Programming Languages and Compilers Commons^™

A Polyglot Approach To Bioinformatics Data Integration: Phylogenetic Analysis Of Hiv-1, Steven Reisman, Catherine Putonti, George K. Thiruvathukal, Konstantin Läufer

Computer Science: Faculty Publications & Other Works

RNA-interference has potential therapeutic use against HIV-1 by targeting highly-functional mRNA sequences that contribute to the virulence of the virus. Empirical work has shown that within cell lines, all of the HIV-1 genes are affected by RNAi-induced gene silencing. While promising, inherent in this treatment is the fact that RNAi sequences must be highly specific. HIV, however, mutates rapidly, leading to the evolution of viral escape mutants. In fact, such strains are under strong selection to include mutations within the targeted region, evading the RNAi therapy and thus increasing the virus’ fitness in the host. Taking a phylogenetic approach, we ...

Spring­11: Pdc In Cs1/2 And A Mobile/Cloud Intermediate Mobile/Cloud Intermediate Software Design Course, Joseph P. Kaylor, Konstantin Läufer, Chandra N. Sekharan, George K. Thiruvathukal

Computer Science: Faculty Publications & Other Works

Recent changes in the environment of Loyola University Chicago’s Department of Computer Science include a better differentiation of our four undergraduate majors, growing interest in computing among science majors, and an increased demand for graduates with mobile and cloud skills. In our continued effort to incorporate parallel and distributed computing topics into the undergraduate curriculum, we are focusing on these three existing courses:

CS1: In response to a request from the physics department, we started to offer a CS1 section aimed at majors in physics and other hard sciences this spring semester. This section includes some material on numerical ...

Building Capable, Energy-Efficient, Flexible Visualization And Sensing Clusters From Commodity Tablets, Thomas Delgado Dias, Xian Yan, Konstantin Läufer, George K. Thiruvathukal

Computer Science: Faculty Publications & Other Works

We explore the application of clusters of commodity tablet devices to problems spanning a “trilogy” of concerns: visualization, sensing, and computation. We conjecture that such clusters provide a low-cost, energy-efficient, flexible, and ultimately effective platform to tackle a wide range of problems within this trilogy. This is a work in progress, and we now elaborate our position and give a preliminary status report.

A wide range of Android tablet devices are available in terms of price and capabilities. “You get what you pay for” w.r.t. display resolution, sensors, and chipset---corresponding to the trilogy. $200 gets one a 1280x800-pixel ...

Network Technologies Used To Aggregate Environmental Data, Paul Stasiuk, Konstantin Läufer, George K. Thiruvathukal

Computer Science: Faculty Publications & Other Works

The goal of the Loyola Weather Service (lws) project is to design and build a system of functioning environmental monitoring widgets that can intelligently and autonomously control the environment around them based on set thresholds and triggers. The widgets will also have the ability to aggregate their data and easily display this data in various ways: through a user interface in the room that the widget is placed, via a web application, and programmatically via a RESTful web service.

Etd Conversion Utility, Logan E. Jewett

Digital Repository Outreach and Workshops

This presentation describes the development and operation of an ETD Conversion Utility created to prepare electronic theses and dissertations (ETD) received from ProQuest for deposit in Iowa State University's Digital Commons-based institutional repository.

Understanding And Expressing Scalable Concurrency, Aaron Joseph Turon

Computer Science Dissertations

The Holy Grail of parallel programming is to provide good speedup while hiding or avoiding the pitfalls of concurrency. But some level in the tower of abstraction must face facts: parallel processors execute code concurrently, and the interplay between concurrent code, synchronization, and the memory subsystem is a major determiner of performance. Effective parallel programming must ultimately be supported by scalable concurrent algorithms—algorithms that tolerate (or even embrace) concurrency for the sake of scaling with available parallelism. This dissertation makes several contributions to the understanding and expression of such algorithms:

• It shows how to understand scalable algorithms in terms ...

Integrated Development And Parallelization Of Automated Dicentric Chromosome Identification Software To Expedite Biodosimetry Analysis, Yanxin Li

University of Western Ontario - Electronic Thesis and Dissertation Repository

Manual cytogenetic biodosimetry lacks the ability to handle mass casualty events. We present an automated dicentric chromosome identification (ADCI) software utilizing parallel computing technology. A parallelization strategy combining data and task parallelism, as well as optimization of I/O operations, has been designed, implemented, and incorporated in ADCI. Experiments on an eight-core desktop show that our algorithm can expedite the process of ADCI by at least four folds. Experiments on Symmetric Computing, SHARCNET, Blue Gene/Q multi-processor computers demonstrate the capability of parallelized ADCI to process thousands of samples for cytogenetic biodosimetry in a few hours. This increase in speed ...

Parallel For Loops On Heterogeneous Resources, Frederick Edward Weber

Doctoral Dissertations

In recent years, Graphics Processing Units (GPUs) have piqued the interest of researchers in scientific computing. Their immense floating point throughput and massive parallelism make them ideal for not just graphical applications, but many general algorithms as well. Load balancing applications and taking advantage of all computational resources in a machine is a difficult challenge, especially when the resources are heterogeneous. This dissertation presents the clUtil library, which vastly simplifies developing OpenCL applications for heterogeneous systems. The core focus of this dissertation lies in clUtil's ParallelFor construct and our novel PINA scheduler which can efficiently load balance work onto ...

Constructing Verifiably Correct Java Programs Using Ocl And Cleanjava, Yoonsik Cheon, Carmen Avila

Departmental Technical Reports (CS)

A recent trend in software development is building a precise model that can be used as a basis for the software development. Such a model may enable an automatic generation of working code, and more importantly it provides a foundation for correctness reasoning of code. In this paper we propose a practical approach for constructing a verifiably correct program from such a model. The key idea of our approach is (a) to systematically translate formally-specified design constraints such as class invariants and operation pre and postconditions to code-level annotations and (b) to use the annotations for the correctness proof of ...

Senior Project Report - Doctest, Stephen Weessies

Computer Engineering

DocTest is a program that, simply put, allows a programmer or user to document STANAG 4586 (a standard for unmanned aerial vehicle interoperability) messages and test the vehicle system at Lockheed Martin [5]. The program is extensible to allow for further development aiding our software team to do what they do best and not get bogged down in tedious but necessary documentation. DocTest is also used to aid in testing, keeping track of the issues and bugs found and creating a document that captures each issue so an issue is not missed or forgotten. This program was made for use ...

Modular Proof Development In Acl2, Carl Eastlund

Computer Science Dissertations

The ACL2 theorem prover combines a first-order dialect of LISP with an automated proof engine for first-order logic. While ACL2 is logically quite powerful, it can be difficult to build and maintain large models due to its ad hoc systems for modularity, namespace management, logical encapsulation, and macro expansion. I propose a new language, Refined ACL2, extending ACL2 with expressive component and macro systems designed to accommodate large-scale proof development and flexible logical abstractions. The component system of Refined ACL2 adapts many features of ML's functors and signatures to ACL2. Components support nesting, parameterization, translucent specification, and refinement of ...

A Dynamic Programming Approach To Achieving An Optimal End State Along A Serial Production Line, Shih-Fen Cheng, Blake Nicholson, Marina A. Epelman, Daniel Reaume, Robert L. Smith

Research Collection School of Information Systems (Open Access)

In modern production systems, it is critical to perform maintenance, calibration, installation, and upgrade tasks during planned downtime. Otherwise, the systems become unreliable and new product introductions are delayed. For reasons of safety, testing, and access, task performance often requires the vicinity of impacted equipment to be left in a specific “end state” when production halts. Therefore, planning the shutdown of a production system to balance production goals against enabling non-production tasks yields a challenging optimization problem. In this paper, we propose a mathematical formulation of this problem and a dynamic programming approach that efficiently finds optimal shutdown policies for ...

Foundations For Behavioral Higher-Order Contracts, Christos Dimoulas

Computer Science Dissertations

Contracts are a popular mechanism for enhancing the interface of components. In the world of first-order functions, programmers embrace contracts because they write them in a familiar language and easily understand them as a pair of a pre-condition andsame expressiveness to programmers but their meaning subtly differs from the familiar first-order notion. For instance, it is unclear what the behavior of dependent contracts for higher-order functions or of contracts for mutable data should be. As a consequence, it is difficult to design monitoring systems for such higher-order worlds.

In response to this problem, this dissertation investigates complete monitors, a formal ...

Certified Cost Bounds For Higher-Order Programs, Norman Danner

Data, code, etc.

The files in this directory comprise a formal development in Coq of a target language, complexity language, translation, and soundness theorem, all of which combine to provide a mechanism for certified cost bounds on higher-order programs. This section is intended to contain the most current version of the development, which may or may not correspond directly to the developments associated with particular papers from this project.

Scaling Contracts To Realistic Languages, Tharpe Stephen Strickland

Computer Science Dissertations

Contracts allow programmers to specify the expected behavior and use of program components separately from the code of the components themselves. Since Bertrand Meyer introduced contracts to working programmers via the Eiffel programming language, Eiffel-like contract systems have been designed for many other object-oriented languages. Contract systems are not limited to object-oriented programming; Findler and Felleisen showed how to add contracts to languages with higher-order functions and formalized the notions of contract boundaries and blame.

Currently, contract systems come with two major omissions: monitoring the invariants of mutable data structures and protecting first-class components, which are used in the construction ...

Dynamic Data Race Detection And Healing, Du Li

Computer Science and Engineering: Theses, Dissertations, and Student Research

Perpetual availability is an important operational goal in today's computer systems. However, achieving this goal is challenging because modern software systems contain faults that can cause them to fail. For example, multi-threading is widely used in modern software to fully utilize the computing capability of multicore processors. However, employing multi-threading can lead to concurrency faults such as deadlock and data race that are notoriously difficult to to isolate, detect, and repair.Data races, which involves two concurrent accesses to the same data where at least one is a write, are the most common concurrency faults.

As our first step ...

Type-Safety For Inverse Imaging Problems, Maryam Moghadas

Open Access Dissertations and Theses

This thesis gives a partial answer to the question: “Can type systems detect modeling errors in scientific computing, particularly for inverse problems derived from physical models?” by considering, in detail, the major aspects of inverse problems in Magnetic Resonance Imaging (MRI). We define a type-system that can capture all correctness properties for MRI inverse problems, including many properties that are not captured with current type-systems, e.g., frames of reference. We implemented a type-system in the Haskell language that can capture the errors arising in translating a mathe- matical model into a linear or nonlinear system, or alternatively into an ...

Validation Dsl For Client-Server Applications, Vitalii M. Fedorenko

Open Access Dissertations and Theses

Given the nature of client-server applications, most use some freeform interface, like web forms, to collect user input. The main difficulty with this approach is that all parameters obtained in this fashion need to be validated and normalized to protect the application from invalid entries. This is the problem addressed here: how to take client input and preprocess it before passing the data to a back-end, which concentrates on business logic. The method of implementation is a rule engine that uses Groovy internal domain-specific language (DSL) for specifying input requirements. We will justify why the DSL is a good fit ...

Analytic Programming With Fmri Data: A Quick-Start Guide For Statisticians Using R, Ani Eloyan, Shanshan Li, John Muschelli, Jim Pekar, Stewart Mostofsky, Brian S. Caffo

Johns Hopkins University, Dept. of Biostatistics Working Papers

Functional magnetic resonance imaging (fMRI) is a thriving field that plays an important role in medical imaging analysis, biological and neuroscience research and practice. This manuscript gives a didactic introduction to the statistical analysis of fMRI data using the R project along with the relevant R code. The goal is to give tatisticians who would like to pursue research in this area a quick start for programming with fMRI data along with the available data visualization tools.