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International Conference on High Performance Computing

作者： Sriram P. Chockalingam Maneesha Aluru Srinivas Aluru Dept. of Computer Science and Engineering Indian Institute of Technology Mumbai India School of Biology Georgia Institute of Technology Atlanta USA School of Computational Science and Engineering Georgia Institute of Technology Atlanta USA

ISBN: (纸本)9781467384872

Reverse-engineering genome-scale gene networks from gene expression data is a principal challenge in systems biology. Mutual information (MI) based methods are favored because of their ability to recover non-linear relationships, low algorithmic complexity, and their successful use in various biological applications such as gene function prediction. In this paper, we present the first ever construction of MI based genome-scale gene networks using MapReduce. We develop the solution for all the stages of a MI-based network construction algorithm using only the map and reduce operations on distributed datasets. Our solution is implemented using Spark, a software that provides a compute and memory abstraction for distributed datasets. We deploy our solution using on-demand virtual instances on Amazon EC2 cloud computing platform, thus demonstrating the use of a rent-by-the-hour ad-hoc cluster for this grand challenge problem in systems biology. Our implementation can scale with the number of virtual instances, and can be used to construct networks of sizes in the range of 2000 to 5000 genes within an hour in a cost effective manner. We demonstrate the capability to construct genome-scale networks by reverse engineering a network of over 17,000 genes for the widely studied model plant Arabidopsis Thaliana.

关键词： Correlation Genomics Bioinformatics Bayes methods Gene expression Complexity theory Random variables

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A multi-fidelity, multi-disciplinary analysis and optimization framework for the design of morphing UAV wings 16th

A multi-fidelity, multi-disciplinary analysis and optimizati...

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16th AIAA/ISSMO Multidisciplinary Analysis and Optimization Conference, 2015

作者： Ciarella, Andrea Tsotskas, Christos Hahn, Marco Werter, Noud P. M. De Breuker, Roeland Beaverstock, Chris S. Friswell, Michael I. Yang, Yosheph Özgen, Serkan Antoniadis, Antonios Tsoutsanis, Panagiotis Drikakis, Dimitris Aircraft Research Association Ltd. Computational Aerodynamics BedfordMK41 7PF United Kingdom Delft University of Technology Aerospace Structures and Computational Mechanics Delft2629 HS Netherlands Swansea University School of Engineering Wales SwanseaSA2 8PP United Kingdom Middle East Technical University Dept. Of Aerospace Engineering Dumlupinar Bulvari Ankara06800 Turkey Institute of Aerospace Sciences Cranfield University Department of Fluid Mechanics and Computational Science Cranfield BedfordshireMK43 0AL United Kingdom Head of Division - Engineering Sciences Department of Fluid Mechanics and Computational Science Institute of Aerospace Sciences Cranfield University Cranfield BedfordshireMK43 0AL United Kingdom

ISBN: (纸本)9781624103681

A framework for the design and optimization of a morphing wing is presented. It allows the user to simplify the design process of a morphing UAV wing with a simple and effective interface with the possibility to easily switch between flight phases and morphing concepts. It consists of two main solvers: a high-fidelity CFD module for detailed RANS simulation and a fast low-fidelity module that solves the aeroelastic problem by coupling a geometrically nonlinear structural model to a potential flow aerodynamic model. The structure of the framework and the methodology used for the design of a morphing UAV wing are detailed. This wing is the focus of the European FP7 CHANGE project and serves as an example of the application of this methodology. © 2015 American Institute of Aeronautics and Astronautics Inc, AIAA. All rights reserved.

关键词： Unmanned aerial vehicles (UAV)

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Boosting classification accuracy of diffusion MRI derived brain networks for the subtypes of mild cognitive impairment using higher order singular value decomposition

Boosting classification accuracy of diffusion MRI derived br...

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IEEE International Symposium on Biomedical Imaging

作者： L. Zhan Y. Liu J. Zhou J. Ye P.M. Thompson Dept. of Neurology University of California Los Angeles CA USA Imaging Genetics Center Keck School of Medicine University of Southern California CA USA Dept. of Computer Science and Engineering Arizona State University Tempe AZ 85287 USA Dept. of Electrical Engineering and Computer Science University of Michigan Ann Arbor MI USA Dept. of Computational Medicine and Bioinformatics

Mild cognitive impairment (MCI) is an intermediate stage between normal aging and Alzheimer's disease (AD), and around 10-15% of people with MCI develop AD each year. More recently, MCI has been further subdivided into early and late stages, and there is interest in identifying sensitive brain imaging biomarkers that help to differentiate stages of MCI. Here, we focused on anatomical brain networks computed from diffusion MRI and proposed a new feature extraction and classification framework based on higher order singular value decomposition and sparse logistic regression. In tests on publicly available data from the Alzheimer's Disease Neuroimaging Initiative, our proposed framework showed promise in detecting brain network differences that help in classifying early versus late MCI.

关键词： Tensile stress Feature extraction Sparse matrices Magnetic resonance imaging Optical fiber networks Diseases Logistics

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The Atacama Cosmology Telescope: A measurement of the cosmic microwave background power spectra at 98 and 150 GHZ

arXiv

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arXiv 2020年

作者： Choi, Steve K. Hasselfield, Matthew Ho, Shuay-Pwu Patty Koopman, Brian Lungu, Marius Abitbol, Maximilian H. Addison, Graeme E. Ade, Peter A.R. Aiola, Simone Alonso, David Amiri, Mandana Amodeo, Stefania Angile, Elio Austermann, Jason E. Baildon, Taylor Battaglia, Nick Beall, James A. Bean, Rachel Becker, Daniel T. Bond, J. Richard Bruno, Sarah Marie Calabrese, Erminia Calafut, Victoria Campusano, Luis E. Carrero, Felipe Chesmore, Grace E. Cho, Hsiao-Mei Clark, Susan E. Cothard, Nicholas F. Crichton, Devin Crowley, Kevin T. Darwish, Omar Datta, Rahul Denison, Edward V. Devlin, Mark J. Duell, Cody J. Duff, Shannon M. Duivenvoorden, Adriaan J. Dunkley, Jo Dünner, Rolando Essinger-Hileman, Thomas Fankhanel, Max Ferraro, Simone Fox, Anna E. Fuzia, Brittany Gallardo, Patricio A. Gluscevic, Vera Golec, Joseph E. Grace, Emily Gralla, Megan Guan, Yilun Hall, Kirsten Halpern, Mark Han, Dongwon Hargrave, Peter Henderson, Shawn Hensley, Brandon Hill, J. Colin Hilton, Gene C. Hilton, Matt Hincks, Adam D. Hložek, Renée Hubmayr, Johannes Huffenberger, Kevin M. Hughes, John P. Infante, Leopoldo Irwin, Kent Jackson, Rebecca Klein, Jeff Knowles, Kenda Kosowsky, Arthur Lakey, Victoria Li, Dale Li, Yaqiong Li, Zack Lokken, Martine Louis, Thibaut MacInnis, Amanda Madhavacheril, Mathew Maldonado, Felipe Mallaby-Kay, Maya Marsden, Danica Maurin, Loïc McMahon, Jeff Menanteau, Felipe Moodley, Kavilan Morton, Tim Naess, Sigurd Namikawa, Toshiya Nati, Federico Newburgh, Laura Nibarger, John P. Nicola, Andrina Niemack, Michael D. Nolta, Michael R. Orlowski-Sherer, John Page, Lyman A. Pappas, Christine G. Partridge, Bruce Phakathi, Phumlani Prince, Heather Puddu, Roberto Qu, Frank J. Rivera, Jesus Robertson, Naomi Rojas, Felipe Salatino, Maria Schaan, Emmanuel Schillaci, Alessandro Schmitt, Benjamin L. Sehgal, Neelima Sherwin, Blake D. Sierra, Carlos Sievers, Jon Sifon, Cristobal Sikhosana, Precious Simon, Sara Spergel, David N. Staggs, Suzanne T. Stevens, Jason Storer, Emilie Sunder, Dhaneshwar D. Switzer, Eric R. Thorne, Ben Thornton, Robe Department of Physics Cornell University IthacaNY14853 United States Department of Astronomy Cornell University IthacaNY14853 United States Joseph Henry Laboratories of Physics Jadwin Hall Princeton University PrincetonNJ08544 United States Center for Computational Astrophysics Flatiron Institute 162 5th Avenue New YorkNY10010 United States Department of Astronomy and Astrophysics The Pennsylvania State University University ParkPA16802 United States Institute for Gravitation and the Cosmos The Pennsylvania State University University ParkPA16802 United States Department of Physics Yale University 217 Prospect St New HavenCT06511 United States Department of Physics and Astronomy University of Pennsylvania 209 South 33rd Street PhiladelphiaPA19104 United States Department of Physics University of Oxford Keble Road OxfordOX1 3RH United Kingdom Dept. of Physics and Astronomy The Johns Hopkins University 3400 N. Charles St. BaltimoreMD21218-2686 United States School of Physics and Astronomy Cardiff University The Parade Wales CardiffCF24 3AA United Kingdom Department of Physics and Astronomy University of British Columbia VancouverBCV6T 1Z4 Canada NIST Quantum Devices Group 325 Broadway Mailcode 817.03 BoulderCO80305 United States Department of Physics University of Michigan Ann Arbor48103 United States Canadian Institute for Theoretical Astrophysics University of Toronto TorontoONM5S 3H8 Canada Universidad de Chile Dept Astronomía Casilla Santiago36-D Chile Sociedad Radiosky Asesorías de Ingeniería Limitada Camino a Toconao 145-A Ayllu de Solor San Pedro de Atacama Chile Department of Physics University of Chicago ChicagoIL60637 United States SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo ParkCA94025 United States Institute for Advanced Study 1 Einstein Dr PrincetonNJ08540 United States Department of Applied and Engineering Physics Cornell University IthacaNY14853 United States Astrophysics Res

We present the temperature and polarization angular power spectra of the CMB measured by the Atacama Cosmology Telescope (ACT) from 5400 deg2 of the 2013-2016 survey, which covers >15000 deg2 at 98 and 150 GHz. For this analysis we adopt a blinding strategy to help avoid confirmation bias and, related to this, show numerous checks for systematic error done before unblinding. Using the likelihood for the cosmological analysis we constrain secondary sources of anisotropy and foreground emission, and derive a "CMB-only" spectrum that extends to = 4000. At large angular scales, foreground emission at 150 GHz is ∼1% of TT and EE within our selected regions and consistent with that found by Planck. Using the same likelihood, we obtain the cosmological parameters for ΛCDM for the ACT data alone with a prior on the optical dept. of τ = 0.065 ± 0.015. ΛCDM is a good fit. The best-fit model has a reduced χ2 of 1.07 (PTE = 0.07) with H0 = 67.9 ± 1.5 km/s/Mpc. We show that the lensing BB signal is consistent with ΛCDM and limit the celestial EB polarization angle to ψP = −0.07◦ ± 0.09◦. We directly cross correlate ACT with Planck and observe generally good agreement but with some discrepancies in TE. All data on which this analysis is based will be publicly released. Copyright © 2020, The Authors. All rights reserved.

关键词： Cosmology

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The Atacama Cosmology Telescope: DR4 maps and cosmological parameters

arXiv

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arXiv 2020年

作者： Aiola, Simone Calabrese, Erminia Maurin, Loïc Naess, Sigurd Schmitt, Benjamin L. Abitbol, Maximilian H. Addison, Graeme E. Ade, Peter A.R. Alonso, David Amiri, Mandana Amodeo, Stefania Angile, Elio Austermann, Jason E. Baildon, Taylor Battaglia, Nick Beall, James A. Bean, Rachel Becker, Daniel T. Bond, J. Richard Bruno, Sarah Marie Calafut, Victoria Campusano, Luis E. Carrero, Felipe Chesmore, Grace E. Cho, Hsiao-Mei Choi, Steve K. Clark, Susan E. Cothard, Nicholas F. Crichton, Devin Crowley, Kevin T. Darwish, Omar Datta, Rahul Denison, Edward V. Devlin, Mark J. Duell, Cody J. Duff, Shannon M. Duivenvoorden, Adriaan J. Dunkley, Jo Dünner, Rolando Essinger-Hileman, Thomas Fankhanel, Max Ferraro, Simone Fox, Anna E. Fuzia, Brittany Gallardo, Patricio A. Gluscevic, Vera Golec, Joseph E. Grace, Emily Gralla, Megan Guan, Yilun Hall, Kirsten Halpern, Mark Han, Dongwon Hargrave, Peter Hasselfield, Matthew Helton, Jakob M. Henderson, Shawn Hensley, Brandon Hill, J. Colin Hilton, Gene C. Hilton, Matt Hincks, Adam D. Hložek, Renée Ho, Shuay-Pwu Patty Hubmayr, Johannes Huffenberger, Kevin M. Hughes, John P. Infante, Leopoldo Irwin, Kent Jackson, Rebecca Klein, Jeff Knowles, Kenda Koopman, Brian Kosowsky, Arthur Lakey, Victoria Li, Dale Li, Yaqiong Li, Zack Lokken, Martine Louis, Thibaut Lungu, Marius MacInnis, Amanda Madhavacheril, Mathew Maldonado, Felipe Mallaby-Kay, Maya Marsden, Danica McMahon, Jeff Menanteau, Felipe Moodley, Kavilan Morton, Tim Namikawa, Toshiya Nati, Federico Newburgh, Laura Nibarger, John P. Nicola, Andrina Niemack, Michael D. Nolta, Michael R. Orlowski-Sherer, John Page, Lyman A. Pappas, Christine G. Partridge, Bruce Phakathi, Phumlani Pisano, Giampaolo Prince, Heather Puddu, Roberto Qu, Frank J. Rivera, Jesus Robertson, Naomi Rojas, Felipe Salatino, Maria Schaan, Emmanuel Schillaci, Alessandro Sehgal, Neelima Sherwin, Blake D. Sierra, Carlos Sievers, Jon Sifon, Cristobal Sikhosana, Precious Simon, Sara Spergel, David N. Staggs, Suzanne T. Stevens, Jason Storer, Emilie Sunder, Dhaneshwar D. Switzer, Center for Computational Astrophysics Flatiron Institute 162 5th Avenue New YorkNY10010 United States Joseph Henry Laboratories of Physics Jadwin Hall Princeton University PrincetonNJ08544 United States School of Physics and Astronomy Cardiff University The Parade Wales CardiffCF24 3AA United Kingdom Université Paris-Saclay CNRS Institut d'astrophysique spatiale Orsay 91405 France Instituto de Astrofísica Centro de Astro-Ingeniería Facultad de Fìsica Pontificia Universidad Católica de Chile Av. Vicuña Mackenna 4860 Macul Santiago7820436 Chile Department of Physics and Astronomy University of Pennsylvania 209 South 33rd Street PhiladelphiaPA19104 United States Department of Physics University of Oxford Keble Road OxfordOX1 3RH United Kingdom Dept. of Physics and Astronomy The Johns Hopkins University 3400 N. Charles St. BaltimoreMD21218-2686 United States Department of Physics and Astronomy University of British Columbia VancouverBCV6T 1Z4 Canada Department of Astronomy Cornell University IthacaNY14853 United States NIST Quantum Devices Group 325 Broadway Mailcode 817.03 BoulderCO80305 United States Department of Physics University of Michigan Ann Arbor48103 United States Canadian Institute for Theoretical Astrophysics University of Toronto TorontoONM5S 3H8 Canada Universidad de Chile Dept Astronomía Casilla Santiago36-D Chile Sociedad Radiosky Asesorías de Ingeniería Limitada Camino a Toconao 145-A Ayllu de Solor San Pedro de Atacama Chile Department of Physics University of Chicago ChicagoIL60637 United States SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo ParkCA94025 United States Department of Physics Cornell University IthacaNY14853 United States Institute for Advanced Study 1 Einstein Dr PrincetonNJ08540 United States Department of Applied and Engineering Physics Cornell University IthacaNY14853 United States Astrophysics Research Centre School of Mathematics Statistics and Computer Scie

We present new arcminute-resolution maps of the Cosmic Microwave Background temperature and polarization anisotropy from the Atacama Cosmology Telescope, using data taken from 2013-2016 at 98 and 150 GHz. The maps cover more than 17,000 deg2, the deepest 600 deg2 with noise levels below 10µK-arcmin. We use the power spectrum derived from almost 6,000 deg2 of these maps to constrain cosmology. The ACT data enable a measurement of the angular scale of features in both the divergence-like polarization and the temperature anisotropy, tracing both the velocity and density at last-scattering. From these one can derive the distance to the last-scattering surface and thus infer the local expansion rate, H0. By combining ACT data with large-scale information from WMAP we measure H0 = 67.6±1.1 km/s/Mpc, at 68% confidence, in excellent agreement with the independently-measured Planck satellite estimate (from ACT alone we find H0 = 67.9 ±1.5 km/s/Mpc). The ΛCDM model provides a good fit to the ACT data, and we find no evidence for deviations: both the spatial curvature, and the departure from the standard lensing signal in the spectrum, are zero to within 1σ;the number of relativistic species, the primordial Helium fraction, and the running of the spectral index are consistent with ΛCDM predictions to within 1.5-2.2σ. We compare ACT, WMAP, and Planck at the parameter level and find good consistency;we investigate how the constraints on the correlated spectral index and baryon density parameters readjust when adding CMB large-scale information that ACT does not measure. The DR4 products presented here will be publicly released on the NASA Legacy Archive for Microwave Background data Analysis. Copyright © 2020, The Authors. All rights reserved.

关键词： Cosmology

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Model of interior finish work of apartment building by using ABM

Computer Software

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Computer Software 2014年第3期31卷 222-233页

作者： Ichikawa, Manabu Deguchi, Hiroshi Tazawa, Shuhei Shide, Kazuya Dept. of Computational Intelligence and Systems Science Tokyo Institute of Technology Japan Takenaka Corporation Japan Architecture and Building Engineering Shibaura Institute of Technology Japan

Recently, there is no significant difference among Japanese general contractors' building techniques. So, general contractors are becoming to focus on management skills of constructing. As there are various employment types, many works and many relations between works, it is very difficult for general contractors to plan the best process planning of works. Once general contractors created a process planning of works, which they think better, there are no ways to evaluate it except constructing a building in the real world according to the created one. In this research, we made a simulation model with agent-based approach to simulate how interior finish works proceeded in the apartment building construction with a planned process of works by the general contractor. And we show some simulation results and discuss about future possibilities of using our simulation model.

关键词： Apartment houses

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Sparsely extracting stored movements to construct interfaces for humanoid end-effector control

Sparsely extracting stored movements to construct interfaces...

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IEEE International Conference on Robotics and Biomimetics

作者： Yuka Ariki Tetsunari Inamura Shiro Ikeda Jun Morimoto Dept. of Science and Engineering Ritsumeikan University Shiga Japan National Institute of Informatics The Graduate School for Advanced Studies Chiyoda-ku Tokyo Japan Institute of Statistical Mathematics Tokyo Japan Dept. of Brain Robot Interface ATR Computational Neuroscience Laboratories Kyoto Japan

ISBN: (纸本)9781467396769

This paper proposes a robot interface design method by which we can control humanoid end-effector movements with such a low-dimensional input device as a gamepad. In our proposed method, first, the numbers of movement trajectories to accomplish different tasks are generated using a simulated robot model and stored in a database. Second, a human user demonstrates the current task-related behavior. Third, the corresponding stored movements for the demonstrated human behavior are sparsely extracted by a sparse coding method. Finally, the sparsely extracted movement bases are linearly combined to generate a novel movement to accomplish a new target task where the linear weight parameters are modulated by the gamepad. We easily generated such complicated hand movements as spiral motions on a small humanoid robot with our proposed interface.

关键词： Spirals Trajectory Humanoid robots databases Encoding Design methodology

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Efficient detection of viral transmission with threshold-based methods

Efficient detection of viral transmission with threshold-bas...

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IEEE International Conference on computational Advances in Bio and Medical sciences (ICCABS)

作者： Inna Rytsareva David S. Campo Yueli Zheng Seth Sims Cansu Tetik Jain Chirag Sriram P. Chockalingam Sharma V. Thankachan Amanda Sue Srinivas Aluru Yury Khudyakov Division of Viral hepatitis Centers for Disease Control and Prevention Atlanta USA Eagle Medical Services Centers for Disease Control and Prevention Atlanta USA School of Computational Science and Engineering Georgia Institute of Technology Atlanta USA Dept. of Computer Science and Engineering IIT Bombay Mumbai India

Hepatitis C is a major public health problem in the United States and worldwide. Outbreaks of hepatitis C virus (HCV) infections associated with unsafe injection practices, drug diversion, and other exposures to blood are difficult to detect and investigate. Molecular analysis has been frequently used in the study of HCV outbreaks and transmission chains; helping identify a cluster of sequences as linked by transmission if their genetic distances are below a previously defined threshold. However, HCV exists as a population of numerous variants in each infected individual and it has been observed that minority variants in the source are often the ones responsible for transmission, a situation that precludes the use of a single sequence per individual because many such transmissions would be missed. The use of Next-Generation Sequencing immensely increases the sensitivity of transmission detection but brings a considerable computational challenge because all sequences need to be compared among all pairs of samples. For instance, our relatively small dataset of 401 samples, a total of 80200 pairwise sample comparisons must be performed, which account for 4.56 x 1010 pairwise sequence comparisons. We present a fast and efficient three-step filtering strategy that removes 85.1% of all the pairwise sample comparisons and 91.0% of all pairwise sequence comparisons, accurately establishing which pairs of HCV samples are below the relatedness threshold This electronic document is a “live” template and already defines the components of your paper [title, text, heads, etc.] in its style sheet.

关键词： Bioinformatics Diseases Filtering Genetics Scientific computing Drugs Sequential analysis

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Empirical evaluation of software development effort estimation based on upper phase development activity

Computer Software

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Computer Software 2014年第2期31卷 129-143页

作者： Tsunoda, Masateru Toda, Koji Fushida, Kyohei Kamei, Yasutaka Ubayashi, Naoyasu Dept. of Informatics Kinki University Japan Dept. of Information and Systems Engineering Fukuoka Institute of Technology Japan Research and Development Headquarters NTT DATA Corporation Japan Graduate School Faculty of Information Science and Electrical Engineering Kyushu University Japan

We focus on effort estimation based on the effort for early phase activities, and built effort estimation models using early phase effort as an explanatory variable, and compared the estimation accuracies of these models to the effort estimation models based on software size. In addition, we built estimation models using both early phase effort and software size. In our experiment, we used ISBSG dataset, which was collected from software development companies, and regarded planning phase effort and requirement analysis effort as early phase effort. The result of the experiment showed that when both software size and sum of planning and requirement analysis phase effort were used as explanatory variables, the estimation accuracy was most improved (Average Balanced Relative Error was improved to 75.4% from 148.4%).

关键词： Software design

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Dependability Issues of Android Games: A First Look via Software Analysis

Dependability Issues of Android Games: A First Look via Soft...

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2015 IEEE Symposium on Service-Oriented System engineering

作者： Jiaojiao Fu Yangfan Zhang Yu Kang School of Computer Science Fudan University Shenzhen Key Laboratory of Rich Media Big Data Analytics and Applications The Chinese University of Hong Kong Fudan University Shanghai Shanghai CN Dept. of Computer Science & Engineering The Chinese University of Hong Kong

Smart phones have surged into popularity in recent years, which has dramatically changed the way people live, work, and have fun. Smart phone games are an important type of Smart phone applications, which attract many software developers. However, they still have not caught much research attention in the software dependability community. In this paper, we study the characteristics of over 2000 Android games with software analysis techniques, with a focus on their dependability issues. Our study suggests that a new security paradigm is of great importance to Smart phone games to prevent potential privilege abuse. Moreover, a new set of testing and debugging approaches should be specifically tailored for Smart phone games, since games are becoming more complicated. Our study also reveals that most games are not specifically optimized according to the user pattern of Smart phones. We expect these open problems can bring more attentions to the software dependability community.

关键词： Games Internet Androids Humanoid robots Libraries Java Software

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