Numerical Analysis and Scientific Computing Commons^™

Probabilistic Robust Route Recovery With Spatio-Temporal Dynamics, Hao Wu, Jiangyun Mao, Weiwei Sun, Baihua Zheng, Hanyuan Zhang, Ziyang Chen, Wei Wang

Research Collection School Of Computing and Information Systems

Vehicle trajectories are one of the most important data in location-based services. The quality of trajectories directly affects the services. However, in the real applications, trajectory data are not always sampled densely. In this paper, we study the problem of recovering the entire route between two distant consecutive locations in a trajectory. Most existing works solve the problem without using those informative historical data or solve it in an empirical way. We claim that a data-driven and probabilistic approach is actually more suitable as long as data sparsity can be well handled. We propose a novel route recovery system in …

Unsupervised Multi-Graph Cross-Modal Hashing For Large-Scale Multimedia Retrieval, Liang Xie, Lei Zhu, Guoqi Chen

Research Collection School Of Computing and Information Systems

With the advance of internet and multimedia technologies, large-scale multi-modal representation techniques such as cross-modal hashing, are increasingly demanded for multimedia retrieval. In cross-modal hashing, three essential problems should be seriously considered. The first is that effective cross-modal relationship should be learned from training data with scarce label information. The second is that appropriate weights should be assigned for different modalities to reflect their importance. The last is the scalability of training process which is usually ignored by previous methods. In this paper, we propose Multi-graph Cross-modal Hashing (MGCMH) by comprehensively considering these three points. MGCMH is unsupervised method which …

Comparison Of Experimental And Theoretical Fully Differential Cross Sections For Single Ionization Of The 2s And 2p States Of Li By O⁸⁺ Ions, Ebrahim Ghanbari-Adivi, Daniel Fischer, Natalia Ferreira, Johannes Goullon, Renate Hubele, Aaron Laforge, Michael Schulz, Don H. Madison

Physics Faculty Research & Creative Works

This paper presents a full three-dimensional (3D) comparison between experiment and theory for 24 MeV O⁸⁺ single ionization of the 2s ground state of lithium and the 2p excited state. Two theoretical approximations are examined: the three-body continuum distorted-wave (3DW) and three-body continuum distorted-wave-eikonal initial state (3DW-EIS). Normally, there is a significant difference between these two approaches and the 3DW-EIS is in much better agreement with experiment. In this case, there is very little difference between the two approaches and both are in very good agreement with experiment. For the excited 2p state, the 3D cross sections would exhibit …

Contact Process With Temporal Disorder, Hatem Barghathi, Thomas Vojta, José A. Hoyos

Physics Faculty Research & Creative Works

We investigate the influence of time-varying environmental noise, i.e., temporal disorder, on the nonequilibrium phase transition of the contact process. Combining a real-time renormalization group, scaling theory, and large scale Monte-Carlo simulations in one and two dimensions, we show that the temporal disorder gives rise to an exotic critical point. At criticality, the effective noise amplitude diverges with increasing time scale, and the probability distribution of the density becomes infinitely broad, even on a logarithmic scale. Moreover, the average density and survival probability decay only logarithmically with time. This infinite-noise critical behavior can be understood as the temporal counterpart of …

R Packages To Aid In Handling Web Access Logs, Oliver Keyes, Bob Rudis, Jay Jacobs

The R Journal

Web access logs contain information on HTTP(S) requests and form a key part of both industry and academic explorations of human behaviour on the internet. But the preparation (reading, parsing and manipulation) of that data is just unique enough to make generalized tools unfit for the task, both in programming time and processing time which are compounded when dealing with large data sets common with web access logs. In this paper we explain and demonstrate a series of packages designed to efficiently read in, parse and munge access log data, allowing researchers to handle URLs and IP addresses easily. These …

Using Decipher V2.0 To Analyze Big Biological Sequence Data In R, Erik S. Wright

The R Journal

In recent years, the cost of DNA sequencing has decreased at a rate that has outpaced improvements in memory capacity. It is now common to collect or have access to many gigabytes of biological sequences. This has created an urgent need for approaches that analyze sequences in subsets without requiring all of the sequences to be loaded into memory at one time. It has also opened opportunities to improve the organization and accessibility of information acquired in sequencing projects. The DECIPHER package offers solutions to these problems by assisting in the curation of large sets of biological sequences stored in …

Progenyclust: An R Package For Progeny Clustering, Chenyue W. Hu, Amina A. Qutub

The R Journal

Identifying the optimal number of clusters is a common problem faced by data scientists in various research fields and industry applications. Though many clustering evaluation techniques have been developed to solve this problem, the recently developed algorithm Progeny Clustering is a much faster alternative and one that is relevant to biomedical applications. In this paper, we introduce an R package progenyClust that implements and extends the original Progeny Clustering algorithm for evaluating clustering stability and identifying the optimal cluster number. We illustrate its applicability using two examples: a simulated test dataset for proof-of-concept, and a cell imaging dataset for demonstrating …

Schemaonread: A Package For Schema-On-Read In R, Michael J. North

The R Journal

SchemaOnRead is a CRAN package that provides an extensible mechanism for importing a wide range of file types into R as well as support for the emerging schema-on-read paradigm in R. The schema-on-read tools within the package include a single function call that recursively reads folders with text, comma separated value, raster image, R data, HDF5, NetCDF, spreadsheet, Weka, Epi Info, Pajek network, R network, HTML, SPSS, Systat, and Stata files. It also recursively reads folders (e.g., schemaOnRead("folder")), returning a nested list of the contained elements. The provided tools can be used as-is or easily customized to implement tool chains …

Cryptrndtest: An R Package For Testing The Cryptographic Randomness, Haydar Demirhan, Nihan Bitirim

The R Journal

n this article, we introduce the R package CryptRndTest that performs eight statistical randomness tests on cryptographic random number sequences. The purpose of the package is to provide software implementing recently proposed cryptographic randomness tests utilizing goodness of-fit tests superior to the usual chi-square test in terms of statistical performance. Most of the tests included in package CryptRndTest are not available in other software packages such as the R package RDieHarder or the C library TestU01. Chi-square, Anderson-Darling, Kolmogorov-Smirnov, and Jarque-Bera goodness-of-fit procedures are provided along with cryptographic randomness tests. CryptRndTest utilizes multiple precision floating numbers for sequences longer than …

Scmamp: Statistical Comparison Of Multiple Algorithms In Multiple Problems, Borja Calvo, Guzmán Santafé

The R Journal

Comparing the results obtained by two or more algorithms in a set of problems is a central task in areas such as machine learning or optimization. Drawing conclusions from these comparisons may require the use of statistical tools such as hypothesis testing. There are some interesting papers that cover this topic. In this manuscript we present scmamp, an R package aimed at being a tool that simplifies the whole process of analyzing the results obtained when comparing algorithms, from loading the data to the production of plots and tables.

Comparing the performance of different algorithms is an essential step …

Swmpr: An R Package For Retrieving, Organizing, And Analyzing Environmental Data For Estuaries, Marcus W. Beck

The R Journal

The System-Wide Monitoring Program (SWMP)was implemented in 1995 by the US National Estuarine Research Reserve System. This program has provided two decades of continuous monitoring data at over 140 fixed stations in 28 estuaries. However, the increasing quantity of data provided by the monitoring network has complicated broad-scale comparisons between systems and, in some cases, prevented simple trend analysis of water quality parameters at individual sites. This article describes the SWMPr package that provides several functions that facilitate data retrieval, organization, and analysis of time series data in the reserve estuaries. Previously unavailable functions for estuaries are also provided to …

Fwdselect: An R Package For Variable Selection In Regression Models, Marta Sestelo, Nora M. Villanueva, Luis Meira-Machado, Javier Roca-Pardiñas

The R Journal

In multiple regression models, when there are a large number (p) of explanatory variables which may o rmay not be relevant for predicting the response, it is useful to be able to reduce the model. To this end, it is necessary to determine the best subset of q (q p) predictors which will establish the model with the best prediction capacity. FWDselect package introduces a new forward stepwise based selection procedure to select the best model in different regression frameworks (parametric or nonparametric). The developed methodology, which can be equally applied to linear models, generalized linear models or generalized additive …

Quickpsy: An R Package To Fit Psychometric Functions For Multiple Groups, Daniel Linares, Joan López-Moliner

The R Journal

quickpsy is a package to parametrically fit psychometric functions. In comparison with previous R packages, quickpsy was built to easily fit and plot data for multiple groups. Here, we describe the standard parametric model used to fit psychometric functions and the standard estimation of its parameters using maximum likelihood. We also provide examples of usage of quickpsy, including how allowing the lapse rate to vary can sometimes eliminate the bias in parameter estimation, but not in general. Finally, we describe some implementation details, such as how to avoid the problems associated to round-off errors in the maximisation of the …

Variable Clustering In High-Dimensional Linear Regression: The R Package Clere, Loïc Yengo, Julien Jacques, Christophe Biernacki, Mickael Canouil

The R Journal

Dimension reduction is one of the biggest challenges in high-dimensional regression models. We recently introduced a new methodology based on variable clustering as a means to reduce dimensionality. We present here the R package clere that implements some refinements of this methodology. An overview of the package functionalities as well as examples to run an analysis are described. Numerical experiments on real data were performed to illustrate the good predictive performance of our parsimonious method compared to standard dimension reduction approaches.

Rtableicc: An R Package For Random Generation Of 22k And Rc Contingency Tables, Haydar Demirhan

The R Journal

In this paper, we describe the R package rTableICC that provides an interface for random generation of 2 2 K and R Ccontingency tables constructed over either intraclass-correlated or uncorrelated individuals. Intraclass correlations arise in studies where sampling units include more than one individual and these individuals are correlated. The package implements random generation of contingency tables over individuals with or without intraclass correlations under various sampling plans. The package include two functions for the generation of K 2 2 tables over product-multinomial sampling schemes and that of 2 2 K tables under Poisson or multinomial sampling plans. It also …

Editorial, Michael Lawrence

The R Journal

On behalf of the editorial board, I am pleased to publish Volume 8, Issue 1 of the R Journal. This issue contains 27 contributed research articles. Each of them either presents an R package, a specific extension of an R package or applications using R packages available from the Comprehensive R Archive Network (CRAN, http:://CRAN.R-project.org). It thus provides a small but current cross-section of the burgeoning R ecosystem.

Singapore In Motion: Insights On Public Transport Service Level Through Farecard And Mobile Data Analytics, Hasan Poonawala, Vinay Kolar, Sebastien Blandin, Laura Wynter, Sambit Sahu

Research Collection School Of Computing and Information Systems

Given the changing dynamics of mobility patterns and rapid growth of cities, transport agencies seek to respond more rapidly to needs of the public with the goal of offering an effective and competitive public transport system. A more data-centric approach for transport planning is part of the evolution of this process. In particular, the vast penetration of mobile phones provides an opportunity to monitor and derive insights on transport usage. Real time and historical analyses of such data can give a detailed understanding of mobility patterns of people and also suggest improvements to current transit systems. On its own, however, …

A Step Towards An Intelligent Digital Training Management System (I-Dtms), Andrew Dugger

Theses and Dissertations

The U.S. Army Digital Training Management System (DTMS) is a web-based system designed to create a single point of entry for units to schedule unit training, manage training resources, and create schedules and master calendars for training. Currently, the U.S. Army uses DTMS to manage unit training and help commanders at each step of the training management process from planning and preparing to execute and assessing the training plans. This research aims to add intelligent features to DTMS through augmenting it with an intelligent decision support system (ITPSS) that utilizes artificial intelligence techniques (case-based reasoning, in particular) to determine if …

Where Is The Goldmine? Finding Promising Business Locations Through Facebook Data Analytics, Jovian Lin, Richard Oentaryo, Ee-Peng Lim, Casey Vu, Adrian Vu, Agus Kwee

Research Collection School Of Computing and Information Systems

If you were to open your own cafe, would you not want to effortlessly identify the most suitable location to set up your shop? Choosing an optimal physical location is a critical decision for numerous businesses, as many factors contribute to the final choice of the location. In this paper, we seek to address the issue by investigating the use of publicly available Facebook Pages data-which include user "check-ins", types of business, and business locations-to evaluate a user-selected physical location with respect to a type of business. Using a dataset of 20,877 food businesses in Singapore, we conduct analysis of …

Word Clouds With Latent Variable Analysis For Visual Comparison Of Documents, Tuan M. V. Le, Hady W. Lauw

Research Collection School Of Computing and Information Systems

Word cloud is a visualization form for text that is recognized for its aesthetic, social, and analytical values. Here, we are concerned with deepening its analytical value for visual comparison of documents. To aid comparative analysis of two or more documents, users need to be able to perceive similarities and differences among documents through their word clouds. However, as we are dealing with text, approaches that treat words independently may impede accurate discernment of similarities among word clouds containing different words of related meanings. We therefore motivate the principle of displaying related words in a coherent manner, and propose to …