a single X-ray image, to reveal a clearer lung texture. We firstly extend the rib suppression problem to the 3D case at the software level. We propose a $\textbf{T}$omosynthesis $\textbf{RI}$b Su$\textbf{P}$pression and $\textbf{L}$ung $\textbf{E}$nhancement $\textbf{Net}$work (TRIPLE-Net) to model the 3D rib component and provide a rib-free DCT. TRIPLE-Net takes the advantages from both 2D and 3D domains, which model the ribs in DCT with the exact FBP procedure and 3D depth information, respectively. The experiments on simulated datasets and clinical data have shown the effectiveness of TRIPLE-Net to preserve lung details as well as improve the imaging quality of pulmonary diseases. Finally, an expert user study confirms our findings.

Quan Quan, Shang Zhao, Qingsong Yao et al.

The augmentation parameters matter to few-shot semantic segmentation since they directly affect the training outcome by feeding the networks with varying perturbated samples. However, searching optimal augmentation parameters for few-shot segmentation models without annotations is a challenge that current methods fail to address. In this paper, we first propose a framework to determine the ``optimal'' parameters without human annotations by solving a distribution-matching problem between the intra-instance and intra-class similarity distribution, with the intra-instance similarity describing the similarity between the original sample of a particular anatomy and its augmented ones and the intra-class similarity representing the similarity between the selected sample and the others in the same class. Extensive experiments demonstrate the superiority of our optimized augmentation in boosting few-shot segmentation models. We greatly improve the top competing method by 1.27\% and 1.11\% on Abd-MRI and Abd-CT datasets, respectively, and even achieve a significant improvement for SSL-ALP on the left kidney by 3.39\% on the Abd-CT dataset.

Quan Quan, Qingsong Yao, Jun Li et al.

Contrastive learning (CL) is a form of self-supervised learning and has been widely used for various tasks. Different from widely studied instance-level contrastive learning, pixel-wise contrastive learning mainly helps with pixel-wise tasks such as medical landmark detection. The counterpart to an instance in instance-level CL is a pixel, along with its neighboring context, in pixel-wise CL. Aiming to build better feature representation, there is a vast literature about designing instance augmentation strategies for instance-level CL; but there is little similar work on pixel augmentation for pixel-wise CL with a pixel granularity. In this paper, we attempt to bridge this gap. We first classify a pixel into three categories, namely low-, medium-, and high-informative, based on the information quantity the pixel contains. Inspired by the ``InfoMin" principle, we then design separate augmentation strategies for each category in terms of augmentation intensity and sampling ratio. Extensive experiments validate that our information-guided pixel augmentation strategy succeeds in encoding more discriminative representations and surpassing other competitive approaches in unsupervised local feature matching. Furthermore, our pretrained model improves the performance of both one-shot and fully supervised models. To the best of our knowledge, we are the first to propose a pixel augmentation method with a pixel granularity for enhancing unsupervised pixel-wise contrastive learning.

Haoran Lai, Qingsong Yao, Zihang Jiang et al.

The advancement of Zero-Shot Learning in the medical domain has been driven forward by using pre-trained models on large-scale image-text pairs, focusing on image-text alignment. However, existing methods primarily rely on cosine similarity for alignment, which may not fully capture the complex relationship between medical images and reports. To address this gap, we introduce a novel approach called Cross-Attention Alignment for Radiology Zero-Shot Classification (CARZero). Our approach innovatively leverages cross-attention mechanisms to process image and report features, creating a Similarity Representation that more accurately reflects the intricate relationships in medical semantics. This representation is then linearly projected to form an image-text similarity matrix for cross-modality alignment. Additionally, recognizing the pivotal role of prompt selection in zero-shot learning, CARZero incorporates a Large Language Model-based prompt alignment strategy. This strategy standardizes diverse diagnostic expressions into a unified format for both training and inference phases, overcoming the challenges of manual prompt design. Our approach is simple yet effective, demonstrating state-of-the-art performance in zero-shot classification on five official chest radiograph diagnostic test sets, including remarkable results on datasets with long-tail distributions of rare diseases. This achievement is attributed to our new image-text alignment strategy, which effectively addresses the complex relationship between medical images and reports. Code and models are available at https://github.com/laihaoran/CARZero.

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.

Wenxin Ma, Qingsong Yao, Xiang Zhang et al.

Unsupervised anomaly detection (UAD) from images strives to model normal data distributions, creating discriminative representations to distinguish and precisely localize anomalies. Despite recent advancements in the efficient and unified one-for-all scheme, challenges persist in accurately segmenting anomalies for further monitoring. Moreover, this problem is obscured by the widely-used AUROC metric under imbalanced UAD settings. This motivates us to emphasize the significance of precise segmentation of anomaly pixels using pAP and DSC as metrics. To address the unsolved segmentation task, we introduce the Unified Anomaly Segmentation (UniAS). UniAS presents a multi-level hybrid pipeline that progressively enhances normal information from coarse to fine, incorporating a novel multi-granularity gated CNN (MGG-CNN) into Transformer layers to explicitly aggregate local details from different granularities. UniAS achieves state-of-the-art anomaly segmentation performance, attaining 65.12/59.33 and 40.06/32.50 in pAP/DSC on the MVTec-AD and VisA datasets, respectively, surpassing previous methods significantly. The codes are shared at https://github.com/Mwxinnn/UniAS.

Fenghe Tang, Qingsong Yao, Wenxin Ma et al.

Medical image segmentation remains a formidable challenge due to the label scarcity. Pre-training Vision Transformer (ViT) through masked image modeling (MIM) on large-scale unlabeled medical datasets presents a promising solution, providing both computational efficiency and model generalization for various downstream tasks. However, current ViT-based MIM pre-training frameworks predominantly emphasize local aggregation representations in output layers and fail to exploit the rich representations across different ViT layers that better capture fine-grained semantic information needed for more precise medical downstream tasks. To fill the above gap, we hereby present Hierarchical Encoder-driven MAE (Hi-End-MAE), a simple yet effective ViT-based pre-training solution, which centers on two key innovations: (1) Encoder-driven reconstruction, which encourages the encoder to learn more informative features to guide the reconstruction of masked patches; and (2) Hierarchical dense decoding, which implements a hierarchical decoding structure to capture rich representations across different layers. We pre-train Hi-End-MAE on a large-scale dataset of 10K CT scans and evaluated its performance across seven public medical image segmentation benchmarks. Extensive experiments demonstrate that Hi-End-MAE achieves superior transfer learning capabilities across various downstream tasks, revealing the potential of ViT in medical imaging applications. The code is available at: https://github.com/FengheTan9/Hi-End-MAE

Zhen Huang, Tao Tang, Ronghao Xu et al.

3D landmark detection is a critical task in medical image analysis, and accurately detecting anatomical landmarks is essential for subsequent medical imaging tasks. However, mainstream deep learning methods in this field struggle to simultaneously capture fine-grained local features and model global spatial relationships, while maintaining a balance between accuracy and computational efficiency. Local feature extraction requires capturing fine-grained anatomical details, while global modeling requires understanding the spatial relationships within complex anatomical structures. The high-dimensional nature of 3D volume further exacerbates these challenges, as landmarks are sparsely distributed, leading to significant computational costs. Therefore, achieving efficient and precise 3D landmark detection remains a pressing challenge in medical image analysis. In this work, We propose a \textbf{H}ybrid \textbf{3}D \textbf{DE}tection \textbf{Net}(H3DE-Net), a novel framework that combines CNNs for local feature extraction with a lightweight attention mechanism designed to efficiently capture global dependencies in 3D volumetric data. This mechanism employs a hierarchical routing strategy to reduce computational cost while maintaining global context modeling. To our knowledge, H3DE-Net is the first 3D landmark detection model that integrates such a lightweight attention mechanism with CNNs. Additionally, integrating multi-scale feature fusion further enhances detection accuracy and robustness. Experimental results on a public CT dataset demonstrate that H3DE-Net achieves state-of-the-art(SOTA) performance, significantly improving accuracy and robustness, particularly in scenarios with missing landmarks or complex anatomical variations. We aready open-source our project, including code, data and model weights.

Rongsheng Wang, Fenghe Tang, Qingsong Yao et al.

Medical vision-language pre-training shows great potential in learning representative features from massive paired radiographs and reports. However, in computed tomography (CT) scans, the distribution of lesions which contain intricate structures is characterized by spatial sparsity. Besides, the complex and implicit relationships between different pathological descriptions in each sentence of the report and their corresponding sub-regions in radiographs pose additional challenges. In this paper, we propose a Similarity-Driven Cross-Granularity Pre-training (SimCroP) framework on chest CTs, which combines similarity-driven alignment and cross-granularity fusion to improve radiograph interpretation. We first leverage multi-modal masked modeling to optimize the encoder for understanding precise low-level semantics from radiographs. Then, similarity-driven alignment is designed to pre-train the encoder to adaptively select and align the correct patches corresponding to each sentence in reports. The cross-granularity fusion module integrates multimodal information across instance level and word-patch level, which helps the model better capture key pathology structures in sparse radiographs, resulting in improved performance for multi-scale downstream tasks. SimCroP is pre-trained on a large-scale paired CT-reports dataset and validated on image classification and segmentation tasks across five public datasets. Experimental results demonstrate that SimCroP outperforms both cutting-edge medical self-supervised learning methods and medical vision-language pre-training methods. Codes and models are available at https://github.com/ToniChopp/SimCroP.

Xiaoqian Zhou, Zhen Huang, Heqin Zhu et al.

Anatomical landmark detection (ALD) from a medical image is crucial for a wide array of clinical applications. While existing methods achieve quite some success in ALD, they often struggle to balance global context with computational efficiency, particularly with high-resolution images, thereby leading to the rise of a natural question: where is the performance limit of ALD? In this paper, we aim to forge performant ALD by proposing a {\bf HY}brid {\bf ATT}ention {\bf Net}work (HYATT-Net) with the following designs: (i) A novel hybrid architecture that integrates CNNs and Transformers. Its core is the BiFormer module, utilizing Bi-Level Routing Attention for efficient attention to relevant image regions. This, combined with Attention Residual Module(ARM), enables precise local feature refinement guided by the global context. (ii) A Feature Fusion Correction Module that aggregates multi-scale features and thus mitigates a resolution loss. Deep supervision with a mean-square error loss on multi-resolution heatmaps optimizes the model. Experiments on five diverse datasets demonstrate state-of-the-art performance, surpassing existing methods in accuracy, robustness, and efficiency. The HYATT-Net provides a promising solution for accurate and efficient ALD in complex medical images. Our codes and data are already released at: \url{https://github.com/ECNUACRush/HYATT-Net}.

Heqin Zhu, Qingsong Yao, Li Xiao et al.

Detecting anatomical landmarks in medical images plays an essential role in understanding the anatomy and planning automated processing. In recent years, a variety of deep neural network methods have been developed to detect landmarks automatically. However, all of those methods are unary in the sense that a highly specialized network is trained for a single task say associated with a particular anatomical region. In this work, for the first time, we investigate the idea of "You Only Learn Once (YOLO)" and develop a universal anatomical landmark detection model to realize multiple landmark detection tasks with end-to-end training based on mixed datasets. The model consists of a local network and a global network: The local network is built upon the idea of universal U-Net to learn multi-domain local features and the global network is a parallelly-duplicated sequential of dilated convolutions that extract global features to further disambiguate the landmark locations. It is worth mentioning that the new model design requires much fewer parameters than models with standard convolutions to train. We evaluate our YOLO model on three X-ray datasets of 1,588 images on the head, hand, and chest, collectively contributing 62 landmarks. The experimental results show that our proposed universal model behaves largely better than any previous models trained on multiple datasets. It even beats the performance of the model that is trained separately for every single dataset. The code is available at https://github.com/MIRACLE-Center/YOLO_Universal_Anatomical_Landmark_Detection

Qingsong Yao, Zecheng He, Hu Han et al.

Recent methods in multiple landmark detection based on deep convolutional neural networks (CNNs) reach high accuracy and improve traditional clinical workflow. However, the vulnerability of CNNs to adversarial-example attacks can be easily exploited to break classification and segmentation tasks. This paper is the first to study how fragile a CNN-based model on multiple landmark detection to adversarial perturbations. Specifically, we propose a novel Adaptive Targeted Iterative FGSM (ATI-FGSM) attack against the state-of-the-art models in multiple landmark detection. The attacker can use ATI-FGSM to precisely control the model predictions of arbitrarily selected landmarks, while keeping other stationary landmarks still, by adding imperceptible perturbations to the original image. A comprehensive evaluation on a public dataset for cephalometric landmark detection demonstrates that the adversarial examples generated by ATI-FGSM break the CNN-based network more effectively and efficiently, compared with the original Iterative FGSM attack. Our work reveals serious threats to patients' health. Furthermore, we discuss the limitations of our method and provide potential defense directions, by investigating the coupling effect of nearby landmarks, i.e., a major source of divergence in our experiments. Our source code is available at https://github.com/qsyao/attack_landmark_detection.

Chao Huang, Hu Han, Qingsong Yao et al.

Fully convolutional neural networks like U-Net have been the state-of-the-art methods in medical image segmentation. Practically, a network is highly specialized and trained separately for each segmentation task. Instead of a collection of multiple models, it is highly desirable to learn a universal data representation for different tasks, ideally a single model with the addition of a minimal number of parameters steered to each task. Inspired by the recent success of multi-domain learning in image classification, for the first time we explore a promising universal architecture that handles multiple medical segmentation tasks and is extendable for new tasks, regardless of different organs and imaging modalities. Our 3D Universal U-Net (3D U$^2$-Net) is built upon separable convolution, assuming that {\it images from different domains have domain-specific spatial correlations which can be probed with channel-wise convolution while also share cross-channel correlations which can be modeled with pointwise convolution}. We evaluate the 3D U$^2$-Net on five organ segmentation datasets. Experimental results show that this universal network is capable of competing with traditional models in terms of segmentation accuracy, while requiring only about $1\%$ of the parameters. Additionally, we observe that the architecture can be easily and effectively adapted to a new domain without sacrificing performance in the domains used to learn the shared parameterization of the universal network. We put the code of 3D U$^2$-Net into public domain. \url{https://github.com/huangmozhilv/u2net_torch/}

Zhen Hang, Yushan Yashengjiang, Junhui Li et al.

PDE-to-solver code generation aims to automatically synthesize executable numerical solvers from partial differential equation (PDE) specifications. This task requires not only understanding the mathematical structure of PDEs, but also selecting appropriate discretization schemes and solver configurations, and correctly implementing the resulting formulations in finite-element method (FEM) libraries. Existing code generation benchmarks mainly evaluate syntactic correctness, or success on predefined test cases. To our knowledge, there is currently no publicly available benchmark specifically for PDE-to-solver code generation, and general-purpose code benchmarks do not fully capture the unique challenges of numerical PDE solution, such as ensuring solver accuracy, efficiency, and compatibility with professional FEM libraries. We introduce PDEAgent-Bench, to the best of our knowledge, the first multi-metric, multi-library benchmark for PDE-to-solver code generation. PDEAgent-Bench contains 645 instances across 6 mathematical categories and 11 PDE families, with common FEM libraries for DOLFINx, Firedrake, and deal.II. Each instance provides an agent-facing problem specification, a reference solution on a prescribed evaluation grid, and case-specific accuracy and runtime targets. PDEAgent-Bench adopts a staged evaluation framework in which generated solvers must sequentially pass executability, numerical accuracy, and computational efficiency checks. Experiments with representative LLMs and code agents show that models can often produce runnable code, but their pass rate drops substantially once accuracy and efficiency requirements are enforced. These results indicate that current agents remain limited in producing numerically reliable and efficient PDE solvers, and that PDEAgent-Bench provides a reproducible testbed grounded in the practical requirements of numerical PDE solving.

Haoran Lai, Zihang Jiang, Qingsong Yao et al.

The development of 3D medical vision-language models holds significant potential for disease diagnosis and patient treatment. However, compared to 2D medical images, 3D medical images, such as CT scans, face challenges related to limited training data and high dimension, which severely restrict the progress of 3D medical vision-language models. To address these issues, we collect a large amount of unlabeled 3D CT data and utilize self-supervised learning to construct a 3D visual foundation model for extracting 3D visual features. Then, we apply 3D spatial convolutions to aggregate and project high-level image features, reducing computational complexity while preserving spatial information. We also construct two instruction-tuning datasets based on BIMCV-R and CT-RATE to fine-tune the 3D vision-language model. Our model demonstrates superior performance compared to existing methods in report generation, visual question answering, and disease diagnosis. Code and data will be made publicly available soon.

Qingsong Yao, Zecheng He, Yuexiang Li et al. · tencent-ai

Deep learning based methods for medical images can be easily compromised by adversarial examples (AEs), posing a great security flaw in clinical decision-making. It has been discovered that conventional adversarial attacks like PGD which optimize the classification logits, are easy to distinguish in the feature space, resulting in accurate reactive defenses. To better understand this phenomenon and reassess the reliability of the reactive defenses for medical AEs, we thoroughly investigate the characteristic of conventional medical AEs. Specifically, we first theoretically prove that conventional adversarial attacks change the outputs by continuously optimizing vulnerable features in a fixed direction, thereby leading to outlier representations in the feature space. Then, a stress test is conducted to reveal the vulnerability of medical images, by comparing with natural images. Interestingly, this vulnerability is a double-edged sword, which can be exploited to hide AEs. We then propose a simple-yet-effective hierarchical feature constraint (HFC), a novel add-on to conventional white-box attacks, which assists to hide the adversarial feature in the target feature distribution. The proposed method is evaluated on three medical datasets, both 2D and 3D, with different modalities. The experimental results demonstrate the superiority of HFC, \emph{i.e.,} it bypasses an array of state-of-the-art adversarial medical AE detectors more efficiently than competing adaptive attacks, which reveals the deficiencies of medical reactive defense and allows to develop more robust defenses in future.

Hanxue Zhang, Haoran Jiang, Qingsong Yao et al.

Despite the success of deep learning in close-set 3D object detection, existing approaches struggle with zero-shot generalization to novel objects and camera configurations. We introduce DetAny3D, a promptable 3D detection foundation model capable of detecting any novel object under arbitrary camera configurations using only monocular inputs. Training a foundation model for 3D detection is fundamentally constrained by the limited availability of annotated 3D data, which motivates DetAny3D to leverage the rich prior knowledge embedded in extensively pre-trained 2D foundation models to compensate for this scarcity. To effectively transfer 2D knowledge to 3D, DetAny3D incorporates two core modules: the 2D Aggregator, which aligns features from different 2D foundation models, and the 3D Interpreter with Zero-Embedding Mapping, which mitigates catastrophic forgetting in 2D-to-3D knowledge transfer. Experimental results validate the strong generalization of our DetAny3D, which not only achieves state-of-the-art performance on unseen categories and novel camera configurations, but also surpasses most competitors on in-domain data.DetAny3D sheds light on the potential of the 3D foundation model for diverse applications in real-world scenarios, e.g., rare object detection in autonomous driving, and demonstrates promise for further exploration of 3D-centric tasks in open-world settings. More visualization results can be found at DetAny3D project page.

Haoran Lai, Zihang Jiang, Qingsong Yao et al.

3D medical images such as computed tomography are widely used in clinical practice, offering a great potential for automatic diagnosis. Supervised learning-based approaches have achieved significant progress but rely heavily on extensive manual annotations, limited by the availability of training data and the diversity of abnormality types. Vision-language alignment (VLA) offers a promising alternative by enabling zero-shot learning without additional annotations. However, we empirically discover that the visual and textural embeddings after alignment endeavors from existing VLA methods form two well-separated clusters, presenting a wide gap to be bridged. To bridge this gap, we propose a Bridged Semantic Alignment (BrgSA) framework. First, we utilize a large language model to perform semantic summarization of reports, extracting high-level semantic information. Second, we design a Cross-Modal Knowledge Interaction module that leverages a cross-modal knowledge bank as a semantic bridge, facilitating interaction between the two modalities, narrowing the gap, and improving their alignment. To comprehensively evaluate our method, we construct a benchmark dataset that includes 15 underrepresented abnormalities as well as utilize two existing benchmark datasets. Experimental results demonstrate that BrgSA achieves state-of-the-art performances on both public benchmark datasets and our custom-labeled dataset, with significant improvements in zero-shot diagnosis of underrepresented abnormalities.

Zikang Xu, Fenghe Tang, Quan Quan et al.

Ensuring fairness in deep-learning-based segmentors is crucial for health equity. Much effort has been dedicated to mitigating unfairness in the training datasets or procedures. However, with the increasing prevalence of foundation models in medical image analysis, it is hard to train fair models from scratch while preserving utility. In this paper, we propose a novel method, Adversarial Privacy-aware Perturbations on Latent Embedding (APPLE), that can improve the fairness of deployed segmentors by introducing a small latent feature perturber without updating the weights of the original model. By adding perturbation to the latent vector, APPLE decorates the latent vector of segmentors such that no fairness-related features can be passed to the decoder of the segmentors while preserving the architecture and parameters of the segmentor. Experiments on two segmentation datasets and five segmentors (three U-Net-like and two SAM-like) illustrate the effectiveness of our proposed method compared to several unfairness mitigation methods.

Haoran Lai, Zihang Jiang, Kun Zhang et al.

Developing 3D vision-language models with robust clinical reasoning remains a challenge due to the inherent complexity of volumetric medical imaging, the tendency of models to overfit superficial report patterns, and the lack of interpretability-aware reward designs. In this paper, we propose Med3D-R1, a reinforcement learning framework with a two-stage training process: Supervised Fine-Tuning (SFT) and Reinforcement Learning (RL). During SFT stage, we introduce a residual alignment mechanism to bridge the gap between high-dimensional 3D features and textual embeddings, and an abnormality re-weighting strategy to emphasize clinically informative tokens and reduce structural bias in reports. In RL stage, we redesign the consistency reward to explicitly promote coherent, step-by-step diagnostic reasoning. We evaluate our method on medical multiple-choice visual question answering using two 3D diagnostic benchmarks, CT-RATE and RAD-ChestCT, where our model attains state-of-the-art accuracies of 41.92\% on CT-RATE and 44.99\% on RAD-ChestCT. These results indicate improved abnormality diagnosis and clinical reasoning and outperform prior methods on both benchmarks. Overall, our approach holds promise for enhancing real-world diagnostic workflows by enabling more reliable and transparent 3D medical vision-language systems.

Xu He, Zhen Huang, Qingsong Yao et al.

Landmark detection plays a crucial role in medical imaging applications such as disease diagnosis, bone age estimation, and therapy planning. However, training models for detecting multiple landmarks simultaneously often encounters the "seesaw phenomenon", where improvements in detecting certain landmarks lead to declines in detecting others. Yet, training a separate model for each landmark increases memory usage and computational overhead. To address these challenges, we propose a novel approach based on the belief that "landmarks are distinct" by training models with pseudo-labels and template data updated continuously during the training process, where each model is dedicated to detecting a single landmark to achieve high accuracy. Furthermore, grounded on the belief that "landmarks are also alike", we introduce an adapter-based fusion model, combining shared weights with landmark-specific weights, to efficiently share model parameters while allowing flexible adaptation to individual landmarks. This approach not only significantly reduces memory and computational resource requirements but also effectively mitigates the seesaw phenomenon in multi-landmark training. Experimental results on publicly available medical image datasets demonstrate that the single-landmark models significantly outperform traditional multi-point joint training models in detecting individual landmarks. Although our adapter-based fusion model shows slightly lower performance compared to the combined results of all single-landmark models, it still surpasses the current state-of-the-art methods while achieving a notable improvement in resource efficiency.

Rongsheng Wang, Qingsong Yao, Zihang Jiang et al.

Despite significant advancements in medical vision-language pre-training, existing methods have largely overlooked the inherent linguistic complexity and imbalanced isssue within medical reports, as well as the complex cross-modality contextual relationships between texts and images. To close this gap, we propose a novel Entity-centered Context-aware Medical Vision-language Pre-training (ECAMP) framework, which establishes a more entity-centered, context-sensitive, and balanced understanding of medical reports to effectively pre-train the vision encoder. We first distill entity-centered context from medical reports utilizing large language models, enabling ECAMP to draw more precise supervision from the text modality. By further incorporating entity-aware re-balanced factor and descriptor masking strategies into masked languange modeling, ECAMP significantly enhances the knowledge of entities within the reports. A context-guided super-resolution task is proposed alongside a multi-scale context fusion design to improve the semantic integration of both coarse and fine-level image representations, which prompts better performance for multi-scale downstream applications. ECAMP integrates these innovations together, leading to significant performance leaps over current state-of-the-art methods and establish a new standard for cross-modality pre-training in medical imaging. The effectiveness of ECAMP is demonstrated by extensive experiments on various domains and organs, which achieves cutting-edge results on multiple tasks including classification, segmentation, and detection across 5 public chest X-ray and 4 fundoscopy datasets respectively.

Quan Quan, Qingsong Yao, Jun Li et al.

The success of deep learning methods relies on the availability of well-labeled large-scale datasets. However, for medical images, annotating such abundant training data often requires experienced radiologists and consumes their limited time. Few-shot learning is developed to alleviate this burden, which achieves competitive performances with only several labeled data. However, a crucial yet previously overlooked problem in few-shot learning is about the selection of template images for annotation before learning, which affects the final performance. We herein propose a novel Sample Choosing Policy (SCP) to select "the most worthy" images for annotation, in the context of few-shot medical landmark detection. SCP consists of three parts: 1) Self-supervised training for building a pre-trained deep model to extract features from radiological images, 2) Key Point Proposal for localizing informative patches, and 3) Representative Score Estimation for searching the most representative samples or templates. The advantage of SCP is demonstrated by various experiments on three widely-used public datasets. For one-shot medical landmark detection, its use reduces the mean radial errors on Cephalometric and HandXray datasets by 14.2% (from 3.595mm to 3.083mm) and 35.5% (4.114mm to 2.653mm), respectively.

Qingsong Yao, Zecheng He, S. Kevin Zhou

Deep neural network based medical image systems are vulnerable to adversarial examples. Many defense mechanisms have been proposed in the literature, however, the existing defenses assume a passive attacker who knows little about the defense system and does not change the attack strategy according to the defense. Recent works have shown that a strong adaptive attack, where an attacker is assumed to have full knowledge about the defense system, can easily bypass the existing defenses. In this paper, we propose a novel adversarial example defense system called Medical Aegis. To the best of our knowledge, Medical Aegis is the first defense in the literature that successfully addresses the strong adaptive adversarial example attacks to medical images. Medical Aegis boasts two-tier protectors: The first tier of Cushion weakens the adversarial manipulation capability of an attack by removing its high-frequency components, yet posing a minimal effect on classification performance of the original image; the second tier of Shield learns a set of per-class DNN models to predict the logits of the protected model. Deviation from the Shield's prediction indicates adversarial examples. Shield is inspired by the observations in our stress tests that there exist robust trails in the shallow layers of a DNN model, which the adaptive attacks can hardly destruct. Experimental results show that the proposed defense accurately detects adaptive attacks, with negligible overhead for model inference.

Qingsong Yao, Quan Quan, Li Xiao et al.

The success of deep learning methods relies on the availability of a large number of datasets with annotations; however, curating such datasets is burdensome, especially for medical images. To relieve such a burden for a landmark detection task, we explore the feasibility of using only a single annotated image and propose a novel framework named Cascade Comparing to Detect (CC2D) for one-shot landmark detection. CC2D consists of two stages: 1) Self-supervised learning (CC2D-SSL) and 2) Training with pseudo-labels (CC2D-TPL). CC2D-SSL captures the consistent anatomical information in a coarse-to-fine fashion by comparing the cascade feature representations and generates predictions on the training set. CC2D-TPL further improves the performance by training a new landmark detector with those predictions. The effectiveness of CC2D is evaluated on a widely-used public dataset of cephalometric landmark detection, which achieves a competitive detection accuracy of 81.01\% within 4.0mm, comparable to the state-of-the-art fully-supervised methods using a lot more than one training image.

Qingsong Yao, Zecheng He, Yi Lin et al.

Deep neural networks (DNNs) for medical images are extremely vulnerable to adversarial examples (AEs), which poses security concerns on clinical decision making. Luckily, medical AEs are also easy to detect in hierarchical feature space per our study herein. To better understand this phenomenon, we thoroughly investigate the intrinsic characteristic of medical AEs in feature space, providing both empirical evidence and theoretical explanations for the question: why are medical adversarial attacks easy to detect? We first perform a stress test to reveal the vulnerability of deep representations of medical images, in contrast to natural images. We then theoretically prove that typical adversarial attacks to binary disease diagnosis network manipulate the prediction by continuously optimizing the vulnerable representations in a fixed direction, resulting in outlier features that make medical AEs easy to detect. However, this vulnerability can also be exploited to hide the AEs in the feature space. We propose a novel hierarchical feature constraint (HFC) as an add-on to existing adversarial attacks, which encourages the hiding of the adversarial representation within the normal feature distribution. We evaluate the proposed method on two public medical image datasets, namely {Fundoscopy} and {Chest X-Ray}. Experimental results demonstrate the superiority of our adversarial attack method as it bypasses an array of state-of-the-art adversarial detectors more easily than competing attack methods, supporting that the great vulnerability of medical features allows an attacker more room to manipulate the adversarial representations.

Qingsong Yao, Li Xiao, Peihang Liu et al.

Scarcity of annotated images hampers the building of automated solution for reliable COVID-19 diagnosis and evaluation from CT. To alleviate the burden of data annotation, we herein present a label-free approach for segmenting COVID-19 lesions in CT via pixel-level anomaly modeling that mines out the relevant knowledge from normal CT lung scans. Our modeling is inspired by the observation that the parts of tracheae and vessels, which lay in the high-intensity range where lesions belong to, exhibit strong patterns. To facilitate the learning of such patterns at a pixel level, we synthesize `lesions' using a set of surprisingly simple operations and insert the synthesized `lesions' into normal CT lung scans to form training pairs, from which we learn a normalcy-converting network (NormNet) that turns an 'abnormal' image back to normal. Our experiments on three different datasets validate the effectiveness of NormNet, which conspicuously outperforms a variety of unsupervised anomaly detection (UAD) methods.