Numerical Analysis and Scientific Computing Commons^™

Pymelt-Px: A Python Script For Modeling Melting Of A Pyroxenite-Peridotite Bilithological Mantle, Ana L. Jimenez Bustos

Department of Earth and Atmospheric Sciences: Dissertations, Theses, and Student Research

The study of oceanic crust formation is a fundamental building block in our understanding of the processes of planetary formation, necessitating an understanding of the melt generation processes that help form oceanic crust. To aid in this purpose, we present pyMeltPX: a bilithological pyroxenite-peridotite mantle modeling script. Although the mantle is primarily comprised of peridotite, pyroxenite is a minor but ubiquitous feature of the mantle and can contribute a disproportionate amount of melt to crustal generation in mid-ocean ridge and ocean island basalt settings. Our model, pyMeltPX, is a python coded, extensible tool based on the Excel calculator by Lambart …

Physics Embedded Neural Network: A Novel Data-Free Numerical Method For Solving Computational Physics Problems, Pawan Gaire

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

A novel approach for solving partial differential equations (PDEs) using neural networks for scientific computing is introduced. The proposed approach, referred to as physics-embedded neural network (PENN), features a unique architecture that incorporates the PDE and boundary conditions information directly within the final fully-connected layer of the feed-forward neural network (NN). The key aspect of PENN is the parallel numerical embedding of a differential equation associated with physical problems within the activation function of the network’s final layer. This integration leads to a new class of computational solvers competitive with classical methods like the Finite Element Method (FEM) and capable …

Radar Precursors To Severe Weather Reports In Left-Moving Supercells, Eric A. Carothers

Department of Earth and Atmospheric Sciences: Dissertations, Theses, and Student Research

While much research has examined dual-polarimetric signatures of right-moving supercells, very little has been done with left-moving supercells. Given that left-moving supercells are thought to be disproportionate producers of large hail, understanding their internal dynamics is vitally important. This study examines differences and trends in the dual-polarimetric signatures of left-moving supercells to identify precursors to severe weather reports. A dataset of left-moving supercells associated with severe weather reports was created. These storms are processed with an automated analysis algorithm that identifies and quantifies the polarimetric signatures in each storm. A method for analysis of differences and trends in their dual-polarization …

Towards Advancing Streamflow And Peak Flow Prediction With Machine Learning: Identifying Infrastructure At Risk, Sudan Pokharel

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Due to climate change and its impact, the need for adaptive strategies for natural disaster mitigation and resource management has never been more urgent. Central to this is water resource management, which is essential for sustainable human activities, ecological balance, and the mitigation of natural hazards like floods. Streamflow is a crucial element of water resource management and plays a vital role in planning and building water infrastructure, implementing emergency response plans, supporting flood mitigation initiatives, and regulating agricultural and industrial use. However, accurate prediction of streamflow still remains a challenge due to the complex non-linear and non-stationary interaction between …

Leaf-Based Varietal Categorization Of Sweetpotato (Ipomoea Batatas L. Lam.), A Potentially Healthful Vegetable, Using Image Processing And K-Means Clustering, Shahidul Islam, Md Towfiqur Rahman, Md Hamidul Rahman, Abdul Momin

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Sweetpotato (Ipomoea batatas Lam) leaves contain higher concentrations of phenolic compounds, flavonoids, and carotenoids that are remarkable in health promotion. However, the nutrient content in sweetpotato leaves varies from variety to variety, and leaf shape and color are the key identifying factors for the varietal classification of sweetpotatoes. So, detecting sweetpotato leaves is essential for the in-situ identification of sweetpotato varieties and for developing intelligent agricultural systems. This study aimed to create a leaf-shape-based varietal classification technique for sweetpotato using image processing techniques coupled with a K-means clustering algorithm. 38 leaf images (RGB) of two sweetpotato cultivars were collected …

In-Season Nitrogen Mmanagement: Leveraging Data Visualization For Precision Agriculture, Chathurika Harshani Narayana

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Effective nitrogen management is vital for sustainable agriculture, impacting both crop yield and environmental health. Traditional methods often use fixed application rates set before planting, which do not adapt to changing crop needs during the season. This can lead to over- or under-application, reducing efficiency and sustainability. While modern tools like sensors, satellites, and UAVs provide valuable real-time data on crop and field conditions, integrating and using this data to guide timely nitrogen decisions remains a major challenge. In-season nitrogen management offers a solution by allowing for dynamic adjustments to nitrogen applications, addressing crop needs as they arise. This approach …

Dirt/Μ: Automated Extraction Of Root Hair Traits Using Combinatorial Optimization, Peter Pietrzyk, Neen Phan-Udom, Chartinun Chutoe, Lise Pingault, Ankita Roy, Marc Libault, Patompong Johns Saengwilai, Alexander Bucksch

Department of Entomology: Faculty Publications

As with phenotyping of any microscopic appendages, such as cilia or antennae, phenotyping of root hairs has been a challenge due to their complex intersecting arrangements in two-dimensional images and the technical limitations of automated measurements. Digital Imaging of Root Traits at Microscale (DIRT/μ) is a newly developed algorithm that addresses this issue by computationally resolving intersections and extracting individual root hairs from two-dimensional microscopy images. This solution enables automatic and precise trait measurements of individual root hairs. DIRT/μ rigorously defines a set of rules to resolve intersecting root hairs and minimizes a newly designed cost function to combinatorically identify …

Multi-Case Study Of Left-Flank Boundaries Within Supercells, Peyton B. Stevenson

Department of Earth and Atmospheric Sciences: Dissertations, Theses, and Student Research

This study investigates the prevalence and significance of forward-flank convergence boundaries (FFCBs) and left-flank convergence boundaries (LFCBs) in shaping the structure and intensity of supercells, using observational data from various field projects. Unlike previous research focusing on individual cases, this study examines a diverse range of cases to provide comprehensive insights into the relationship between these boundaries and supercell characteristics such as intensity, longevity, and tornadogenesis. By analyzing high-resolution surface data, the research addresses the frequency, location, and intensity of these boundaries, and their impact on pseudo vertical vorticity, pseudo convergence, and density gradients. A total of 228 boundary identifications …

Star-Based Reachability Analysis Of Binary Neural Networks On Continuous Input, Mykhailo Ivashchenko

School of Computing: Dissertations, Theses, and Student Research

Deep Neural Networks (DNNs) have become a popular instrument for solving various real-world problems. DNNs’ sophisticated structure allows them to learn complex representations and features. However, architecture specifics and floating-point number usage result in increased computational operations complexity. For this reason, a more lightweight type of neural networks is widely used when it comes to edge devices, such as microcomputers or microcontrollers – Binary Neural Networks (BNNs). Like other DNNs, BNNs are vulnerable to adversarial attacks; even a small perturbation to the input set may lead to an errant output. Unfortunately, only a few approaches have been proposed for verifying …

Weakly Supervised Attention-Based Recognition Under Spectral, Turbulence, And Resource Variations, Kshitij Naresh Nikhal

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

While supervised optimization paradigms are ubiquitous across diverse recognition systems, the risk of over-fitting and increasing bias have limited their applicability.

This dissertation focuses on unsupervised learning—learning without precisely curated data—and argues that unsupervised learning methods can enable both discriminability and generalizability. Through the use of attention-based machine learning and advanced clustering, unsupervised methods are able to focus on fine-grained information in images without any explicit supervision. The dissertation introduces a domain-bridging framework for tasks like cross-spectrum matching and long-range recognition, utilizing intra-domain clustering and inter-domain matching to generate pseudo-labels. Additionally, a hash-based network is proposed to accelerate the search …

Quantitative Verification For Massive Linear Systems, Qing Liu

School of Computing: Dissertations, Theses, and Student Research

The verification of linear systems has been an active area of research for decades. Reachability analysis is a key component in verification problems. It involves computing the system’s reachable set, the set of reachable states in the state space from a given set of initial states. Most verification methods primarily focus on qualitative verification, which answers whether or not a system may violate specified safety conditions. This paper extends this qualitative verification to quantitative verification by introducing a novel approach, employing probabilistic stars (Probstars) to compute reachable sets, which augment traditional star sets by integrating Gaussian-distributed random variables with …

On Dyadic Parity Check Codes And Their Generalizations, Meraiah Martinez

Department of Mathematics: Dissertations, Theses, and Student Research

In order to communicate information over a noisy channel, error-correcting codes can be used to ensure that small errors don’t prevent the transmission of a message. One family of codes that has been found to have good properties is low-density parity check (LDPC) codes. These are represented by sparse bipartite graphs and have low complexity graph-based decoding algorithms. Various graphical properties, such as the girth and stopping sets, influence when these algorithms might fail. Additionally, codes based on algebraically structured parity check matrices are desirable in applications due to their compact representations, practical implementation advantages, and tractable decoder performance analysis. …

Snowmass 2021 Computational Frontier Compf4 Topical Group Report Storage And Processing Resource Access, W. Bhimji, D. Carder, E. Dart, J. Duarte, I. Fisk, R. Gardner, C. Guok, B. Jayatilaka, T. Lehman, M. Lin, C. Maltzahn, S. Mckee, M. S. Neubauer, O. Rind, O. Shadura, N. V. Tran, P. Van Gemmeren, G. Watts, B. A. Weaver, F. Würthwein

Holland Computing Center: Faculty Publications

The Snowmass 2021 CompF4 topical group’s scope is facilities R&D, where we consider “facilities” as the hardware and software infrastructure inside the data centers plus the networking between data centers, irrespective of who owns them, and what policies are applied for using them. In other words, it includes commercial clouds, federally funded High Performance Computing (HPC) systems for all of science, and systems funded explicitly for a given experimental or theoretical program. However, we explicitly consider any data centers that are integrated into data acquisition systems or trigger of the experiments out of scope here. Those systems tend to have …

Collaborative Computing Support For Analysis Facilities Exploiting Software As Infrastructure Techniques, Maria Acosta Flechas, Garhan Attebury, Kenneth Bloom, Brian Bockelman, Lindsey Gray, Burt Holzman, Carl Lundstedt, Oksana Shadura, Nicholas Smith, John Thiltges

Holland Computing Center: Faculty Publications

Prior to the public release of Kubernetes it was difficult to conduct joint development of elaborate analysis facilities due to the highly non-homogeneous nature of hardware and network topology across compute facilities. However, since the advent of systems like Kubernetes and OpenShift, which provide declarative interfaces for building fault-tolerant and self-healing deployments of networked software, it is possible for multiple institutes to collaborate more effectively since resource details are abstracted away through various forms of hardware and software virtualization. In this whitepaper we will outline the development of two analysis facilities: “Coffea-casa” at University of Nebraska Lincoln and the “Elastic …

News From The Bioconductor Project, Bioconductor Core Team

The R Journal

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor 3.14 was released on 27 October, 2021. It is compatible with R 4.1.0 and consists of 2083 software packages, 408 experiment data packages, 904 up-to-date annotation packages, and 29 workflows.

Changes In R, Tomas Kalibera, Sebastian Meyer, Kurt Hornik, Gennadiy Starostin, Luke Tierney

The R Journal

We present important changes in the development version of R (referred to as R-devel, to become R 4.2) and give a summary of the new search engine interfaced by RSiteSearch(). Some statistics on bug tracking activities in 2021 are also provided.

Rpese: Risk And Performance Estimators Standard Errors With Serially Dependent Data, Anthony-Alexander Christidis, R Douglas Martin

The R Journal

The R package RPESE (Risk and Performance Estimators Standard Errors) implements a new method for computing accurate standard errors of risk and performance estimators when returns are serially dependent. The new method makes use of the representation of a risk or performance estimator as a summation of a time series of influence-function (IF) transformed returns, and computes estimator standard errors using a sophisticated method of estimating the spectral density at frequency zero of the time series of IF-transformed returns. Two additional packages used by RPESE are introduced, namely RPEIF which computes and provides graphical displays of the IF of risk …

The Vote Package: Single Transferable Vote And Other Electoral Systems In R, Adrian E. Raftery, Hana ŠevčÍková, Bernard W. Silverman

The R Journal

We describe the vote package in R, which implements the plurality (or first-past-the-post), two-round runoff, score, approval, and Single Transferable Vote (STV) electoral systems, as well as methods for selecting the Condorcet winner and loser. We emphasize the STV system, which we have found to work well in practice for multi-winner elections with small electorates, such as committee and council elections, and the selection of multiple job candidates. For single-winner elections, STV is also called Instant Runoff Voting (IRV), Ranked Choice Voting (RCV), or the alternative vote (AV) system. The package also implements the STV system with equal preferences, for …

Volume Approximation And Sampling For Convex Polytopes In R, Apostolos Chalkis, Vissarion Fisikopoulos

The R Journal

Sampling from high-dimensional distributions and volume approximation of convex bodies are fundamental operations that appear in optimization, finance, engineering, artificial intelligence, and machine learning. In this paper, we present volesti, an R package that provides efficient, scalable algorithms for volume estimation, uniform, and Gaussian sampling from convex polytopes. volesti scales to hundreds of dimensions, handles efficiently three different types of polyhedra and provides non existing sampling routines to R. We demonstrate the power of volesti by solving several challenging problems using the R language

Bssm: Bayesian Inference Of Non-Linear And Non-Gaussian State Space Models In R, Jouni Helske, Matti Vihola

The R Journal

We present an R package bssm for Bayesian non-linear/non-Gaussian state space modeling. Unlike the existing packages, bssm allows for easy-to-use approximate inference based on Gaussian approximations such as the Laplace approximation and the extended Kalman filter. The package also accommodates discretely observed latent diffusion processes. The inference is based on fully automatic, adaptive Markov chain Monte Carlo (MCMC) on the hyperparameters, with optional importance sampling post-correction to eliminate any approximation bias. The package also implements a direct pseudo-marginal MCMC and a delayed acceptance pseudo-marginal MCMC using intermediate approximations. The package offers an easy-to-use interface to define models with linear-Gaussian state …

Openskies - Integration Of Aviation Data Into The R Ecosystem, Rafael Ayala, Daniel Ayala, Lara Sellés Vidal, David Ruiz

The R Journal

Aviation data has become increasingly more accessible to the public thanks to the adoption of technologies such as Automatic Dependent Surveillance-Broadcast (ADS-B) and Mode S, which provide aircraft information over publicly accessible radio channels. Furthermore, the OpenSky Network provides multiple public resources to access such air traffic data from a large network of ADS-B receivers. Here, we present openSkies, the first R package for processing public air traffic data. The package provides an interface to the OpenSky Network resources, standardized data structures to represent the different entities involved in air traffic data, and functionalities to analyze and visualize such …

Passed: Calculate Power And Sample Size For Two Sample Tests, Jinpu Li, Ryan .. Knigge, Kaiyi Chen, Emily V. Leary

The R Journal

Power and sample size estimation are critical aspects of study design to demonstrate minimized risk for subjects and justify the allocation of time, money, and other resources. Researchers often work with response variables that take the form of various distributions. Here, we present an R package, PASSED, that allows flexibility with seven common distributions and multiple options to accommodate sample size or power analysis. The relevant statistical theory, calculations, and examples for each distribution using PASSED are discussed in this paper.

Automatic Time Series Forecasting With Ata Method In R: Ataforecasting Package, Ali Sabri Taylan, Güçkan Yapar, Hanife Taylan Selamlar

The R Journal

Ata method is a new univariate time series forecasting method that provides innovative solutions to issues faced during the initialization and optimization stages of existing methods. The Ata method’s forecasting performance is superior to existing methods in terms of easy implementation and accurate forecasting. It can be applied to non-seasonal or deseasonalized time series, where the deseasonalization can be performed via any preferred decomposition method. The R package ATAforecasting was developed as a comprehensive toolkit for automatic time series forecasting. It focuses on modeling all types of time series components with any preferred Ata methods and handling seasonality patterns by …

A New Versatile Discrete Distribution, Rolf Turner

The R Journal

This paper introduces a new flexible distribution for discrete data. Approximate moment estimators of the parameters of the distribution, to be used as starting values for numerical optimization procedures, are discussed. “Exact” moment estimation, effected via a numerical procedure, and maximum likelihood estimation, are considered. The quality of the results produced by these estimators is assessed via simulation experiments. Several examples are given of fitting instances of the new distribution to real and simulated data. It is noted that the new distribution is a member of the exponential family. Expressions for the gradient and Hessian of the log-likelihood of the …

Robustbf: An R Package For Robust Solution To The Behrens-Fisher Problem, Gamze Güven, ŞÜkrü Acıtaş, Hatice ŞAmkar, Birdal ŞEnoğLu

The R Journal

Welch’s two-sample t-test based on least squares (LS) estimators is generally used to test the equality of two normal means when the variances are not equal. However, this test loses its power when the underlying distribution is not normal. In this paper, two different tests are proposed to test the equality of two long-tailed symmetric (LTS) means under heterogeneous variances. Adaptive modified maximum likelihood (AMML) estimators are used in developing the proposed tests since they are highly efficient under LTS distribution. An R package called RobustBF is given to show the implementation of these tests. Simulated Type I error rates …

Volesti: Volume Approximation And Sampling For Convex Polytopes In R, Apostolos Chalkis, Vissarion Fisikopoulos

The R Journal

Sampling from high-dimensional distributions and volume approximation of convex bodies are fundamental operations that appear in optimization, finance, engineering, artificial intelligence, and machine learning. In this paper, we present volesti, an R package that provides efficient, scalable algorithms for volume estimation, uniform, and Gaussian sampling from convex polytopes. volesti scales to hundreds of dimensions, handles efficiently three different types of polyhedra and provides non existing sampling routines to R. We demonstrate the power of volesti by solving several challenging problems using the R language.

Passed: Calculate Power And Sample Size For Two Sample Tests, University Of Missouri Li, Ryan P. Knigge, Kaiyi Chen, Emily V. Leary

The R Journal

Power and sample size estimation are critical aspects of study design to demonstrate minimized risk for subjects and justify the allocation of time, money, and other resources. Researchers often work with response variables that take the form of various distributions. Here, we present an R package, PASSED, that allows flexibility with seven common distributions and multiple options to accommodate sample size or power analysis. The relevant statistical theory, calculations, and examples for each distribution using PASSED are discussed in this paper.

Robust And Efficient Optimization Using A Marquardt-Levenberg Algorithm With R Package Marqlevalg, Viviane Philipps, Boris P. Hejblum, Mélanie Prague, Daniel Commenges, Cécile Proust-Lima

The R Journal

Implementations in R of classical general-purpose algorithms for local optimization generally have two major limitations which cause difficulties in applications to complex problems: too loose convergence criteria and too long calculation time. By relying on a Marquardt-Levenberg algorithm (MLA), a Newton-like method particularly robust for solving local optimization problems, we provide with marqLevAlg package an efficient and general-purpose local optimizer which (i) prevents convergence to saddle points by using a stringent convergence criterion based on the relative distance to minimum/maximum in addition to the stability of the parameters and of the objective function; and (ii) reduces the computation time in …

Emss: New Em-Type Algorithms For The Heckman Selection Model In R, Kexuan Yang, Sang Kyu Lee, Jun Zhao, Hyoung-Moon Kim

The R Journal

When investigators observe non-random samples from populations, sample selectivity problems may occur. The Heckman selection model is widely used to deal with selectivity problems. Based on the EM algorithm, Zhao et al. (2020) developed three algorithms, namely, ECM, ECM(NR), and ECME(NR), which also have the EM algorithm’s main advantages: stability and ease of implementation. This paper provides the implementation of these three new EM-type algorithms in the package EMSS and illustrates the usage of the package on several simulated and real data examples. The comparison between the maximum likelihood estimation method (MLE) and three new EM-type algorithms in robustness issues …

Bayessenmc: An R Package For Bayesian Sensitivity Analysis Of Misclassification, Jinhui Yang, Lifeng Lin, Haitao Chu

The R Journal

In case–control studies, the odds ratio is commonly used to summarize the association between a binary exposure and a dichotomous outcome. However, exposure misclassification frequently appears in case–control studies due to inaccurate data reporting, which can produce bias in measures of association. In this article, we implement a Bayesian sensitivity analysis of misclassification to provide a full posterior inference on the corrected odds ratio under both non-differential and differential misclassification. We present an R (R Core Team, 2018) package BayesSenMC, which provides user-friendly functions for its implementation. The usage is illustrated by a real data analysis on the association between …