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Training, testing and benchmarking medical AI models using Clinical AIBench

BenchCouncil Transactions on Benchmarks, Standards and Evaluations 2022年第1期2卷 100037-100037页

作者： Huang, Yunyou Miao, Xiuxia Zhang, Ruchang Ma, Li Liu, Wenjing Zhang, Fan Guan, Xianglong Liang, Xiaoshuang Lu, Xiangjiang Tang, Suqing Zhang, Zhifei Guangxi Key Lab of Multi-Source Information Mining & Security School of Computer Science and Engineering & School of Software Guangxi Normal University Guilin China State Key Laboratory of Computer Architecture Institute of Computing Technology Chinese Academy of Sciences Beijing China Guilin Medical University Guilin China Department of Physiology and Pathophysiology Capital Medical University Beijing China Faculty of Education Guangxi Normal University Guilin China International Open Benchmark Council Beijing China

AI technology has been used in many clinical research fields, but most AI technologies are difficult to land in real-world clinical settings. In most current clinical AI research settings, the diagnosis task is to identify different types of diseases among the given ones. However, the diagnosis in real-world settings needs dynamically developing inspection strategies based on the existing resources of medical institutions and identifying different kinds of diseases out of many possibilities. To promote the development of different clinical AI technologies and the implementation of clinical applications, we propose a benchmark named Clinical AIBench for developing, verifying, and evaluating clinical AI technologies in real-world clinical settings. Specifically, Clinical AIBench can be used for: (1) Model training and testing: Researchers can use the data to train and test their models. (2)Model evaluation: Researchers can use Clinical AIBench to objectively, fairly, and comparably evaluate various models of different researchers. (3) Clinical value evaluation: Researchers can use the clinical indicators provided by Clinical AIBench to evaluate the clinical value of models, which will be applied in real-world clinical settings. For convenience, Clinical AIBench provides three different levels of clinical settings: restricted clinical setting, which is named closed clinical setting, data island clinical setting, and real-world clinical setting, which is called open clinical setting. In addition, Clinical AIBench covers three diseases: Alzheimer's disease, COVID-19, and dental. Clinical AIBench provides python APIs to researchers. The data and source code are publicly available from the project website https://***/clinical_aibench/. © 2022 The Authors

关键词： COVID-19

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Using Determinant Point Process in Generative Adversarial Networks for SSVEP Signals Synthesis

Using Determinant Point Process in Generative Adversarial Ne...

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Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： Junkongshuai Wang Lu Wang Jiaguan Han Wei Mu Pengchao Wang Xueze Zhang Gege Zhan Lihua Zhang Zhongxue Gan Xiaoyang Kang MOE Frontiers Center for Brain Science State Key Laboratory of Medical Neurobiology Institute of AI and Robotics Academy for Engineering & Technology Laboratory for Neural Interface and Brain Computer Interface Engineering Research Center of AI & Robotics Ministry of Education Shanghai Engineering Research Center of AI & Robotics Fudan University Shanghai China Ji Hua Laboratory Foshan China Yiwu Research Institute of Fudan University Yiwu City China Research Center for Intelligent Sensing Zhejiang Lab Hangzhou China

Steady-state visual evoked potential (SSVEP) is one of the main paradigms of brain-computer interface (BCI). However, the acquisition method of SSVEP can cause subject fatigue and discomfort, leading to the insufficiency of SSVEP databases. Inspired by generative determinantal point process (GDPP), we utilize the determinantal point process in generative adversarial network (GAN) to generate SSVEP signals. We investigate the ability of the method to synthesize signals from the Benchmark dataset. We further use some evaluation metrics to verify its validity. Results prove that the usage of this method significantly improved the authenticity of generated data and the accuracy (97.636%) of classification using deep learning in SSVEP data augmentation.

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CodeRAG: Supportive Code Retrieval on Bigraph for Real-World Code Generation

arXiv

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arXiv 2025年

作者： Li, Jia Shi, Xianjie Zhang, Kechi Li, Lei Li, Ge Tao, Zhengwei Liu, Fang Tao, Chongyang Jin, Zhi Key Lab of High Confidence Software Technology Peking University MoE School of Computer Science Peking University China The University of Hong Kong Hong Kong School of Computer Science and Engineering State Key Laboratory of Complex & Critical Software Environment Beihang University China Beihang University China

Large language models (LLMs) have shown promising performance in automated code generation, especially excelling in simple tasks such as generating standalone codes. Different from simple tasks, real-world code generation usually depends on specific programming environment (e.g., code repositories). It contains complex dependencies and domain knowledge, which is needed for LLMs when generating target code snippets. In this paper, we propose CodeRAG, a retrieval-augmented code generation (RAG) framework to comprehensively retrieve supportive codes for real-world code generation. Beginning with the requirement, CodeRAG first constructs a requirement graph for the current repository, and retrieves sub- and similar- requirement nodes of the target requirement on the graph. Meanwhile, it models the repository into a DS-code graph. CodeRAG then maps these relevant requirement nodes into their corresponding code nodes, and treats these code nodes as archors for LLM reasoning on DS-code graph. Finally, CodeRAG introduces a code-oriented agentic reasoning process, seamlessly allowing LLMs to reason and comprehensively retrieve for supportive codes which LLMs’ need for generating correct programs. Experiments show that CodeRAG achieves significant improvements (i.e., increasing 40.90 and 37.79 Pass@1 on GPT-4o and Gemini-Pro on DevEval) compared to no RAG scenarios. Further tests on reasoning LLMs (i.e., QwQ-32B) confirm CodeRAG’s adaptability and efficacy across various types of LLMs. In addition, CodeRAG outperforms commercial programming products such as Copilit and Cursor. We further investigate the performance of our framework on different dependency types, and observe that CodeRAG is superior in generating examples where target codes invoke predefined cross-file code snippets. These results demonstrate CodeRAG’s potential in solving real-world repo-level coding challenges. Copyright © 2025, The Authors. All rights reserved.

关键词： Report generators

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Large language models for diabetes training:a prospective study

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science Bulletin 2025年第6期70卷 934-942页

作者： Haoxuan Li Zehua Jiang Zhouyu Guan Yuqian Bao Yuexing Liu Tingting Hu Jiajia Li Ruhan Liu Liang Wu Di Cheng Hongwei Ji Yong Wang Ya-Xing Wang Carol Y.Cheung Yingfeng Zheng Jihong Wang Zhen Li Weibing Wu Cynthia Ciwei Lim Yong Mong Bee Hong Chang Tan Elif I.Ekinci David C.Klonoff Justin B.Echouffo-Tcheugui Nestoras Mathioudakis Leonor Corsino Rafael Simó Charumathi Sabanayagam Gavin Siew Wei Tan Ching-Yu Cheng Tien Yin Wong Huating Li Chun Cai Lijuan Mao Lee-Ling Lim Yih-Chung Tham Bin Sheng Weiping Jia Shanghai University of Sport Shanghai 200438China School of Clinical Medicine Beijing Tsinghua Changgung HospitalTsinghua MedicineTsinghua UniversityBeijing 100084China Beijing Visual Science and Translational Eye Research Institute(BERI) Tsinghua MedicineTsinghua UniversityBeijing 100084China Shanghai Belt and Road International Joint Laboratory of Intelligent Prevention and Treatment for Metabolic Diseases Department of Computer Science and EngineeringSchool of ElectronicInformationand Electrical EngineeringShanghai Jiao Tong UniversityDepartment of Endocrinology and MetabolismShanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai Diabetes InstituteShanghai Clinical Center for DiabetesShanghai 200240China MoE Key Lab of Artificial Intelligence Artificial Intelligence InstituteShanghai Jiao Tong UniversityShanghai 200240China Department of Cardiology the Affiliated Hospital of Qingdao UniversityQingdao 266011China CEMS NCMISHCMSMADISAcademy of Mathematics and Systems ScienceChinese Academy of SciencesBeijing 100190China School of Mathematics University of Chinese Academy of SciencesChinese Academy of SciencesBeijing 100049China Key Laboratory of Systems Health Science of Zhejiang Province School of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou 310024China Beijing Institute of Ophthalmology Beijing Tongren HospitalCapital Medical UniversityBeijing Ophthalmology and Visual Sciences Key LaboratoryBeijing 100730China k.Department of Ophthalmology and Visual Sciences The Chinese University of Hong KongHong Kong 999077China State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat-sen UniversityGuangdong Provincial Key Laboratory of Ophthalmology and Visual ScienceGuangdong Provincial Clinical Research Center for Ocular DiseasesGuangzhou 510060China Department of Renal Medicine Singapore General HospitalSingHealth-Duke Academic Medical CentreSingapore169

Diabetes poses a considerable global health challenge,with varying levels of diabetes knowledge among healthcare professionals,highlighting the importance of diabetes *** Language Models(LLMs)provide new insights into diabetes training,but their performance in diabetes-related queries remains uncertain,especially outside the English language like *** first evaluated the performance of ten LLMs:ChatGPT-3.5,ChatGPT-4.0,Google Bard,LlaMA-7B,LlaMA2-7B,Baidu ERNIE Bot,Ali Tongyi Qianwen,MedGPT,HuatuoGPT,and Chinese LlaMA2-7B on diabetes-related queries,based on the Chinese National Certificate Examination for Primary Diabetes Care in China(NCE-CPDC)and the English Specialty Certificate Examination in Endocrinology and Diabetes of Membership of the Royal College of Physicians of the United ***,we assessed the training of primary care physicians(PCPs)without and with the assistance of ChatGPT-4.0 in the NCE-CPDC examination to ascertain the reliability of LLMs as medical *** found that ChatGPT-4.0 outperformed other LLMs in the English examination,achieving a passing accuracy of 62.50%,which was significantly higher than that of Google Bard,LlaMA-7B,and *** the NCE-CPFC examination,ChatGPT-4.0,Ali Tongyi Qianwen,Baidu ERNIE Bot,Google Bard,MedGPT,and ChatGPT-3.5 successfully passed,whereas LlaMA2-7B,HuatuoGPT,Chinese LLaMA2-7B,and LlaMA-7B ***-4.0(84.82%)surpassed all PCPs and assisted most PCPs in the NCE-CPDC examination(improving by 1%–6.13%).In summary,LLMs demonstrated outstanding competence for diabetes-related questions in both the Chinese and English language,and hold great potential to assist future diabetes training for physicians globally.

关键词： Diabetes Diabetestraining Largelanguagemodels Primarydiabetescare Prospectivestudy

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Runtime Permission Issues in Android Apps: Taxonomy, Practices, and Ways Forward

arXiv

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arXiv 2021年

作者： Wang, Ying Wang, Yibo Wang, Sinan Liu, Yepang Xu, Chang Cheung, Shing-Chi Yu, Hai Zhu, Zhiliang The Software College Northeasthern University China The Department of Computer Science and Engineering Guangdong Provincial Key Laboratory of Brain-inspired Intelligent Computation Southern University of Science and Technology Shenzhen China The State Key Lab for Novel Software Technology The Department of Computer Science and Technology Nanjing University China The Department of Computer Science and Engineering The Hong Kong University of Science and Technology Hong Kong Hong Kong

Android introduces a new permission model that allows apps to request permissions at runtime rather than at the installation time since 6.0 (Marshmallow, API level 23). While this runtime permission model provides users with greater flexibility in controlling an app’s access to sensitive data and system features, it brings new challenges to app development. First, as users may grant or revoke permissions at any time while they are using an app, developers need to ensure that the app properly checks and requests required permissions before invoking any permission-protected APIs. Second, Android’s permission mechanism keeps evolving and getting customized by device manufacturers. Developers are expected to comprehensively test their apps on different Android versions and device models to make sure permissions are properly requested in all situations. Unfortunately, these requirements are often impractical for developers. In practice, many Android apps suffer from various runtime permission issues (ARP issues). While existing studies have explored ARP issues, the understanding of such issues is still preliminary. To better characterize ARP issues, we performed an empirical study using 135 Stack Overflow posts that discuss ARP issues and 199 real ARP issues archived in popular open-source Android projects on GitHub. Via analyzing the data, we observed 11 types of ARP issues that commonly occur in Android apps. For each type of issues, we systematically studied: (1) how they can be manifested, (2) how pervasive and serious they are in real-world apps, and (3) how they can be fixed. We also analyzed the evolution trend of different types of issues from 2015 to 2020 to understand their impact on the Android ecosystem. Furthermore, we conducted a field survey and in-depth interviews among practitioners, to gain insights from industrial practices and learn practitioners’ requirements of tools that can help combat ARP issues. Finally, to understand the strengths and weaknesse

关键词： Android (operating system)

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Bionic Soft Fingers with Hybrid Variable Stiffness Mechanisms for Multimode Grasping

Bionic Soft Fingers with Hybrid Variable Stiffness Mechanism...

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IEEE International Conference on Robotics and Automation (ICRA)

作者： Xiangbo Wang Tianran Zhang Hongze Yu Zhenwei Wen Lide Fang Huaping Liu Fuchun Sun Lixue Tang Bin Fang College of Quality and Technical Supervision Hebei University Baoding China School of Artificial Intelligence Beijing University of Posts and Telecommunications Beijing China School of Mechanical Engineering & Automation Beihang University Beijing China International School Beijing University of Posts and Telecommunications Beijing China Department of Computer Science and Technology Beijing National Research Center for Information Science and Technology Institute for Artificial Intelligence State Key Lab of Intelligent Technology and Systems Tsinghua University Beijing China School of Biomedical Engineering Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application Capital Medical University Beijing China

ISBN: (数字)9798350384574

ISBN: (纸本)9798350384581

This paper presents a novel Bionic Soft Finger (BSF) that aims to overcome the limitations of conventional rigid manipulators in terms of adaptability and safety, as well as the challenges faced by soft hands regarding carrying capacity and stability. The BSF design uses a hybrid variable stiffness mechanism combining memory alloy actuators with particle jamming to achieve the desired bending angle and actuator stiffness. Our innovative approach utilizes a bionic finger design that incorporates a memory alloy skeleton and a water-cooled recirculation system, leading to a substantial reduction in the time required for each operation. Through the integration of particle jamming, we have enhanced the overall stiffness and performance of the manipulator, enabling load capacities of up to 3N per finger and more than twice the stiffness of a normal condition. Additionally, our design enables multimode grasping and incorporates a liquid metal strain sensor (METT) for real-time monitoring of finger bending angles. Comparative analyses demonstrate that our design exhibits superior stiffness and enables five-mode grasping in comparison to pneumatic actuators. We believe that bionic soft fingers present a promising solution for enhancing adaptability, safety, and performance in human-robot interaction applications.

关键词： Metals Grasping Bending Manipulators Stability analysis Skeleton Real-time systems

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Improving Adversarial Robustness via Mutual Information Estimation

arXiv

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arXiv 2022年

作者： Zhou, Dawei Wang, Nannan Gao, Xinbo Han, Bo Wang, Xiaoyu Zhan, Yibing Liu, Tongliang State Key Laboratory of Integrated Services Networks School of Telecommunications Engineering Xidian University China Chongqing Key Laboratory of Image Cognition Chongqing University of Posts and Telecommunications China Department of Computer Science Hong Kong Baptist University Hong Kong The Chinese University of Hong Kong Shenzhen China JD Explore Academy China TML Lab Sydney AI Centre The University of Sydney Australia

Deep neural networks (DNNs) are found to be vulnerable to adversarial noise. They are typically misled by adversarial samples to make wrong predictions. To alleviate this negative effect, in this paper, we investigate the dependence between outputs of the target model and input adversarial samples from the perspective of information theory, and propose an adversarial defense method. Specifically, we first measure the dependence by estimating the mutual information (MI) between outputs and the natural patterns of inputs (called natural MI) and MI between outputs and the adversarial patterns of inputs (called adversarial MI), respectively. We find that adversarial samples usually have larger adversarial MI and smaller natural MI compared with those w.r.t. natural samples. Motivated by this observation, we propose to enhance the adversarial robustness by maximizing the natural MI and minimizing the adversarial MI during the training process. In this way, the target model is expected to pay more attention to the natural pattern that contains objective semantics. Empirical evaluations demonstrate that our method could effectively improve the adversarial accuracy against multiple attacks. Copyright © 2022, The Authors. All rights reserved.

关键词： Information theory

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Asymptotically unbiased instance-wise regularized partial AUC optimization: theory and algorithm 22

Asymptotically unbiased instance-wise regularized partial AU...

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Proceedings of the 36th International Conference on Neural Information Processing Systems

作者： Huiyang Shao Qianqian Xu Zhiyong Yang Shilong Bao Qingming Huang Key Lab of Intell. Info. Process. Inst. of Comput. Tech. CAS and School of Computer Science and Tech. University of Chinese Academy of Sciences Key Lab of Intell. Info. Process. Inst. of Comput. Tech. CAS School of Computer Science and Tech. University of Chinese Academy of Sciences State Key Lab of Info. Security Inst. of Info. Engineering CAS and School of Cyber Security University of Chinese Academy of Sciences Key Lab of Intell. Info. Process. Inst. of Comput. Tech. CAS and School of Computer Science and Tech. University of Chinese Academy of Sciences and BDKM University of Chinese Academy of Sciences and Peng Cheng Laboratory

ISBN: (纸本)9781713871088

The Partial Area Under the ROC Curve (PAUC), typically including One-way Partial AUC (OPAUC) and Two-way Partial AUC (TPAUC), measures the average performance of a binary classifier within a specific false positive rate and/or true positive rate interval, which is a widely adopted measure when decision constraints must be considered. Consequentiy, PAUC optimization has naturally attracted increasing attention in the machine learning community within the last few years. Nonetheless, most of the existing methods could only optimize PAUC approximately, leading to inevitable biases that are not controllable. Fortunately, a recent work presents an unbiased formulation of the PAUC optimization problem via distributional robust optimization. However, it is based on the pair-wise formulation of AUC, which suffers from the limited scalability w.r.t. sample size and a slow convergence rate, especially for TPAUC. To address this issue, we present a simpler reformulation of the problem in an asymptotically unbiased and instance-wise manner. For both OPAUC and TPAUC, we come to a nonconvex strongly concave minimax regularized problem of instance-wise functions. On top of this, we employ an efficient solver enjoys a linear per-iteration computational complexity w.r.t. the sample size and a time-complexity of O(ε-1/3) to reach a ε stationary point. Furthermore, we find that the minimax reformulation also facilitates the theoretical analysis of generalization error as a byproduct. Compared with the existing results, we present new error bounds that are much easier to prove and could deal with hypotheses with real-valued outputs. Finally, extensive experiments on several benchmark datasets demonstrate the effectiveness of our method.

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Reler: Relearning Controversial Regions to Accurately Segment Nasopharyngeal Carcinoma

Reler: Relearning Controversial Regions to Accurately Segmen...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Guihua Tao Haojiang Li Dandan Lu Ziqin Ling Lizhi Liu Hongmin Cai School of Computer Science and Engineering South China University of Technology Guangzhou China State Key Laboratory of Oncology in South China Collaborative Innovation Center for Cancer Medicine Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy Sun Yat-sen University Cancer Center Sun Yat-sen University Guangzhou China Brain and Affective Cognitive Research Center Pazhou Lab Guangzhou China

ISBN: (数字)9781665468190

ISBN: (纸本)9781665468206

Accurate nasopharyngeal carcinoma (NPC) segmentation is significant in preventing local recurrence and improving patients’ survival rates. However, existing deep learning-based methods often yield unsatisfactory segmentation results, especially in fine-grained detail. Because NPC is a tiny and infiltrative tumor with a huge background, traditional deep neural networks tend to be dominated by salient information, thus missing the fine-grained details of NPC. To achieve accurate NPC segmentation, a relearning controversial regions method (Reler) is proposed. It consists of three modules, including the controversial features generator (CFG), controversial features finding module (CFF), and controversial regions arbitration module (CRA). First, CFG constructs global and local feature extractors to generate two types of different features. Then, CFF finds the controversial features and corresponding regions by comparing the global and local features’ estimates of the segmentation results of the same input regions. Next, the CRA focuses on controversial features, relearns new features, and produces new segmentation results through a proposed Transformer-based self-attention network. Finally, the uncontroversial segmentation results from CFF and CRA are combined as the final segmentation results. Extensive experiments are conducted on a large NPC dataset containing 6342 images from 596 patients. The experimental results show that the proposed method Reler is effective and superior to the nine state-of-the-art methods.

关键词： Learning systems Deep learning Image segmentation Neural networks Feature extraction Transformers Generators

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Repetitive nonoverlapping sequential pattern mining

arXiv

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arXiv 2023年

作者： Geng, Meng Wu, Youxi Li, Yan Liu, Jing Fournier-Viger, Philippe Zhu, Xingquan Wu, Xindong School of Artificial Intelligence Hebei University of Technology Tianjin300401 China School of Economics and Management Hebei University of Technology Tianjin300401 China State Key Laboratory of Reliability and Intelligence of Electrical Equipment Hebei University of Technology Tianjin300401 China Shenzhen University Shenzhen China Department of Computer & Electrical Engineering and Computer Science Florida Atlantic University FL33431 United States Research Center for Knowledge Engineering The Zhejiang Lab Hangzhou311121 China

Sequential pattern mining (SPM) is an important branch of knowledge discovery that aims to mine frequent sub-sequences (patterns) in a sequential database. Various SPM methods have been investigated, and most of them are classical SPM methods, since these methods only consider whether or not a given pattern occurs within a sequence. Classical SPM can only find the common features of sequences, but it ignores the number of occurrences of the pattern in each sequence, i.e., the degree of interest of specific users. To solve this problem, this paper addresses the issue of repetitive nonoverlapping sequential pattern (RNP) mining and proposes the RNP-Miner algorithm. To reduce the number of candidate patterns, RNP-Miner adopts an itemset pattern join strategy. To improve the efficiency of support calculation, RNP-Miner utilizes the candidate support calculation algorithm based on the position dictionary. To validate the performance of RNP-Miner, 10 competitive algorithms and 20 sequence databases were selected. The experimental results verify that RNP-Miner outperforms the other algorithms, and using RNPs can achieve a better clustering performance than raw data and classical frequent patterns. All the algorithms were developed using the PyCharm environment and can be downloaded from https://***/wuc567/Pattern-Mining/tree/master/RNPMiner. Copyright © 2023, The Authors. All rights reserved.

关键词： Clustering algorithms

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