Numerical Analysis and Scientific Computing Commons^™

Automatic Media Segmentation Within Ieee 1599–2008, Antonello D'Aguanno, Luca A. Ludovico, Davide Andrea Mauro

Computer Sciences and Electrical Engineering Faculty Research

This paper deals with the automatic extraction of synchronization data from IEEE 1599-2008, an XML-based standard aiming at a comprehensive description of music. Within such format, audio tracks and video contents related to the same music piece can be referred to the occurrence of symbolic music events. In this way, digital objects are mutually synchronized, too. The goal is to show how timing information can be easily extracted from an IEEE 1599-2008 file, converted into a suitable format, and finally employed in a multimedia editing environment in order to produce an automatic segmentation of media objects.

Appearance Based Stage Recognition Of Drosophila Embryos, Gopi Chand Nutakki

Masters Theses & Specialist Projects

Stages in Drosophila development denote the time after fertilization at which certain specific events occur in the developmental cycle. Stage information of a host embryo, as well as spatial information of a gene expression region is indispensable input for the discovery of the pattern of gene-gene interaction. Manual labeling of stages is becoming a bottleneck under the circumstance of high throughput embryo images. Automatic recognition based on the appearances of embryos is becoming a more desirable scheme. This problem, however, is very challenging due to severe variations of illumination and gene expressions. In this research thesis, we propose an appearance …

The R Journal (December 2010) 2(2): Complete Issue, The R Foundation

The R Journal

Contributed Research Articles

Solving Differential Equations in R, Karline Soetaert, Thomas Petzoldt and R. Woodrow Setzer

Source References, Duncan Murdoch

hglm: A Package for Fitting Hierarchical Generalized Linear Models, Lars Rönnegård, Xia Shen and Moudud Alam

dclone: Data Cloning in R, Péter Sólymos

stringr: Modern, Consistent String Processing, Hadley Wickham

Bayesian Estimation of the GARCH(1,1) Model with Student-t Innovations, David Ardia and Lennart F. Hoogerheide

cudaBayesreg: Bayesian Computation in CUDA, Adelino Ferreira da Silva

binGroup: A Package for Group Testing, Christopher R. Bilder, Boan Zhang, Frank Schaarschmidt, and Joshua M. Tebbs

The RecordLinkage Package: Detecting Errors in Data, Murat Sariyar …

The Recordlinkage Package: Detecting Errors In Data, Murat Sariyar, Andreas Borg

The R Journal

Record linkage deals with detecting homonyms and mainly synonyms in data. The package RecordLinkage provides means to per form and evaluate different record linkage methods. A stochastic framework is implemented which calculates weights through an EM algorithm. The determination of the necessary thresholds in this model can be achieved by tools of extreme value theory. Furthermore, machine learning methods are utilized, including decision trees (rpart), bootstrap aggregating (bagging), ada boost (ada), neural nets (nnet) and support vector machines (svm). The generation of record pairs and comparison patterns from single data …

Bingroup: A Package For Group Testing, Christopher R. Bilder, Boan Zhang, Frank Schaarschmidt, Joshua M. Tebbs

The R Journal

When the prevalence of a disease or of some other binary characteristic is small, group testing (also known as pooled testing) is frequently used to estimate the prevalence and/or to identify individuals as positive or negative. We have developed the binGroup package as the first package designed to address the estimation problem in group testing. We present functions to estimate an overall prevalence for a homogeneous population. Also, for this set ting, we have functions to aid in the very important choice of the group size. When individuals come from a heterogeneous population, our group testing regression functions can be …

Stringr: Modern, Consistent String Processing, Hadley Wickham

The R Journal

String processing is not glamorous, but it is frequently used in data cleaning and preparation. The existing string functions in R are powerful, but not friendly. To remedy this, the stringr package provides string functions that are simpler and more consistent, and also fixes some functionality that R is missing compared to other programming languages.

Source References, Duncan Murdoch

The R Journal

Since version 2.10.0, R includes expanded support for source references in R code and ‘.Rd’ files. This paper describes the origin and purposes of source references, and current and future support for them.

Mapping And Measuring Country Shapes, Nils B. Weidmann, Kristian Skrede Gleditsch

The R Journal

The article introduces the cshapes R package, which includes our CShapes dataset of contemporary and historical country boundaries, as well as computational tools for computing geographical measures from these maps. We provide an overview of the need for considering spatial dependence in comparative re search, how this requires appropriate historical maps, and detail how the cshapes associated R package cshapes can contribute to these ends. We illustrate the use of the package for drawing maps, computing spatial variables for countries, and generating weights matrices for spatial statistics.

Dclone: Data Cloning In R, Péter Sólymos

The R Journal

The dclone R package contains low level functions for implementing maximum likelihood estimating procedures for complex models using data cloning and Bayesian Markov Chain Monte Carlo methods with support for JAGS, WinBUGS and OpenBUGS.

Solving Differential Equations In R, Karline Soetaert, Thomas Petzoldt, R. Woodrow Setzer

The R Journal

Although R is still predominantly applied for statistical analysis and graphical representation, it is rapidly becoming more suitable for mathematical computing. One of the fields where considerable progress has been made recently is the solution of differential equations. Here we give a brief overview of differential equations that can now be solved by R.

Spikeslab: Prediction And Variable Selection Using Spike And Slab Regression, Hemant Ishwaran, Udaya B. Kogalur, J. Sunil Rao

The R Journal

Weighted generalized ridge regression offers unique advantages in correlated high dimensional problems. Such estimators can be efficiently computed using Bayesian spike and slab models and are effective for prediction. For sparse variable selection, a generalization of the elastic net can be used in tandem with these Bayesian estimates. In this article, we de scribe the R-software package spikeslab for implementing this new spike and slab prediction and variable selection methodology.

Hglm: A Package For Fitting Hierarchical Generalized Linear Models, Lars Rönnegård, Xia Shen, Moudud Alam

The R Journal

We present the hglm package for fit ting hierarchical generalized linear models. It can be used for linear mixed models and generalized linear mixed models with random effects for a variety of links and a variety of distributions for both the outcomes and the random effects. Fixed effects can also be fitted in the dispersion part of the model.

Bayesian Estimation Of The Garch(1,1) Model With Student-T Innovations, David Ardia, Lennart F. Hoogerheide

The R Journal

This note presents the R package bayesGARCH which provides functions for the Bayesian estimation of the parsimonious and effective GARCH(1,1) model with Student-t innovations. The estimation procedure is fully automatic and thus avoids the tedious task of tuning an MCMC sampling algorithm. The usage of the package is shown in an empirical application to exchange rate log-returns

Online Reproducible Research: An Application To Multivariate Analysis Of Bacterial Dna Fingerprint Data, Jean Thioulouse, Claire Valiente-Moro, Lionel Zenner

The R Journal

This paper presents an example of online reproducible multivariate data analysis. This example is based on a web page providing an online computing facility on a server. HTML forms contain editable R code snippets that can be executed in any web browser thanks to the Rweb software. The example is based on the multivariate analysis of DNA fingerprints of the internal bacterial flora of the poultry red mite Dermanyssus gallinae. Several multivariate data analysis methods from the ade4 package are used to compare the fingerprints of mite pools coming from various poultry farms. All the computations and graphical displays …

Cudabayesreg: Bayesian Computation In Cuda, Adelino Ferreira Da Silva

The R Journal

Graphical processing units are rapidly gaining maturity as powerful general parallel computing devices. The package cudaBayesreg uses GPU–oriented procedures to improve the performance of Bayesian computations. The paper motivates the need for devising high performance computing strategies in the con text of fMRI data analysis. Some features of the package for Bayesian analysis of brain fMRI data are illustrated. Comparative computing performance figures between sequential and parallel implementations are presented as well.

Ensemble-Based Method For Task 2: Predicting Traffic Jam, Jingrui He, Qing He, Grzegorz Swirszcz, Yiannis Kamarianakis, Rick Lawrence, Wei Shen, Laura Wynter

Research Collection School Of Computing and Information Systems

In this paper, we describe our solution for ICDM 2010 Contest Task 2 (Jams), where the task is to predict future where the next traffic jams will occur in morning rush hour, given data gathered during the initial phase of this peak period. Our solution, which is based on an ensemble approach, finished Second in the final evaluation.

Toward Effective Concept Representation In Decision Support To Improve Patient Safety, Tze-Yun Leong

Research Collection School Of Computing and Information Systems

Patient safety is an emerging, major health care discipline with significance accentuated in the influential Institute of Medicine (IOM) reports in the United States “To Err is Human” and “Crossing the Quality Chasm”. These reports highlighted the danger and prevalence of medical errors and preventable adverse events, explained the three main sources of system-related, human factors-related and cognitive-related errors, and recommended the use of information and decision support technologies to help alleviate the problem. A number of studies and reports from all over the world with similar findings have since followed, culminating in the 55th World Health Assembly Resolution on …

A Structure First Image Inpainting Approach Based On Self-Organizing Map (Som), Bo Chen, Zhaoxia Wang, Ming Bai, Quan Wang, Zhen Sun

Research Collection School Of Computing and Information Systems

This paper presents a structure first image inpainting method based on self-organizing map (SOM). SOM is employed to find the useful structure information of the damaged image. The useful structure information which includes relevant edges of the image is used to simulate the structure information of the lost or damaged area in the image. The structure information is described by distinct or indistinct curves in an image in this paper. The obtained target curves separate the damaged area of the image into several parts. As soon as each part of the damaged image is restored respectively, the damaged image is …

Automobile Exhaust Gas Detection Based On Fuzzy Temperature Compensation System, Zhiyong Wang, Hao Ding, Fufei Hao, Zhaoxia Wang, Zhen Sun, Shujin Li

Research Collection School Of Computing and Information Systems

A temperature compensation scheme of detecting automobile exhaust gas based on fuzzy logic inference is presented in this paper. The principles of the infrared automobile exhaust gas analyzer and the influence of the environmental temperature on analyzer are discussed. A fuzzy inference system is designed to improve the measurement accuracy of the measurement equipment by reducing the measurement errors caused by environmental temperature. The case studies demonstrate the effectiveness of the proposed method. The fuzzy compensation scheme is promising as demonstrated by the simulation results in this paper.

Sequence Alignment Based Analysis Of Player Behavior In Massively Multiplayer Online Role-Playing Games (Mmorpgs), Kyong Jin Shim, Jaideep Srivastava

Research Collection School Of Computing and Information Systems

This study proposes a sequence alignment-based behavior analysis framework (SABAF) developed for predicting inactive game players that either leave the game permanently or stop playing the game for a long period of time. Sequence similarity scores and derived statistics form profile databases of inactive players and active players from the past. SABAF uses global and local sequence alignment algorithms and a unique scoring scheme to measure similarity between activity sequences. SABAF is tested on the game player activity data of Ever Quest II, a popular massively multiplayer online role-playing game developed by Sony Online Entertainment. SABAF consists of the following …

Chemical Plume Tracing By Discrete Fourier Analysis And Particle Swarm Optimization, Eugene Jun Jie Neo, Eldin Wee Chuan Lim

Australian Security and Intelligence Conference

A novel methodology for solving the chemical plume tracing problem that utilizes data from a network of stationary sensors has been developed in this study. During a toxic chemical release and dispersion incident, the imperative need of first responders is to determine the physical location of the source of chemical release in the shortest possible time. However, the chemical plume that develops from the source of release may evolve into a highly complex distribution over the entire contaminated region, making chemical plume tracing one of the most challenging problems known to date. In this study, the discrete Fourier series method …

Would Position Limits Have Made Any Difference To The 'Flash Crash' On May 6, 2010, Wing Bernard Lee, Shih-Fen Cheng, Annie Koh

Research Collection School Of Computing and Information Systems

On May 6, 2010, the US equity markets experienced a brief but highly unusual drop in prices across a number of stocks and indices. The Dow Jones Industrial Average (DJIA) fell by approximately 9% in a matter of minutes, and several stocks were traded down sharply before recovering a short time later. Earlier research by Lee, Cheng and Koh (2010) identified the conditions under which a “flash crash” can be triggered by systematic traders running highly similar trading strategies, especially when they are “crowding out” other liquidity providers in the market. The authors contend that the events of May 6, …

Program Transformations For Information Personalization, Saverio Perugini, Naren Ramakrishnan

Computer Science Faculty Publications

Personalization constitutes the mechanisms necessary to automatically customize information content, structure, and presentation to the end user to reduce information overload. Unlike traditional approaches to personalization, the central theme of our approach is to model a website as a program and conduct website transformation for personalization by program transformation (e.g., partial evaluation, program slicing). The goal of this paper is study personalization through a program transformation lens and develop a formal model, based on program transformations, for personalized interaction with hierarchical hypermedia. The specific research issues addressed involve identifying and developing program representations and transformations suitable for classes of hierarchical …

Context Modeling For Ranking And Tagging Bursty Features In Text Streams, Xin Zhao, Jing Jiang, Jing He, Xiaoming Li, Hongfei Yan, Dongdong Shan

Research Collection School Of Computing and Information Systems

Bursty features in text streams are very useful in many text mining applications. Most existing studies detect bursty features based purely on term frequency changes without taking into account the semantic contexts of terms, and as a result the detected bursty features may not always be interesting or easy to interpret. In this paper we propose to model the contexts of bursty features using a language modeling approach. We then propose a novel topic diversity-based metric using the context models to find newsworthy bursty features. We also propose to use the context models to automatically assign meaningful tags to bursty …

Finding Unusual Review Patterns Using Unexpected Rules, Nitin Jindal, Bing Liu, Ee Peng Lim

Research Collection School Of Computing and Information Systems

In recent years, opinion mining attracted a great deal of research attention. However, limited work has been done on detecting opinion spam (or fake reviews). The problem is analogous to spam in Web search [1, 9 11]. However, review spam is harder to detect because it is very hard, if not impossible, to recognize fake reviews by manually reading them [2]. This paper deals with a restricted problem, i.e., identifying unusual review patterns which can represent suspicious behaviors of reviewers. We formulate the problem as finding unexpected rules. The technique is domain independent. Using the technique, we analyzed an Amazon.com …

Detecting Product Review Spammers Using Rating Behaviors, Ee Peng Lim, Viet-An Nguyen, Nitin Jindal, Bing Liu, Hady Wirawan Lauw

Research Collection School Of Computing and Information Systems

This paper aims to detect users generating spam reviews or review spammers. We identify several characteristic be- haviors of review spammers and model these behaviors so as to detect the spammers. In particular, we seek to model the following behaviors. First, spammers may target specific products or product groups in order to maximize their im- pact. Second, they tend to deviate from the other reviewers in their ratings of products. We propose scoring methods to measure the degree of spam for each reviewer and apply them on an Amazon review dataset. We then select a sub- set of highly suspicious …

Mining Interesting Link Formation Rules In Social Networks, Cane Wing-Ki Leung, Ee Peng Lim, David Lo, Jianshu Weng

Research Collection School Of Computing and Information Systems

Link structures are important patterns one looks out for when modeling and analyzing social networks. In this paper, we propose the task of mining interesting Link Formation rules (LF-rules) containing link structures known as Link Formation patterns (LF-patterns). LF-patterns capture various dyadic and/or triadic structures among groups of nodes, while LF-rules capture the formation of a new link from a focal node to another node as a postcondition of existing connections between the two nodes. We devise a novel LF-rule mining algorithm, known as LFR-Miner, based on frequent subgraph mining for our task. In addition to using a support-confidence framework …

Mining Collaboration Patterns From A Large Developer Network, Didi Surian, David Lo, Ee Peng Lim

Research Collection School Of Computing and Information Systems

In this study, we extract patterns from a large developer collaborations network extracted from Source Forge. Net at high and low level of details. At the high level of details, we extract various network-level statistics from the network. At the low level of details, we extract topological sub-graph patterns that are frequently seen among collaborating developers. Extracting sub graph patterns from large graphs is a hard NP-complete problem. To address this challenge, we employ a novel combination of graph mining and graph matching by leveraging network-level properties of a developer network. With the approach, we successfully analyze a snapshot of …

Shortest Path Computation On Air Indexes, Georgios Kellaris, Kyriakos Mouratidis

Research Collection School Of Computing and Information Systems

Shortest path computation is one of the most common queries in location-based services that involve transportation net- works. Motivated by scalability challenges faced in the mo- bile network industry, we propose adopting the wireless broad- cast model for such location-dependent applications. In this model the data are continuously transmitted on the air, while clients listen to the broadcast and process their queries locally. Although spatial problems have been considered in this environment, there exists no study on shortest path queries in road networks. We develop the rst framework to compute shortest paths on the air, and demonstrate the practicality and …

A Biologically-Inspired Cognitive Agent Model Integrating Declarative Knowledge And Reinforcement Learning, Ah-Hwee Tan, Gee-Wah Ng

Research Collection School Of Computing and Information Systems

The paper proposes a biologically-inspired cognitive agent model, known as FALCON-X, based on an integration of the Adaptive Control of Thought (ACT-R) architecture and a class of self-organizing neural networks called fusion Adaptive Resonance Theory (fusion ART). By replacing the production system of ACT-R by a fusion ART model, FALCON-X integrates high-level deliberative cognitive behaviors and real-time learning abilities, based on biologically plausible neural pathways. We illustrate how FALCON-X, consisting of a core inference area interacting with the associated intentional, declarative, perceptual, motor and critic memory modules, can be used to build virtual robots for battles in a simulated RoboCode …