Programming Languages and Compilers Commons^™

Peptides: A Package For Data Mining Of Antimicrobial Peptides, Daniel Osorio, Paola Rondón-Villarreal, Rodrigo Torres

The R Journal

Antimicrobial peptides (AMP) are a promising source of antibiotics with a broad spectrum activity against bacteria and low incidence of developing resistance. The mechanism by which an AMPexecutes its function depends on a set of computable physicochemical properties from the amino acid sequence. The Peptides package was designed to allow the quick and easy computation of ten structural characteristics own of the antimicrobial peptides, with the aim of generating data to increase the accuracy in classification and design of new amino acid sequences. Moreover, the options to read and plot XVG output files from GROMACS molecular dynamics package are included.

Correspondence Analysis On Generalised Aggregated Lexical Tables (Ca-Galt) In The Factominer Package, Belchin Kostov, Mónica Bécue-Bertaut, François Husson

The R Journal

Correspondence analysis on generalised aggregated lexical tables (CA-GALT) is a method that generalizes classical CA-ALT to the case of several quantitative, categorical and mixed variables. It aims to establish a typology of the external variables and a typology of the events from their mutual relationships. In order to do so, the influence of external variables on the lexical choices is untangled cancelling the associations among them, and to avoid the instability issued from multicollinearity, they are substituted by their principal components. The CaGalt function, implemented in the FactoMineR package, provides numerous numerical and graphical outputs. Confidence ellipses are also provided …

Rdrobust: An R Package For Robust Nonparametric Inference In Regression-Discontinuity Designs, Sebastian Calonico, Matias D. Cattaneo, Rocío Titiunik

The R Journal

This article describes the R package rdrobust, which provides data-driven graphical and in ference procedures for RD designs. The package includes three main functions: rdrobust, rdbwselect and rdplot. The first function (rdrobust) implements conventional local-polynomial RD treatment effect point estimators and confidence intervals, as well as robust bias-corrected confidence intervals, for average treatment effects at the cutoff. This function covers sharp RD, sharp kink RD, fuzzy RD and fuzzy kink RD designs, among other possibilities. The second function (rdbwselect) implements several bandwidth selectors proposed in the RD literature. The third function (rdplot) provides data-driven optimal choices of evenly-spaced and …

News From The Bioconductor Project, Bioconductor Team

The R Journal

The Bioconductor project provides tools for the analysis and comprehension of high throughput genomic data. The 1024 software packages available in Bioconductor can be viewed at http://bioconductor.org/packages/. Navigate packages using ‘biocViews’ terms and title search. Each package has an html page with a description, links to vignettes, reference manuals, and usage statistics. Start using Bioconductor version 3.1 by installing R 3.2.1 and evaluating the commandS

Implementing Persistent O(1) Stacks And Queues In R, Shawn T. O'Neil

The R Journal

True to their functional roots, most R functions are side-effect-free, and users expect datatypes to be persistent. However, these semantics complicate the creation of efficient and dynamic data structures. Here, we describe the implementation of stack and queue data structures satisfying these conditions in R, available in the CRAN package rstackdeque. Guided by important work in purely functional languages, we look at both partially- and fully-persistent versions of queues, comparing their performance characteristics. Finally, we illustrate the usefulness of such dynamic structures with examples of generating and solving mazes.

Showtext: Using System Fonts In R Graphics, Yixuan Qiu

The R Journal

This article introduces the showtext package that makes it easy to use system fonts in R graphics. Unlike other methods to embedfonts into graphics, showtext converts text into raster images or polygons, and then adds them to the plot canvas. This method produces platform-independent image files that do not rely on the fonts that create them. It supports a large number of font formats and Rgraphics devices, and meanwhile provides convenient features such as using web fonts and integrating with knitr. This article provides an elaborate introduction to the showtext package, including its design, usage, and examples.

Editorial, Bettina Grün

The R Journal

On behalf of the editorial board, I am pleased to publish Volume 7, Issue 1 of the R Journal. This issue contains 16 contributed research articles. Each of them either presents an R package, a specific extension of an R package or applications using R packages available from the Comprehensive R Archive Network (CRAN, http:://CRAN.R-project.org). It thus provides a small insight into the wide variety of functionality covered currently by the more than 6800 packages available from CRAN.

Manipulation Of Discrete Random Variables With Discreterv, Eric Hare, Andreas Buja, Heike Hofmann

The R Journal

A prominent issue in statistics education is the sometimes large disparity between the theoretical and the computational coursework. discreteRV is an R package for manipulation of discrete random variables which uses clean and familiar syntax similar to the mathematical notation in introductory probability courses. The package offers functions that are simple enough for users with little experience with statistical programming, but has more advanced features which are suitable for a large number of more complex applications. In this paper, we introduce and motivate discreteRV, describe its functionality, and provide reproducible examples illustrating its use.

A Cultural Diffusion Model For The Rise And Fall Of Programming Languages, Sergi Valverde, Ricard V. Solé

Human Biology Open Access Pre-Prints

Our interaction with complex computing machines is mediated by programming languages (PLs) which constitute one of the major innovations in the evolution of technology. PLs allowed a flexible, scalable and fast use of hardware and are largely responsible for shaping the history of information technology since the rise of computers in the 1950s. The rapid growth and impact of computers was followed closely by the development of programming languages. As it occurs with natural, human languages, they emerged and got extinct. There has been always a diversity of coexisting PLs that somewhat compete among them, while occupying special niches. Here …

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

The R Journal

Here I introduce package cmvnorm, a complex generalization of the mvtnorm package. A complex generalization of the Gaussian process is suggested and numerical results presented using the package. An application in the context of approximating the Weierstrass-function using a complex Gaussian process is given.

Verifying Parameterized Timed Security Protocols, Li Li, Jun Sun, Yang Liu, Jin Song Dong

Research Collection School Of Computing and Information Systems

Quantitative timing is often explicitly used in systems for better security, e.g., the credentials for automatic website logon often has limited lifetime. Verifying timing relevant security protocols in these systems is very challenging as timing adds another dimension of complexity compared with the untimed protocol verification. In our previous work, we proposed an approach to check the correctness of the timed authentication in security protocols with fixed timing constraints. However, a more difficult question persists, i.e., given a particular protocol design, whether the protocol has security flaws in its design or it can be configured secure with proper parameter values? …

Introducing Faceted Exception Handling For Dynamic Information Flow, Sri Tej Narala

Master's Projects

JavaScript is most commonly used as a part of web browsers, especially client- side scripts interacting with the user. JavaScript is also the source of many security problems, which includes cross-site scripting attacks. The primary challenge is that code from untrusted sources run with full privileges on the client side, thus lead- ing to security breaches. This paper develops information flow controls with proper exception handling to prevent violations of data confidentiality and integrity.

Faceted values are a mechanism to handle dynamic information flow security in a way that overcomes the limitations caused by dynamic execution, but previous work has …

Adding Syntax Parameters To The Sweet.Js Macro Library For Javascript, Vimal Kumar

Master's Projects

Lisp and Scheme have demonstrated the power of macros to enable programmers to evolve and craft languages. A macro is a rule or pattern that specifies how a certain input sequence should be mapped to an output sequence according to some defined procedure. Using a macro system a programmer can introduce new syntactic elements to the programming language. Macros found in a program are expanded by a macro expander and allow a programmer to enable code reuse. Mozilla Sweet.JS provides a way for developers to enrich their JavaScript code by adding new syntax to the language through the use of …

Operational Semantics For Featherweight Lua, Hanshu Lin

Master's Projects

Lua is a small, embedded language to provide scripting in other languages. De- spite a clean, minimal syntax, it is still too complex for formal reasoning because of some syntactic sugar or specific syntax structures in Lua.

This thesis develops Featherweight Lua (FWLua), following the tradition of lan- guages like Featherweight Java[1] and Featherweight JavaScript[2]. The goal is to develop a core of language features that, while remaining simple enough for formal reasoning, also remain faithful to the central characteristics of the language. Specifi- cally for Lua, the core features that are essential for our modeling include:

∙ First-class functions …

Heuristic Collective Learning For Efficient And Robust Emergence Of Social Norms, Jianye Hao, Jun Sun, Dongping Huang, Yi Cai, Chao Yu

Research Collection School Of Computing and Information Systems

In multiagent systems, social norms is a useful technique in regulating agents’ behaviors to achieve coordination or cooperation among agents. One important research question is to investigate how a desirable social norm can be evolved in a bottom-up manner through local interactions. In this paper, we propose two novel learning strategies under the collective learning framework: collective learning EV-l and collective learning EV-g, to efficiently facilitate the emergence of social norms. Experimental results show that both learning strategies can support the emergence of desirable social norms more efficiently in a much broader range of multiagent interaction scenarios than previous work, …

Wip, Armon Nayeraini

Computer Science and Computer Engineering Undergraduate Honors Theses

Games have been shown to be capable tools in teaching. Additionally, programming can be a hard skill to learn. The objective of this research was to create a game that helps student learn coding concepts by playing a video game. The result of our work is a fully functional game that introduces the beginning concepts of programming: sequential, conditional, iterative operations.

Compression Of Video Tracking And Bandwidth Balancing Routing In Wireless Multimedia Sensor Networks, Yin Wang, Jianjun Yang, Ju Shen, Bryson Payne, Juan Guo, Kun Hua

Computer Science Faculty Publications

There has been a tremendous growth in multimedia applications over wireless networks. Wireless Multimedia Sensor Networks(WMSNs) have become the premier choice in many research communities and industry. Many state-of-art applications, such as surveillance, traffic monitoring, and remote heath care are essentially video tracking and transmission in WMSNs. The transmission speed is constrained by the big file size of video data and fixed bandwidth allocation in constant routing paths. In this paper, we present a CamShift based algorithm to compress the tracking of videos. Then we propose a bandwidth balancing strategy in which each sensor node is able to dynamically select …

Locating Potential Aspect Interference Using Clustering Analysis, Brian Todd Bennett

CCAC Theses and Dissertations

Software design continues to evolve from the structured programming paradigm of the 1970s and 1980s and the object-oriented programming (OOP) paradigm of the 1980s and 1990s. The functional decomposition design methodology used in these paradigms reduced the prominence of non-functional requirements, which resulted in scattered and tangled code to address non-functional elements. Aspect-oriented programming (AOP) allowed the removal of crosscutting concerns scattered throughout class code into single modules known as aspects. Aspectization resulted in increased modularity in class code, but introduced new types of problems that did not exist in OOP. One such problem was aspect interference, in which aspects …

Design, Programming, And User-Experience, Kaila G. Manca

Honors Scholar Theses

This thesis is a culmination of my individualized major in Human-Computer Interaction. As such, it showcases my knowledge of design, computer engineering, user-experience research, and puts into practice my background in psychology, com- munications, and neuroscience.

I provided full-service design and development for a web application to be used by the Digital Media and Design Department and their students.This process involved several iterations of user-experience research, testing, concepting, branding and strategy, ideation, and design. It lead to two products.

The first product is full-scale development and optimization of the web appli- cation.The web application adheres to best practices. It was …

Making Your Popcorn And Enjoying It Too, Sean Anderson, Adam C. Northam

Velma K. Waters Library Faculty Publications

No abstract provided.

Java Animated Software For Teaching The Frank-Wolfe Algorithm For Static Traffic Network Equilibrium, Zhi Li

Computational Modeling & Simulation Engineering Theses & Dissertations

The popular Frank-Wolfe (FW) algorithm for solving the network equilibrium problems plays an important role in transportation simulation. Not only has the basic Frank Wolfe algorithm been studied, but also other variations of the FW algorithm (such as Conjugate Frank Wolfe and Bi-Conjugate Frank Wolfe algorithms) have been extensively studied by the research communities.

In this work, the basic Frank Wolfe algorithm is re-visited for the purpose of developing a useful, user-friendly, and appealing Java computer animation for enhancing the teaching effectiveness of this fundamental transportation static network equilibrium algorithm. Since the shortest path (SP) algorithms (such as the well-known …

Leading Undergraduate Students To Big Data Generation, Jianjun Yang, Ju Shen

Computer Science Faculty Publications

People are facing a flood of data today. Data are being collected at unprecedented scale in many areas, such as networking, image processing, virtualization, scientific computation, and algorithms. The huge data nowadays are called Big Data. Big data is an all encompassing term for any collection of data sets so large and complex that it becomes difficult to process them using traditional data processing applications. In this article, the authors present a unique way which uses network simulator and tools of image processing to train students abilities to learn, analyze, manipulate, and apply Big Data. Thus they develop students hands-on …

Hole Detection And Shape-Free Representation And Double Landmarks Based Geographic Routing In Wireless Sensor Networks, Jianjun Yang, Zongming Fei, Ju Shen

Computer Science Faculty Publications

In wireless sensor networks, an important issue of geographic routing is “local minimum” problem, which is caused by a “hole” that blocks the greedy forwarding process. Existing geographic routing algorithms use perimeter routing strategies to find a long detour path when such a situation occurs. To avoid the long detour path, recent research focuses on detecting the hole in advance, then the nodes located on the boundary of the hole advertise the hole information to the nodes near the hole. Hence the long detour path can be avoided in future routing. We propose a heuristic hole detecting algorithm which identifies …

Privacycanary: Privacy-Aware Recommenders With Adaptive Input Obfuscation, Thivya Kandappu, Arik Friedman, Roksan Borelli, Vijay Sivaraman

Research Collection School Of Computing and Information Systems

Recommender systems are widely used by online retailers to promote products and content that are most likely to be of interest to a specific customer. In such systems, users often implicitly or explicitly rate products they have consumed, and some form of collaborative filtering is used to find other users with similar tastes to whom the products can be recommended. While users can benefit from more targeted and relevant recommendations, they are also exposed to greater risks of privacy loss, which can lead to undesirable financial and social consequences. The use of obfuscation techniques to preserve the privacy of user …

The Expression Problem, Gracefully, Andrew P. Black

Computer Science Faculty Publications and Presentations

The “Expression Problem” was brought to prominence by Wadler in 1998. It is widely regarded as illustrating that the two mainstream approaches to data abstraction — procedural abstraction and type abstraction— are complementary, with the strengths of one being the weaknesses of the other. Despite an extensive literature, the origin of the problem remains ill-understood. I show that the core problem is in fact the use of global constants, and demonstrate that an important aspect of the problem goes away when Java is replaced by a language like Grace, which eliminates them.

The Grace Programming Language Draft Specification Version 0.5. 2025, 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. For discussion and rationale, see http://gracelang.org.

Metalogic Notes, Saverio Perugini

Computer Science Working Papers

A collection of notes, formulas, theorems, postulates and terminology in symbolic logic, syntactic notions, semantic notions, linkages between syntax and semantics, soundness and completeness, quantified logic, first-order theories, Goedel's First Incompleteness Theorem and more.

Statistics Notes, Saverio Perugini

Computer Science Working Papers

A collection of terms, definitions, formulas and explanations about statistics.

Injective Type Families For Haskell, Jan Stolarek, Simon Peyton Jones, Richard A. Eisenberg

Computer Science Faculty Research and Scholarship

Haskell, as implemented by the Glasgow Haskell Compiler (GHC), allows expressive type-level programming. The most popular type- level programming extension is TypeFamilies, which allows users to write functions on types. Yet, using type functions can cripple type inference in certain situations. In particular, lack of injectivity in type functions means that GHC can never infer an instantiation of a type variable appearing only under type functions. In this paper, we describe a small modification to GHC that allows type functions to be annotated as injective. GHC naturally must check validity of the injectivity annotations. The algorithm to do so is …

Math In The Dark: Tools For Expressing Mathematical Content By Visually Impaired Students, Patricia M. Mcdermott-Wells

CCAC Theses and Dissertations

Blind and visually impaired students are under-represented in the science, technology, engineering, and mathematics disciplines of higher education and the workforce. This is due primarily to the difficulties they encounter in trying to succeed in mathematics courses. While there are sufficient tools available to create Braille content, including the special Nemeth Braille used in the U.S. for mathematics constructs, there are very few tools to allow a blind or visually impaired student to create his/her own mathematical content in a manner that sighted individuals can use. The software tools that are available are isolated, do not interface well with other …