Computer Sciences Commons^™

Fclust: An R Package For Fuzzy Clustering, Maria Brigida Ferraro, Paolo Giordani, Alessio Serafini

The R Journal

Fuzzy clustering methods discover fuzzy partitions where observations can be softly assigned to more than one cluster. The package fclust is a toolbox for fuzzy clustering in the R programming language. It not only implements the widely used fuzzy k-means (FkM) algorithm, but also many FkM variants. Fuzzy cluster similarity measures, cluster validity indices and cluster visualization tools are also offered. In the current version, all the functions are rewritten in the C++ language allowing their application in large-size problems. Moreover, new fuzzy relational clustering algorithms for partitioning qualitative/mixed data are provided together with an improved version of the so-called …

Mdfs: Multidimensional Feature Selection In R, Radosław Piliszek, Krzysztof Mnich, Szymon Migacz, Paweł Tabaszewski, Andrzej Sułecki, Aneta Polewko-Klim, Witold Rudnicki

The R Journal

Identification of informative variables in an information system is often performed using simple one-dimensional filtering procedures that discard information about interactions between variables. Such an approach may result in removing some relevant variables from consideration. Here we present an R package MDFS (MultiDimensional Feature Selection) that performs identification of informative variables taking into account synergistic interactions between multiple descriptors and the decision variable. MDFS is an implementation of an algorithm based on information theory (Mnich and Rudnicki, 2017). The computational kernel of the package is implemented in C++. A high-performance version implemented in CUDA C is also available. The application …

Connecting R With D3 For Dynamic Graphics, To Explore Multivariate Data With Tours, Michael Kipp, Ursula Laa, Dianne Cook

The R Journal

The tourr package in R has several algorithms and displays for showing multivariate data as a sequence of low-dimensional projections. It can display as a movie but has no capacity for interaction, such as stop/go, change tour type, drop/add variables. The tourrGui package provides these sorts of controls, but the interface is programmed with the dated RGtk2 package. This work explores using custom messages to pass data from R to D3 for viewing, using the Shiny framework. This is an approach that can be generally used for creating all sorts of interactive graphics.

Matching With Clustered Data: The Cmatching Package In R, Massimo Cannas, Bruno Arpino

The R Journal

Matching is a well known technique to balance covariates distribution between treated and control units in non-experimental studies. In many fields, clustered data are a very common occurrence in the analysis of observational data and the clustering can add potentially interesting information. Matching algorithms should be adapted to properly exploit the hierarchical structure. In this article we present the CMatching package implementing matching algorithms for clustered data. The package provides functions for obtaining a matched dataset along with estimates of most common parameters of interest and model-based standard errors. A propensity score matching analysis, relating math proficiency with homework completion …

Identifying And Testing Recursive Vs. Interdependent Links In Simultaneous Equation Models Via The Sire Package, Gianmarco Vacca, Maria Grazia Zoia

The R Journal

Simultaneous equation models (SEMs) are composed of relations which either represent unidirectional links, which entail a causal interpretation, or bidirectional links, due to feedback loops, which lead to the notion of interdependence. The issue is of prominent interest in several respects. Investigating the causal structure of a SEM, on the one hand, brings to light the theoretical assumptions behind the model and, on the other hand, pilots the choice of the befitting estimation method and of which policy to implement. This paper provides an operational method to distinguish causal relations from interdependent ones in SEMs, such as macro-econometric models, models …

Rssampling: A Pioneering Package For Ranked Set Sampling, Busra Sevinc, Bekir Cetintav, Melek Esemen, Selma Gurler

The R Journal

Ranked set sampling (RSS) is an advanced data collection method when the exact measurement of an observation is difficult and/or expensive used in a number of research areas, e.g., environment, bioinformatics, ecology, etc. In this method, random sets are drawn from a population and the units in sets are ranked with a ranking mechanism which is based on a visual inspection or a concomitant variable. Because of the importance of working with a good design and easy analysis, there is a need for a software tool which provides sampling designs and statistical inferences based on RSS and its modifications. This …

Title: Ipwerrory: An R Package For Estimation Of Average Treatment Effect With Misclassified Binary Outcome, Di Shu, Grace Y. Yi

The R Journal

It has been well documented that ignoring measurement error may result in severely biased inference results. In recent years, there has been limited but increasing research on causal inference with measurement error. In the presence of misclassified binary outcome variable, Shu and Yi (2017) considered the inverse probability weighted estimation of the average treatment effect and proposed valid estimation methods to correct for misclassification effects for various settings. To expedite the application of those methods for situations where misclassification in the binary outcome variable is a real concern, we implement correction methods proposed by Shu and Yi (2017) and develop …

Semicomprisks: An R Package For The Analysis Of Independent And Cluster-Correlated Semi-Competing Risks Data, Danilo Alvares, Sebastien Haneuse, Catherine Lee, Kyu Ha Lee

The R Journal

Semi-competing risks refer to the setting where primary scientific interest lies in estimation and inference with respect to a non-terminal event, the occurrence of which is subject to a terminal event. In this paper, we present the R package SemiCompRisks that provides functions to perform the analysis of independent/clustered semi-competing risks data under the illness-death multi-state model. The package allows the user to choose the specification for model components from a range of options giving users substantial flexibility, including: accelerated failure time or proportional hazards regression models; parametric or non-parametric specifications for baseline survival functions; parametric or non-parametric specifications for …

R News, R Core Team

The R Journal

CHANGES IN R 3.6.1

Fixed Point Acceleration In R, Stuart Baumann, Margaryta Klymak

The R Journal

t A fixed point problem is one where we seek a vector, X, for a function, f, such that f(X) = X. The solution of many such problems can be accelerated by using a fixed point acceleration algorithm. With the release of the FixedPoint package there is now a number of algorithms available in R that can be used for accelerating the finding of a fixed point of a function. These algorithms include Newton acceleration, Aitken acceleration and Anderson acceleration as well as epsilon extrapolation methods and minimal polynomial methods. This paper demonstrates the use of fixed point accelerators in …

Nowcasting: An R Package For Predicting Economic Variables Using Dynamic Factor Models, Serge De Valk, Daiane De Mattos, Pedro Ferreira

The R Journal

The nowcasting package provides the tools to make forecasts of monthly or quarterly economic variables using dynamic factor models. The objective is to help the user at each step of the forecasting process, starting with the construction of a database, all the way to the interpretation of the forecasts. The dynamic factor model adopted in this package is based on the articles from Giannone et al. (2008) and Banbura et al. (2011). Although there exist several other dynamic factor model packages available for R, ours provides an environment to easily forecast economic variables and interpret results.

Unival: An Fa-Based R Package For Assessing Essential Unidimensionality Using External Validity Information, Pere J. Ferrando, Urbano Lorenzo-Seva, David Navarro-Gonzalez

The R Journal

The unival package is designed to help researchers decide between unidimensional and correlated-factors solutions in the factor analysis of psychometric measures. The novelty of the approach is its use of external information, in which multiple factor scores and general factor scores are related to relevant external variables or criteria. The unival package’s implementation comes from a series of procedures put forward by Ferrando and Lorenzo-Seva (2019) and new methodological developments proposed in this article. We assess models fitted using unival by means of a simulation study extending the results obtained in the original proposal. Its usefulness is also assessed through …

Optimparallel: An R Package Providing A Parallel Version Of The L-Bfgs-B Optimization Method, Florian Gerber, Reinhard Furrer

The R Journal

The R package optimParallel provides a parallel version of the L-BFGS-B optimization method of optim(). The main function of the package is optimParallel(), which has the same usage and output as optim(). Using optimParallel() can significantly reduce the optimization time, especially when the evaluation time of the objective function is large and no analytical gradient is available. We introduce the R package and illustrate its implementation, which takes advantage of the lexical scoping mechanism of R.

Integration Of Networks And Pathways With Starbiotrek Package, Claudia Cava, Isabella Castiglioni

The R Journal

High-throughput genomic technologies bring to light a comprehensive hallmark of molecular changes of a disease. It is increasingly evident that genes are not isolated from each other and the identification of a gene signature can only partially elucidate the de-regulated biological functions in a disease. The comprehension of how groups of genes (pathways) are related to each other (pathway-cross talk) could explain biological mechanisms causing diseases. Biological pathways are important tools to identify gene interactions and decrease the large number of genes to be studied by partitioning them into smaller groups. Furthermore, recent scientific studies have demonstrated that an integration …

Whats For Dynr: A Package For Linear And Nonlinear Dynamic Modeling In R, Lu Ou, Michael D. Hunter, Sy-Miin Chow

The R Journal

Intensive longitudinal data in the behavioral sciences are often noisy, multivariate in nature, and may involve multiple units undergoing regime switches by showing discontinuities interspersed with continuous dynamics. Despite increasing interest in using linear and nonlinear differential/difference equation models with regime switches, there has been a scarcity of software packages that are fast and freely accessible. We have created an R package called dynr that can handle a broad class of linear and nonlinear discrete- and continuous-time models, with regime-switching properties and linear Gaussian measurement functions, in C, while maintaining simple and easy-to-learn model specification functions in R. We present …

Swgee: An R Package For Analyzing Longitudinal Data With Response Missingness And Covariate Measurement Error, Juan Xiong, Grace Y. Yi

The R Journal

Though longitudinal data often contain missing responses and error-prone covariates, relatively little work has been available to simultaneously correct for the effects of response missingness and covariate measurement error on analysis of longitudinal data. Yi (2008) proposed a simulation based marginal method to adjust for the bias induced by measurement error in covariates as well as by missingness in response. The proposed method focuses on modeling the marginal mean and variance structures, and the missing at random mechanism is assumed. Furthermore, the distribution of covariates are left unspecified. These features make the proposed method applicable to a broad settings. In …

Simcorrmix: Simulation Of Correlated Data With Multiple Variable Types Including Continuous And Count Mixture Distributions, Allison Fialkowski, Hemant Tiwari

The R Journal

The SimCorrMix package generates correlated continuous (normal, non-normal, and mixture), binary, ordinal, and count (regular and zero-inflated, Poisson and Negative Binomial) variables that mimic real-world data sets. Continuous variables are simulated using either Fleishman’s third-order or Headrick’s fifth-order power method transformation. Simulation occurs at the component level for continuous mixture distributions, and the target correlation matrix is specified in terms of correlations with components. However, the package contains functions to approximate expected correlations with continuous mixture variables. There are two simulation pathways which calculate intermediate correlations involving count variables differently, increasing accuracy under a wide range of parameters. The package …

The R Journal (June 2019) 11(1): Complete Issue, The R Foundation

The R Journal

Editorial, Michael J. Kane

Contributed Research Articles

atable: Create Tables for Clinical Trial Reports, Armin Ströbel

Connecting R with D3 for Dynamic Graphics, to Explore Multivariate Data with Tours, Michael Kipp, Ursula Laa, and Dianne Cook

Optimization Routines for Enforcing One-to-One Matches in Record Linkage Problems, Diego Moretti, Luca Valentino, and Tiziana Tuoto

mixedsde: A Package to Fit Mixed Stochastic Differential Equations, Charlotte Dion, Simone Hermann, and Adeline Samson

Indoor Positioning and Fingerprinting: The R Package ipft, Emilio Sansano, Raúl Montoliu, Óscar Belmonte, and Joaquín Torres-Sospedra

RobustGaSP: Robust Gaussian Stochastic Process Emulation in R, Mengyang Gu, Jesus Palomo, and James …

Design And Analysis Of An Instrumenting Profiler For Webassembly, Chandler Gifford

Master's Theses

This thesis presents the design, implementation, and analysis of WasmProf, an instrumenting profiler for WebAssembly programs. WebAssembly is a compiled language designed for use on the web that, at the time of this writing, is still being actively developed. At present, performance analysis for WebAssembly programs mostly consists of browsers’ built-in sampling profilers. These profilers work well in many cases but only give a statistical estimation of the distribution of function calls and are, therefore, not well-suited for more fine-grained analysis. The WasmProf instrumenting profiler fills this analysis gap. WasmProf is capable of tracking the number of calls made and …

Corrn: Cooperative Reflection Removal Network, Renjie Wen, Boxin Shi, Haoliang Li, Ling-Yu Duan, Ah-Hwee Tan, Alex C. Kot

Research Collection School Of Computing and Information Systems

Removing the undesired reflections from images taken through the glass is of broad application to various computer vision tasks. Non-learning based methods utilize different handcrafted priors such as the separable sparse gradients caused by different levels of blurs, which often fail due to their limited description capability to the properties of real-world reflections. In this paper, we propose a network with the feature-sharing strategy to tackle this problem in a cooperative and unified framework, by integrating image context information and the multi-scale gradient information. To remove the strong reflections existed in some local regions, we propose a statistic loss by …

Impact Of Http Cookie Violations In Web Archives, Sawood Alam, Michele C. Weigle, Michael L. Nelson

Computer Science Faculty Publications

Certain HTTP Cookies on certain sites can be a source of content bias in archival crawls. Accommodating Cookies at crawl time, but not utilizing them at replay time may cause cookie violations, resulting in defaced composite mementos that never existed on the live web. To address these issues, we propose that crawlers store Cookies with short expiration time and archival replay systems account for values in the Vary header along with URIs.

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

Publications and Research

Streaming APIs are becoming more pervasive in mainstream Object-Oriented programming languages. For example, the Stream API introduced in Java 8 allows for functional-like, MapReduce-style operations in processing both finite and infinite data structures. However, using this API efficiently involves subtle considerations like determining when it is best for stream operations to run in parallel, when running operations in parallel can be less efficient, and when it is safe to run in parallel due to possible lambda expression side-effects. In this paper, we present an automated refactoring approach that assists developers in writing efficient stream code in a semantics-preserving fashion. The …

3d Canopy Model Reconstruction From Unmanned Aerial System And Automated Single Tree Extraction, Hai Ha Duong

Graduate Theses/Dissertations

This project aims to develop and assess methodology for spatial modeling and extracting individual trees from high spatial resolution Digital Surface Model (DSMs) derived from unmanned aerial system (UAS) or drone-based aerial photos. Those results could be used for monitoring of vegetative response of forests, grasslands and vineyards to regional and localized fluctuations in climate and seasonality. The primary objective of this research is to extract 3D spatial information using drone-based aerial imagery through photogrammetric methods. UAS flights were taken place at phenologically critical times over several locations owned and managed by Missouri State University (MSU). The 3D DSM can …

Declassification Of Faceted Values In Javascript, Shreya Gangishetty

Master's Projects

This research addresses the issues with protecting sensitive information at the language level using information flow control mechanisms (IFC). Most of the IFC mechanisms face the challenge of releasing sensitive information in a restricted or limited manner. This research uses faceted values, an IFC mechanism that has shown promising flexibility for downgrading the confidential information in a secure manner, also called declassification.

In this project, we introduce the concept of first-class labels to simplify the declassification of faceted values. To validate the utility of our approach we show how the combination of faceted values and first-class labels can build various …

Shared-Environment Call-By-Need, George W. Stelle

Computer Science ETDs

Call-by-need semantics formalize the wisdom that work should be done at most once. It frees programmers to focus more on the correctness of their code, and less on the operational details. Because of this property, programmers of lazy functional languages rely heavily on their compiler to both preserve correctness and generate high-performance code for high level abstractions. In this dissertation I present a novel technique for compiling call-by-need semantics by using shared environments to share results of computation. I show how the approach enables a compiler that generates high-performance code, while staying simple enough to lend itself to formal reasoning. …

Examining Augmented Virtuality Impairment Simulation For Mobile App Accessibility Design, Tsu Wei, Kenny (Zhu Shuwei, Kenny) Choo, Rajesh Krishna Balan, Rajesh Krishna Balan

Research Collection School Of Computing and Information Systems

With mobile apps rapidly permeating all aspects of daily living with use by all segments of the population, it is crucial to support the evaluation of app usability for specific impaired users to improve app accessibility. In this work, we examine the effects of using our augmented virtuality impairment simulation system–Empath-D–to support experienced designer-developers to redesign a mockup of commonly used mobile application for cataract-impaired users, comparing this with existing tools that aid designing for accessibility. We show that the use of augmented virtuality for assessing usability supports enhanced usability challenge identification, finding more defects and doing so more accurately …

Visualization And Machine Learning Techniques For Nasa’S Em-1 Big Data Problem, Antonio P. Garza Iii, Jose Quinonez, Misael Santana, Nibhrat Lohia

SMU Data Science Review

In this paper, we help NASA solve three Exploration Mission-1 (EM-1) challenges: data storage, computation time, and visualization of complex data. NASA is studying one year of trajectory data to determine available launch opportunities (about 90TBs of data). We improve data storage by introducing a cloud-based solution that provides elasticity and server upgrades. This migration will save $120k in infrastructure costs every four years, and potentially avoid schedule slips. Additionally, it increases computational efficiency by 125%. We further enhance computation via machine learning techniques that use the classic orbital elements to predict valid trajectories. Our machine learning model decreases trajectory …

Seeing Eye To Eye: A Machine Learning Approach To Automated Saccade Analysis, Maigh Attre

Honors Scholar Theses

Abnormal ocular motility is a common manifestation of many underlying pathologies particularly those that are neurological. Dynamics of saccades, when the eye rapidly changes its point of fixation, have been characterized for many neurological disorders including concussions, traumatic brain injuries (TBI), and Parkinson’s disease. However, widespread saccade analysis for diagnostic and research purposes requires the recognition of certain eye movement parameters. Key information such as velocity and duration must be determined from data based on a wide set of patients’ characteristics that may range in eye shapes and iris, hair and skin pigmentation [36]. Previous work on saccade analysis has …

Teaching Introductory Programming Concepts Through A Gesture-Based Interface, Lora Streeter

Graduate Theses and Dissertations

Computer programming is an integral part of a technology driven society, so there is a tremendous need to teach programming to a wider audience. One of the challenges in meeting this demand for programmers is that most traditional computer programming classes are targeted to university/college students with strong math backgrounds. To expand the computer programming workforce, we need to encourage a wider range of students to learn about programming.

The goal of this research is to design and implement a gesture-driven interface to teach computer programming to young and non-traditional students. We designed our user interface based on the feedback …

Towards Zero Knowledge Learning For Cross Language Api Mappings, Duy Quoc Nghi Bui

Research Collection School Of Computing and Information Systems

Programmers often need to migrate programs from one language or platform to another in order to implement functionality, instead of rewriting the code from scratch. However, most techniques proposed to identify API mappings across languages and facilitate automated program translation require manually curated parallel corpora that contain already mapped API seeds or functionally-equivalent code using the APIs in two different languages so that the techniques can have an anchor to map APIs. To alleviate the need of curating parallel data and to generalize the applicability of program translation techniques, we develop a new automated approach for identifying API mappings across …