Numerical Analysis and Scientific Computing Commons^™

Coxphmic: An R Package For Sparse Estimation Of Cox Proportional Hazards Models Via Approximated Information Criteria, Razieh Nabi, Xiaogang Su

The R Journal

In this paper, we describe an R package named coxphMIC, which implements the sparse estimation method for Cox proportional hazards models via approximated information criterion (Su et al., 2016). The developed methodology is named MIC which stands for “Minimizing approximated Information Criteria". A reparameterization step is introduced to enforce sparsity while at the same time keeping the objective function smooth. As a result, MIC is computationally fast with a superior performance in sparse estimation. Furthermore, the reparameterization tactic yields an additional advantage in terms of circumventing post-selection inference (Leeb and Pötscher, 2005). The MIC method and its R implementation …

Isogenegui: Multiple Approaches For Dose-Response Analysis Of Microarray Data Using R, Martin Otava, Rudradev Sengupta, Ziv Shkedy, Dan Lin, Setia Pramana, Tobias Verbeke, Philippe Haldermans, Ludwig A. Hothorn, Daniel Gerhard, Rebecca M. Kuiper, Florian Klinglmueller, Adetayo Kasim

The R Journal

The analysis of transcriptomic experiments with ordered covariates, such as dose-response data, has become a central topic in bioinformatics, in particular in omics studies. Consequently, multiple R packages on CRAN and Bioconductor are designed to analyse microarray data from various perspectives under the assumption of order restriction. We introduce the new R package IsoGene Graphical User Interface (IsoGeneGUI), an extension of the original IsoGene package that includes methods from most of available R packages designed for the analysis of order restricted microarray data, namely orQA, ORIClust, goric and ORCME. The methods included in the new …

Gsympoint: An R Package To Estimate The Generalized Symmetry Point, An Optimal Cut-Off Point For Binary Classification In Continuous Diagnostic Tests, Mónica López-Ratón, Elisa M. Molanes-López, Emilio Letón, Carmen Cadarso-Suárez

The R Journal

In clinical practice, it is very useful to select an optimal cutpoint in the scale of a continuous biomarker or diagnostic test for classifying individuals as healthy or diseased. Several methods for choosing optimal cutpoints have been presented in the literature, depending on the ultimate goal. One of these methods, the generalized symmetry point, recently introduced, generalizes the symmetry point by incorporating the misclassification costs. Two statistical approaches have been proposed in the literature for estimating this optimal cutpoint and its associated sensitivity and specificity measures, a parametric method based on the generalized pivotal quantity and a nonparametric method based …

News From The Bioconductor Project, Bioconductor Core Team

The R Journal

The Bioconductor project provides tools for the analysis and comprehension of high throughput genomic data. Bioconductor 3.5 was released on 25 April, 2017. It is compatible with R 3.4 and consists of 1383 software packages, 316 experiment data packages, and 911 up-to-date annotation packages. The release announcement includes descriptions of 88 new packages, and updated NEWS files for many additional packages. Start using Bioconductor by installing the most recent version of R and evaluating the commands

Bayesbinmix: An R Package For Model Based Clustering Of Multivariate Binary Data, Panagiotis Papastamoulis, Magnus Rattray

The R Journal

The BayesBinMix package offers a Bayesian framework for clustering binary data with or without missing values by fitting mixtures of multivariate Bernoulli distributions with an unknown number of components. It allows the joint estimation of the number of clusters and model parameters using Markov chain Monte Carlo sampling. Heated chains are run in parallel and accelerate the convergence to the target posterior distribution. Identifiability issues are addressed by implementing label switching algorithms. The package is demonstrated and benchmarked against the Expectation Maximization algorithm using a simulation study as well as a real dataset.

Compress: A Comprehensive Framework Of Trajectory Compression In Road Networks, Yunheng Han, Weiwei Sun, Baihua Zheng

Research Collection School Of Computing and Information Systems

More and more advanced technologies have become available to collect and integrate an unprecedented amount of data from multiple sources, including GPS trajectories about the traces of moving objects. Given the fact that GPS trajectories are vast in size while the information carried by the trajectories could be redundant, we focus on trajectory compression in this article. As a systematic solution, we propose a comprehensive framework, namely, COMPRESS (Comprehensive Paralleled Road-Network-Based Trajectory Compression), to compress GPS trajectory data in an urban road network. In the preprocessing step, COMPRESS decomposes trajectories into spatial paths and temporal sequences, with a thorough justification …

On Self-Selection Biases In Online Product Reviews, Nan Hu, Paul A. Pavlou, Jie Zhang

Research Collection School Of Computing and Information Systems

Online product reviews help consumers infer product quality, and the mean (average) rating is often used as a proxy for product quality. However, two self-selection biases, acquisition bias (mostly consumers with a favorable predisposition acquire a product and hence write a product review) and underreporting bias (consumers with extreme, either positive or negative, ratings are more likely to write reviews than consumers with moderate product ratings), render the mean rating a biased estimator of product quality, and they result in the well-known J-shaped (positively skewed, asymmetric, bimodal) distribution of online product reviews. To better understand the nature and consequences of …

The Acquisition And Analysis Of Electroencephalogram Data For The Classification Of Benign Partial Epilepsy Of Childhood With Centrotemporal Spikes, Jessica A. Scarborough

Master's Theses

In this thesis, I will expand upon each step in the process of acquiring and analyzing electroencephalogram (EEG) for the classification of benign childhood epilepsy with centrotemporal spikes. Despite huge advancements in the field of health informatics—natural language processing, machine learning, predictive modeling—there are significant barriers to the access of clinical data. These barriers include information blocking, privacy policy concerns, and a lack of stakeholder support. We will see that these roadblocks are all responsible for stunting biomedical research in some way, including my own experiences in acquiring the data for the second chapter of this thesis.

This second chapter …

Comparing Tensorflow Deep Learning Performance Using Cpus, Gpus, Local Pcs And Cloud, John Lawrence, Jonas Malmsten, Andrey Rybka, Daniel A. Sabol, Ken Triplin

Publications and Research

Deep learning is a very computational intensive task. Traditionally GPUs have been used to speed-up computations by several orders of magnitude. TensorFlow is a deep learning framework designed to improve performance further by running on multiple nodes in a distributed system. While TensorFlow has only been available for a little over a year, it has quickly become the most popular open source machine learning project on GitHub. The open source version of TensorFlow was originally only capable of running on a single node while Google’s proprietary version only was capable of leveraging distributed systems. This has now changed. In this …

Optimized Forecasting Of Dominant U.S. Stock Market Equities Using Univariate And Multivariate Time Series Analysis Methods, Michael Schwartz

Computational and Data Sciences Theses

This dissertation documents an investigation into forecasting U.S. stock market equities via two very different time series analysis techniques: 1) autoregressive integrated moving average (ARIMA), and 2) singular spectrum analysis (SSA). Approximately 40% of the S&P 500 stocks are analyzed. Forecasts are generated for one and five days ahead using daily closing prices. Univariate and multivariate structures are applied and results are compared. One objective is to explore the hypothesis that a multivariate model produces superior performance over a univariate configuration. Another objective is to compare the forecasting performance of ARIMA to SSA, as SSA is a relatively recent development …

Electrodynamical Modeling For Light Transport Simulation, Michael G. Saunders

Undergraduate Honors Theses

Modernity in the computer graphics community is characterized by a burgeoning interest in physically based rendering techniques. That is to say that mathematical reasoning from first principles is widely preferred to ad hoc, approximate reasoning in blind pursuit of photorealism. Thereby, the purpose of our research is to investigate the efficacy of explicit electrodynamical modeling by means of the generalized Jones vector given by Azzam [1] and the generalized Jones matrix given by Ortega-Quijano & Arce-Diego [2] in the context of stochastic light transport simulation for computer graphics. To augment the status quo path tracing framework with such a modeling …

Molecular Dynamics Simulations Of Dna-Functionalized Nanoparticle Building Blocks On Gpus, Tyler Landon Fochtman

Graduate Theses and Dissertations

This thesis discusses massively parallel molecular dynamics simulations of nBLOCKs using graphical processing units. nBLOCKs are nanoscale building blocks composed of gold nanoparticles functionalized with single-stranded DNA molecules. To explore greater simulation time scales we implement our nBLOCK computational model as an extension to the coarse grain molecular simulator oxDNA. oxDNA is parameterized to match the thermodynamics of DNA strand hybridization as well as the mechanics of single stranded DNA and double stranded DNA. In addition to an in-depth review of our implementation details we also provide results of the model validation and performance tests. These validation and performance tests …

Evaluating A Personal Stress Monitoring System, Sneha Gogineni

Theses and Dissertations

Now-a-days, Life is generally much more stressful than in the past. "Stress" is the word that we use when we feel that we are overloaded mentally in our thoughts and wonder whether we can really cope with those placed upon us. Sometimes, stress gets us going and they are good for us but at other times, it could be the cause to undermine both our mental and physical health. The way we respond to a challenge can be considered as a kind of stress. Part of our response to a challenge is physiological and affects our own physical state. When …

A Comparative Study Of Cognitive Systems For Learning, Praneetha Mandava

Theses and Dissertations

Learning is the modification of a behavioral tendency by experience. Memory and reasoning are the most important aspects for learning in humans; information is temporarily stored in the short-term memory and processed, compared with existing memories and stored in long-term memory, and can be re-used when needed. One way to describe an organized pattern of thought or behavior and the categories of information along with their relationships is by using schemas. A cognitive script is one form of a schema that evolves over multiple exposures to the same set of stimuli and/or repeated enactment of a particular behavior. This research …

Continuous Top-K Monitoring On Document Streams, Leong Hou U, Junjie Zhang, Kyriakos Mouratidis, Ye Li

Research Collection School Of Computing and Information Systems

The efficient processing of document streams plays an important role in many information filtering systems. Emerging applications, such as news update filtering and social network notifications, demand presenting end-users with the most relevant content to their preferences. In this work, user preferences are indicated by a set of keywords. A central server monitors the document stream and continuously reports to each user the top-k documents that are most relevant to her keywords. Our objective is to support large numbers of users and high stream rates, while refreshing the top-k results almost instantaneously. Our solution abandons the traditional frequency-ordered indexing approach. …

Who Will Leave The Company?: A Large-Scale Industry Study Of Developer Turnover By Mining Monthly Work Report, Lingfeng Bao, Zhenchang Xing, Xin Xia, David Lo, Shanping Li

Research Collection School Of Computing and Information Systems

Software developer turnover has become a big challenge for information technology (IT) companies. The departure of key software developers might cause big loss to an IT company since they also depart with important business knowledge and critical technical skills. Understanding developer turnover is very important for IT companies to retain talented developers and reduce the loss due to developers' departure. Previous studies mainly perform qualitative observations or simple statistical analysis of developers' activity data to understand developer turnover. In this paper, we investigate whether we can predict the turnover of software developers in non-open source companies by automatically analyzing monthly …

A Neural Network Model For Semi-Supervised Review Aspect Identification, Ying Ding, Changlong Yu, Jing Jiang

Research Collection School Of Computing and Information Systems

Aspect identification is an important problem in opinion mining. It is usually solved in an unsupervised manner, and topic models have been widely used for the task. In this work, we propose a neural network model to identify aspects from reviews by learning their distributional vectors. A key difference of our neural network model from topic models is that we do not use multinomial word distributions but instead embedding vectors to generate words. Furthermore, to leverage review sentences labeled with aspect words, a sequence labeler based on Recurrent Neural Networks (RNNs) is incorporated into our neural network. The resulting model …

Persona Generation From Aggregated Social Media Data, Soon-Gyo Jung, Jisun An, Haewoon Kwak, Moeed Ahmad, Lene Nielsen, Bernard J. Jansen

Research Collection School Of Computing and Information Systems

We develop a methodology for persona generation using real time social media data for the distribution of products via online platforms. From a large social media account containing more than 30 million interactions from users from 181 countries engaging with more than 4,200 digital products produced by a global media corporation, we demonstrate that our methodology can first identify both distinct and impactful user segments and then create persona descriptions by automatically adding pertinent features, such as names, photos, and personal attributes. We validate our approach by implementing the methodology into an actual working system that leverages large scale online …

A Parallelized Method For Solving Large Scale Integer Linear Optimization Problems Using Cut-And-Solve With Applications To Cgwas, John Brandenburg

Theses

The commercial solver CPLEX has been one of the top solvers of mixed-integer and purely integer linear problems for some time. Its method of solving, Branch-and-Cut, has been shown to be highly effective, but has its limits in terms of input sizes which are tractable, and cannot be effectively parallelized beyond a small number. Here we present a different method of solution, Cut-and-Solve, which utilizes the power of CPLEX to effectively parallelize any mixed-integer or integer linear problem. We have utilized Cut-and-Solve in a novel way to offer optimal solution guarantees more quickly. We will show comparisons of Cut-and-Solve to …

Network Exploration Of Correlated Multivariate Protein Data For Alzheimer's Disease Association, Matthew J. Lane

Theses

Alzheimer Disease (AD) is difficult to diagnose by using genetic testing or other traditional methods. Unlike diseases with simple genetic risk components, there exists no single marker determining as to whether someone will develop AD. Furthermore, AD is highly heterogeneous and different subgroups of individuals develop the disease due to differing factors. Traditional diagnostic methods using perceivable cognitive deficiencies are often too little too late due to the brain having suffered damage from decades of disease progression. In order to observe AD at early stages prior to the observation of cognitive deficiencies, biomarkers with greater accuracy are required. By using …

Inelastic Rate Coefficients For Collisions Of C₆Hˉ With H₂ And He, Kyle M. Walker, François Lique, Fabien Dumouchel, Richard Dawes

Chemistry Faculty Research & Creative Works

The recent detection of anions in the interstellar medium has shown that they exist in a variety of astrophysical environments -- circumstellar envelopes, cold dense molecular clouds and star-forming regions. Both radiative and collisional processes contribute to molecular excitation and de-excitation in these regions so that the ‘local thermodynamic equilibrium’ approximation, where collisions cause the gas to behave thermally, is not generally valid. Therefore, along with radiative coefficients, collisional excitation rate coefficients are needed to accurately model the anionic emission from these environments. We focus on the calculation of state-to-state rate coefficients of the C₆H^- molecule in …

A Robust And Secure Video Steganography Method In Dwt-Dct Domains Based On Multiple Object Tracking And Ecc, Ramadhan J. Mstafa, Khaled M. Elleithy, Eman Abdelfattah

School of Computer Science & Engineering Faculty Publications

Over the past few decades, the art of secretly embedding and communicating digital data has gained enormous attention because of the technological development in both digital contents and communication. The imperceptibility, hiding capacity, and robustness against attacks are three main requirements that any video steganography method should take into consideration. In this paper, a robust and secure video steganographic algorithm in discrete wavelet transform (DWT) and discrete cosine transform (DCT) domains based on the multiple object tracking (MOT) algorithm and error correcting codes is proposed. The secret message is preprocessed by applying both Hamming and Bose, Chaudhuri, and Hocquenghem codes …

Predicting The Impact Of Software Engineering Topics: An Empirical Study, Santonu Sarkar, Rumana Lakdawala, Subhajit Datta

Research Collection School Of Computing and Information Systems

Predicting the future is hard, more so in active research areas. In this paper, we customize an established model for citation prediction of research papers and apply it on research topics. We argue that research topics, rather than individual publications, have wider relevance in the research ecosystem, for individuals as well as organizations. In this study, topics are extracted from a corpus of software engineering publications covering 55,000+ papers written by more than 70,000 authors across 56 publication venues, over a span of 38 years, using natural language processing techniques. We demonstrate how critical aspects of the original paper-based prediction …

Modeling Topics And Behavior Of Microbloggers: An Integrated Approach, Tuan Anh Hoang, Ee-Peng Lim

Research Collection School Of Computing and Information Systems

Microblogging encompasses both user-generated content and behavior. When modeling microblogging data, one has to consider personal and background topics, as well as how these topics generate the observed content and behavior. In this article, we propose the Generalized Behavior-Topic (GBT) model for simultaneously modeling background topics and users' topical interest in microblogging data. GBT considers multiple topical communities (or realms) with different background topical interests while learning the personal topics of each user and the user's dependence on realms to generate both content and behavior. This differentiates GBT from other previous works that consider either one realm only or content …

Assessing The Language Of Chat For Teamwork Dialogue, Antonette Shibani, Elizabeth Koh, Vivian Lai, Kyong Jin Shim

Research Collection School Of Computing and Information Systems

In technology enhanced language learning, many pedagogical activities involve students in online discussion such as synchronous chat, in order to help them practice their language skills. Besides developing the language competency of students, it is also crucial to nurture their teamwork competencies for today's global and complex environment. Language communication is an important glue of teamwork. In order to assess the language of chat for teamwork dimensions, several text mining methods are pos sible. However, difficulties arise such as pre-processing being a black box and classification approaches and algorithms being dependent on the context. To address these issues, the study …

Characterizing Malicious Android Apps By Mining Topic-Specific Data Flow Signatures, Xinli Yang, David Lo, Li Li, Xin Xia, Tegawendé F. Bissyande, Jacques Klein

Research Collection School Of Computing and Information Systems

Context: State-of-the-art works on automated detection of Android malware have leveraged app descriptions to spot anomalies w.r.t the functionality implemented, or have used data flow information as a feature to discriminate malicious from benign apps. Although these works have yielded promising performance,we hypothesize that these performances can be improved by a better understanding of malicious behavior. Objective: To characterize malicious apps, we take into account both information on app descriptions,which are indicative of apps’ topics, and information on sensitive data flow, which can be relevant todiscriminate malware from benign apps. Method: In this paper, we propose a topic-specific approach to …

Comparative Relation Generative Model, Maksim Tkachenko, Hady W. Lauw

Research Collection School Of Computing and Information Systems

Online reviews are important decision aids to consumers. Other than helping users to evaluate individual products, reviews also support comparison shopping by comparing two (or more) products based on a specific aspect. However, making a comparison across two different reviews, written by different authors, is not always equitable due to the different standards and preferences of authors. Therefore, we focus on comparative sentences, whereby two products are compared directly by a review author within a sentence. We study the problem of comparative relation mining. Given a set of comparative sentences, each relating a pair of entities, our objective is three-fold: …

Ten Simple Rules For Responsible Big Data Research, Matthew Zook, Solon Barocas, Danah Boyd, Kate Crawford, Emily Keller, Seeta Peña Gangadharan, Alyssa Goodman, Rachelle Hollander, Barbara A. Koenig, Jacob Metcalf, Arvind Narayanan, Alondra Nelson, Frank Pasquale

Geography Faculty Publications

No abstract provided.

Designing Novel Nanostructured Permanent Magnets, Ali Al Kadhim

UNO Student Research and Creative Activity Fair

Rare earth element based alloys have been the source of high performance magnetic alloys, and have played a paramount role in the development of various technologies, including: memory devices (such as credit cards, random-access memory), sensors, and various biomedical applications. However, there is a tremendous need to replace rare earth metals with material with powerful magnetic properties. Our group recently found CrTe-based materials that show very promising magnetic properties in nanostructured form. The magnetic modeling of such material in nanostructured form prior to their fabrication demonstrates their magnetic properties in bulk form. In this project, we investigate the behavior of …

Optimizing Campus Mobility With A Focus On Sustainability: A Graph Theory Approach To Intra-Campus Transportation Networks, Quinn M. Nelson

UNO Student Research and Creative Activity Fair

The idea of public transportation is supported by most in theory but often heavily criticized by users when put into application. There are common tensions that are related to public transportation, as described by frequent users: unreliable, too crowded, and slow. The University of Nebraska-Omaha (UNO) is a growing metropolitan institution that uses a shuttle system to transport students among their three campuses daily. As of 2015, the current total student enrollment is approximately 16,000; UNO plans to enroll 20,000 students by 2020. The expected student growth is also reflected by the current construction of new buildings and expansion of …