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Designing Computing System Architecture and Models for the HL-LHC era

Journal of Physics: Conference Series 2015年第3期664卷

作者： L Bauerdick B Bockelman P Elmer S Gowdy M Tadel F Würthwein Fermilab Batavia IL 60510 USA Computer Science & Engineering University of Nebraska-Lincoln Lincoln NE 68588 USA Department of Physics Princeton University Princeton NJ 08540 USA Department of Physics UCSD La Jolla CA 92093 USA

This paper describes a programme to study the computing model in CMS after the next long shutdown near the end of the decade.

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Erratum to: Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain

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Molecular neurodegeneration 2016年第1期11卷 42页

作者： Philipp A Jaeger Kurt M Lucin Markus Britschgi Badri Vardarajan Ruo-Pan Huang Elizabeth D Kirby Rachelle Abbey Bradley F Boeve Adam L Boxer Lindsay A Farrer NiCole Finch Neill R Graff-Radford Elizabeth Head Matan Hofree Ruochun Huang Hudson Johns Anna Karydas David S Knopman Andrey Loboda Eliezer Masliah Ramya Narasimhan Ronald C Petersen Alexei Podtelezhnikov Suraj Pradhan Rosa Rademakers Chung-Huan Sun Steven G Younkin Bruce L Miller Trey Ideker Tony Wyss-Coray Department of Neurology and Neurological Sciences Stanford University School of Medicine Stanford CA USA. pjaeger@ucsd.edu. Institute of Chemistry and Biochemistry Free University Berlin Berlin Germany. pjaeger@ucsd.edu. Departments of Bioengineering and Medicine University of California La Jolla San Diego CA USA. pjaeger@ucsd.edu. Department of Neurology and Neurological Sciences Stanford University School of Medicine Stanford CA USA. Present address: Biology Department Eastern Connecticut State University Willimantic CT USA. Present address: Roche Pharma Research and Early Development NORD DTA Roche Innovation Center Basel Basel Switzerland. Department of Medicine (Biomedical Genetics) Boston University Schools of Medicine Boston MA USA. RayBiotech Guangzhou China. RayBiotech Norcrosse GA USA. Department of Neurology Mayo Clinic Rochester MN USA. Department of Neurology University of California San Francisco San Francisco CA USA. Departments of Neurology Ophthalmology Genetics and Genomics Epidemiology and Biostatistics Boston University Schools of Medicine and Public Health Boston MA USA. Department of Neuroscience Mayo Clinic Jacksonville FL USA. Department of Neurology Mayo Clinic Jacksonville FL USA. Departments of Pharmacology and Nutritional Sciences and Sanders-Brown Center on Aging University of Kentucky Lexington KY USA. Department of Computer Science and Engineering University of California La Jolla San Diego CA USA. Genetics and Pharmacogenomics Merck Research Laboratories West Point PA USA. Department of Pathology University of California La Jolla San Diego CA USA. Departments of Bioengineering and Medicine University of California La Jolla San Diego CA USA. Department of Neurology and Neurological Sciences Stanford University School of Medicine Stanford CA USA. twc@stanford.edu. Center for Tissue Regeneration Repair and Restoration VA Palo Alto Health Care System Palo Alto CA USA. twc@stanford.edu.

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Margins, shrinkage, and boosting

Margins, shrinkage, and boosting

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30th International Conference on Machine Learning, ICML 2013

作者： Telgarsky, Matus Department of Computer Science and Engineering UCSD 9500 Gilman Drive San Diego CA 92093-0404 United States

ISBN: (纸本)9781629933061

This manuscript shows that AdaBoost and its immediate variants can produce approximate maximum margin classifiers simply by scaling step size choices with a fixed small constant. In this way, when the unscaled step size is an optimal choice, these results provide guarantees for Friedman's empirically successful "shrinkage" procedure for gradient boosting (Friedman, 2000). Guarantees are also provided for a variety of other step sizes, affirming the intuition that increasingly regularized line searches provide improved margin guarantees. The results hold for the exponential loss and similar losses, most notably the logistic loss. Copyright 2013 by the author(s).

关键词： Shrinkage

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Sibelia: A scalable and comprehensive synteny block generation tool for closely related microbial genomes

Sibelia: A scalable and comprehensive synteny block generati...

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13th Workshop on Algorithms in Bioinformatics, WABI 2013

作者： Minkin, Ilya Patel, Anand Kolmogorov, Mikhail Vyahhi, Nikolay Pham, Son Department of Computer Science and Engineering UCSD San Diego CA United States St. Petersburg Academic University St. Petersburg Russia

ISBN: (纸本)9783642404528

Comparing strains within the same microbial species has proven effective in the identification of genes and genomic regions responsible for virulence, as well as in the diagnosis and treatment of infectious diseases. In this paper, we present Sibelia, a tool for finding synteny blocks in multiple closely related microbial genomes using iterative de Bruijn graphs. Unlike most other tools, Sibelia can find synteny blocks that are repeated within genomes as well as blocks shared by multiple genomes. It represents synteny blocks in a hierarchy structure with multiple layers, each of which representing a different granularity level. Sibelia has been designed to work efficiently with a large number of microbial genomes;it finds synteny blocks in 31 S. aureus genomes within 31 minutes and in 59 *** genomes within 107 minutes on a standard desktop. Sibelia software is distributed under the GNU GPL v2 license and is available at: https://***/bioinf/Sibelia. Sibelia's web-server is available at: http://***/software/sibelia. © 2013 Springer-Verlag.

关键词： Escherichia coli

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Residential energy simulation and scheduling: A case study approach

Residential energy simulation and scheduling: A case study a...

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IEEE Symposium on computers and Communications (ISCC)

作者： Jagannathan Venkatesh Baris Aksanli Tajana Šimunić Rosing Computer Science & Engineering Department UCSD La Jolla USA

Residential energy contributes to 38% of the total energy consumption of the United States [1]. Current research aims to reduce consumption through time-of-use (TOU) pricing or by providing energy information to consumers. Industrial innovations are focused on energy efficiency and automated control of appliances. However, to date, quantifying the benefits of current and future technology improvements in residential energy management is difficult. This work presents HomeSim, a simulation platform aimed at residential energy modeling that can compare and quantify these results. The subsequent case studies leverage HomeSim to explore current and future technologies, including distributed batteries, renewable sources, smart appliances, cost-aware scheduling, and peak power reduction.

关键词： Batteries Home appliances Green products Computational modeling Monitoring

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Implementation and implications of a stealth hard-drive backdoor 13

Implementation and implications of a stealth hard-drive back...

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29th Annual computer Security Applications Conference, ACSAC 2013

作者： Zaddach, Jonas Kurmus, Anil Balzarotti, Davide Blass, Erik-Oliver Francillon, Aurélien Goodspeed, Travis Gupta, Moitrayee Koltsidas, Ioannis EURECOM 06560 Sophia Antipolis France IBM Research - Zurich 8803 Rüschlikon Switzerland College of Computer and Information Science Northeastern University Boston MA United States Department of Computer Science and Engineering UCSD San Diego CA United States

ISBN: (纸本)9781450320153

Modern workstations and servers implicitly trust hard disks to act as well-behaved block devices. This paper analyzes the catastrophic loss of security that occurs when hard disks are not trustworthy. First, we show that it is possible to compromise the firmware of a commercial off-the-shelf hard drive, by resorting only to public information and reverse engineering. Using such a compromised firmware, we present a stealth rootkit that replaces arbitrary blocks from the disk while they are written, providing a data replacement backdoor. The measured performance overhead of the compromised disk drive is less than 1% compared with a normal, non-malicious disk drive. We then demonstrate that a remote attacker can even establish a communication channel with a compromised disk to infiltrate commands and to ex-filtrate data. In our example, this channel is established over the Internet to an unmodified web server that relies on the compromised drive for its storage, passing through the original webserver, database server, database storage engine, filesystem driver, and block device driver. Additional experiments, performed in an emulated disk-drive environment, could automatically extract sensitive data such as/etc/shadow (or a secret key file) in less than a minute. This paper claims that the difficulty of implementing such an attack is not limited to the area of government cyber-warfare;rather, it is well within the reach of moderately funded criminals, botnet herders and academic researchers.

关键词： Hard disk storage

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Canonical correlation approach to common spatial patterns

Canonical correlation approach to common spatial patterns

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International IEEE/EMBS Conference on Neural engineering, CNE

作者： Eunho Noh Virginia R. de Sa Department of Electrical & Computer Engineering UCSD La Jolla CA Faculty of Cognitive Science UCSD La Jolla CA

Common spatial patterns (CSPs) are a way of spatially filtering EEG signals to increase the discriminability between the filtered variance/power between the two classes. The proposed canonical correlation approach to CSP (CCACSP) utilizes temporal information in the time series, in addition to exploiting the covariance structure of the different classes, to find filters which maximize the bandpower difference between the classes. We show with simulated data, that the unsupervised canonical correlation analysis (CCA) algorithm is better able to extract the original class-discriminative sources than the CSP algorithm in the presence of large amounts of additive Gaussian noise (while the CSP algorithm is better at very low noise levels) and that our CCACSP algorithm is a hybrid, yielding good performance at all noise levels. Finally, experiments on data from the BCI competitions confirm the effectiveness of the CCACSP algorithm and a merged CSP/CCACSP algorithm (mCCACSP).

关键词： Electroencephalography Correlation Noise Algorithm design and analysis Eigenvalues and eigenfunctions Error analysis Covariance matrices

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A comprehensive approach to reduce the energy cost of network of datacenters

A comprehensive approach to reduce the energy cost of networ...

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IEEE Symposium on computers and Communications (ISCC)

作者： Baris Aksanli Jagannathan Venkatesh Tajana Rosing Inder Monga Computer Science & Engineering Department UCSD USA Energy Sciences Network LBNL USA

Several studies have proposed job migration over the wide area network (WAN) to reduce the energy of networks of datacenters by taking advantage of different electricity prices and load demands. Each study focuses on only a small subset of network parameters and thus their results may have large errors. For example, datacenters usually have long-term power contracts instead of paying market prices. However, previous work neglects these contracts, thus overestimating the energy savings by 2.3x. We present a comprehensive approach to minimize the energy cost of networks of datacenters by modeling performance of the workloads, power contracts, local renewable energy sources, different routing options for WAN and future router technologies. Our method can reduce the energy cost of datacenters by up to 28%, while reducing the error in the energy cost estimation by 2.6x.

关键词： Green products Carbon dioxide Bandwidth Power measurement Availability Schedules Hardware

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Study of visual stimulus waveforms via forced van der Pol oscillator model for SSVEP-based brain-computer interfaces

Study of visual stimulus waveforms via forced van der Pol os...

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2013 International Conference on Communications, Circuits and Systems, ICCCAS 2013

作者： Wang, Yanchen Wong, Ngai Wang, Yu-Te Wang, Yijun Huang, Xiaoxia Huang, Liya Jung, Tzyy-Ping Mandell, Arnold J. Cheng, Chung-Kuan Department of Electrical and Electronic Engineering University of Hong Kong Pokfulam Hong Kong San Diego CA United States Swartz Center of Computational Neuroscience UCSD United States Department of Computer Science and Engineering Shanghai Maritime University Shanghai China Nanjing University of Posts and Telecommunications Nanjing Jiangsu China Multimedia Imaging Laboratory Department of Psychiatry UCSD and the Fetzer Franklin Fund Kalamazoo MI United States

ISBN: (纸本)9781479930517

Visual stimulus design is a central problem for practical brain-computer interfaces (BCIs) based on steady state visually evoked potentials (SSVEPs). In this study, we compare the performances of three differing stimulus waveforms: sine wave, square wave of 50% duty cycle, and the output of the autonomous van der Pol oscillator. The human brain SSVEP is modeled with a forced van der Pol oscillator in which these three driving waveforms are individually applied. In doing so, we use binary search to yield equation parameters that predictably generates frequency maxima in the desired ratio. We compare the minimum amplitude required for each stimulus to activate a corresponding local maximum within the relevant frequency band. We then compute and graph a suitably defined signal-to-noise ratio (SNR) in relation to stimulus frequency for the three waveforms in order to ascertain their relative rates of synchronization. This theoretical exploration has its aim to provide a guideline to the development of an optimal visual stimulus pattern for use in real life SSVEP-based BCI applications. © 2013 IEEE.

关键词： Electrophysiology

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Digital Archaeological Landscapes & Replicated Artifacts: Questions of Analytical & Phenomenological Authenticity & Ethical Policies in CyberArchaeology

Digital Archaeological Landscapes & Replicated Artifacts: Qu...

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International Congress on Digital Heritage

作者： Ashley M. Richter Vid Petrovic David Vanoni Steven M. Parish Falko Kuester Thomas E. Levy Department of Anthropology Center of Interdisciplinary Science for Art Architecture UCSD branch of the California Institute of Telecommunications and Information Technology Department of Anthropology University of California San Diego Department of Computer Science & Engineering UCSD branch of the California Institute of Telecommunications and Information Technology Departments of Computer Science & Engineering & Structural Engineering UCSD branch of the California Institute of Telecommunications and Information Technology

As cyberarchaeology pushes the boundaries of digital replication of space, objects, and arguably, time itself, it simultaneously adjusts mankind's perception of these things, their connection to the individual and to culture, and our ability to analyze these increasingly solid intangible data sets. When considered as part of the evolving global modernist perspective, and as something valuable as a comparative analytical tool- these are useful developments. However, with every innovation, comes a price. And in creating virtually solid simulacra of cultural heritage, we must consider the implications of the removed authenticities cyberarchaeologists are creating. How might the ability to have a virtual copy affect international conservation policies for archaeological sites and collected artifacts? What does a virtual and potentially 3D printable version of an artifact mean to the economics of looting? How might digital augmentation in museums be balanced so as not to replace the real artifacts themselves? In developing the interdisciplinary and collaborative big-system cyberarchaeological methodologies and systems like those at the Center of Interdisciplinary science for Art, Architecture, and Archaeology at the University of California, San Diego, the ethical implications of reactions to digitization and digital analysis are being concurrently evaluated so that some flexible contingencies can be built in as a safety measure to protect the authentic from the misuse of its heterotopic virtual counterparts.

关键词： Component Authenticity Digital artifact Replica Replicated artifact Archaeological landscape Point cloud Mesh 3D printing Technology Holodeck Virtual reality CISA3 ucsd

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