Programming Languages and Compilers Commons^™

Support Vector Machines For Survival Analysis With R, Césaire J.K. Fouodo, Inke R. König, Claus Weihs, Andreas Ziegler, Marvin N. Wright

The R Journal

This article introduces the R package survivalsvm, implementing support vector machines for survival analysis. Three approaches are available in the package: The regression approach takes censoring into account when formulating the inequality constraints of the support vector problem. In the ranking approach, the inequality constraints set the objective to maximize the concordance index for comparable pairs of observations. The hybrid approach combines the regression and ranking constraints in a single model. We describe survival support vector machines and their implementation, provide examples and compare the prediction performance with the Cox proportional hazards model, random survival forests and gradient boosting using …

Mglm: An R Package For Multivariate Categorical Data Analysis, Juhyun Kim, Yiwen Zhang, Joshua Day, Hua Zhou

The R Journal

Data with multiple responses is ubiquitous in modern applications. However, few tools are available for regression analysis of multivariate counts. The most popular multinomial-logit model has a very restrictive mean-variance structure, limiting its applicability to many data sets. This article introduces an R package MGLM, short for multivariate response generalized linear models, that expands the current tools for regression analysis of polytomous data. Distribution fitting, random number generation, regression, and sparse regression are treated in a unifying framework. The algorithm, usage, and implementation details are discussed.

Cchs: An R Package For Stratified Case-Cohort Studies, Edmund Jones

The R Journal

The cchs package contains a function, also called cchs, for analyzing data from a stratified case-cohort study, as used in epidemiology. For data from this type of study, cchs calculates Estimator III of Borgan et al. (2000), which is a score-unbiased estimator for the regression coefficients in the Cox proportional hazards model. From the user’s point of view, the function is similar to coxph (in the survival package) and other widely used model-fitting functions. Convenient software has not previously been available for Estimator III since it is complicated to calculate. SAS and S-Plus code-fragments for the calculation have been published, …

Small Area Disease Risk Estimation And Visualization Using R, Paula Moraga

The R Journal

Small area disease risk estimation is essential for disease prevention and control. In this paper, we demonstrate how R can be used to obtain disease risk estimates and quantify risk factors using areal data. We explain how to define disease risk models and how to perform Bayesian inference using the INLA package. We also show how to make interactive maps of estimates using the leaflet package to better understand the disease spatial patterns and communicate the results. We show an example of lung cancer risk in Pennsylvania, United States, in year 2002, and demonstrate that R represents an excellent tool …

Semiparametric Generalized Linear Models With The Gldrm Package, Michael J. Wurm, Paul J. Rathouz

The R Journal

This paper introduces a new algorithm to estimate and perform inferences on a recently proposed and developed semiparametric generalized linear model (glm). Rather than selecting a particular parametric exponential family model, such as the Poisson distribution, this semiparametric glm assumes that the response is drawn from the more general exponential tilt family. The regression coefficients and unspecified reference distribution are estimated by maximizing a semiparametric likelihood. The new algorithm incorporates several computational stability and efficiency improvements over the algorithm originally proposed. In particular, the new algorithm performs well for either small or large support for the nonparametric response distribution. The …

Ratingscalereduction Package: Stepwise Rating Scale Item Reduction Without Predictability Loss, Waldemar W. Koczkodaj, Feng Li, Alicja Wolny–Dominiak

The R Journal

This study presents an innovative method for reducing the number of rating scale items without predictability loss. The “area under the receiver operator curve” method (AUC ROC) is used for the stepwise method of reducing items of a rating scale. RatingScaleReduction R package contains the presented implementation. Differential evolution (a metaheuristic for optimization) was applied to one of the analyzed datasets to illustrate that the presented stepwise method can be used with other classifiers to reduce the number of rating scale items (variables). The targeted areas of application are decision making, data mining, machine learning, and psychometrics.

News From The Bioconductor Project, Bioconductor Core Team

The R Journal

The Bioconductor project provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor 3.7 was released on 1 May, 2018. It is compatible with R 3.5.1 and consists of 1560 software packages, 342 experiment data packages, and 919 up-to-date annotation packages. The release announcement includes descriptions of 98 new software packages and updated NEWS files for many additional packages. Start using Bioconductor by installing the most recent version of R and evaluating the commands

A System For An Accountable Data Analysis Process In R, Jonathan Gelfond, Martin Goros, Brian Hernandez, Alex Bokov

The R Journal

Efficiently producing transparent analyses may be difficult for beginners or tedious for the experienced. This implies a need for computing systems and environments that can efficiently satisfy reproducibility and accountability standards. To this end, we have developed a system, R package, and R Shiny application called adapr (Accountable Data Analysis Process in R) that is built on the principle of accountable units. An accountable unit is a data file (statistic, table or graphic) that can be associated with a provenance, meaning how it was created, when it was created and who created it, and this is similar to the ’verifiable …

Mmpf: Monte-Carlo Methods For Prediction Functions, Zachary M. Jones

The R Journal

Machine learning methods can often learn high-dimensional functions which generalize well but are not human interpretable. The mmpf package marginalizes prediction functions using Monte-Carlo methods, allowing users to investigate the behavior of these learned functions, as on a lower dimensional subset of input features: partial dependence and variations thereof. This makes machine learning methods more useful in situations where accurate prediction is not the only goal, such as in the social sciences where linear models are commonly used because of their interpretability.

Many methods for estimating prediction functions produce estimated functions which are not directly human-interpretable because of their complexity: …

Generalized Additive Model Multiple Imputation By Chained Equations With Package Imputerobust, Daniel Salfran, Martin Spiess

The R Journal

Data analysis, common to all empirical sciences, often requires complete data sets. Unfortunately, real world data collection will usually result in data values not being observed. We present a package for robust multiple imputation (the ImputeRobust package) that allows the use of generalized additive models for location, scale, and shape in the context of chained equations. The paper describes the basics of the imputation technique which builds on a semi-parametric regression model (GAMLSS) and the algorithms and functions provided with the corresponding package. Furthermore, some illustrative examples are provided.

Fhdi: An R Package For Fractional Hot Deck Imputation, Jongho Im, In Ho Cho, Jae Kwang Kim

The R Journal

Fractional hot deck imputation (FHDI), proposed by Kalton and Kish (1984) and investigated by Kim and Fuller (2004), is a tool for handling item nonresponse in survey sampling. In FHDI, each missing item is filled with multiple observed values yielding a single completed data set for subsequent analyses. An R package FHDI is developed to perform FHDI and also the fully efficient fractional imputation (FEFI) method of (Fuller and Kim, 2005) to impute multivariate missing data with arbitrary missing patterns. FHDI substitutes missing items with a few observed values jointly obtained from a set of donors whereas the FEFI uses …

The R Journal (July 2018) 10(1): Complete Issue, The R Foundation

The R Journal

Editorial, John Verzani

Contributed Research Articles

A System for an Accountable Data Analysis Process in R, Jonathan Gelfond, Martin Goros, Brian Hernandez and Alex Bokov

RealVAMS: An R Package for Fitting a Multivariate Value-added Model (VAM), Jennifer Broatch, Jennifer Green, and Andrew Karl

InfoTrad: An R Package for Estimating the Probability of Informed Trading, Duygu Çelik and Murat Tiniç

RatingScaleReduction Package: Stepwise Rating Scale Item Reduction without Predictability Loss, Waldemar W. Koczkodaj, Feng Li, and Alicja Wolny-Dominiak

mmpf: Monte-Carlo Methods for Prediction Functions, Zachary M. Jones

Generalized Additive Model Multiple Imputation by Chained Equations with Package ImputeRobust, Daniel Salfran and …

Stackelberg Security Games: Looking Beyond A Decade Of Success, Arunesh Sinha, Fei Fang, Bo An, Christopher Kiekintveld, Milind Tambe

Research Collection School Of Computing and Information Systems

The Stackelberg Security Game (SSG) model has been immensely influential in security research since it was introduced roughly a decade ago. Furthermore, deployed SSG-based applications are one of most successful examples of game theory applications in the real world. We present a broad survey of recent technical advances in SSG and related literature, and then look to the future by highlighting the new potential applications and open research problems in SSG.

Static Analysis Of Context Leaks In Android Applications, Flavio Toffalini, Jun Sun, Martín Cohoa

Research Collection School Of Computing and Information Systems

Android native applications, written in Java and distributed in APK format, are widely used in mobile devices. Their specific pattern of use lets the operating system control the creation and destruction of key resources, such as activities and services (contexts). Programmers are not supposed to interfere with such lifecycle events. Otherwise contexts might be leaked, i.e. they will never be deallocated from memory, or be deallocated too late, leading to memory exhaustion and frozen applications. In practice, it is easy to write incorrect code, which hinders garbage collection of contexts and subsequently leads to context leakage.In this work, we present …

Overfitting In Automated Program Repair: Challenges And Solutions, Dinh Xuan Bach Le

Dissertations and Theses Collection (Open Access)

This chapter discusses the main problem and motivation of this dissertation. It also discusses a quantification of various research issues directly related to the dissertation. A summary of works done will also be presented along with the structure of the dissertation.

Funqual: User-Defined, Statically-Checked Call Graph Constraints In C++, Andrew P. Nelson

Master's Theses

Static analysis tools can aid programmers by reporting potential programming mistakes prior to the execution of a program. Funqual is a static analysis tool that reads C++17 code ``in the wild'' and checks that the function call graph follows a set of rules which can be defined by the user. This sort of analysis can help the programmer to avoid errors such as accidentally calling blocking functions in time-sensitive contexts or accidentally allocating memory in heap-sensitive environments. To accomplish this, we create a type system whereby functions can be given user-defined type qualifiers and where users can define their own …

Compiler Optimization Effects On Register Collisions, Jonathan S. Tan

Master's Theses

We often want a compiler to generate executable code that runs as fast as possible. One consideration toward this goal is to keep values in fast registers to limit the number of slower memory accesses that occur. When there are not enough physical registers available for use, values are ``spilled'' to the runtime stack. The need for spills is discovered during register allocation wherein values in use are mapped to physical registers. One factor in the efficacy of register allocation is the number of values in use at one time (register collisions). Register collision is affected by compiler optimizations that …

An Empirical Study Of Alias Analysis Techniques, Andrew T. Tran

Master's Theses

As software projects become larger and more complex, software optimization at that scale is only feasible through automated means. One such component of software optimization is alias analysis, which attempts to determine which variables in a program refer to the same area in memory, and is used to relocate instructions to improve performance without interfering with program execution. Several alias analyses have been proposed over the past few decades, with varying degrees of precision and time and space complexity, but few studies have been conducted to compare these techniques with one another, nor to measure with program data to confirm …

Poster: Towards Safe Refactoring For Intelligent Parallelization Of Java 8 Streams, Yiming Tang, Raffi Khatchadourian, Mehdi Bagherzadeh, Syed Ahmed

Publications and Research

The Java 8 Stream API sets forth a promising new programming model that incorporates functional-like, MapReduce-style features into a mainstream programming language. However, using streams correctly and efficiently may involve subtle considerations. In this poster, we present our ongoing work and preliminary results towards an automated refactoring approach that assists developers in writing optimal stream code. The approach, based on ordering and typestate analysis, determines when it is safe and advantageous to convert streams to parallel and optimize a parallel streams.

Less-Java, More Learning: Language Design For Introductory Programming, Zamua Nasrawt

Senior Honors Projects, 2010-2019

Less-Java is a new procedural programming language with static, strong, and inferred typing, native unit testing, and support for basic object-oriented constructs. These features make programming in Less-Java more intuitive than traditional introductory languages, which will allow professors to dedicate more class time to overarching computer science concepts and less to syntax and language-specific quirks.