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computational intelligence, cyber security and computational models: Proceedings of ICC3 2015

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International Conference on computational Intelligence, Cyber Security and computational Models, ICC3 2015

作者： Senthilkumar, Muthukrishnan Ramasamy, Vijayalakshmi Sheen, Shina Veeramani, C. Bonato, Anthony Batten, Lynn Applied Mathematics and Computational Sciences PSG College of Technology Coimbatore Tamil Nadu India Department of Mathematics Ryerson University TorontoON Canada School of Information Technology Deakin University Melbourne Australia

computational Intelligence, Cyber Security and computational Models 1

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丛书名： Advances in Intelligent Systems and Computing

2016年

作者： Muthukrishnan Senthilkumar Vijayalakshmi Ramasamy Shina Sheen C. Veeramani Anthony Bonato Lynn Batten

PairClone: A Bayesian subclone caller based on mutation Pairs

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arXiv 2017年

作者： Zhou, Tianjian Müller, Peter Sengupta, Subhajit Ji, Yuan Department of Statistics and Data Sciences University of Texas Austin United States Department of Mathematics University of Texas Austin United States Program for Computational Genomics and Medicine NorthShore University HealthSystem Department of Public Health Sciences University of Chicago

Tumor cell populations can be thought of as being composed of homogeneous cell subpopulations, with each subpopulation being characterized by overlapping sets of single nucleotide variants (SNVs). Such subpopulations are known as subclones and are an important target for precision medicine. Reconstructing such subclones from next-generation sequencing (NGS) data is one of the major challenges in precision medicine. We present PairClone as a new tool to implement this reconstruction. The main idea of PairClone is to model short reads mapped to pairs of proximal SNVs. In contrast, most existing methods use only marginal reads for unpaired SNVs. Using Bayesian nonparametric models, we estimate posterior probabilities of the number, genotypes and population frequencies of subclones in one or more tumor sample. We use the categorical Indian buffet process (cIBP) as a prior probability model for subclones that are represented as vectors of categorical matrices that record the corresponding sets of mutation pairs. Performance of PairClone is assessed using simulated and real datasets. An open source software package can be obtained at http://***/pairclone. Copyright © 2017, The Authors. All rights reserved.

关键词： Matrix algebra

Molecular dynamics simulation of strong shock waves propagating in dense deuterium, taking into consideration effects of excited electrons

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Physical Review E 2017年第2期95卷 023201-023201页

作者： Hao Liu Yin Zhang Wei Kang Ping Zhang Huiling Duan X. T. He HEDPS Center for Applied Physics and Technology College of Engineering Peking University Beijing 100871 China Department of Mechanics and Engineering Science College of Engineering Peking University Beijing 100871 China Collaborative Innovation Center of IFSA (CICIFSA) Shanghai Jiao Tong University Shanghai 200240 China Institute of Applied Physics and Computational Mathematics Beijing 100088 China

We present a molecular dynamics simulation of shock waves propagating in dense deuterium with the electron force field method [J. T. Su and W. A. Goddard, Phys. Rev. Lett. 99, 185003 (2007)], which explicitly takes the excitation of electrons into consideration. Nonequilibrium features associated with the excitation of electrons are systematically investigated. We show that chemical bonds in D2 molecules lead to a more complicated shock wave structure near the shock front, compared with the results of classical molecular dynamics simulation. Charge separation can bring about accumulation of net charges on large scales, instead of the formation of a localized dipole layer, which might cause extra energy for the shock wave to propagate. In addition, the simulations also display that molecular dissociation at the shock front is the major factor that accounts for the “bump” structure in the principal Hugoniot. These results could help to build a more realistic picture of shock wave propagation in fuel materials commonly used in the inertial confinement fusion.

关键词： Shock waves Shock waves & discontinuities in plasma Inertially confined plasmas Molecular dynamics

Correction to: Constraint-based causal discovery with mixed data

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International Journal of Data Science and Analytics 2018年第1期6卷 31-31页

作者： Michail Tsagris Giorgos Borboudakis Vincenzo Lagani Ioannis Tsamardinos Department of Computer Science University of Crete Heraklion Greece Gnosis Data Analysis (Gnosis DA) University of Crete Heraklion Greece Institute of Applied and Computational Mathematics Foundation for Research and Technology Hellas Greece

The article “Constraint-based causal discovery with mixed data,” written by Michail Tsagris, Giorgos Borboudakis, Vincenzo Lagani, and Ioannis Tsamardinos, was originally published electronically on the publisher’s...

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Symmetrized importance samplers for stochastic differential equations

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arXiv 2017年

作者： Leach, Andrew Lin, Kevin K. Morzfeld, Matthias Program in Applied Mathematics University of Arizona 617 N. Santa Rita Ave. TucsonAZ85721 United States Department of Mathematics University of Arizona 617 N. Santa Rita Ave. TucsonAZ85721 United States

We study a class of importance sampling methods for stochastic differential equations (SDEs). A small-noise analysis is performed, and the results suggest that a simple symmetrization procedure can significantly improve the performance of our importance sampling schemes when the noise is not too large. We demonstrate that this is indeed the case for a number of linear and nonlinear examples. Potential applications, e.g., data assimilation, are discussed. Copyright © 2017, The Authors. All rights reserved.

关键词： Importance sampling

Snowmass 2021 CMB-S4 White Paper

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arXiv 2022年

作者： Abazajian, Kevork Abdulghafour, Arwa Addison, Graeme E. Adshead, Peter Ahmed, Zeeshan Ajello, Marco Akerib, Daniel Allen, Steven W. Alonso, David Alvarez, Marcelo Amin, Mustafa A. Amiri, Mandana Anderson, Adam Ansarinejad, Behzad Archipley, Melanie Arnold, Kam S. Ashby, Matt Aung, Han Baccigalupi, Carlo Baker, Carina Bakshi, Abhishek Bard, Debbie Barkats, Denis Barron, Darcy Barry, Peter S. Bartlett, James G. Barton, Paul Thakur, Ritoban Basu Battaglia, Nicholas Beall, Jim Bean, Rachel Beck, Dominic Belkner, Sebastian Benabed, Karim Bender, Amy N. Benson, Bradford A. Besuner, Bobby Bethermin, Matthieu Bhimani, Sanah Bianchini, Federico Biquard, Simon Birdwell, Ian Bischoff, Colin A. Bleem, Lindsey Bocaz, Paulina Bock, James J. Bocquet, Sebastian Boddy, Kimberly K. Richard Bond, J. Borrill, Julian Bouchet, François R. Brinckmann, Thejs Brown, Michael L. Bryan, Sean Buza, Victor Byrum, Karen Calabrese, Erminia Calafut, Victoria Caldwell, Robert Carlstrom, John E. Carron, Julien Cecil, Thomas Challinor, Anthony Chan, Victor Chang, Clarence L. Chapman, Scott Charles, Eric Chauvin, Eric Cheng, Cheng Chesmore, Grace Cheung, Kolen Chinone, Yuji Chluba, Jens Cho, Hsiao-Mei Sherry Choi, Steve Clancy, Justin Clark, Susan Cooray, Asantha Coppi, Gabriele Corlett, John Coulton, Will Crawford, Thomas M. Crites, Abigail Cukierman, Ari Cyr-Racine, Francis-Yan Dai, Wei-Ming Daley, Cail Dart, Eli Daues, Gregorg de Haan, Tijmen Deaconu, Cosmin Delabrouille, Jacques Derylo, Greg Devlin, Mark Di Valentino, Eleonora Dierickx, Marion Dober, Brad Doriese, Randy Duff, Shannon Dutcher, Daniel Dvorkin, Cora Dünner, Rolando Eftekhari, Tarraneh Eimer, Joseph El Bouhargani, Hamza Elleflot, Tucker Emerson, Nick Errard, Josquin Essinger-Hileman, Thomas Fabbian, Giulio Fanfani, Valentina Fasano, Alessandro Feng, Chang Ferraro, Simone Filippini, Jeffrey P. Flauger, Raphael Flaugher, Brenna Fraisse, Aurelien A. Frisch, Josef Frolov, Andrei Galitzki, Nicholas Gallardo, Patricio A. Galli, Silvia Ganga, Ken Gerbino, Martina Giannakopoulos, Christos G University of California IrvineCA92697 United States School of Physics The University of Melbourne ParkvilleVIC3010 Australia Johns Hopkins University BaltimoreMD21218 United States Illinois Center for Advanced Studies of the Universe Department of Physics University of Illinois at Urbana-Champaign UrbanaIL61801 United States SLAC National Accelerator Laboratory Menlo ParkCA94025 United States Clemson University ClemsonSC29634 United States Stanford University StanfordCA94305 United States University of Oxford OxfordOX1 3RH United Kingdom University of California BerkeleyCA94720 United States Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Department of Physics & Astronomy Rice University HoustonTX77005 United States University of British Columbia VancouverBCV6T 1Z1 Canada Fermi National Accelerator Laboratory BataviaIL60510 United States University of California La Jolla San DiegoCA92093 United States Harvard-Smithsonian Center for Astrophysics CambridgeMA02138 United States Department of Physics Yale University New HavenCT06520 United States SISSA International School for Advanced Studies Via Bonomea 265 Trieste34136 Italy IFPU - Institute for Fundamental Physics of the Universe Via Beirut 2 Trieste34014 Italy Department of Physics Harvard University CambridgeMA02138 United States Department of Physics and Astronomy University of New Mexico AlbuquerqueNM87131 United States Argonne National Laboratory LemontIL60439 United States School of Physics and Astronomy Cardiff University The Parade CardiffCF24 3AA United Kingdom CNRS IN2P3 Université Paris Diderot Paris Cedex 1375205 France California Institute of Technology PasadenaCA91125 United States Cornell University IthacaNY14853 United States National Institute of Standards and Technology Boulder CO80305 United States Département de Physique Théorique et CAP Université de Genève Genève 4CH-1211 Switzerland CNRS Sorbonne Un

The science case for CMB-S4 remains as exciting as ever, as evidenced by DOE CD-0 "Mission Need" approval and by the strong endorsement by the 2020 Decadal Survey of Astronomy and Astrophysics. In fact, the science case has become stronger as scientists spanning the particle physics and cosmology communities have explored the potential of the transformational measurements CMB-S4 will make to achieve its threshold-crossing science goals. The technology is well understood and field tested. The CMB-S4 Collaboration and Integrated Project Office are established and highly functioning. The project is well developed, has been extensively reviewed, and is on path to achieve DOE CD-1 and NSF PDR on the timescale of a year, depending on funding. © 2022, CC BY.

关键词： Astrophysics

On trees, tanglegrams, and tangled chains 28

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On trees, tanglegrams, and tangled chains

28th International Conference on Formal Power Series and Algebraic Combinatorics, FPSAC 2016

作者： Billey, Sara C. Konvalinka, Matjaž Matsen, Frederick A. Department of Mathematics University of Washington SeattleWA98195 United States Department of Mathematics University of Ljubljana & Institute for Mathematics Physics and Mechanics Ljubljana Slovenia Computational Biology Program Fred Hutchinson Cancer Research Center SeattleWA98109 United States

Tanglegrams are a class of graphs arising in computer science and in biological research on cospeciation and coevolution. They are formed by identifying the leaves of two rooted binary trees. The embedding of the trees in the plane is irrelevant for this application. We give an explicit formula to count the number of distinct binary rooted tanglegrams with n matched leaves, along with a simple asymptotic formula and an algorithm for choosing a tanglegram uniformly at random. The enumeration formula is then extended to count the number of tangled chains of binary trees of any length. This work gives a new formula for the number of binary trees with n leaves. Several open problems and conjectures are included along with pointers to several followup articles that have already appeared. © 2016 Discrete mathematics and Theoretical Computer Science (DMTCS), Nancy, France to reconstruct the historical associations between the phylogenies of host and parasite under a model of parasites switching hosts, which is an instance of the more general problem of cophylogeny estimation.

关键词： Binary trees

Millimeter light curves of Sagittarius A∗ observed during the 2017 Event Horizon Telescope campaign

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arXiv 2022年

作者： Wielgus, Maciek Marchili, Nicola Martí-Vidal, Iván Keating, Garrett K. Ramakrishnan, Venkatessh Tiede, Paul Fomalont, Ed Issaoun, Sara Neilsen, Joey Nowak, Michael A. Blackburn, Lindy Gammie, Charles F. Goddi, Ciriaco Haggard, Daryl Lee, Daeyoung Moscibrodzka, Monika Tetarenko, Alexandra J. Bower, Geoffrey C. Chan, Chi-Kwan Chatterjee, Koushik Chesler, Paul M. Dexter, Jason Doeleman, Sheperd S. Georgiev, Boris Gurwell, Mark Johnson, Michael D. Marrone, Daniel P. Mus, Alejandro Psaltis, Dimitrios Ripperda, Bart Witzel, Gunther Akiyama, Kazunori Alberdi, Antxon Alef, Walter Algaba, Juan Carlos Anantua, Richard Asada, Keiichi Azulay, Rebecca Bach, Uwe Baczko, Anne-Kathrin Ball, David Baloković, Mislav Barrett, John Bauböck, Michi Benson, Bradford A. Bintley, Dan Blundell, Raymond Boland, Wilfred Bouman, Katherine L. Boyce, Hope Bremer, Michael Brinkerink, Christiaan D. Brissenden, Roger Britzen, Silke Broderick, Avery E. Broguiere, Dominique Bronzwaer, Thomas Bustamante, Sandra Byun, Do-Young Carlstrom, John E. Ceccobello, Chiara Chael, Andrew Chatterjee, Shami Chen, Ming-Tang Chen, Yongjun Cho, Ilje Christian, Pierre Conroy, Nicholas S. Conway, John E. Cordes, James M. Crawford, Thomas M. Crew, Geoffrey B. Cruz-Osorio, Alejandro Cui, Yuzhu Davelaar, Jordy de Laurentis, Mariafelicia Deane, Roger Dempsey, Jessica Desvignes, Gregory Dhruv, Vedant Dzib, Sergio A. Eatough, Ralph P. Emami, Razieh Falcke, Heino Farah, Joseph Fish, Vincent L. Alyson Ford, H. Fraga-Encinas, Raquel Freeman, William T. Friberg, Per Fromm, Christian M. Fuentes, Antonio Galison, Peter García, Roberto Gentaz, Olivier Gold, Roman Gómez-Ruiz, Arturo I. Gómez, José L. Gu, Minfeng Hada, Kazuhiro Haworth, Kari Hecht, Michael H. Hesper, Ronald Ho, Luis C. Ho, Paul Honma, Mareki Huang, Chih-Wei L. Huang, Lei Hughes, David H. Ikeda, Shiro Violette Impellizzeri, C.M. Inoue, Makoto James, David J. Jannuzi, Buell T. Janssen, Michael Jeter, Britton Jiang, Wu Jiménez-Rosales, Alejandra Jorstad, Svetlana Joshi, Abhishek V. Jung, Taehyun Karami, Mansour Karupp Max-Planck-Institut für Radioastronomie Auf dem Hügel 69 BonnD-53121 Germany Italian ALMA Regional Centre INAF-Istituto di Radioastronomia Via P. Gobetti 101 BolognaI-40129 Italy Departament d’Astronomia i Astrofísica Universitat de València C. Dr. Moliner 50 Burjassot ValènciaE-46100 Spain Observatori Astronòmic Universitat de València C. Catedrático José Beltrán 2 Paterna ValenciaE-46980 Spain Center for Astrophysics Harvard & Smithsonian 60 Garden Street CambridgeMA02138 United States Astronomy Department Universidad de Concepción Casilla 160-C Concepción Chile Finnish Centre for Astronomy with ESO University of Turku FI-20014 Finland Aalto University Metsähovi Radio Observatory Metsähovintie 114 KylmäläFI-02540 Finland Harvard University 20 Garden Street CambridgeMA02138 United States National Radio Astronomy Observatory 520 Edgemont Road CharlottesvilleVA22903 United States NASA Hubble Fellowship Program Einstein Fellow United States Villanova University Mendel Science Center Rm. 263B 800 E Lancaster Ave VillanovaPA19085 United States Physics Department Washington University CB 1105 St LouisMO63130 United States Department of Physics University of Illinois 1110 West Green Street UrbanaIL61801 United States Department of Astronomy University of Illinois at Urbana-Champaign 1002 West Green Street UrbanaIL61801 United States Dipartimento di Fisica Università degli Studi di Cagliari SP Monserrato-Sestu km 0.7 MonserratoI-09042 Italy INAF - Osservatorio Astronomico di Cagliari Via della Scienza 5 CA Selargius09047 Italy Department of Physics McGill University 3600 rue University MontréalQCH3A 2T8 Canada McGill Space Institute McGill University 3550 rue University MontréalQCH3A 2A7 Canada Radboud University P.O. Box 9010 Nijmegen6500 GL Netherlands Department of Physics and Astronomy Texas Tech University LubbockTX79409-1051 United States Institute of Astronomy and Astrophysics Academia Sinica 645 N. A’oho

The Event Horizon Telescope (EHT) observed the compact radio source, Sagittarius A∗ (Sgr A∗), in the Galactic Center on 2017 April 5-11 in the 1.3 millimeter wavelength band. At the same time, interferometric array data from the Atacama Large Millimeter/submillimeter Array and the Submillimeter Array were collected, providing Sgr A∗ light curves simultaneous with the EHT observations. These data sets, complementing the EHT very-long-baseline interferometry, are characterized by a cadence and signal-to-noise ratio previously unattainable for Sgr A∗ at millimeter wavelengths, and they allow for the investigation of source variability on timescales as short as a minute. While most of the light curves correspond to a low variability state of Sgr A∗, the April 11 observations follow an X-ray flare, and exhibit strongly enhanced variability. All of the light curves are consistent with a red noise process, with a power spectral density (PSD) slope measured to be between -2 and -3 on timescales between 1 min and several hours. Our results indicate a steepening of the PSD slope for timescales shorter than 0.3 h. The spectral energy distribution is flat at 220 GHz and there are no time-lags between the 213 and 229 GHz frequency bands, suggesting low optical depth for the event horizon scale source. We characterize Sgr A∗’s variability, highlighting the different behavior observed just after the X-ray flare, and use Gaussian process modeling to extract a decorrelation timescale and a PSD slope. We also investigate the systematic calibration uncertainties by analyzing data from independent data reduction pipelines. © 2022, CC BY.

关键词： Signal to noise ratio