Other Computer Sciences Commons^™

Novel Computational Methods For Transcript Reconstruction And Quantification Using Rna-Seq Data, Yan Huang

Theses and Dissertations--Computer Science

The advent of RNA-seq technologies provides an unprecedented opportunity to precisely profile the mRNA transcriptome of a specific cell population. It helps reveal the characteristics of the cell under the particular condition such as a disease. It is now possible to discover mRNA transcripts not cataloged in existing database, in addition to assessing the identities and quantities of the known transcripts in a given sample or cell. However, the sequence reads obtained from an RNA-seq experiment is only a short fragment of the original transcript. How to recapitulate the mRNA transcriptome from short RNA-seq reads remains a challenging problem. We …

Current Practices For Product Usability Testing In Web And Mobile Applications, Spencer W. Black

Honors Theses and Capstones

Software usability testing is a key methodology that ensures applications are intuitive and easy to use for the target audience. Usability testing has direct benefits for companies as usability improvements often are fundamental to the success of a product. A standard usability test study includes the following five steps: obtain suitable participants, design test scripts, conduct usability sessions, interpret test outcomes, and produce recommendations. Due to the increasing importance for more usable applications, effective techniques to develop usable products, as well as technologies to improve usability testing, have been widely utilized. However, as companies are developing more cross-platform web and …

Preface To "Intertwingled: The Work And Influence Of Ted Nelson", Douglas R. Dechow, Daniele C. Struppa

Mathematics, Physics, and Computer Science Faculty Books and Book Chapters

This is the preface to "Intertwingled: The Work and Influence of Ted Nelson", which examines and honors the work and influence of the computer visionary and re-imagines its meaning for the future. Emerging from a conference held in 2014 at Chapman University, it includes contributions from world-renowned computer scientists and media figures.

The full text of this book is available on an open access basis at Springer.

The blog for the Intertwingled Conference can be read here.

Electronic Health Record Simulator, Samuel M. Brown

Williams Honors College, Honors Research Projects

The Electronic Health Record Simulator is exactly that; it is meant to simulate an EHR (like those found in hospitals and clinics) for use in an academic setting. Its purpose is to familiarize students with the operation of real-world EHRs in order to better prepare them for the workforce. It allows instructors to create fictional patients (with full lab values), and allows students to fill in information as in a real EHR.

Creating A Mobile Game, Timothy Jasany

Williams Honors College, Honors Research Projects

The world we live in today is one that revolves around technology. Whether you are checking your email or paying a bill, most of these actions can be accomplished through the use of technology. One of the most powerful pieces of technology is a cell phone, which can accomplish most tasks any other device can do. Since this piece of technology is growing better and better each day I decided to learn how to program android devices. Cell phones are becoming more widely used by the general public, which I think means that in the near future that cell phones …

Choice Of Human–Computer Interaction Mode In Stroke Rehabilitation, Hossein Mousavi Hondori, Maryam Khademi, Lucy Dodakian, Alison Mackenzie, Cristina V. Lopes, Steven C. Cramer

Physical Therapy Faculty Articles and Research

Background and Objective. Advances in technology are providing new forms of human–computer interaction. The current study examined one form of human–computer interaction, augmented reality (AR), whereby subjects train in the real-world workspace with virtual objects projected by the computer. Motor performances were compared with those obtained while subjects used a traditional human–computer interaction, that is, a personal computer (PC) with a mouse. Methods. Patients used goal-directed arm movements to play AR and PC versions of the Fruit Ninja video game. The 2 versions required the same arm movements to control the game but had different cognitive demands. With …

Positive Fragments Of Coalgebraic Logics, Adriana Balan, Alexander Kurz, Jirí Velebil

Engineering Faculty Articles and Research

Positive modal logic was introduced in an influential 1995 paper of Dunn as the positive fragment of standard modal logic. His completeness result consists of an axiomatization that derives all modal formulas that are valid on all Kripke frames and are built only from atomic propositions, conjunction, disjunction, box and diamond. In this paper, we provide a coalgebraic analysis of this theorem, which not only gives a conceptual proof based on duality theory, but also generalizes Dunn's result from Kripke frames to coalgebras for weak-pullback preserving functors. To facilitate this analysis we prove a number of category theoretic results on …

Presenting Distributive Laws, Marcello M. Bonsangue, Helle H. Hansen, Alexander Kurz, Jurriaan Rot

Engineering Faculty Articles and Research

Distributive laws of a monad T over a functor F are categorical tools for specifying algebra-coalgebra interaction. They proved to be important for solving systems of corecursive equations, for the specification of well-behaved structural operational semantics and, more recently, also for enhancements of the bisimulation proof method. If T is a free monad, then such distributive laws correspond to simple natural transformations. However, when T is not free it can be rather difficult to prove the defining axioms of a distributive law. In this paper we describe how to obtain a distributive law for a monad with an equational presentation …

Extensions Of Functors From Set To V-Cat, Adriana Balan, Alexander Kurz, Jirí Velebil

Engineering Faculty Articles and Research

We show that for a commutative quantale V every functor Set --> V-cat has an enriched left- Kan extension. As a consequence, coalgebras over Set are subsumed by coalgebras over V-cat. Moreover, one can build functors on V-cat by equipping Set-functors with a metric.

Approximation Of Nested Fixpoints, Alexander Kurz

Engineering Faculty Articles and Research

The question addressed in this paper is how to correctly approximate infinite data given by systems of simultaneous corecursive definitions. We devise a categorical framework for reasoning about regular datatypes, that is, datatypes closed under products, coproducts and fixpoints. We argue that the right methodology is on one hand coalgebraic (to deal with possible nontermination and infinite data) and on the other hand 2-categorical (to deal with parameters in a disciplined manner). We prove a coalgebraic version of Bekic lemma that allows us to reduce simultaneous fixpoints to a single fix point. Thus a possibly infinite object of interest is …

Coalgebraic Semantics Of Reflexive Economics (Dagstuhl Seminar 15042), Samson Abramsky, Alexander Kurz, Pierre Lescanne, Viktor Winschel

Engineering Faculty Articles and Research

This report documents the program and the outcomes of Dagstuhl Seminar 15042 “Coalgebraic Semantics of Reflexive Economics”.

Improving Energy Efficiency And Quality Of Service In An Integrated Wireless-Optical Broadband Access Network, Maha Shihab Ahmed

Theses: Doctorates and Masters

Exponential growth in the volume of wireless data, boosted by the growing popularity of mobile devices such as smart phones and tablets, is forcing telecommunication industries to rethink network design, and focus on developing high capacity mobile broadband networks. Accordingly, researchers have undertaken developmental work for an integrated wireless-optical broadband access network (WOBAN). Passive optical networks (PONs) and fourth generation (4G) wireless networks are two major candidate technologies for the WOBAN. PON is a wired access technology, well-known for its high capacity, whereas 4G is a wireless broadband access technology, popular for its ease of deployment and ability to offer …

Synthesis Of Irreversible Incompletely Specified Multi-Output Functions To Reversible Eosops Circuits With Pse Gates, Robert Adrian Fiszer

Dissertations and Theses

As quantum computers edge closer to viability, it becomes necessary to create logic synthesis and minimization algorithms that take into account the particular aspects of quantum computers that differentiate them from classical computers. Since quantum computers can be functionally described as reversible computers with superposition and entanglement, both advances in reversible synthesis and increased utilization of superposition and entanglement in quantum algorithms will increase the power of quantum computing.

One necessary component of any practical quantum computer is the computation of irreversible functions. However, very little work has been done on algorithms that synthesize and minimize irreversible functions into a …

A Partner-Matching Framework For Social Activity Communities, Chunyu Ai, Wei Zhong, Mingyuan Yan, Feng Gu

Publications and Research

A lot of daily activities require more than one person to participate and collaborate with each other; however, for many people, it is not easy to find good partners to engage in activities with one another. With the rapid growth of social network applications, more and more people get used to creating connections with people on the social network. Therefore, designing social network framework for partner-matching is significant in helping people to easily find good partners. In this paper, we proposed a framework which can match partners for an active community. In order to improve the matching performance, all users …

Using Spectral Analysis To Evaluate Flute Tone Quality, Ron Yorita

Master's Theses

Many skilled flutists place a high priority on "good" tone quality, or timbre. Timbre can be defined as the audible difference in character that a listener perceives for two notes played at the same pitch. Different timbres are determined by the combination and balance of harmonics that comprise a note. Unlike pitch and rhythm, timbre is difficult to objectively quantify. This project explores (1) how tone quality is described by skilled flutists, (2) whether the harmonic spectrum has some correlation with tone quality, (3) whether certain harmonic spectra are preferred, or considered "good".

Thirty-one flutists ranging from high school students …

Ranking Methods For Global Optimization Of Molecular Structures, John Norman Mcmeen Jr

Electronic Theses and Dissertations

This work presents heuristics for searching large sets of molecular structures for low-energy, stable systems. The goal is to find the globally optimal structures in less time or by consuming less computational resources. The strategies intermittently evaluate and rank structures during molecular dynamics optimizations, culling possible weaker solutions from evaluations earlier, leaving better solutions to receive more simulation time. Although some imprecision was introduced from not allowing all structures to fully optimize before ranking, the strategies identify metrics that can be used to make these searches more efficient when computational resources are limited.

High-Resolution Digital 3d Models Of Algar Do Penico Chamber: Limitations, Challenges, And Potential, Ivo Silvestre M.Sc., José I. Rodrigues Phd, Mauro Figueiredo Phd, Cristina Veiga-Pires Phd

International Journal of Speleology

The study of karst and its geomorphological structures is important for understanding the relationships between hydrology and climate over geological time. In that context, we conducted a terrestrial laser-scan survey to map geomorphological structures in the karst cave of Algar do Penico in southern Portugal. The point cloud data set obtained was used to generate 3D meshes with different levels of detail, allowing the limitations of mapping capabilities to be explored.

In addition to cave mapping, the study focuses on 3D-mesh analysis, including the development of two algorithms for determination of stalactite extremities and contour lines, and on the interactive …

Cubic Spline Interpolation By Solving A Recurrence Equation Instead Of A Tridiagonal Matrix, Peter Revesz

School of Computing: Conference and Workshop Papers

The cubic spline interpolation method is proba- bly the most widely-used polynomial interpolation method for functions of one variable. However, the cubic spline method requires solving a tridiagonal matrix-vector equation with an O(n) computational time complexity where n is the number of data measurements. Even an O(n) time complexity may be too much in some time-ciritical applications, such as continuously estimating and updating the flight paths of moving objects. This paper shows that under certain boundary conditions the tridiagonal matrix solving step of the cubic spline method could be entirely eliminated and instead the coefficients of the unknown cubic polynomials …

Designing A Bayer Filter With Smooth Hue Transition Interpolation Using The Xilinx System Generator, Zhiqiang Li, Peter Revesz

School of Computing: Conference and Workshop Papers

This paper describes the design of a Bayer filter with smooth hue transition using the System Generator for DSP. We describe and compare experimentally two different designs, one based on a MATLAB implementation and the other based on a modification of the Bayer filter using bilinear interpolation.

A Game-Theoretic Analysis Of The Nuclear Non-Proliferation Treaty, Peter Revesz

School of Computing: Conference and Workshop Papers

Although nuclear non-proliferation is an almost universal human desire, in practice, the negotiated treaties appear unable to prevent the steady growth of the number of states that have nuclear weapons. We propose a computational model for understanding the complex issues behind nuclear arms negotiations, the motivations of various states to enter a nuclear weapons program and the ways to diffuse crisis situations.