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iMetaOmics 2024年第1期2卷

作者： Yiming Zhang Bian Bian Manabu Okumura Department of Information and Communications Engineering School of Engineering Institute of Science Tokyo Yokohama Japan Department of Computational Biology and Medical Sciences Graduate School of Frontier Sciences The University of Tokyo Kashiwa Japan Artificial Intelligence Research Center National Institute of Advanced Industrial Science and Technology (AIST) Tokyo Japan Department of Data Science School of Frontier Engineering Kitasato University Sagamihara Japan

The emergence of self-supervised deep language models has revolutionized natural language processing tasks and has recently extended its applications to biological sequence analysis. Traditional language models, primarily based on Transformer architectures, demonstrate substantial effectiveness in various applications. However, these models are inherently constrained by the attention mechanism's quadratic computational complexity, , which limits their efficiency and leads to high computational costs. To address these limitations, we introduce ProtHyena, a novel approach that leverages the Hyena operator in protein language modeling. This innovative methodology alternates between subquadratic long convolutions and element-wise gating operations, which circumvents the constraints imposed by attention mechanisms and reduces computational complexity to subquadratic levels. This enables faster and more memory-efficient modeling of protein sequences. ProtHyena can achieve state-of-the-art results and comparable performance in 8 downstream tasks, including protein engineering (protein fluorescence and stability prediction), protein property prediction (neuropeptide cleavage, signal peptide, solubility, disorder, gene function prediction), protein structure prediction, with only 1.6 M parameters. The architecture of ProtHyena represents a highly efficient solution for protein language modeling, offering a promising avenue for fast and efficient analysis of protein sequences. Novel Architecture: ProtHyena applies Hyena architecture for protein language modeling, outperforming traditional attention-based models with lower computational costs and fewer parameters. State-of-the-Art Performance: Achieves leading results across classification and regression tasks, excelling with diverse protein sequences. Efficiency: Optimized for faster training and lower memory usage, enabling scalable modeling of long protein sequences.

关键词： Hyena architecture protein language model protein pre-training

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AdAUC: End-to-end Adversarial AUC Optimization Against Long-tail Problems

arXiv

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arXiv 2022年

作者： Hou, Wenzheng Xu, Qianqian Yang, Zhiyong Bao, Shilong He, Yuan Huang, Qingming Key Laboratory of Intelligent Information Processing Institute of Computing Technology CAS Beijing China School of Computer Science and Technology University of Chinese Academy of Sciences Beijing China State Key Laboratory of Information Security Institute of Information Engineering CAS Beijing China School of Cyber Security University of Chinese Academy of Sciences Beijing China Alibaba Group Beijing China Key Laboratory of Big Data Mining and Knowledge Management Chinese Academy of Sciences Beijing China Artificial Intelligence Research Center Peng Cheng Laboratory Shenzhen China

It is well-known that deep learning models are vulnerable to adversarial examples. Existing studies of adversarial training have made great progress against this challenge. As a typical trait, they often assume that the class distribution is overall balanced. However, long-tail datasets are ubiquitous in a wide spectrum of applications, where the amount of head class instances is larger than the tail classes. Under such a scenario, AUC is a much more reasonable metric than accuracy since it is insensitive toward class distribution. Motivated by this, we present an early trial to explore adversarial training methods to optimize AUC. The main challenge lies in that the positive and negative examples are tightly coupled in the objective function. As a direct result, one cannot generate adversarial examples without a full scan of the dataset. To address this issue, based on a concavity regularization scheme, we reformulate the AUC optimization problem as a saddle point problem, where the objective becomes an instance-wise function. This leads to an end-to-end training protocol. Furthermore, we provide a convergence guarantee of the proposed algorithm. Our analysis differs from the existing studies since the algorithm is asked to generate adversarial examples by calculating the gradient of a min-max problem. Finally, the extensive experimental results show the performance and robustness of our algorithm in three long-tail datasets. © 2022, CC BY.

关键词： Deep learning

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Optimizing biomedical ontology alignment in lexical vector space

Optimizing biomedical ontology alignment in lexical vector s...

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作者： Xue, Xingsi Wu, Xiaojing Fujian Key Lab for Automotive Electronics and Electric Drive Fujian University of Technology Fuzhou Fujian Minhou China College of Information Science and Engineering Fujian University of Technology Fuzhou Fujian Minhou China Intelligent Information Processing Research Center Fujian University of Technology Fuzhou Fujian Minhou China Institute of Artificial Intelligence Fujian University of Technology Fuzhou Fujian Minhou China Fujian Provincial Key Laboratory of Big Data Mining and Applications Fujian University of Technology Fuzhou Fujian Minhou China

Biomedical ontology matching dedicates to find two heterogeneous ontologies' alignment and address their heterogeneity problem. Typically, a biomedical ontology has various biomedical concepts that are described with various labels and datatype property names, which forms a lexical space where each label or datatype property represents one dimension. Therefore, it is an effective way to present two biomedical concepts in a vector space, and use the cosine distance to measure their similarity. In this work, we present two biomedical concepts in a lexical vector space which is constructed with their inner and context concepts' lexical information, and then utilize two vector's cosine distance to measure similarity value. Then, we propose a compact Evolutionary Algorithm (cEA) to find the concept correspondences. The experiment uses Ontology Alignment Evaluation Initiative (OAEI)'s testing cases, and the expeirmental results with Vector space Based Ontology Matcher (VBOM), Genetic Algorithm based Ontology Matcher (GAOM) and OAEI's participants show the effectiveness of our proposal. © 2020 - IOS Press and the authors. All rights reserved.

关键词： Vector spaces

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Heavy metals prediction in coastal marine sediments using hybridized machine learning models with metaheuristic optimization algorithm

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Chemosphere 2024年 352卷 141329页

作者： Yaseen, Zaher Mundher Melini Wan Mohtar, Wan Hanna Homod, Raad Z. Alawi, Omer A. Abba, Sani I. Oudah, Atheer Y. Togun, Hussein Goliatt, Leonardo Ul Hassan Kazmi, Syed Shabi Tao, Hai Civil and Environmental Engineering Department King Fahd University of Petroleum and Minerals Dhahran 31261 Saudi Arabia Interdisciplinary Research Center for Membranes and Water Security King Fahd University of Petroleum & Minerals (KFUPM) Dhahran Saudi Arabia Department of Civil Engineering Faculty of Engineering and Built Environment Universiti Kebangsaan Malaysia UKM Selangor Bangi 43600 Malaysia Environmental Management Centre Institute of Climate Change Universiti Kebangsaan Malaysia Selangor UKM Bangi 43600 Malaysia Department of Oil and Gas Engineering Basrah University for Oil and Gas Basra Iraq Department of Thermofluids School of Mechanical Engineering Universiti Teknologi Malaysia UTM Skudai Johor Bahru 81310 Malaysia Department of Computer Sciences College of Education for Pure Science University of Thi-Qar Nasiriyah 64001 Iraq Information and Communication Technology Research Group Scientific Research Center Al-Ayen University Nasiriyah 64001 Iraq Department of Mechanical Engineering College of Engineering University of Baghdad Baghdad Iraq Computational and Applied Mechanics Department Federal University of Juiz de Fora 36036-900 Brazil Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention and Guangdong Provincial Key Laboratory of Marine Biotechnology Shantou University Shantou 515063 China School of Computer and Information Qiannan Normal University for Nationalities Guizhou Duyun 558000 China Institute of Big Data Application and Artificial Intelligence Qiannan Normal University for Nationalities Guizhou Duyun 558000 China Faculty of Data Science and Information Technology INTI International University 71800 Malaysia

This study proposes different standalone models viz: Elman neural network (ENN), Boosted Tree algorithm (BTA), and f relevance vector machine (RVM) for modeling arsenic (As (mg/kg)) and zinc (Zn (mg/kg)) in marine sediments owing to anthropogenic activities. A heuristic algorithm based on the potential of RVM and a flower pollination algorithm (RVM-FPA) was developed to improve the prediction performance. Several evaluation indicators and graphical methods coupled with visualized cumulative probability function (CDF) were used to evaluate the accuracy of the models. Akaike (AIC) and Schwarz (SCI) information criteria based on Dickey-Fuller (ADF) and Philip Perron (PP) tests were introduced to check the reliability and stationarity of the data. The prediction performance in the verification phase indicated that RVM-M2 (PBAIS = -o.0465, MAE = 0.0335) and ENN-M2 (PBAIS = 0.0043, MAE = 0.0322) emerged as the best model for As (mg/kg) and Zn (mg/kg), respectively. In contrast with the standalone approaches, the simulated hybrid RVM-FPA proved merit and the most reliable, with a 5 % and 18 % predictive increase for As (mg/kg) and Zn (mg/kg), respectively. The study's findings validated the potential for estimating complex HMs through intelligent data-driven models and heuristic optimization. The study also generated valuable insights that can inform the decision-makers and stockholders for environmental management strategies. © 2024 Elsevier Ltd

关键词： Artificial intelligence Heavy metals Sensitivity analysis Soil contamination

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Redefining pandemic preparedness:Multidisciplinary insights from the CERP modelling workshop in infectious diseases,workshop report

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Infectious Disease Modelling 2024年第2期9卷 501-518页

作者： Marta C.Nunes Edward Thommes Holger Fröhlich Antoine Flahault Julien Arino Marc Baguelin Matthew Biggerstaff Gaston Bizel-Bizellot Rebecca Borchering Giacomo Cacciapaglia Simon Cauchemez Alex Barbier-Chebbah Carsten Claussen Christine Choirat Monica Cojocaru Catherine Commaille-Chapus Chitin Hon Jude Kong Nicolas Lambert Katharina B.Lauer Thorsten Lehr Cédric Mahe Vincent Marechal Adel Mebarki Seyed Moghadas Rene Niehus Lulla Opatowski Francesco Parino Gery Pruvost Andreas Schuppert Rodolphe Thiébaut Andrea Thomas-Bachli Cecile Viboud Jianhong Wu Pascal Crépey Laurent Coudeville Center of Excellence in Respiratory Pathogens(CERP) Hospices Civils de Lyon(HCL)and Centre International de Recherche en Infectiologie(CIRI)Équipe SantéPubliqueÉpidémiologie etÉcologieÉvolutive des Maladies Infectieuses(PHE3ID)Inserm U1111CNRS UMR5308ENS de LyonUniversitéClaude Bernard Lyon 1LyonFrance South African Medical Research Council Vaccines&Infectious Diseases Analytics Research UnitFaculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa New Products and Innovation(NPI) Sanofi Vaccines(Global)TorontoOntarioCanada Department of Mathematics and Statistics University of GuelphGuelphOntarioCanada Fraunhofer Institute for Algorithms and Scientific Computing(SCAI) Department of BioinformaticsSchloss BirlinghovenSankt AugustinGermany University of Bonn Bonn-Aachen International Center for IT(b-it)BonnGermany Institute of Global Health Faculty of MedicineUniversity of GenevaGenevaSwitzerland and Swiss School of Public HealthZürichSwitzerland Department of Mathematics University of ManitobaWinnipegManitobaCanada MRC Centre for Global Infectious Disease Analysis School of Public HealthImperial College LondonLondonUK Centre for Mathematical Modelling of Infectious Diseases Department of Infectious Disease EpidemiologyLondon School of Hygiene&Tropical MedicineLondonUK National Center for Immunization and Respiratory Diseases(NCIRD) US Centers for Disease Control and Prevention(CDC)AtlantaGAUSA Departement of Computational Biology Departement of Global HealthInstitut PasteurParisFrance Institut de Physique des Deux Infinis de Lyon(IP2I) UMR5822IN2P3/CNRSUniversitéClaude Bernard Lyon 1VilleurbanneFrance Mathematical Modelling of Infectious Diseases Unit Institut PasteurUniversitéParis CitéUMR2000 CNRSParisFrance Decision and Bayesian Computation Institut PasteurUniversitéParis CitéCNRS UMR 3571France Fraunhofer-Institute for Translational Medicine and Pharmacology HamburgGermany Institute of Global Health Faculty of MedicineUniversity of

In July 2023,the center of Excellence in Respiratory Pathogens organized a two-day workshop on infectious diseases modelling and the lessons learnt from the Covid-19 *** report summarizes the rich discussions that occurred during the *** workshop participants discussed multisource data integration and highlighted the benefits of combining traditional surveillance with more novel data sources like mobility data,social media,and wastewater *** advancements were noted in the development of predictive models,with examples from various countries showcasing the use of machine learning and artificial intelligence in detecting and monitoring disease *** role of open collaboration between various stakeholders in modelling was stressed,advocating for the continuation of such partnerships beyond the pandemic.A major gap identified was the absence of a common international framework for data sharing,which is crucial for global pandemic ***,the workshop underscored the need for robust,adaptable modelling frameworks and the integration of different data sources and collaboration across sectors,as key elements in enhancing future pandemic response and preparedness.

关键词： Modelling Covid-19 Infectious diseases Pandemic preparedness Workshop

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NTIRE 2023 Challenge on Light Field Image Super-Resolution: dataset, Methods and Results

arXiv

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arXiv 2023年

作者： Wang, Yingqian Wang, Longguang Liang, Zhengyu Yang, Jungang Timofte, Radu Guo, Yulan Jin, Kai Wei, Zeqiang Yang, Angulia Guo, Sha Gao, Mingzhi Zhou, Xiuzhuang Van Duong, Vinh Huu, Thuc Nguyen Yim, Jonghoon Jeon, Byeungwoo Liu, Yutong Cheng, Zhen Xiao, Zeyu Xu, Ruikang Xiong, Zhiwei Liu, Gaosheng Jin, Manchang Yue, Huanjing Yang, Jingyu Gao, Chen Zhang, Shuo Chang, Song Lin, Youfang Chao, Wentao Wang, Xuechun Wang, Guanghui Duan, Fuqing Xia, Wang Wang, Yan Xia, Peiqi Wang, Shunzhou Lu, Yao Cong, Ruixuan Sheng, Hao Yang, Da Chen, Rongshan Wang, Sizhe Cui, Zhenglong Chen, Yilei Lu, Yongjie Cai, Dongjun An, Ping Salem, Ahmed Ibrahem, Hatem Yagoub, Bilel Kang, Hyun-Soo Zeng, Zekai Wu, Heng National University of Defense Technology China Aviation University of Air Force China University of Würzburg Germany ETH Zürich Switzerland The Shenzhen Campus of Sun Yat-Sen University Sun Yat-Sen University China Bigo Technology Pte. Ltd Singapore Smart Medical Innovation Lab Beijing University of Posts and Telecommunications China Global Explorer Ltd. Suzhou China National Engineering Research Center of Visual Technology School of Computer Science Peking University China School of Artificial Intelligence Beijing University of Posts and Telecommunications China Department of Electrical and Computer Engineering Sungkyunkwan University Korea Republic of University of Science and Technology of China China School of Electrical and Information Engineering Tianjin University China Beijing Key Lab of Traffic Data Analysis and Mining School of Computer and Information Technology Beijing Jiaotong University China Beijing Normal University China Toronto Metropolitan University Canada Beijing Institute of Technology China Shenzhen MSU-BIT University China State Key Laboratory of Virtual Reality Technology and Systems School of Computer Science and Engineering Beihang University China Beihang Hangzhou Innovation Institute Yuhang China Faculty of Applied Sciences Macao Polytechnic University China School of Communication and Information Engineering Shanghai University China School of Information and Communication Engineering Chungbuk National University Korea Republic of Guangdong University of Technology China

In this report, we summarize the first NTIRE challenge on light field (LF) image super-resolution (SR), which aims at super-resolving LF images under the standard bicubic degradation with a magnification factor of 4. This challenge develops a new LF dataset called NTIRE-2023 for validation and test, and provides a toolbox called BasicLFSR to facilitate model development. Compared with single image SR, the major challenge of LF image SR lies in how to exploit complementary angular information from plenty of views with varying disparities. In total, 148 participants have registered the challenge, and 11 teams have successfully submitted results with PSNR scores higher than the baseline method LF-InterNet [1]. These newly developed methods have set new state-of-the-art in LF image SR, e.g., the winning method achieves around 1 dB PSNR improvement over the existing state-of-the-art method DistgSSR [2]. We report the solutions proposed by the participants, and summarize their common trends and useful tricks. We hope this challenge can stimulate future research and inspire new ideas in LF image SR. © 2023, CC BY-SA.

关键词： Image enhancement

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Assessing Trustworthy AI in Times of COVID-19: Deep Learning for Predicting a Multiregional Score Conveying the Degree of Lung Compromise in COVID-19 Patients

IEEE Transactions on Technology and Society

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IEEE Transactions on technology and Society 2022年第4期3卷 272-289页

作者： Allahabadi, Himanshi Amann, Julia Balot, Isabelle Beretta, Andrea Binkley, Charles Bozenhard, Jonas Bruneault, Frederick Brusseau, James Candemir, Sema Cappellini, Luca Alessandro Chakraborty, Subrata Cherciu, Nicoleta Cociancig, Christina Coffee, Megan Ek, Irene Espinosa-Leal, Leonardo Farina, Davide Fieux-Castagnet, Genevieve Frauenfelder, Thomas Gallucci, Alessio Giuliani, Guya Golda, Adam Van Halem, Irmhild Hildt, Elisabeth Holm, Sune Kararigas, Georgios Krier, Sebastien A. Kuhne, Ulrich Lizzi, Francesca Madai, Vince I. Markus, Aniek F. Masis, Serg Mathez, Emilie Wiinblad Mureddu, Francesco Neri, Emanuele Osika, Walter Ozols, Matiss Panigutti, Cecilia Parent, Brendan Pratesi, Francesca Moreno-Sanchez, Pedro A. Sartor, Giovanni Savardi, Mattia Signoroni, Alberto Sormunen, Hanna-Maria Spezzatti, Andy Srivastava, Adarsh Stephansen, Annette F. Theng, Lau Bee Tithi, Jesmin Jahan Tuominen, Jarno Umbrello, Steven Vaccher, Filippo Vetter, Dennis Westerlund, Magnus Wurth, Renee Zicari, Roberto V. Ey Netherlands Enterprise Intelligence Department Amsterdam1083 HP Netherlands Eth Zurich Health Ethics and Policy Lab Department of Health Sciences and Technology Zürich8092 Switzerland Center for Diplomatic and Strategic Studies Postgraduate Studies in Diplomacy and International Relations Paris75015 France Pisa56124 Italy Hackensack Meridian Health Bioethics Center EdisonNJ08820 United States University of Oxford Faculty of Philosophy OxfordOX2 6GG United Kingdom Collège André- Laurendeau Philosophie Department MontrealQCH8N 2J4 Canada Université du Québec À Montréal École des Médias MontrealQCH2L 2C4 Canada Pace University Philosophy Department New YorkNY10038 United States The Ohio State University Wexner Medical Center Department of Radiology ColumbusOH43210 United States Humanitas Research Hospital Department of Radiology Milan20089 Italy Humanitas University Department of Biomedical Sciences Milan20089 Italy University of New England Faculty of Science Agriculture Business and Law ArmidaleNSW2351 Australia University of Technology Sydney Faculty of Engineering and Information Technology SydneyNSW2007 Australia Scuola Superiore Sant'Anna European Centre of Excellence on the Regulation of Robotics and Ai Pisa56127 Italy University of Bremen Group of Computer Architecture Bremen28359 Germany New York University Grossman School of Medicine Division of Infectious Diseases and Immunology Department of Medicine New YorkNY10016 United States Digital Institute Ai Research Section Stockholm16731 Sweden Arcada University of Applied Sciences Department of Business Management and Analytics Helsinki00550 Finland University of Brescia Radiological Sciences and Public Health Department of Medical and Surgical Specialties Brescia25121 Italy Sncf Reseau Sa Ethique Groupe La Plaine93418 France Institute of Diagnostic and Interventional Radiology University Hospital Zurich Zürich8091 Switzerland Eindhoven University of Tech

This article's main contributions are twofold: 1) to demonstrate how to apply the general European Union's High-Level Expert Group's (EU HLEG) guidelines for trustworthy AI in practice for the domain of healthcare and 2) to investigate the research question of what does 'trustworthy AI' mean at the time of the COVID-19 pandemic. To this end, we present the results of a post-hoc self-assessment to evaluate the trustworthiness of an AI system for predicting a multiregional score conveying the degree of lung compromise in COVID-19 patients, developed and verified by an interdisciplinary team with members from academia, public hospitals, and industry in time of pandemic. The AI system aims to help radiologists to estimate and communicate the severity of damage in a patient's lung from Chest X-rays. It has been experimentally deployed in the radiology department of the ASST Spedali Civili clinic in Brescia, Italy, since December 2020 during pandemic time. The methodology we have applied for our post-hoc assessment, called Z-Inspection®, uses sociotechnical scenarios to identify ethical, technical, and domain-specific issues in the use of the AI system in the context of the pandemic. © 2020 IEEE.

关键词： COVID-19

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Automatic autism spectrum disorder detection using artificial intelligence methods with MRI neuroimaging: A review

arXiv

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arXiv 2022年

作者： Moridian, Parisa Ghassemi, Navid Jafari, Mahboobeh Salloum-Asfar, Salam Sadeghi, Delaram Khodatars, Marjane Shoeibi, Afshin Khosravi, Abbas Ling, Sai Ho Subasi, Abdulhamit Alizadehsani, Roohallah Gorriz, Juan M. Abdulla, Sara A. Acharya, U. Rajendra Faculty of Engineering Science and Research Branch Islamic Azad University Tehran Iran Computer Engineering Department Ferdowsi University of Mashhad Mashhad Iran Electrical and Computer Engineering Faculty Semnan University Semnan Iran Neurological Disorders Research Center Qatar Biomedical Research Institute Hamad Bin Khalifa University Qatar Foundation Doha Qatar Dept. of Medical Engineering Mashhad Branch Islamic Azad University Mashhad Iran Data Science and Computational Intelligence Institute University of Granada Granada Spain Deakin University GeelongVIC Australia UltimoNSW Australia Institute of Biomedicine Faculty of Medicine University of Turku Turku Finland Dept. of Computer Science College of Engineering Effat University Jeddah Saudi Arabia Ngee Ann Polytechnic Singapore Singapore Department of Biomedical Informatics and Medical Engineering Asia University Taichung Taiwan Department of Biomedical Engineering School of Science and Technology Singapore University of Social Sciences Singapore

Autism spectrum disorder (ASD) is a brain condition characterized by diverse signs and symptoms that appear in early childhood. ASD is also associated with communication deficits and repetitive behavior in affected individuals. Various ASD detection methods have been developed, including neuroimaging modalities and psychological tests. Among these methods, magnetic resonance imaging (MRI) imaging modalities are of paramount importance to physicians. Clinicians rely on MRI modalities to diagnose ASD accurately. The MRI modalities are non-invasive methods that include functional (fMRI) and structural (sMRI) neuroimaging methods. However, diagnosing ASD with fMRI and sMRI for specialists is often laborious and time-consuming;therefore, several computer-aided design systems (CADS) based on artificial intelligence (AI) have been developed to assist specialist physicians. Conventional machine learning (ML) and deep learning (DL) are the most popular schemes of AI used for diagnosing ASD. This study aims to review the automated detection of ASD using AI. We review several CADS that have been developed using ML techniques for the automated diagnosis of ASD using MRI modalities. There has been very limited work on the use of DL techniques to develop automated diagnostic models for ASD. A summary of the studies developed using DL is provided in the Supplementary Appendix. Then, the challenges encountered during the automated diagnosis of ASD using MRI and AI techniques are described in detail. Additionally, a graphical comparison of studies using ML and DL to diagnose ASD automatically is discussed. We suggest future approaches to detecting ASDs using AI techniques and MRI neuroimaging. © 2022, CC BY-NC-ND.

关键词： Magnetic resonance imaging

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DeePMD-kit v3: A Multiple-Backend Framework for Machine Learning Potentials

arXiv

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arXiv 2025年

作者： Zeng, Jinzhe Zhang, Duo Peng, Anyang Zhang, Xiangyu He, Sensen Wang, Yan Liu, Xinzijian Bi, Hangrui Li, Yifan Cai, Chun Zhang, Chengqian Du, Yiming Zhu, Jia-Xin Mo, Pinghui Huang, Zhengtao Zeng, Qiyu Shi, Shaochen Qin, Xuejian Yu, Zhaoxi Luo, Chenxing Ding, Ye Liu, Yun-Pei Shi, Ruosong Wang, Zhenyu Bore, Sigbjørn Løland Chang, Junhan Deng, Zhe Ding, Zhaohan Han, Siyuan Jiang, Wanrun Ke, Guolin Liu, Zhaoqing Lu, Denghui Muraoka, Koki Oliaei, Hananeh Singh, Anurag Kumar Que, Haohui Xu, Weihong Xu, Zhangmancang Zhuang, Yong-Bin Dai, Jiayu Giese, Timothy J. Jia, Weile Xu, Ben York, Darrin M. Zhang, Linfeng Wang, Han School of Artificial Intelligence and Data Science Unversity of Science and Technology of China Hefei China 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 Beijing China Baidu Inc. Beijing China Department of Computer Science University of Toronto TorontoON Canada Department of Chemistry Princeton University PrincetonNJ08540 United States University of Chinese Academy of Sciences Beijing100871 China State Key Laboratory of Physical Chemistry of Solid Surfaces iChEM College of Chemistry and Chemical Engineering Xiamen University Xiamen361005 China College of Integrated Circuits Hunan University Changsha410082 China State Key Laboratory of Advanced Technology for Materials Synthesis and Processing Center for Smart Materials and Device Integration School of Material Science and Engineering Wuhan University of Technology Wuhan430070 China College of Science National University of Defense Technology Changsha410073 China Hunan Key Laboratory of Extreme Matter and Applications National University of Defense Technology Changsha410073 China ByteDance Research Beijing100098 China Ningbo Institute of Materials Technology and Engineering Chinese Academy of Sciences Ningbo315201 China College of Materials Science and Opto-Electronic Technology University of Chinese Academy of Sciences Beijing100049 China Key Laboratory of Theoretical and Computational Photochemistry of Ministry of Education College of Chemistry Beijing Normal University Beijing100875 China Department of Geosciences Princeton University PrincetonNJ08544 United States Department of Applied Physics and Applied Mathematics Columbia University New YorkNY10027 United States IKKEM Fujian Xiamen361005 China Graduate

In recent years, machine learning potentials (MLPs) have become indispensable tools in physics, chemistry, and materials science, driving the development of software packages for molecular dynamics (MD) simulations and related applications. These packages, typically built on specific machine learning frameworks such as TensorFlow, PyTorch, or JAX, face integration challenges when advanced applications demand communication across different frameworks. The previous TensorFlow-based implementation of DeePMD-kit exemplified these limitations. In this work, we introduce DeePMD-kit version 3, a significant update featuring a multi-backend framework that supports TensorFlow, PyTorch, JAX, and PaddlePaddle backends, and demonstrate the versatility of this architecture through the integration of other MLPs packages and of Differentiable Molecular Force Field. This architecture allows seamless backend switching with minimal modifications, enabling users and developers to integrate DeePMD-kit with other packages using different machine learning frameworks. This innovation facilitates the development of more complex and interoperable workflows, paving the way for broader applications of MLPs in scientific research. Copyright © 2025, The Authors. All rights reserved.

关键词： Molecular dynamics

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Scientific discovery in the age of artificial intelligence

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NATURE 2023年第7978期621卷 E33-E33页

作者： Wang, Hanchen Fu, Tianfan Du, Yuanqi Gao, Wenhao Huang, Kexin Liu, Ziming Chandak, Payal Liu, Shengchao Van Katwyk, Peter Deac, Andreea Anandkumar, Anima Bergen, Karianne Gomes, Carla P. Ho, Shirley Kohli, Pushmeet Lasenby, Joan Leskovec, Jure Liu, Tie-Yan Manrai, Arjun Marks, Debora Ramsundar, Bharath Song, Le Sun, Jimeng Tang, Jian Velickovic, Petar Welling, Max Zhang, Linfeng Coley, Connor W. Bengio, Yoshua Zitnik, Marinka Department of Engineering University of Cambridge Cambridge UK Department of Computing and Mathematical Sciences California Institute of Technology Pasadena CA USA NVIDIA Santa Clara CA USA Department of Computational Science and Engineering Georgia Institute of Technology Atlanta GA USA Department of Computer Science Cornell University Ithaca NY USA Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA USA Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA USA Department of Computer Science Stanford University Stanford CA USA Department of Physics Massachusetts Institute of Technology Cambridge MA USA Harvard-MIT Program in Health Sciences and Technology Cambridge MA USA Mila – Quebec AI Institute Montreal Quebec Canada Université de Montréal Montreal Quebec Canada HEC Montréal Montreal Quebec Canada CIFAR AI Chair Toronto Ontario Canada Department of Earth Environmental and Planetary Sciences Brown University Providence RI USA Data Science Institute Brown University Providence RI USA Center for Computational Astrophysics Flatiron Institute New York NY USA Department of Astrophysical Sciences Princeton University Princeton NJ USA Department of Physics Carnegie Mellon University Pittsburgh PA USA Department of Physics and Center for Data Science New York University New York NY USA Google DeepMind London UK Department of Computer Science and Technology University of Cambridge Cambridge UK Microsoft Research Beijing China Department of Biomedical Informatics Harvard Medical School Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Harvard Data Science Initiative Cambridge MA USA Kempner Institute for the Study of Natural and Artificial Intelligence Harvard University Cambridge MA USA Department of Systems Biology Harvard Medical School Boston MA USA Deep Forest Sciences Palo Alto CA USA BioMap Beijing China Mo

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