Digital Commons Network^™

Predicting Flavonoid Ugt Regioselectivity With Graphical Residue Models And Machine Learning., Arthur Rhydon Jackson

Electronic Theses and Dissertations

Machine learning is applied to a challenging and biologically significant protein classification problem: the prediction of flavonoid UGT acceptor regioselectivity from primary protein sequence. Novel indices characterizing graphical models of protein residues are introduced. The indices are compared with existing amino acid indices and found to cluster residues appropriately. A variety of models employing the indices are then investigated by examining their performance when analyzed using nearest neighbor, support vector machine, and Bayesian neural network classifiers. Improvements over nearest neighbor classifications relying on standard alignment similarity scores are reported.

Noninvasive Estimation Of Pulmonary Artery Pressure Using Heart Sound Analysis, Aaron W. Dennis

Theses and Dissertations

Right-heart catheterization is the most accurate method for estimating pulmonary artery pressure (PAP). Because it is an invasive procedure it is expensive, exposes patients to the risk of infection, and is not suited for long-term monitoring situations. Medical researchers have shown that PAP influences the characteristics of heart sounds. This suggests that heart sound analysis is a potential noninvasive solution to the PAP estimation problem. This thesis describes the development of a prototype system, called PAPEr, which estimates PAP noninvasively using heart sound analysis. PAPEr uses patient data with machine learning algorithms to build models of how PAP affects heart …

Creating Insanity In Learning Systems: Addressing Ambiguity Effects Of Predicting Non-Linear Continuous Valued Functions With Reconstructabilty Analysis From Large Categorically Valued Input Data Sets, William D. Eisenhauer

Systems Science Friday Noon Seminar Series

Being told to give two different, and potentially counter, responses to the same stimulus can set up a double bind in humans, leading to a type of insanity. So what how do you deal with it when it comes up quite frequently in modeling through simplification and removal of predictive variables?

In his current dissertation research Ike Eisenhauer is using reconstructability analysis to implement K-System, U-System, and B-System approaches to predict a continuously valued function through discrete categorically valued input variables [e.g. textual data]. One of the key issues is how to address the inability of K-Systems and U-Systems to …

A Neural Network Approach To Border Gateway Protocol Peer Failure Detection And Prediction, Cory B. White

Master's Theses

The size and speed of computer networks continue to expand at a rapid pace, as do the corresponding errors, failures, and faults inherent within such extensive networks. This thesis introduces a novel approach to interface Border Gateway Protocol (BGP) computer networks with neural networks to learn the precursor connectivity patterns that emerge prior to a node failure. Details of the design and construction of a framework that utilizes neural networks to learn and monitor BGP connection states as a means of detecting and predicting BGP peer node failure are presented. Moreover, this framework is used to monitor a BGP network …

Learning Condition-Specific Networks, Sushmita Roy

Computer Science ETDs

Condition-specific cellular networks are networks of genes and proteins that describe functional interactions among genes occurring under different environmental conditions. These networks provide a systems-level view of how the parts-list (genes and proteins) interact within the cell as it functions under changing environmental conditions and can provide insight into mechanisms of stress response, cellular differentiation and disease susceptibility. The principle challenge, however, is that cellular networks remain unknown for most conditions and must be inferred from activity levels of genes (mRNA levels) under different conditions. This dissertation aims to develop computational approaches for inferring, analyzing and validating cellular networks of …

Automatic Red Tide Detection Using Modis Satellite Images, Wijian Cheng

USF Tampa Graduate Theses and Dissertations

Red tides pose a significant economic and environmental threat in the Gulf of Mexico. Detecting red tide is important for understanding this phenomenon. In this thesis, machine learning approaches based on Random Forests, Support Vector Machines and K-Nearest Neighbors have been evaluated for red tide detection from MODIS satellite images. Detection results using machine learning algorithms were compared to ship collected ground truth red tide data. This work has three major contributions. First, machine learning approaches outperformed two of the latest thresholding red tide detection algorithms based on bio-optical characterization by more than 10% in terms of F measure and …

A Unified Multi-Functional Dynamic Spectrum Access Framework: Tutorial, Theory And Multi-Ghz Wideband Testbed, Robert Qiu, Nan Guo, Husheng Li, Zhiqiang Wu, Vasu Chakravarthy, Yu Song, Zhen Hu, Peng Zhang, Zhe Chen

Electrical Engineering Faculty Publications

Dynamic spectrum access is a must-have ingredient for future sensors that are ideally cognitive. The goal of this paper is a tutorial treatment of wideband cognitive radio and radar—a convergence of (1) algorithms survey, (2) hardware platforms survey, (3) challenges for multi-function (radar/communications) multi-GHz front end, (4) compressed sensing for multi-GHz waveforms—revolutionary A/D, (5) machine learning for cognitive radio/radar, (6) quickest detection, and (7) overlay/underlay cognitive radio waveforms. One focus of this paper is to address the multi-GHz front end, which is the challenge for the next-generation cognitive sensors. The unifying theme of this paper is to spell out the …

Intentional Learning Agent Architecture, Budhitama Subagdja, Liz Sonenberg, Iyad Rahwan

Research Collection School Of Computing and Information Systems

Dealing with changing situations is a major issue in building agent systems. When the time is limited, knowledge is unreliable, and resources are scarce, the issue becomes more challenging. The BDI (Belief-Desire-Intention) agent architecture provides a model for building agents that addresses that issue. The model can be used to build intentional agents that are able to reason based on explicit mental attitudes, while behaving reactively in changing circumstances. However, despite the reactive and deliberative features, a classical BDI agent is not capable of learning. Plans as recipes that guide the activities of the agent are assumed to be static. …

Predictive Decoding Of Neural Data, Yaroslav O. Halchenko

Dissertations

In the last five decades the number of techniques available for non-invasive functional imaging has increased dramatically. Researchers today can choose from a variety of imaging modalities that include EEG, MEG, PET, SPECT, MRI, and fMRI.

This doctoral dissertation offers a methodology for the reliable analysis of neural data at different levels of investigation. By using statistical learning algorithms the proposed approach allows single-trial analysis of various neural data by decoding them into variables of interest. Unbiased testing of the decoder on new samples of the data provides a generalization assessment of decoding performance reliability. Through consecutive analysis of the …

A Strategy Oriented, Machine Learning Approach To Automatic Quality Assessment Of Wikipedia Articles, Gabriel De La Calzada

Master's Theses

This work discusses an approach to modeling and measuring information quality of Wikipedia articles. The approach is based on the idea that the quality of Wikipedia articles with distinctly different profiles needs to be measured using different information quality models. To implement this approach, a software framework written in the Java language was developed to collect and analyze information of Wikipedia articles.

We report on our initial study, which involved two categories of Wikipedia articles: ”stabilized” (those, whose content has not undergone major changes for a significant period of time) and ”controversial” (articles that have undergone vandalism, revert wars, or …

Bootstrapping Events And Relations From Text, Ting Liu

Legacy Theses & Dissertations (2009 - 2024)

Information Extraction (IE) is a technique for automatically extracting structured data from text documents. One of the key analytical tasks is extraction of important and relevant information from textual sources. While information is plentiful and readily available, from the Internet, news services, media, etc., extracting the critical nuggets that matter to business or to national security is a cognitively demanding and time consuming task. Intelligence and business analysts spend many hours poring over endless streams of text documents pulling out reference to entities of interest (people, locations, organizations) as well as their relationships as reported in text. Such extracted "information …

Machine Learned Melody Matching Using Strictly Relative Musical Abstractions, Michael Joseph Kolta

Legacy Theses & Dissertations (2009 - 2024)

We implement and evaluate a machine learning approach to improve systems for searching a database of music via melodic sample. We explore symbolic and aural input queries and test our prototypes with extensive user surveys. Our main contribution is to combine the following four elements. First is to create a unique musical abstraction that accounts for both pitch and rhythm in a relative manner. Second, our system allows for approximate matching of imperfect queries via the utilization of the Smith-Waterman algorithm that was originally designed for approximate matching of molecular subsequences, such as DNA samples. Third is to design our …

Quantum Inductive Learning And Quantum Logic Synthesis, Martin Lukac

Dissertations and Theses

Since Quantum Computer is almost realizable on large scale and Quantum Technology is one of the main solutions to the Moore Limit, Quantum Logic Synthesis (QLS) has become a required theory and tool for designing Quantum Logic Circuits. However, despite its growth, there is no any unified aproach to QLS as Quantum Computing is still being discovered and novel applications are being identified.

The intent of this study is to experimentally explore principles of Quantum Logic Synthesis and its applications to Inductive Machine Learning. Based on algorithmic approach, I first design a Genetic Algorithm for Quantum Logic Synthesis that is …

Using Student Mood And Task Performance To Train Classifier Algorithms To Select Effective Coaching Strategies Within Intelligent Tutoring Systems (Its), Robert Sottilare

Electronic Theses and Dissertations

The ultimate goal of this research was to improve student performance by adjusting an Intelligent Tutoring System's (ITS) coaching strategy based on the student's mood. As a step toward this goal, this study evaluated the relationships between each student's mood variables (pleasure, arousal, dominance and mood intensity), the coaching strategy selected by the ITS and the student's performance. Outcomes included methods to increase the perception of the intelligent tutor to allow it to adapt coaching strategies (methods of instruction) to the student's affective needs to mitigate barriers to performance (e.g. negative affect) during the one-to-one tutoring process. The study evaluated …

Concept Learning By Example Decomposition, Sameer Joshi

Electronic Theses and Dissertations

For efficient understanding and prediction in natural systems, even in artificially closed ones, we usually need to consider a number of factors that may combine in simple or complex ways. Additionally, many modern scientific disciplines face increasingly large datasets from which to extract knowledge (for example, genomics). Thus to learn all but the most trivial regularities in the natural world, we rely on different ways of simplifying the learning problem. One simplifying technique that is highly pervasive in nature is to break down a large learning problem into smaller ones; to learn the smaller, more manageable problems; and then to …

Analyses Of Crash Occurence And Injury Severities On Multi Lane Highways Using Machine Learning Algorithms, Abhishek Das

Electronic Theses and Dissertations

Reduction of crash occurrence on the various roadway locations (mid-block segments; signalized intersections; un-signalized intersections) and the mitigation of injury severity in the event of a crash are the major concerns of transportation safety engineers. Multi lane arterial roadways (excluding freeways and expressways) account for forty-three percent of fatal crashes in the state of Florida. Significant contributing causes fall under the broad categories of aggressive driver behavior; adverse weather and environmental conditions; and roadway geometric and traffic factors. The objective of this research was the implementation of innovative, state-of-the-art analytical methods to identify the contributing factors for crashes and injury …

Development Of A Workflow For The Comparison Of Classification Techniques, Zanifa Omary

Masters

As the interest in machine learning and data mining springs up, the problem of how to assess learning algorithms and compare classifiers become more pressing. This has been associated with the lack of comprehensive and complete workflow depending on the project scale to provide guidance to its users. This means the success or failure of the project can be highly dependent on the person or team carrying it. The standard practice adopted by many researchers and experimenters has been to follow steps or phases from existing workflows such as CRISP-DM, KDD and SASSEMMA. However, as machine learning and data mining …

Development Of A Workflow For The Comparison Of Classification Techniques, Zanifa Omary

Dissertations

As the interest in machine learning and data mining springs up, the problem of how to assess learning algorithms and compare classifiers become more pressing. This has been associated with the lack of comprehensive and complete workflow depending on the project scale to provide guidance to its users. This means the success or failure of the project can be highly dependent on the person or team carrying it.

The standard practice adopted by many researchers and experimenters has been to follow steps or phases from existing workflows such as CRISP-DM, KDD and SASSEMMA. However, as machine learning and data mining …

Classifier System Learning Of Good Database Schema, Mitsuru Tanaka

LSU New Orleans Theses and Dissertations

This thesis presents an implementation of a learning classifier system which learns good database schema. The system is implemented in Java using the NetBeans development environment, which provides a good control for the GUI components. The system contains four components: a user interface, a rule and message system, an apportionment of credit system, and genetic algorithms. The input of the system is a set of simple database schemas and the objective for the classifier system is to keep the good database schemas which are represented by classifiers. The learning classifier system is given some basic knowledge about database concepts or …

Clustering Via Supervised Support Vector Machines, Sepehr Merat

LSU New Orleans Theses and Dissertations

An SVM-based clustering algorithm is introduced that clusters data with no a priori knowledge of input classes. The algorithm initializes by first running a binary SVM classifier against a data set with each vector in the set randomly labeled. Once this initialization step is complete, the SVM confidence parameters for classification on each of the training instances can be accessed. The lowest confidence data (e.g., the worst of the mislabeled data) then has its labels switched to the other class label. The SVM is then re-run on the data set (with partly re-labeled data). The repetition of the above process …

Classification Algorithms On The Cell Processor, Mateusz Wyganowski

Theses

The rapid advancement in the capacity and reliability of data storage technology has allowed for the retention of virtually limitless quantity and detail of digital information. Massive information databases are becoming more and more widespread among governmental, educational, scientific, and commercial organizations. By segregating this data into carefully defined input (e.g.: images) and output (e.g.: classification labels) sets, a classification algorithm can be used develop an internal expert model of the data by employing a specialized training algorithm. A properly trained classifier is capable of predicting the output for future input data from the same input domain that it was …

Scaling Ant Colony Optimization With Hierarchical Reinforcement Learning Partitioning, Erik J. Dries, Gilbert L. Peterson

Faculty Publications

This paper merges hierarchical reinforcement learning (HRL) with ant colony optimization (ACO) to produce a HRL ACO algorithm capable of generating solutions for large domains. This paper describes two specific implementations of the new algorithm: the first a modification to Dietterich’s MAXQ-Q HRL algorithm, the second a hierarchical ant colony system algorithm. These implementations generate faster results, with little to no significant change in the quality of solutions for the tested problem domains. The application of ACO to the MAXQ-Q algorithm replaces the reinforcement learning, Q-learning, with the modified ant colony optimization method, Ant-Q. This algorithm, MAXQ-AntQ, converges to solutions …

Detection Of Marine Vehicles In Images And Video Of Open Sea, Sergiy Fefilatyev

USF Tampa Graduate Theses and Dissertations

This work presents a new technique for automatic detection of marine vehicles in images and video of open sea. Users of such system include border guards, military, port safety, flow management, and sanctuary protection personnel. The source of images and video is a digital camera or a camcorder which is placed on a buoy or stationary mounted in a harbor facility. The system is intended to work autonomously, taking images of the surrounding ocean surface and analyzing them for the presence of marine vehicles. The goal of the system is to detect an approximate window around the ship. The proposed …

Active Learning For E-Rulemaking: Public Comment Categorization, Stephen Purpura, Claire Cardie, Jesse Simons

Cornell e-Rulemaking Initiative Publications

We address the e-rulemaking problem of reducing the manual labor required to analyze public comment sets. In current and previous work, for example, text categorization techniques have been used to speed up the comment analysis phase of e-rulemaking - by classifying sentences automatically, according to the rule-specific issues [2] or general topics that they address [7, 8]. Manually annotated data, however, is still required to train the supervised inductive learning algorithms that perform the categorization. This paper, therefore, investigates the application of active learning methods for public comment categorization: we develop two new, general-purpose, active learning techniques to selectively sample …

Matching Records In Multiple Databases Using A Hybridization Of Several Technologies., Xiaoyi Wang 1962-

Electronic Theses and Dissertations

A major problem with integrating information from multiple databases is that the same data objects can exist in inconsistent data formats across databases and a variety of attribute variations, making it difficult to identify matching objects using exact string matching. In this research, a variety of models and methods have been developed and tested to alleviate this problem. A major motivation for this research is that the lack of efficient tools for patient record matching still exists for health care providers. This research is focused on the approximate matching of patient records with third party payer databases. This is a …

Evolution And Field Application Of A Plankton Imaging System, Andrew Walker Remsen

USF Tampa Graduate Theses and Dissertations

Understanding the processes controlling the distribution and abundance of zooplankton has been a primary concern of oceanographers and has driven the development of numerous technologies to more accurately quantify these parameters. This study investigates the potential of a new plankton imaging sensor, the shadowed image particle profiling and evaluation recorder (SIPPER), that I helped develop at the University of South Florida, to address that concern. In the first chapter, results from the SIPPER are compared against concurrently sampling plankton nets and the optical plankton counter (OPC), the most widely used optical zooplankton sampling sensor in the field. It was found …

Context-Aware Statistical Debugging: From Bug Predictors To Faulty Control Flow Paths, Lingxiao Jiang, Zhendong Su

Research Collection School Of Computing and Information Systems

Effective bug localization is important for realizing automated debugging. One attractive approach is to apply statistical techniques on a collection of evaluation profiles of program properties to help localize bugs. Previous research has proposed various specialized techniques to isolate certain program predicates as bug predictors. However, because many bugs may not be directly associated with these predicates, these techniques are often ineffective in localizing bugs. Relevant control flow paths that may contain bug locations are more informative than stand-alone predicates for discovering and understanding bugs. In this paper, we propose an approach to automatically generate such faulty control flow paths …

Parallelization Of Ant Colony Optimization Via Area Of Expertise Learning, Adrian A. De Freitas

Theses and Dissertations

Ant colony optimization algorithms have long been touted as providing an effective and efficient means of generating high quality solutions to NP-hard optimization problems. Unfortunately, while the structure of the algorithm is easy to parallelize, the nature and amount of communication required for parallel execution has meant that parallel implementations developed suffer from decreased solution quality, slower runtime performance, or both. This thesis explores a new strategy for ant colony parallelization that involves Area of Expertise (AOE) learning. The AOE concept is based on the idea that individual agents tend to gain knowledge of different areas of the search space …

Solar Activity Detection And Prediction Using Image Processing And Machine Learning Techniques, Gang Fu

Dissertations

The objective of the research in this dissertation is to develop the methods for automatic detection and prediction of solar activities, including prominence eruptions, emerging flux regions and solar flares. Image processing and machine learning techniques are applied in this study. These methods can be used for automatic observation of solar activities and prediction of space weather that may have great influence on the near earth environment.

The research presented in this dissertation covers the following topics: i) automatic detection of prominence eruptions (PBs), ii) automatic detection of emerging flux regions (EFRs), and iii) automatic prediction of solar flares.

In …

Active Learning For Part-Of-Speech Tagging: Accelerating Corpus Annotation, George Busby, Marc Carmen, James Carroll, Robbie Haertel, Deryle W. Lonsdale, Peter Mcclanahan, Eric K. Ringger, Kevin Seppi

Faculty Publications

In the construction of a part-of-speech annotated corpus, we are constrained by a fixed budget. A fully annotated corpus is required, but we can afford to label only a subset. We train a Maximum Entropy Markov Model tagger from a labeled subset and automatically tag the remainder. This paper addresses the question of where to focus our manual tagging efforts in order to deliver an annotation of highest quality. In this context, we find that active learning is always helpful. We focus on Query by Uncertainty (QBU) and Query by Committee (QBC) and report on experiments with several baselines and …