Numerical Analysis and Scientific Computing Commons^™

Vibrational Energy Levels Of The Simplest Criegee Intermediate (Ch₂Oo) From Full-Dimensional Lanczos, Mctdh, And Multimode Calculations, Hua-Gen Yu, Steve Alexandre Ndengué, Jun Li, Richard Dawes, Hua Guo

Chemistry Faculty Research & Creative Works

Accurate vibrational energy levels of the simplest Criegee intermediate (CH₂OO) were determined on a recently developed ab initio based nine-dimensional potential energy surface using three quantum mechanical methods. the first is the iterative Lanczos method using a conventional basis expansion with an exact Hamiltonian. the second and more efficient method is the multi-configurational time-dependent Hartree (MCTDH) method in which the potential energy surface is refit to conform to the sums-of-products requirement of MCTDH. Finally, the energy levels were computed with a vibrational self-consistent field/virtual configuration interaction method in MULTIMODE. the low-lying levels obtained from the three methods are …

Distributed Caching Using The Htcondor Cached, Derek J. Weitzel, Brian Bockelman, David Swanson

Holland Computing Center: Faculty Publications

A batch processing job in a distributed system has three clear steps, stage-in, execution, and stage-out. As data sizes have increased, the stage-in time has also increased. In order to optimize stage-in time for shared inputs, we propose the CacheD, a caching mechanism for high throughput computing. Along with caching on worker nodes for rapid transfers, we also introduce a novel transfer method to distribute shared caches to multiple worker nodes utilizing BitTorrent. We show that our caching method significantly improves workflow completion times by minimizing stage-in time while being non-intrusive to the computational resources, allowing for opportunistic resources to …

Automatic Video Self Modeling For Voice Disorder, Ju Shen, Changpeng Ti, Anusha Raghunathan, Sen-Ching S. Cheung, Rita Patel

Computer Science Faculty Publications

Video self modeling (VSM) is a behavioral intervention technique in which a learner models a target behavior by watching a video of him- or herself. In the field of speech language pathology, the approach of VSM has been successfully used for treatment of language in children with Autism and in individuals with fluency disorder of stuttering. Technical challenges remain in creating VSM contents that depict previously unseen behaviors. In this paper, we propose a novel system that synthesizes new video sequences for VSM treatment of patients with voice disorders. Starting with a video recording of a voice-disorder patient, the proposed …

Improving Patient Flow With Data-Driven Patient Prioritization Method In The Emergency Department, Kar Way Tan, Sean Shao Wei Lam

Research Collection School Of Computing and Information Systems

We aim to improve the length-of-stay (LOS) of patients in the Emergency Department (ED) ambulatory care area. We propose the use of real-time computerized physician order entry data and ED patient flow management system to estimate the consultation time of patients re-entering the queue to consult a doctor again after receiving treatment or results of tests. The estimation allows decision-makers to apply dynamic prioritization strategies that help the ED to identify patients who can complete their ED treatment process quickly, freeing up resources in the ED and lowering overall LOS.

Interference Effects For Intermediate Energy Electron-Impact Ionization Of H₂ And N₂ Molecules, Zehra Nur Ozer, Hari Chaluvadi, Don H. Madison, Mevlut Dogan

Physics Faculty Research & Creative Works

We have studied electron impact ionization of H₂ and N₂ molecules at intermediate energies to look for possible two center interference effects experimentally and theoretically. Here we report a study of the interference factor I for 250 eV electron-impact ionization. The experimental measurements are performed using a crossed-beam-type electron-electron coincidence spectrometer and theoretical calculations are obtained using the Molecular Three Body Distorted Wave Approximation (M3DW). We found that the I-factor demonstrated strong evidence for two-center interference effects for both H₂ and N₂. We also found that the I-factor is more sensitive to projectile angular scans …

No Thermal Anomalies In The Mantle Transition Zone Beneath An Incipient Continental Rift: Evidence From The First Receiver Function Study Across The Okavango Rift Zone, Botswana, Youqiang Yu, Kelly H. Liu, M. Moidaki, Cory A. Reed, Stephen S. Gao

Geosciences and Geological and Petroleum Engineering Faculty Research & Creative Works

Mechanisms leading to the initiation and early-stage development of continental rifts remain enigmatic, in spite of numerous studies. Among the various rifting models, which were developed mostly based on studies of mature rifts, far-field stresses originating from plate interactions (passive rifting) and nearby active mantle upwelling (active rifting) are commonly used to explain rift dynamics. Situated atop of the hypothesized African Superplume, the incipient Okavango Rift Zone (ORZ) of northern Botswana is ideal to investigate the role of mantle plumes in rift initiation and development, as well as the interaction between the upper and lower mantle. The ORZ developed within …

Structured Learning From Heterogeneous Behavior For Social Identity Linkage, Siyuan Liu, Shuhui Wang, Feida Zhu

Research Collection School Of Computing and Information Systems

Social identity linkage across different social media platforms is of critical importance to business intelligence by gaining from social data a deeper understanding and more accurate profiling of users. In this paper, we propose a solution framework, HYDRA, which consists of three key steps: (I) we model heterogeneous behavior by long-term topical distribution analysis and multi-resolution temporal behavior matching against high noise and information missing, and the behavior similarity are described by multi-dimensional similarity vector for each user pair; (II) we build structure consistency models to maximize the structure and behavior consistency on users' core social structure across different platforms, …

Message Passing For Collective Graphical Models, Tao Sun, Daniel Sheldon, Akshat Kumar

Research Collection School Of Computing and Information Systems

Collective graphical models (CGMs) are a formalism for inference and learning about a population of independent and identically distributed individuals when only noisy aggregate data are available. We highlight a close connection between approximate MAP inference in CGMs and marginal inference in standard graphical models. The connection leads us to derive a novel Belief Propagation (BP) style algorithm for collective graphical models. Mathematically, the algorithm is a strict generalization of BP—it can be viewed as an extension to minimize the Bethe free energy plus additional energy terms that are non-linear functions of the marginals. For CGMs, the algorithm is much …

Real Time Mission Planning, Emad William Saad, Stefan Richard Bieniawski, Paul Edward Riley Pigg, John Lyle Vian, Paul Michael Robinette, Donald C. Wunsch

Electrical and Computer Engineering Faculty Research & Creative Works

The different advantageous embodiments provide a system comprising a number of computers, a graphical user interface, first program code stored on the computer, and second program code stored on the computer. The graphical user interface is executed by a computer in the number of computers. The computer is configured to run the first program code to define a mission using a number of mission elements. The computer is configured to run the second program code to generate instructions for a number of assets to execute the mission and monitor the number of assets during execution of the mission.

Preface, Gennady Fridman, Jeremy Levesley, Ivan Tyukin, Donald C. Wunsch

Electrical and Computer Engineering Faculty Research & Creative Works

In August 2014 a conference on “Model reduction across disciplines” was held in Leicester, UK. As a scientific field, model reduction is an important part of mathematical modelling and data analysis with very wide areas of applications. The main scientific goal of the conference was to facilitate interdisciplinary discussion of model reduction and coarse-graining methodologies in order to reveal their general mathematical nature. This time, however, the conference had an additional personal and more profound mission – it was dedicated to the 60th birthday of Professor Alexander Gorban (albeit with some delay) whose fantastic achievements in applying model reduction techniques …

Changes In R, R Core Team

The R Journal

CHANGES IN R 3.2.1

CHANGES IN R 3.2.0

CHANGES IN R 3.1.3

Changes On Cran, Kurt Hornik, Achim Zeileis

The R Journal

New packages in CRAN task views

New contributed packages

Other changes

R Foundation News, Kurt Hornik

The R Journal

Donations

New Supporting Institutions

New Supporting Members

Identifying Complex Causal Dependencies In Configurational Data With Coincidence Analysis, Michael Baumgartner, Alrik Thiem

The R Journal

We present cna, a package for performing Coincidence Analysis (CNA). CNA is a configurational comparative method for the identification of complex causal dependencies—in particular, causal chains and common cause structures—in configurational data. After a brief introduction to the method’s theoretical background and main algorithmic ideas, we demonstrate the use of the package by means of an artificial and a real-life data set. Moreover, we outline planned enhancements of the package that will further increase its applicability.

Fslr: Connecting The Fsl Software With R, John Muschelli, Elizabeth Sweeney, Martin Lindquist, Ciprian Crainiceanu

The R Journal

We present the package fslr, a set of R functions that interface with FSL (FMRIB Software Library), a commonly-used open-source software package for processing and analyzing neuroimaging data. The fslr package performs operations on ‘nifti’ image objects in R using command-line functions from FSL, and returns R objects back to the user. fslr allows users to develop image processing and analysis pipelines based on FSL functionality while interfacing with the functionality provided by R. We present an example of the analysis of structural magnetic resonance images, which demonstrates how R users can leverage the functionality of FSL without switching …

The R Journal (June 2015) 7(1): Complete Issue, The R Foundation

The R Journal

Editorial, Bettina Grün

Contributed Research Articles

Peptides: A Package for Data Mining of Antimicrobial Peptides, Daniel Osorio, Paola Rondón-Villarreal, and Rodrigo Torres

fanplot: An R Package for Visualising Sequential Distributions, Guy J. Abel

sparkTable: Generating Graphical Tables for Websites and Documents with R, Alexander Kowarik, Bernhard Meindl, and Matthias Templ

rdrobust: An R Package for Robust Nonparametric Inference in Regression-Discontinuity Designs, Sebastian Calonico, Matias D. Cattaneo, and Rocío Titiunik

Frames2: A Package for Estimation in Dual Frame Surveys, Antonio Arcos, David Molina, Maria Giovanna Ranalli, and María del Mar Rueda

The Complex Multivariate Gaussian Distribution, Robin K. S. Hankin

sae: …

R As An Environment For Reproducible Analysis Of Dna Amplification Experiments, Stefan Rödiger, Michał Burdukiewicz, Konstantin Blagodatskikh, Michael Jahn, Peter Schierack

The R Journal

There is an ever-increasing number of applications, which use quantitative PCR (qPCR) or digital PCR (dPCR) to elicit fundamentals of biological processes. Moreover, quantitative isothermal amplification (qIA) methods have become more prominent in life sciences and point-of-care diagnostics. Additionally, the analysis of melting data is essential during many experiments. Several software packages have been developed for the analysis of such datasets. In most cases, the software is either distributed as closed source software or as monolithic block with little freedom to perform highly customized analysis procedures. We argue, among others, that R is an excellent foundation for reproducible and transparent …

Sae: An R Package For Small Area Estimation, Isabel Molina, Yolanda Marhuenda

The R Journal

We describe the R package sae for small area estimation. This package can be used to obtain model-based estimates for small areas based on a variety of models at the area and unit levels, along with basic direct and indirect estimates. Mean squared errors are estimated by analytical approximations in simple models and applying bootstrap procedures in more complex models. We describe the package functions and show how to use them through examples.

Frames2: A Package For Estimation In Dual Frame Surveys, Antonio Arcos, David Molina, Maria Giovanna Ranalli, Maria Del Mar Rueda

The R Journal

Data from complex survey designs require special consideration with regard to estimation of finite population parameters and corresponding variance estimation procedures, as a consequence of significant departures from the simple random sampling assumption. In the past decade a number of statistical software packages have been developed to facilitate the analysis of complex survey data. All these statistical software packages are able to treat samples selected from one sampling frame containing all population units. Dual frame surveys are very useful when it is not possible to guarantee a complete coverage of the target population and may result in considerable cost savings …

Sparktable: Generating Graphical Tables For Websites And Documents With R, Alexander Kowarik, Bernhard Meindl, Matthias Templ

The R Journal

Visual analysis of data is important to understand the main characteristics, main trends and relationships in data sets and it can be used to assess the data quality. Using the R package sparkTable, statistical tables holding quantitative information can be enhanced by including spark-type graphs such as sparklines [] and sparkbars [].

These kind of graphics are well-known in literature and are considered as simple, intense and illustrative graphs that are small enough to fit in a single line. Thus, they can easily enrich tables and texts with additional information in a comprehensive visual way.

The R package sparkTable …