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arXiv 2019年

作者： Ye, Cong Slavakis, Konstantinos Patil, Pratik V. Muldoon, Sarah F. Medaglia, John NY14260 United States Department of Mathematics Computational and Data-Enabled Science and Engineering Program University at Buffalo SUNY NY14260 United States Department of Psychology Drexel University PA19104 United States Perelman School of Medicine University of Pennsylvania PA19104 United States

Recent advances in neuroscience and in the technology of functional magnetic resonance imaging (fMRI) and electro-encephalography (EEG) have propelled a growing interest in brain-network clustering via time-series analysis. Notwithstanding, most of the brain-network clustering methods revolve around state clustering and/or node clustering (a.k.a. community detection or topology inference) within states. This work answers first the need of capturing non-linear nodal dependencies by bringing forth a novel feature-extraction mechanism via kernel autoregressive-moving-average modeling. The extracted features are mapped to the Grassmann manifold (Grassmannian), which consists of all linear subspaces of a fixed rank. By virtue of the Riemannian geometry of the Grassmannian, a unifying clustering framework is offered to tackle all possible clustering problems in a network: Cluster multiple states, detect communities within states, and even identify/track subnetwork state sequences. The effectiveness of the proposed approach is underlined by extensive numerical tests on synthetic and real fMRI/EEG data which demonstrate that the advocated learning method compares favorably versus several state-of-the-art clustering schemes. Copyright © 2019, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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Deterministic guarantees for Burer–Monteiro factorizations of smooth semidefinite programs

arXiv

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arXiv 2018年

作者： Boumal, Nicolas Voroninski, Vladislav Bandeira, Afonso S. Mathematics Department Program in Applied and Computational Mathematics Princeton University Department of Mathematics Center for Data Science Courant Institute of Mathematical Sciences New York University

We consider semidefinite programs (SDPs) with equality constraints. The variable to be optimized is a positive semidefinite matrix X of size n. Following the Burer–Monteiro approach, we optimize a factor Y of size n× p instead, such that X = YY. This ensures positive semidefiniteness at no cost and can reduce the dimension of the problem if p is small, but results in a non-convex optimization problem with a quadratic cost function and quadratic equality constraints in Y. In this paper, we show that if the set of constraints on Y regularly defines a smooth manifold, then, despite non-convexity, first- and second-order necessary optimality conditions are also sufficient, provided p is large enough. For smaller values of p, we show a similar result holds for almost all (linear) cost functions. Under those conditions, a global optimum Y maps to a global optimum X = YY of the SDP. We deduce old and new consequences for SDP relaxations of the generalized eigenvector problem, the trust-region subproblem and quadratic optimization over several spheres, as well as for the Max-Cut and Orthogonal-Cut SDPs which are common relaxations in stochastic block modeling and synchronization of rotations. Copyright © 2018, The Authors. All rights reserved.

关键词： Stochastic systems

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External exposome and incident asthma across the life course in 14 European cohorts: a prospective analysis within the EXPANSE project

The Lancet Regional Health - Europe

引用

The Lancet Regional Health - Europe 2025年 54卷

作者： Yu, Zhebin Kress, Sara Blay, Natalia Gregor, Petr Kukk, Hanna-Maria Leskien, Miriam Majewska, Renata Oosterwegel, Max J. Szabó, Daniel ten Have, Margreet Klánová, Jana Mikeš, Ondřej Bergström, Anna Bussalleu, Alonso de Cid, Rafael Dalecka, Andrea Dadvand, Payam van Dorsselaer, Saskia Fischer, Krista de Hoogh, Kees Koppelman, Gerard H. Kronberg, Jaanika Metspalu, Andres Milani, Lili Esko, Tõnu Metspalu, Mait Lakerveld, Jeroen Ljungman, Petter Merid, Simon Kebede Macek, Pawel Manczuk, Marta Merritt, Anne-Sophie Pac, Agnieszka Palta, Priit Pershagen, Göran Peters, Annette Pikhart, Hynek Saucy, Apolline Schikowski, Tamara Shen, Youchen Standl, Marie Tonne, Cathryn Vermeulen, Roel Vlaanderen, Jelle Vonk, Judith M. Wolf, Kathrin Ek, Carl Henrik Gruzieva, Olena Gehring, Ulrike Melén, Erik Institute of Environmental Medicine Karolinska Institutet Stockholm Sweden IUF – Leibniz Research Institute for Environmental Medicine Düsseldorf Germany Genomes for Life-GCAT Lab CORE Program Germans Trias I Pujol Research Institute (IGTP) Badalona Spain Grup de Recerca en Impacte de Les Malalties Cròniques I Les Seves Trajectòries (GRIMTra) (IGTP) Badalona Spain RECETOX Faculty of Science Masaryk University Brno Czech Republic Institute of Genomics University of Tartu Estonia Institute of Mathematics and Statistics University of Tartu Estonia Institute of Epidemiology Helmholtz Zentrum München - German Research Center for Environmental Health Neuherberg Germany Institute for Medical Information Processing Biometry and Epidemiology Medical Faculty Ludwig-Maximilians-Universität München Munich Germany Chair of Epidemiology and Preventive Medicine Jagiellonian University Medical College Kraków Poland Institute for Risk Assessment Sciences Utrecht University Utrecht Netherlands Netherlands Institute of Mental Health and Addiction Utrecht Netherlands Centre for Occupational and Environmental Medicine Region Stockholm Stockholm Sweden Swiss Tropical and Public Health Institute Allschwil Switzerland University of Basel Basel Switzerland ISGlobal Barcelona Spain Universitat Pompeu Fabra (UPF) Barcelona Spain CIBER Epidemiología y Salud Pública Spain University of Groningen University Medical Center Groningen Beatrix Children's Hospital Department of Pediatric Pulmonology and Pediatric Allergology Groningen Netherlands University of Groningen University Medical Center Groningen Groningen Research Institute for Asthma and COPD (GRIAC) Groningen Netherlands Department of Epidemiology and Data Science Amsterdam UMC Location Vrije Universiteit Amsterdam Amsterdam Netherlands Department of Cardiology Danderyd Hospital Stockholm Sweden Department of Clinical Sciences and Education Södersjukhuset Karolinska Institutet Stockholm Sweden Collegium Medicum Jan Koc

Background: The joint impact of exposure to multiple urban environmental factors on asthma remains unclear. Methods: We analysed data from 14 European cohorts to assess the impact of the urban exposome on asthma incidence across the life course. We linked three external exposome domains (air pollution, built environment, ambient temperature) to the participants’ home addresses at baseline. We performed k-means clustering within each domain and assessed associations of clusters with asthma adjusting for potentially relevant covariates in cohort-specific analyses, with subsequent separate meta-analyses for birth and adult cohorts. An environmental risk score using a coefficient-weighted sum approach was used to assess the impact of combining the three domains. Findings: A total of 7428 incident asthma cases were identified among 349,037 participants (from birth up to age 70+). Overall, we observed higher risks of asthma for clusters characterized by high particulate matter and nitrogen dioxide exposure in adults (OR_meta = 1.13, 95%CI:1.01–1.25), and clusters characterized by high built-up area and low levels of greenness in both children and adults (OR_meta = 1.36, 95%CI: 1.14–1.64 for birth cohorts and OR_meta = 1.15, 95%CI: 1.03–1.28 for adult cohorts, respectively). The joint exposure using the environment risk score combining the three domains was consistently associated with higher risks of incident asthma (OR_meta = 1.13, 95%CI: 1.07–1.20 for birth cohorts, OR_meta = 1.15, 95%CI: 1.10–1.20 for adult cohorts per 20% increase). On average 11.6% of the incident asthma cases could be attributed to environmental risk score above cohort-specific median levels. Interpretation: Multiple environmental exposures jointly contribute to incident asthma risk across the life course. Urban planning accounting for these factors may help mitigate asthma development. Funding: This study was funded by the European Union's Horizon 2

关键词： Asthma Cohort Exposome Life course

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Publisher Correction: Global estimates on the number of people blind or visually impaired by cataract: a meta-analysis from 2000 to 2020

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Eye (London, England) 2024年第11期38卷 2229-2231页

作者： Konrad Pesudovs Hugh R. Taylor Tabassom Sedighi Rupert R. A. Bourne Shahina Pardhan Van Charles Lansingh John H. Kempen Ian Tapply Arthur G. Fernandes Maria Vittoria Cicinelli Alessandro Arrigo Nicolas Leveziel Serge Resnikoff Seth Flaxman Mukkharram M. Bikbov Tasanee Braithwaite Alain Bron Ching-Yu Cheng Monte A. Del Monte Joshua R. Ehrlich Leon B. Ellwein David Friedman João M. Furtado Gus Gazzard Ronnie George M. Elizabeth Hartnett Jost B. Jonas Rim Kahloun Moncef Khairallah Rohit C. Khanna Janet Leasher Julie-Anne Little Vinay Nangia Michal Nowak Tunde Peto Pradeep Ramulu Fotis Topouzis Mitiadis Tsilimbaris Ya Xing Wang Ningli Wang Paul Svitil Briant Theo Vos Katrin Burkart Kaleb Coberly Xiaochen Dai Stephen S. Lim Tomislav Mestrovic Ali H. Mokdad Christopher J. L. Murray Jaimie D. Steinmetz Awoke Misganaw Yohannes Habtegiorgis Abate Mohammad Abdollahi Mozhan Abdollahi Ayele Mamo Abebe Olumide Abiodun Richard Gyan Aboagye Woldu Aberhe Abrha Hasan Abualruz Hiwa Abubaker Ali Eman Abu-Gharbieh Salahdein Aburuz Tadele Girum Girum Adal Mesafint Molla Adane Isaac Yeboah Addo Qorinah Estiningtyas Sakilah Adnani Muhammad Sohail Afzal Muhammad Umair Shahin Aghamiri Bright Opoku Ahinkorah Aqeel Ahmad Sajjad Ahmad Ali Ahmadi Siamak Sabour Ayman Ahmed Haroon Ahmed Ahmad Samir Alfaar Abid Ali Syed Shujait Shujait Ali Awais Altaf Hubert Amu Emmanuel Manu Sofia Androudi Rodrigo Anguita Abhishek Anil Rimple Jeet Kaur Muhammad Aaqib Shamim Saeid Anvari Anayochukwu Edward Anyasodor Francis Appiah Jalal Arabloo Haleh Ayatollahi Mosab Arafat Damelash Areda Reza Arefnezhad Brhane Berhe Aregawi Akeza Awealom Asgedom Tahira Ashraf Seyyed Shamsadin Athari Bantalem Tilaye Tilaye Atinafu Birhan Tsegaw Taye Maha Moh’d Wahbi Atout Alok Atreya Ahmed Y. Azzam Hassan Babamohamadi Sara Bagherieh Yogesh Bahurupi Atif Amin Baig Shumaila Nargus Biswajit Banik Mainak Bardhan Saurav Basu Kavita Batra Nebiyou Simegnew Bayileyegn Fatemeh Bazvand Addisu Shunu Beyene Awoke Masrie Asrat Derese Devidas S. Bhagat Akshaya Srikanth Bhagavathula Pankaj Bh Medicine & Health University of New South Wales Sydney NSW Australia School of Optometry and Vision Science University of New South Wales Sydney NSW Australia School of Population and Global Health University of Melbourne Carlton VIC Australia Vision and Eye Research Institute Anglia Ruskin University Cambridge UK HelpMeSee Instituto Mexicano de Oftalmologia Santiago de Querétaro Mexico University of Miami Gables FL USA University of Utah Salt Lake City UT USA Chief Medical Office HelpMeSee New York NY USA Mexican Institute of Ophthalmology Queretaro Mexico Department of Ophthalmology Massachusetts Eye and Ear/Shepens Eye Research Institute/Harvard Medical School Boston MA USA Eye Unit MyungSung Christian Medical Center (MCM) Comprehensive Specialized Hospital and MyungSun Medical College Addis Ababa Ethiopia Department of Ophthalmology Addis Ababa University Addis Ababa Ethiopia Sight for Souls Bellevue WA USA Department of Ophthalmology Harvard University Boston MA USA Eye Unit MyungSung Medical College Addis Ababa Ethiopia Addenbrooke’s Hospital Cambridge UK Department of Ophthalmology Cambridge University Hospitals Cambridge UK Federal University of Sao Paolo Sao Paolo SP Brazil University of Calgary Calgary AB Canada Department of Ophthalmology and Visual Sciences Federal University of São Paulo Sao Paulo Brazil School of Medicine Vita-Salute San Raffaele University Milan Italy Department of Ophthalmology IRCCS San Raffaele Scientific Institute Milan Italy Department of Ophthalmology San Raffaele Scientific Institute Milano Italy IRCCS San Raffaele Scientific Institute Vita-Salute University Milan Italy Scientific Institute San Raffaele Hospital Vita-Salute University Milan Italy University of Poitiers Poitiers France CHU de Poitiers Poitiers France Ophthalmology Department CHU de Poitiers (Poitiers University Hospital) Poitiers France Unité 1084 National Institute of Health and Medical Research (INSERM) Poitiers France

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THE ARCTIC

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Bulletin of the American Meteorological Society 2024年第8期105卷 S277-S330页

作者： Druckenmiller, M.L. Thoman, R.L. Moon, T.A. National Snow and Ice Data Center Cooperative Institute for Research in Environmental Sciences University of Colorado Boulder Boulder Colorado International Arctic Research Center University of Alaska Fairbanks Fairbanks Alaska National Snow and Ice Data Center Cooperative Institute for Research in Environmental Sciences University of Colorado Boulder Colorado Section for Glaciers Ice and Snow Norwegian Water Resources and Energy Directorate Oslo Norway School of Informatics Computing and Cyber Systems Northern Arizona University Flagstaff Arizona Biospherical Instruments Inc. San Diego California Geophysical Institute University of Alaska Fairbanks Fairbanks Alaska Plant Soils and Climate Department Utah State University Logan Utah Norwegian Institute for Nature Research Trondheim Norway FRAM – High North Research Centre for Climate and the Environment Tromsø Norway Geological Survey of Denmark and Greenland (GEUS) Copenhagen Denmark NOAA/NWS Alaska Region Anchorage Alaska Alaska Native Tribal Health Consortium Anchorage Alaska Geological Survey of Canada Natural Resources Canada Ottawa Canada NOAA Chemical Sciences Laboratory Boulder Colorado Arctic Geophysics Department University Centre in Svalbard Longyearbyen Norway Geology Department University Centre in Svalbard Longyearben Norway Centre National de Recherches Météorologiques Météo-France/CNRS Toulouse France Climate Research Division Environment and Climate Change Canada Toronto Canada Norwegian Polar Institute Fram Centre Tromsø Norway Danish Meteorological Institute Copenhagen Denmark Department of Physics University of Toronto Toronto Canada Department of Environmental Sciences University of Virginia Charlottesville Virginia Department of Geographical Sciences University of Maryland College Park Maryland University of Liège Liège Belgium Environment and Climate Change Canada Toronto Canada Northern Rocky Mountain Science Center U.S. Geological Survey Bozeman Montana Arctic C

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Reconciling emergences: An information-theoretic approach to identify causal emergence in multivariate data

arXiv

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arXiv 2020年

作者： Rosas, Fernando E. Mediano, Pedro A.M. Jensen, Henrik J. Seth, Anil K. Barrett, Adam B. Carhart-Harris, Robin L. Bor, Daniel Center for Psychedelic Research Department of Brain Science Imperial College London SW7 2DD United Kingdom Data Science Institute Imperial College London LondonSW7 2AZ United Kingdom Center for Complexity Science Imperial College London LondonSW7 2AZ United Kingdom Department of Psychology University of Cambridge CambridgeCB2 3EB United Kingdom Department of Mathematics Imperial College London LondonSW7 2AZ United Kingdom Institute of Innovative Research Tokyo Institute of Technology Yokohama226-8502 Japan Sackler Center for Consciousness Science Department of Informatics University of Sussex BrightonBN1 9RH United Kingdom CIFAR Azrieli Program on Brain Mind and Consciousness TorontoM5G 1M1 Canada Data Intensive Science Centre Department of Physics and Astronomy University of Sussex BrightonBN1 9QH United Kingdom Center for Psychedelic Research Department of Brain Science Imperial College London LondonSW7 2DD United Kingdom

The broad concept of emergence is instrumental in various of the most challenging open scientific questions - yet, few quantitative theories of what constitutes emergent phenomena have been proposed. This article introduces a formal theory of causal emergence in multivariate systems, which studies the relationship between the dynamics of parts of a system and macroscopic features of interest. Our theory provides a quantitative definition of downward causation, and introduces a complementary modality of emergent behaviour - which we refer to as causal decoupling. Moreover, the theory allows practical criteria that can be efficiently calculated in large systems, making our framework applicable in a range of scenarios of practical interest. We illustrate our findings in a number of case studies, including Conway's Game of Life, Reynolds' flocking model, and neural activity as measured by electrocorticography. Copyright © 2020, The Authors. All rights reserved.

关键词： Neurons

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End-to-end symmetry preserving inter-atomic potential energy model for finite and extended systems 32

End-to-end symmetry preserving inter-atomic potential energy...

引用

32nd Conference on Neural Information Processing Systems, NeurIPS 2018

作者： Zhang, Linfeng Han, Jiequn Wang, Han Saidi, Wissam A. Car, Roberto Weinan, E. Program in Applied and Computational Mathematics Princeton University United States Institute of Applied Physics and Computational Mathematics China CAEP Software Center for High Performance Numerical Simulation China Department of Mechanical Engineering and Materials Science University of Pittsburgh United States Department of Chemistry Department of Physics Princeton University United States Princeton Institute for the Science and Technology of Materials Princeton University United States Department of Mathematics Princeton University United States Beijing Institute of Big Data Research China

Machine learning models are changing the paradigm of molecular modeling, which is a fundamental tool for material science, chemistry, and computational biology. Of particular interest is the inter-atomic potential energy surface (PES). Here we develop Deep Potential - Smooth Edition (DeepPot-SE), an end-to-end machine learning-based PES model, which is able to efficiently represent the PES of a wide variety of systems with the accuracy of ab initio quantum mechanics models. By construction, DeepPot-SE is extensive and continuously differentiable, scales linearly with system size, and preserves all the natural symmetries of the system. Further, we show that DeepPot-SE describes finite and extended systems including organic molecules, metals, semiconductors, and insulators with high fidelity. © 2018 Curran Associates Inc..All rights reserved.

关键词： Potential energy

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Search for K: Assessing Five Topic-Modeling Approaches to 120,000 Canadian Articles

Search for K: Assessing Five Topic-Modeling Approaches to 12...

引用

IEEE International Conference on Big data

作者： Qiang Fu Yufan Zhuang Jiaxin Gu Yushu Zhu Huihui Qin Xin Guo Department of Sociology The University of British Columbia Vancouver BC Canada Data Science Institute Columbia University New York NY USA Urban Studies Program and School of Public Policy Simon Fraser University Vancouver BC Canada Department of Applied Mathematics The Hong Kong Polytechnic University Hong Kong China

ISBN: (数字)9781728108582

ISBN: (纸本)9781728108599

Topic modeling has been an important field in natural language processing (NLP) and recently witnessed great methodological advances. Yet, the development of topic modeling is still, if not increasingly, challenged by two critical issues. First, despite intense efforts toward nonparametric/post-training methods, the search for the optimal number of topics K remains a fundamental question in topic modeling and warrants input from domain experts. Second, with the development of more sophisticated models, topic modeling is now ironically been treated as a black box and it becomes increasingly difficult to tell how research findings are informed by data, model specifications, or inference algorithms. Based on about 120,000 newspaper articles retrieved from three major Canadian newspapers (Globe and Mail, Toronto Star, and National Post) since 1977, we employ five methods with different model specifications and inference algorithms (Latent Semantic Analysis, Latent Dirichlet Allocation, Principal Component Analysis, Factor Analysis, Nonnegative Matrix Factorization) to identify discussion topics. The optimal topics are then assessed using three measures: coherence statistics, held-out likelihood (loss), and graph-based dimensionality selection. Mixed findings from this research complement advances in topic modeling and provide insights into the choice of optimal topics in social science research.

关键词： Principal component analysis Covariance matrices data models Matrix decomposition Loading Analytical models Semantics

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Ten quick tips for deep learning in biology

arXiv

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arXiv 2021年

作者： Lee, Benjamin D. Gitter, Anthony Greene, Casey S. Raschka, Sebastian Maguire, Finlay Titus, Alexander J. Kessler, Michael D. Lee, Alexandra J. Chevrette, Marc G. Stewart, Paul Allen Britto-Borges, Thiago Cofer, Evan M. Yu, Kun-Hsing Carmona, Juan Jose Fertig, Elana J. Kalinin, Alexandr A. Signal, Beth Lengerich, Benjamin J. Triche, Timothy J. Boca, Simina M. In-Q-Tel Labs School of Engineering and Applied Sciences Harvard University Department of Genetics Harvard Medical School United States Department of Biostatistics and Medical Informatics University of Wisconsin-Madison MadisonWI United States Morgridge Institute for Research MadisonWI United States Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Biochemistry and Molecular Genetics University of Colorado School of Medicine AuroraCO United States Center for Health AI University of Colorado School of Medicine AuroraCO United States Department of Statistics University of Wisconsin Madison United States Faculty of Computer Science Dalhousie University Canada University of New Hampshire Bioeconomy.XYZ United States Department of Oncology Johns Hopkins University United States Institute for Genome Sciences University of Maryland School of Medicine United States Genomics and Computational Biology Graduate Program University of Pennsylvania United States Department of Systems Pharmacology and Translational Therapeutics University of Pennsylvania United States Wisconsin Institute for Discovery Department of Plant Pathology University of Wisconsin-Madison United States Department of Biostatistics and Bioinformatics Moffitt Cancer Center TampaFL United States Section of Bioinformatics and Systems Cardiology Klaus Tschira Institute for Integrative Computational Cardiology University Hospital Heidelberg Germany University Hospital Heidelberg Germany Lewis-Sigler Institute for Integrative Genomics Princeton University PrincetonNJ United States Graduate Program in Quantitative and Computational Biology Princeton University PrincetonNJ United States Department of Biomedical Informatics Harvard Medical School United States Department of Pathology Brigham and Women's Hospital United States Philips Healthcare CambridgeMA United States Philips Research

Machine learning is a modern approach to problem-solving and task automation. In particular, machine learning is concerned with the development and applications of algorithms that can recognize patterns in data and use them for predictive modeling. Artificial neural networks are a particular class of machine learning algorithms and models that evolved into what is now described as deep learning. Given the computational advances made in the last decade, deep learning can now be applied to massive data sets and in innumerable contexts. Therefore, deep learning has become its own subfield of machine learning. In the context of biological research, it has been increasingly used to derive novel insights from high-dimensional biological data. To make the biological applications of deep learning more accessible to scientists who have some experience with machine learning, we solicited input from a community of researchers with varied biological and deep learning interests. These individuals collaboratively contributed to this manuscript's writing using the GitHub version control platform and the Manubot manuscript generation toolset. The goal was to articulate a practical, accessible, and concise set of guidelines and suggestions to follow when using deep learning. In the course of our discussions, several themes became clear: the importance of understanding and applying machine learning fundamentals as a baseline for utilizing deep learning, the necessity for extensive model comparisons with careful evaluation, and the need for critical thought in interpreting results generated by deep learning, among others. © 2021, CC BY.

关键词： Learning algorithms

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Deep Potential Molecular Dynamics: A Scalable Model with the Accuracy of Quantum Mechanics

引用

Physical Review Letters 2018年第14期120卷 143001-143001页

作者： Linfeng Zhang Jiequn Han Han Wang Roberto Car Weinan E Department of Mathematics and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA and Center for Data Science Beijing International Center for Mathematical Research Peking University Beijing Institute of Big Data Research Beijing 100871 People’s Republic of China

We introduce a scheme for molecular simulations, the deep potential molecular dynamics (DPMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data. The neural network model preserves all the natural symmetries in the problem. It is first-principles based in the sense that there are no ad hoc components aside from the network model. We show that the proposed scheme provides an efficient and accurate protocol in a variety of systems, including bulk materials and molecules. In all these cases, DPMD gives results that are essentially indistinguishable from the original data, at a cost that scales linearly with system size.

关键词： Classical statistical mechanics Density functional theory First-principles calculations Interatomic & molecular potentials Learning Neuronal networks Potential energy surfaces Solid-state chemistry Thermal properties Van der Waals interaction Molecular dynamics

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