Benchmarking R Packages For Calculation Of Persistent Homology,
2021
Case Western Reserve University
Benchmarking R Packages For Calculation Of Persistent Homology, Eashwar V. Somasundaram, Shael E. Brown, Adam Litzler, Jacob G. Scott, Raoul R. Wadhwa
The R Journal
Several persistent homology software libraries have been implemented in R. Specifically, the Dionysus, GUDHI, and Ripser libraries have been wrapped by the TDA and TDAstats CRAN packages. These software represent powerful analysis tools that are computationally expensive and, to our knowledge, have not been formally benchmarked. Here, we analyze runtime and memory growth for the 2 R packages and the 3 underlying libraries. We find that datasets with less than 3 dimensions can be evaluated with persistent homology fastest by the GUDHI library in the TDA package. For higher-dimensional datasets, the Ripser library in the TDAstats package is the fastest. …
Unidimensional And Multidimensional Methods For Recurrence Quantification Analysis With Crqa,
2021
University of East London
Unidimensional And Multidimensional Methods For Recurrence Quantification Analysis With Crqa, Moreno I. Coco, Dan Mønster, Giuseppe Leonardi, Rick Dale, Sebastian Wallot
The R Journal
Recurrence quantification analysis is a widely used method for characterizing patterns in time series. This article presents a comprehensive survey for conducting a wide range of recurrence-based analyses to quantify the dynamical structure of single and multivariate time series and capture coupling properties underlying leader-follower relationships. The basics of recurrence quantification analysis (RQA) and all its variants are formally introduced step-by-step from the simplest auto-recurrence to the most advanced multivariate case. Importantly, we show how such RQA methods can be deployed under a single computational framework in R using a substantially renewed version of our crqa 2.0 package. This package …
Exprior: An R Package For The Formulation Of Ex-Situ Priors,
2021
University Potsdam
Exprior: An R Package For The Formulation Of Ex-Situ Priors, Falk Heße, Karina Cucchi, Nura Kawa, Yoram Rubin
The R Journal
The exPrior package implements a procedure for formulating informative priors of geostatistical properties for a target field site, called ex-situ priors and introduced in Cucchi et al. (2019). The procedure uses a Bayesian hierarchical model to assimilate multiple types of data coming from multiple sites considered as similar to the target site. This prior summarizes the information contained in the data in the form of a probability density function that can be used to better inform further geostatistical investigations at the site. The formulation of the prior uses ex-situ data, where the data set can either be gathered by the …
A Method For Deriving Information From Running R Code,
2021
Statistics Netherlands
A Method For Deriving Information From Running R Code, Mark P. J. Van Der Loo
The R Journal
It is often useful to tap information from a running R script. Obvious use cases include monitoring the consumption of resources (time, memory) and logging. Perhaps less obvious cases include tracking changes in R objects or collecting the output of unit tests. In this paper, we demonstrate an approach that abstracts the collection and processing of such secondary information from the running R script. Our approach is based on a combination of three elements. The first element is to build a customized way to evaluate code. The second is labeled local masking and it involves temporarily masking a user-facing function …
Conference Report Of Why R? Turkey 2021,
2021
Eskisehir Technical University
Conference Report Of Why R? Turkey 2021, Mustafa Cavus, Olgun Aydin, Ozan Evkaya, Ozancan Ozdemir, Deniz Bezer, Ugur Dar
The R Journal
The Why R? Turkey 2021 as a three-day online conference was organized to bring together researchers and professionals from Turkey on April 16-17-18, 2021. We hereby aimed to promote the R community in Turkey by bringing R users with different backgrounds such as genetics, sociology, finance, economy, bio-statistics. There were 8 thematic sessions and 18 invited speakers. In this article, it is aimed to describe the preparation phase, technical details, and the impact of the conference on audience.
News From The Forwards Taskforce,
2021
University of Warwick
News From The Forwards Taskforce, Heather Turner
The R Journal
Forwards is an R Foundation taskforce working to widen the participation of underrepresented groups in the R project and in related activities, such as the useR! conference. This report rounds up activities of the taskforce during the first half of 2021.
R Foundation News,
2021
Universität Zürich
R Foundation News, Torsten Hothorn
The R Journal
Membership fees and donations received between 2021-01-29 and 2021-07-05.
Changes In R 4.0–4.1,
2021
Czech Technical University
Changes In R 4.0–4.1, Tomas Kalibera, Sebastian Meyer, Kurt Hornik
The R Journal
We give a selection of the most important changes in R 4.1.0. Some statistics on source code commits and bug tracking activities are also provided.
Delving Deep Into Many-To-Many Attention For Few-Shot Video Object Segmentation,
2021
Singapore Management University
Delving Deep Into Many-To-Many Attention For Few-Shot Video Object Segmentation, Haoxin Chen, Hanjie Wu, Nanxuan Zhao, Sucheng Ren, Shengfeng He
Research Collection School Of Computing and Information Systems
This paper tackles the task of Few-Shot Video Object Segmentation (FSVOS), i.e., segmenting objects in the query videos with certain class specified in a few labeled support images. The key is to model the relationship between the query videos and the support images for propagating the object information. This is a many-to-many problem and often relies on full-rank attention, which is computationally intensive. In this paper, we propose a novel Domain Agent Network (DAN), breaking down the full-rank attention into two smaller ones. We consider one single frame of the query video as the domain agent, bridging between the support …
Pitcher Effectiveness: A Step Forward For In Game Analytics And Pitcher Evaluation,
2021
Chapman University
Pitcher Effectiveness: A Step Forward For In Game Analytics And Pitcher Evaluation, Christopher Watkins, Vincent Berardi, Cyril Rakovski
Mathematics, Physics, and Computer Science Faculty Articles and Research
With the introduction of Statcast in 2015, baseball analytics have become more precise. Statcast allows every play to be accurately tracked and the data it generates is easily accessible through Baseball Savant, which opens the opportunity for improved performance statistics to be developed. In this paper we propose a new tool, Pitcher Effectiveness, that uses Statcast data to evaluate starting pitchers dynamically, based on the results of in-game outcomes after each pitch. Pitcher Effectiveness successfully predicts instances where starting pitchers give up several runs, which we believe make it a new and important tool for the in-game and post-game evaluation …
High-Order Flexible Multirate Integrators For Multiphysics Applications,
2021
Southern Methodist University
High-Order Flexible Multirate Integrators For Multiphysics Applications, Rujeko Chinomona
Mathematics Theses and Dissertations
Traditionally, time integration methods within multiphysics simulations have been chosen to cater to the most restrictive dynamics, sometimes at a great computational cost. Multirate integrators accurately and efficiently solve systems of ordinary differential equations that exhibit different time scales using two or more time steps. In this thesis, we explore three classes of time integrators that can be classified as one-step multi-stage multirate methods for which the slow dynamics are evolved using a traditional one step scheme and the fast dynamics are solved through a sequence of modified initial value problems. Practically, the fast dynamics are subcycled using a small …
Using Deep Learning For Children Brain Image Analysis,
2021
University of Arkansas, Fayetteville
Using Deep Learning For Children Brain Image Analysis, Rafael Toche Pizano
Computer Science and Computer Engineering Undergraduate Honors Theses
Analyzing the correlation between brain volumetric/morphometry features and cognition/behavior in children is important in the field of pediatrics as identifying such relationships can help identify children who may be at risk for illnesses. Understanding these relationships can not only help identify children who may be at risk of illnesses, but it can also help evaluate strategies that promote brain development in children. Currently, one way to do this is to use traditional statistical methods such as a correlation analysis, but such an approach does not make it easy to generalize and predict how brain volumetric/morphometry will impact cognition/behavior. One of …
A Comparison Of Word Embedding Techniques For Similarity Analysis,
2021
University of Arkansas, Fayetteville
A Comparison Of Word Embedding Techniques For Similarity Analysis, Tyler Gerth
Computer Science and Computer Engineering Undergraduate Honors Theses
There have been a multitude of word embedding techniques developed that allow a computer to process natural language and compare the relationships between different words programmatically. In this paper, similarity analysis, or the testing of words for synonymic relations, is used to compare several of these techniques to see which performs the best. The techniques being compared all utilize the method of creating word vectors, reducing words down into a single vector of numerical values that denote how the word relates to other words that appear around it. In order to get a holistic comparison, multiple analyses were made, with …
Improving Bayesian Graph Convolutional Networks Using Markov Chain Monte Carlo Graph Sampling,
2021
University of Arkansas, Fayetteville
Improving Bayesian Graph Convolutional Networks Using Markov Chain Monte Carlo Graph Sampling, Aneesh Komanduri
Computer Science and Computer Engineering Undergraduate Honors Theses
In the modern age of social media and networks, graph representations of real-world phenomena have become incredibly crucial. Often, we are interested in understanding how entities in a graph are interconnected. Graph Neural Networks (GNNs) have proven to be a very useful tool in a variety of graph learning tasks including node classification, link prediction, and edge classification. However, in most of these tasks, the graph data we are working with may be noisy and may contain spurious edges. That is, there is a lot of uncertainty associated with the underlying graph structure. Recent approaches to modeling uncertainty have been …
Trunctrimmer: A First Step Towards Automating Standard Bioinformatic Analysis,
2021
University of Arkansas, Fayetteville
Trunctrimmer: A First Step Towards Automating Standard Bioinformatic Analysis, Z. Gunner Lawless, Dana Dittoe, Dale R. Thompson, Steven C. Ricke
Computer Science and Computer Engineering Undergraduate Honors Theses
Bioinformatic analysis is a time-consuming process for labs performing research on various microbiomes. Researchers use tools like Qiime2 to help standardize the bioinformatic analysis methods, but even large, extensible platforms like Qiime2 have drawbacks due to the attention required by researchers. In this project, we propose to automate additional standard lab bioinformatic procedures by eliminating the existing manual process of determining the trim and truncate locations for paired end 2 sequences. We introduce a new Qiime2 plugin called TruncTrimmer to automate the process that usually requires the researcher to make a decision on where to trim and truncate manually after …
Using Large Pre-Trained Language Models To Track Emotions Of Cancer Patients On Twitter,
2021
University of Arkansas, Fayetteville
Using Large Pre-Trained Language Models To Track Emotions Of Cancer Patients On Twitter, Will Baker
Computer Science and Computer Engineering Undergraduate Honors Theses
Twitter is a microblogging website where any user can publicly release a message, called a tweet, expressing their feelings about current events or their own lives. This candid, unfiltered feedback is valuable in the spaces of healthcare and public health communications, where it may be difficult for cancer patients to divulge personal information to healthcare teams, and randomly selected patients may decline participation in surveys about their experiences. In this thesis, BERTweet, a state-of-the-art natural language processing (NLP) model, was used to predict sentiment and emotion labels for cancer-related tweets collected in 2019 and 2020. In longitudinal plots, trends in …
Tripdecoder: Study Travel Time Attributes And Route Preferences Of Metro Systems From Smart Card Data,
2021
Singapore Management University
Tripdecoder: Study Travel Time Attributes And Route Preferences Of Metro Systems From Smart Card Data, Xiancai Tian, Baihua Zheng, Yazhe Wang, Hsao-Ting Huang, Chih-Cheng Hung
Research Collection School Of Computing and Information Systems
In this paper, we target at recovering the exact routes taken by commuters inside a metro system that are not captured by an Automated Fare Collection (AFC) system and hence remain unknown. We strategically propose two inference tasks to handle the recovering, one to infer the travel time of each travel link that contributes to the total duration of any trip inside a metro network and the other to infer the route preferences based on historical trip records and the travel time of each travel link inferred in the previous inference task. As these two inference tasks have interrelationship, most …
Robot: Robustness-Oriented Testing For Deep Learning Systems,
2021
Zhejiang University
Robot: Robustness-Oriented Testing For Deep Learning Systems, Jingyi Wang, Jialuo Chen, Youcheng Sun, Xingjun Ma, Dongxia Wang, Jun Sun, Peng Cheng
Research Collection School Of Computing and Information Systems
Recently, there has been a significant growth of interest in applying software engineering techniques for the quality assurance of deep learning (DL) systems. One popular direction is deep learning testing, where adversarial examples (a.k.a. bugs) of DL systems are found either by fuzzing or guided search with the help of certain testing metrics. However, recent studies have revealed that the commonly used neuron coverage metrics by existing DL testing approaches are not correlated to model robustness. It is also not an effective measurement on the confidence of the model robustness after testing. In this work, we address this gap by …
The Effect Of Initial Conditions On The Weather Research And Forecasting Model,
2021
Stephen F Austin State University
The Effect Of Initial Conditions On The Weather Research And Forecasting Model, Aaron D. Baker
Electronic Theses and Dissertations
Modeling our atmosphere and determining forecasts using numerical methods has been a challenge since the early 20th Century. Most models use a complex dynamical system of equations that prove difficult to solve by hand as they are chaotic by nature. When computer systems became more widely adopted and available, approximating the solution of these equations, numerically, became easier as computational power increased. This advancement in computing has caused numerous weather models to be created and implemented across the world. However a challenge of approximating these solutions accurately still exists as each model have varying set of equations and variables to …
Corn Co-Product Logistics: An Application Of Linear Programming,
2021
University of Nebraska-Lincoln
Corn Co-Product Logistics: An Application Of Linear Programming, Dmitry Kalashnikov Adams
Department of Agricultural Economics: Dissertations, Theses, and Student Research
The purpose of this thesis is not to explore new ways to apply or to study the general field of linear programming. Rather the emphasis is on applying a particular type of linear programming to a specific problem. In this thesis the classic case of linear programing - the transportation problem – is used to optimize corn co-product logistics between six ethanol producing facilities. At the core, the problem of corn germ logistics lies in transporting products from areas of excess supply to areas with excess demand. The challenge of optimizing corn germ logistics lies in managing transportation between producing …
