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SRBench++: Principled Benchmarking of Symbolic Regression With Domain-Expert Interpretation

IEEE Transactions on evolutionary Computation 2024年 1-1页

作者： de Franca, F.O. Virgolin, M. Kommenda, M. Majumder, M.S. Cranmer, M. Espada, G. Ingelse, L. Fonseca, A. Landajuela, M. Petersen, B. Glatt, R. Mundhenk, N. Lee, C.S. Hochhalter, J.D. Randall, D.L. Kamienny, P. Zhang, H. Dick, G. Simon, A. Burlacu, B. Kasak, Jaan Machado, Meera Wilstrup, Casper Cavaz, W.G.L. Federal University of ABC Santo Andre Brazil Evolutionary Intelligence group Centrum Wiskunde and Informatica Science Park Amsterdam Netherlands University of Applied Sciences Upper Austria Hagenberg Austria Computational Health Informatics Program Boston Children’s Hospital Harvard Medical School Boston USA Center for Computational Astrophysics Flatiron Institute and Department of Astrophysical Sciences of Princeton University USA LASIGE Faculdade de Ciências Universidade de Lisboa Lisboa Portugal Computational Engineering Division Lawrence Livermore National Laboratory Livermore USA Department of Mechanical Engineering University of Utah Utah USA Meta FAIR France Victoria University of Wellington School of Engineering and Computer Science New Zealand University of otago Department of Information Science New Zealand Institut für Angewandte Physik Universität TübingenMax Planck Institute for Intelligent Systems Tübingen Germany Abzu AI Orient Plads 1 Nordhavn Denmark

Symbolic regression searches for analytic expressions that accurately describe studied phenomena. The main promise of this approach is that it may return an interpretable model that can be insightful to users, while maintaining high accuracy. The current standard for benchmarking these algorithms is SRBench, which evaluates methods on hundreds of datasets that are a mix of real-world and simulated processes spanning multiple domains. At present, the ability of SRBench to evaluate interpretability is limited to measuring the size of expressions on real-world data, and the exactness of model forms on synthetic data. In practice, model size is only one of many factors used by subject experts to determine how interpretable a model truly is. Furthermore, SRBench does not characterize algorithm performance on specific, challenging sub-tasks of regression such as feature selection and evasion of local minima. In this work, we propose and evaluate an approach to benchmarking SR algorithms that addresses these limitations of SRBench by 1) incorporating expert evaluations of interpretability on a domain-specific task, and 2) evaluating algorithms over distinct properties of data science tasks. We evaluate 12 modern symbolic regression algorithms on these benchmarks and present an in-depth analysis of the results, discuss current challenges of symbolic regression algorithms and highlight possible improvements for the benchmark itself. Authors

关键词： Benchmarking

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Opportunities and challenges for monitoring terrestrial biodiversity in the robotics age

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Nature Ecology and Evolution 2025年第6期9卷 1031-1042页

作者： Pringle, Stephen Dallimer, Martin Goddard, Mark A. Le Goff, Léni K. Hart, Emma Langdale, Simon J. Fisher, Jessica C. Abad, Sara-Adela Ancrenaz, Marc Angeoletto, Fabio Auat Cheein, Fernando Austen, Gail E. Bailey, Joseph J. Baldock, Katherine C. R. Banin, Lindsay F. Banks-Leite, Cristina Barau, Aliyu S. Bashyal, Reshu Bates, Adam J. Bicknell, Jake E. Bielby, Jon Bosilj, Petra Bush, Emma R. Butler, Simon J. Carpenter, Dan Clements, Christopher F. Cully, Antoine Davies, Kendi F. Deere, Nicolas J. Dodd, Michael Drinkwater, Rosie Driscoll, Don A. Dutilleux, Guillaume Dyrmann, Mads Edwards, David P. Farhadinia, Mohammad S. Faruk, Aisyah Field, Richard Fletcher, Robert J. Foster, Chris W. Fox, Richard Francksen, Richard M. Franco, Aldina M. A. Gainsbury, Alison M. Gardner, Charlie J. Giorgi, Ioanna Griffiths, Richard A. Hamaza, Salua Hanheide, Marc Hayward, Matt W. Hedblom, Marcus Helgason, Thorunn Heon, Sui P. Hughes, Kevin A. Hunt, Edmund R. Ingram, Daniel J. Jackson-Mills, George Jowett, Kelly Keitt, Timothy H. Kloepper, Laura N. Kramer-Schadt, Stephanie Labisko, Jim Labrosse, Frédéric Lawson, Jenna Lecomte, Nicolas de Lima, Ricardo F. Littlewood, Nick A. Marshall, Harry H. Masala, Giovanni L. Maskell, Lindsay C. Matechou, Eleni Mazzolai, Barbara McConnell, Alistair Melbourne, Brett A. Miriyev, Aslan Nana, Eric Djomo Ossola, Alessandro Papworth, Sarah Parr, Catherine L. Payo-Payo, Ana Perry, Gad Pettorelli, Nathalie Pillay, Rajeev Potts, Simon G. Prendergast-Miller, Miranda T. Qie, Lan Rolley-Parnell, Persie Rossiter, Stephen J. Rowcliffe, Marcus Rumble, Heather Sadler, Jon P. Sandom, Christopher J. Sanyal, Asiem Schrodt, Franziska Sethi, Sarab S. Shabrani, Adi Siddall, Robert Smith, Simón C. Snep, Robbert P. H. Soulsbury, Carl D. Stanley, Margaret C. Stephens, Philip A. Stephenson, P.J. Struebig, Matthew J. Studley, Matthew Svátek, Martin Tang, Gilbert Taylor, Nicholas K. Umbers, Kate D. L. Ward, Robert J. White, Patrick J. C. Whittingham, Mark J. Wich, Serge Williams, Christopher D. Yakubu, Ibrahim B. Yoh, Natalie Durrell Institute of Conservation and Ecology (DICE) School of Natural Sciences University of Kent Canterbury United Kingdom Centre for Environmental Policy Imperial College London London United Kingdom Department of Geography and Environmental Sciences Northumbria University Newcastle upon Tyne United Kingdom School of Computing Engineering and the Built Environment Edinburgh Napier University Edinburgh United Kingdom Synthotech Ltd Milner Court Hornbeam Square Harrogate United Kingdom Mechanical Engineering Department University College London London United Kingdom HUTAN SWD Kota Kinabalu Malaysia Programa de Pós-Graduação em Gestão e Tecnologia Ambiental da Universidade Federal de Rondonópolis Rondonópolis Brazil Department of Engineering Harper Adams University Newport United Kingdom Applied Ecology Research Group School of Life Sciences Anglia Ruskin University Cambridge United Kingdom Centre for Ecology and Hydrology Penicuik United Kingdom Department of Life Sciences Imperial College London Silwood Park Campus Ascot United Kingdom Department of Urban and Regional Planning Faculty of Earth and Environmental Sciences Bayero University Kano Nigeria Greenhood Nepal Kathmandu Nepal Animal Rural & Environmental Sciences Nottingham Trent University Nottinghamshire United Kingdom School of Biological and Environmental Sciences Liverpool John Moores University Liverpool United Kingdom Lincoln Centre for Autonomous Systems University of Lincoln Lincoln United Kingdom Royal Botanic Garden Edinburgh Edinburgh United Kingdom School of Biological Sciences University of East Anglia Norwich Research Park Norwich United Kingdom Digital Ecology Limited Bristol United Kingdom School of Biological Sciences University of Bristol Bristol United Kingdom Department of Computing Imperial College London London United Kingdom Department of Ecology and Evolutionary Biology University of Colorado Boulder CO United States Faculty of Science Technology Engineering

With biodiversity loss escalating globally, a step change is needed in our capacity to accurately monitor species populations across ecosystems. Robotic and autonomous systems (RAS) offer technological solutions that may substantially advance terrestrial biodiversity monitoring, but this potential is yet to be considered systematically. We used a modified Delphi technique to synthesize knowledge from 98 biodiversity experts and 31 RAS experts, who identified the major methodological barriers that currently hinder monitoring, and explored the opportunities and challenges that RAS offer in overcoming these barriers. Biodiversity experts identified four barrier categories: site access, species and individual identification, data handling and storage, and power and network availability. Robotics experts highlighted technologies that could overcome these barriers and identified the developments needed to facilitate RAS-based autonomous biodiversity monitoring. Some existing RAS could be optimized relatively easily to survey species but would require development to be suitable for monitoring of more ‘difficult’ taxa and robust enough to work under uncontrolled conditions within ecosystems. Other nascent technologies (for instance, new sensors and biodegradable robots) need accelerated research. Overall, it was felt that RAS could lead to major progress in monitoring of terrestrial biodiversity by supplementing rather than supplanting existing methods. Transdisciplinarity needs to be fostered between biodiversity and RAS experts so that future ideas and technologies can be codeveloped effectively. © The Author(s) 2025.

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Learning, visualizing and exploring 16S rRNA structure using an attention-based deep neural network

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PLoS Computational Biology 2021年第9期17卷 e1009345-e1009345页

作者： Zhao, Zhengqiao Woloszynek, Stephen Agbavor, Felix Mell, Joshua Chang Sokhansanj, Bahrad A. Rosen, Gail L. Ecological and Evolutionary Signal-Processing and Informatics Laboratory Department of Electrical and Computer Engineering College of Engineering Drexel University PhiladelphiaPA United States Beth Israel Deaconess Medical Center BostonMA United States Harvard Medical School BostonMA United States School of Biomedical Engineering Science and Health Systems Drexel University PhiladelphiaPA United States College of Medicine Drexel University PhiladelphiaPA United States

Recurrent neural networks with memory and attention mechanisms are widely used in natural language processing because they can capture short and long term sequential information for diverse tasks. We propose an integrated deep learning model for microbial DNA sequence data, which exploits convolutional neural networks, recurrent neural networks, and attention mechanisms to predict taxonomic classifications and sample-associated attributes, such as the relationship between the microbiome and host phenotype, on the read/ sequence level. In this paper, we develop this novel deep learning approach and evaluate its application to amplicon sequences. We apply our approach to short DNA reads and full sequences of 16S ribosomal RNA (rRNA) marker genes, which identify the heterogeneity of a microbial community sample. We demonstrate that our implementation of a novel attention- based deep network architecture, Read2Pheno, achieves read-level phenotypic prediction. Training Read2Pheno models will encode sequences (reads) into dense, meaningful representations: learned embedded vectors output from the intermediate layer of the network model, which can provide biological insight when visualized. The attention layer of Read2Pheno models can also automatically identify nucleotide regions in reads/sequences which are particularly informative for classification. As such, this novel approach can avoid pre/post-processing and manual interpretation required with conventional approaches to microbiome sequence classification. We further show, as proof-of-concept, that aggregating read-level information can robustly predict microbial community properties, host phenotype, and taxonomic classification, with performance at least comparable to conventional approaches. An implementation of the attention-based deep learning network is available at https://***/EESI/sequence_attention (a python package) and https://***/ EESI/seq2att (a command line tool). Copyright: © 2021 Zhao et

关键词： Classification (of information)

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Performance and energy-aware bi-objective tasks scheduling for cloud data centers

arXiv

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arXiv 2021年

作者： Materwala, Huned Ismail, Leila Intelligent Distributed Computing and Systems Research Laboratory Department of Computer Science and Software Engineering College of Information Technology United Arab Emirates University Al Ain Abu Dhabi15551 United Arab Emirates National Water and Energy Center United Arab Emirates University Al Ain Abu Dhabi United Arab Emirates

Cloud computing enables remote execution of users' tasks. The pervasive adoption of cloud computing in smart cities' services and applications requires timely execution of tasks adhering to Quality of Services (QoS). However, the increasing use of computing servers exacerbates the issues of high energy consumption, operating costs, and environmental pollution. Maximizing the performance and minimizing the energy in a cloud data center is challenging. In this paper, we propose a performance and energy optimization bi-objective algorithm to tradeoff the contradicting performance and energy objectives. An evolutionary algorithm-based multi-objective optimization is for the first time proposed using system performance counters. The performance of the proposed model is evaluated using a realistic cloud dataset in a cloud computing environment. Our experimental results achieve higher performance and lower energy consumption compared to a state-of-the-art algorithm. © 2021, CC BY.

关键词： Energy efficiency

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Interpretable Symbolic Regression for Data science: Analysis of the 2022 Competition

arXiv

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arXiv 2023年

作者： de Franca, F.O. Virgolin, M. Kommenda, M. Majumder, M.S. Cranmer, M. Espada, G. Ingelse, L. Fonseca, A. Landajuela, M. Petersen, B. Glatt, R. Mundhenk, N. Lee, C.S. Hochhalter, J.D. Randall, D.L. Kamienny, P. Zhang, H. Dick, G. Simon, A. Burlacu, B. Kasak, Jaan Machado, Meera Wilstrup, Casper La Cava, W.G. Federal University of ABC Santo Andre Brazil Evolutionary Intelligence Group Centrum Wiskunde & Informatica Science Park 123 Amsterdam Netherlands Computational Health Informatics Program Boston Children's Hospital Harvard Medical School Boston United States University of Applied Sciences Upper Austria Hagenberg Austria Center for Computational Astrophysics Flatiron Institute Department of Astrophysical Sciences Princeton University United States LASIGE Faculdade de Ciências Universidade de Lisboa Lisboa Portugal Computational Engineering Division Lawrence Livermore National Laboratory Livermore United States University of Utah Department of Mechanical Engineering Utah United States Meta FAIR France Victoria University of Wellington School of Engineering and Computer Science New Zealand University of otago Department of Information Science New Zealand Institut für Angewandte Physik Universität Tübingen Max Planck Institute for Intelligent Systems Tübingen Germany Abzu AI Orient Plads 1 Nordhavn 2150 Denmark

Symbolic regression searches for analytic expressions that accurately describe studied phenomena. The main attraction of this approach is that it returns an interpretable model that can be insightful to users. Historically, the majority of algorithms for symbolic regression have been based on evolutionary algorithms. However, there has been a recent surge of new proposals that instead utilize approaches such as enumeration algorithms, mixed linear integer programming, neural networks, and Bayesian optimization. In order to assess how well these new approaches behave on a set of common challenges often faced in real-world data, we hosted a competition at the 2022 Genetic and evolutionary Computation Conference consisting of different synthetic and real-world datasets which were blind to entrants. For the real-world track, we assessed interpretability in a realistic way by using a domain expert to judge the trustworthiness of candidate models. We present an in-depth analysis of the results obtained in this competition, discuss current challenges of symbolic regression algorithms and highlight possible improvements for future competitions. Copyright © 2023, The Authors. All rights reserved.

关键词： Machine learning

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Challenges in Cybersecurity: Lessons from Biological Defense systems

SSRN

引用

SSRN 2023年

作者： Schrom, Edward Kinzig, Ann P. Forrest, Stephanie Graham, Andrea L. Levin, Simon A. Bergstrom, Carl T. Castillo-Chavez, Carlos Collins, James P. de Boer, Rob J. Doupé, Adam Ensafi, Roya Feldman, Stuart Grenfell, Bryan T. Halderman, J. Alex Huijben, Silvie Maley, Carlo Moses, Melanie Perelson, Alan S. Perrings, Charles Plotkin, Joshua Rexford, Jennifer Tiwari, Mohit Department of Ecology and Evolutionary Biology Princeton University PrincetonNJ08544 United States School of Life Sciences Arizona State University TempeAZ85287 United States Biodesign Center for Biocomputation Security and Society Arizona State University TempeAZ85287 United States School of Computing and Augmented Intelligence Arizona State University TempeAZ85287 United States Santa Fe Institute Santa FeNM87501 United States Department of Biology University of Washington SeattleWA98195 United States School of Human Evolution and Social Change Arizona State University TempeAZ85287 United States Theoretical Biology and Bioinformatics Utrecht University Utrecht3584 CH Netherlands Center for Cybersecurity and Trusted Foundations Global Security Initiative Arizona State University TempeAZ85287 United States Department of Electrical Engineering and Computer Science Computer Science and Engineering Division University of Michigan Ann ArborMI48109 United States Schmidt Futures New YorkNY10011 United States Princeton School of Public and International Affairs Princeton University PrincetonNJ08544 United States Center for Computer Security and Society University of Michigan Ann ArborMI48109 United States Arizona Cancer Evolution Center Arizona State University TempeAZ85287 United States Department of Computer Science University of New Mexico AlbuquerqueNM87131 United States Department of Biology University of New Mexico AlbuquerqueNM87131 United States Theoretical Biology and Biophysics Group Los Alamos National Laboratory Los AlamosNM87545 United States Department of Biology University of Pennsylvania PhiladelphiaPA19104 United States Department of Computer Science Princeton University PrincetonNJ08540 United States Department of Electrical and Computer Engineering University of Texas AustinTX78712 United States

Defending against novel, repeated, or unpredictable attacks, while avoiding attacks on the ‘self’, are the central problems of both mammalian immune systems and computer systems. Both systems have been studied in great detail, but with little exchange of information across the different disciplines. Here, we present a conceptual framework for structured comparisons across the fields of biological immunity and cybersecurity, by framing the context of defense, considering different (combinations of) defensive strategies, and evaluating defensive performance. Throughout this paper, we pose open questions for further exploration. We hope to spark the interdisciplinary discovery of general principles of optimal defense, which can be understood and applied in biological immunity, cybersecurity, and other defensive realms. © 2023, The Authors. All rights reserved.

关键词： Cybersecurity

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Iterated Problem Reformulation for evolutionary Large-Scale Multiobjective Optimization

Iterated Problem Reformulation for Evolutionary Large-Scale ...

引用

Congress on evolutionary Computation

作者： Cheng He Ran Cheng Ye Tian Xingyi Zhang Department of Computer Science and Engineering University Key Laboratory of Evolving Intelligent Systems of Guangdong Province Southern University of Science and Technology Shenzhen China Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education Institutes of Physical Science and Information Technology Anhui University Hefei China Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education School of Computer Science and Technology Anhui University Hefei China

ISBN: (数字)9781728169293

ISBN: (纸本)9781728169309

Due to the curse of dimensionality, two main issues remain challenging for applying evolutionary algorithms (EAs) to large-scale multiobjective optimization. The first issue is how to improve the efficiency of EAs for reducing computation cost. The second one is how to improve the diversity maintenance of EAs to avoid local optima. Nevertheless, these two issues are somehow conflicting with each other, and thus it is crucial to strike a balance between them in practice. Thereby, we propose an iterated problem reformulation based EA for large-scale multiobjective optimization, where the problem reformulation based method and the decomposition based method are used iteratively to address the aforementioned issues. The proposed method is compared with several state-of-the-art EAs on a variety of large-scale multiobjective optimization problems. Experimental results demonstrate the effectiveness of our proposed iterated method in large-scale multiobjective optimization.

关键词： Sociology Convergence Pareto optimization Indexes computer science

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Preface

Lecture Notes in Networks and Systems

引用

Lecture Notes in Networks and systems 2023年 729 LNNS卷 v-vi页

作者： Vasant, Pandian Weber, Gerhard-Wilhelm Arefin, Mohammad Shamsul Rodriguez-Aguilar, Roman Panchenko, Vladimir Munapo, Elias Thomas, J. Joshua Faculty of Electrical and Electronics Engineering Modeling Evolutionary Algorithms Simulation and Artificial Intelligence Ton Duc Thang University Ho Chi Minh City Viet Nam Department of Computer Science Chittagong University of Engineering and Technology Chittagong Bangladesh Laboratory of Non-traditional Energy Systems Department of Theoretical and Applied Mechanics Federal Scientific Agroengineering Center VIM Russian University of Transport Moscow Russia Department of Computer Science UOW Malaysia KDU Penang University College George Town Malaysia Faculty of Engineering Management Poznań University of Technology Poznan Poland School of Economics and Decision Sciences North West University Mmabatho South Africa Facultad de Ciencias Económicas y Empresariales School of Economic and Business Sciences Universidad Panamericana Mexico City Mexico

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Challenges in cybersecurity: Lessons from biological defense systems

arXiv

引用

arXiv 2021年

作者： Schrom, Edward Kinzig, Ann Forrest, Stephanie Graham, Andrea L. Levin, Simon A. Bergstrom, Carl T. Castillo-Chavez, Carlos Collins, James P. De Boer, Rob J. Doupé, Adam Ensafi, Roya Feldman, Stuart Grenfell, Bryan T. Halderman, J. Alex Huijben, Silvie Maley, Carlo Moses, Melanie Perelson, Alan S. Perrings, Charles Plotkin, Joshua Rexford, Jennifer Tiwari, Mohit Department of Ecology and Evolutionary Biology Princeton University 106A Guyot Hall PrincetonNJ08544 United States School of Life Sciences Arizona State University TempeAZ85287 United States Julie Ann Wrigley Global Institute of Sustainability Arizona State University TempeAZ85287 United States Biodesign Center for Biocomputation Security and Society Arizona State University TempeAZ85287 United States School of Computing Informatics and Decision Sciences Engineering Arizona State University TempeAZ85287 United States Santa Fe Institute Santa FeNM87501 United States Department of Biology University of Washington SeattleWA98195 United States Arizona State University TempeAZ85287 United States Theoretical Biology and Bioinformatics Utrecht University Utrecht3584 CH Netherlands Center for Cybersecurity and Digital Forensics Global Security Initiative Arizona State University TempeAZ85287 United States Department of Electrical Engineering and Computer Science Computer Science and Engineering Division University of Michigan Ann ArborMI48109 United States Schmidt Futures New YorkNY10011 United States Princeton School of Public and International Affairs Princeton University PrincetonNJ08544 United States Center for Computer Security and Society University of Michigan Ann ArborMI48109 United States Center for Evolution and Medicine School of Life Sciences Arizona State University TempeAZ85287 United States Arizona Cancer Evolution Center Arizona State University TempeAZ85287 United States Department of Computer Science University of New Mexico AlbuquerqueNM87131 United States University of New Mexico Department of Computer Science AlbuquerqueNM87131 United States Department of Biology University of New Mexico AlbuquerqueNM87131 United States Theoretical Biology and Biophysics Group Los Alamos National Laboratory Los AlamosNM87545 United States Department of Biology University of Pennsylvania PhiladelphiaPA19104 Unite

We explore the commonalities between methods for assuring the security of computer systems (cybersecurity) and the mechanisms that have evolved through natural selection to protect vertebrates against pathogens, and how insights derived from studying the evolution of natural defenses can inform the design of more effective cybersecurity systems. More generally, security challenges are crucial for the maintenance of a wide range of complex adaptive systems, including financial systems, and again lessons learned from the study of the evolution of natural defenses can provide guidance for the protection of such *** Codes A.0. Copyright © 2021, The Authors. All rights reserved.

关键词： Cybersecurity

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The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2

引用

四川生理科学杂志 2022年第7期44卷 1299-1299页

作者： Jonathan E Pekar Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA 92093 USA Department of Biomedical Informatics University of California San Diego La Jolla CA 92093 USA Department of Human Genetics David Geffen School of Medicine University of California Los Angeles Los Angeles CA 90095 USA Department of Immunology and Microbiology The Scripps Research Institute La Jolla CA 92037 USA Department of Computer Science and Engineering University of California San Diego La Jolla CA 92093 USA Department of Mathematics University of California San Diego La Jolla CA 92093 USA Department of Ecology and Evolutionary Biology University of Arizona Tucson AZ 85721 USA W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health Baltimore MD 21205 USA New York City Public Health Laboratory New York City Department of Health and Mental Hygiene New York NY 11101 USA Department of Microbiology Institute for Viral Diseases Biosafety Center College of Medicine Korea University Seoul South Korea BK21 Graduate Program Department of Biomedical Sciences Korea University College of Medicine Seoul 02841 Republic of Korea National Public Health Laboratory National Centre for Infectious Diseases Singapore Malaysia Genome and Vaccine Institute Jalan Bangi 43000 Kajang Selangor Malaysia Department of Medicine University of California San Diego La Jolla CA 92093 USA Department of Microbiology and Immunology School of Medicine Tulane University New Orleans LA 70112 USA Zalgen Labs Frederick MD 21703 USA Global Virus Network (GVN) Baltimore MD 21201 USA Sydney Institute for Infectious Diseases School of Life and Environmental Sciences and School of Medical Sciences The University of Sydney Sydney NSW 2006 Australia Institute of Evolutionary Biology University of Edinburgh King’s Buildings Edinburgh EH9 3FL UK Department of Biomathematics David Geffen School of Medicine Un

Understanding the circumstances that lead to pandemics is important for their prevention. Here, we analyze the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pandemic. We show that SARS-CoV-2 genomic diversity before February 2020 likely comprised only two distinct viral lineages, denoted A and B. Phylodynamic rooting methods, coupled with epidemic simulations, reveal that these lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses around 18 November 2019 (23 October-8 December), while the separate introduction of lineage A likely occurred within weeks of this event.

关键词： epidemiology likely acute

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