Theory and Algorithms Commons^™

Motif-Cluster: A Spatial Clustering Package For Repetitive Motif Binding Patterns, Mengyuan Zhou

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Previous efforts in using genome-wide analysis of transcription factor binding sites (TFBSs) have overlooked the importance of ranking potential significant regulatory regions, especially those with repetitive binding within a local region. Identifying these homogenous binding sites is critical because they have the potential to amplify the binding affinity and regulation activity of transcription factors, impacting gene expression and cellular functions. To address this issue, we developed an open-source tool Motif-Cluster that prioritizes and visualizes transcription factor regulatory regions by incorporating the idea of local motif clusters. Motif-Cluster can rank the significant transcription factor regulatory regions without the need for experimental …

Partitions Of R^N With Maximal Seclusion And Their Applications To Reproducible Computation, Jason Vander Woude

Department of Mathematics: Dissertations, Theses, and Student Research

We introduce and investigate a natural problem regarding unit cube tilings/partitions of Euclidean space and also consider broad generalizations of this problem. The problem fits well within a historical context of similar problems and also has applications to the study of reproducibility in randomized computation.

Given $k\in\mathbb{N}$ and $\epsilon\in(0,\infty)$, we define a $(k,\epsilon)$-secluded unit cube partition of $\mathbb{R}^{d}$ to be a unit cube partition of $\mathbb{R}^{d}$ such that for every point $\vec{p}\in\R^d$, the closed $\ell_{\infty}$ $\epsilon$-ball around $\vec{p}$ intersects at most $k$ cubes. The problem is to construct such partitions for each dimension $d$ with the primary goal of minimizing …

Chatgpt As Metamorphosis Designer For The Future Of Artificial Intelligence (Ai): A Conceptual Investigation, Amarjit Kumar Singh (Library Assistant), Dr. Pankaj Mathur (Deputy Librarian)

Library Philosophy and Practice (e-journal)

Abstract

Purpose: The purpose of this research paper is to explore ChatGPT’s potential as an innovative designer tool for the future development of artificial intelligence. Specifically, this conceptual investigation aims to analyze ChatGPT’s capabilities as a tool for designing and developing near about human intelligent systems for futuristic used and developed in the field of Artificial Intelligence (AI). Also with the helps of this paper, researchers are analyzed the strengths and weaknesses of ChatGPT as a tool, and identify possible areas for improvement in its development and implementation. This investigation focused on the various features and functions of ChatGPT that …

Ubjective Information And Survival In A Simulated Biological System, Tyler S. Barker, Massimiliano Pierobon, Peter J. Thomas

School of Computing: Faculty Publications

Information transmission and storage have gained traction as unifying concepts to characterize biological systems and their chances of survival and evolution at multiple scales. Despite the potential for an information-based mathematical framework to offer new insights into life processes and ways to interact with and control them, the main legacy is that of Shannon’s, where a purely syntactic characterization of information scores systems on the basis of their maximum information efficiency. The latter metrics seem not entirely suitable for biological systems, where transmission and storage of different pieces of information (carrying different semantics) can result in different chances of survival. …

Information Extraction And Classification On Journal Papers, Lei Yu

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

The importance of journals for diffusing the results of scientific research has increased considerably. In the digital era, Portable Document Format (PDF) became the established format of electronic journal articles. This structured form, combined with a regular and wide dissemination, spread scientific advancements easily and quickly. However, the rapidly increasing numbers of published scientific articles requires more time and effort on systematic literature reviews, searches and screens. The comprehension and extraction of useful information from the digital documents is also a challenging task, due to the complex structure of PDF.

To help a soil science team from the United States …

Unsupervised Data Mining Technique For Clustering Library In Indonesia, Robbi Rahim, Joseph Teguh Santoso, Sri Jumini, Gita Widi Bhawika, Daniel Susilo, Danny Wibowo

Library Philosophy and Practice (e-journal)

Organizing school libraries not only keeps library materials, but helps students and teachers in completing tasks in the teaching process so that national development goals are in order to improve community welfare by producing quality and competitive human resources. The purpose of this study is to analyze the Unsupervised Learning technique in conducting cluster mapping of the number of libraries at education levels in Indonesia. The data source was obtained from the Ministry of Education and Culture which was processed by the Central Statistics Agency (abbreviated as BPS) with url: bps.go.id/. The data consisted of 34 records where the attribute …

Algorithms Of Oppression [Uno Pa Theory Proseminar Presentation], Sue Ann Gardner

University of Nebraska-Lincoln Libraries: Conference Presentations and Speeches

Slides of two classes taught in the Theory Proseminar in the School of Public Administration at the University of Nebraska at Omaha by Sue Ann Gardner on February 11 and 18, 2020.

Connects information theory to applicable knowledge frameworks in public administration. Includes an in-depth discussion of the concepts addressed in Samiya Umoja Noble's book Algorithms of Oppression (published by New York University Press, New York, New York, United States, 2018) in the context of public administration and public academic libraries.

Improved Evolutionary Support Vector Machine Classifier For Coronary Artery Heart Disease Prediction Among Diabetic Patients, Narasimhan B, Malathi A Dr

Library Philosophy and Practice (e-journal)

Soft computing paves way many applications including medical informatics. Decision support system has gained a major attention that will aid medical practitioners to diagnose diseases. Diabetes mellitus is hereditary disease that might result in major heart disease. This research work aims to propose a soft computing mechanism named Improved Evolutionary Support Vector Machine classifier for CAHD risk prediction among diabetes patients. The attribute selection mechanism is attempted to build with the classifier in order to reduce the misclassification error rate of the conventional support vector machine classifier. Radial basis kernel function is employed in IESVM. IESVM classifier is evaluated through …

Pascal's Triangle Modulo N And Its Applications To Efficient Computation Of Binomial Coefficients, Zachary Warneke

Honors Theses

In this thesis, Pascal's Triangle modulo n will be explored for n prime and n a prime power. Using the results from the case when n is prime, a novel proof of Lucas' Theorem is given. Additionally, using both the results from the exploration of Pascal's Triangle here, as well as previous results, an efficient algorithm for computation of binomial coefficients modulo n (a choose b mod n) is described, and its time complexity is analyzed and compared to naive methods. In particular, the efficient algorithm runs in O(n log(a)) time (as opposed to …

The Global Disinformation Order: 2019 Global Inventory Of Organised Social Media Manipulation, Samantha Bradshaw, Philip N. Howard

Copyright, Fair Use, Scholarly Communication, etc.

Executive Summary

Over the past three years, we have monitored the global organization of social media manipulation by governments and political parties. Our 2019 report analyses the trends of computational propaganda and the evolving tools, capacities, strategies, and resources.

1. Evidence of organized social media manipulation campaigns which have taken place in 70 countries, up from 48 countries in 2018 and 28 countries in 2017. In each country, there is at least one political party or government agency using social media to shape public attitudes domestically.

2.Social media has become co-opted by many authoritarian regimes. In 26 countries, computational propaganda …

Modular Scheduling System For Westside School District, Tyler Bienhoff

Honors Theses

Westside School district offers a modular scheduling system for their high school that is more similar to a college schedule than the typical high school system. Due to the complexity of their master schedule each semester, there are no commercially available products that can assist in creating a schedule. Hence, this thesis discusses a scheduling algorithm and management system that was built specifically for Westside High School with the potential to be expanded for use by other interested schools. The first part of the paper is focused on gathering input from students and faculty for which courses and how many …

Design And Implementation Of A Stand-Alone Tool For Metabolic Simulations, Milad Ghiasi Rad

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

In this thesis, we present the design and implementation of a stand-alone tool for metabolic simulations. This system is able to integrate custom-built SBML models along with external user’s input information and produces the estimation of any reactants participating in the chain of the reactions in the provided model, e.g., ATP, Glucose, Insulin, for the given duration using numerical analysis and simulations. This tool offers the food intake arguments in the calculations to consider the personalized metabolic characteristics in the simulations. The tool has also been generalized to take into consideration of temporal genomic information and be flexible for simulation …

Incremental Phylogenetics By Repeated Insertions: An Evolutionary Tree Algorithm, Peter Revesz, Zhiqiang Li

School of Computing: Faculty Publications

We introduce the idea of constructing hypothetical evolutionary trees using an incremental algorithm that inserts species one-by-one into the current evolutionary tree. The method of incremental phylogenetics by repeated insertions lead to an algorithm that can be used on DNA, RNA and amino acid sequences. According to experimental results on both synthetic and biological data, the new algorithm generates more accurate evolutionary trees than the UPGMA and the Neighbor Joining algorithms.

A Mitochondrial Dna-Based Computational Model Of The Spread Of Human Populations, Peter Revesz

School of Computing: Faculty Publications

This paper presents a mitochondrial DNA-based computational model of the spread of human populations. The computation model is based on a new measure of the relatedness of two populations that may be both heterogeneous in terms of their set of mtDNA haplogroups. The measure gives an exponentially increasing weight for the similarity of two haplogroups with the number of levels shared in the mtDNA classification tree. In an experiment, the computational model is applied to the study of the relatedness of seven human populations ranging from the Neolithic through the Bronze Age to the present. The human populations included in …

A Systems Approach To Animal Communication, Eileen A. Hebets, Andrew B. Barron, Christopher N. Balakrishnan, Mark E. Hauber, Paul H. Mason, Kim L. Hoke

Eileen Hebets Publications

Why animal communication displays are so complex and how they have evolved are active foci of research with a long and rich history. Progress towards an evolutionary analysis of signal complexity, however, has been constrained by a lack of hypotheses to explain similarities and/or differences in signalling systems across taxa. To address this, we advocate incorporating a systems approach into studies of animal communication—an approach that includes comprehensive experimental designs and data collection in combination with the implementation of systems concepts and tools. A systems approach evaluates overall display architecture, including how components interact to alter function, and how function …

An Incremental Phylogenetic Tree Algorithm Based On Repeated Insertions Of Species, Peter Revesz, Zhiqiang Li

CSE Conference and Workshop Papers

In this paper, we introduce a new phylogenetic tree algorithm that generates phylogenetic trees by repeatedly inserting species one-by-one. The incremental phylogenetic tree algorithm can work on proteins or DNA sequences. Computer experiments show that the new algorithm is better than the commonly used UPGMA and Neighbor Joining algorithms.

A Comparative Study Of Underwater Robot Path Planning Algorithms For Adaptive Sampling In A Network Of Sensors, Sreeja Banerjee

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Monitoring lakes, rivers, and oceans is critical to improving our understanding of complex large-scale ecosystems. We introduce a method of underwater monitoring using semi-mobile underwater sensor networks and mobile underwater robots in this thesis. The underwater robots can move freely in all dimension while the sensor nodes are anchored to the bottom of the water column and can move only up and down along the depth of the water column. We develop three different algorithms to optimize the path of the underwater robot and the positions of the sensors to improve the overall quality of sensing of an area of …

Ultimate Codes: Near-Optimal Mds Array Codes For Raid-6, Zhijie Huang, Hong Jiang, Chong Wang, Ke Zhou, Yuhong Zhao

CSE Technical Reports

As modern storage systems have grown in size and complexity, RAID-6 is poised to replace RAID-5 as the dominant form of RAID architectures due to its ability to protect against double disk failures. Many excellent erasure codes specially designed for RAID-6 have emerged in recent years. However, all of them have limitations. In this paper, we present a class of near perfect erasure codes for RAID-6, called the Ultimate codes. These codes encode, update and decode either optimally or nearly optimally, regardless of what the code length is. This implies that utilizing these codes we can build highly efficient and …

S-Code: Lowest Density Mds Array Codes For Raid-6, Zhijie Huang, Hong Jiang, Ke Zhou, Yuhong Zhao, Chong Wang

CSE Technical Reports

RAID, a storage architecture designed to exploit I/O parallelism and provide data reliability, has been deployed widely in computing systems as a storage building block. In large scale storage systems, in particular, RAID-6 is gradually replacing RAID-5 as the dominant form of disk arrays due to its capability of tolerating concurrent failures of any two disks. MDS (maximum distance separable) array codes are the most popular erasure codes that can be used for implementing RAID-6, since they enable optimal storage efficiency and efficient encoding and decoding algorithms. In this paper, we propose a new class of MDS array codes called …

Decaf: A New Event Detection Logic For The Purpose Of Fusing Delineated-Continuous Spatial Information, Kerry Q. Hart

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Geospatial information fusion is the process of synthesizing information from complementary data sources located at different points in space and time. Spatial phenomena are often measured at discrete locations by sensor networks, technicians, and volunteers; yet decisions often require information about locations where direct measurements do not exist. Traditional methods assume the spatial phenomena to be either discrete or continuous, an assumption that underlies and informs all subsequent analysis. Yet certain phenomena defy this dichotomy, alternating as they move across spatial and temporal scales. Precipitation, for example, appears continuous at large scales, but it can be temporally decomposed into discrete …

Information In Biological Systems And The Fluctuation Theorem, Yaşar Demirel

Department of Chemical and Biomolecular Engineering: Faculty Publications

Some critical trends in information theory, its role in living systems and utilization in fluctuation theory are discussed. The mutual information of thermodynamic coupling is incorporated into the generalized fluctuation theorem by using information theory and nonequilibrium thermodynamics. Thermodynamically coupled dissipative structures in living systems are capable of degrading more energy, and processing complex information through developmental and environmental constraints. The generalized fluctuation theorem can quantify the hysteresis observed in the amount of the irreversible work in nonequilibrium regimes in the presence of information and thermodynamic coupling.

Algorithms For Grid Graphs In The Mapreduce Model, Taylor P. Spangler

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

The MapReduce programming paradigm has seen widespread use in analyzing large data sets. Often these large data sets can be formulated as graphs. Many algorithms, such as filtering based algorithms, are designed to work efficiently for dense graphs - graphs with substantially more number of edges than the number of vertices. These algorithms are not optimized for sparse graphs - graphs where the number of edges is of the same order as the number of vertices. However, sparse graphs are also common in big data sets. In this thesis we present algorithms for maximal matching, approximate edge covering, and approximate …

Retrieval Of Sub-Pixel-Based Fire Intensity And Its Application For Characterizing Smoke Injection Heights And Fire Weather In North America, David Peterson

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

For over two decades, satellite sensors have provided the locations of global fire activity with ever-increasing accuracy. However, the ability to measure fire intensity, know as fire radiative power (FRP), and its potential relationships to meteorology and smoke plume injection heights, are currently limited by the pixel resolution. This dissertation describes the development of a new, sub-pixel-based FRP calculation (FRP_f) for fire pixels detected by the MODerate Resolution Imaging Spectroradiometer (MODIS) fire detection algorithm (Collection 5), which is subsequently applied to several large wildfire events in North America. The methodology inherits an earlier bi-spectral algorithm for retrieving sub-pixel …

Combinatorics Using Computational Methods, Derrick Stolee

Department of Mathematics: Dissertations, Theses, and Student Research

Computational combinatorics involves combining pure mathematics, algorithms, and computational resources to solve problems in pure combinatorics. This thesis provides a theoretical framework for combinatorial search, which is then applied to several problems in combinatorics. Some results in space-bounded computational complexity are also presented.

Isomorph-Free Generation Of 2-Connected Graphs With Applications, Derrick Stolee

CSE Technical Reports

Many interesting graph families contain only 2-connected graphs, which have ear decompositions. We develop a technique to generate families of unlabeled 2-connected graphs using ear augmentations and apply this technique to two problems. In the first application, we search for uniquely Kr-saturated graphs and find the list of uniquely K4-saturated graphs on at most 12 vertices, supporting current conjectures for this problem. In the second application, we verify the Edge Reconstruction Conjecture for all 2-connected graphs on at most 12 vertices. This technique can be easily extended to more problems concerning 2-connected graphs.

A First Practical Algorithm For High Levels Of Relational Consistency, Shant Karakashian, Robert J. Woodward, Christopher Reesons, Berthe Y. Choueiry, Christian Bessiere

CSE Conference and Workshop Papers

Consistency properties and algorithms for achieving them are at the heart of the success of Constraint Programming. In this paper, we study the relational consistency property R(∗,m)C, which is equivalent to m-wise consistency proposed in relational databases. We also define wR(∗,m)C, a weaker variant of this property. We propose an algorithm for enforcing these properties on a Constraint Satisfaction Problem by tightening the existing relations and without introducing new ones. We empirically show that wR(∗,m)C solves in a backtrack-free manner all the instances of some CSP benchmark classes, thus hinting at the tractability of those classes.

Adaptive Interpolation Algorithms For Temporal-Oriented Datasets, Jun Gao

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Spatiotemporal datasets can be classified into two categories: temporal-oriented and spatial-oriented datasets depending on whether missing spatiotemporal values are closer to the values of its temporal or spatial neighbors. We present an adaptive spatiotemporal interpolation model that can estimate the missing values in both categories of spatiotemporal datasets. The key parameters of the adaptive spatiotemporal interpolation model can be adjusted based on experience.