Jiaxin Zhuang

Jia-Xin Zhuang, Luyang Luo, Hao Chen · cmu

Masked autoencoder (MAE) is a promising self-supervised pre-training technique that can improve the representation learning of a neural network without human intervention. However, applying MAE directly to volumetric medical images poses two challenges: (i) a lack of global information that is crucial for understanding the clinical context of the holistic data, (ii) no guarantee of stabilizing the representations learned from randomly masked inputs. To address these limitations, we propose the \textbf{G}lobal-\textbf{L}ocal \textbf{M}asked \textbf{A}uto\textbf{E}ncoder (GL-MAE), a simple yet effective self-supervised pre-training strategy. In addition to reconstructing masked local views, as in previous methods, GL-MAE incorporates global context learning by reconstructing masked global views. Furthermore, a complete global view is integrated as an anchor to guide the reconstruction and stabilize the learning process through global-to-global consistency learning and global-to-local consistency learning. Finetuning results on multiple datasets demonstrate the superiority of our method over other state-of-the-art self-supervised algorithms, highlighting its effectiveness on versatile volumetric medical image segmentation tasks, even when annotations are scarce. Our codes and models will be released upon acceptance.

Jia-Xin Zhuang, Xiansong Huang, Yang Yang et al.

In this paper, we present OpenMedIA, an open-source toolbox library containing a rich set of deep learning methods for medical image analysis under heterogeneous Artificial Intelligence (AI) computing platforms. Various medical image analysis methods, including 2D/3D medical image classification, segmentation, localisation, and detection, have been included in the toolbox with PyTorch and/or MindSpore implementations under heterogeneous NVIDIA and Huawei Ascend computing systems. To our best knowledge, OpenMedIA is the first open-source algorithm library providing compared PyTorch and MindSpore implementations and results on several benchmark datasets. The source codes and models are available at https://git.openi.org.cn/OpenMedIA.

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.

Jia-Xin Zhuang, Jiabin Cai, Jianguo Zhang et al.

Automated medical image classification is the key component in intelligent diagnosis systems. However, most medical image datasets contain plenty of samples of common diseases and just a handful of rare ones, leading to major class imbalances. Currently, it is an open problem in intelligent diagnosis to effectively learn from imbalanced training data. In this paper, we propose a simple yet effective framework, named \textbf{C}lass \textbf{A}ttention to \textbf{RE}gions of the lesion (CARE), to handle data imbalance issues by embedding attention into the training process of \textbf{C}onvolutional \textbf{N}eural \textbf{N}etworks (CNNs). The proposed attention module helps CNNs attend to lesion regions of rare diseases, therefore helping CNNs to learn their characteristics more effectively. In addition, this attention module works only during the training phase and does not change the architecture of the original network, so it can be directly combined with any existing CNN architecture. The CARE framework needs bounding boxes to represent the lesion regions of rare diseases. To alleviate the need for manual annotation, we further developed variants of CARE by leveraging the traditional saliency methods or a pretrained segmentation model for bounding box generation. Results show that the CARE variants with automated bounding box generation are comparable to the original CARE framework with \textit{manual} bounding box annotations. A series of experiments on an imbalanced skin image dataset and a pneumonia dataset indicates that our method can effectively help the network focus on the lesion regions of rare diseases and remarkably improves the classification performance of rare diseases.

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.

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.

Yanqi Wu, Xinhua Lu, Runhe Lai et al.

Recent studies show that using potential out-of-distribution (OOD) labels from large corpora as auxiliary information can improve OOD detection in vision-language models (VLMs). However, these methods often fail when real-world OOD samples fall outside the predefined OOD label set. To address this limitation, we propose DynProto, a novel approach that learns OOD prototypes dynamically during testing using only in-distribution (ID) information. DynProto is inspired by a key observation: OOD samples predicted as the same ID class tend to cluster in the feature space. With this insight, we leverage easy-to-detect OOD samples as ``anchors'' to find their harder-to-detect, similar counterparts. To this end, DynProto introduces two modules: \textbf{Coarse OOD Pattern Capturing Module} caches OOD patterns that are easily confused with each ID class during testing, and \textbf{Fine-grained OOD Pattern Refinement Module} subsequently clusters these patterns within each cache and aggregates them into representative OOD prototypes. By measuring similarity to ID and dynamic OOD prototypes, DynProto enables accurate OOD detection. DynProto significantly outperforms prior methods across multiple benchmarks. On ImageNet OOD benchmark, DynProto reduces FPR95 by 11.60\% and improves AUROC by 4.70\%. Moreover, the framework is architecture-agnostic and can be integrated into various backbones.

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/.

Yuting Gao, Jia-Xin Zhuang, Shaohui Lin et al.

While self-supervised representation learning (SSL) has received widespread attention from the community, recent research argue that its performance will suffer a cliff fall when the model size decreases. The current method mainly relies on contrastive learning to train the network and in this work, we propose a simple yet effective Distilled Contrastive Learning (DisCo) to ease the issue by a large margin. Specifically, we find the final embedding obtained by the mainstream SSL methods contains the most fruitful information, and propose to distill the final embedding to maximally transmit a teacher's knowledge to a lightweight model by constraining the last embedding of the student to be consistent with that of the teacher. In addition, in the experiment, we find that there exists a phenomenon termed Distilling BottleNeck and present to enlarge the embedding dimension to alleviate this problem. Our method does not introduce any extra parameter to lightweight models during deployment. Experimental results demonstrate that our method achieves the state-of-the-art on all lightweight models. Particularly, when ResNet-101/ResNet-50 is used as teacher to teach EfficientNet-B0, the linear result of EfficientNet-B0 on ImageNet is very close to ResNet-101/ResNet-50, but the number of parameters of EfficientNet-B0 is only 9.4\%/16.3\% of ResNet-101/ResNet-50. Code is available at https://github. com/Yuting-Gao/DisCo-pytorch.

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.

Jia-Xin Zhuang, Wanying Tao, Jianfei Xing et al.

Deep learning models have shown their superior performance in various vision tasks. However, the lack of precisely interpreting kernels in convolutional neural networks (CNNs) is becoming one main obstacle to wide applications of deep learning models in real scenarios. Although existing interpretation methods may find certain visual patterns which are associated with the activation of a specific kernel, those visual patterns may not be specific or comprehensive enough for interpretation of a specific activation of kernel of interest. In this paper, a simple yet effective optimization method is proposed to interpret the activation of any kernel of interest in CNN models. The basic idea is to simultaneously preserve the activation of the specific kernel and suppress the activation of all other kernels at the same layer. In this way, only visual information relevant to the activation of the specific kernel is remained in the input. Consistent visual information from multiple modified inputs would help users understand what kind of features are specifically associated with specific kernel. Comprehensive evaluation shows that the proposed method can help better interpret activation of specific kernels than widely used methods, even when two kernels have very similar activation regions from the same input image.

Yuqiao Xian, Jia-Xin Zhuang, Fufu Yu

This is a technical report for CVPR 2021 AliProducts Challenge. AliProducts Challenge is a competition proposed for studying the large-scale and fine-grained commodity image recognition problem encountered by worldleading ecommerce companies. The large-scale product recognition simultaneously meets the challenge of noisy annotations, imbalanced (long-tailed) data distribution and fine-grained classification. In our solution, we adopt stateof-the-art model architectures of both CNNs and Transformer, including ResNeSt, EfficientNetV2, and DeiT. We found that iterative data cleaning, classifier weight normalization, high-resolution finetuning, and test time augmentation are key components to improve the performance of training with the noisy and imbalanced dataset. Finally, we obtain 6.4365% mean class error rate in the leaderboard with our ensemble model.