Numerical Analysis and Scientific Computing Commons^™

Conference Report: Latinr 2018, Laura Acion, Natalia Da Silva, Riva Quiroga

The R Journal

LatinR <- Latin American Conference about the Use of R in Research + Development (LatinR) was an international conference whose goal was bringing together the Latin Ameri can R community. The inagural LatinR took place at the Universidad de Palermo in Buenos Aires, Argentina, on September 3 to 5, 2018. About 100 participants from more than 10 differ ent countries (e.g., Argentina, Uruguay, Chile, Peru, Ecuador, Brazil, Costa Rica, Venezuela, Spain, United States, Canada) attended LatinR.

LatinR will be an annual meeting that will rotate among different countries in Latin America. LatinR 2019 will be hosted by the Universidad Católica de Chile in Santiago de Chile on September 25 to 27

Explanations Of Model Predictions With Live And Breakdown Packages, Mateusz Staniak, Przemysław Biecek

The R Journal

Complex models are commonly used in predictive modeling. In this paper we present R packages that can be used for explaining predictions from complex black box models and attributing parts of these predictions to input features. We introduce two new approaches and corresponding packages for such attribution, namely live and breakDown. We also compare their results with existing implementations of state-of-the-art solutions, namely, lime (Pedersen and Benesty, 2018) which implements Locally Interpretable Model-agnostic Explanations and iml (Molnar et al., 2018) which implements Shapley values.

Downside Risk Evaluation With The R Package Gas, David Ardia, Kris Boudt, Leopoldo Catania

The R Journal

Financial risk managers routinely use non–linear time series models to predict the downside risk of the capital under management. They also need to evaluate the adequacy of their model using so–called backtesting procedures. The latter involve hypothesis testing and evaluation of loss functions. This paper shows how the R package GAS can be used for both the dynamic prediction and the evaluation of downside risk. Emphasis is given to the two key financial downside risk measures: Value-at-Risk (VaR) and Expected Shortfall (ES). High-level functions for: (i) prediction, (ii) backtesting, and (iii) model comparison are discussed, and code examples are provided. …

Dot-Pipe: An S3 Extensible Pipe For R, John Mount, Nina Zumel

The R Journal

Pipe notation is popular with a large league of R users, with magrittr being the dominant realization. However, this should not be enough to consider piping in R as a settled topic that is not subject to further discussion, experimentation, or possibility for improvement. To promote innovation opportunities, we describe the wrapr R package and “dot-pipe” notation, a well behaved sequencing operator with S3 extensibility. We include a number of examples of using this pipe to interact with and extend other R packages.

Rfsa: An R Package For Finding Best Subsets And Interactions, Joshua Lambert, Liyu Gong, Corrine F. Elliott, Katherine Thompson, Arnold Stromberg

The R Journal

Herein we present the R package rFSA, which implements an algorithm for improved variable selection. The algorithm searches a data space for models of a user-specified form that are statistically optimal under a measure of model quality. Many iterations afford a set of feasible solutions (or candidate models) that the researcher can evaluate for relevance to his or her questions of interest. The algorithm can be used to formulate new or to improve upon existing models in bioinformatics, health care, and myriad other fields in which the volume of available data has outstripped researchers’ practical and computational ability to explore …

R Foundation News, Torsten Hothorn

The R Journal

Donations and members

Donations

Supporting benefactors

Supporting institutions

Supporting members

Conference Report: R / Medicine Report, Joseph Rickert, Naras Balasubramanian, Michael Kane

The R Journal

R has found widespread use and is flourishing in bioinformatics, the pharmaceutical industry, clinical trials, and basic science labs. While R is being adopted in clinical informatics, its potential has not yet been realized. We believe R will fundamentally transform the space because of its strengths in making new methods available, the availability of tools for reproducible research, its interfaces to other languages, and it’s ability to disseminate new approaches through web interfaces and packaging for rapid prototyping of ideas and implementations.

Moreover, while large number of clinicians, scientists, and statisticians contribute to data driven medical science, communication between individuals …

Automatic Identification Of Animals In The Wild: A Comparative Study Between C-Capsule Networks And Deep Convolutional Neural Networks., Joel Kamdem Teto, Ying Xie

Master of Science in Computer Science Theses

The evolution of machine learning and computer vision in technology has driven a lot of

improvements and innovation into several domains. We see it being applied for credit decisions, insurance quotes, malware detection, fraud detection, email composition, and any other area having enough information to allow the machine to learn patterns. Over the years the number of sensors, cameras, and cognitive pieces of equipment placed in the wilderness has been growing exponentially. However, the resources (human) to leverage these data into something meaningful are not improving at the same rate. For instance, a team of scientist volunteers took 8.4 years, …

Multi-Resolution Analysis Of Large Molecular Structures And Interactions, Kasra Manavi

Computer Science ETDs

Simulation of large molecular structures and their interactions has become a major component of modern biomolecular research. Methods to simulate these type of molecules span a wide array of resolutions, from all atom molecular dynamics to model interaction energetics to systems of linear equations to evaluate population kinetics. In recent years, there has been an acceleration of molecular structural information production, primarily from x-ray crystallography and electron microscopy. This data has provided modelers the ability to produce better representations of these molecular structures. The purpose of this research is to take advantage of this information to develop multi-resolution models for …

A Multi-Task Approach To Incremental Dialogue State Tracking, Anh Duong Trinh, Robert J. Ross, John D. Kelleher

Conference papers

Incrementality is a fundamental feature of language in real world use. To this point, however, the vast majority of work in automated dialogue processing has focused on language as turn based. In this paper we explore the challenge of incremental dialogue state tracking through the development and analysis of a multi-task approach to incremental dialogue state tracking. We present the design of our incremental dialogue state tracker in detail and provide evaluation against the well known Dialogue State Tracking Challenge 2 (DSTC2) dataset. In addition to a standard evaluation of the tracker, we also provide an analysis of the Incrementality …

Reaction Simulations: A Rapid Development Framework, Brendan Drake Donohoe

Shared Knowledge Conference

Chemical Reaction Networks (CRNs) are a popular tool in the chemical sciences for providing a means of analyzing and modeling complex reaction systems. In recent years, CRNs have attracted attention in the field of molecular computing for their ability to simulate the components of a digital computer. The reactions within such networks may occur at several different scales relative to one another – at rates often too difficult to directly measure and analyze in a laboratory setting. To facilitate the construction and analysis of such networks, we propose a reduced order model for simulating such networks as a system of …

Analyzing And Modeling Users In Multiple Online Social Platforms, Roy Lee Ka Wei

Dissertations and Theses Collection (Open Access)

This dissertation addresses the empirical analysis on user-generated data from multiple online social platforms (OSPs) and modeling of latent user factors in multiple OSPs setting.

In the first part of this dissertation, we conducted cross-platform empirical studies to better understand user's social and work activities in multiple OSPs. In particular, we proposed new methodologies to analyze users' friendship maintenance and collaborative activities in multiple OSPs. We also apply the proposed methodologies on real-world OSP datasets, and the findings from our empirical studies have provided us with a better understanding on users' social and work activities which are previously not uncovered …

Centroid-Amenities: An Interactive Visual Analytical Tool For Exploring And Analyzing Amenities In Singapore, Xue Qian Jazreel Siew, Sean Jia Ming Koh

Research Collection School Of Computing and Information Systems

Planning for civic amenities in a fast-changing urban setting such as Singapore is never an easy task. And as urban planners look toward more data-driven approaches toward urban planning, so grows the demand for more flexible geospatial analytics tools to facilitate a more iterative and granular approach toward urban planning. Such specific tools however, are not always readily available as plugins for traditional desktop GIS software, as numerous customizations must be made to model specific temporal planning scenarios for quick analysis, which could prove both costly and time-consuming. Hence, to address this need, open-source tools such as R Shiny could …

Latent Dirichlet Allocation For Textual Student Feedback Analysis, Swapna Gottipati, Venky Shankararaman, Jeff Lin

Research Collection School Of Computing and Information Systems

Education institutions collect feedback from students upon course completion and analyse it to improve curriculum design, delivery methodology and students' learning experience. A large part of feedback comes in the form textual comments, which pose a challenge in quantifying and deriving insights. In this paper, we present a novel approach of the Latent Dirichlet Allocation (LDA) model to address this difficulty in handling textual student feedback. The analysis of quantitative part of student feedback provides generalratings and helps to identify aspects of the teaching that are successful and those that can improve. The reasons for the failure or success, however, …

A Survey Of Software Metric Use In Research Software Development, Nasir U. Eisty, George K. Thiruvathukal, Jeffrey C. Carver

Computer Science: Faculty Publications and Other Works

Background: Breakthroughs in research increasingly depend on complex software libraries, tools, and applications aimed at supporting specific science, engineering, business, or humanities disciplines. The complexity and criticality of this software motivate the need for ensuring quality and reliability. Software metrics are a key tool for assessing, measuring, and understanding software quality and reliability. Aims: The goal of this work is to better understand how research software developers use traditional software engineering concepts, like metrics, to support and evaluate both the software and the software development process. One key aspect of this goal is to identify how the set of metrics …

Introducing The Fractional Differentiation For Clinical Data-Justified Prostate Cancer Modelling Under Iad Therapy, Ozlem Ozturk Mizrak

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Mathematical Modeling And Simulation With Deep Learning Methods Of Cancer Growth For Patient-Specific Therapy, Vishal Kobla, Joshua P. Smith, Pranav Unni, Padmanabhan Seshaiyer

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Automating Intention Mining, Qiao Huang, Xin Xia, David Lo, Gail C. Murphy

Research Collection School Of Computing and Information Systems

Developers frequently discuss aspects of the systems they are developing online. The comments they post to discussions form a rich information source about the system. Intention mining, a process introduced by Di Sorbo et al., classifies sentences in developer discussions to enable further analysis. As one example of use, intention mining has been used to help build various recommenders for software developers. The technique introduced by Di Sorbo et al. to categorize sentences is based on linguistic patterns derived from two projects. The limited number of data sources used in this earlier work introduces questions about the comprehensiveness of intention …

An Evaluation Of Geotagged Twitter Data During Hurricane Irma Using Sentiment Analysis And Topic Modeling For Disaster Resilience, Ike Robert Vayansky

Electronic Theses and Dissertations

Disasters require quick response times, thought-out preparations, overall community, and government support. These efforts will ensure prevention of loss of life and reduce possible damages. The United States has been battered by multiple major hurricanes in the recent years and multiple avenues of disaster response efforts were being tested. Hurricane Irma can be recognized as the most popular hurricane in terms of social media attention. Irma made landfall in Florida as a Category 4 storm and preparation measures taken were intensive thus providing a good measure to evaluate in terms of efficacy. The effectiveness of the response methods utilized are …

Sufat: An Analytics Tool For Gaining Insights From Student Feedback Comments, Siddhant Pyasi, Swapna Gottipati, Venky Shankararaman

Research Collection School Of Computing and Information Systems

Teacher evaluation is a vital element inimproving student learning outcomes. Course and instructor feedback given bystudents, provides insights that can help improve student learning outcomes andteaching quality. Teaching and course evaluation systems help to collectquantitative and qualitative feedback from students. Since manually analysingthe qualitative feedback is painstaking and a tedious process, usually, onlythe quantitative feedback is often used for evaluating the course and theinstructor. However, useful knowledge is hidden in the qualitative comments, inthe form of sentiments and suggestions that can provide valuable insights tohelp plan improvements in the course content and delivery. In order toefficiently gather, analyse and provide …