Programming Languages and Compilers Commons^™

Smr: An R Package For Computing The Externally Studentized Normal Midrange Distribution, Ben Dêivide, Oliveira Batista, Daniel Furtado Ferreira

The R Journal

The main purpose of this paper is to present the main algorithms underlining the con struction and implementation of the SMR package, whose aim is to compute studentized normal midrange distribution. Details on the externally studentized normal midrange and standardized normal midrange distributions are also given. The package follows the same structure as the prob ability functions implemented in R. That is: the probability density function (dSMR), the cumulative distribution function (pSMR), the quantile function (qSMR) and the random number generating function (rSMR). Pseudocode and illustrative examples of how to use the package are presented.

Sgof: An R Package For Multiple Testing Problems, Irene Castro-Conde, Jacob De Uña-Álvarez

The R Journal

In this paper we present a new R package called sgof for multiple hypothesis testing. The principal aim of this package is to implement SGoF-type multiple testing methods, known to be more powerful than the classical false discovery rate (FDR) and family-wise error rate (FWER) based methods in certain situations, particularly when the number of tests is large. This package includes Bi nomial and Conservative SGoF and the Bayesian and Beta-Binomial SGoF multiple testing procedures, which are adaptations of the original SGoF method to the Bayesian setting and to possibly correlated tests, respectively. The sgof package also implements the Benjamini-Hochberg …

Ngspatial: A Package For Fitting The Centered Autologistic And Sparse Spatial Generalized Linear Mixed Models For Areal Data, John Hughes

The R Journal

Two important recent advances in areal modeling are the centered autologistic model and the sparse spatial generalized linear mixed model (SGLMM), both of which are reparameterizations of traditional models. The reparameterizations improve regression inference by alleviating spatial confounding, and the sparse SGLMM also greatly speeds computing by reducing the dimension of the spatial random effects. Package ngspatial (’ng’ = non-Gaussian) provides routines for fitting these new models. The package supports composite likelihood and Bayesian inference for the centered autologistic model, and Bayesian inference for the sparse SGLMM.

Phaser: An R Package For Phase Plane Analysis Of Autonomous Ode Systems, Michael J. Grayling

The R Journal

When modelling physical systems, analysts will frequently be confronted by differential equations which cannot be solved analytically. In this instance, numerical integration will usually be the only way forward. However, for autonomous systems of ordinary differential equations (ODEs) in one or two dimensions, it is possible to employ an instructive qualitative analysis foregoing this requirement, using so-called phase plane methods. Moreover, this qualitative analysis can even prove to be highly useful for systems that can be solved analytically, or will be solved numerically anyway. The package phaseR allows the user to perform such phase plane analyses: determining the stability of …

Study Of Parallel Programming Models On Computer Clusters With Accelerators, Chenggang Lai

Graduate Theses and Dissertations

In order to reach exascale computing capability, accelerators have become a crucial part in developing supercomputers. This work examines the potential of two latest acceleration technologies, Intel Many Integrated Core (MIC) Architecture and Graphics Processing Units (GPUs). This thesis applies three benchmarks under 3 different configurations, MPI+CPU, MPI+GPU, and MPI+MIC. The benchmarks include intensely communicating application, loosely communicating application, and embarrassingly parallel application. This thesis also carries out a detailed study on the scalability and performance of MIC processors under two programming models, i.e., offload model and native model, on the Beacon computer cluster.

According to different benchmarks, the results …

Alternative Approaches To Correction Of Malapropisms In Aiml Based Conversational Agents, Walter A. Brock

CCAC Theses and Dissertations

The use of Conversational Agents (CAs) utilizing Artificial Intelligence Markup Language (AIML) has been studied in a number of disciplines. Previous research has shown a great deal of promise. It has also documented significant limitations in the abilities of these CAs. Many of these limitations are related specifically to the method employed by AIML to resolve ambiguities in the meaning and context of words. While methods exist to detect and correct common errors in spelling and grammar of sentences and queries submitted by a user, one class of input error that is particularly difficult to detect and correct is the …

Web Application Vulnerability Prediction Using Hybrid Program Analysis And Machine Learning, Lwin Khin Shar, Lionel Briand, Hee Beng Kuan Tan

Research Collection School Of Computing and Information Systems

Due to limited time and resources, web software engineers need support in identifying vulnerable code. A practical approach to predicting vulnerable code would enable them to prioritize security auditing efforts. In this paper, we propose using a set of hybrid (staticþdynamic) code attributes that characterize input validation and input sanitization code patterns and are expected to be significant indicators of web application vulnerabilities. Because static and dynamic program analyses complement each other, both techniques are used to extract the proposed attributes in an accurate and scalable way. Current vulnerability prediction techniques rely on the availability of data labeled with vulnerability …

A Catalog Of While Loop Specification Patterns, Aditi Barua, Yoonsik Cheon

Departmental Technical Reports (CS)

This document provides a catalog of while loop patterns along with their skeletal specifications. The specifications are written in a functional form known as intended functions. The catalog can be used to derive specifications of while loops by first matching the loops to the cataloged patterns and then instantiating the skeletal specifications of the matched patterns. Once their specifications are formulated and written, the correctness of while loops can be proved rigorously or formally using the functional program verification technique in which a program is viewed as a mathematical function from one program state to another.

Safe Zero-Cost Coercions For Haskell, Joachim Breitner, Richard A. Eisenberg, Simon Peyton Jones, Stephanie Weirich

Computer Science Faculty Research and Scholarship

Generative type abstractions – present in Haskell, OCaml, and other languages – are useful concepts to help prevent programmer errors. They serve to create new types that are distinct at compile time but share a run-time representation with some base type. We present a new mechanism that allows for zero-cost conversions between generative type abstractions and their representations, even when such types are deeply nested. We prove type safety in the presence of these conversions and have implemented our work in GHC.

Event Analytics, Jin Song Dong, Jun Sun, Yang Liu, Yuan-Fang Li

Research Collection School Of Computing and Information Systems

The process analysis toolkit (PAT) integrates the expressiveness of state, event, time, and probability-based languages with the power of model checking. PAT is a self-contained reasoning system for system specification, simulation, and verification. PAT currently supports a wide range of 12 different expressive modeling languages with many application domains and has attracted thousands of registered users from hundreds of organizations. In this invited talk, we will present the PAT system and its vision on “Event Analytics” (EA) which is beyond “Data Analytics”. The EA research is based on applying model checking to event planning, scheduling, prediction, strategy analysis and decision …

Applying Genetic Programming To Bytecode And Assembly, Eric Collom

Scholarly Horizons: University of Minnesota, Morris Undergraduate Journal

Traditional genetic programming (GP) is typically not used to perform unrestricted evolution on entire programs at the source code level. Instead, only small sections within programs are usually evolved. Not being able to evolve whole programs is an issue since it limits the flexibility of what can be evolved. Evolving programs in either bytecode or assembly language is a method that has been used to perform unrestricted evolution. This paper provides an overview of applying genetic programming to Java bytecode and x86 assembly. Two examples of how this method has been implemented will be explored. We will also discuss experimental …

An Overview Of The Current State Of The Test-First Vs. Test-Last Debate, Christopher M. Thomas

Scholarly Horizons: University of Minnesota, Morris Undergraduate Journal

When it comes to software development, perhaps one of the most important and time consuming processes is that of software testing. In fact, early studies on software testing estimated that it could consume fifty percent or more of development costs for a product. Because of this, the ability to optimize testing to reduce testing costs can be very valuable. In this paper we compare two popular methods, test-last testing, often used in waterfall software development processes, and test-first testing, often used in Agile test driven software development methods, by reviewing recent studies on the subject. In this review we discuss …

Improved Microrobotic Control Through Image Processing And Automated Hardware Interfacing, Archit R. Aggarwal, Wuming Jing, David J. Cappelleri

The Summer Undergraduate Research Fellowship (SURF) Symposium

Untethered submilliliter-sized robots (microrobots) are showing potential use in different industrial, manufacturing and medical applications. A particular type of these microrobots, magnetic robots, have shown improved performance in power and control capabilities compared to the other thermal and electrostatic based robots. However, the magnetic robot designs have not been assessed in a robust manner to understand the degree of control in different environments and their application feasibility. This research project seeks to develop a custom control software interface to provide a holistic tool for researchers to evaluate the microrobotic performance through advance control features. The software deliverable involved two main …

A Palm Vein Identification System Based On Gabor Wavelet Features, Ran Wang, Guoyou Wang, Zhong Chen, Zhigang Zeng, Yong Wang

Research Collection School Of Computing and Information Systems

As a new and promising biometric feature, thermal palm vein pattern has drawn lots of attention in research and application areas. Many algorithms have been proposed for authentication since palm vein has special characteristics, such as liveness detection and hard to forgery. However, the detection accuracy of palm vein quite depends on the preprocessing and feature representation, which is supposed to be translation and rotation invariant to some extent. In this paper, we proposed an effective method for palm vein identification based on Gabor wavelet features which contains five steps: image acquisition, ROI detection, image preprocessing, features extraction, and matching. …

Structure Preserving Large Imagery Reconstruction, Ju Shen, Jianjun Yang, Sami Taha Abu Sneineh, Bryson Payne, Markus Hitz

Computer Science Faculty Publications

With the explosive growth of web-based cameras and mobile devices, billions of photographs are uploaded to the internet. We can trivially collect a huge number of photo streams for various goals, such as image clustering, 3D scene reconstruction, and other big data applications. However, such tasks are not easy due to the fact the retrieved photos can have large variations in their view perspectives, resolutions, lighting, noises, and distortions. Furthermore, with the occlusion of unexpected objects like people, vehicles, it is even more challenging to find feature correspondences and reconstruct realistic scenes. In this paper, we propose a structure-based image …

Diamonds Are A Girl's Best Friend: Partial Order Reduction For Timed Automata With Abstractions, Henri Hansen, Shang-Wei Lin, Yang Liu, Truong Khanh Nguyen, Jun Sun

Research Collection School Of Computing and Information Systems

A major obstacle for using partial order reduction in the context of real time verification is that the presence of clocks and clock constraints breaks the usual diamond structure of otherwise independent transitions. This is especially true when information of the relative values of clocks is preserved in the form of diagonal constraints. However, when diagonal constraints are relaxed by a suitable abstraction, some diamond structure is re-introduced in the zone graph. In this article, we introduce a variant of the stubborn set method for reducing an abstracted zone graph. Our method works with all abstractions, but especially targets situations …

Changes On Cran, Kurt Hornik, Achim Zeileis

The R Journal

New packages in CRAN task views

New contributed packages

Other changes

Web Technologies Task View, Patrick Mair, Scott Chamberlain

The R Journal

This article presents the CRAN Task View on Web Technologies. We describe the most important aspects of Web Technologies and Web Scraping and list some of the packages that are currently available on CRAN. Finally, we plot the network of Web Technology related package dependencies.

Oligomask: A Framework For Assessing And Removing The Effect Of Genetic Variants On Microarray Probes, Daniel Bottomly, Beth Wilmot, Shannon K. Mcweeney

The R Journal

As expression microarrays are typically designed relative to a reference genome, any individual genetic variant that overlaps a probe’s genomic position can possibly cause a reduction in hybridization due to the probe no longer being a perfect match to a given sample’s mRNA at that locus. If the samples or groups used in a microarray study differ in terms of genetic variants, the results of the microarray experiment can be negatively impacted. The oligoMask package is an R/SQLite framework which can utilize publicly available genetic variants and works in conjunction with the oligo package to read in the expression data …

Rotations: An R Package For So(3) Data, Bryan Stanfill, Heike Hofmann, Ulrike Genschel

The R Journal

In this article we introduce the rotations package which provides users with the ability to simulate, analyze and visualize three-dimensional rotation data. More specifically it includes four commonly used distributions from which to simulate data, four estimators of the central orientation, six confidence region estimation procedures and two approaches to visualizing rotation data. All of these features are available for two different parameterizations of rotations: three-by-three matrices and quaternions. In addition, two datasets are included that illustrate the use of rotation data in practice