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arXiv 2020年

作者： Dodds, Peter Sheridan Minot, Joshua R. Arnold, Michael V. Alshaabi, Thayer Adams, Jane Lydia Dewhurst, David Rushing Gray, Tyler J. Frank, Morgan R. Reagan, Andrew J. Danforth, Christopher M. Computational Story Lab Vermont Complex Systems Center MassMutual Center of Excellence for Complex Systems and Data Science Vermont Advanced Computing Center University of Vermont BurlingtonVT05405 United States Department of Computer Science University of Vermont BurlingtonVT05405 United States Santa Fe Institute 1399 Hyde Park Rd Santa FeNM87501 United States Department of Mathematics & Statistics University of Vermont BurlingtonVT05405 United States Institute for Data Systems and Society Massachusetts Institute of Technology CambridgeMA02139 United States MassMutual Data Science AmherstMA01002 United States Computational Story Lab Vermont Complex Systems Center MassMutual Center of Excellence for Complex Systems and Data Science Vermont Advanced Computing Center University of Vermont BurlingtonVT05405 United States Department of Mathematics & Statistics University of Vermont BurlingtonVT05405 United States

Complex systems often comprise many kinds of components which vary over many orders of magnitude in size: Populations of cities in countries, individual and corporate wealth in economies, species abundance in ecologies, word frequency in natural language, and node degree in complex networks. Here, we introduce ‘allotaxonometry’ along with ‘rank-turbulence divergence’ (RTD), a tunable instrument for comparing any two ranked lists of components. We analytically develop our rank-based divergence in a series of steps, and then establish a rank-based allotaxonograph which pairs a map-like histogram for rank-rank pairs with an ordered list of components according to divergence contribution. We explore the performance of rank-turbulence divergence, which we view as an instrument of ‘type calculus’, for a series of distinct settings including: Language use on Twitter and in books, species abundance, baby name popularity, market capitalization, performance in sports, mortality causes, and job titles. We provide a series of supplementary flipbooks which demonstrate the tunability and storytelling power of rank-based allotaxonometry. Copyright © 2020, The Authors. All rights reserved.

关键词： Turbulence

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DeePMD-kit v2: A software package for Deep Potential models

arXiv

引用

arXiv 2023年

作者： Zeng, Jinzhe Zhang, Duo Lu, Denghui Mo, Pinghui Li, Zeyu Chen, Yixiao Rynik, Marián Huang, Li'ang Li, Ziyao Shi, Shaochen Wang, Yingze Ye, Haotian Tuo, Ping Yang, Jiabin Ding, Ye Li, Yifan Tisi, Davide Zeng, Qiyu Bao, Han Xia, Yu Huang, Jiameng Muraoka, Koki Wang, Yibo Chang, Junhan Yuan, Fengbo Bore, Sigbjørn Løland Cai, Chun Lin, Yinnian Wang, Bo Xu, Jiayan Zhu, Jia-Xin Luo, Chenxing Zhang, Yuzhi Goodall, Rhys E.A. Liang, Wenshuo Singh, Anurag Kumar Yao, Sikai Zhang, Jingchao Wentzcovitch, Renata Han, Jiequn Liu, Jie Jia, Weile York, Darrin M. Weinan, E. Car, Roberto Zhang, Linfeng Wang, Han Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854 United States AI for Science Institute Beijing100080 China DP Technology Beijing100080 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China HEDPS CAPT College of Engineering Peking University Beijing100871 China College of Electrical and Information Engineering Hunan University Changsha China Yuanpei College Peking University Beijing100871 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ08540 United States Department of Experimental Physics Comenius University Mlynská Dolina F2 Bratislava842 48 Slovakia Center for Quantum Information Institute for Interdisciplinary Information Sciences Tsinghua University Beijing100084 China Center for Data Science Peking University Beijing100871 China ByteDance Research Zhonghang Plaza No. 43 North 3rd Ring West Road Haidian District Beijing China College of Chemistry and Molecular Engineering Peking University Beijing100871 China Baidu Inc. Beijing China Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University Zhejiang Hangzhou China Westlake AI Therapeutics Lab Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Hangzhou China Department of Chemistry Princeton University PrincetonNJ08544 United States SISSA Scuola Internazionale Superiore di Studi Avanzati Trieste34136 Italy Laboratory of Computational Science and Modeling Institute of Materials École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Department of Physics National University of Defense Technology Hunan Changsha410073 China State Key Lab of Processors Institute of Computing Technology Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China School of Electronics Engineerin

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, Deep Potential - Range Correction (DPRc), Deep Potential Long Range (DPLR), GPU support for customized operators, model compression, non-von Neumann molecular dynamics (NVNMD), and improved usability, including documentation, compiled binary packages, graphical user interfaces (GUI), and application programming interfaces (API). This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, the article benchmarks the accuracy and efficiency of different models and discusses ongoing developments. © 2023, CC BY-NC-ND.

关键词： Molecular dynamics

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Navigating the challenges in creating complex data systems: a development philosophy

arXiv

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arXiv 2022年

作者： Dittmer, Sören Roberts, Michael Gilbey, Julian Biguri, Ander Preller, Jacobus Rudd, James H.F. Aston, John A.D. Schönlieb, Carola-Bibiane Selby, Ian Breger, Anna Thorpe, Matthew Weir-McCall, Jonathan R. Gkrania-Klotsas, Effrossyni Korhonen, Anna Jefferson, Emily Langs, Georg Yang, Guang Prosch, Helmut Stanczuk, Jan Tang, Jing Babar, Judith Sánchez, Lorena Escudero Teare, Philip Patel, Mishal Wassin, Marcel Holzer, Markus Walton, Nicholas Lió, Pietro Shadbahr, Tolou Sala, Evis Department of Applied Mathematics and Theoretical Physics University of Cambridge Cambridge United Kingdom Addenbrooke’s Hospital Cambridge University Hospitals NHS Trust Cambridge United Kingdom Department of Medicine University of Cambridge Cambridge United Kingdom Department of Pure Mathematics and Mathematical Statistics University of Cambridge Cambridge United Kingdom ZeTeM University of Bremen Bremen Germany Department of Radiology University of Cambridge Cambridge United Kingdom Faculty of Mathematics University of Vienna Austria Department of Mathematics University of Manchester Manchester United Kingdom Royal Papworth Hospital Cambridge Royal Papworth Hospital NHS Foundation Trust Cambridge United Kingdom Language Technology Laboratory University of Cambridge Cambridge United Kingdom Population Health and Genomics School of Medicine University of Dundee Dundee United Kingdom Department of Biomedical Imaging and Image-guided Therapy Computational Imaging Research Lab Medical University of Vienna Vienna Austria National Heart and Lung Institute Imperial College London London United Kingdom Research Program in Systems Oncology Faculty of Medicine University of Helsinki Helsinki Finland Data Science & Artificial Intelligence AstraZeneca Cambridge United Kingdom Clinical Pharmacology & Safety Sciences AstraZeneca Cambridge United Kingdom Contextflow GmbH Vienna Austria Institute of Astronomy University of Cambridge Cambridge United Kingdom Department of Computer Science and Technology University of Cambridge Cambridge United Kingdom

In this perspective, we argue that despite the democratization of powerful tools for data science and machine learning over the last decade, developing the code for a trustworthy and effective data science system (DSS) is getting harder. Perverse incentives and a lack of widespread software engineering (SE) skills are among many root causes we identify that naturally give rise to the current systemic crisis in reproducibility of DSSs. We analyze why SE and building large complex systems is, in general, hard. Based on these insights, we identify how SE addresses those difficulties and how we can apply and generalize SE methods to construct DSSs that are fit for purpose. We advocate two key development philosophies, namely that one should incrementally grow – not biphasically plan and build – DSSs, and one should always employ two types of feedback loops during development: one which tests the code’s correctness and another that evaluates the code’s efficacy. Copyright © 2022, The Authors. All rights reserved.

关键词： Software engineering

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Convex hull algorithms based on some variational models

arXiv

引用

arXiv 2019年

作者： Li, Lingfeng Luo, Shousheng Tai, Xue-Cheng Yang, Jiang Department of Mathematics Hong Kong Baptist University Hong Kong Department of Mathematics Southern University of Science and Technology Shenzhen China Beijing Computational Science Research Center Beijing China School of Mathematics and Statistics Data Analysis Technology Lab Henan University Kaifeng China

Seeking the convex hull of an object is a very fundamental problem arising from various tasks. In this work, we propose two variational convex hull models using level set representation for 2-dimensional data. The first one is an exact model, which can get the convex hull of one or multiple objects. In this model, the convex hull is characterized by the zero sublevel-set of a convex level set function, which is non-positive at every given point. By minimizing the area of the zero sublevel-set, we can find the desired convex hull. The second one is intended to get convex hull of objects with outliers. Instead of requiring all the given points are included, this model penalizes the distance from each given point to the zero sublevel-set. Literature methods are not able to handle outliers. For the solution of these models, we develop efficient numerical schemes using alternating direction method of multipliers. Numerical examples are given to demonstrate the advantages of the proposed methods. Copyright © 2019, The Authors. All rights reserved.

关键词： Numerical methods

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Storywrangler: A massive exploratorium for sociolinguistic, cultural, socioeconomic, and political timelines using Twitter

arXiv

引用

arXiv 2020年

作者： Alshaabi, Thayer Adams, Jane L. Arnold, Michael V. Minot, Joshua R. Dewhurst, David R. Reagan, Andrew J. Danforth, Christopher M. Dodds, Peter Sheridan Vermont Complex Systems Center Computational Story Lab University of Vermont BurlingtonVT05405 United States Department of Computer Science University of Vermont BurlingtonVT05405 United States Charles River Analytics CambridgeMA02138 United States MassMutual Data Science AmherstMA01002 United States Department of Mathematics & Statistics University of Vermont BurlingtonVT05405 United States

In real-time, Twitter strongly imprints world events, popular culture, and the day-to-day, recording an ever growing compendium of language change. Vitally, and absent from many standard corpora such as books and news archives, Twitter also encodes popularity and spreading through retweets. Here, we describe Storywrangler, an ongoing curation of over 100 billion tweets containing 1 trillion 1-grams from 2008 to 2021. For each day, we break tweets into 1-, 2-, and 3-grams across 100+ languages, generating frequencies for words, hashtags, handles, numerals, symbols, and emojis. We make the dataset available through an interactive time series viewer, and as downloadable time series and daily distributions. Although Storywrangler leverages Twitter data, our method of tracking dynamic changes in n-grams can be extended to any temporally evolving corpus. Illustrating the instrument’s potential, we present example use cases including social amplification, the sociotechnical dynamics of famous individuals, box office success, and social unrest. Copyright © 2020, The Authors. All rights reserved.

关键词： Social networking (online)

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Classification of datasets with imputed missing values: does imputation quality matter?

arXiv

引用

arXiv 2022年

作者： Shadbahr, Tolou Roberts, Michael Stanczuk, Jan Gilbey, Julian Teare, Philip Dittmer, Sören Thorpe, Matthew Torné, Ramon Viñas Sala, Evis Lió, Pietro Patel, Mishal Rudd, James H.F. Mirtti, Tuomas Rannikko, Antti Sakari Aston, John A.D. Tang, Jing Schönlieb, Carola-Bibiane Selby, Ian Breger, Anna Weir-McCall, Jonathan R. Gkrania-Klotsas, Effrossyni Korhonen, Anna Jefferson, Emily Langs, Georg Yang, Guang Prosch, Helmut Preller, Jacobus Stanczuk, Jan Babar, Judith Sánchez, Lorena Escudero Wassin, Marcel Holzer, Markus Walton, Nicholas Research Program in Systems Oncology Faculty of Medicine University of Helsinki Helsinki Finland Department of Applied Mathematics and Theoretical Physics University of Cambridge Cambridge United Kingdom Data Science & Artificial Intelligence AstraZeneca Cambridge United Kingdom Department of Mathematics University of Manchester Manchester United Kingdom Department of Computer Science and Technology University of Cambridge Cambridge United Kingdom Department of Radiology University of Cambridge Cambridge United Kingdom Clinical Pharmacology & Safety Sciences AstraZeneca Cambridge United Kingdom Department of Medicine University of Cambridge Cambridge United Kingdom Department of Pathology University of Helsinki Helsinki University Hospital Finland iCAN-Digital Precision Cancer Medicine Flagship Helsinki Finland Department of Urology University of Helsinki Helsinki University Hospital Helsinki Finland Department of Pure Mathematics and Mathematical Statistics University of Cambridge Cambridge United Kingdom ZeTeM University of Bremen Bremen Germany Faculty of Mathematics University of Vienna Austria Royal Papworth Hospital Cambridge Royal Papworth Hospital NHS Foundation Trust Cambridge United Kingdom Addenbrooke’s Hospital Cambridge University Hospitals NHS Trust Cambridge United Kingdom Language Technology Laboratory University of Cambridge Cambridge United Kingdom Population Health and Genomics School of Medicine University of Dundee Dundee United Kingdom Department of Biomedical Imaging and Image-guided Therapy Computational Imaging Research Lab Medical University of Vienna Vienna Austria National Heart and Lung Institute Imperial College London London United Kingdom Contextflow GmbH Vienna Austria Institute of Astronomy University of Cambridge Cambridge United Kingdom

Classifying samples in incomplete datasets is a common aim for machine learning practitioners, but is non-trivial. Missing data is found in most real-world datasets and these missing values are typically imputed using established methods, followed by classification of the now complete, imputed, samples. The focus of the machine learning researcher is then to optimise the downstream classification performance. In this study, we highlight that it is imperative to consider the quality of the imputation. We demonstrate how the commonly used measures for assessing quality are flawed and propose a new class of discrepancy scores which focus on how well the method recreates the overall distribution of the data. To conclude, we highlight the compromised interpretability of classifier models trained using poorly imputed data. All code and data used in this paper are also released publicly at [inserted upon publication]. © 2022, CC BY.

关键词： Classification (of information)

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Probability-turbulence divergence: A tunable allotaxonometric instrument for comparing heavy-tailed categorical distributions

arXiv

引用

arXiv 2020年

作者： Dodds, Peter Sheridan Minot, Joshua R. Arnold, Michael V. Alshaabi, Thayer Adams, Jane Lydia Reagan, Andrew J. Danforth, Christopher M. Computational Story Lab Vermont Complex Systems Center MassMutual Center of Excellence for Complex Systems and Data Science University of Vermont BurlingtonVT05401 United States Vermont Advanced Computing Center University of Vermont BurlingtonVT05401 United States Department of Computer Science University of Vermont BurlingtonVT05401 United States Santa Fe Institute 1399 Hyde Park Rd Santa FeNM87501 United States MassMutual Data Science AmherstMA01002 United States Howard Hughes Medical Institute University of California Berkeley BerkeleyCA94720 United States Data Visualization Lab Khoury College of Computer Sciences Northeastern University BostonMA United States Department of Mathematics & Statistics University of Vermont BurlingtonVT05401 United States

Real-world complex systems often comprise many distinct types of elements as well as many more types of networked interactions between elements. When the relative abundances of types can be measured well, we further observe heavy-tailed categorical distributions for type frequencies. For the comparison of type frequency distributions of two systems or a system with itself at different time points in time—a facet of allotaxonometry—a great range of probability divergences are available. Here, we introduce and explore ‘probability-turbulence divergence’, a tunable, straightforward, and interpretable instrument for comparing normalizable categorical frequency distributions. We model probability-turbulence divergence (PTD) after rank-turbulence divergence (RTD). While probability-turbulence divergence is more limited in application than rank-turbulence divergence, it is more sensitive to changes in type frequency. We build allotaxonographs to display probability turbulence, incorporating a way to visually accommodate zero probabilities for ‘exclusive types’ which are types that appear in only one system. We explore comparisons of example distributions taken from literature, social media, and ecology. We show how probability-turbulence divergence either explicitly or functionally generalizes many existing kinds of distances and measures, including, as special cases, L(p) norms, the Sørensen-Dice coefficient (the F1 statistic), and the Hellinger distance. We discuss similarities with the generalized entropies of Rényi and Tsallis, and the diversity indices (or Hill numbers) from ecology. We close with thoughts on open problems concerning the optimization of the tuning of rank- and probability-turbulence divergence. Copyright © 2020, The Authors. All rights reserved.

关键词： Normal distribution

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data-driven method for 3D axis-symmetric object reconstruction from single cone-beam projection data

arXiv

引用

arXiv 2019年

作者： Luo, Shousheng Meng, Ruyue Wei, Suhua Cai, Jian-Feng Tai, Xue-Cheng Wang, Yang School of Mathematics and Statistics Data Analysis Technology Lab of Henan University Henan University Kaifeng China School of Mathematics and Statistics Henan University Kaifeng China Institute of Applied Physics and Computational Mathematics Beijing China Department of Mathematics Hong Kong University of Science and Technology Hong Kong Department of Mathematics Hong Kong Baptist University Hong Kong

In this paper we consider 3D axis-symmetric (AS) object reconstruction from single cone-beam x-ray projection data. Traditional x-ray CT fails to capture fleeting state of material due to the long time for data acquisition at all angles. Therefore, AS object is devised to investigate the instant deformation of material under pulse change of environment because single projection data is enough to reconstruct its inner structure. Previous reconstruction methods are layer by layer, and ignore the longitudinal tilt of x-ray paths. We propose a regularization method using adaptive tight frame to reconstruct the 3D AS object structure simultaneously. Alternating direction method is adopted to solve the proposed model. More importantly, a numerical algorithm is developed to compute imaging matrix. Experiments on simulation data verify the effectiveness of our method. Copyright © 2019, The Authors. All rights reserved.

关键词： Computerized tomography

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Evolving ab initio trading strategies in heterogeneous environments

arXiv

引用

arXiv 2019年

作者： Dewhurst, David Rushing Li, Yi Bogdan, Alexander Geng, Jasmine MassMutual Center of Excellence in Complex Systems and Data Science University of Vermont BurlingtonVT05405 United States Vermont Complex Systems Center Computational Story Lab Department of Mathematics and Statistics University of Vermont BurlingtonVT05405 United States MassMutual Data Science BostonMA02210 United States

Securities markets are quintessential complex adaptive systems in which heterogeneous agents compete in an attempt to maximize returns. Species of trading agents are also subject to evolutionary pressure as entire classes of strategies become obsolete and new classes emerge. Using an agent-based model of interacting heterogeneous agents as a flexible environment that can endogenously model many diverse market conditions, we subject deep neural networks to evolutionary pressure to create dominant trading agents. After analyzing the performance of these agents and noting the emergence of anomalous superdiffusion through the evolutionary process, we construct a method to turn high-fitness agents into trading algorithms. We backtest these trading algorithms on real high-frequency foreign exchange data, demonstrating that elite trading algorithms are consistently profitable in a variety of market conditions-even though these algorithms had never before been exposed to real financial data. These results provide evidence to suggest that developing ab initio trading strategies by repeated simulation and evolution in a mechanistic market model may be a practical alternative to explicitly training models with past observed market data. Copyright © 2019, The Authors. All rights reserved.

关键词： Autonomous agents

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PLUMED Tutorials: a collaborative, community-driven learning ecosystem

arXiv

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arXiv 2024年

作者： Tribello, Gareth A. Bonomi, Massimiliano Bussi, Giovanni Camilloni, Carlo Armstrong, Blake I. Arsiccio, Andrea Aureli, Simone Ballabio, Federico Bernetti, Mattia Bonati, Luigi Brookes, Samuel G.H. Faidon Brotzakis, Z. Capelli, Riccardo Ceriotti, Michele Chan, Kam-Tung Cossio, Pilar Dasetty, Siva Donadio, Davide Ensing, Bernd Ferguson, Andrew L. Fraux, Guillaume Gale, Julian D. Gervasio, Francesco Luigi Giorgino, Toni Herringer, Nicholas S.M. Hocky, Glen M. Hoff, Samuel E. Invernizzi, Michele Languin-Cattoën, Olivier Leone, Vanessa Limongelli, Vittorio Lopez-Acevedo, Olga Marinelli, Fabrizio Martinez, Pedro Febrer Masetti, Matteo Mehdi, Shams Michaelides, Angelos Murtada, Mhd Hussein Parrinello, Michele Piaggi, Pablo M. Pietropaolo, Adriana Pietrucci, Fabio Pipolo, Silvio Pritchard, Claire Raiteri, Paolo Raniolo, Stefano Rapetti, Daniele Rizzi, Valerio Rydzewski, Jakub Salvalaglio, Matteo Schran, Christoph Seal, Aniruddha Zadeh, Armin Shayesteh Silva, Tomás F.D. Spiwok, Vojtěch Stirnemann, Guillaume Sucerquia, Daniel Tiwary, Pratyush Valsson, Omar Vendruscolo, Michele Voth, Gregory A. White, Andrew D. Wu, Jiangbo Centre for Quantum Materials and Technology School of Mathematics and Physics Queen’s University Belfast United Kingdom Institut Pasteur Université Paris Cité CNRS UMR 3528 Computational Structural Biology Unit Paris France Via Bonomea 265 Trieste34136 Italy Department of Biosciences University of Milano Milano Italy School of Molecular and Life Sciences Curtin University GPO Box U1987 PerthWA6845 Australia Coriolis Pharma Fraunhoferstrasse 18b Martinsried82152 Germany School of Pharmaceutical Sciences University of Geneva Rue Michel-Servet 1 GenevaCH-1206 Switzerland Institute of Pharmaceutical Sciences of Western Switzerland University of Geneva GenevaCH-1206 Switzerland Swiss Bioinformatics Institute University of Geneva GenevaCH-1206 Switzerland Via Celoria 26 Milan20133 Italy Department of Biomolecular Sciences University of Urbino "Carlo Bo" Piazza Rinascimento 6 Urbino61029 Italy Department of Pharmacy and Biotechnology Alma Mater Studiorum University of Bologna Via Belmeloro 6 Bologna40126 Italy Atomistic Simulations Italian Institute of Technology Genova Italy Yusuf Hamied Department of Chemistry University of Cambridge CambridgeCB2 1EW United Kingdom Institute for Bioinnovation Biomedical Sciences Research Center "Alexander Fleming" Vari16672 Greece Laboratory of Computational Science and Modeling Institut des Matériaux École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Department of Chemistry University of California Davis DavisCA95616 United States Center for Computational Mathematics Flatiron Institute New YorkNY10010 United States Center for Computational Biology Flatiron Institute New YorkNY10010 United States Pritzker School of Molecular Engineering University of Chicago ChicagoIL60637 United States AI4Science Lab Informatics Institute University of Amsterdam Science Park 904 Amsterdam1098 XH Netherlands Computational Chemistry Group Van’t Hoff Institute for Molecular Sciences Unive

In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software users presents several challenges. Common methods like direct knowledge transfer and in-person workshops are limited in reach and comprehensiveness. Furthermore, while the COVID-19 pandemic highlighted the benefits of online training, traditional online tutorials can quickly become outdated and may not cover all the software’s functionalities. To address these issues, here we introduce "PLUMED Tutorials", a collaborative model for developing, sharing, and updating online tutorials. This initiative utilizes repository management and continuous integration to ensure compatibility with software updates. Moreover, the tutorials are interconnected to form a structured learning path and are enriched with automatic annotations to provide broader context. This paper illustrates the development, features, and advantages of PLUMED Tutorials, aiming to foster an open community for creating and sharing educational resources. © 2024, CC BY.

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