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arXiv 2025年

作者： Sun, Yingying Jun, A. Liu, Zhiwei Sun, Rui Qian, Liujia Payne, Samuel H. Bittremieux, Wout Ralser, Markus Li, Chen Chen, Yi Dong, Zhen Perez-Riverol, Yasset Khan, Asif Sander, Chris Aebersold, Ruedi Vizcaíno, Juan Antonio Krieger, Jonathan R. Yao, Jianhua Wen, Han Zhang, Linfeng Zhu, Yunping Xuan, Yue Sun, Benjamin Boyang Qiao, Liang Hermjakob, Henning Tang, Haixu Gao, Huanhuan Deng, Yamin Zhong, Qing Chang, Cheng Bandeira, Nuno Li, Ming Weinan, E. Sun, Siqi Yang, Yuedong Omenn, Gilbert S. Zhang, Yue Xu, Ping Fu, Yan Liu, Xiaowen Overall, Christopher M. Wang, Yu Deutsch, Eric W. Chen, Luonan Cox, Jürgen Demichev, Vadim He, Fuchu Huang, Jiaxing Jin, Huilin Liu, Chao Li, Nan Luan, Zhongzhi Song, Jiangning Yu, Kaicheng Wan, Wanggen Wang, Tai Zhang, Kang Zhang, Le Bell, Peter A. Mann, Matthias Zhang, Bing Guo, Tiannan Affiliated Hangzhou First People’s Hospital State Key Laboratory of Medical Proteomics School of Medicine Westlake University Zhejiang Province Hangzhou China Westlake Center for Intelligent Proteomics Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Province Hangzhou China Biology Department Brigham Young University ProvoUT84602 United States Department of Computer Science University of Antwerp Antwerp2020 Belgium Department of Biochemistry CharitéUniversitätsmedizin Berlin Berlin Germany Biomedicine Discovery Institute Department of Biochemistry and Molecular Biology Monash University MelbourneVICVIC 3800 Australia Wellcome Genome Campus Hinxton CambridgeCB10 1SD United Kingdom Harvard Medical School Ludwig Center at Harvard United States Harvard Medical School Broad Institute Ludwig Center at Harvard Dana-Farber Cancer Institute United States Department of Biology Institute of Molecular Systems Biology ETH Zürich Zürich Switzerland Bruker Ltd. MiltonONL9T 6P4 Canada AI for Life Sciences Lab Tencent Shenzhen518057 China State Key Laboratory of Medical Proteomics AI for Science Institute Beijing100080 China Beijing Institute of Lifeomics Beijing102206 China Thermo Fisher Scientific GmbH Hanna-Kunath Str. 11 Bremen28199 Germany Informatics and Predictive Sciences Research Bristol Myers Squibb United States Department of Chemistry Fudan University Songhu Road 2005 Shanghai200438 China Department of Computer Science Luddy School of Informatics Computing and Engineering Indiana University IN47408 United States ProCan® Children’s Medical Research Institute Faculty of Medicine and Health The University of Sydney WestmeadNSW Australia La Jolla CA United States Central China Institute of Artificial Intelligence University of Waterloo Canada AI for Science Institute Center for Machine Learning Research School of Mathematical Sciences Peking University China Research Institute of Intelligent Complex Systems Fudan U

Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new challenges and opportunities in biological discovery. Here, we highlight key areas where AI is driving innovation, from data analysis to new biological insights. These include developing an AI-friendly ecosystem for proteomics data generation, sharing, and analysis;improving peptide and protein identification and quantification;characterizing protein-protein interactions and protein complexes;advancing spatial and perturbation proteomics;integrating multi-omics data;and ultimately enabling AI-empowered virtual cells. © 2025, CC BY.

关键词： Biotic

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An Early Stage Researcher's Primer on systems Medicine Terminology

Network and Systems Medicine

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Network and systems Medicine 2021年第1期4卷 2-50页

作者： Zanin, Massimiliano Aitya, Nadim A.A. Basilio, José Baumbach, Jan Benis, Arriel Behera, Chandan K. Bucholc, Magda Castiglione, Filippo Chouvarda, Ioanna Comte, Blandine Dao, Tien-Tuan Ding, Xuemei Pujos-Guillot, Estelle Filipovic, Nenad Finn, David P. Glass, David H. Harel, Nissim Iesmantas, Tomas Ivanoska, Ilinka Joshi, Alok Boudjeltia, Karim Zouaoui Kaoui, Badr Kaur, Daman Maguire, Liam P. McClean, Paula L. McCombe, Niamh De Miranda, João Luís Moisescu, Mihnea Alexandru Pappalardo, Francesco Polster, Annikka Prasad, Girijesh Rozman, Damjana Sacala, Ioan Sanchez-Bornot, Jose M. Schmid, Johannes A. Sharp, Trevor Solé-Casals, Jordi Spiwok, Vojtěch Spyrou, George M. Stalidzans, Egils Stres, Blaa Sustersic, Tijana Symeonidis, Ioannis Tieri, Paolo Todd, Stephen Van Steen, Kristel Veneva, Milena Wang, Da-Hui Wang, Haiying Wang, Hui Watterson, Steven Wong-Lin, Kongfatt Yang, Su Zou, Xin Schmidt, Harald H.H.W. Centro de Tecnología Biomédica Universidad Politécnica de Madrid Madrid Spain Intelligent Systems Research Centre School of Computing Engineering and Intelligent Systems Ulster University Ulster United Kingdom Center for Physiology and Pharmacology Institute of Vascular Biology and Thrombosis Research Medical University of Vienna Vienna Austria TUM School of Life Sciences Weihenstephan Technical University of Munich Freising Germany Holon Israel CNR National Research Council IAC Institute for Applied Computing Rome Italy Lab of Computing Medical Informatics and Biomedical Imaging Technologies School of Medicine Aristotle University of Thessaloniki Thessaloniki Greece Université Clermont Auvergne INRAE UNH Plateforme d'Exploration du Métabolisme MetaboHUB Clermont Clermont-Ferrand France Université de Technologie de Compiègne Compiègne France Labex MS2T Control of Technological Systems-of-Systems CNRS and Université de Technologie de Compiègne Compiègne France Faculty of Engineering University of Kragujevac Kragujevac Serbia Kragujevac Serbia Steinbeis Advanced Risk Technologies Institute Doo Kragujevac Kragujevac Serbia Pharmacology and Therapeutics School of Medicine Galway Neuroscience Centre National University of Ireland Galway Ireland School of Computing Ulster University Ulster United Kingdom Holon Israel Department of Mathematics and Natural Sciences Kaunas University of Technology Kaunas Lithuania Faculty of Computer Science and Engineering Ss. Cyril and Methodius University Skopje Macedonia Medicine Faculty Université Libre de Bruxelles CHU de Charleroi Charleroi Belgium Northern Ireland Centre for Stratified Medicine Biomedical Sciences Research Institute Ulster University Ulster United Kingdom Escola Superior de Tecnologia e Gestão Instituto Politécnico de Portalegre Portalegre Portugal Instituto Superior Técnico Universidade de Lisboa Lisboa Portugal Faculty of Automatic Control and Computers University Politehnica of B

Background: systems Medicine is a novel approach to medicine, that is, an interdisciplinary field that considers the human body as a system, composed of multiple parts and of complex relationships at multiple levels, and further integrated into an environment. Exploring systems Medicine implies understanding and combining concepts coming from diametral different fields, including medicine, biology, statistics, modeling and simulation, and data science. Such heterogeneity leads to semantic issues, which may slow down implementation and fruitful interaction between these highly diverse fields. Methods: In this review, we collect and explain more than100 terms related to systems Medicine. These include both modeling and data science terms and basic systems medicine terms, along with some synthetic definitions, examples of applications, and lists of relevant references. Results: This glossary aims at being a first aid kit for the systems Medicine researcher facing an unfamiliar term, where he/she can get a first understanding of them, and, more importantly, examples and references for digging into the topic. © Massimiliano Zanin et al., 2021;Published by Mary Ann Liebert, Inc. 2021.

关键词： Semantics

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EcoLens: Visual analysis of urban region dynamics using traffic data

arXiv

引用

arXiv 2019年

作者： Jin, Zhuochen Cao, Nan Shi, Yang Tong, Hanghang Wu, Yingcai Intelligent Big Data Visualization Lab Tongji University Shanghai China School of Computing Informatics and Decision Systems Engineering Arizona State University United States College of Computer Science and Technology Zhejiang University Hangzhou Zhejiang China

The rapid development of urbanization during the past decades has significantly improved people's lives but also introduced new challenges on effective functional urban planning and transportation management. The functional regions defined based on a static boundary rarely reflect an individual's daily experience of the space in which they live and visit for a variety of purposes. Fortunately, the increasing availability of spatiotemporal data provides unprecedented opportunities for understanding the structure of an urban area in terms of people's activity pattern and how they form the latent regions over time. These ecological regions, where people temporarily share a similar moving behavior during a short period of time, could provide insights into urban planning and smart-city services. However, existing solutions are limited in their capacity of capturing the evolutionary patterns of dynamic latent regions within urban context. In this work, we introduce an interactive visual analysis approach, EcoLens, that allows analysts to progressively explore and analyze the complex dynamic segmentation patterns of a city using traffic data. We propose an extended non-negative Matrix Factorization based algorithm smoothed over both spatial and temporal dimensions to capture the spatiotemporal dynamics of the city. The algorithm also ensures the orthogonality of its result to facilitate the interpretation of different patterns. A suite of visualizations is designed to illustrate the dynamics of city segmentation and the corresponding interactions are added to support the exploration of the segmentation patterns over time. We evaluate the effectiveness of our system via case studies using a real-world dataset and a qualitative interview with the domain expert. Copyright © 2019, The Authors. All rights reserved.

关键词： Non-negative matrix factorization

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Scene Classification via Learning a Multi-Branch Convolutional Network

Scene Classification via Learning a Multi-Branch Convolution...

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IEEE International Conference on systems, Man and Cybernetics

作者： Xiaoyong Bian Chunfang Chen Yang Chen Xiongjun Fei Jingshan Tang Intelligent Information Processing and Real-time Industrial Systems Hubei Province Key Laboratory School of Computer Science and Technology Wuhan University of Science and Technology and Institute of Big Data Science and Engineering Wuhan University of Science and Technology Wuhan China School of Information Science and Engineering and Engineering Research Center for Metallurgical Automation and Measurement Technology of Ministry of Education Wuhan University of Science and Technology Wuhan China School of Technology Michigan Technological University Michigan USA

Efficient and accurate classification of high-resolution scene remains a challenge of within-class diversity and between-class similarity due to rich image variations in viewpoint, object pose, spatial resolution and background. To address these issues, we propose a multi-branch convolutional neural network (MB-CNN), which focuses on tackling the problem of learning the appropriate representation of a high-resolution scene that is rich enough to discriminate between different semantic classes. First, pyramid scene parsing network (PSPNet) with minor modification is introduced to gather global object information. Then, an attention net is proposed to highlight transformation invariance and key regions for attention feature extraction. Finally, above two branches are fused with original input branch to learn consistently semantic class information and generate powerful predictions. Our approach achieves better performance favorably against state-of-the-arts on two publicly available scene datasets.

关键词： Conferences Cybernetics

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DPHL:A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

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Genomics, Proteomics & Bioinformatics 2020年第2期18卷 104-119页

作者： Tiansheng Zhu Yi Zhu Yue Xuan Huanhuan Gao Xue Cai Sander R.Piersma Thang V.Pham Tim Schelfhorst Richard R.G.D.Haas Irene V.Bijnsdorp Rui Sun Liang Yue Guan Ruan Qiushi Zhang Mo Hu Yue Zhou Winan J.Van Houdt Tessa Y.S.Le Large Jacqueline Cloos Anna Wojtuszkiewicz Danijela Koppers-Lalic Franziska Bottger Chantal Scheepbouwer Ruud H.Brakenhoff Geert J.L.H.van Leenders Jan N.M.Ijzermans John W.M.Martens Renske D.M.Steenbergen Nicole C.Grieken Sathiyamoorthy Selvarajan Sangeeta Mantoo Sze S.Lee Serene J.Y.Yeow Syed M.F.Alkaff Nan Xiang Yaoting Sun Xiao Yi Shaozheng Dai Wei Liu Tian Lu Zhicheng Wu Xiao Liang Man Wang Yingkuan Shao Xi Zheng Kailun Xu Qin Yang Yifan Meng Cong Lu Jiang Zhu Jin'e Zheng Bo Wang Sai Lou Yibei Dai Chao Xu Chenhuan Yu Huazhong Ying Tony K.Lim Jianmin Wu Xiaofei Gao Zhongzhi Luan Xiaodong Teng Peng Wu Shi'ang Huang Zhihua Tao Narayanan G.Iyer Shuigeng Zhou Wenguang Shao Henry Lam Ding Ma Jiafu Ji Oi L.Kon Shu Zheng Ruedi Aebersold Connie R.Jimenez Tiannan Guo Zhejiang Provincial Laboratory of Life Sciences and Biomedicine Westlake UniversityHangzhou 310024China Key Laboratory of Structural Biology of Zhejiang Province School of Life SciencesWestlake UniversityHangzhou 310024China Institute of Basic Medical Sciences Westlake Institute for Advanced StudyHangzhou 310024China School of Computer Science Shanghai Key Laboratory of Intelligent Information ProcessingFudan UniversityShanghai 200433China Thermo Fisher Scientific(BREMEN)GmbH Bremen 28195Germany OncoProteomics Laboratory Department of Medical OncologyVU University Medical CenterVU UniversityAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamUrologyCancer Center AmsterdamAmsterdam 1011The Netherlands Thermo Fisher Scientific Shanghai 201206China The Netherlands Cancer Institute Surgical OncologyAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamSurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamPediatric Oncology/HematologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamHematologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamMedical OncologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamNeurosurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamPathologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamOtolaryngology/Head and Neck SurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Erasmus MC University Medical Center PathologyRotterdam 1016LVThe Netherlands Erasmus MC University Medical Center SurgeryRotterdam 1016LVThe Netherlands Erasmus MC University Medical Center Medical OncologyRotterdam 1016LVThe Netherlands Department of Anatomical Pathology Singapore General HospitalSingapore 169608Singapore Division of Medical Scie

To address the increasing need for detecting and validating protein biomarkers in clinical specimens,mass spectrometry(MS)-based targeted proteomic techniques,including the selected reaction monitoring(SRM),parallel reaction monitoring(PRM),and massively parallel dataindependent acquisition(DIA),have been *** optimal performance,they require the fragment ion spectra of targeted peptides as prior *** this report,we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue *** build the spectral resource,we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on *** then applied the workflow to generate DPHL,a comprehensive DIA pan-human library,from 1096 data-dependent acquisition(DDA)MS raw files for 16 types of cancer *** extensive spectral resource was then applied to a proteomic study of 17 prostate cancer(PCa)***,PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was *** a second application,the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma(DLBCL)patients and 18 healthy control *** expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by *** data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker *** is freely accessible at https://***/page/***?id=IPX0001400000.

关键词： data-independent acquisition Parallel reaction monitoring Spectral library Prostate cancer Diffuse large B cell lymphoma

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Deep Learning in Digital Breast Tomosynthesis: Current Status, Challenges, and Future Trends

MedComm

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MedComm 2025年第6期6卷 e70247页

作者： Wang, Ruoyun Chen, Fanxuan Chen, Haoman Lin, Chenxing Shuai, Jincen Wu, Yutong Ma, Lixiang Hu, Xiaoqu Wu, Min Wang, Jin Zhao, Qi Shuai, Jianwei Pan, Jingye Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine Vision and Brain Health) Wenzhou Institute University of Chinese Academy of Sciences Wenzhou China Wenzhou Medical University Wenzhou China UCSC Baskin School of Engineering University of California Santa Cruz CA United States Key Laboratory of Intelligent Treatment and Life Support for Critical Diseases of Zhejiang Province Wenzhou China Department of Anatomy Histology & Embryology School of Basic Medical Sciences Fudan University Shanghai China Department of Medicine Harvard Medical School and Brigham and Women's Hospital Boston MA United States Joint Research Centre on Medicine The Affiliated Xiangshan Hospital of Wenzhou Medical University Ningbo China Stony Brook University Stony Brook NY United States School of Computer Science and Software Engineering University of Science and Technology Liaoning Anshan China Department of Big Data in Health Science The First Affiliated Hospital of Wenzhou Medical University Wenzhou China Zhejiang Engineering Research Center for Hospital Emergency and Process Digitization Wenzhou China

The high-resolution three-dimensional (3D) images generated with digital breast tomosynthesis (DBT) in the screening of breast cancer offer new possibilities for early disease diagnosis. Early detection is especially important as the incidence of breast cancer increases. However, DBT also presents challenges in terms of poorer results for dense breasts, increased false positive rates, slightly higher radiation doses, and increased reading times. Deep learning (DL) has been shown to effectively increase the processing efficiency and diagnostic accuracy of DBT images. This article reviews the application and outlook of DL in DBT-based breast cancer screening. First, the fundamentals and challenges of DBT technology are introduced. The applications of DL in DBT are then grouped into three categories: diagnostic classification of breast diseases, lesion segmentation and detection, and medical image generation. Additionally, the current public databases for mammography are summarized in detail. Finally, this paper analyzes the main challenges in the application of DL techniques in DBT, such as the lack of public datasets and model training issues, and proposes possible directions for future research, including large language models, multisource domain transfer, and data augmentation, to encourage innovative applications of DL in medical imaging. © 2025 The Author(s). MedComm published by Sichuan International Medical Exchange & Promotion Association (SCIMEA) and John Wiley & Sons Australia, Ltd.

关键词： deep learning digital breast tomosynthesis early breast cancer screening medical image analysis public database

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Understanding adversarial attacks on deep learning based medical image analysis systems

arXiv

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arXiv 2019年

作者： Ma, Xingjun Niu, Yuhao Gu, Lin Wang, Yisen Zhao, Yitian Bailey, James Lu, Feng State Key Laboratory of VR Technology and Systems School of CSE Beihang University Beijing China School of Computing and Information Systems The University of Melbourne ParkvilleVIC3010 Australia Beijing Advanced Innovation Center for Big Data-Based Precision Medicine Beihang University Beijing China National Institute of Informatics Tokyo101-8430 Japan Department of Computer Science and Engineering Shanghai Jiao Tong University Shanghai China Cixi Instuitue of Biomedical Engineering Ningbo Institute of Industrial Technology Chinese Academy of Sciences Ningbo China

Deep neural networks (DNNs) have become popular for medical image analysis tasks like cancer diagnosis and lesion detection. However, a recent study demonstrates that medical deep learning systems can be compromised by carefully-engineered adversarial examples/attacks with small imperceptible perturbations. This raises safety concerns about the deployment of these systems in clinical settings. In this paper, we provide a deeper understanding of adversarial examples in the context of medical images. We find that medical DNN models can be more vulnerable to adversarial attacks compared to models for natural images, according to two different viewpoints. Surprisingly, we also find that medical adversarial attacks can be easily detected, i.e., simple detectors can achieve over 98% detection AUC against state-of-the-art attacks, due to fundamental feature differences compared to normal examples. We believe these findings may be a useful basis to approach the design of more explainable and secure medical deep learning systems. Copyright © 2019, The Authors. All rights reserved.

关键词： Deep neural networks

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Foundation models and intelligent decision-making: Progress, challenges, and perspectives

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Innovation 2025年第6期6卷 100948页

作者： Huang, Jincai Xu, Yongjun Wang, Qi Wang, Qi [Cheems] Liang, Xingxing Wang, Fei Zhang, Zhao Wei, Wei Zhang, Boxuan Huang, Libo Chang, Jingru Ma, Liantao Ma, Ting Liang, Yuxuan Zhang, Jie Guo, Jian Jiang, Xuhui Fan, Xinxin An, Zhulin Li, Tingting Li, Xuefei Shao, Zezhi Qian, Tangwen Sun, Tao Diao, Boyu Yang, Chuanguang Yu, Chenqing Wu, Yiqing Li, Mengxian Zhang, Haifeng Zeng, Yongcheng Zhang, Zhicheng Zhu, Zhengqiu Lv, Yiqin Li, Aming Chen, Xu An, Bo Xiao, Wei Bai, Chenguang Mao, Yuxing Yin, Zhigang Gui, Sheng Su, Wentao Zhu, Yinghao Gao, Junyi He, Xinyu Li, Yizhou Jin, Guangyin Ao, Xiang Zhai, Xuehao Tan, Haoran Yun, Lijun Shi, Hongquan Li, Jun Fan, Changjun Huang, Kuihua Harrison, Ewen Leung, Victor C.M. Qiu, Sihang Dong, Yanjie Zheng, Xiaolong Wang, Gang Zheng, Yu Wang, Yuanzhuo Guo, Jiafeng Wang, Lizhe Cheng, Xueqi Wang, Yaonan Yang, Shanlin Fu, Mengyin Fei, Aiguo Institute of Computing Technology Chinese Academy of Sciences Beijing100190 China Department of Automation Tsinghua University Beijing100084 China Huazhong University of Science and Technology Wuhan430074 China School of Automation Beijing Institute of Technology Beijing100081 China School of Information Science and Engineering Dalian Polytechnic University Dalian116034 China National Engineering Research Center for Software Engineering Peking University Beijing100871 China Department of Oral Implantology Peking University School and Hospital of Stomatology Beijing100081 China Guangzhou511453 China College of Information and Electrical Engineering China Agricultural University Beijing100083 China IDEA Research International Digital Economy Academy Shenzhen518057 China Institute of Automation Chinese Academy of Sciences Beijing100190 China The State Key Laboratory of Multimodal Artificial Intelligence Systems Institute of Automation Chinese Academy of Sciences Beijing100190 China College of Science National University of Defense Technology Changsha410073 China Center for Systems and Control College of Engineering Peking University Beijing100871 China Gaoling School of Artificial Intelligence Renmin University of China Beijing100872 China College of Systems Engineering National University of Defense Technology Changsha410073 China Laboratory for Big Data and Decision National University of Defense Technology Changsha410073 China College of Computing and Data Science Nanyang Technological University Singapore639798 Singapore School of Electrical Engineering Chongqing University Chongqing400044 China Department of Mathematics The University of Hong Kong Hong Kong SAR999077 China School of Food Science and Technology Dalian Polytechnic University Dalian116034 China Centre for Medical Informatics University of Edinburgh EdinburghEH16 4UX United Kingdom Department of Stomatology Peking Union Medical College Hospital Chinese Academ

intelligent decision-making (IDM) is a cornerstone of artificial intelligence (AI) designed to automate or augment decision processes. Modern IDM paradigms integrate advanced frameworks to enable intelligent agents to make effective and adaptive choices and decompose complex tasks into manageable steps, such as AI agents and high-level reinforcement learning. Recent advances in multimodal foundation-based approaches unify diverse input modalities—such as vision, language, and sensory data—into a cohesive decision-making process. Foundation models (FMs) have become pivotal in science and industry, transforming decision-making and research capabilities. Their large-scale, multimodal data-processing abilities foster adaptability and interdisciplinary breakthroughs across fields such as healthcare, life sciences, and education. This survey examines IDM's evolution, advanced paradigms with FMs and their transformative impact on decision-making across diverse scientific and industrial domains, highlighting the challenges and opportunities in building efficient, adaptive, and ethical decision systems. © 2025 The Authors

关键词： Reinforcement learning

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MedShapeNet - A Large-Scale dataset of 3D Medical Shapes for Computer Vision

arXiv

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arXiv 2023年

作者： Li, Jianning Zhou, Zongwei Yang, Jiancheng Pepe, Antonio Gsaxner, Christina Luijten, Gijs Qu, Chongyu Zhang, Tiezheng Chen, Xiaoxi Li, Wenxuan Wodzinski, Marek Friedrich, Paul Xie, Kangxian Jin, Yuan Ambigapathy, Narmada Nasca, Enrico Solak, Naida Melito, Gian Marco Vu, Viet Duc Memon, Afaque R. Schlachta, Christopher De Ribaupierre, Sandrine Patel, Rajnikant Eagleson, Roy Chen, Xiaojun Mächler, Heinrich Kirschke, Jan Stefan de la Rosa, Ezequiel Christ, Patrick Ferdinand Li, Hongwei Bran Ellis, David G. Aizenberg, Michele R. Gatidis, Sergios Küstner, Thomas Shusharina, Nadya Heller, Nicholas Andrearczyk, Vincent Depeursinge, Adrien Hatt, Mathieu Sekuboyina, Anjany Löffler, Maximilian Liebl, Hans Dorent, Reuben Vercauteren, Tom Shapey, Jonathan Kujawa, Aaron Cornelissen, Stefan Langenhuizen, Patrick Ben-Hamadou, Achraf Rekik, Ahmed Pujades, Sergi Boyer, Edmond Bolelli, Federico Grana, Costantino Lumetti, Luca Salehi, Hamidreza Ma, Jun Zhang, Yao Gharleghi, Ramtin Beier, Susann Sowmya, Arcot Garza-Villarreal, Eduardo A. Balducci, Thania Angeles-Valdez, Diego Souza, Roberto Rittner, Leticia Frayne, Richard Ji, Yuanfeng Ferrari, Vincenzo Chatterjee, Soumick Dubost, Florian Schreiber, Stefanie Mattern, Hendrik Speck, Oliver Haehn, Daniel John, Christoph Nürnberger, Andreas Pedrosa, João Ferreira, Carlos Aresta, Guilherme Cunha, António Campilho, Aurélio Suter, Yannick Garcia, Jose Lalande, Alain Vandenbossche, Vicky Van Oevelen, Aline Duquesne, Kate Mekhzoum, Hamza Vandemeulebroucke, Jef Audenaert, Emmanuel Krebs, Claudia van Leeuwen, Timo Vereecke, Evie Heidemeyer, Hauke Röhrig, Rainer Hölzle, Frank Badeli, Vahid Krieger, Kathrin Gunzer, Matthias Chen, Jianxu van Meegdenburg, Timo Dada, Amin Balzer, Miriam Fragemann, Jana Jonske, Frederic Rempe, Moritz Malorodov, Stanislav Bahnsen, Fin H. Seibold, Constantin Jaus, Alexander Marinov, Zdravko Jaeger, Paul F. Stiefelhagen, Rainer Santos, Ana Sofia Lindo, Mariana Ferreira, André Alves, Victor Kamp, Michael Abourayya, Amr Nensa, Felix Hörst, Fabian Brehmer, Alexander Hein Girardetstraße 2 Essen45131 Germany Graz University of Technology Inffeldgasse 16c Graz8010 Austria Graz Austria The Department of Computer Science Johns Hopkins University Malone Hall 3400 N Charles St BaltimoreMD21218 United States Rte Cantonale Lausanne1015 Switzerland The Department of Measurement and Electronics AGH University of Science and Technology Krakow Poland Sierre Switzerland Department of Biomedical Engineering University of Basel Hegenheimermattweg Allschwil167C CH-4123 Switzerland The Boston College 140 Commonwealth Ave Chestnut HillMA02467 United States University Hospital B7-200 339 Windermere Road LondonN6A 5A5 Canada The Department of Radiology Renji Hospital School of Medicine Shanghai Jiao Tong University Shanghai200240 China The Research Center for Connected Healthcare Big Data ZhejiangLab Zhejiang Hangzhou311121 China The Faculty of Statistics Technical University Dortmund August-Schmidt-Straße 1 Dortmund44227 Germany The Institute of Mechanics Graz University of Technology Kopernikusgasse 24/IV Graz8010 Austria The Institute of Biomedical Manufacturing and Life Quality Engineering State Key Laboratory of Mechanical System and Vibration School of Mechanical Engineering Shanghai Jiao Tong University 800 Dongchuan Road Shanghai200240 China The Department of Cardiac Surgery Medical University Graz Auenbruggerplatz 29 Graz8036 Austria The Department of Diagnostic and Interventional Radiology University Hospital Giessen Justus-Liebig-University Giessen Klinikstraße 33 Giessen35392 Germany The Department of Mechanical Engineering Mehran University of Engineering and Technology Jamshoro Sindh76062 Pakistan The Institute of Medical Robotics Shanghai Jiao Tong University Shanghai China The Geschäftsführender Oberarzt Abteilung für Interventionelle und Diagnostische Neuroradiologie Universitätsklinikum der Technischen Universität München Ismaningerstr. 22 München81675 Germany icometrix Kolonel Be

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 datasets with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://***/ and https://***/Jianningli/*** Codes 68T01 © 2023, CC BY.

关键词： Large dataset

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Kiwifruit detection in field images using Faster R-CNN with VGG16

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IFAC-PapersOnLine 2019年第30期52卷 76-81页

作者： Zhenzhen Song Longsheng Fu Jingzhu Wu Zhihao Liu Rui Li Yongjie Cui College of Mechanical and Electronic Engineering Northwest A&F University Yangling 712100 China College of Mechanical and Electronic Engineering Northwest A&F University Yangling 712100 China Key Laboratory of Agricultural Internet of Things Ministry of Agriculture Yangling 712100 China Shaanxi Key Laboratory of Agricultural Information Perception and Intelligent Service Yangling 712100 China Center for Precision & Automated Agricultural Systems Washington State University Prosser WA 99350 USA Beijing Key Laboratory of Big Data Technology for Food Safety Beijing Technology and Business University Beijing 100048 China

Kiwifruit is widely planted in Shaanxi, China, accounting for approximately 70% of the local production, and 33% of the global. Harvesting kiwifruits in China relies mainly on manual picking, and it is labor-intensive. To develop a machine vision system for harvesting robot which can work all day, kiwifruit images were captured in an orchard at different timing, morning, afternoon, and night, with or without flash, respectively. Kiwifruit images of 2400 were divided into training (1440) and testing (960) groups. A Faster R-CNN model implemented by VGG16 were constructed and trained. The average precision of VGG16 model was 87.61%, and the kiwifruit images collected under different timing and lighting conditions were detected well. In the end, the performance of the proposed method was compared with ZFNet in the same image dataset. It suggested that the proposed method achieved higher detection average precision than ZFNet (72.50%). This system is able to detect different categories of fruit in the field effectively and provides strong support for the harvesting robot, which can work all day round during the busy season.

关键词： image detection kiwifruit VGG16 Faster R-CNN ZFNet data augmentation

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