Jiaxin Zhuang

Zhongying Deng, Cheng Tang, Ziyan Huang et al. · pku

Foundation models have demonstrated remarkable success across diverse domains and tasks, primarily due to the thrive of large-scale, diverse, and high-quality datasets. However, in the field of medical imaging, the curation and assembling of such medical datasets are highly challenging due to the reliance on clinical expertise and strict ethical and privacy constraints, resulting in a scarcity of large-scale unified medical datasets and hindering the development of powerful medical foundation models. In this work, we present the largest survey to date of medical image datasets, covering over 1,000 open-access datasets with a systematic catalog of their modalities, tasks, anatomies, annotations, limitations, and potential for integration. Our analysis exposes a landscape that is modest in scale, fragmented across narrowly scoped tasks, and unevenly distributed across organs and modalities, which in turn limits the utility of existing medical image datasets for developing versatile and robust medical foundation models. To turn fragmentation into scale, we propose a metadata-driven fusion paradigm (MDFP) that integrates public datasets with shared modalities or tasks, thereby transforming multiple small data silos into larger, more coherent resources. Building on MDFP, we release an interactive discovery portal that enables end-to-end, automated medical image dataset integration, and compile all surveyed datasets into a unified, structured table that clearly summarizes their key characteristics and provides reference links, offering the community an accessible and comprehensive repository. By charting the current terrain and offering a principled path to dataset consolidation, our survey provides a practical roadmap for scaling medical imaging corpora, supporting faster data discovery, more principled dataset creation, and more capable medical foundation models.

Jiaxin Zhuang, Luyang Luo, Zhixuan Chen et al.

Deep-learning (DL) based methods are playing an important role in the task of abdominal organs and tumors segmentation in CT scans. However, the large requirements of annotated datasets heavily limit its development. The FLARE23 challenge provides a large-scale dataset with both partially and fully annotated data, which also focuses on both segmentation accuracy and computational efficiency. In this study, we propose to use the strategy of Semi-Supervised Learning (SSL) and iterative pseudo labeling to address FLARE23. Initially, a deep model (nn-UNet) trained on datasets with complete organ annotations (about 220 scans) generates pseudo labels for the whole dataset. These pseudo labels are then employed to train a more powerful segmentation model. Employing the FLARE23 dataset, our approach achieves an average DSC score of 89.63% for organs and 46.07% for tumors on online validation leaderboard. For organ segmentation, We obtain 0.9007\% DSC and 0.9493\% NSD. For tumor segmentation, we obtain 0.3785% DSC and 0.2842% NSD. Our code is available at https://github.com/USTguy/Flare23.

Jinlun Ye, Jiang Liao, Runhe Lai et al.

Vision-language models (VLMs) such as CLIP exhibit strong Out-of-distribution (OOD) detection capabilities by aligning visual and textual representations. Recent CLIP-based test-time adaptation methods further improve detection performance by incorporating external OOD labels. However, such labels are finite and fixed, while the real OOD semantic space is inherently open-ended. Consequently, fixed labels fail to represent the diverse and evolving OOD semantics encountered in test streams. To address this limitation, we introduce Test-time Textual Learning (TTL), a framework that dynamically learns OOD textual semantics from unlabeled test streams, without relying on external OOD labels. TTL updates learnable prompts using pseudo-labeled test samples to capture emerging OOD knowledge. To suppress noise introduced by pseudo-labels, we introduce an OOD knowledge purification strategy that selects reliable OOD samples for adaptation while suppressing noise. In addition, TTL maintains an OOD Textual Knowledge Bank that stores high-quality textual features, providing stable score calibration across batches. Extensive experiments on two standard benchmarks with nine OOD datasets demonstrate that TTL consistently achieves state-of-the-art performance, highlighting the value of textual adaptation for robust test-time OOD detection. Our code is available at https://github.com/figec/TTL.

Pedro R. A. S. Bassi, Wenxuan Li, Yucheng Tang et al.

How can we test AI performance? This question seems trivial, but it isn't. Standard benchmarks often have problems such as in-distribution and small-size test sets, oversimplified metrics, unfair comparisons, and short-term outcome pressure. As a consequence, good performance on standard benchmarks does not guarantee success in real-world scenarios. To address these problems, we present Touchstone, a large-scale collaborative segmentation benchmark of 9 types of abdominal organs. This benchmark is based on 5,195 training CT scans from 76 hospitals around the world and 5,903 testing CT scans from 11 additional hospitals. This diverse test set enhances the statistical significance of benchmark results and rigorously evaluates AI algorithms across various out-of-distribution scenarios. We invited 14 inventors of 19 AI algorithms to train their algorithms, while our team, as a third party, independently evaluated these algorithms on three test sets. In addition, we also evaluated pre-existing AI frameworks--which, differing from algorithms, are more flexible and can support different algorithms--including MONAI from NVIDIA, nnU-Net from DKFZ, and numerous other open-source frameworks. We are committed to expanding this benchmark to encourage more innovation of AI algorithms for the medical domain.

Jiaxin Zhuang, Leon Yan, Zhenwei Zhang et al. · tsinghua

Time series anomaly detection (TSAD) is becoming increasingly vital due to the rapid growth of time series data across various sectors. Anomalies in web service data, for example, can signal critical incidents such as system failures or server malfunctions, necessitating timely detection and response. However, most existing TSAD methodologies rely heavily on manual feature engineering or require extensive labeled training data, while also offering limited interpretability. To address these challenges, we introduce a pioneering framework called the Time Series Anomaly Multimodal Analyzer (TAMA), which leverages the power of Large Multimodal Models (LMMs) to enhance both the detection and interpretation of anomalies in time series data. By converting time series into visual formats that LMMs can efficiently process, TAMA leverages few-shot in-context learning capabilities to reduce dependence on extensive labeled datasets. Our methodology is validated through rigorous experimentation on multiple real-world datasets, where TAMA consistently outperforms state-of-the-art methods in TSAD tasks. Additionally, TAMA provides rich, natural language-based semantic analysis, offering deeper insights into the nature of detected anomalies. Furthermore, we contribute one of the first open-source datasets that includes anomaly detection labels, anomaly type labels, and contextual description, facilitating broader exploration and advancement within this critical field. Ultimately, TAMA not only excels in anomaly detection but also provides a comprehensive approach for understanding the underlying causes of anomalies, pushing TSAD forward through innovative methodologies and insights.

Linshan Wu, Jiaxin Zhuang, Hao Chen

The scarcity of annotations poses a significant challenge in medical image analysis. Large-scale pre-training has emerged as a promising label-efficient solution, owing to the utilization of large-scale data, large models, and advanced pre-training techniques. However, its development in medical images remains underexplored. The primary challenge lies in harnessing large-scale unlabeled data and learning high-level semantics without annotations. We observe that 3D medical images exhibit consistent geometric context, i.e., consistent geometric relations between different organs, which leads to a promising way for learning consistent representations. Motivated by this, we introduce a simple-yet-effective Volume Contrast (VoCo) framework to leverage geometric context priors for self-supervision. Given an input volume, we extract base crops from different regions to construct positive and negative pairs for contrastive learning. Then we predict the contextual position of a random crop by contrasting its similarity to the base crops. In this way, VoCo encodes the inherent geometric context into model representations, facilitating high-level semantic learning without annotations. Specifically, we (1) introduce the largest medical pre-training dataset PreCT-160K; (2) investigate scaling laws and propose guidelines for tailoring different model sizes to various medical tasks; (3) build a benchmark encompassing 48 medical tasks. Extensive experiments highlight the superiority of VoCo. Codes at https://github.com/Luffy03/Large-Scale-Medical.

Linshan Wu, Jiaxin Zhuang, Hao Chen

Pan-cancer screening in large-scale CT scans remains challenging for existing AI methods, primarily due to the difficulty of localizing diverse types of tiny lesions in large CT volumes. The extreme foreground-background imbalance significantly hinders models from focusing on diseased regions, while redundant focus on healthy regions not only decreases the efficiency but also increases false positives. Inspired by radiologists' glance and focus diagnostic strategy, we introduce GF-Screen, a Glance and Focus reinforcement learning framework for pan-cancer screening. GF-Screen employs a Glance model to localize the diseased regions and a Focus model to precisely segment the lesions, where segmentation results of the Focus model are leveraged to reward the Glance model via Reinforcement Learning (RL). Specifically, the Glance model crops a group of sub-volumes from the entire CT volume and learns to select the sub-volumes with lesions for the Focus model to segment. Given that the selecting operation is non-differentiable for segmentation training, we propose to employ the segmentation results to reward the Glance model. To optimize the Glance model, we introduce a novel group relative learning paradigm, which employs group relative comparison to prioritize high-advantage predictions and discard low-advantage predictions within sub-volume groups, not only improving efficiency but also reducing false positives. In this way, for the first time, we effectively extend cutting-edge RL techniques to tackle the specific challenges in pan-cancer screening. Extensive experiments on 16 internal and 7 external datasets across 9 lesion types demonstrated the effectiveness of GF-Screen. Notably, GF-Screen leads the public validation leaderboard of MICCAI FLARE25 pan-cancer challenge, surpassing the FLARE24 champion solution by a large margin (+25.6% DSC and +28.2% NSD).

Xuefeng Ni, Linshan Wu, Jiaxin Zhuang et al.

3D medical image analysis is pivotal in numerous clinical applications. However, the scarcity of labeled data and limited generalization capabilities hinder the advancement of AI-empowered models. Radiology reports are easily accessible and can serve as weakly-supervised signals. However, large-scale vision-language pre-training (VLP) remains underexplored in 3D medical image analysis. Specifically, the insufficient investigation into multi-grained radiology semantics and their correlations across patients leads to underutilization of large-scale volume-report data. Considering intra-patient cross-modal semantic consistency and inter-patient semantic correlations, we propose a multi-task VLP method, MG-3D, pre-trained on large-scale data (47.1K), addressing the challenges by the following two aspects: 1) Establishing the correspondence between volume semantics and multi-grained medical knowledge of each patient with cross-modal global alignment and complementary modality-guided local reconstruction, ensuring intra-patient features of different modalities cohesively represent the same semantic content; 2) Correlating inter-patient visual semantics based on fine-grained report correlations across patients, and keeping sensitivity to global individual differences via contrastive learning, enhancing the discriminative feature representation. Furthermore, we delve into the scaling law to explore potential performance improvements. Comprehensive evaluations across nine uni- and cross-modal clinical tasks are carried out to assess model efficacy. Extensive experiments on both internal and external datasets demonstrate the superior transferability, scalability, and generalization of MG-3D, showcasing its potential in advancing feature representation for 3D medical image analysis. Code will be available: https://github.com/Xuefeng-Ni/MG-3D.

Jiawei Zhang, Jiaxin Zhuang, Cheng Jin et al.

The recent emergence of diffusion models has significantly advanced the precision of learnable priors, presenting innovative avenues for addressing inverse problems. Since inverse problems inherently entail maximum a posteriori estimation, previous works have endeavored to integrate diffusion priors into the optimization frameworks. However, prevailing optimization-based inverse algorithms primarily exploit the prior information within the diffusion models while neglecting their denoising capability. To bridge this gap, this work leverages the diffusion process to reframe noisy inverse problems as a two-variable constrained optimization task by introducing an auxiliary optimization variable. By employing gradient truncation, the projection gradient descent method is efficiently utilized to solve the corresponding optimization problem. The proposed algorithm, termed ProjDiff, effectively harnesses the prior information and the denoising capability of a pre-trained diffusion model within the optimization framework. Extensive experiments on the image restoration tasks and source separation and partial generation tasks demonstrate that ProjDiff exhibits superior performance across various linear and nonlinear inverse problems, highlighting its potential for practical applications. Code is available at https://github.com/weigerzan/ProjDiff/.

Fanxu Meng, Hao Cheng, Jiaxin Zhuang et al.

Although residual connection enables training very deep neural networks, it is not friendly for online inference due to its multi-branch topology. This encourages many researchers to work on designing DNNs without residual connections at inference. For example, RepVGG re-parameterizes multi-branch topology to a VGG-like (single-branch) model when deploying, showing great performance when the network is relatively shallow. However, RepVGG can not transform ResNet to VGG equivalently because re-parameterizing methods can only be applied to linear blocks and the non-linear layers (ReLU) have to be put outside of the residual connection which results in limited representation ability, especially for deeper networks. In this paper, we aim to remedy this problem and propose to remove the residual connection in a vanilla ResNet equivalently by a reserving and merging (RM) operation on ResBlock. Specifically, the RM operation allows input feature maps to pass through the block while reserving their information and merges all the information at the end of each block, which can remove residual connections without changing the original output. As a plug-in method, RM Operation basically has three advantages: 1) its implementation makes it naturally friendly for high ratio network pruning. 2) it helps break the depth limitation of RepVGG. 3) it leads to better accuracy-speed trade-off network (RMNet) compared to ResNet and RepVGG. We believe the ideology of RM Operation can inspire many insights on model design for the community in the future. Code is available at: https://github.com/fxmeng/RMNet.

Jiaxin Zhuang, Linshan Wu, Qiong Wang et al.

The Vision Transformer (ViT) has demonstrated remarkable performance in Self-Supervised Learning (SSL) for 3D medical image analysis. Masked AutoEncoder (MAE) for feature pre-training can further unleash the potential of ViT on various medical vision tasks. However, due to large spatial sizes with much higher dimensions of 3D medical images, the lack of hierarchical design for MAE may hinder the performance of downstream tasks. In this paper, we propose a novel \textit{Mask in Mask (MiM)} pre-training framework for 3D medical images, which aims to advance MAE by learning discriminative representation from hierarchical visual tokens across varying scales. We introduce multiple levels of granularity for masked inputs from the volume, which are then reconstructed simultaneously ranging at both fine and coarse levels. Additionally, a cross-level alignment mechanism is applied to adjacent level volumes to enforce anatomical similarity hierarchically. Furthermore, we adopt a hybrid backbone to enhance the hierarchical representation learning efficiently during the pre-training. MiM was pre-trained on a large scale of available 3D volumetric images, \textit{i.e.,} Computed Tomography (CT) images containing various body parts. Extensive experiments on thirteen public datasets demonstrate the superiority of MiM over other SSL methods in organ/lesion/tumor segmentation and disease classification. We further scale up the MiM to large pre-training datasets with more than 10k volumes, showing that large-scale pre-training can further enhance the performance of downstream tasks. The improvement also concluded that the research community should pay more attention to the scale of the pre-training dataset towards the healthcare foundation model for 3D medical images.

Xiaoyu Zheng, Jing Wen, Jiaxin Zhuang et al.

Polarization, as a new optical imaging tool, has been explored to assist in the diagnosis of pathology. Moreover, converting the polarimetric Mueller Matrix (MM) to standardized stained images becomes a promising approach to help pathologists interpret the results. However, existing methods for polarization-based virtual staining are still in the early stage, and the diffusion-based model, which has shown great potential in enhancing the fidelity of the generated images, has not been studied yet. In this paper, a Regulated Bridge Diffusion Model (RBDM) for polarization-based virtual staining is proposed. RBDM utilizes the bidirectional bridge diffusion process to learn the mapping from polarization images to other modalities such as H\&E and fluorescence. And to demonstrate the effectiveness of our model, we conduct the experiment on our manually collected dataset, which consists of 18,000 paired polarization, fluorescence and H\&E images, due to the unavailability of the public dataset. The experiment results show that our model greatly outperforms other benchmark methods. Our dataset and code will be released upon acceptance.

Linshan Wu, Jiaxin Zhuang, Yanning Zhou et al.

Tumor is a leading cause of death worldwide, with an estimated 10 million deaths attributed to tumor-related diseases every year. AI-driven tumor recognition unlocks new possibilities for more precise and intelligent tumor screening and diagnosis. However, the progress is heavily hampered by the scarcity of annotated datasets, which demands extensive annotation efforts by radiologists. To tackle this challenge, we introduce FreeTumor, an innovative Generative AI (GAI) framework to enable large-scale tumor synthesis for mitigating data scarcity. Specifically, FreeTumor effectively leverages a combination of limited labeled data and large-scale unlabeled data for tumor synthesis training. Unleashing the power of large-scale data, FreeTumor is capable of synthesizing a large number of realistic tumors on images for augmenting training datasets. To this end, we create the largest training dataset for tumor synthesis and recognition by curating 161,310 publicly available Computed Tomography (CT) volumes from 33 sources, with only 2.3% containing annotated tumors. To validate the fidelity of synthetic tumors, we engaged 13 board-certified radiologists in a Visual Turing Test to discern between synthetic and real tumors. Rigorous clinician evaluation validates the high quality of our synthetic tumors, as they achieved only 51.1% sensitivity and 60.8% accuracy in distinguishing our synthetic tumors from real ones. Through high-quality tumor synthesis, FreeTumor scales up the recognition training datasets by over 40 times, showcasing a notable superiority over state-of-the-art AI methods including various synthesis methods and foundation models. These findings indicate promising prospects of FreeTumor in clinical applications, potentially advancing tumor treatments and improving the survival rates of patients.

Linshan Wu, Yuxiang Nie, Sunan He et al.

The integration of AI-assisted biomedical image analysis into clinical practice demands AI-generated findings that are not only accurate but also interpretable to clinicians. However, existing biomedical AI models generally lack the ability to simultaneously generate diagnostic findings and localize corresponding biomedical objects. This limitation makes it challenging for clinicians to correlate AI-generated findings with visual evidence (e.g., tiny lesions) in images and interpret the results of AI models. To address this challenge, we introduce UniBiomed, the first universal foundation model for grounded biomedical image interpretation, which is capable of generating accurate diagnostic findings and simultaneously segmenting the corresponding biomedical targets. UniBiomed is based on a novel integration of Multi-modal Large Language Model and Segment Anything Model, which can effectively unify diverse biomedical tasks in universal training for advancing grounded interpretation. To develop UniBiomed, we curate a large-scale dataset comprising over 27 million triplets of images, region annotations, and text descriptions across ten biomedical imaging modalities. Extensive validation on 70 internal and 14 external datasets demonstrated the state-of-the-art performance of UniBiomed in diverse biomedical tasks, including image segmentation, disease recognition, region-aware diagnosis, vision question answering, and report generation. In summary, UniBiomed is a powerful and versatile biomedical foundation model, unlocking the untapped grounded interpretation capability for optimizing AI-assisted biomedical image analysis.

Yao Du, Jiaxin Zhuang, Xiaoyu Zheng et al.

Histopathology image analysis is fundamental to digital pathology, with hematoxylin and eosin (H&E) staining as the gold standard for diagnostic and prognostic assessments. While H&E imaging effectively highlights cellular and tissue structures, it lacks sensitivity to birefringence and tissue anisotropy, which are crucial for assessing collagen organization, fiber alignment, and microstructural alterations--key indicators of tumor progression, fibrosis, and other pathological conditions. To bridge this gap, we construct a polarization imaging system and curate a new dataset of over 13,000 paired Polar-H&E images. Visualizations of polarization properties reveal distinctive optical signatures in pathological tissues, underscoring its diagnostic value. Building on this dataset, we propose PolarHE, a dual-modality fusion framework that integrates H&E with polarization imaging, leveraging the latter ability to enhance tissue characterization. Our approach employs a feature decomposition strategy to disentangle common and modality specific features, ensuring effective multimodal representation learning. Through comprehensive validation, our approach significantly outperforms previous methods, achieving an accuracy of 86.70% on the Chaoyang dataset and 89.06% on the MHIST dataset. These results demonstrate that polarization imaging is a powerful and underutilized modality in computational pathology, enriching feature representation and improving diagnostic accuracy. PolarHE establishes a promising direction for multimodal learning, paving the way for more interpretable and generalizable pathology models.

Linshan Wu, Jiaxin Zhuang, Xuefeng Ni et al.

AI-driven tumor analysis has garnered increasing attention in healthcare. However, its progress is significantly hindered by the lack of annotated tumor cases, which requires radiologists to invest a lot of effort in collecting and annotation. In this paper, we introduce a highly practical solution for robust tumor synthesis and segmentation, termed FreeTumor, which refers to annotation-free synthetic tumors and our desire to free patients that suffering from tumors. Instead of pursuing sophisticated technical synthesis modules, we aim to design a simple yet effective tumor synthesis paradigm to unleash the power of large-scale data. Specifically, FreeTumor advances existing methods mainly from three aspects: (1) Existing methods only leverage small-scale labeled data for synthesis training, which limits their ability to generalize well on unseen data from different sources. To this end, we introduce the adversarial training strategy to leverage large-scale and diversified unlabeled data in synthesis training, significantly improving tumor synthesis. (2) Existing methods largely ignored the negative impact of low-quality synthetic tumors in segmentation training. Thus, we employ an adversarial-based discriminator to automatically filter out the low-quality synthetic tumors, which effectively alleviates their negative impact. (3) Existing methods only used hundreds of cases in tumor segmentation. In FreeTumor, we investigate the data scaling law in tumor segmentation by scaling up the dataset to 11k cases. Extensive experiments demonstrate the superiority of FreeTumor, e.g., on three tumor segmentation benchmarks, average $+8.9\%$ DSC over the baseline that only using real tumors and $+6.6\%$ DSC over the state-of-the-art tumor synthesis method. Code will be available.