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ADaCGH2: parallelized analysis of (big) CNA data

BIOINFORMATICS 2014年第12期30卷 1759-1761页

作者： Diaz-Uriarte, Ramon Univ Autonoma Madrid Dept Biochem Inst Invest Biomed Alberto Sols UAM CSIC Madrid 28029 Spain

Motivation: Studies of genomic DNA copy number alteration can deal with datasets with several million probes and thousands of subjects. Analyzing these data with currently available software (e.g. as available from BioConductor) can be extremely slow and may not be feasible because of memory requirements. Results: We have developed a BioConductor package, ADaCGH2, that parallelizes the main segmentation algorithms (using forking on multicore computers or parallelization via message passing interface, etc., in clusters of computers) and uses ff objects for reading and data storage. We show examples of data with 6 million probes per array;we can analyze data that would otherwise not fit in memory, and compared with the non-parallelized versions we can achieve speed-ups of 25-40 times on a 64-cores machine.

关键词： DNA copy number variations GENOMICS computer algorithms DATA analysis

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Triviality of φ₄⁴ theory in a finite volume scheme adapted to the broken phase

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PHYSICS LETTERS B 2014年 733卷 11-14页

作者： Siefert, Johannes Wolff, Ulli Humboldt Univ Inst Phys D-12489 Berlin Germany

We study the standard one-component phi(4)(4)-theory in four dimensions. A renormalized coupling is defined in a finite size renormalization scheme which becomes the standard scheme of the broken phase for large volumes. Numerical simulations are reported using the worm algorithm in the limit of infinite bare coupling. The cutoff dependence of the renormalized coupling closely follows the perturbative Callan Symanzik equation and the triviality scenario is hence further supported. (C) 2014 The Authors. Published by Elsevier B.V.

关键词： FINITE volume method DIMENSIONS RENORMALIZATION (Physics) computer simulation PERTURBATION (Quantum dynamics) computer algorithms

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On the complexity of stream equality

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JOURNAL OF FUNCTIONAL PROGRAMMING 2014年第2-3期24卷 166-217页

作者： Endrullis, Jorg Hendriks, Dimitri Bakhshi, Rena Rosu, Grigore Vrije Univ Amsterdam Amsterdam Netherlands Univ Illinois Urbana IL USA Univ Alexandru Ioan Cuza Iasi Romania

We study the complexity of deciding the equality of streams specified by systems of equations. There are several notions of stream models in the literature, each generating a different semantics of stream equality. We pinpoint the complexity of each of these notions in the arithmetical or analytical hierarchy. Their complexity ranges from low levels of the arithmetical hierarchy such Pi(0)(2) for the most relaxed stream models, to levels of the analytical hierarchy such as Pi(1)(1) and up to subsuming the entire analytical hierarchy for more restrictive but natural stream models. Since all these classes properly include both the semi-decidable and co-semi-decidable classes, it follows that regardless of the stream semantics employed, there is no complete proof system or algorithm for determining equality or inequality of streams. We also discuss several related problems, such as the existence and uniqueness of stream solutions for systems of equations, as well as the equality of such solutions.

关键词： COMPUTATIONAL complexity STREAM (computer hardware description language) computer algorithms UNIQUENESS (Mathematics) MATHEMATICAL proofs EXISTENCE theorems

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A Semiparametric Bayesian Model for Detecting Synchrony Among Multiple Neurons

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NEURAL COMPUTATION 2014年第9期26卷 2025-2051页

作者： Shahbaba, Babak Zhou, Bo Lan, Shiwei Ombao, Hernando Moorman, David Behseta, Sam Univ Calif Irvine Dept Stat Irvine CA 92697 USA Univ Massachusetts Dept Psychol Amherst MA 01003 USA Calif State Univ Fullerton Dept Math Fullerton CA 92834 USA

We propose a scalable semiparametric Bayesian model to capture dependencies among multiple neurons by detecting their cofiring (possibly with some. lag time) patterns over time. After discretizing time so there is at most one spike at each interval, the resulting sequence of Is (spike) and Os (silence) for each neuron is modeled using the logistic function of a continuous latent variable with a gaussian process prior. For multiple neurons, the corresponding marginal distributions are coupled to their joint probability distribution using a parametric copula model. The advantages of our approach are as follows. The nonparametric component (i.e., the gaussian process model) provides a flexible framework for modeling the underlying firing rates, and the parametric component (i.e., the copula model) allows us to make inferences regarding both contemporaneous and lagged relationships among neurons. Using the copula model, we construct multivariate probabilistic models by separating the modeling of univariate marginal distributions from the modeling of a dependence structure among variables. Our method is easy to implement using a computationally efficient sampling algorithm that can be easily extended to high-dimensional problems. Using simulated data, we show that our approach could correctly capture temporal dependencies in firing rates and identify synchronous neurons. We also apply our model to spike train data obtained from prefrontal cortical areas.

关键词： NEURONS BAYESIAN analysis GAUSSIAN processes computer algorithms DISTRIBUTION (Probability theory) PARAMETER estimation

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Workload orchestration and optimization for software defined environments

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IBM JOURNAL OF RESEARCH AND DEVELOPMENT 2014年第2-3期58卷 11:1-11:12页

作者： Arnold, W. C. Arroyo, D. J. Segmuller, W. Spreitzer, M. Steinder, M. Tantawi, A. N. IBM Corp Div Res Thomas J Watson Res Ctr Yorktown Hts NY 10598 USA

The software defined environment (SDE) provides a powerful programmable interface to a cloud infrastructure through an abstraction of compute, network, and storage resources. A workload refers to the application to be deployed in such an infrastructure. To take advantage of the SDE interface, the workload is described using a declarative workload definition language and is then deployed in the infrastructure through an automated workload orchestration and optimization layer. This paper describes the architecture and algorithms that make up this layer. Given a definition of the workload, including the virtual components of the application and their resource needs, as well as other meta-information relating to factors such as performance, availability, and privacy, the function of the workload orchestration and optimization layer is to map virtual resources to physical resources and realize such a mapping in the infrastructure. This mapping, known as placement, is optimized so that the infrastructure is efficiently utilized, and the workload requirements are satisfied. We present the overall architecture of the workload orchestration and optimization runtime. We focus on the workload placement problem and describe our optimization framework. Then, we consider a real application, IBM Connections, as a use-case to demonstrate the orchestration and optimization functionalities.

关键词： computer networks -- Workload SOFTWARE-defined networking (computer network technology) CLOUD computing CLOUD storage computer algorithms

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Iterative acquisition method based on Grey code for weak global positioning system signal

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IET RADAR SONAR AND NAVIGATION 2014年第3期8卷 220-226页

作者： Wang, Jianhui Ou, Gang Zhang, Yonghu Natl Univ Def Technol Satellite Nav Res & Dev Ctr Changsha 410073 Hunan Peoples R China

For weak global positioning system signal, long coherent integration can improve the acquisition performance effectively, but the unknown data bits restrict the coherent integration interval within a data bit. Data bits estimation can extend coherent integration interval over multiple data bits with more Doppler frequency search bins. To lighten the calculation burden of data bit combinations searching, an iterative acquisition algorithm is presented based on ordering data bit combinations by Grey code. Modified block-accumulating coherent integration over extended interval (BACIX) algorithm is also presented, which has linear complexity and better performance than BACIX algorithm.

关键词： GLOBAL Positioning System BINARY codes DOPPLER radar BIT rate (Telecommunication) ITERATIVE methods (Mathematics) computer algorithms DATA acquisition systems

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Model Predictive Control for the Quantum Series-Parallel LCC-Type Resonant Converter with Capacitive Output Filter

Model Predictive Control for the Quantum Series-Parallel LCC...

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IEEE 15th Workshop on Control and Modeling for Power Electronics (COMPEL)

作者： Barth, Tobias Weber, Jens Bernet, Steffen Tech Univ Dresden Fac Elect & Comp Engn Inst Power Engn Chair Power Elect D-01062 Dresden Germany

ISBN: (纸本)9781479921478

This paper presents a model predictive control for the quantum series-parallel LCC-type resonant converter. A hybrid model for the converter including the autonomous change of the systems structure by the output rectifier of the converter is derived. By solving the piecewise linear state equations for the possible input voltages, generated by an II-bridge, the change of the output voltage can be calculated. The maximum resonant current and the voltage across the series-resonant capacitor at the next zero crossing of the resonant current can be estimated, too. Simulation results and measurements show the effectiveness of the control algorithm with constrained resonant current and multistep prediction.

关键词： Capacitors Integrated circuit modeling Mathematical model Predictive control RLC circuits Switches Voltage control Predictive control RLC CIRCUITS output filter integrated circuit modelling Capacitors Voltage regulation computer algorithms Switches Mathematical Model resonant converter Converters series-parallel Hybrid modes output voltage Input Voltage

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A Sensorless Physiological Control Algorithm for Left Ventricular Assist Device for Heart Failure Patients

A Sensorless Physiological Control Algorithm for Left Ventri...

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IEEE Conference on Control Applications (CCA)

作者： Bakouri, Mohsen A. Savkin, Andrey V. Alomari, Abdul-Hakeem H. Univ New S Wales Sch Elect Engn & Telecommun Sydney NSW 2052 Australia

ISBN: (纸本)9781479974092

In order to evaluate ventricular assist devices in heart failure (HF) patients, an optimised lumped parameter model of cardiovascular system (CVS) in conjunction with left ventricle assist devices (LVAD) was used to investigate different control strategies. This paper presents the design of an advanced physiological method for the control of average pump flow in LVADs. The purpose of the proposed control method is to automatically adjust the pump speed to meet for changes in physiological demand. We propose an innovative approach combining a feed-forward and a dynamic sliding mode control (SMC) to determine an appropriate pump flow. Sensor-less measurement of pulse width modulation (PWM) signal is used as inputs to the dynamical model for pump flow estimation previously developed and verified in our laboratory using dogs data. The performance of the proposed control method is tested by carefully examining the immediate response of the controllers to short term of circulatory changes ranging from rest to exercise in CVS - LVAD interactions. Simulation results demonstrate that the developed controller properly tracks the desired reference flow in presence of model uncertainties and external disturbances for LVADs.

关键词： Blood Control systems Heart Hemodynamics Mathematical model Physiology Pulse width modulation Pulse width modulation control systems Control Methods Hemodynamics Physiology Mathematical Model Left Ventricular Assist Device Heart computer algorithms Pumps Blood Heart Failure Controllers external disturbance model uncertainty

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Adaptive Control of a Tilt - Roll Rotor Quadrotor UAV

Adaptive Control of a Tilt - Roll Rotor Quadrotor UAV

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International Conference on Unmanned Aircraft Systems (ICUAS)

作者： Senkul, Fatih Altug, Erdinc Istanbul Tech Univ Syst Dynam & Control Grad Program TR-80626 Istanbul Turkey Istanbul Tech Univ Dept Mech Engn TR-80626 Istanbul Turkey

ISBN: (纸本)9781479923762

In recent years quadrotor unmanned aerial vehicles are being used in various different studies. A regular quadrotor has fixed rotors. This inability to tilt its rotors lead to limited success in trajectory tracking due to controlling 6 DOF systems only with 4 input parameters. There are some studies on tilt rotor and tilt-roll rotor quadrotors that can compensate for versatile conditions. Some of these proposed quadrotors are able to hover and position hold at user defined desired angles unlike regular quadrotors. This study presents the design and control of a novel quadrotor system that can tilt its rotors independently so that it can adaptively update its rotor angles and speeds to compensate for more chaotic and realistic scenarios. After deriving the mathematical model, the designed control algorithms are explained by comparing with the latter studies' abilities. Proposed quadrotor with adaptive control is compared with regular and non-adaptive tilt-roll rotor type multicopters, in various simulations. The results show that the proposed design has clear advantages in certain situations, especially when environmental limitations and hardware inconsistencies and inefficiencies exist.

关键词： adaptive control Rotors Unmanned Aerial Vehicle drone honey bees TILT Regular trajectory tracking computer algorithms input parameter rotor angle SCROLL

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Adaptive Vibration Cancellation in Adaptive Optics: an Experimental Validation 13

Adaptive Vibration Cancellation in Adaptive Optics: an Exper...

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13th European Control Conference (ECC)

作者： Muradore, Riccardo Pettazzi, Lorenzo Fedrigo, Enrico Univ Verona Dept Comp Sci I-37100 Verona Italy European Southern Observ ESO Dept Adapt Opt Munich Germany

ISBN: (纸本)9783952426913

Mechanical vibrations have a deleterious effect on the performance of high accuracy astronomical instruments. In particular the future generation of astronomical instruments is designed to deliver images of unprecedent accuracy and are therefore expected to be even more sensitive to telescope vibrations. It is then necessary to implement mechanical and software counter actions to mitigate their effect and to guarantee the expected accuracy and resolution. In this paper we report on the implementation of an adaptive control algorithm for the vibration rejection in single conjugated and laser tomography adaptive optics systems. The proposed approach can be easily adapted to the two different AO control architectures delivering the expected performance. Experimental validations at the telescope are also reported.

关键词： Adaptive optics Frequency measurement Sensors Telescopes Vibration measurement Vibrations adaptive optics Telescopes Vibration frequency measurement vibration monitoring Astronomical instruments Sensors Mechanical Vibration computer algorithms

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