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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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DPA-2:a large atomic model as a multitask learner

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npj computational Materials 2024年第1期10卷 185-199页

作者： Duo Zhang Xinzijian Liu Xiangyu Zhang Chengqian Zhang Chun Cai Hangrui Bi Yiming Du Xuejian Qin Anyang Peng Jiameng Huang Bowen Li Yifan Shan Jinzhe Zeng Yuzhi Zhang Siyuan Liu Yifan Li Junhan Chang Xinyan Wang Shuo Zhou Jianchuan Liu Xiaoshan Luo Zhenyu Wang Wanrun Jiang Jing Wu Yudi Yang Jiyuan Yang Manyi Yang Fu-Qiang Gong Linshuang Zhang Mengchao Shi Fu-Zhi Dai Darrin M.York Shi Liu Tong Zhu Zhicheng Zhong Jian Lv Jun Cheng Weile Jia Mohan Chen Guolin Ke Weinan E Linfeng Zhang Han Wang AI for Science Institute BeijingP.R.China DP Technology BeijingP.R.China Academy for Advanced Interdisciplinary Studies Peking UniversityBeijingP.R.China State Key Lab of Processors Institute of Computing TechnologyChinese Academy of SciencesBeijingP.R.China University of Chinese Academy of Sciences BeijingP.R.China HEDPS CAPTCollege of EngineeringPeking UniversityBeijingP.R.China Ningbo Institute of Materials Technology and Engineering Chinese Academy of SciencesNingboP.R.China CAS Key Laboratory of Magnetic Materials and Devices and Zhejiang Province Key Laboratory of Magnetic Materials and Application Technology Chinese Academy of SciencesNingboP.R.China School of Electronics Engineering and Computer Science Peking UniversityBeijingP.R.China Shanghai Engineering Research Center of Molecular Therapeutics&New Drug Development School of Chemistry and Molecular EngineeringEast China Normal UniversityShanghaiP.R.China Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine and Department of Chemistry and Chemical BiologyRutgers UniversityPiscatawayNJUSA Department of Chemistry Princeton UniversityPrincetonNJUSA College of Chemistry and Molecular Engineering Peking UniversityBeijingP.R.China Yuanpei College Peking UniversityBeijingP.R.China School of Electrical Engineering and Electronic Information Xihua UniversityChengduP.R.China State Key Laboratory of Superhard Materials College of PhysicsJilin UniversityChangchunP.R.China Key Laboratory of Material Simulation Methods&Software of Ministry of Education College of PhysicsJilin UniversityChangchunP.R.China International Center of Future Science Jilin UniversityChangchunP.R.China Key Laboratory for Quantum Materialsof Zhejiang Province Department of PhysicsSchool of ScienceWestlake UniversityHangzhouP.R.China Atomistic Simulations Italian Institute of TechnologyGenovaItaly State Key Laboratory of Physical Chemistry of Solid Surface iChEMCollege of Chemistry and Chemical EngineeringXiame

The rapid advancements in artificial intelligence(AI)are catalyzing transformative changes in atomic modeling,simulation,and ***-driven potential energy models havedemonstrated the capability to conduct large-scale,long-duration simulations with the accuracy of ab initio electronic structure ***,the model generation process remains a bottleneck for large-scale *** propose a shift towards a model-centric ecosystem,wherein a large atomic model(LAM),pretrained across multiple disciplines,can be efficiently fine-tuned and distilled for various downstream tasks,thereby establishing a new framework for molecular *** this study,we introduce the DPA-2 architecture as a prototype for ***-trained on a diverse array of chemical and materials systemsusing a multi-task approach,DPA-2demonstrates superior generalization capabilities across multiple downstream tasks compared to the traditional single-task pre-training and fine-tuning *** approach sets the stage for the development and broad application of LAMs in molecular and materials simulation research.

关键词： DPA establishing thereby

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DPA-2: a large atomic model as a multi-task learner

arXiv

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arXiv 2023年

作者： Zhang, Duo Liu, Xinzijian Zhang, Xiangyu Zhang, Chengqian Cai, Chun Bi, Hangrui Du, Yiming Qin, Xuejian Peng, Anyang Huang, Jiameng Li, Bowen Shan, Yifan Zeng, Jinzhe Zhang, Yuzhi Liu, Siyuan Li, Yifan Chang, Junhan Wang, Xinyan Zhou, Shuo Liu, Jianchuan Luo, Xiaoshan Wang, Zhenyu Jiang, Wanrun Wu, Jing Yang, Yudi Yang, Jiyuan Yang, Manyi Gong, Fu-Qiang Zhang, Linshuang Shi, Mengchao Dai, Fu-Zhi York, Darrin M. Liu, Shi Zhu, Tong Zhong, Zhicheng Lv, Jian Cheng, Jun Jia, Weile Chen, Mohan Ke, Guolin Weinan, E. Zhang, Linfeng Wang, Han AI for Science Institute Beijing100080 China DP Technology Beijing100080 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China State Key Lab of Processors Institute of Computing Technology Chinese Academy of Sciences Beijing100871 China University of Chinese Academy of Sciences Beijing100871 China HEDPS CAPT College of Engineering Peking University Beijing100871 China Ningbo Institute of Materials Technology and Engineering Chinese Academy of Sciences Ningbo315201 China CAS Key Laboratory of Magnetic Materials and Devices Zhejiang Province Key Laboratory of Magnetic Materials and Application Technology Chinese Academy of Sciences Ningbo315201 China School of Electronics Engineering and Computer Science Peking University Beijing100871 China Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development School of Chemistry and Molecular Engineering East China Normal University Shanghai200062 China Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854 United States Department of Chemistry Princeton University PrincetonNJ08540 United States College of Chemistry and Molecular Engineering Peking University Beijing100871 China Yuanpei College Peking University Beijing100871 China School of Electrical Engineering and Electronic Information Xihua University Chengdu610039 China State Key Laboratory of Superhard Materials College of Physics Jilin University Changchun130012 China Key Laboratory of Material Simulation Methods & Software of Ministry of Education College of Physics Jilin University Changchun130012 China International Center of Future Science Jilin University Changchun130012 China Key Laboratory for Quantum Materials of Zhejiang Province Department of Physics School of Science Westlake University Zhejiang Hangzhou310030 China Atomistic Simulations Italia

The rapid advancements in artificial intelligence (AI) are catalyzing transformative changes in atomic modeling, simulation, and design. AI-driven potential energy models have demonstrated the capability to conduct large-scale, long-duration simulations with the accuracy of ab initio electronic structure methods. However, the model generation process remains a bottleneck for large-scale applications. We propose a shift towards a model-centric ecosystem, wherein a large atomic model (LAM), pre-trained across multiple disciplines, can be efficiently fine-tuned and distilled for various downstream tasks, thereby establishing a new framework for molecular modeling. In this study, we introduce the DPA-2 architecture as a prototype for LAMs. Pre-trained on a diverse array of chemical and materials systems using a multi-task approach, DPA-2 demonstrates superior generalization capabilities across multiple downstream tasks compared to the traditional single-task pre-training and fine-tuning methodologies. Our approach sets the stage for the development and broad application of LAMs in molecular and materials simulation research. Copyright © 2023, The Authors. All rights reserved.

关键词： Multi-task learning

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