Computer Sciences Commons^™

Extracting Development Tasks To Navigate Software Documentation, Christoph Treude, Martin P. Robillard, Barthélémy Dagenais

Research Collection School Of Computing and Information Systems

Knowledge management plays a central role in many software development organizations. While much of the important technical knowledge can be captured in documentation, there often exists a gap between the information needs of software developers and the documentation structure. To help developers navigate documentation, we developed a technique for automatically extracting tasks from software documentation by conceptualizing tasks as specific programming actions that have been described in the documentation. More than 70 percent of the tasks we extracted from the documentation of two projects were judged meaningful by at least one of two developers. We present TaskNavigator, a user interface …

Integrated Low-Rank-Based Discriminative Feature Learning For Recognition, Pan Zhou, Zhouchen Lin, Chao Zhang

Research Collection School Of Computing and Information Systems

Feature learning plays a central role in pattern recognition. In recent years, many representation-based feature learning methods have been proposed and have achieved great success in many applications. However, these methods perform feature learning and subsequent classification in two separate steps, which may not be optimal for recognition tasks. In this paper, we present a supervised low-rank-based approach for learning discriminative features. By integrating latent low-rank representation (LatLRR) with a ridge regression-based classifier, our approach combines feature learning with classification, so that the regulated classification error is minimized. In this way, the extracted features are more discriminative for the recognition …

Protein Domain Linker Prediction: A Direction For Detecting Protein-Protein Interactions, Maad Mohammad Shatnawi

Dissertations

Protein chains are generally long and consist of multiple domains. Domains are the basic elements of protein structures that can exist, evolve, and function independently. The accurate and reliable identification of protein domains and their interactions has very important impacts in several protein research areas. The accurate prediction of protein domains is a fundamental stage in both experimental and computational proteomics. The knowledge of domains is an initial stage of protein tertiary structure prediction which can give insight into the way in which proteins work. The knowledge of domains is also useful in classifying proteins, understanding their structures, functions and …

Gpuhelib And Distributedhelib: Distributed Computing Variants Of Helib, A Homomorphic Encryption Library, Ethan Andrew Frame

Master's Theses

Homomorphic Encryption, an encryption scheme only developed in the last five years, allows for arbitrary operations to be performed on encrypted data. Using this scheme, a user can encrypt data, and send it to an online service. The online service can then perform an operation on the data and generate an encrypted result. This encrypted result is then sent back to the user, who decrypts it. This decryption produces the same data as if the operation performed by the online service had been performed on the unencrypted data. This is revolutionary because it allows for users to rely on online …

Continuous Monitoring Of Enterprise Risks: A Delphi Feasibility Study, Robert Baksa

Dissertations

A constantly evolving regulatory environment, increasing market pressure to improve operations, and rapidly changing business conditions are creating the need for ongoing assurance that organizational risks are continually and adequately mitigated. Enterprises are perpetually exposed to fraud, poor decision making and/or other inefficiencies that can lead to significant financial loss and/or increased levels of operating risk. Increasingly, Information Systems are being harnessed to reinvent the risk management process. One promising technology is Continuous Auditing, which seeks to transform the audit process from periodic reviews of a few transactions to a continuous review of all transactions. However, the highly integrated, rapidly …

Data Mining In Computational Proteomics And Genomics, Yang Song

Dissertations

This dissertation addresses data mining in bioinformatics by investigating two important problems, namely peak detection and structure matching. Peak detection is useful for biological pattern discovery while structure matching finds many applications in clustering and classification.

The first part of this dissertation focuses on elastic peak detection in 2D liquid chromatographic mass spectrometry (LC-MS) data used in proteomics research. These data can be modeled as a time series, in which the X-axis represents time points and the Y-axis represents intensity values. A peak occurs in a set of 2D LC-MS data when the sum of the intensity values in a …

Designing Novel Abstraction Networks For Ontology Summarization And Quality Assurance, Christopher Ochs

Dissertations

Biomedical ontologies are complex knowledge representation systems. Biomedical ontologies support interdisciplinary research, interoperability of medical systems, and Electronic Healthcare Record (EHR) encoding. Ontologies represent knowledge using concepts (entities) linked by relationships. Ontologies may contain hundreds of thousands of concepts and millions of relationships. For users, the size and complexity of ontologies make it difficult to comprehend “the big picture” of an ontology's content. For ontology editors, size and complexity make it difficult to uncover errors and inconsistencies. Errors in an ontology will ultimately affect applications that utilize the ontology.

In prior studies abstraction networks (AbNs) were developed to provide a …

Information Filtering By Multiple Examples, Mingzhu Zhu

Dissertations

A key to successfully satisfy an information need lies in how users express it using keywords as queries. However, for many users, expressing their information needs using keywords is difficult, especially when the information need is complex. Search By Multiple Examples (SBME), a promising method for overcoming this problem, allows users to specify their information needs as a set of relevant documents rather than as a set of keywords.

Most of the studies on SBME adopt the Positive Unlabeled learning (PU learning) techniques by treating the user's provided examples (denoted as query examples) as positive set and the entire data …

Assessing Learning Outcomes And Social Capital Formation Resulting From The Use And Sharing Of Internet Knowledge Resources, Regina S. Collins

Dissertations

Today’s “digital natives” use the Internet to address most, if not all, their learning-related knowledge needs. This research evaluates the outcomes of formal learning activities requiring students to use, manage, share, and consolidate Internet knowledge resources (such as websites, videos, and blogs) to achieve both individual and group learning. This research takes an integrative approach to learning, capturing learner cognitive, interpersonal, and intrapersonal characteristics as well as the impact of the digital environment by evaluating the technological affordances of two different systems supporting such learning activities. This research also examines pedagogical modifications that would best integrate course assignments utilizing Internet …

Entity Recommendations Using Hierarchical Knowledge Bases, Siva Kumar Cheekula, Pavan Kapanipathi, Derek Doran, Prateek Jain, Amit P. Sheth

Kno.e.sis Publications

Recent developments in recommendation algorithms have focused on integrating Linked Open Data to augment traditional algorithms with background knowledge. These developments recognize that the integration of Linked Open Data may or better performance, particularly in cold start cases. In this paper, we explore if and how a specific type of Linked Open Data, namely hierarchical knowledge, may be utilized for recommendation systems. We propose a content-based recommendation approaches that adapts a spreading activation algorithm over the DBpedia category structure to identify entities of interest to the user. Evaluation of the algorithm over the Movielens dataset demonstrates that our method yields …

Exact Genome Alignment, Nandini Ghosh

Theses

The increase in the volume of genomic data due to the decrease in the cost of whole genome sequencing techniques has opened up new avenues of research in the field of Bioinformatics, like comparative genomics and evolutionary dynamics. The fundamental task in these studies is to align the genome sequences accurately. Sequence alignment helps to identify regions of similarity between the sequences to establish their functional, evolutionary and structural relationship. The thesis investigates the performance of two sequence alignment programs LASTZ, a hash table based faster method and SSEARCH, a slower but more rigorous Smith-Waterman based approach, on whole genome …

Unsupervised Gene Regulatory Network Inference On Microarray Data, Nidhi Radia

Theses

Obtaining gene regulatory networks (GRNs) from expression data is a challenging and crucial task. Many computational methods and algorithms have been developed to infer gene networks for gene expression data, which are usually obtained from microarray experiments. A gene network is a method to depict the relation among clusters of genes. To infer gene networks, the unsupervised method is used in this study. The two types of data used are time-series data and steady-state data. The data is analyzed using various tools containing different algorithms and concepts. GRNs from time-series data tools are obtained using the Time-delayed Algorithm for the …

Identifying Modifier Genes In Sma Model Mice, Weiting Xu

Theses

Spinal Muscular Atrophy (SMA) involves the loss of nerve cells called motor neurons in the spinal cord and is classified as a motor neuron disease, it affects 1 in 5000-10000 newborns, one of the leading genetic causes of infant death in USA. Mutations in the SMN1, UBA1, DYNC1H1 and VAPB genes cause spinal muscular atrophy. Extra copies of the SMN2 gene modify the severity of spinal muscular atrophy. Mutations in SMN1 (Motor Neuron 1) mainly causes SMA (Autosomal recessive inheritance). SMN1 gene mutations lead to a shortage of the SMN protein and SMN protein forms SMN complex …

Designing For Mistrust, Eric Gossett

ACMS Conference Proceedings 2015

The 2014 ACM North Central Region programming contest contained a problem about a group of v bandits who want to use multiple locks to seal their treasure and distribute keys in such a way that no group of less than m bandits can open all the locks. The problem asks for an algorithm that will determine the number of locks needed for any set of parameters (v, m). I will present an analytic solution that produces a minimum number of locks, a recurrence relation solution, and a constructive algorithm that can print out a table showing the …

The Mathematics Of Evolution, Steven R. Lay

ACMS Conference Proceedings 2015

Like many universities, Lee University has a non-major’s course for liberal arts students. The course typically includes a potpourri of topics: logical thinking, scientific notation, linear functions, estimation, and probability. At Lee, we have found a way to conclude the course that applies these varied topics to an issue designed to engage student interest and promote critical thinking. We have developed a series of three lessons on “The Mathematics of Evolution.” The first lesson is on radiometric dating. The second lesson is on the origin and progression of life. And the third lesson deals with the nature of the DNA …

A Triune Philosophy Of Mathematics, Dusty Wilson

ACMS Conference Proceedings 2015

What is mathematics and is it discovered or invented? The Humanist, Platonist, and Foundationalist each provide answers. But are the options within the philosophy of mathematics so limited? Rather than viewing and describing mathematics in a mutually exclusive manner, each of these approaches includes components of truth from a greater triune philosophy of mathematics. This talk will introduce this inclusive triune paradigm through which to explore fundamental questions about mathematics.

Software Engineering I: Teaching Challenges, Paul C. Grabow

ACMS Conference Proceedings 2015

The term software engineering can be traced to the late 1960s in response to large-scale, software development problems. Since then it has evolved as a discipline, both within industry and the academy. There have been distinct educational successes: “Standard practice” has matured (and found its way into more textbooks),the ACM and IEEE Computer Society have published curriculum guidelines, computer science programs commonly offer at least one software engineering course, and software engineering degrees (undergraduate or graduate) are more common. However, software engineering still presents a challenge. The term itself has become contorted by companies (and society in general); software has …

Mystery Of The Infinite: Developing A Mathematically Based Summer Scholars Program, Christopher Micklewright

ACMS Conference Proceedings 2015

For the past two years, the Templeton Honors College, at Eastern University, has been conducting a Summer Scholars Program for high school students. The program, which has offered courses in a variety of topics, brings students to campus for an intensive residential program, coupled with pre-program and post-program work, for which students can earn college credit. In summer 2014, I helped to develop a mathematically based course, to include rigorous study of discrete mathematics, as well as a variety of lectures and extracurricular activities integrating faith and philosophy with mathematics. In this presentation, I will give an overview of the …

The Best Religious Calendar, Andrew Simoson

ACMS Conference Proceedings 2015

Many religions have deep roots in the rhythms of the moon. And ever since at least the fifth century BC man has known that the moon repeats itself every n = 19 years. Is this integer valuen the best of all choices?Easter follows such a calendar. We briefly show that 19 is second best. And then we run time backwards, and give a rationale as to why a certain species of cicada has a life cycle of 17 years. The answer involves the moon, the Farey series, and Kepler’s laws of motion.

Math, God And Politics—A Fight Over Geometry In 19th Century Italy, Donna Pierce

ACMS Conference Proceedings 2015

In 1839 a polemic, reminiscent of the Renaissance public challenges over mathematical problems, was issued by the leader of the synthetic school of geometry, Vincent Flauti, to the analytical school, headed by Fortunato Padula. Three geometric problems were proposed, all carefully chosen to guarantee a victory for the synthetic school. The judges were from the Royal Academy of Sciences, men also favorable to the synthetic method. Why then did the analytics take up this challenge, and who were the real victors? This was not just a fight over the ‘correct’ way to do geometry, it was a fight over politics, …

Experiencing A Paradigm Shift: Teaching Statistics Through Simulation-Based Inference, Dave Klanderman, Mandi Maxwell, Nathan Tintle

ACMS Conference Proceedings 2015

For decades, statistics has been taught as an application of formulas, making use of normal and other distributions, and relying heavily on algebraic skills of students, in short, emphasizing mathematical thinking. More recently, several textbook author teams have published statistics books that place an increased emphasis on simulation and randomization methods, and a corresponding decreased emphasis on the algebraic manipulation in formulas (e.g., Lock et al., 2012; Tintle et al., 2015) as a way to encourage better statistical thinking.This session describes simulation-based inference curricula more fully, reports on the necessary steps towards implementation of such an approach, and provides both …

On Random Numbers And God’S Nature, James Bradley

ACMS Conference Proceedings 2015

I start with mathematical Platonism, an ancient stream of thought that views numbers as transcending physical reality. I join this to recent insights into mathematical randomness from theoretical computer science. Joining these streams – one ancient, one recent – yields the surprising conclusion that randomness, defined in a particular way, is part of the nature of God. I then explore some of the implications of this conclusion for our understanding of the doctrine of God’s infinitude.

Parables To A Mathematician, Melvin Royer

ACMS Conference Proceedings 2015

Jesus frequently used parables in His ministry, usually short narratives illustrating the outcomes of people’s choices. In John 3:12 and Matthew 13:10-15, He explained that one reason was to be sure that people who genuinely wanted to understand His message would be able to do so. Since most of His audience was familiar with an agrarian economy, Jesus spoke extensively of wheat, fish, trees, wine, debt, tenants, lamps, etc. Many people have speculated on parables Jesus might have used had He lived in a different society. This non-scholarly (but hopefully thought-provoking) talk will propose parables targeted toward groups of mathematicians …

Cell Representations Of The Configuration Space For Planning Optimal Paths, Ajay Kannan

Dartmouth College Undergraduate Theses

This paper proposes sampling techniques to approximate the configuration space for optimal motion planning. We sample valid configurations in the workspace and construct path subconvex cells in the free configuration space. The radius of each cell is calculated using lower bounds on the robot’s minimum time to collision. Using theorems about path convexity, the shortest paths found between any two points in the decomposed space are guaranteed to be safe. Experimental results are provided for a planar arm.

God: One, Daniel Kiteck

ACMS Conference Proceedings 2015

I see the most mathematically significant verse as Deut. 6:4 where God says He is ONE. (And I don’t believe that it is an accident that the greatest commandment to love God with all we are immediately follows.) What is the concept of “one” in relationship to God? Is God dependent on the concept of “one?” What if “one” is ultimately always a comparison going back to God? God is also commonly viewed as infinite. How is this connected to our understanding of the mathematical continuum? Could this help us see how God is foundational both to discrete and continuous …

The Math Olympian, By Richard Hoshino. A Review, Moriah Magcalas, Kyle Spyksma

ACMS Conference Proceedings 2015

This presentation will be a review of the novel The Math Olympian written by ACMS member Richard Hoshino.

Mathematics Without Apologies: A Portrait Of A Problematic Vocation By Michael Harris. A Review, Jeremy Case

ACMS Conference Proceedings 2015

The subtitle of Mathematics without Apologies by Michael Harris is a “Portrait of a Problematic Vocation,”and that problematic vocation involves pure mathematics. What do pure mathematicians do, and why should they do it? Harris critiques the usual answers of truth, beauty, and potential applications as he gives a contemporary revision of G.H. Hardys’ A Mathematicians Apology. Described as a post-post-modern book, Mathematics without Apologies provides a cultural, sociological, philosophical and psychological landscape of the profession and the life of a mathematician. We will explore whether a romantic view of the profession satisfactorily answers the questions and how it might …

The Remarkable Mrs. Somerville, Richard Stout

ACMS Conference Proceedings 2015

As a woman growing up in the late eighteenth century, Mary Somerville (1780-1872) was denied access to most formal education and getting a university education was completely out of the question. Yet her interests in nature, science, and mathematics, coupled with an intense curiosity and tenacious desire to learn led her to eventually be known and respected by scientists, mathematicians, and intellectuals in both Britain and France. She is one of the important woman in the history of mathematics, even though she did not publish original work. However, she was a talented writer, producing several significant works, including Mechanism of …

Ten Mathematicians Who Recognized God’S Hand In Their Work, Dale L. Mcintyre

ACMS Conference Proceedings 2015

Scottish philosopher David Hume (1711-1776) once observed that

“Whoever is moved by faith to assent to [the Christian religion], is conscious of a continued miracle in his own person, which subverts all the principles of his understanding, and gives him a determination to believe what is most contrary to custom and experience.” [Hume]

Evidently Humes cynical pronouncement did not apply to Euler, Cauchy, Cantor, and other profound thinkers who believed God had commissioned and equipped them to glorify Him in their pursuit of truth through mathematics And based on their extraordinary achievements the principles of their understanding do not appear …

Home Primes And Foreign Primes, Nicholas Zoller

ACMS Conference Proceedings 2015

Home primes and foreign primes are produced by a simple recipe that blends prime factorizations with recursion. The home prime of a positive integer n is formed by concatenating the prime factors of n in non-decreasing order. If the resulting integer is prime, then we have found the home prime of n. If not, then we repeat the process as many times as needed to obtain a prime. For instance, 35 = 5·7. After concatenation, we have 57 = 3·19, which is followed by 319 = 11·29, which is followed by 1129, which is prime. Thus, the home prime …