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Researcher profile

Junde Wu

Junde Wu contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Computer Visioneess.IVquant-phArtificial IntelligenceMachine Learningmath-phmath.FAmath.MP

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Published work

18 published item(s)

preprint2026arXiv

BioMedArena: An Open-source Toolkit for Building and Evaluating Biomedical Deep Research Agents

Building a deep research agent today is an exercise in glue code: the same backbone evaluated on the same benchmark can report different accuracies in different papers because harness and tool registry all differ, and integrating a new foundation model into a comparable evaluation surface costs weeks of model-specific engineering. We call this the per-paper engineering tax and release BioMedArena, an open-source toolkit that not only alleviates it but also provides an arena for fair comparison of different foundation models when evaluating them as deep-research agents. BioMedArena decouples six layers of biomedical agent evaluation -- benchmark loading, tool exposure, tool selection, execution mode, context management, and scoring -- and exposes 147 biomedical benchmarks and 75 biomedical tools across 9 functional families. Adding a new model, benchmark, or tool reduces to registering a few-line provider adapter. We further provide 6 agent harnesses with 6 context-management strategies, which provide 12 backbones with competitive research capabilities and significantly improved performance, achieving state-of-the-art (SOTA) results on 8 representative biomedical benchmarks, with an average lift of +15.03 percentage points over prior SOTA. The toolkit, configurations, and per-task traces are available at https://github.com/AI-in-Health/BioMedArena

0 citations0 reviewsNo code linkedOpen access
preprint2023arXiv

Medical SAM Adapter: Adapting Segment Anything Model for Medical Image Segmentation

The Segment Anything Model (SAM) has recently gained popularity in the field of image segmentation due to its impressive capabilities in various segmentation tasks and its prompt-based interface. However, recent studies and individual experiments have shown that SAM underperforms in medical image segmentation, since the lack of the medical specific knowledge. This raises the question of how to enhance SAM's segmentation capability for medical images. In this paper, instead of fine-tuning the SAM model, we propose the Medical SAM Adapter (Med-SA), which incorporates domain-specific medical knowledge into the segmentation model using a light yet effective adaptation technique. In Med-SA, we propose Space-Depth Transpose (SD-Trans) to adapt 2D SAM to 3D medical images and Hyper-Prompting Adapter (HyP-Adpt) to achieve prompt-conditioned adaptation. We conduct comprehensive evaluation experiments on 17 medical image segmentation tasks across various image modalities. Med-SA outperforms several state-of-the-art (SOTA) medical image segmentation methods, while updating only 2\% of the parameters. Our code is released at https://github.com/KidsWithTokens/Medical-SAM-Adapter.

0 citations0 reviewsNo code linkedOpen access
preprint2023arXiv

MedSegDiff: Medical Image Segmentation with Diffusion Probabilistic Model

Diffusion probabilistic model (DPM) recently becomes one of the hottest topic in computer vision. Its image generation application such as Imagen, Latent Diffusion Models and Stable Diffusion have shown impressive generation capabilities, which aroused extensive discussion in the community. Many recent studies also found it is useful in many other vision tasks, like image deblurring, super-resolution and anomaly detection. Inspired by the success of DPM, we propose the first DPM based model toward general medical image segmentation tasks, which we named MedSegDiff. In order to enhance the step-wise regional attention in DPM for the medical image segmentation, we propose dynamic conditional encoding, which establishes the state-adaptive conditions for each sampling step. We further propose Feature Frequency Parser (FF-Parser), to eliminate the negative effect of high-frequency noise component in this process. We verify MedSegDiff on three medical segmentation tasks with different image modalities, which are optic cup segmentation over fundus images, brain tumor segmentation over MRI images and thyroid nodule segmentation over ultrasound images. The experimental results show that MedSegDiff outperforms state-of-the-art (SOTA) methods with considerable performance gap, indicating the generalization and effectiveness of the proposed model. Our code is released at https://github.com/WuJunde/MedSegDiff.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Calibrate the inter-observer segmentation uncertainty via diagnosis-first principle

On the medical images, many of the tissues/lesions may be ambiguous. That is why the medical segmentation is typically annotated by a group of clinical experts to mitigate the personal bias. However, this clinical routine also brings new challenges to the application of machine learning algorithms. Without a definite ground-truth, it will be difficult to train and evaluate the deep learning models. When the annotations are collected from different graders, a common choice is majority vote. However such a strategy ignores the difference between the grader expertness. In this paper, we consider the task of predicting the segmentation with the calibrated inter-observer uncertainty. We note that in clinical practice, the medical image segmentation is usually used to assist the disease diagnosis. Inspired by this observation, we propose diagnosis-first principle, which is to take disease diagnosis as the criterion to calibrate the inter-observer segmentation uncertainty. Following this idea, a framework named Diagnosis First segmentation Framework (DiFF) is proposed to estimate diagnosis-first segmentation from the raw images.Specifically, DiFF will first learn to fuse the multi-rater segmentation labels to a single ground-truth which could maximize the disease diagnosis performance. We dubbed the fused ground-truth as Diagnosis First Ground-truth (DF-GT).Then, we further propose Take and Give Modelto segment DF-GT from the raw image. We verify the effectiveness of DiFF on three different medical segmentation tasks: OD/OC segmentation on fundus images, thyroid nodule segmentation on ultrasound images, and skin lesion segmentation on dermoscopic images. Experimental results show that the proposed DiFF is able to significantly facilitate the corresponding disease diagnosis, which outperforms previous state-of-the-art multi-rater learning methods.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Characterizing entanglement using quantum discord over state extensions

We propose a framework to characterize entanglement with quantum discord, both asymmetric and symmetric, over state extensions. In particular, we show that the minimal Bures distance of discord over state extensions is equivalent to Bures distance of entanglement. This equivalence places quantum discord at a more primitive position than entanglement conceptually in the sense that entanglement can be interpreted as an irreducible part of discord over all state extensions. Based on this equivalence, we also offer an operational meaning of Bures distance of entanglement by connecting it to quantum state discriminations. Moreover, for the relative entropy part, we prove that the entanglement measure introduced by Devi and Rajagopal [A. R. U. Devi and A. K. Rajagopal, Phys. Rev. Lett. 100, 140502 (2008)] is actually equivalent to the relative entropy of entanglement. We also provide several quantifications of entanglement based on discord measures.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Contrastive Centroid Supervision Alleviates Domain Shift in Medical Image Classification

Deep learning based medical imaging classification models usually suffer from the domain shift problem, where the classification performance drops when training data and real-world data differ in imaging equipment manufacturer, image acquisition protocol, patient populations, etc. We propose Feature Centroid Contrast Learning (FCCL), which can improve target domain classification performance by extra supervision during training with contrastive loss between instance and class centroid. Compared with current unsupervised domain adaptation and domain generalization methods, FCCL performs better while only requires labeled image data from a single source domain and no target domain. We verify through extensive experiments that FCCL can achieve superior performance on at least three imaging modalities, i.e. fundus photographs, dermatoscopic images, and H & E tissue images.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Dataset and Evaluation algorithm design for GOALS Challenge

Glaucoma causes irreversible vision loss due to damage to the optic nerve, and there is no cure for glaucoma.OCT imaging modality is an essential technique for assessing glaucomatous damage since it aids in quantifying fundus structures. To promote the research of AI technology in the field of OCT-assisted diagnosis of glaucoma, we held a Glaucoma OCT Analysis and Layer Segmentation (GOALS) Challenge in conjunction with the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) 2022 to provide data and corresponding annotations for researchers studying layer segmentation from OCT images and the classification of glaucoma. This paper describes the released 300 circumpapillary OCT images, the baselines of the two sub-tasks, and the evaluation methodology. The GOALS Challenge is accessible at https://aistudio.baidu.com/aistudio/competition/detail/230.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

One Hyper-Initializer for All Network Architectures in Medical Image Analysis

Pre-training is essential to deep learning model performance, especially in medical image analysis tasks where limited training data are available. However, existing pre-training methods are inflexible as the pre-trained weights of one model cannot be reused by other network architectures. In this paper, we propose an architecture-irrelevant hyper-initializer, which can initialize any given network architecture well after being pre-trained for only once. The proposed initializer is a hypernetwork which takes a downstream architecture as input graphs and outputs the initialization parameters of the respective architecture. We show the effectiveness and efficiency of the hyper-initializer through extensive experimental results on multiple medical imaging modalities, especially in data-limited fields. Moreover, we prove that the proposed algorithm can be reused as a favorable plug-and-play initializer for any downstream architecture and task (both classification and segmentation) of the same modality.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Progressive Hard-case Mining across Pyramid Levels for Object Detection

In object detection, multi-level prediction (e.g., FPN) and reweighting skills (e.g., focal loss) have drastically improved one-stage detector performance. However, the synergy between these two techniques is not fully explored in a unified framework. We find that, during training, the one-stage detector's optimization is not only restricted to the static hard-case mining loss (gradient drift) but also suffered from the diverse positive samples' proportions split by different pyramid levels (level discrepancy). Under this concern, we propose Hierarchical Progressive Focus (HPF) consisting of two key designs: 1) progressive focus, a more flexible hard-case mining setting calculated adaptive to the convergence progress, 2) hierarchical sampling, automatically generating a set of progressive focus for level-specific target optimization. Based on focal loss with ATSS-R50, our approach achieves 40.5 AP, surpassing the state-of-the-art QFL (Quality Focal Loss, 39.9 AP) and VFL (Varifocal Loss, 40.1 AP). Our best model achieves 55.1 AP on COCO test-dev, obtaining excellent results with only a typical training setting. Moreover, as a plug-and-play scheme, HPF can cooperate well with recent advances, providing a stable performance improvement on nine mainstream detectors.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

REFUGE2 Challenge: A Treasure Trove for Multi-Dimension Analysis and Evaluation in Glaucoma Screening

With the rapid development of artificial intelligence (AI) in medical image processing, deep learning in color fundus photography (CFP) analysis is also evolving. Although there are some open-source, labeled datasets of CFPs in the ophthalmology community, large-scale datasets for screening only have labels of disease categories, and datasets with annotations of fundus structures are usually small in size. In addition, labeling standards are not uniform across datasets, and there is no clear information on the acquisition device. Here we release a multi-annotation, multi-quality, and multi-device color fundus image dataset for glaucoma analysis on an original challenge -- Retinal Fundus Glaucoma Challenge 2nd Edition (REFUGE2). The REFUGE2 dataset contains 2000 color fundus images with annotations of glaucoma classification, optic disc/cup segmentation, as well as fovea localization. Meanwhile, the REFUGE2 challenge sets three sub-tasks of automatic glaucoma diagnosis and fundus structure analysis and provides an online evaluation framework. Based on the characteristics of multi-device and multi-quality data, some methods with strong generalizations are provided in the challenge to make the predictions more robust. This shows that REFUGE2 brings attention to the characteristics of real-world multi-domain data, bridging the gap between scientific research and clinical application.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

SeATrans: Learning Segmentation-Assisted diagnosis model via Transformer

Clinically, the accurate annotation of lesions/tissues can significantly facilitate the disease diagnosis. For example, the segmentation of optic disc/cup (OD/OC) on fundus image would facilitate the glaucoma diagnosis, the segmentation of skin lesions on dermoscopic images is helpful to the melanoma diagnosis, etc. With the advancement of deep learning techniques, a wide range of methods proved the lesions/tissues segmentation can also facilitate the automated disease diagnosis models. However, existing methods are limited in the sense that they can only capture static regional correlations in the images. Inspired by the global and dynamic nature of Vision Transformer, in this paper, we propose Segmentation-Assisted diagnosis Transformer (SeATrans) to transfer the segmentation knowledge to the disease diagnosis network. Specifically, we first propose an asymmetric multi-scale interaction strategy to correlate each single low-level diagnosis feature with multi-scale segmentation features. Then, an effective strategy called SeA-block is adopted to vitalize diagnosis feature via correlated segmentation features. To model the segmentation-diagnosis interaction, SeA-block first embeds the diagnosis feature based on the segmentation information via the encoder, and then transfers the embedding back to the diagnosis feature space by a decoder. Experimental results demonstrate that SeATrans surpasses a wide range of state-of-the-art (SOTA) segmentation-assisted diagnosis methods on several disease diagnosis tasks.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Solvable dilation model of $\cal PT$-symmetric systems

The dilation method is a practical way to experimentally simulate non-Hermitian, especially $\cal PT$-symmetric quantum systems. However, the time-dependent dilation problem cannot be explicitly solved in general. In this paper, we present a simple yet non-trivial exactly solvable dilation problem with two dimensional time-dependent $\cal PT$-symmetric Hamiltonian. Our system is initially set in the unbroken $\cal PT$-symmetric phase and later goes across the so-called exceptional point and enters the broken $\cal PT$-symmetric phase. For this system, the dilated Hamiltonian and the evolution of $\cal PT$-symmetric system are analytically worked out. Our result clearly showed that the exceptional points do not have much physical relevance in a \textit{time-dependent} system.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

The Local Orthogonality between Quantum States and Entanglement Decomposition

In the paper, we show that when a quantum state can be decomposed as a convex combination of locally orthogonal mixed states, its entanglement can be decomposed into the entanglement of these mixed states without losing them. The obtained result generalizes a corresponding one proved by Horodecki [Acta Phys. Slov. 48, 141 (1998).]. But, for the entanglement cost it requires certain conditions for holding the decomposition, and the distillable entanglement only has a week result as inequality. Finally, we presented an example to show that the conditions of our conclusions are existence.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Universal, transferable and targeted adversarial attacks

Deep Neural Networks have been found vulnerable re-cently. A kind of well-designed inputs, which called adver-sarial examples, can lead the networks to make incorrectpredictions. Depending on the different scenarios, goalsand capabilities, the difficulties of the attacks are different.For example, a targeted attack is more difficult than a non-targeted attack, a universal attack is more difficult than anon-universal attack, a transferable attack is more difficultthan a nontransferable one. The question is: Is there existan attack that can meet all these requirements? In this pa-per, we answer this question by producing a kind of attacksunder these conditions. We learn a universal mapping tomap the sources to the adversarial examples. These exam-ples can fool classification networks to classify all of theminto one targeted class, and also have strong transferability.Our code is released at: xxxxx.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Leveraging Undiagnosed Data for Glaucoma Classification with Teacher-Student Learning

Recently, deep learning has been adopted to the glaucoma classification task with performance comparable to that of human experts. However, a well trained deep learning model demands a large quantity of properly labeled data, which is relatively expensive since the accurate labeling of glaucoma requires years of specialist training. In order to alleviate this problem, we propose a glaucoma classification framework which takes advantage of not only the properly labeled images, but also undiagnosed images without glaucoma labels. To be more specific, the proposed framework is adapted from the teacher-student-learning paradigm. The teacher model encodes the wrapped information of undiagnosed images to a latent feature space, meanwhile the student model learns from the teacher through knowledge transfer to improve the glaucoma classification. For the model training procedure, we propose a novel training strategy that simulates the real-world teaching practice named as 'Learning To Teach with Knowledge Transfer (L2T-KT)', and establish a 'Quiz Pool' as the teacher's optimization target. Experiments show that the proposed framework is able to utilize the undiagnosed data effectively to improve the glaucoma prediction performance.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

TR-GAN: Topology Ranking GAN with Triplet Loss for Retinal Artery/Vein Classification

Retinal artery/vein (A/V) classification lays the foundation for the quantitative analysis of retinal vessels, which is associated with potential risks of various cardiovascular and cerebral diseases. The topological connection relationship, which has been proved effective in improving the A/V classification performance for the conventional graph based method, has not been exploited by the deep learning based method. In this paper, we propose a Topology Ranking Generative Adversarial Network (TR-GAN) to improve the topology connectivity of the segmented arteries and veins, and further to boost the A/V classification performance. A topology ranking discriminator based on ordinal regression is proposed to rank the topological connectivity level of the ground-truth, the generated A/V mask and the intentionally shuffled mask. The ranking loss is further back-propagated to the generator to generate better connected A/V masks. In addition, a topology preserving module with triplet loss is also proposed to extract the high-level topological features and further to narrow the feature distance between the predicted A/V mask and the ground-truth. The proposed framework effectively increases the topological connectivity of the predicted A/V masks and achieves state-of-the-art A/V classification performance on the publicly available AV-DRIVE dataset.

0 citations0 reviewsNo code linkedOpen access
preprint2019arXiv

Integrating neural networks into the blind deblurring framework to compete with the end-to-end learning-based methods

Recently, end-to-end learning-based methods based on deep neural network (DNN) have been proven effective for blind deblurring. Without human-made assumptions and numerical algorithms, they are able to restore images with fewer artifacts and better perceptual quality. However, in practice, we also find some of their drawbacks. Without the theoretical guidance, these methods can not perform well when the motion is complex and sometimes generate unreasonable results. In this paper, for overcoming these drawbacks, we integrate deep convolution neural networks into conventional deblurring framework. Specifically, we build Stacked Estimation Residual Net (SEN) to estimate the motion flow map and Recurrent Prior Generative and Adversarial Net (RP-GAN) to learn the implicit image prior in the optimization model. Comparing with state-of-the-art end-to-end learning-based methods, our method restores reasonable details and shows better generalization ability.

0 citations0 reviewsNo code linkedOpen access