Computer Sciences Commons^™

Interpreting Attention-Based Models For Natural Language Processing, Steven J. Signorelli Jr

Dartmouth College Undergraduate Theses

Large pre-trained language models (PLMs) such as BERT and XLNet have revolutionized the field of natural language processing (NLP). The interesting thing is that they are pre- trained through unsupervised tasks, so there is a natural curiosity as to what linguistic knowledge these models have learned from only unlabeled data. Fortunately, these models’ architectures are based on self-attention mechanisms, which are naturally interpretable. As such, there is a growing body of work that uses attention to gain insight as to what linguistic knowledge is possessed by these models. Most attention-focused studies use BERT as their subject, and consequently the field …

Why Dilated Convolutional Neural Networks: A Proof Of Their Optimality, Jonatan Contreras, Martine Ceberio, Vladik Kreinovich

Departmental Technical Reports (CS)

One of the most effective image processing techniques is the use of convolutional neural networks that use convolutional layers. In each such layer, the value of the output at each point is a combination of input data corresponding to several neighboring points. To improve the accuracy, researchers have developed a version of this technique, in which only data from some of the neighboring points is processed. It turns out that the most efficient case -- called dilated convolution -- is when we select the neighboring points whose differences in both coordinates are divisible by some constant l. In this paper, …

Distributing Participation In Design: Addressing Challenges Of A Global Pandemic, Jerry Alan Fails

Computer Science Faculty Publications and Presentations

Participatory Design (PD) – whose inclusive benefits are broadly recognised in design – can be very challenging, especially when involving children. The recent COVID-19 pandemic has given rise to further barriers to PD with such groups. One key barrier is the advent of social distancing and government-imposed social restrictions due to the additional risks posed for e.g. children and families vulnerable to COVID-19. This disrupts traditional in-person PD (which involves close socio-emotional and often physical collaboration between participants and researchers). However, alongside such barriers, we have identified opportunities for new and augmented approaches to PD across distributed geographies, backgrounds, ages …

How Social Media And Embedded Recommender Algorithm Fostered Political Issues, Yan Shi

School of Professional Studies

Social media plays a significant role in social communication and interaction, connecting people from different continents and facilitating information flaws worldwide. Meanwhile, along with the evolution of embedded recommender algorithms that clustering people with similar demographic features, social media has become the most important means of communication for modern society. However, the prosper of interconnecting platforms also have potential flows alongside. One of the major issues is the unexpected political consequence. This paper delivers the first comprehensive analysis of the political impacts posed by social media and embedded recommending algorithms. The article identifies three major political concerns through literature review, …

Promoting And Teaching Responsible Leadership In Software Engineering, Devender Goyal, Luiz Fernando Capretz

Electrical and Computer Engineering Publications

As software and computer technology is becoming more prominent and pervasive in all spheres of life, many researchers and industry folks are realizing the importance of teaching soft skills and values to CS and SE students. Many researchers and leaders, from both academic and non-academic world, are also calling for software researchers and practitioners to seriously consider human values, like respect, integrity, compassion, justice, and honesty when building software, both for greater social good and also for financial considerations. In this paper, we propose and wish to promote teaching soft skills, values, and responsibilities to students, which we term as …

How General Is Fuzzy Decision Making?, Olga Kosheleva, Vladik Kreinovich

Departmental Technical Reports (CS)

In many practical situations, users describe their preferences in imprecise (fuzzy) terms. In such situations, fuzzy techniques are a natural way to describe these preferences in precise terms.

Of course, this description is only an approximation to the ideal decision making that a person would perform if we took time to elicit his/her exact preferences. How accurate is this approximation? When can fuzzy decision making -- potentially -- describe the exact decision making, and when there is a limit to the accuracy of fuzzy approximations?

In this paper, we show that decision making can be precisely described in fuzzy terms …

Green Computing: Three Examples Of How Non-Trivial Mathematical Analysis Can Help, Olga Kosheleva, Vladik Kreinovich

Departmental Technical Reports (CS)

Environment-related problems are extremely important for mankind, the fate of humanity itself depends on our ability to solve these problems. These problems are complex, we cannot solve them without using powerful computers. Thus, in the environmental research, environment-related computing is one of the main computing-related research directions. Another direction is related to the fact that computing itself can be (and currently is) harmful for the environment. How to make computing more environment-friendly, how to move towards green computing -- this is the second important direction. A third direction is motivated by the very complexity of environmental systems: it is difficult …

Is It Fair That Advanced Workers Get Paid Disproportionally More: Economic Analysis, Olga Kosheleva, Sean R. Aguilar

Departmental Technical Reports (CS)

On the one hand, everyone agrees that economics should be fair, that workers should get equal pay for equal work. Any instance of unfairness causes a strong disagreement. On the other hand, in many companies, advanced workers -- who produce more than others -- get paid dispropotionally more for their work, and this does not seem to cause any negative feelings. In this paper, we analyze this situation from the economic viewpoint. We show that from this viewpoint, additional payments for advanced workers indeed make economic sense, benefit everyone, and thus -- in contrast to the naive literal interpretation of …

M^3, Catherine Mingmin Wei, Syrsha Anne Harvey

Computer Science and Software Engineering

M^3 aims to raise students' interest in physics through an interactive and fun video game. Originally planned as a segment in the Cal Poly SLO Seeds in STEM workshop, M^3 is designed with middle and high school students as the intended audience.

Pier Ocean Pier, Brandon J. Nowak

Computer Engineering

Pier Ocean Peer is a weatherproof box containing a Jetson Nano, connected to a cell modem and camera, and powered by a Lithium Iron Phosphate battery charged by a 50W solar panel. This system can currently provide photos to monitor the harbor seal population that likes to haul out at the base of the Cal Poly Pier, but more importantly it provides a platform for future expansion by other students either though adding new sensors directly to the Jetson Nano or by connecting to the jetson nano remotely through a wireless protocol of their choice.

Analyzing Dependence Between Point Processes In Time Using Indtestpp, Ana C. Cebrián, Jesús Asín

The R Journal

The need to analyze the dependence between two or more point processes in time appears in many modeling problems related to the occurrence of events, such as the occurrence of climate events at different spatial locations or synchrony detection in spike train analysis. The package IndTestPP provides a general framework for all the steps in this type of analysis, and one of its main features is the implementation of three families of tests to study independence given the intensities of the processes, which are not only useful to assess independence but also to identify factors causing dependence. The package also …

Distr6: R6 Object-Oriented Probability Distributions Interface In R, Raphael Sonabend, Franz J. Király

The R Journal

distr6 is an object-oriented (OO) probability distributions interface leveraging the extensibility and scalability of R6 and the speed and efficiency of Rcpp. Over 50 probability distributions are currently implemented in the package with ‘core’ methods, including density, distribution, and generating functions, and more ‘exotic’ ones, including hazards and distribution function anti-derivatives. In addition to simple distributions, distr6 supports compositions such as truncation, mixtures, and product distributions. This paper presents the core functionality of the package and demonstrates examples for key use-cases. In addition, this paper provides a critical review of the object-oriented programming paradigms in R and describes some …

Krippendorffsalpha: An R Package For Measuring Agreement Using Krippendorff's Alpha Coefficient, John Hughes

The R Journal

R package krippendorffsalpha provides tools for measuring agreement using Krippendorff’s α coefficient, a well-known nonparametric measure of agreement (also called inter-rater reliability and various other names). This article first develops Krippendorff’s α in a natural way and situates α among statistical procedures. Then, the usage of package krippendorffsalpha is illustrated via analyses of two datasets, the latter of which was collected during an imaging study of hip cartilage. The package permits users to apply the α methodology using built-in distance functions for the nominal, ordinal, interval, or ratio levels of measurement. User-defined distance functions are also supported. The fitting function …

The R Package Smicd: Statistical Methods For Interval-Censored Data, Paul Walter

The R Journal

The package allows the use of two new statistical methods for the analysis of intervalcensored data: 1) direct estimation/prediction of statistical indicators and 2) linear (mixed) regression analysis. Direct estimation of statistical indicators, for instance, poverty and inequality indicators, is facilitated by a non parametric kernel density algorithm. The algorithm is able to account for weights in the estimation of statistical indicators. The standard errors of the statistical indicators are estimated with a non parametric bootstrap. Furthermore, the package offers statistical methods for the estimation of linear and linear mixed regression models with an interval-censored dependent variable, particularly random slope …

Finding Optimal Normalizing Transformations Via Bestnormalize, Ryan A. Peterson

The R Journal

The bestNormalize R package was designed to help users find a transformation that can effectively normalize a vector regardless of its actual distribution. Each of the many normalization techniques that have been developed has its own strengths and weaknesses, and deciding which to use until data are fully observed is difficult or impossible. This package facilitates choosing between a range of possible transformations and will automatically return the best one, i.e., the one that makes data look the most normal. To evaluate and compare the normalization efficacy across a suite of possible transformations, we developed a statistic based on a …

Robustness In Network (Robin): An R Package For Comparison And Validation Of Communities, Valeria Policastro, Dario Righelli, Annamaria Carissimo, Luisa Cutillo, Italia De Feis

The R Journal

In network analysis, many community detection algorithms have been developed. However, their implementation leaves unaddressed the question of the statistical validation of the results. Here, we present robin (ROBustness In Network), an R package to assess the robustness of the community structure of a network found by one or more methods to give indications about their reliability. The procedure initially detects if the community structure found by a set of algorithms is statistically significant and then compares two selected detection algorithms on the same graph to choose the one that better fits the network of interest. We demonstrate the use …

Indexnumber: An R Package For Measuring The Evolution Of Magnitudes, Alejandro Saavedra-Nieves, Paula Saavedra-Nieves

The R Journal

Index numbers are descriptive statistical measures useful in economic settings for comparing simple and complex magnitudes registered, usually in two time periods. Although this theory has a large history, it still plays an important role in modern today’s societies where big amounts of economic data are available and need to be analyzed. After a detailed revision on classical index numbers in literature, this paper is focused on the description of the R package IndexNumber with strong capabilities for calculating them. Two of the four real data sets contained in this library are used for illustrating the determination of the index …

Pdynmc: A Package For Estimating Linear Dynamic Panel Data Models Based On Nonlinear Moment Conditions, Markus Fritsch, Andrew Adrian Yu Pua, Joachim Schnurbus

The R Journal

This paper introduces pdynmc, an R package that provides users sufficient flexibility and precise control over the estimation and inference in linear dynamic panel data models. The package primarily allows for the inclusion of nonlinear moment conditions and the use of iterated GMM; additionally, visualizations for data structure and estimation results are provided. The current implementation reflects recent developments in literature, uses sensible argument defaults, and aligns commercial and noncommercial estimation commands. Since the understanding of the model assumptions is vital for setting up plausible estimation routines, we provide a broad introduction of linear dynamic panel data models directed towards …

Benchmarking R Packages For Calculation Of Persistent Homology, Eashwar V. Somasundaram, Shael E. Brown, Adam Litzler, Jacob G. Scott, Raoul R. Wadhwa

The R Journal

Several persistent homology software libraries have been implemented in R. Specifically, the Dionysus, GUDHI, and Ripser libraries have been wrapped by the TDA and TDAstats CRAN packages. These software represent powerful analysis tools that are computationally expensive and, to our knowledge, have not been formally benchmarked. Here, we analyze runtime and memory growth for the 2 R packages and the 3 underlying libraries. We find that datasets with less than 3 dimensions can be evaluated with persistent homology fastest by the GUDHI library in the TDA package. For higher-dimensional datasets, the Ripser library in the TDAstats package is the fastest. …

Unidimensional And Multidimensional Methods For Recurrence Quantification Analysis With Crqa, Moreno I. Coco, Dan Mønster, Giuseppe Leonardi, Rick Dale, Sebastian Wallot

The R Journal

Recurrence quantification analysis is a widely used method for characterizing patterns in time series. This article presents a comprehensive survey for conducting a wide range of recurrence-based analyses to quantify the dynamical structure of single and multivariate time series and capture coupling properties underlying leader-follower relationships. The basics of recurrence quantification analysis (RQA) and all its variants are formally introduced step-by-step from the simplest auto-recurrence to the most advanced multivariate case. Importantly, we show how such RQA methods can be deployed under a single computational framework in R using a substantially renewed version of our crqa 2.0 package. This package …

The Bdpar Package: Big Data Pipelining Architecture For R, Miguel Ferreiro-Díaz, Tomás R. Cotos-Yáñez, José R. Méndez, David Ruano-Ordás

The R Journal

In the last years, big data has become a useful paradigm for taking advantage of multiple sources to find relevant knowledge in real domains (such as the design of personalized marketing campaigns or helping to palliate the effects of several fatal diseases). Big data programming tools and methods have evolved over time from a MapReduce to a pipeline-based archetype. Concretely the use of pipelining schemes has become the most reliable way of processing and analyzing large amounts of data. To this end, this work introduces bdpar, a new highly customizable pipeline-based framework (using the OOP paradigm provided by R6 …

Exprior: An R Package For The Formulation Of Ex-Situ Priors, Falk Heße, Karina Cucchi, Nura Kawa, Yoram Rubin

The R Journal

The exPrior package implements a procedure for formulating informative priors of geostatistical properties for a target field site, called ex-situ priors and introduced in Cucchi et al. (2019). The procedure uses a Bayesian hierarchical model to assimilate multiple types of data coming from multiple sites considered as similar to the target site. This prior summarizes the information contained in the data in the form of a probability density function that can be used to better inform further geostatistical investigations at the site. The formulation of the prior uses ex-situ data, where the data set can either be gathered by the …

Linear Regression With Stationary Errors: The R Package Slm, Emmanuel Caron, Jérôme Dedecker, Bertrand Michel

The R Journal

This paper introduces the R package slm, which stands for Stationary Linear Models. The package contains a set of statistical procedures for linear regression in the general context where the error process is strictly stationary with a short memory. We work in the setting of Hannan (1973), who proved the asymptotic normality of the (normalized) least squares estimators (LSE) under very mild conditions on the error process. We propose different ways to estimate the asymptotic covariance matrix of the LSE and then to correct the type I error rates of the usual tests on the parameters (as well as confidence …

A Method For Deriving Information From Running R Code, Mark P. J. Van Der Loo

The R Journal

It is often useful to tap information from a running R script. Obvious use cases include monitoring the consumption of resources (time, memory) and logging. Perhaps less obvious cases include tracking changes in R objects or collecting the output of unit tests. In this paper, we demonstrate an approach that abstracts the collection and processing of such secondary information from the running R script. Our approach is based on a combination of three elements. The first element is to build a customized way to evaluate code. The second is labeled local masking and it involves temporarily masking a user-facing function …

Npcure: An R Package For Nonparametric Inference In Mixture Cure Models, Ana López-Cheda, M Amalia Jácome, Ignacio López-De-Ullibarri

The R Journal

Mixture cure models have been widely used to analyze survival data with a cure fraction. They assume that a subgroup of the individuals under study will never experience the event (cured subjects). So, the goal is twofold: to study both the cure probability and the failure time of the uncured individuals through a proper survival function (latency). The R package npcure implements a completely nonparametric approach for estimating these functions in mixture cure models, considering right-censored survival times. Nonparametric estimators for the cure probability and the latency as functions of a covariate are provided. Bootstrap bandwidth selectors for the estimators …

Seedcca: An Integrated R-Package For Canonical Correlation Analysis And Partial Least Squares, Bo-Young Kim, Yunju Im, Jae Keun Yoo

The R Journal

Canonical correlation analysis (CCA) has a long history as an explanatory statistical method in high-dimensional data analysis and has been successfully applied in many scientific fields such as chemometrics, pattern recognition, genomic sequence analysis, and so on. The so-called seedCCA is a newly developed R package that implements not only the standard and seeded CCA but also partial least squares. The package enables us to fit CCA to large-p and small-n data. The paper provides a complete guide. Also, the seeded CCA application results are compared with the regularized CCA in the existing R package. It is believed that the …

Conference Report Of Why R? Turkey 2021, Mustafa Cavus, Olgun Aydin, Ozan Evkaya, Ozancan Ozdemir, Deniz Bezer, Ugur Dar

The R Journal

The Why R? Turkey 2021 as a three-day online conference was organized to bring together researchers and professionals from Turkey on April 16-17-18, 2021. We hereby aimed to promote the R community in Turkey by bringing R users with different backgrounds such as genetics, sociology, finance, economy, bio-statistics. There were 8 thematic sessions and 18 invited speakers. In this article, it is aimed to describe the preparation phase, technical details, and the impact of the conference on audience.

News From The Forwards Taskforce, Heather Turner

The R Journal

Forwards is an R Foundation taskforce working to widen the participation of underrepresented groups in the R project and in related activities, such as the useR! conference. This report rounds up activities of the taskforce during the first half of 2021.

Changes On Cran, Kurt Hornik, Uwe Ligges, Achim Zeileis

The R Journal

In the past 6 months, 1290 new packages were added to the CRAN package repository. 116 packages were unarchived and 467 were archived. The following shows the growth of the number of active packages in the CRAN package repository

Regularized Transformation Models: The Tramnet Package, Lucas Kook, Torsten Hothorn

The R Journal

The tramnet package implements regularized linear transformation models by combining the flexible class of transformation models from tram with constrained convex optimization implemented in CVXR. Regularized transformation models unify many existing and novel regularized regression models under one theoretical and computational framework. Regularization strategies implemented for transformation models in tramnet include the Lasso, ridge regression, and the elastic net and follow the parameterization in glmnet. Several functionalities for optimizing the hyperparameters, including model-based optimization based on the mlrMBO package, are implemented. A multitude of S3 methods is deployed for visualization, handling, and simulation purposes. This work aims at illustrating all …