Programming Languages and Compilers Commons^™

Geospatial Point Density, Paul F. Evangelista, David Beskow

The R Journal

This paper introduces a spatial point density algorithm designed to be explainable, meaning ful, and efficient. Originally designed for military applications, this technique applies to any spatial point process where there is a desire to clearly understand the measurement of density and maintain fidelity of the point locations. Typical spatial density plotting algorithms, such as kernel density estimation, implement some type of smoothing function that often results in a density value that is difficult to interpret. The purpose of the visualization method in this paper is to understand spatial point activity density with precision and meaning. The temporal tendency of …

Perflearner: Learning From Bug Reports To Understand And Generate Performance Test Frames, Xue Han, Tingting Yu, David Lo

Research Collection School Of Computing and Information Systems

Software performance is important for ensuring the quality of software products. Performance bugs, defined as programming errors that cause significant performance degradation, can lead to slow systems and poor user experience. While there has been some research on automated performance testing such as test case generation, the main idea is to select workload values to increase the program execution times. These techniques often assume the initial test cases have the right combination of input parameters and focus on evolving values of certain input parameters. However, such an assumption may not hold for highly configurable real-word applications, in which the combinations …

Towards Automated Domain-Oriented Lexicon Construction And Dimension Reduction For Arabic Sentiment Analysis, Hasan A. Alshahrani

Dissertations

Sentiment analysis is a type of text mining that uses Natural Language Processing (NLP) tools to identify and label opinionated text. There are two main approaches of sentiment analysis: lexicon-based, and statistical approach. In our research, we use the lexicon-based approach because the lexicon contains sentiment words and phrases which are the main linguistic units to express sentiments. More specifically, we work with domain-oriented lexicons as they are more efficient than general ones because the polarity is heavily driven by domains.

Arabic language has a degree of uniqueness that makes it hard to be processed with the available cross-language tools …

Effectiveness Of Physical Robot Versus Robot Simulator In Teaching Introductory Programming, Oka Kurniawan, Norman Tiong Seng Lee, Subhajit Datta, Nachamma Sockalingam, Pey Lin Leong

Research Collection School Of Computing and Information Systems

This study reports the use of a physical robot and robot simulator in an introductory programming course in a university and measures students' programming background conceptual learning gain and learning experience. One group used physical robots in their lessons to complete programming assignments, while the other group used robot simulators. We are interested in finding out if there is any difference in the learning gain and experiences between those that use physical robots as compared to robot simulators. Our results suggest that there is no significant difference in terms of students' learning between the two approaches. However, the control group …

Feature-Based Transfer Learning In Natural Language Processing, Jianfei Yu

Dissertations and Theses Collection (Open Access)

In the past few decades, supervised machine learning approach is one of the most important methodologies in the Natural Language Processing (NLP) community. Although various kinds of supervised learning methods have been proposed to obtain the state-of-the-art performance across most NLP tasks, the bottleneck of them lies in the heavy reliance on the large amount of manually annotated data, which is not always available in our desired target domain/task. To alleviate the data sparsity issue in the target domain/task, an attractive solution is to find sufficient labeled data from a related source domain/task. However, for most NLP applications, due to …

Exploring The Impact Of Pretrained Bidirectional Language Models On Protein Secondary Structure Prediction, Dillon G. Daudert

Masters Theses

Protein secondary structure prediction (PSSP) involves determining the local conformations of the peptide backbone in a folded protein, and is often the first step in resolving a protein's global folded structure. Accurate structure prediction has important implications for understanding protein function and de novo protein design, with progress in recent years being driven by the application of deep learning methods such as convolutional and recurrent neural networks. Language models pretrained on large text corpora have been shown to learn useful representations for feature extraction and transfer learning across problem domains in natural language processing, most notably in instances where the …

Testfordep: An R Package For Modern Distribution-Free Tests And Visualization Tools For Independence, Jeffrey C. Miecznikowski, En-Shuo Hsu, Yanhua Chen, Albert Vexler

The R Journal

This article introduces testforDEP, a portmanteau R package implementing for the first time several modern tests and visualization tools for independence between two variables. While classical tests for independence are in the base R packages, there have been several recently developed tests for independence that are not available in R. This new package combines the classical tests including Pearson’s product moment correlation coefficient method, Kendall’s τ rank correlation coefficient method and Spearman’s ρ rank correlation coefficient method with modern tests consisting of an empirical likelihood based test, a density-based empirical likelihood ratio test, Kallenberg data-driven test, maximal information coefficient …

Clustmixtype: User-Friendly Clustering Of Mixed-Type Data In R, Gero Szepannek

The R Journal

Clustering algorithms are designed to identify groups in data where the traditional emphasis has been on numeric data. In consequence, many existing algorithms are devoted to this kind of data even though a combination of numeric and categorical data is more common in most business applications. Recently, new algorithms for clustering mixed-type data have been proposed based on Huang’s k-prototypes algorithm. This paper describes the R package clustMixType which provides an implementation of k-prototypes in R.

Profile Likelihood Estimation Of The Correlation Coefficient In The Presence Of Left, Right Or Interval Censoring And Missing Data, Yanming Li, Brenda W. Gillespie, Kerby Shedden, John A. Gillespie

The R Journal

We discuss implementation of a profile likelihood method for estimating a Pearson correlation coefficient from bivariate data with censoring and/or missing values. The method is implemented in an R package clikcorr which calculates maximum likelihood estimates of the correlation coefficient when the data are modeled with either a Gaussian or a Student t-distribution, in the presence of left, right, or interval censored and/or missing data. The R package includes functions for conducting inference and also provides graphical functions for visualizing the censored data scatter plot and profile log likelihood function. The performance of clikcorr in a variety of circumstances is …

Basis-Adaptive Selection Algorithm In Dr-Package, Jae Keun Yoo

The R Journal

Sufficient dimension reduction (SDR) turns out to be a useful dimension reduction tool in high-dimensional regression analysis. Weisberg (2002) developed the dr-package to implement the four most popular SDR methods. However, the package does not provide any clear guidelines as to which method should be used given a data. Since the four methods may provide dramatically different dimension reduction results, the selection in the dr-package is problematic for statistical practitioners. In this paper, a basis-adaptive selection algorithm is developed in order to relieve this issue. The basic idea is to select an SDR method that provides the highest …

Revengc: An R Package To Reverse Engineer Summarized Data, Samantha Duchscherer, Robert Stewart, Marie Urban

The R Journal

Decoupled (e.g. separate averages) and censored (e.g. > 100 species) variables are continually reported by many well-established organizations, such as the World Health Organization (WHO), Centers for Disease Control and Prevention (CDC), and World Bank. The challenge therefore is to infer what the original data could have been given summarized information. We present an R package that reverse engineers censored and/or decoupled data with two main functions. The cnbinom.pars() function estimates the average and dispersion parameter of a censored univariate frequency table. The rec() function reverse engineers summarized data into an uncensored bivariate table of probabilities.

Stplanr: A Package For Transport Planning, Robin Lovelace, Richard Ellison

The R Journal

Tools for transport planning should be flexible, scalable, and transparent. The stplanr package demonstrates and provides a home for such tools, with an emphasis on spatial transport data and non-motorized modes. The stplanr package facilitates common transport planning tasks including: downloading and cleaning transport datasets; creating geographic “desire lines” from origin-destination (OD) data; route assignment, locally and interfaces to routing services such as CycleStreets.net; calculation of route segment attributes such as bearing and aggregate flow; and ‘travel watershed’ analysis. This paper demonstrates this functionality using reproducible examples on real transport datasets. More broadly, the experience of developing and using R …

Lmridge: A Comprehensive R Package For Ridge Regression, Muhammad Imdad Ullah, Bahauddin Zakariya University Aslam, Saima Atlaf

The R Journal

The ridge regression estimator, one of the commonly used alternatives to the conventional ordinary least squares estimator, avoids the adverse effects in the situations when there exists some considerable degree of multicollinearity among the regressors. There are many software packages available for estimation of ridge regression coefficients. However, most of them display limited methods to estimate the ridge biasing parameters without testing procedures. Our developed package, lmridge can be used to estimate ridge coefficients considering a range of different existing biasing parameters, to test these coefficients with more than 25 ridge related statistics, and to present different graphical displays of …

Sdpt3r: Semidefinite Quadratic Linear Programming In R, Adam Rahman

The R Journal

We present the package sdpt3r, an R implementation of the Matlab package SDPT3 (Toh et al., 1999). The purpose of the software is to solve semidefinite quadratic linear programming (SQLP) problems, which encompasses problems such as D-optimal experimental design, the nearest correlation matrix problem, and distance weighted discrimination, as well as problems in graph theory such as finding the maximum cut or Lovasz number of a graph.

Current optimization packages in R include Rdsdp, Rcsdp, scs, cccp, and Rmosek. Of these, scs and Rmosek solve a similar suite of problems. In addition to these …

Bnclassify: Learning Bayesian Network Classifiers, Bojan Mihaljević, Concha Bielza, Pedro Larrañaga

The R Journal

The bnclassify package provides state-of-the art algorithms for learning Bayesian network classifiers from data. For structure learning it provides variants of the greedy hill-climbing search, a well-known adaptation of the Chow-Liu algorithm and averaged one-dependence estimators. It provides Bayesian and maximum likelihood parameter estimation, as well as three naive-Bayes specific methods based on discriminative score optimization and Bayesian model averaging. The implementation is efficient enough to allow for time-consuming discriminative scores on medium sized data sets. The bnclassify package provides utilities for model evaluation, such as cross-validated accuracy and penalized log-likelihood scores, and analysis of the underlying networks, including network …

Conference Report: Latinr 2018, Laura Acion, Natalia Da Silva, Riva Quiroga

The R Journal

LatinR <- Latin American Conference about the Use of R in Research + Development (LatinR) was an international conference whose goal was bringing together the Latin Ameri can R community. The inagural LatinR took place at the Universidad de Palermo in Buenos Aires, Argentina, on September 3 to 5, 2018. About 100 participants from more than 10 differ ent countries (e.g., Argentina, Uruguay, Chile, Peru, Ecuador, Brazil, Costa Rica, Venezuela, Spain, United States, Canada) attended LatinR.

LatinR will be an annual meeting that will rotate among different countries in Latin America. LatinR 2019 will be hosted by the Universidad Católica de Chile in Santiago de Chile on September 25 to 27

Explanations Of Model Predictions With Live And Breakdown Packages, Mateusz Staniak, Przemysław Biecek

The R Journal

Complex models are commonly used in predictive modeling. In this paper we present R packages that can be used for explaining predictions from complex black box models and attributing parts of these predictions to input features. We introduce two new approaches and corresponding packages for such attribution, namely live and breakDown. We also compare their results with existing implementations of state-of-the-art solutions, namely, lime (Pedersen and Benesty, 2018) which implements Locally Interpretable Model-agnostic Explanations and iml (Molnar et al., 2018) which implements Shapley values.

Downside Risk Evaluation With The R Package Gas, David Ardia, Kris Boudt, Leopoldo Catania

The R Journal

Financial risk managers routinely use non–linear time series models to predict the downside risk of the capital under management. They also need to evaluate the adequacy of their model using so–called backtesting procedures. The latter involve hypothesis testing and evaluation of loss functions. This paper shows how the R package GAS can be used for both the dynamic prediction and the evaluation of downside risk. Emphasis is given to the two key financial downside risk measures: Value-at-Risk (VaR) and Expected Shortfall (ES). High-level functions for: (i) prediction, (ii) backtesting, and (iii) model comparison are discussed, and code examples are provided. …

Dot-Pipe: An S3 Extensible Pipe For R, John Mount, Nina Zumel

The R Journal

Pipe notation is popular with a large league of R users, with magrittr being the dominant realization. However, this should not be enough to consider piping in R as a settled topic that is not subject to further discussion, experimentation, or possibility for improvement. To promote innovation opportunities, we describe the wrapr R package and “dot-pipe” notation, a well behaved sequencing operator with S3 extensibility. We include a number of examples of using this pipe to interact with and extend other R packages.

Rfsa: An R Package For Finding Best Subsets And Interactions, Joshua Lambert, Liyu Gong, Corrine F. Elliott, Katherine Thompson, Arnold Stromberg

The R Journal

Herein we present the R package rFSA, which implements an algorithm for improved variable selection. The algorithm searches a data space for models of a user-specified form that are statistically optimal under a measure of model quality. Many iterations afford a set of feasible solutions (or candidate models) that the researcher can evaluate for relevance to his or her questions of interest. The algorithm can be used to formulate new or to improve upon existing models in bioinformatics, health care, and myriad other fields in which the volume of available data has outstripped researchers’ practical and computational ability to explore …