Computer Sciences Commons^™

Health Monitoring Of Atlas Data Center Clusters And Failure Analysis, Meenakshi Balasubramanian

Computer Science and Engineering Theses - Archive

Monitoring the health of data center clusters is an integral part of any industrial facility. ATLAS is one of the High Energy Physics experiments at the Large Hadron Collider (LHC) at CERN. ATLAS DDM (Distributed Data Management) is a system that manages data transfer, staging, deletions and experimental data on the LHC grid. Currently, the DDM system relies on Rucio software, with Cloud based object storage and No-SQL solutions. It is a cumbersome process in the current system, to fetch and analyze the transfer, staging and deletion metrics of a specific site for any regional center. In this thesis, a …

Monitoring Of Swt2 Data Clusters For The Atlas Experiment, Antara Ray

Computer Science and Engineering Theses - Archive

Monitoring of the South West Tier 2 RSEs is done by CERN with the help of Rucio. The challenge faced by the team monitoring the servers at the University of Texas site was that the monitoring data is pictorially represented and provided to them in GIF format. In this work we focus on creating an interactive site that will not only monitor the data at the local RSEs but also create a platform to analyze the data storage systems. It turn it will also create alerts whenever during monitoring an aberration from expected behavior is noticed either in the storage …

Topological And Feature Based Identification Of Hole Boundaries In Point Cloud Data And Differentiation Between Surface And Physical Holes, Aaqif Muhtasim

Computer Science and Engineering Theses - Archive

With the advent of autonomous agents becoming prominent in everyday lives, the importance of processing the surroundings into understandable features becomes more and more important. 3D point clouds play a major role in the perception of such agents and thus having the ability to correctly decipher features from point clouds is crucial to the planning of actions that the agent would need to undertake. This thesis analyzes holes found in point clouds. Based on two approaches that center around topological data analysis and local point set features respectively. It studies how each of the methods works and how a combination …

Generating An Adaptive Path Using Rrt Sampling And Potential Functions With Directional Nearest Neighbors, Sandeep Chahal

Computer Science and Engineering Theses - Archive

Planning algorithms have attained omnipresent successes in several fields including robotics, animation, manufacturing, drug design, computational biology and aerospace applications. Path Planning is an essential component for autonomous robots. The problem involves searching the configuration space and constructing a desired collision-free path that connects two states (the start and the goal) for a robot to gradually navigate from one state to another. In global path planners, the complete path is computed prior to the robot set off. Sampling based planning like Rapidly Expanding Random Trees (RRT) and Probabilistic Road Maps (PRM) used for single or multi-query planning has gained popularity …

Text Mining On Twitter Data To Evaluate Sentiment, Srijanee Niyogi

Computer Science and Engineering Theses - Archive

Social media platforms have been a major part of our daily lives. But with the freedom of expression there is no way one can check whether the posts/tweets/expressions are classified on which polarity. Since Twitter is one of the biggest social platforms for microblogging, hence the experiment was done on this platform. There are several topics that are popular over the internet like sports, politics, finance, technology are chosen as the source of the experiment. These tweets were collected over a span of time for more than 2 months via a cron job. Every tweet can be divided into three …

Samu: Design And Implementation Of Frequency Selectivity-Aware Multi-User Mimo For Wlans, Yongjiu Du, Yan Shi, Ehsan Aryafar, Pengfei Cui, Joseph Camp, Mung Chiang

Computer Science Faculty Publications and Presentations

The traffic demand of wireless networks is expected to increase 1000-fold over the next decade. In anticipation of such increasing data demand for dense networks with a large number of stations, IEEE 802.11ax has introduced key technologies for capacity improvement including Orthogonal Frequency-Division Multiple Access (OFDMA), multi-user multi-input multi-output (MU-MIMO), and greater bandwidth. However, IEEE 802.11ax has yet to fully define a specific scheduling framework, on which the throughput improvement of networks significantly depends. Even within a 20 MHz of bandwidth, users experience heterogeneous channel orthogonality characteristics across sub-carriers, which prevents access points (APs) from achieving the ideal multi-user gain. …

Comparison Mining From Text, Maksim Tkachenko

Dissertations and Theses Collection (Open Access)

Online product reviews are important factors of consumers' purchase decisions. They invade more and more spheres of our life, we have reviews on books, electronics, groceries, entertainments, restaurants, travel experiences, etc. More than 90 percent of consumers read online reviews before they purchase products as reported by various consumers surveys. This observation suggests that product review information enhances consumer experience and helps them to make better-informed purchase decisions. There is an enormous amount of online reviews posted on e-commerce platforms, such as Amazon, Apple, Yelp, TripAdvisor. They vary in information and may be written with different experiences and preferences.

If …

Empathetic Computing For Inclusive Application Design, Kenny Choo Tsu Wei

Dissertations and Theses Collection (Open Access)

The explosive growth of the ecosystem of personal and ambient computing de- vices coupled with the proliferation of high-speed connectivity has enabled ex- tremely powerful and varied mobile computing applications that are used every- where. While such applications have tremendous potential to improve the lives of impaired users, most mobile applications have impoverished designs to be inclusive– lacking support for users with specific disabilities. Mobile app designers today haveinadequate support to design existing classes of apps to support users with specific disabilities, and more so, lack the support to design apps that specifically target these users. One way to resolve …

Building A Versatile Deduplication System, Zhichao Yan

Computer Science and Engineering Dissertations - Archive

With the development of the Internet and information technology, a large amount of unstructured data is generated and stored in various storage systems. In particular, data reduction techniques such as compression and deduplication have become an effective way to address the combined challenges of explosive growth in data volume but lagging network bandwidth growth to increase the space and bandwidth efficiency of various storage systems. However, we have found that existing deduplication systems cannot effectively process compressed data and image data because existing deduplication systems only analyze the hash value of the bitstream to detect redundant data. At the same …

Defending Neural Networks Against Adversarial Examples, Armon Barton

Computer Science and Engineering Dissertations - Archive

Deep learning is becoming a technology central to the safety of cars, the security of networks, and the correct functioning of many other types of systems. Unfortunately, attackers can create adversarial examples, small perturbations to inputs that trick deep neural networks into making a misclassification. Researchers have explored various defenses against this attack, but many of them have been broken. The most robust approaches are Adversarial Training and its extension, Adversarial Logit Pairing, but Adversarial Training requires generating and training on adversarial examples from any possible attack. This is not only expensive, but it is inherently vulnerable to novel attack …

Large-Scale Deep Learning With Application In Medical Imaging And Bio-Informatics, Zheng Xu

Computer Science and Engineering Dissertations - Archive

With the recent advancement of the deep learning technology in the artificial intelligence area, nowadays people's lives have been drastically changed. However, the success of deep learning technology mostly relies on large-scale high-quality data-sets. The complexity of deeper model and larger scale datasets have brought us significant challenges. Inspired by this trend, in this dissertation, we focus on developing efficient and effective large-scale deep learning techniques in solving real-world problems, like cell detection in hyper-resolution medical image or drug screening from millions of compound candidates. With respect to the hyper-resolution medical imaging cell detection problem, the challenges are mainly the …

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 …

Smm: An R Package For Estimation And Simulation Of Discrete-Time Semi-Markov Models, Vlad Stefan Barbu, Caroline Bérard, Dominique Cellier, Mathilde Sautreuil, Nicolas Vergne

The R Journal

Semi-Markov models, independently introduced by Lévy (1954), Smith (1955) and Takacs (1954), are a generalization of the well-known Markov models. For semi-Markov models, sojourn times can be arbitrarily distributed, while sojourn times of Markov models are constrained to be exponentially distributed (in continuous time) or geometrically distributed (in discrete time). The aim of this paper is to present the R package SMM, devoted to the simulation and estimation of discrete-time multi-state semi-Markov and Markov models. For the semi-Markov case we have considered: parametric and non-parametric estimation; with and without censoring at the beginning and/or at the end of sample …

Fica: Fastica Algorithms And Their Improved Variants, Jari Miettinen, Klaus Nordhausen, Sara Taskinen

The R Journal

In independent component analysis (ICA) one searches for mutually independent nongaussian latent variables when the components of the multivariate data are assumed to be linear combinations of them. Arguably, the most popular method to perform ICA is FastICA. There are two classical versions, the deflation-based FastICA where the components are found one by one, and the symmetric FastICA where the components are found simultaneously. These methods have been implemented previously in two R packages, fastICA and ica. We present the R package fICA and compare it to the other packages. Additional features in fICA include optimization of the extraction order …

Snowboot: Bootstrap Methods For Network Inference, Yuzhou Chen, Yulia R. Gel, Vyacheslav Lyubchich, Kusha Nezafati

The R Journal

Complex networks are used to describe a broad range of disparate social systems and natural phenomena, from power grids to customer segmentation to human brain connectome. Challenges of parametric model specification and validation inspire a search for more data-driven and flexible nonparametric approaches for inference of complex networks. In this paper we discuss methodology and R implementation of two bootstrap procedures on random networks, that is, patchwork bootstrap of Thompson et al. (2016) and Gel et al. (2017) and vertex bootstrap of Snijders and Borgatti (1999). To our knowledge, the new R package snowboot is the first implementation of the …

Addhaz: Contribution Of Chronic Diseases To The Disability Burden Using R, Renata Tiene De Carvalho Yokota, Caspar Wn Looman, Wilma Johanna Nusselder, Herman Van Oyen, Geert Molenberghs

The R Journal

The increase in life expectancy followed by the burden of chronic diseases contributes to disability at older ages. The estimation of how much chronic conditions contribute to disability can be useful to develop public health strategies to reduce the burden. This paper introduces the R package addhaz, which is based on the attribution method (Nusselder and Looman, 2004) to partition disability into the additive contributions of diseases using cross-sectional data. The R package includes tools to fit the additive hazard model, the core of the attribution method, to binary and multinomial outcomes. The models are fitted by maximizing the …

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 …

Changes In R, R Core Team

The R Journal

CHANGES IN R 3.5.2

CHANGES IN R 3.5.1

Conference Report: Why R? 2018, Michał Burdukiewicz, Marta Karas, Leon Eyrich Jessen, Marcin KosińSki, Bernd Bischl, Stefan Rödiger

The R Journal

The primary purpose of the Why R? 2018 conference was to provide R programming language enthusiasts with an opportunity to meet and discuss experiences in R software development and analysis applications, for both academia and industry professionals. The event was held 2-5 August, 2018 in a city of Wroclaw, a strong academic and business center of Poland. The total of approximately 250 people from 6 countries attended the main conference event. Additionally, approximately 540 R users attended the pre-meetings in eleven cities across Europe (Figure 2).

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

Shinyitemanalysis For Teaching Psychometrics And To Enforce Routine Analysis Of Educational Tests, Patrícia Martinková, Adéla Drabinová

The R Journal

This work introduces ShinyItemAnalysis, an R package and an online shiny application for psychometric analysis of educational tests and items. ShinyItemAnalysis covers a broad range of psychometric methods and offers data examples, model equations, parameter estimates, interpretation of results, together with a selected R code, and is therefore suitable for teaching psychometric concepts with R. Furthermore, the application aspires to be an easy-to-use tool for analysis of educational tests by allowing the users to upload and analyze their own data and to automatically generate analysis reports in PDF or HTML. We argue that psychometric analysis should be a routine …

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 …

Networktoolbox: Methods And Measures For Brain, Cognitive, And Psychometric Network Analysis In R, Alexander P. Christensen

The R Journal

This article introduces the NetworkToolbox package for R. Network analysis offers an intuitive perspective on complex phenomena via models depicted by nodes (variables) and edges (correlations). The ability of networks to model complexity has made them the standard approach for modeling the intricate interactions in the brain. Similarly, networks have become an increasingly attractive model for studying the complexity of psychological and psychopathological phenomena. NetworkToolbox aims to provide researchers with state-of-the-art methods and measures for estimating and analyzing brain, cognitive, and psychometric networks. In this article, I introduce NetworkToolbox and provide a tutorial for applying some the package’s functions to …

Dynamic Simulation And Testing For Single-Equation Cointegrating And Stationary Autoregressive Distributed Lag Models, Soren Jordan, Andrew Q. Philips

The R Journal

While autoregressive distributed lag models allow for extremely flexible dynamics, interpreting the substantive significance of complex lag structures remains difficult. In this paper we discuss dynamac (dynamic autoregressive and cointegrating models), an R package designed to assist users in estimating, dynamically simulating, and plotting the results of a variety of autoregressive distributed lag models. It also contains a number of post-estimation diagnostics, including a test for cointegration for when researchers are estimating the error-correction variant of the autoregressive distributed lag model.

Bnsp: An R Package For Fitting Bayesian Semiparametric Regression Models And Variable Selection, Georgios Papageorgiou

The R Journal

The R package BNSP provides a unified framework for semiparametric location-scale regression and stochastic search variable selection. The statistical methodology that the package is built upon utilizes basis function expansions to represent semiparametric covariate effects in the mean and variance functions, and spike-slab priors to perform selection and regularization of the estimated effects. In addition to the main function that performs posterior sampling, the package includes functions for assessing convergence of the sampler, summarizing model fits, visualizing covariate effects and obtaining predictions for new responses or their means given feature/covariate vectors.

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 …

Rcss: R Package For Optimal Convex Stochastic Switching, Juri Hinz, Jeremy Yee

The R Journal

The R package rcss provides users with a tool to approximate the value functions in the Bellman recursion under certain assumptions that guarantee desirable convergence properties. This R package represents the first software implementation of these methods using matrices and nearest neighbors. This package also employs a pathwise dynamic method to gauge the quality of these value function approximations. Statistical analysis can be performed on the results to obtain other useful practical insights. This paper describes rcss version 1.6.

Idmtpreg: Regression Model For Progressive Illness Death Data, Leyla Azarang, Manuel Oviedo De La Fuente

The R Journal

The progressive illness-death model is frequently used in medical applications. For example, the model may be used to describe the disease process in cancer studies. We have developed a new R package called idmTPreg to estimate regression coefficients in datasets that can be described by the progressive illness-death model. The motivation for the development of the package is a recent contribution that enables the estimation of possibly time-varying covariate effects on the transition probabilities for a progressive illness-death data. The main feature of the package is that it befits both non-Markov and Markov progressive illness-death data. The package implements the …

Conference Report: R / Medicine Report, Joseph Rickert, Naras Balasubramanian, Michael Kane

The R Journal

R has found widespread use and is flourishing in bioinformatics, the pharmaceutical industry, clinical trials, and basic science labs. While R is being adopted in clinical informatics, its potential has not yet been realized. We believe R will fundamentally transform the space because of its strengths in making new methods available, the availability of tools for reproducible research, its interfaces to other languages, and it’s ability to disseminate new approaches through web interfaces and packaging for rapid prototyping of ideas and implementations.

Moreover, while large number of clinicians, scientists, and statisticians contribute to data driven medical science, communication between individuals …