Computer Sciences Commons^™

Mvn: An R Package For Assessing Multivariate Normality, Selcuk Korkmaz, Dincer Goksuluk, Gokmen Zararsiz

The R Journal

Assessing the assumption of multivariate normality is required by many parametric multivariate statistical methods, such as MANOVA, linear discriminant analysis, principal component analysis, canonical correlation, etc. It is important to assess multivariate normality in order to proceed with such statistical methods. There are many analytical methods proposed for checking multivariate normality. However, deciding which method to use is a challenging process, since each method may give different results under certain conditions. Hence, we may say that there is no best method, which is valid under any condition, for normality checking. In addition to numerical results, it is very useful to …

Ngspatial: A Package For Fitting The Centered Autologistic And Sparse Spatial Generalized Linear Mixed Models For Areal Data, John Hughes

The R Journal

Two important recent advances in areal modeling are the centered autologistic model and the sparse spatial generalized linear mixed model (SGLMM), both of which are reparameterizations of traditional models. The reparameterizations improve regression inference by alleviating spatial confounding, and the sparse SGLMM also greatly speeds computing by reducing the dimension of the spatial random effects. Package ngspatial (’ng’ = non-Gaussian) provides routines for fitting these new models. The package supports composite likelihood and Bayesian inference for the centered autologistic model, and Bayesian inference for the sparse SGLMM.

Coordinate-Based Meta-Analysis Of Fmri Studies With R, Andrea Stocco

The R Journal

This paper outlines how to conduct a simple meta-analysis of neuroimaging foci of activation in R. In particular, the first part of this paper reviews the nature of fMRI data, and presents a brief overview of the existing packages that can be used to analyze fMRI data in R. The second part illustrates how to handle fMRI data by showing how to visualize the results of different neuroimaging studies in a so-called orthographic view, where the spatial distribution of the foci of activation from different fMRI studies can be inspected visually.

Functional MRI (fMRI) is one of the most important …

Bshazard: A Flexible Tool For Nonparametric Smoothing Of The Hazard Function, Paola Rebora, Agus Salim, Marie Reilly

The R Journal

The hazard function is a key component in the inferential process in survival analysis and relevant for describing the pattern of failures. However, it is rarely shown in research papers due to the difficulties in nonparametric estimation. We developed the bshazard package to facilitate the computation of a nonparametric estimate of the hazard function, with data-driven smoothing. The method accounts for left truncation, right censoring and possible covariates. B-splines are used to estimate the shape of the hazard within the generalized linear mixed models frame work. Smoothness is controlled by imposing an autoregressive structure on the baseline hazard coefficients. This …

Prinsimp, Jonathan Zhang, Nancy Heckman, Davor Cubranic, Joel G. Kingsolver, Travis Gaydos, J.S. Marron

The R Journal

Principal Components Analysis (PCA) is a common way to study the sources of variation in a high-dimensional data set. Typically, the leading principal components are used to understand the variation in the data or to reduce the dimension of the data for subsequent analysis. The remaining principal components are ignored since they explain little of the variation in the data. However, the space spanned by the low variation principal components may contain interesting structure, structure that PCA cannot find. Prinsimp is an R package that looks for interesting structure of low variability. “Interesting” is defined in terms of a simplicity …

Phaser: An R Package For Phase Plane Analysis Of Autonomous Ode Systems, Michael J. Grayling

The R Journal

When modelling physical systems, analysts will frequently be confronted by differential equations which cannot be solved analytically. In this instance, numerical integration will usually be the only way forward. However, for autonomous systems of ordinary differential equations (ODEs) in one or two dimensions, it is possible to employ an instructive qualitative analysis foregoing this requirement, using so-called phase plane methods. Moreover, this qualitative analysis can even prove to be highly useful for systems that can be solved analytically, or will be solved numerically anyway. The package phaseR allows the user to perform such phase plane analyses: determining the stability of …

Taming Pitchf/X Data With Xml2r And Pitchrx, Carson Sievert

The R Journal

XML2R is a framework that reduces the effort required to transform XML content into tables in a way that preserves parent to child relationships. pitchRx applies XML2R’s grammar for XML manipulation to Major League Baseball Advanced Media (MLBAM)’s Gameday data. With pitchRx, one can easily obtain and store Gameday data in a remote database. The Gameday website hosts a wealth of XML data, but perhaps most interesting is PITCHf/x. Among other things, PITCHf/x data can be used to recreate a baseball’s flight path from a pitcher’s hand to home plate. With pitchRx, one can easily create animations …

Applying Spartan To Understand Parameter Uncertainty In Simulations, Kieran Alden, Mark Read, Paul S. Andrews, Jon Timmis, Mark Coles

The R Journal

In attempts to further understand the dynamics of complex systems, the application of computer simulation is becoming increasingly prevalent. Whereas a great deal of focus has been placed in the development of software tools that aid researchers develop simulations, similar focus has not been applied in the creation of tools that perform a rigorous statistical analysis of results generated through simulation: vital in understanding how these results offer an insight into the captured system. This encouraged us to develop spartan, a package of statistical techniques designed to assist researchers in understanding the relationship between their simulation and the real system. …

Replication And Knowledge Production In Empirical Software Engineering Research, Jonathan L. Krein

Theses and Dissertations

Although replication is considered an indispensable part of the scientific method in software engineering, few replication studies are published each year. The rate of replication, however, is not surprising given that replication theory in software engineering is immature. Not only are replication taxonomies varied and difficult to reconcile, but opinions on the role of replication contradict. In general, we have no clear sense of how to build knowledge via replication, particularly given the practical realities of our research field. Consequently, most replications in software engineering yield little useful information. In particular, the vast majority of external replications (i.e., replications performed …

Framework To Implement Authentication, Authorization And Secure Communications In A Multiuser Collaborative Cax Environment, Francis Mensah

Theses and Dissertations

Computer Aided Design (CAD) applications have historically been based on a single user per application architecture. Although this architecture is still popular to date, it does have several drawbacks. First of all the single user CAD architecture inhibits a concurrent engineering design process where several designers can work on the same model simultaneously. This limitation introduces time inefficiency especially when a project involves geographically dispersed designers. A solution to these drawbacks could be a transition from the traditional single user CAD architecture to a multiuser collaborative architecture. Advances in computer networking technologies, especially relating to the Internet, have provided the …

Classifying And Cataloging Cyber-Security Incidents Within Cyber-Physical Systems, William B. Miller

Theses and Dissertations

In the past, there were perceived delineations between the cyber world and the physical world. We are becoming increasingly aware of the overlap between these two worlds, and the overlap itself is increasing. The overlap between these two worlds is known as cyber-physical systems. There have been several incidents involving cyber-physical systems and the number of these incidents is increasing dramatically. In the past there has been no effort to identify methods for describing these incidents in the unique context of cyber-physical systems. This research provides a taxonomy for classifying these incidents that focuses on cross domain, impact oriented analysis. …

The Bioluminescence Heterozygous Genome Assembler, Jared Calvin Price

Theses and Dissertations

High-throughput DNA sequencing technologies are currently revolutionizing the fields of biology and medicine by elucidating the structure and function of the components of life. Modern DNA sequencing machines typically produce relatively short reads of DNA which are then assembled by software in an attempt to produce a representation of the entire genome. Due to the complex structure of all but the smallest genomes, especially the abundant presence of exact or almost exact repeats, all genome assemblers introduce errors into the final sequence and output a relatively large set of contigs instead of full-length chromosomes (a contig is a DNA sequence …

Peanut Butter Jelly: An Animated Short Film, Alexander Beaty

All Theses

Peanut Butter Jelly is an animated short film based on the concept of two species of Jellyfish clashing over a jar of peanut butter. The production spanned a year and involved the artistic effort of 12 Digital Production Arts graduate students as well as a support team of 10 students from various programs within the University.

I’Ve Heard You Have Problems: Cellular Signal Monitoring Through Ue Participatory Sensing, Huiguang Liang, Hyong Kim, Hwee-Pink Tan, Wai-Leong Yeow

Research Collection School Of Computing and Information Systems

The operating environment of cellular networks can be in a constant state of change. One Singaporean operator expressed difficulty with the coverage assertion (CA) problem of whether regulated minimum coverage is met, especially in urban areas. Currently, the operator manually appraises coverage through laborious and expensive walk/drive-tests. In this paper, we propose Tattle, a distributed, low-cost and comprehensive cellular network measurement collection and processing framework. We exemplify Tattle by leveraging on participating UEs to report on network coverage in real-time. Tattle exploits wireless local-area interfaces to exchange RSCP measurements amongst devices to preserve the co-locality of readings and conserve power. …

Unisense: A Unified And Sustainable Sensing And Transport Architecture For Large Scale And Heterogeneous Sensor Networks, Yunye Jin, Hwee-Pink Tan

Research Collection School Of Computing and Information Systems

In this paper, we propose UNISENSE, a unified and sustainable sensing and transport architecture for large scale and heterogeneous sensor networks. The proposed architecture incorporates seven principal components, namely, application profiling, node architecture, intelligent network design, network management, deep sensing, generalized participatory sensing, and security. We describe the design and implementation for each component. We also present the deployment and performance of the UNISENSE architecture in four practical applications.

X-Ray Emission Produced In Charge-Exchange Collisions Between Highly Charged Ions And Argon: Role Of The Multiple Electron Capture, Sebastian Otranto, N. D. Cariatore, Ronald E. Olson

Physics Faculty Research & Creative Works

In this work we use the classical trajectory Monte Carlo method within an eight-electron scheme to theoretically study photonic spectra that follow charge-exchange processes between highly charged ions of charge states 10+, 17+, 18+, and 36+ with neutral argon. The energy range considered is 18 eV/amu to 4 keV/amu, covering typical electron beam ion traps and solar wind energies. The role played by multiple electron capture processes for the different collision systems under consideration is explicitly analyzed and its contribution separated as arising from radiative decay and autoionizing multiple capture. For the present collision systems we find that multiple electron …

The R Journal (December 2014) 6(2): Complete Issue, The R Foundation

The R Journal

Editorial, Deepayan Sarkar

Contributed Research Articles

Coordinate-Based Meta-Analysis of fMRI Studies with R, Andrea Stocco

Automatic Conversion of Tables to LongForm Dataframes, Jimmy Oh

Prinsimp, Jonathan Zhang, Nancy Heckman, Davor Cubranic, Joel G. Kingsolver, Travis Gaydos, and J. S. Marron

phaseR: An R Package for Phase Plane Analysis of Autonomous ODE Systems, Michael J. Grayling

Flexible R Functions for Processing Accelerometer Data, with Emphasis on NHANES 2003-2006, Dane R. Van Domelen and W. Stephen Pittard

Applying spartan to Understand Parameter Uncertainty in Simulations, Kieran Alden, Mark Read, Paul S. Andrews, Jon Timmis, and Mark Coles

ngspatial: A Package for Fitting …

Using Spectral Analysis To Evaluate Flute Tone Quality, Ron Yorita

Master's Theses

Many skilled flutists place a high priority on "good" tone quality, or timbre. Timbre can be defined as the audible difference in character that a listener perceives for two notes played at the same pitch. Different timbres are determined by the combination and balance of harmonics that comprise a note. Unlike pitch and rhythm, timbre is difficult to objectively quantify. This project explores (1) how tone quality is described by skilled flutists, (2) whether the harmonic spectrum has some correlation with tone quality, (3) whether certain harmonic spectra are preferred, or considered "good".

Thirty-one flutists ranging from high school students …

An Approximation Algorithm For The Stable Marriagae Problem With Ties And Incomplete Lists, Rommel Jalasutram

All Dissertations

Consider the bipartite matching problem with two sets of participants: men (L) and women (R). Each person participating has a strict and complete preference list over participants from the other set. The goal is to pair men and women such that no one can improve their partner by breaking away from the centralized matching scheme. Problems that exhibit this flavor are commonly classified as ordinal matchings. Gale and Shapley showed how to obtain such a matching (otherwise known as a “stable” matching). Generalizations of this model have found relevance in several centralized matching schemes such as the National Residency Matching …

Information-Theoretic Limits For Density Estimation, James Brofos

Computer Science Technical Reports

This paper is concerned with the information-theoretical limits of density estimation for Gaussian random variables with data drawn independently and with identical distributions. We apply Fano's inequality to the space of densities and an arbitrary estimator. We derive necessary conditions on the sample size for reliable density recovery and for reliable density estimation. These conditions are true simultaneously for both finitely and infinitely dimensional density spaces.

Underwater God Rays From A Custom Volume Renderer, Gowthaman Ilango

All Theses

Peanut Butter Jelly, directed by Alexander Beaty, is a 51 second computer-animated short film produced by Digital Production Arts. The plot focuses on a fight sequence between a pirate jelly fish and a flyboy jelly fish over a peanut butter jar. The production demanded a photo-realistic computer generated underwater environment, which lead to the need for a custom built volume renderer to render high quality god rays. This thesis illustrates the requirement for a customized volume renderer for the production, the algorithm, and the implementation of the renderer. It also describes a tool created for Maya 2012 which gives the …

Aspccgtk: Towards Syntactic Parsing With Semantic Disambiguation, Yuliya Lierler, Peter Schueller

Computer Science Faculty Publications

Natural language expressions are often ambiguous, allowing multiple interpretations. In this note we describe an approach that integrates syntactic analysis with semantic constraints in a system called ASPCCGTK. This system is based on Answer Set Programming — a popular declarative constraint programming paradigm.

Theoretical And Experimental (E, 2e) Study Of Electron-Impact Ionization Of Laser-Aligned Mg Atoms, Sadek Amami, Andrew J. Murray, Al Stauffer, Kate Nixon, Gregory Armstrong, James Colgan, Don H. Madison

Physics Faculty Research & Creative Works

We have performed calculations of the fully differential cross sections for electron-impact ionization of magnesium atoms. Three theoretical approximations, the time-dependent close coupling, the three-body distorted wave, and the distorted wave Born approximation, are compared with experiment in this article. Results will be shown for ionization of the 3s ground state of Mg for both asymmetric and symmetric coplanar geometries. Results will also be shown for ionization of the 3p state which has been excited by a linearly polarized laser which produces a charge cloud aligned perpendicular to the laser beam direction and parallel to the linear polarization. Theoretical and …

The Application Of P-Bar Theory In Transformation-Based Error-Driven Learning, Bryant Harold Walley

Master's Theses

In P-bar Theory, Perkins et al. (2014) proposed a rule based method for determining the context of a partext (i.e., a part of a text document).

In Transformation-Based Error-Driven Learning and Natural Language Processing: A Case Study in Part-of-Speech Tagging Brill (1995) demonstrates a method of error-driven learning applied to individual words at the sentence level to determine the part of speech each word represents.

We combine these two concepts providing a transformation-based error-driven learning algorithm to improve the results obtained from the static rules Perkins proposed and determine if the rule order prediction will provide additional metadata.

Reinforcement Learning Of Distributed Surveillance Plans, Madhavi Chittireddy

Master's Theses

This thesis describes the design and implementation of a Reinforcement Learning algorithm on a camera surveillance model which is used to know the stackelberg strategies of attacker and defender. This reinforcement learning algorithm is compared with the uniform policy and hill climbing algorithms by executing them on a common set of different data files, generated programmatically with various combinations of problem size, location, and orientation transitions as well as rewards of attacker and defender. The comparison includes the time taken to obtain better stackelberg policy and the resulted final pay-off of the defender. This thesis shows that the reinforcement learning …

Integrability And Exact Solutions For A (2+1)-Dimensional Variable-Coefficient Kdv Equation, Zhang Yu, Xu Gui-Qiong

Applications and Applied Mathematics: An International Journal (AAM)

By using the WTC method and symbolic computation, we apply the Painlevé test for a (2+1)-dimensional variable-coefficient Kortweg-de Vries (KdV) equation, and the considered equation is found to possess the Painlevé property without any parametric constraints. The auto-Bǎcklund transformation and several types of exact solutions are obtained by using the Painlevé truncated expansion method. Finally, the Hirota’s bilinear form is presented and multi-soliton solutions are also constructed.

Towards Intelligent Caring Agents For Aging-In-Place: Issues And Challenges, Di Wang, Budhitama Subagdja, Yilin Kang, Ah-Hwee Tan

Research Collection School Of Computing and Information Systems

The aging of the world’s population presents vast societal and individual challenges. The relatively shrinking workforce to support the growing population of the elderly leads to a rapidly increasing amount of technological innovations in the field of elderly care. In this paper, we present an integrated framework consisting of various intelligent agents with their own expertise and responsibilities working in a holistic manner to assist, care, and accompany the elderly around the clock in the home environment. To support the independence of the elderly for Aging-In-Place (AIP), the intelligent agents must well understand the elderly, be fully aware of the …

From Cells To Streets: Estimating Mobile Paths With Cellular-Side Data, Qatar Computing Research Institute, University Of Birmingham, Seattle University Of Washington, Haewoon Kwak

Research Collection School Of Computing and Information Systems

Through their normal operation, cellular networks are a repository of continuous location information from their subscribed devices. Such information, however, comes at a coarse granularity both in terms of space, as well as time. For otherwise inactive devices, location information can be obtained at the granularity of the associated cellular sector, and at infrequent points in time, that are sensitive to the structure of the network itself, and the level of mobility of the device. In this paper, we are asking the question of whether such sparse information can help to identify the paths followed by mobile connected devices throughout …

A Deep Search Architecture For Capturing Product Ontologies, Tejeshwar Sangameswaran

Graduate Theses and Dissertations

This thesis describes a method to populate very large product ontologies quickly. We discuss a deep search architecture to text-mine online e-commerce market places and build a taxonomy of products and their corresponding descriptions and parent categories. The goal is to automatically construct an open database of products, which are aggregated from different online retailers. The database contains extensive metadata on each object, which can be queried and analyzed. Such a public database currently does not exist; instead the information currently resides siloed within various organizations. In this thesis, we describe the tools, data structures and software architectures that allowed …

A Smart Web Crawler For A Concept Based Semantic Search Engine, Vinay Kancherla

Master's Projects

The internet is a vast collection of billions of web pages containing terabytes of information arranged in thousands of servers using HTML. The size of this collection itself is a formidable obstacle in retrieving information necessary and relevant. This made search engines an important part of our lives. Search engines strive to retrieve information as relevant as possible to the user. One of the building blocks of search engines is the Web Crawler. A web crawler is a bot that goes around the internet collecting and storing it in a database for further analysis and arrangement of the data.

The …