Theory and Algorithms Commons^™

Spiking Neural Networks: Neuron Models, Plasticity, And Graph Applications, Shaun Donachy

Theses and Dissertations

Networks of spiking neurons can be used not only for brain modeling but also to solve graph problems. With the use of a computationally efficient Izhikevich neuron model combined with plasticity rules, the networks possess self-organizing characteristics. Two different time-based synaptic plasticity rules are used to adjust weights among nodes in a graph resulting in solutions to graph prob- lems such as finding the shortest path and clustering.

Metalogic Notes, Saverio Perugini

Computer Science Working Papers

A collection of notes, formulas, theorems, postulates and terminology in symbolic logic, syntactic notions, semantic notions, linkages between syntax and semantics, soundness and completeness, quantified logic, first-order theories, Goedel's First Incompleteness Theorem and more.

Statistics Notes, Saverio Perugini

Computer Science Working Papers

A collection of terms, definitions, formulas and explanations about statistics.

Feature Selection And Classification Methods For Decision Making: A Comparative Analysis, Osiris Villacampa

CCAC Theses and Dissertations

The use of data mining methods in corporate decision making has been increasing in the past decades. Its popularity can be attributed to better utilizing data mining algorithms, increased performance in computers, and results which can be measured and applied for decision making. The effective use of data mining methods to analyze various types of data has shown great advantages in various application domains. While some data sets need little preparation to be mined, whereas others, in particular high-dimensional data sets, need to be preprocessed in order to be mined due to the complexity and inefficiency in mining high dimensional …

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 …

Operator Calculus Algorithms For Multi-Constrained Paths, Jamila Ben Slimane, Rene' Schott, Ye Qiong Song, G. Stacey Staples, Evangelia Tsiontsiou

SIUE Faculty Research, Scholarship, and Creative Activity

Classical approaches to multi-constrained routing problems generally require construction of trees and the use of heuristics to prevent combinatorial explosion. Introduced here is the notion of constrained path algebras and their application to multi-constrained path problems. The inherent combinatorial properties of these algebras make them useful for routing problems by implicitly pruning the underlying tree structures. Operator calculus (OC) methods are generalized to multiple non-additive constraints in order to develop algorithms for the multi constrained path problem and multi constrained optimization problem. Theoretical underpinnings are developed first, then algorithms are presented. These algorithms demonstrate the tremendous simplicity, flexibility and speed …

Singular Value Computation And Subspace Clustering, Qiao Liang

Theses and Dissertations--Mathematics

In this dissertation we discuss two problems. In the first part, we consider the problem of computing a few extreme eigenvalues of a symmetric definite generalized eigenvalue problem or a few extreme singular values of a large and sparse matrix. The standard method of choice of computing a few extreme eigenvalues of a large symmetric matrix is the Lanczos or the implicitly restarted Lanczos method. These methods usually employ a shift-and-invert transformation to accelerate the speed of convergence, which is not practical for truly large problems. With this in mind, Golub and Ye proposes an inverse-free preconditioned Krylov subspace method, …

The Module Isomorphism Problem Reconsidered, Peter A. Brooksbank

Faculty Journal Articles

Algorithms to decide isomorphism of modules have been honed continually over the last 30 years, and their range of applicability has been extended to include modules over a wide range of rings. Highly efficient computer implementations of these algorithms form the bedrock of systems such as GAP and MAGMA, at least in regard to computations with groups and algebras. By contrast, the fundamental problem of testing for isomorphism between other types of algebraic structures -- such as groups, and almost any type of algebra -- seems today as intractable as ever. What explains the vastly different complexity status of the …

Intersection Of Art And Science, Petronio Bendito, Tim Korb

Lawson Building Exhibitions on the Intersection of Art and Science

The Intersection of Art and Science exhibition is an interdisciplinary educational project that examines a wide range of expressive approaches explored by international artists working at the intersection of art, mathematics, computer science, and technology. It is a joint collaboration between the Department of Computer Science and the Patti and Rusty Rueff School of Visual and Performing Arts at Purdue University. Featured artists: Sergio Albiac, Anne Burns, Conan Chadbourne, Hans Dehlinger, Brian Evans, Richard Hassell, Patrick Bingham-Hall, John Arden Hiigli, So Yoon Lym, Gabriel Meyer, and Robert M. Spann. The exhibition was curated by Dr. Petronio Bendito and Dr. Tim …

Parameters Estimation Of Material Constitutive Models Using Optimization Algorithms, Kiswendsida Jules Kere

Williams Honors College, Honors Research Projects

Optimization Algorithms are very useful for solving engineering problems. Indeed, optimization algorithms can be used to optimize engineering designs in terms of safety and economy. Understanding the proprieties of materials in engineering designs is very important in order to make designs safe. Materials are not really perfectly homogeneous and there are heterogeneous distributions in most materials. In this paper, Self-OPTIM which is an inverse constitutive parameter identification framework will be used to identify parameters of a linear elastic material constitutive model. Data for Self-OPTIM will be obtained using ABAQUS simulation of a dog-bone uniaxial test. Optimization Algorithms will be used …

Exploring Algorithmic Musical Key Recognition, Nathan J. Levine

CMC Senior Theses

The following thesis outlines the goal and process of algorithmic musical key detection as well as the underlying music theory. This includes a discussion of signal-processing techniques intended to most accurately detect musical pitch, as well as a detailed description of the Krumhansl-Shmuckler (KS) key-finding algorithm. It also describes the Java based implementation and testing process of a musical key-finding program based on the KS algorithm. This thesis provides an analysis of the results and a comparison with the original algorithm, ending with a discussion of the recommended direction of further development.

What Is Answer Set Programming To Propositional Satisfiability, Yuliya Lierler

Computer Science Faculty Publications

Propositional satisfiability (or satisfiability) and answer set programming are two closely related subareas of Artificial Intelligence that are used to model and solve difficult combinatorial search problems. Satisfiability solvers and answer set solvers are the software systems that find satisfying interpretations and answer sets for given propositional formulas and logic programs, respectively. These systems are closely related in their common design patterns. In satisfiability, a propositional formula is used to encode problem specifications in a way that its satisfying interpretations correspond to the solutions of the problem. To find solutions to a problem it is then sufficient to use a …

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) …

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 …

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 …

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 …