Computer Sciences Commons^™

A Comparison Of Cloud Computing Database Security Algorithms, Joseph A. Hoeppner

UNF Graduate Theses and Dissertations

The cloud database is a relatively new type of distributed database that allows companies and individuals to purchase computing time and memory from a vendor. This allows a user to only pay for the resources they use, which saves them both time and money. While the cloud in general can solve problems that have previously been too costly or time-intensive, it also opens the door to new security problems because of its distributed nature. Several approaches have been proposed to increase the security of cloud databases, though each seems to fall short in one area or another.

This thesis presents …

Hash-Map-Eradicator: Filtering Non-Target Sequences From Next Generation Sequencing Reads, Jonathon Brenner, Catherine Putonti

Bioinformatics Faculty Publications

Contemporary DNA sequencing technologies are continuously increasing throughput at ever decreasing costs. Moreover, due to recent advances in sequencing technology new platforms are emerging. As such computational challenges persist. The average read length possible has taken a giant leap forward with the PacBio and Nanopore solutions. Regardless of the platform used, impurities within the DNA preparation of the sample - be it from unintentional contaminants or pervasive symbiots - remains an issue. We have developed a new tool, HAsh-MaP-ERadicator (HAMPER), for the detection and removal of non-target, contaminating DNA sequences. Integrating hash-based and mapping-based strategies, HAMPER is both memory and …

Adaptive Graph Construction For Isomap Manifold Learning, Loc Tran, Zezhong Zheng, Guoquing Zhou, Jiang Li, Karen O. Egiazarian (Ed.), Sos S. Agaian (Ed.), Atanas P. Gotchev (Ed.)

Electrical & Computer Engineering Faculty Publications

Isomap is a classical manifold learning approach that preserves geodesic distance of nonlinear data sets. One of the main drawbacks of this method is that it is susceptible to leaking, where a shortcut appears between normally separated portions of a manifold. We propose an adaptive graph construction approach that is based upon the sparsity property of the ℓ₁ norm. The ℓ₁ enhanced graph construction method replaces k-nearest neighbors in the classical approach. The proposed algorithm is first tested on the data sets from the UCI data base repository which showed that the proposed approach performs better than …

Learning Emotions: A Software Engine For Simulating Realistic Emotion In Artificial Agents, Douglas Code

Senior Independent Study Theses

This paper outlines a software framework for the simulation of dynamic emotions in simulated agents. This framework acts as a domain-independent, black-box solution for giving actors in games or simulations realistic emotional reactions to events. The emotion management engine provided by the framework uses a modified Fuzzy Logic Adaptive Model of Emotions (FLAME) model, which lets it manage both appraisal of events in relation to an individual’s emotional state, and learning mechanisms through which an individual’s emotional responses to a particular event or object can change over time. In addition to the FLAME model, the engine draws on the design …

Graph-Based Regularization In Machine Learning: Discovering Driver Modules In Biological Networks, Xi Gao

Theses and Dissertations

Curiosity of human nature drives us to explore the origins of what makes each of us different. From ancient legends and mythology, Mendel's law, Punnett square to modern genetic research, we carry on this old but eternal question. Thanks to technological revolution, today's scientists try to answer this question using easily measurable gene expression and other profiling data. However, the exploration can easily get lost in the data of growing volume, dimension, noise and complexity. This dissertation is aimed at developing new machine learning methods that take data from different classes as input, augment them with knowledge of feature relationships, …

A Dynamic Programming Algorithm For Finding The Optimal Placement Of A Secondary Structure Topology In Cryo-Em Data, Abhishek Biswas, Desh Ranjan, Mohammad Zubair, Jing He

Computer Science Faculty Publications

The determination of secondary structure topology is a critical step in deriving the atomic structures from the protein density maps obtained from electron cryomicroscopy technique. This step often relies on matching the secondary structure traces detected from the protein density map to the secondary structure sequence segments predicted from the amino acid sequence. Due to inaccuracies in both sources of information, a pool of possible secondary structure positions needs to be sampled. One way to approach the problem is to first derive a small number of possible topologies using existing matching algorithms, and then find the optimal placement for each …

An Adaptive Gradient Method For Online Auc Maximization, Yi Ding, Peilin Zhao, Steven C. H. Hoi, Yew-Soon Ong

Research Collection School Of Computing and Information Systems

Learning for maximizing AUC performance is an important research problem in machine learning. Unlike traditional batch learning methods for maximizing AUC which often suffer from poor scalability, recent years have witnessed some emerging studies that attempt to maximize AUC by single-pass online learning approaches. Despite their encouraging results reported, the existing online AUC maximization algorithms often adopt simple stochastic gradient descent approaches, which fail to exploit the geometry knowledge of the data observed in the online learning process, and thus could suffer from relatively slow convergence. To overcome the limitation of the existing studies, in this paper, we propose a …

Designing A Portfolio Of Parameter Configurations For Online Algorithm Selection, Aldy Gunawan, Hoong Chuin Lau, Mustafa Misir

Research Collection School Of Computing and Information Systems

Algorithm portfolios seek to determine an effective set of algorithms that can be used within an algorithm selection framework to solve problems. A limited number of these portfolio studies focus on generating different versions of a target algorithm using different parameter configurations. In this paper, we employ a Design of Experiments (DOE) approach to determine a promising range of values for each parameter of an algorithm. These ranges are further processed to determine a portfolio of parameter configurations, which would be used within two online Algorithm Selection approaches for solving different instances of a given combinatorial optimization problem effectively. We …

Algorithm Selection Via Ranking, Jayadi Oentaryo Richard, Handoko Stephanus Daniel, Hoong Chuin Lau

Research Collection School Of Computing and Information Systems

The abundance of algorithms developed to solve different problems has given rise to an important research question: How do we choose the best algorithm for a given problem? Known as algorithm selection, this issue has been prevailing in many domains, as no single algorithm can perform best on all problem instances. Traditional algorithm selection and portfolio construction methods typically treat the problem as a classification or regression task. In this paper, we present a new approach that provides a more natural treatment of algorithm selection and portfolio construction as a ranking task. Accordingly, we develop a Ranking-Based Algorithm Selection (RAS) …

De Novo Protein Structure Modeling And Energy Function Design, Lin Chen

Computer Science Theses & Dissertations

The two major challenges in protein structure prediction problems are (1) the lack of an accurate energy function and (2) the lack of an efficient search algorithm. A protein energy function accurately describing the interaction between residues is able to supervise the optimization of a protein conformation, as well as select native or native-like structures from numerous possible conformations. An efficient search algorithm must be able to reduce a conformational space to a reasonable size without missing the native conformation. My PhD research studies focused on these two directions.

A protein energy function—the distance and orientation dependent energy function of …

Sorting By Block Moves, Jici Huang

UNF Graduate Theses and Dissertations

The research in this thesis is focused on the problem of Block Sorting, which has applications in Computational Biology and in Optical Character Recognition (OCR). A block in a permutation is a maximal sequence of consecutive elements that are also consecutive in the identity permutation. BLOCK SORTING is the process of transforming an arbitrary permutation to the identity permutation through a sequence of block moves. Given an arbitrary permutation π and an integer m, the Block Sorting Problem, or the problem of deciding whether the transformation can be accomplished in at most m block moves has been shown to be …

Concurrent Localized Wait-Free Operations On A Red Black Tree, Vitaliy Kubushyn

UNLV Theses, Dissertations, Professional Papers, and Capstones

A red-black tree is a type of self-balancing binary search tree. Some wait-free algorithms have been proposed for concurrently accessing and modifying a red-black tree from multiple threads in shared memory systems. Most algorithms presented utilize the concept of a "window", and are entirely top-down implementations. Top-down algorithms like these have to operate on large portions of the tree, and operations on nodes that would otherwise not overlap at all still have to compete with and help one another.

A wait-free framework is proposed for obtaining ownership of small portions of the tree at a time in a bottom-up manner. …

Spectral Decomposition Of The Scattered Light Due To Deposits On The Solar Panel Surface, And Cross Correlated To Power Loss, Suzanna Ho

UNLV Theses, Dissertations, Professional Papers, and Capstones

The electric energy generated by solar panels declines due to dust particulates, bird deposits, water spots, and other contaminants that inhibit sunlight absorption and promote light scattering. As part of our research, we use cameras to capture images of solar panels, and analyze the images to detect the amount of scattered light. The more scattered light there is, the less light there is to penetrate the solar panel glass and reach the part of the panel that converts incident light to electric energy; therefore, less energy is generated. In this paper, we discuss the classification algorithm we developed to classify …

Feasibility Of Scalable Quantum Computers, Benjamin N. Goodberry

Selected Honors Theses

No abstract provided.

Band Selection For Hyperspectral Images Using Probabilistic Memetic Algorithm, Liang Feng, Ah-Hwee Tan, Meng-Hiot Lim, Si Wei Jiang

Research Collection School Of Computing and Information Systems

Band selection plays an important role in identifying the most useful and valuable information contained in the hyperspectral images for further data analysis such as classification, clustering, etc. Memetic algorithm (MA), among other metaheuristic search methods, has been shown to achieve competitive performances in solving the NP-hard band selection problem. In this paper, we propose a formal probabilistic memetic algorithm for band selection, which is able to adaptively control the degree of global exploration against local exploitation as the search progresses. To verify the effectiveness of the proposed probabilistic mechanism, empirical studies conducted on five well-known hyperspectral images against two …

Networked Employment Discrimination, Tamara Kneese

Media Studies

Employers often struggle to assess qualified applicants, particularly in contexts where they receive hundreds of applications for job openings. In an effort to increase efficiency and improve the process, many have begun employing new tools to sift through these applications, looking for signals that a candidate is “the best fit.” Some companies use tools that offer algorithmic assessments of workforce data to identify the variables that lead to stronger employee performance, or to high employee attrition rates, while others turn to third party ranking services to identify the top applicants in a labor pool. Still others eschew automated systems, but …

Comparison Of Optimization Techniques In Large Scale Transportation Problems, Tapojit Kumar

Journal of Undergraduate Research at Minnesota State University, Mankato

The Transportation Problem is a classic Operations Research problem where the objective is to determine the schedule for transporting goods from source to destination in a way that minimizes the shipping cost while satisfying supply and demand constraints. Although it can be solved as a Linear Programming problem, other methods exist. Linear Programming makes use of the Simplex Method, an algorithm invented to solve a linear program by progressing from one extreme point of the feasible polyhedron to an adjacent one. The algorithm contains tactics like pricing and pivoting. For a Transportation Problem, a simplified version of the regular Simplex …

Comparison Of Sequence Alignment Algorithms, Tejas Gandhi

Journal of Undergraduate Research at Minnesota State University, Mankato

The fact that biological sequences can be represented as strings belonging to a finite alphabet (A, C, G, and T for DNA) plays an important role in connecting biology to computer science. String representation allows researchers to apply various string comparison techniques available in computer science. As a result, various applications have been developed that facilitate the task of sequence alignment. The problem of finding sequence alignments consists of finding the best match between two biological sequences. A best match can infer an evolutionary relationship and functional similarity. However, there is a lack of research on how reliable and efficient …

Improved Storm Data Processing Through Parallel Computing Approaches, Shauna Smith

Journal of Undergraduate Research at Minnesota State University, Mankato

A previous research study conducted at Michigan Technological University by Dr. Deborah Nykanen and her colleague Dr. Daniel Harris analyzed storm data in order to develop algorithms that will allow coarse resolution rainfall forecasted by weather models to be optimally used in high resolution hydrology models with the goal of improving stream flow predictions and early detection algorithms that can be used to warn communities about potential flash floods. This research was performed by analyzing a series of independent radar images derived from Weather Surveillance Radar-1988 Doppler (WSR-88D) data obtained from Dr. James A. Smith at Princeton University using a …

Verification Of Costless Merge Pairing Heaps, Joshua Vander Hook

Journal of Undergraduate Research at Minnesota State University, Mankato

Most algorithms’ performance is limited by the data structures they use. Internal algorithms then decide the performance of the data structure. This cycle continues until fundamental results, verified by analysis and experiment, prevent further improvement. In this paper I examine one specific example of this. The focus of this work is primarily on a new variant of the pairing heap. I will review the new implementation, compare its theoretical performance, and discuss my original contribution: the first preliminary data on its experimental performance. It is instructive to provide some background information, followed by a formal definition of heaps in 1.1. …

Improved Microrobotic Control Through Image Processing And Automated Hardware Interfacing, Archit R. Aggarwal, Wuming Jing, David J. Cappelleri

The Summer Undergraduate Research Fellowship (SURF) Symposium

Untethered submilliliter-sized robots (microrobots) are showing potential use in different industrial, manufacturing and medical applications. A particular type of these microrobots, magnetic robots, have shown improved performance in power and control capabilities compared to the other thermal and electrostatic based robots. However, the magnetic robot designs have not been assessed in a robust manner to understand the degree of control in different environments and their application feasibility. This research project seeks to develop a custom control software interface to provide a holistic tool for researchers to evaluate the microrobotic performance through advance control features. The software deliverable involved two main …

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

School of Computing: 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 …

Approaches For Generating 2d Shapes, Pratik Shankar Hada

UNLV Theses, Dissertations, Professional Papers, and Capstones

Constructing a two dimensional shape from given a set of point sites is a well known problem in computation geometry. We present a critical review of the existing algorithms for constructing polygonal shapes. We present a new approach calledinward dentingfor constructing simple polygons. We then extend the proposed approach for modeling polygons with holes. This is the

first known algorithm for modeling holes in the interior of 2d shapes. We also present experimental investigations of the quality of the solutions generated by the proposed algorithms.

For this we implemented the proposed algorithms in Java programming language. The prototype program can …

A Taxonomy Of Polynomially Solvable Shop Problems With Limited Number Of Machines Or Jobs, Megha Sairam Darapuneni

UNLV Theses, Dissertations, Professional Papers, and Capstones

Among shop scheduling problems, job shop and mixed shop are one of the most general models encompassing open shop and flow shop. Many job shop problems are NP hard, but there are numerous cases, which possess polynomial solutions when the number of jobs or the number of machines (or both) is limited.

This thesis gives an overview of methods and algorithms for solving - in polynomial time - such special shop problems, including open, flow, job shop and mixed shop. The tools used include Monge interchange, dynamic programming, greedy techniques and sweep line algorithms and the primary focus of this …

A Characterization Of Open Shop Scheduling Problems Using The Hall Theorem And Network Flow, Arunasri Chitti

UNLV Theses, Dissertations, Professional Papers, and Capstones

Open shop scheduling problems are combinatorial problems where jobs with certain processing requirements on a number of different machines must be arranged in such a way that objectives related to completion time are optimized. Such problems have applications over a wide spectrum including such as communications, routing and manufacturing.

Many open shop problems are NP-hard but there are a number of special cases which possess polynomial solutions in the case of few machines or few jobs or when preemption of jobs is permitted. Many such solutions are based in the theory of matching or Hall's theorem, or more generally network …

Multi-Valued Argumentation Frameworks, Pierpaolo Dondio

Conference papers

In this paper we explore how the seminal Dung’s abstract argumentation framework can be extended to handle arguments containing gradual concepts. We allow arguments to have a degree of truth associated with them and we investigate the degree of truth to which each argument can be considered accepted, rejected and undecided by an abstract argumentation semantics. We propose a truth-compositional recursive computation, and we discuss examples using the major multi-valued logics such as Godel’s, Zadeh’s and Łukasiewicz's logic. The findings are a contribution in the field of non-monotonic approximate reasoning and they also represent a well-grounded proposal towards the introduction …

Structure Preserving Large Imagery Reconstruction, Ju Shen, Jianjun Yang, Sami Taha Abu Sneineh, Bryson Payne, Markus Hitz

Computer Science Faculty Publications

With the explosive growth of web-based cameras and mobile devices, billions of photographs are uploaded to the internet. We can trivially collect a huge number of photo streams for various goals, such as image clustering, 3D scene reconstruction, and other big data applications. However, such tasks are not easy due to the fact the retrieved photos can have large variations in their view perspectives, resolutions, lighting, noises, and distortions. Furthermore, with the occlusion of unexpected objects like people, vehicles, it is even more challenging to find feature correspondences and reconstruct realistic scenes. In this paper, we propose a structure-based image …

Evaluation Of Ct Images Created Using A New Metal Artifact Reduction Reconstruction Algorithm For Radiation Therapy Treatment Planning, John Niemkiewicz, Andrew G. Palmiotti, Marc S. Miner, Lee E. Stunja, Jenelle Bergene

Department of Radiation Oncology

No abstract provided.

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

School of Computing: 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

School of Computing: 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 …