Computer Sciences Commons^™

Network Technologies Used To Aggregate Environmental Data, Paul Stasiuk, Konstantin Läufer, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

The goal of the Loyola Weather Service (lws) project is to design and build a system of functioning environmental monitoring widgets that can intelligently and autonomously control the environment around them based on set thresholds and triggers. The widgets will also have the ability to aggregate their data and easily display this data in various ways: through a user interface in the room that the widget is placed, via a web application, and programmatically via a RESTful web service.

Distortion Tolerant Source Code Using Viterbi Algorithm, Christopher Hankins

Electrical Engineering Undergraduate Honors Theses

Convolutional codes are used in digital communication systems in order to protect information from distortion and increase system reliability. One of the most efficient methods for decoding convolutional codes is based on the Viterbi Algorithm. Considering the fundamental similarities between these channel codes and source codes, it is logical to postulate that the Viterbi Algorithm may also provide a basis for the implementation of an efficient lossy source code. In this thesis, the Viterbi Algorithm is used to used to compress digital data from a symmetric Bernoulli source. The Viterbi source code is simulated and shown to produce results which …

Cjc: An Extensible Checker For The Cleanjava Annotation Language, Cesar Yeep

Departmental Technical Reports (CS)

CleanJava is a formal annotation language for the Java programming language to support a Cleanroom-style functional program verification technique that views programs as mathematical functions. It needs a suite of support tools including a checker that can parse annotations and check them for syntactic and static semantic correctness. The two key requirements of the checker are flexibility and extensibility. Since the language is still under development and refinement, it should be flexible to facilitate language experimentation and accommodate language changes. It should be also extensible to provide base code for developing more advanced support tools like an automated theorem prover. …

Efficient Architectures For Retrieving Mixed Data With Rest Architecture Style And Html5 Support, Koushik Maddipudi

Masters Theses & Specialist Projects

Software as a service is an emerging but important aspect of the web. Web
Services play a vital role in providing it. Web Services are commonly provided in one of two architectural styles: a "REpresentational State Transfer" (REST), or using the "Simple Object Access Protocol" (SOAP.) Originally most web content was text and small images. But more recent services involve complex data structures including text, images, audio, and video. The task of optimizing data to provide delivery of these structures is a complex one, involving both theoretical and practical aspects. In this thesis work, I have considered two architectures developed …

Tower Of Babel: A Crowdsourcing Game Building Sentiment Lexicons For Resource-Scarce Languages, Yoonsung Hong, Haewoon Kwak, Youngmin Baek, Sue. Moon

Research Collection School Of Computing and Information Systems

With the growing amount of textual data produced by online social media today, the demands for sentiment analysis are also rapidly increasing; and, this is true for worldwide. However, non-English languages often lack sentiment lexicons, a core resource in performing sentiment analysis. Our solution, Tower of Babel (ToB), is a language-independent sentiment-lexicon-generating crowdsourcing game. We conducted an experiment with 135 participants to explore the difference between our solution and a conventional manual annotation method. We evaluated ToB in terms of effectiveness, efficiency, and satisfactions. Based on the result of the evaluation, we conclude that sentiment classification via ToB is accurate, …

A Polyglot Approach To Bioinformatics Data Integration: Phylogenetic Analysis Of Hiv-1, Steven Reisman, Catherine Putonti, George K. Thiruvathukal, Konstantin Läufer

Computer Science: Faculty Publications and Other Works

RNA-interference has potential therapeutic use against HIV-1 by targeting highly-functional mRNA sequences that contribute to the virulence of the virus. Empirical work has shown that within cell lines, all of the HIV-1 genes are affected by RNAi-induced gene silencing. While promising, inherent in this treatment is the fact that RNAi sequences must be highly specific. HIV, however, mutates rapidly, leading to the evolution of viral escape mutants. In fact, such strains are under strong selection to include mutations within the targeted region, evading the RNAi therapy and thus increasing the virus’ fitness in the host. Taking a phylogenetic approach, we …

Senior Project Report - Doctest, Stephen Weessies

Computer Engineering

DocTest is a program that, simply put, allows a programmer or user to document STANAG 4586 (a standard for unmanned aerial vehicle interoperability) messages and test the vehicle system at Lockheed Martin [5]. The program is extensible to allow for further development aiding our software team to do what they do best and not get bogged down in tedious but necessary documentation. DocTest is also used to aid in testing, keeping track of the issues and bugs found and creating a document that captures each issue so an issue is not missed or forgotten. This program was made for use …

Object-Oriented Programming: Some History, And Challenges For The Next Fifty Years, Andrew P. Black

Computer Science Faculty Publications and Presentations

Object-oriented programming is inextricably linked to the pioneering work of Ole-Johan Dahl and Kristen Nygaard on the design of the Simula language, which started at the Norwegian Computing Centre in the Spring of 1961. However, object-orientation, as we think of it today—fifty years later—is the result of a complex interplay of ideas, constraints and people. Dahl and Nygaard would certainly recognize it as their progeny, but might also be amazed at how much it has grown up. This article is based on a lecture given on 22nd August 2011, on the occasion of the scientific opening of the Ole-Johan …

Constructing Verifiably Correct Java Programs Using Ocl And Cleanjava, Yoonsik Cheon, Carmen Avila

Departmental Technical Reports (CS)

A recent trend in software development is building a precise model that can be used as a basis for the software development. Such a model may enable an automatic generation of working code, and more importantly it provides a foundation for correctness reasoning of code. In this paper we propose a practical approach for constructing a verifiably correct program from such a model. The key idea of our approach is (a) to systematically translate formally-specified design constraints such as class invariants and operation pre and postconditions to code-level annotations and (b) to use the annotations for the correctness proof of …

Verifying Linearizability Via Optimized Refinement Checking, Yang Liu, Wei Chen, Yanhong A. Liu, Jun Sun, Shao Jie Zhang, Jin Song Dong Dong

Research Collection School Of Computing and Information Systems

Linearizability is an important correctness criterion for implementations of concurrent objects. Automatic checking of linearizability is challenging because it requires checking that: 1) All executions of concurrent operations are serializable, and 2) the serialized executions are correct with respect to the sequential semantics. In this work, we describe a method to automatically check linearizability based on refinement relations from abstract specifications to concrete implementations. The method does not require that linearization points in the implementations be given, which is often difficult or impossible. However, the method takes advantage of linearization points if they are given. The method is based on …

Modeling And Verifying Hierarchical Real-Time Systems Using Stateful Timed Csp, Jun Sun, Yang Liu, Jin Song Dong, Yan Liu, Ling Shi, Étienne André

Research Collection School Of Computing and Information Systems

Modeling and verifying complex real-time systems are challenging research problems. The de facto approach is based on Timed Automata, which are finite state automata equipped with clock variables. Timed Automata are deficient in modeling hierarchical complex systems. In this work, we propose a language called Stateful Timed CSP and an automated approach for verifying Stateful Timed CSP models. Stateful Timed CSP is based on Timed CSP and is capable of specifying hierarchical real-time systems. Through dynamic zone abstraction, finite-state zone graphs can be generated automatically from Stateful Timed CSP models, which are subject to model checking. Like Timed Automata, Stateful …

Modules And Dialects As Objects In Grace, Michael Homer, James Noble, Kim B. Bruce, Andrew P. Black

Computer Science Faculty Publications and Presentations

Grace is a gradually typed, object-oriented language for use in education; consonant with that use, we have tried to keep Grace as simple and straightforward as possible. Grace needs a module system for several reasons: to teach students about modular program design, to organise large programs, especially its self-hosted implementation, to provide access to resources defined in other languages, and to support different “dialects”—language subsets, or domain specific languages, for particular parts of the curriculum. Grace already has several organising constructs; this paper describes how Grace uses two of them, objects and lexical scope, to provide modules and dialects.

Interactive Ambient Visualizations For Soft Advice, Emerson Murphy-Hill, Titus Barik, Andrew P. Black

Computer Science Faculty Publications and Presentations

Some software packages offer the user soft advice: recommendations that are intended to help the user create high quality artifacts, but which may turn out to be bad advice. It is left to the user to determine whether the soft advice really will improve quality, and to decide whether or not to adopt it. Visualizations can help the user in making this decision, but we believe that conventional visualizations are less than ideal. In this paper, we describe an interactive ambient visualization to help users identify, understand and interpret soft advice.

Our visualization was developed to help programmers interpret code …

The Grace Programming Language Draft Specification Version 0.3.1261, Andrew P. Black, Kim B. Bruce, James Noble

Computer Science Faculty Publications and Presentations

This is a specification of the Grace Programming Language. This specification is notably incomplete, and everything is subject to change.

Symbolic Model-Checking Of Stateful Timed Csp Using Bdd And Digitization, Truong Khanh Nguyen, Jun Sun, Yang Liu, Jin Song Dong

Research Collection School Of Computing and Information Systems

Stateful Timed CSP has been recently proposed to model (and verify) hierarchical real-time systems. It is an expressive modeling language which combines data structure/operations, complicated control flows (modeled using compositional process operators adopted from Timed CSP), and real-time requirements like deadline and within. It has been shown that Stateful Timed CSP is equivalent to closed timed automata with silent transitions, which implies that the timing constraints of Stateful Timed CSP can be captured using explicit tick events, through digitization. In order to tackle the state space explosion problem, we develop a BDD-based symbolic model checking approach to verify Stateful Timed …

Dependently Typed Programming With Singletons, Richard A. Eisenberg, Stephanie Weirich

Computer Science Faculty Research and Scholarship

Haskell programmers have been experimenting with dependent types for at least a decade, using clever encodings that push the limits of the Haskell type system. However, the cleverness of these encodings is also their main drawback. Although the ideas are in- spired by dependently typed programs, the code looks significantly different. As a result, GHC implementors have responded with ex- tensions to Haskell’s type system, such as GADTs, type families, and datatype promotion. However, there remains a significant dif- ference between programming in Haskell and in full-spectrum de- pendently typed languages. Haskell enforces a phase separation be- tween runtime values …

The R Journal (December 2012) 4(2): Complete Issue, The R Foundation

The R Journal

Contributing Articles

What's in a Name? Paul Murrell

It's Not What You Draw, It's What You Don't Draw, Paul Murrell

Debugging grid Graphics, Paul Murrell and Velvet Ly

frailtyHL: A Package for Fitting Frailty Models with H-likelihood, Il Do Ha, Maengseok Noh, and Youngjo Lee

influence.ME: Tools for Detecting Influential Data in Mixed Effects Models, Rense Nieuwenhuis, Manfred te Grotenhuis and Ben Pelzer

The crs Package: Nonparametric Regression Splines for Continuous and Categorical Predictors, Zhenghua Nie and Jeffrey S. Racine

Rfit: Rank-based Estimation for Linear Models, John D. Kloke and Joseph W. McKean

Graphical Markov Models with Mixed Graphs in …

The Crs Package: Nonparametric Regression Splines For Continuous And Categorical Predictors, Zhenghua Nie, Jeffery S. Racine

The R Journal

A new package crs is introduced for computing nonparametric regression (and quantile) splines in the presence of both continuous and categorical predictors. B-splines are employed in the regression model for the continuous predictors and kernel weighting is employed for the categorical predictors. We also de velop a simple R interface to NOMAD, which is a mixed integer optimization solver used to compute optimal regression spline solutions.

Influence.Me: Tools For Detecting Influential Data In Mixed Effects Models, Rense Nieuwenhuis, Manfred Te Grotenhuis, Ben Pelzer

The R Journal

influence.ME provides tools for detecting influential data in mixed effects models. The application of these models has become common practice, but the development of diagnostic tools has lagged behind. influence.ME calculates standardized measures of influential data for the point estimates of generalized mixed effects models, such as DFBETAS, Cook’s distance, as well as percentile change and a test for changing levels of significance. influence.ME calculates these measures of influence while ac counting for the nesting structure of the data. The package and measures of influential data are introduced, a practical example is given, and strategies for dealing with influential data …

Graphical Markov Models With Mixed Graphs In R, Kayvan Sadeghi, Giovanni M. Marchetti

The R Journal

In this paper we provide a short tuto rial illustrating the new functions in the package ggm that deal with ancestral, summary and ribbonless graphs. These are mixed graphs (containing three types of edges) that are important because they capture the modified independence structure after marginalisation over, and conditioning on, nodes of directed acyclic graphs. We provide functions to verify whether a mixed graph implies that A is independent of B given C for any disjoint sets of nodes and to generate maximal graphs inducing the same independence structure of non-maximal graphs. Finally, we provide functions to decide on the …

What's In A Name?, Paul Murrell

The R Journal

Any shape that is drawn using the grid graphics package can have a name associated with it. If a name is provided, it is possible to access, query, and modify the shape after it has been drawn. These facilities allow for very detailed customisations of plots and also for very general transformations of plots that are drawn by packages based on grid.

Frailtyhl: A Package For Fitting Frailty Models With H-Likelihood, Il Do Ha, Maengseok Noh, Youngjo Lee

The R Journal

We present the frailtyHL package for fitting semi-parametric frailty models using h likelihood. This package allows lognormal or gamma frailties for random-effect distribution, and it fits shared or multilevel frailty models for correlated survival data. Functions are provided to format and summarize the frailtyHL results. The estimates of fixed effects and frailty parameters and their standard errors are calculated. We illustrate the use of our package with three well known data sets and compare our results with various alternative R-procedures.

Rfit: Rank-Based Estimation For Linear Models, John D. Kloke, Joseph W. Mckeen

The R Journal

In the nineteen seventies, Jureĉková and Jaeckel proposed rank estimation for linear models. Since that time, several authors have developed inference and diagnostic methods for these estimators. These rank-based estimators and their associated inference are highly efficient and are robust to outliers in response space. The methods include estimation of standard errors, tests of general linear hypotheses, confidence intervals, diagnostic procedures including studentized residuals, and measures of influential cases. We have developed an R package, Rfit, for computing of these robust procedures. In this paper we highlight the main features of the pack age. The package uses standard linear …

It's Not What You Draw, It's What You Don't Draw, Paul Murrell

The R Journal

The R graphics engine has new support for drawing complex paths via the functions polypath() and grid.path(). This article explains what is meant by a complex path and demonstrates the usefulness of complex paths in drawing non-trivial shapes, logos, customised data symbols, and maps.

Debugging Grid Graphics, Paul Murrell, Velvet Ly

The R Journal

A graphical scene that has been produced using the grid graphics package consists of grobs (graphical objects) and viewports. This article describes functions that allow the exploration and inspection of the grobs and viewports in a grid scene, including several functions that are available in a new package called gridDe bug. The ability to explore the grobs and view ports in a grid scene is useful for adding more drawing to a scene that was produced using grid and for understanding and debugging the grid code that produced a scene.

The State Of Naming Conventions In R, Rasmus Bååth

The R Journal

Most programming language communities have naming conventions that are generally agreed upon, that is, a set of rules that governs how functions and variables are named. This is not the case with R, and a review of unofficial style guides and naming convention us age on CRAN shows that a number of different naming conventions are currently in use. Some naming conventions are, however, more popular than others and as a newcomer to the R community or as a developer of a new package this could be useful to consider when choosing what naming convention to adopt.

Dynamic Data Race Detection And Healing, Du Li

School of Computing: Dissertations, Theses, and Student Research

Perpetual availability is an important operational goal in today's computer systems. However, achieving this goal is challenging because modern software systems contain faults that can cause them to fail. For example, multi-threading is widely used in modern software to fully utilize the computing capability of multicore processors. However, employing multi-threading can lead to concurrency faults such as deadlock and data race that are notoriously difficult to to isolate, detect, and repair.Data races, which involves two concurrent accesses to the same data where at least one is a write, are the most common concurrency faults.

As our first step, we investigate …

Effective Computer Programming Instruction For Pre-University Albanian Students, Robert Mccloud, Ardiana Sula

School of Computer Science & Engineering Faculty Publications

The relationship between pre-university students and technology is frequently overrated. While we receive glowing reports about how young people are knowledgeable about computers, the truth is that their knowledge is typically about computer content and the manipulation of applications. Young students too often treat the actual programming and understanding of computers as a sort of magical mystery.

In this paper we look at a new Albanian initiative to identify and nurture the most talented of our pre-university students. In particular we look at contributions to the goal of making Albanians the most talented programmers in this area of Europe.

The …

Fame, Soft Flock Formation Control For Collective Behavior Studies And Rapid Games Development, Choon Sing Ho, Yew-Soon Ong, Xianshun Chen, Ah-Hwee Tan

Research Collection School Of Computing and Information Systems

We present FAME, a comprehensive C# software library package providing soft formation control for large flocks of agents. While many existing available libraries provide means to create flocks of agent equipped with simple steering behavior, none so far, to the best of our knowledge, provides an easy and hassle free approach to control the formation of the flock. Here, besides the basic flocking mechanisms, FAME provides an extensive range of advanced features that gives enhanced soft formation control over multiple flocks. These soft formation features include defining flocks in any user-defined formation, automated self-organizing agent within formation, manipulating formation shape …

Automatic Generation Of Provably Correct Embedded Systems, Shang-Wei Lin, Yang Liu, Pao-Ann Hsiung, Jun Sun, Jin Song Dong

Research Collection School Of Computing and Information Systems

With the demand for new and complicated features, embedded systems are becoming more and more difficult to design and verify. Even if the design of a system is verified, how to guarantee the consistency between the design and its implementation remains a big issue. As a solution, we propose a framework that can help a system designer to model his or her embedded system using a high-level modeling language, verify the design of the system, and automatically generate executable software codes whose behavior semantics are consistent with that of the high-level model. We use two case studies to demonstrate the …