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Analysis of english free association network reveals mechanisms of efficient solution of remote association tests

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arXiv 2020年

作者： Valba, O.V. Gorsky, A.S. Nechaev, Sergei K. Tamm, M.V. Department of Applied Mathematics MIEM National Research University Higher School of Economics Moscow123458 Russia Kharkevich Institute for Information Transmission Problems RAS Moscow Institute of Physics and Technology Dolgoprudny141700 Russia Interdisciplinary Scientific Center Poncelet CNRS UMI 2615 Moscow119002 Russia P.N. Lebedev Physical Institute RAS Moscow119991 Russia Faculty of Physics Lomonosov Moscow State University Moscow119992 Russia

We study correlations between the structure and properties of a free association network of the English language, and solutions of psycholinguistic Remote Association Tests (RATs). We show that average hardness of individual RATs is largely determined by relative positions of test words (stimuli and response) on the free association network. We argue that the solution of RATs can be interpreted as a first passage search problem on a network whose vertices are words and links are associations between words. We propose different heuristic search algorithms and demonstrate that in"easily-solving" RATs (those that are solved in 15 seconds by more than 64% subjects) the solution is governed by"strong" network links (i.e. strong associations) directly connecting stimuli and response, and thus the efficient strategy consist in activating such strong links. In turn, the most efficient mechanism of solving medium and hard RATs consists of preferentially following sequence of"moderately weak" associations. Copyright © 2020, The Authors. All rights reserved.

关键词： Heuristic algorithms

Phase-field crystal model for heterostructures

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Physical Review B 2019年第16期100卷 165412-165412页

作者： Petri Hirvonen Vili Heinonen Haikuan Dong Zheyong Fan Ken R. Elder Tapio Ala-Nissila QTF Centre of Excellence Department of Applied Physics Aalto University School of Science P.O. Box 11000 FIN-00076 Aalto Espoo Finland Department of Mathematics Massachusetts Institute of Technology 77 Massachusetts Avenue Cambridge Massachusetts 02139-4307 USA School of Mathematics and Physics Bohai University Jinzhou 121000 China Department of Physics Oakland University Rochester Michigan 48309 USA Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences Loughborough University Loughborough Leicestershire LE11 3TU United Kingdom

Atomically thin two-dimensional heterostructures are a promising, novel class of materials with ground-breaking properties. The possibility of choosing many constituent components and their proportions allows optimization of these materials to specific requirements. The wide adaptability comes with a cost of large parameter space making it hard to experimentally test all the possibilities. Instead, efficient computational modeling is needed. However, large range of relevant time and length scales related to physics of polycrystalline materials poses a challenge for computational studies. To this end, we present an efficient and flexible phase-field crystal model to describe the atomic configurations of multiple atomic species and phases coexisting in the same physical domain. We extensively benchmark the model for two-dimensional binary systems in terms of their elastic properties and phase boundary configurations and their energetics. As a concrete example, we demonstrate modeling lateral heterostructures of graphene and hexagonal boron nitride. We consider both idealized bicrystals and large-scale systems with random phase distributions. We find consistent relative elastic moduli and lattice constants, as well as realistic continuous interfaces and faceted crystal shapes. Zigzag-oriented interfaces are observed to display the lowest formation energy.

关键词： Crystal defects Crystal structure Elastic modulus Line defects Microstructure Nanocrystals Polycrystals Graphene Heterostructures Honeycomb lattice Monolayer films Polycrystalline materials Solid-solid interfaces Coarse graining

Nonuniform 3D finite difference elastic wave simulation on staggered grids

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arXiv 2020年

作者： Gao, Longfei Ghattas, Omar Keyes, David Oden Institute for Computational Engineering and Sciences The University of Texas at Austin AustinTX78712 United States Oden Institute for Computational Engineering and Sciences Jackson School of Geosciences Department of Mechanical Engineering The University of Texas at Austin AustinTX78712 United States Applied Mathematics and Computational Science Program Extreme Computing Research Center King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia

We present an approach to simulate the 3D isotropic elastic wave propagation using nonuniform finite difference discretization on staggered grids. Specifically, we consider simulation domains composed of layers of uniform grids with different grid spacings, separated by nonconforming interfaces. We demonstrate that this layer-wise finite difference discretization has the potential to significantly reduce the simulation cost, compared to its fully uniform counterpart. Stability of such a discretization is achieved by using specially designed difference operators, which are variants of the standard difference operators with adaptations near boundaries or interfaces, and penalty terms, which are appended to the discretized wave system to weakly impose boundary or interface conditions. Combined with specially designed interpolation operators, the discretized wave system is shown to preserve the energy conserving property of the continuous elastic wave equation, and a fortiori ensure the stability of the simulation. Numerical examples are presented to demonstrate the efficacy of the proposed simulation approach. © 2020, CC BY.

关键词： Elastic waves

Methodology to construct large realizations of perfectly hyperuniform disordered packings

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Physical Review E 2019年第5期99卷 052141-052141页

作者： Jaeuk Kim Salvatore Torquato Department of Physics Princeton University Princeton New Jersey 08544 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Princeton Institute for the Science and Technology of Materials Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

Disordered hyperuniform packings (or dispersions) are unusual amorphous two-phase materials that are endowed with exotic physical properties. Such hyperuniform systems are characterized by an anomalous suppression of volume-fraction fluctuations at infinitely long-wavelengths, compared to ordinary disordered materials. While there has been growing interest in such singular states of amorphous matter, a major obstacle has been an inability to produce large samples that are perfectly hyperuniform due to practical limitations of conventional numerical and experimental methods. To overcome these limitations, we introduce a general theoretical methodology to construct perfectly hyperuniform packings in d-dimensional Euclidean space Rd. Specifically, beginning with an initial general tessellation of space by disjoint cells that meets a “bounded-cell” condition, hard particles of general shape are placed inside each cell such that the local-cell particle packing fractions are identical to the global packing fraction. We prove that the constructed packings with a polydispersity in size are perfectly hyperuniform in the infinite-sample-size limit, regardless of particle shapes, positions, and numbers per cell. We use this theoretical formulation to devise an efficient and tunable algorithm to generate extremely large realizations of such packings. We employ two distinct initial tessellations: Voronoi as well as sphere tessellations. Beginning with Voronoi tessellations, we show that our algorithm can remarkably convert extremely large nonhyperuniform packings into hyperuniform ones in R2 and R3. Implementing our theoretical methodology on sphere tessellations, we establish the hyperuniformity of the classical Hashin-Shtrikman multiscale coated-spheres structures, which are known to be two-phase media microstructures that possess optimal effective transport and elastic properties. A consequence of our work is a rigorous demonstration that packings that have identical tessella

关键词： Fluctuations & noise

European first-year university students accept evolution but lack substantial knowledge about it: a standardized European cross-country assessment

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Evolution: Education and Outreach 2021年第1期14卷 1-22页

作者： Kuschmierz, Paul Beniermann, Anna Bergmann, Alexander Pinxten, Rianne Aivelo, Tuomas Berniak-Woźny, Justyna Bohlin, Gustav Bugallo-Rodriguez, Anxela Cardia, Pedro Cavadas, Bento Filipe Barreiras Pinto Cebesoy, Umran Betul Cvetković, Dragana D. Demarsy, Emilie Đorđević, Mirko S. Drobniak, Szymon M. Dubchak, Liudmyla Dvořáková, Radka M. Fančovičová, Jana Fortin, Corinne Futo, Momir Geamănă, Nicoleta Adriana Gericke, Niklas Grasso, Donato A. Lendvai, Ádám Z. Mavrikaki, Evangelia Meneganzin, Andra Mogias, Athanasios Möller, Andrea Mota, Paulo G. Naciri, Yamama Németh, Zoltán Ożańska-Ponikwia, Katarzyna Paolucci, Silvia Pap, Péter László Petersson, Maria Pietrzak, Barbara Pievani, Telmo Pobric, Alma Porozovs, Juris Realdon, Giulia Sá-Pinto, Xana Savković, Uroš B. Sicard, Mathieu Sofonea, Mircea T. Sorgo, Andrej Stermin, Alexandru N. Tăușan, Ioan Torkar, Gregor Türkmen, Lütfullah Tutnjević, Slavica Uitto, Anna E. Varga, Mirna Vazquez-Ben, Lucia Venetis, Constantinos Viguera, Enrique Virtbauer, Lisa Christine Vutsova, Albena Yruela, Inmaculada Zandveld, Jelle Graf, Dittmar Institute for Didactics of Biology Justus-Liebig-University Giessen Giessen Germany Institute for Biology Teaching and Learning Research in Biology Education Humboldt-Universität Zu Berlin Berlin Germany Faculty of Life Science Department of Biology University of Leipzig Leipzig Germany Didactica Research Unit Faculty of Social Sciences & Behavioural Ecology & Ecophysiology Group Department of Biology University of Antwerp Antwerp Belgium Organismal and Evolutionary Biology Research Program University of Helsinki Helsinki Finland University of Information Technology and Management in Rzeszów Rzeszów Poland Public & Science (VA) Stockholm Sweden Department of Pedagogy and Didactics University of A Coruña A Coruña Spain Escola Superior de Educação Politécnico do Porto Porto Portugal Department of Science and Mathematics Polytechnic Institute of Santarém/School of Education Santarém Portugal Faculty of Education/Department of Mathematics and Science Education Usak University Uşak Turkey Chair of Genetics and Evolution Faculty of Biology University of Belgrade Belgrade Serbia Department of Botany and Plant Biology University of Geneva Geneva Switzerland Department of Evolutionary Biology Institute for Biological Research “Siniša Stanković” - National Institute of Republic of Serbia University of Belgrade Belgrade Serbia Institute of Environmental Sciences Jagiellonian University Kraków Poland Department of Parliamentarism and Political Management National Academy for Public Administration Under the President of Ukraine Kyiv Ukraine Department of Teaching and Didactics of Biology Charles University Praha Czech Republic Department of Biology Faculty of Education Trnava University Trnava Slovakia Laboratory of Didactic André Revuz University of Paris Paris France Institut Ruđer Bošković/Division of Molecular Biology Zagreb Croatia Department/Research Center in Systems Ecology and Sustainability University of Bucharest Bucharest Romania Department of Envir

Background: Investigations of evolution knowledge and acceptance and their relation are central to evolution education research. Ambiguous results in this field of study demonstrate a variety of measuring issues, for instance differently theorized constructs, or a lack of standardized methods, especially for cross-country comparisons. In particular, meaningful comparisons across European countries, with their varying cultural backgrounds and education systems, are rare, often include only few countries, and lack standardization. To address these deficits, we conducted a standardized European survey, on 9200 first-year university students in 26 European countries utilizing a validated, comprehensive questionnaire, the “Evolution Education Questionnaire”, to assess evolution acceptance and knowledge, as well as influencing factors on evolution acceptance. Results: We found that, despite European countries’ different cultural backgrounds and education systems, European first-year university students generally accept evolution. At the same time, they lack substantial knowledge about it, even if they are enrolled in a biology-related study program. Additionally, we developed a multilevel-model that determines religious faith as the main influencing factor in accepting evolution. According to our model, knowledge about evolution and interest in biological topics also increase acceptance of evolution, but to a much lesser extent than religious faith. The effect of age and sex, as well as the country’s affiliation, students’ denomination, and whether or not a student is enrolled in a biology-related university program, is negligible. Conclusions: Our findings indicate that, despite all their differences, most of the European education systems for upper secondary education lead to acceptance of evolution at least in university students. It appears that, at least in this sample, the differences in knowledge between countries reflect neither the extent to which school curricul

关键词： Acceptance Assessment Attitude Europe Evolution Higher education Knowledge Multilevel modeling Religious faith Socioscientific issues

Rotation in Event Horizon Telescope Movies

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arXiv 2023年

作者： Conroy, Nicholas S. Bauböck, Michi Dhruv, Vedant Lee, Daeyoung Broderick, Avery E. Chan, Chi-Kwan Georgiev, Boris Joshi, Abhishek V. Prather, Ben Gammie, Charles F. Department of Astronomy University of Illinois at Urbana-Champaign 1002 West Green Street UrbanaIL61801 United States Department of Physics University of Illinois at Urbana-Champaign 1110 West Green Street UrbanaIL61801 United States Illinois Center for the Advanced Study of the Universe University of Illinois at Urbana-Champaign 1110 West Green St. UrbanaIL61801 United States Perimeter Institute for Theoretical Physics 31 Caroline Street North WaterlooONN2L 2Y5 Canada Department of Physics and Astronomy University of Waterloo 200 University Avenue West WaterlooONN2L 3G1 Canada Waterloo Centre for Astrophysics University of Waterloo WaterlooONN2L 3G1 Canada Steward Observatory Department of Astronomy University of Arizona 933 N. Cherry Ave. TucsonAZ85721 United States Data Science Institute University of Arizona 1230 N. Cherry Ave. TucsonAZ85721 United States Program in Applied Mathematics University of Arizona 617 N. Santa Rita TucsonAZ85721 United States Los Alamos National Lab Los AlamosNM87545 United States NCSA University of Illinois at Urbana-Champaign 1205 W. Clark St. UrbanaIL61801 United States

The Event Horizon Telescope (EHT) has produced images of M87* and Sagittarius A*, and will soon produce time sequences of images, or movies. In anticipation of this, we describe a technique to measure the rotation rate, or pattern speed Ωp, from movies using an autocorrelation technique. We validate the technique on Gaussian random field models with a known rotation rate and apply it to a library of synthetic images of Sgr A* based on general relativistic magnetohydrodynamics simulations. We predict that EHT movies will have Ωp ≈ 1◦ per GMc−3, which is of order 15% of the Keplerian orbital frequency in the emitting region. We can plausibly attribute the slow rotation seen in our models to the pattern speed of inward-propagating spiral shocks. We also find that Ωp depends strongly on inclination. Application of this technique will enable us to compare future EHT movies with the clockwise rotation of Sgr A* seen in near-infrared flares by GRAVITY. Pattern speed analysis of future EHT observations of M87* and Sgr A* may also provide novel constraints on black hole inclination and spin, as well as an independent measurement of black hole mass. © 2023, CC BY.

关键词： Black holes

Deterministic guarantees for Burer–Monteiro factorizations of smooth semidefinite programs

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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

Deep Generative Models for Fast Photon Shower Simulation in ATLAS

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Computing and Software for Big Science 2024年第1期8卷 1-40页

作者： Aad, G. Abbott, B. Abbott, D.C. Abud, A. Abed Abeling, K. Abhayasinghe, D.K. Abidi, S.H. Aboulhorma, A. Abramowicz, H. Abreu, H. Abulaiti, Y. Hoffman, A. C. Abusleme Acharya, B.S. Achkar, B. Adam, L. Bourdarios, C. Adam Adamczyk, L. Adamek, L. Addepalli, S.V. Adelman, J. Adiguzel, A. Adorni, S. Adye, T. Affolder, A.A. Afik, Y. Agaras, M.N. Agarwala, J. Aggarwal, A. Agheorghiesei, C. Aguilar-Saavedra, J.A. Ahmad, A. Ahmadov, F. Ahmed, W.S. Ai, X. Aielli, G. Aizenberg, I. Akbiyik, M. Åkesson, T.P.A. Akimov, A.V. Khoury, K. Al Alberghi, G.L. Albert, J. Albicocco, P. Verzini, M. J. Alconada Alderweireldt, S. Aleksa, M. Aleksandrov, I.N. Alexa, C. Alexopoulos, T. Alfonsi, A. Alfonsi, F. Alhroob, M. Ali, B. Ali, S. Aliev, M. Alimonti, G. Allaire, C. Allbrooke, B.M.M. Allport, P.P. Aloisio, A. Alonso, F. Alpigiani, C. Camelia, E. Alunno Estevez, M. Alvarez Alviggi, M.G. Coutinho, Y. Amaral Ambler, A. Ambroz, L. Amelung, C. Amidei, D. Santos, S. P. Amor Dos Amoroso, S. Amos, K.R. Amrouche, C.S. Ananiev, V. Anastopoulos, C. Andari, N. Andeen, T. Anders, J.K. Andrean, S.Y. Andreazza, A. Angelidakis, S. Angerami, A. Anisenkov, A.V. Annovi, A. Antel, C. Anthony, M.T. Antipov, E. Antonelli, M. Antrim, D.J.A. Anulli, F. Aoki, M. Pozo, J. A. Aparisi Aparo, M.A. Bella, L. Aperio Appelt, C. Aranzabal, N. Ferraz, V. Araujo Arcangeletti, C. Arce, A.T.H. Arena, E. Arguin, J.-F. Argyropoulos, S. Arling, J.-H. Armbruster, A.J. Arnaez, O. Arnold, H. Tame, Z. P. Arrubarrena Artoni, G. Asada, H. Asai, K. Asai, S. Asbah, N.A. Asimakopoulou, E.M. Assahsah, J. Assamagan, K. Astalos, R. Atkin, R.J. Atkinson, M. Atlay, N.B. Atmani, H. Atmasiddha, P.A. Augsten, K. Auricchio, S. Austrup, V.A. Avner, G. Avolio, G. Ayoub, M.K. Azuelos, G. Babal, D. Bachacou, H. Bachas, K. Bachiu, A. Backman, F. Badea, A. Bagnaia, P. Bahmani, M. Bailey, A.J. Bailey, V.R. Baines, J.T. Bakalis, C. Baker, O.K. Bakker, P.J. Bakos, E. Gupta, D. Bakshi Balaji, S. Balasubramanian, R. Baldin, E.M. Balek, P. Ballabene, E. Balli, F. Baltes, L.M. Balunas, W.K. Balz, J. Banas Department of Physics University of Adelaide Adelaide Australia Department of Physics University of Alberta Edmonton AB Canada Department of Physics Ankara University Ankara Turkey Division of Physics TOBB University of Economics and Technology Ankara Turkey LAPP Université Savoie Mont Blanc CNRS/IN2P3 Annecy France APC Université Paris Cité CNRS/IN2P3 Paris France High Energy Physics Division Argonne National Laboratory Argonne IL United States Department of Physics University of Arizona Tucson AZ United States Department of Physics University of Texas at Arlington Arlington TX United States Physics Department National and Kapodistrian University of Athens Athens Greece Physics Department National Technical University of Athens Zografou Greece Department of Physics University of Texas at Austin Austin TX United States Institute of Physics Azerbaijan Academy of Sciences Baku Azerbaijan Institut de Física d’Altes Energies (IFAE) Barcelona Institute of Science and Technology Barcelona Spain Institute of High Energy Physics Chinese Academy of Sciences Beijing China Physics Department Tsinghua University Beijing China Department of Physics Nanjing University Nanjing China University of Chinese Academy of Science (UCAS) Beijing China Institute of Physics University of Belgrade Belgrade Serbia Department for Physics and Technology University of Bergen Bergen Norway Physics Division Lawrence Berkeley National Laboratory Berkeley CA United States Institut für Physik Humboldt Universität zu Berlin Berlin Germany Albert Einstein Center for Fundamental Physics and Laboratory for High Energy Physics University of Bern Bern Switzerland School of Physics and Astronomy University of Birmingham Birmingham United Kingdom Department of Physics Bogazici University Istanbul Turkey Department of Physics Engineering Gaziantep University Gaziantep Turkey Department of Physics Istanbul University Istanbul Turkey Istinye University Sariyer Istanbul

The need for large-scale production of highly accurate simulated event samples for the extensive physics programme of the ATLAS experiment at the Large Hadron Collider motivates the development of new simulation techniques. Building on the recent success of deep learning algorithms, variational autoencoders and generative adversarial networks are investigated for modelling the response of the central region of the ATLAS electromagnetic calorimeter to photons of various energies. The properties of synthesised showers are compared with showers from a full detector simulation using geant4. Both variational autoencoders and generative adversarial networks are capable of quickly simulating electromagnetic showers with correct total energies and stochasticity, though the modelling of some shower shape distributions requires more refinement. This feasibility study demonstrates the potential of using such algorithms for ATLAS fast calorimeter simulation in the future and shows a possible way to complement current simulation techniques. © The Author(s) 2024.

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Interpretable network propagation with application to expanding the repertoire of human proteins that interact with SARS-CoV-2

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arXiv 2020年

作者： Law, Jeffrey N. Akers, Kyle Tasnina, Nure Della Santina, Catherine M. Deutsch, Shay Kshirsagar, Meghana Klein-Seetharaman, Judith Crovella, Mark Rajagopalan, Padmavathy Kasif, Simon Murali, T.M. Interdisciplinary Ph.D. Program in Genetics Bioinformatics and Computational Biology BlacksburgVA United States Department of Computer Science Virginia Tech BlacksburgVA United States Department of Biomedical Engineering Boston University BostonMA United States Department of Mathematics University of California Los AngelesCA United States AI for Good Lab Microsoft RedmondWA United States Department of Chemistry Colorado School of Mines GoldenCO United States Department of Computer Science Boston University BostonMA United States Department of Chemical Engineering Virginia Tech BlacksburgVA United States

Background: Network propagation has been widely used for nearly 20 years to predict gene functions and phenotypes. Despite the popularity of this approach, little attention has been paid to the question of provenance tracing in this context, e.g., determining how much any experimental observation in the input contributes to the score of every prediction. Results: We design a network propagation framework with two novel components and apply it to predict human proteins that directly or indirectly interact with SARS-CoV-2 proteins. First, we trace the provenance of each prediction to its experimentally validated sources, which in our case are human proteins experimentally determined to interact with viral proteins. Second, we design a technique that helps to reduce the manual adjustment of parameters by users. We find that for every top-ranking prediction, the highest contribution to its score arises from a direct neighbor in a human protein-protein interaction network. We further analyze these results to develop functional insights on SARS-CoV-2 that expand on known biology such as the connection between endoplasmic reticulum stress, HSPA5, and anti-clotting agents. Conclusions: We examine how our provenance tracing method can be generalized to a broad class of network-based algorithms. We provide a useful resource for the SARS-CoV-2 community that implicates many previously undocumented proteins with putative functional relationships to viral infection. This resource includes potential drugs that can be opportunistically repositioned to target these proteins. We also discuss how our overall framework can be extended to other, newly-emerging viruses. © 2020, CC BY-NC-SA.

关键词： SARS