Computer Sciences Commons^™

View-Dependent Data Prefetching For Interactive Visualization Of Large-Scale 3d Scientific Data, Jin Wang

School of Computing: Dissertations, Theses, and Student Research

One of the most significant challenges for today's interactive visualization is the efficient analysis and visualization of large-scale data, and I/O becomes a significant performance bottleneck. This thesis proposes a new data management policy to support interactive large-scale visual analytics. Our method can characterize user's data access patterns according to their data-dependent and view-dependent visualization operations, and leverage application knowledge to derive a novel scheme to predict data access during the interactive operations. Based on the prediction results, we develop a data replacement policy to exploit data locality and minimize data movement across multiple levels of a memory hierarchy. We …

Document Images And Machine Learning: A Collaboratory Between The Library Of Congress And The Image Analysis For Archival Discovery (Aida) Lab At The University Of Nebraska, Lincoln, Ne, Yi Liu, Chulwoo Pack, Leen-Kiat Soh, Elizabeth Lorang

School of Computing: Conference and Workshop Papers

This presentation summarized and presented preliminary results from the first weeks of work conducted by the Aida research team in response to Library of Congress funding notice ID 030ADV19Q0274, “The Library of Congress – Pre-processing Pilot.” It includes overviews of projects on historic document segmentation, document classification, document quality assessment, figure and graph extraction from historic documents, text-line extraction from figures, subject and objective quality assesments, and digitization type differentiation.

Learnfca: A Fuzzy Fca And Probability Based Approach For Learning And Classification, Suraj Ketan Samal

School of Computing: Dissertations, Theses, and Student Research

Formal concept analysis(FCA) is a mathematical theory based on lattice and order theory used for data analysis and knowledge representation. Over the past several years, many of its extensions have been proposed and applied in several domains including data mining, machine learning, knowledge management, semantic web, software development, chemistry ,biology, medicine, data analytics, biology and ontology engineering.

This thesis reviews the state-of-the-art of theory of Formal Concept Analysis(FCA) and its various extensions that have been developed and well-studied in the past several years. We discuss their historical roots, reproduce the original definitions and derivations with illustrative examples. Further, we provide …

Analysis Of Social Unrest Events Using Spatio-Temporal Data Clustering And Agent-Based Modelling, Sudeep Basnet

School of Computing: Dissertations, Theses, and Student Research

Social unrest such as appeals, protests, conflicts, fights and mass violence can result from a wide ranging of diverse factors making the analysis of causal relationships challenging, with high complexity and uncertainty. Unrest events can result in significant changes in a society ranging from new policies and regulations to regime change. Widespread unrest often arises through a process of feedback and cascading of a collection of past events over time, in regions that are close to each other. Understanding the dynamics of these social events and extrapolating their future growth will enable analysts to detect or forecast major societal events. …

Distributed Edge Bundling For Large Graphs, Yves Tuyishime

School of Computing: Dissertations, Theses, and Student Research

Graphs or networks are widely used to depict the relationships between data entities in diverse scientific and engineering applications. A direct visualization (such as node-link diagram) of a graph with a large number of nodes and edges often incurs visual clutter. To address this issue, researchers have developed edge bundling algorithms that visually merge similar edges into curved bundles and can effectively reveal high-level edge patterns with reduced visual clutter. Although the existing edge bundling algorithms achieve appealing results, they are mostly designed for a single machine, and thereby the size of a graph they can handle is limited by …

Exploring Eye Tracking Data On Source Code Via Dual Space Analysis, Li Zhang

School of Computing: Dissertations, Theses, and Student Research

Eye tracking is a frequently used technique to collect data capturing users' strategies and behaviors in processing information. Understanding how programmers navigate through a large number of classes and methods to find bugs is important to educators and practitioners in software engineering. However, the eye tracking data collected on realistic codebases is massive compared to traditional eye tracking data on one static page. The same content may appear in different areas on the screen with users scrolling in an Integrated Development Environment (IDE). Hierarchically structured content and fluid method position compose the two major challenges for visualization. We present a …

Impact Of Robotic Challenges On Fifth Grade Problem Solving, Julie Rankin

Department of Teaching, Learning, and Teacher Education: Theses and Other Student Research

This action research project was designed to investigate the impact of educational robotics in a fifth grade rural classroom. The integration of science, technology, engineering, and math in education (STEM) has sparked an increase of robotics in the classroom. The purpose of the study was to determine if problem-solving skills can be impacted through continuing involvement with challenges using various educational robotics and programming tools. The study sought to answer two research questions: (1) How does the introduction of robotics challenges in a fifth-grade classroom impact students’ problem solving skills? (2) How do robotics in the classroom impact student interest …

Dimensional Analysis Of Robot Software Without Developer Annotations, John-Paul W. Ore

School of Computing: Dissertations, Theses, and Student Research

Robot software risks the hazard of dimensional inconsistencies. These inconsistencies occur when a program incorrectly manipulates values representing real-world quantities. Incorrect manipulation has real-world consequences that range in severity from benign to catastrophic. Previous approaches detect dimensional inconsistencies in programs but require extra developer effort and technical complications. The extra effort involves developers creating type annotations for every variable representing a real-world quantity that has physical units, and the technical complications include toolchain burdens like specialized compilers or type libraries.

To overcome the limitations of previous approaches, this thesis presents novel methods to detect dimensional inconsistencies without developer annotations. We …

The Design And Implementation Of Aida: Ancient Inscription Database And Analytics System, M. Parvez Rashid

School of Computing: Dissertations, Theses, and Student Research

AIDA, the Ancient Inscription Database and Analytic system can be used to translate and analyze ancient Minoan language. The AIDA system currently stores three types of ancient Minoan inscriptions: Linear A, Cretan Hieroglyph and Phaistos Disk inscriptions. In addition, AIDA provides candidate syllabic values and translations of Minoan words and inscriptions into English. The AIDA system allows the users to change these candidate phonetic assignments to the Linear A, Cretan Hieroglyph and Phaistos symbols. Hence the AIDA system provides for various scholars not only a convenient online resource to browse Minoan inscriptions but also provides an analysis tool to explore …

New Algorithms For Large Datasets And Distributions, Sutanu Gayen

School of Computing: Dissertations, Theses, and Student Research

In this dissertation, we make progress on certain algorithmic problems broadly over two computational models: the streaming model for large datasets and the distribution testing model for large probability distributions.

First we consider the streaming model, where a large sequence of data items arrives one by one. The computer needs to make one pass over this sequence, processing every item quickly, in a limited space. In Chapter 2 motivated by a bioinformatics application, we consider the problem of estimating the number of low-frequency items in a stream, which has received only a limited theoretical work so far. We give an …

User Privacy Leakage In Location-Based Mobile Ad Services, Qicheng Lin

School of Computing: Dissertations, Theses, and Student Research

The online advertising ecosystem leverages its massive data collection capability to learn the properties of users for targeted ad deliveries. Many Android app developers include ad libraries in their apps as a way of monetization. These ad libraries contain advertisements from the sell-side platforms, which collect an extensive set of sensitive information to provide more relevant advertisements for their customers. Existing efforts have investigated the increasingly pervasive private data collection of mobile ad networks over time. However, there lacks a measurement study to evaluate the scale of privacy leakage of ad networks across different geographical areas. In this work, we …

"Flagella Base Model" And "Flagellin Monomer", Brandon Lasalle, Rebecca Roston

3-D Printed Model Structural Files

"Flagella Base Model" and "Flagellin monomer"

Description: This is a teaching model of the proteins that make a bacterial flagella. All models are depicted in space-fill. The Flagellin monomer and the Flagella base can slot together to show protein quaternary structure and filamentous protein assembly.

Printable models are already uploaded to Shapeways.com in the MacroMolecules shop under the names "Flagella Base Model" and "Flagellin monomer".

This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following material: Processed Versatile Plastic (Strong & Flexible Plastic).

Model designer: Brandon Lasalle Authors: Brandon Lasalle and Rebecca Roston …

Scheduling And Prefetching In Hadoop With Block Access Pattern Awareness And Global Memory Sharing With Load Balancing Scheme, Sai Suman

School of Computing: Dissertations, Theses, and Student Research

Although several scheduling and prefetching algorithms have been proposed to improve data locality in Hadoop, there has not been much research to increase cluster performance by targeting the issue of data locality while considering the 1) cluster memory, 2) data access patterns and 3) real-time scheduling issues together.

Firstly, considering the data access patterns is crucial because the computation might access some portion of the data in the cluster only once while the rest could be accessed multiple times. Blindly retaining data in memory might eventually lead to inefficient memory utilization.

Secondly, several studies found that the cluster memory goes …

Bincor: An R Package For Estimating The Correlation Between Two Unevenly Spaced Time Series, Josue M. Polanco-Martinez, Martin A. Medina-Elizalde, Maria Fernanda Sanchez Goni, Manfred Mudelsee

The R Journal

This paper presents a computational program named BINCOR (BINned CORrelation) for estimating the correlation between two unevenly spaced time series. This program is also applicable to the situation of two evenly spaced time series not on the same time grid. BINCOR is based on a novel estimation approach proposed by Mudelsee (2010) for estimating the correlation between two climate time series with different timescales. The idea is that autocorrelation (e.g. an AR1 process) means that memory enables values obtained on different time points to be correlated. Binned correlation is performed by resampling the time series under study into time bins …

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

The R Journal

In the past 8 months, 1524 new packages were added to the CRAN package repository. 71 packages were unarchived and 302 were archived. The following shows the growth of the number of active packages in the CRAN package repository:

R Foundation News, Torsten Hothorn

The R Journal

Membership fees and donations received between 2019-01-07 and 2019-09-04

Ciuupi: An R Package For Computing Confidence Intervals That Utilize Uncertain Prior Information, Mainzer Kabaila, Paul Kabaila

The R Journal

We have created the R package ciuupi to compute confidence intervals that utilize uncertain prior information in linear regression. Unlike post-model-selection confidence intervals, the confidence interval that utilizes uncertain prior information (CIUUPI) implemented in this package has, to an excellent approximation, coverage probability throughout the parameter space that is very close to the desired minimum coverage probability. Furthermore, when the uncertain prior information is correct, the CIUUPI is, on average, shorter than the standard confidence interval constructed using the full linear regression model. In this paper we provide motivating examples of scenarios where the CIUUPI may be used. We then …

R Package For Geometric Shadow Calculations In An Urban Environment, Michael Dorman, Evyatar Erell, Adi Vulkan, Itai Kloog

The R Journal

This paper introduces the shadow package for R. The package provides functions for shadow-related calculations in the urban environment, namely shadow height, shadow footprint and Sky View Factor (SVF) calculations, as well as a wrapper function to estimate solar radiation while taking shadow effects into account. All functions operate on a layer of polygons with a height attribute, also known as “extruded polygons” or 2.5D vector data. Such data are associated with accuracy limitations in representing urban environments. However, unlike 3D models, polygonal layers of building outlines along with their height are abundantly available and their processing does not require …

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

The R Journal

Methods based on Received Signal Strength Indicator (RSSI) fingerprinting are in the forefront among several techniques being proposed for indoor positioning. This paper introduces the R package ipft, which provides algorithms and utility functions for indoor positioning using fingerprinting techniques. These functions are designed for manipulation of RSSI fingerprint data sets, estimation of positions, comparison of the performance of different positioning models, and graphical visualization of data. Well-known machine learning algorithms are implemented in this package to perform analysis and estimations over RSSI data sets. The paper provides a description of these algorithms and functions, as well as examples of …

Time-Series Clustering In R Using The Dtwclust Package, Alexis Sardá-Espinosa

The R Journal

Most clustering strategies have not changed considerably since their initial definition. The common improvements are either related to the distance measure used to assess dissimilarity, or the function used to calculate prototypes. Time-series clustering is no exception, with the Dynamic Time Warping distance being particularly popular in that context. This distance is computationally expensive, so many related optimizations have been developed over the years. Since no single clustering algorithm can be said to perform best on all datasets, different strategies must be tested and compared, so a common infrastructure can be advantageous. In this manuscript, a general overview of shape-based …

Editorial, Norm Matloff

The R Journal

On behalf of the Editorial Board, I am pleased to present Volume 10, Issue 1 of the R Journal. This issue contains 36 contributed articles. The majority of which cover new or newly enhanced packages on CRAN.

Optimization Routines For Enforcing One-To-One Matches In Record Linkage Problems, Diego Moretti, Luca Valentino, Tiziana Tuoto

The R Journal

Record linkage aims at quickly and accurately identifying if two records represent the same real world entity. In many applications, we are interested in restricting the linkage results to "1 to 1" links, that is a single record does not appear more than once in the output. This can be dealt with the transport algorithm. The optimization problem, however, grows quadratically in the size of the input, quickly becoming untreatable for cases with a few thousand records. This paper compares different solutions, provided by some R packages for linear programming solvers. The comparison is done in terms of memory usage …

Robustgasp: Robust Gaussian Stochastic Process Emulation In R, Mengyang Gu, Jesus Palomo, James O. Berger

The R Journal

Gaussian stochastic process (GaSP) emulation is a powerful tool for approximating computationally intensive computer models. However, estimation of parameters in the GaSP emulator is a challenging task. No closed-form estimator is available and many numerical problems arise with standard estimates, e.g., the maximum likelihood estimator. In this package, we implement a marginal posterior mode estimator, for special priors and parameterizations. This estimation method that meets the robust parameter estimation criteria was discussed in Gu et al. (2018); mathematical reasons are provided therein to explain why robust parameter estimation can greatly improve predictive performance of the emulator. In addition, inert inputs …

Mixedsde: A Package To Fit Mixed Stochastic Differential Equations, Charlotte Dion, Simone Hermann, Adeline Samson

The R Journal

Stochastic differential equations (SDEs) are useful to model continuous stochastic processes. When (independent) repeated temporal data are available, variability between the trajectories can be modeled by introducing random effects in the drift of the SDEs. These models are useful to analyze neuronal data, crack length data, pharmacokinetics, financial data, to cite some applications among other. The R package focuses on the estimation of SDEs with linear random effects in the drift. The goal is to estimate the common density of the random effects from repeated discrete observations of the SDE. The package mixedsde proposes three estimation methods: a Bayesian parametric, …

Atable: Create Tables For Clinical Trial Reports, Armin Ströbel

The R Journal

Examining distributions of variables is the first step in the analysis of a clinical trial before more specific modelling can begin. Reporting these results to stakeholders of the trial is an essential part of a statistician’s work. The atable package facilitates these steps by offering easy-to-use but still flexible functions.

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 …