In recent years, the collection of genomic data has skyrocketed and databases of genomic data are growing at a faster rate than ever before. Although many computational methods have been developed to interpret these data, they tend to struggle to process the ever increasing file sizes that are being produced and fail to take advantage of the advances in multi-core processors by using parallel processing. In some instances, loss of accuracy has been a necessary trade off to allow faster computation of the data. This thesis discusses one such algorithm that has been developed and how changes were made to allow larger input file sizes and reduce the time required to achieve a result without sacrificing accuracy. An information entropy based algorithm was used as a basis to demonstrate these techniques. The algorithm dissects the distinctive patterns underlying genomic data efficiently requiring no a priori knowledge, and thus is applicable in a variety of biological research applications. This research describes how parallel processing and object-oriented programming techniques were used to process larger files in less time and achieve a more accurate result from the algorithm. Through object oriented techniques, the maximum allowable input file size was significantly increased from 200 …

This thesis presents algorithms to utilize the wireless bandwidth efficiently and at the same time meet the quality of service (QoS) requirements of the users. In the proposed algorithms we present an adaptive frame structure based upon the airlink frame loss probability and control the admission of call requests into the system based upon the load on the system and the QoS requirements of the incoming call requests. The performance of the proposed algorithms is studied by developing analytical formulations and simulation experiments. Finally we present an admission control algorithm which uses an adaptive delay computation algorithm to compute the queuing delay for each class of traffic and adapts the service rate and the reliability in the estimates based upon the deviation in the expected and obtained performance. We study the performance of the call admission control algorithm by simulation experiments. Simulation results for the adaptive frame structure algorithm show an improvement in the number of users in the system but there is a drop in the system throughput. In spite of the lower throughput the adaptive frame structure algorithm has fewer QoS delay violations. The adaptive call admission control algorithm adapts the call dropping probability of different classes of …

Wireless sensor networks are composed of sensor nodes, which can monitor an environment and observe events of interest. These networks are applied in various fields including but not limited to environmental, industrial and habitat monitoring. In many applications, the exact location of the sensor nodes is unknown after deployment. Localization is a process used to find sensor node's positional coordinates, which is vital information. The localization is generally assisted by anchor nodes that are also sensor nodes but with known locations. Anchor nodes generally are expensive and need to be optimally placed for effective localization. Passive localization is one of the localization techniques where the sensor nodes silently listen to the global events like thunder sounds, seismic waves, lighting, etc. According to previous studies, the ideal location to place anchor nodes was on the perimeter of the sensor network. This may not be the case in passive localization, since the function of anchor nodes here is different than the anchor nodes used in other localization systems. I do extensive studies on positioning anchor nodes for effective localization. Several simulations are run in dense and sparse networks for proper positioning of anchor nodes. I show that, for effective passive localization, the …

Shadows in indoor scenarios are usually characterized with multiple light sources that produce complex shadow patterns of a single object. Without removing shadow, the foreground object tends to be erroneously segmented. The inconsistent hue and intensity of shadows make automatic removal a challenging task. In this thesis, a dynamic thresholding and transfer learning-based method for removing shadows is proposed. The method suppresses light shadows with a dynamically computed threshold and removes dark shadows using an online learning strategy that is built upon a base classifier trained with manually annotated examples and refined with the automatically identified examples in the new videos. Experimental results demonstrate that despite variation of lighting conditions in videos our proposed method is able to adapt to the videos and remove shadows effectively. The sensitivity of shadow detection changes slightly with different confidence levels used in example selection for classifier retraining and high confidence level usually yields better performance with less retraining iterations.

This dissertation addresses the general problem of recognition of acoustic signals which may be derived from speech, sonar, or acoustic phenomena. The specific problem of recognizing speech is the main focus of this research. The intention is to design a recognition system for a definite number of discrete words. For this purpose specifically, eight isolated words from the T1MIT database are selected. Four medium length words "greasy," "dark," "wash," and "water" are used. In addition, four short words are considered "she," "had," "in," and "all." The recognition system addresses the following issues: filtering or preprocessing, training, and decision-making. The preprocessing phase uses linear predictive coding of order 12. Following the filtering process, a vector quantization method is used to further reduce the input data and generate a finite inductive sequence of symbols representative of each input signal. The sequences generated by the vector quantization process of the same word are factored, and a single ruling or reference template is generated and stored in a codebook. This system introduces a new modeling technique which relies heavily on the basic concept that all finite sequences are finitely inductive. This technique is used in the training stage. In order to accommodate the variabilities …

Globally distributed software teams are widespread throughout industry. But finding reliable methods that can properly assess a team's activities is a real challenge. Methods such as surveys and manual coding of activities are too time consuming and are often unreliable. Recent advances in information retrieval and linguistics, however, suggest that automated and/or semi-automated text classification algorithms could be an effective way of finding differences in the communication patterns among individuals and groups. Communication among group members is frequent and generates a significant amount of data. Thus having a web-based tool that can automatically analyze the communication patterns among global software teams could lead to a better understanding of group performance. The goal of this thesis, therefore, is to compare automatic and semi-automatic measures of communication and evaluate their effectiveness in classifying different types of group activities that occur within a global software development project. In order to achieve this goal, we developed a web-based component that can be used to help clean and classify communication activities. The component was then used to compare different automated text classification techniques on various group activities to determine their effectiveness in correctly classifying data from a global software development team project.

Vehicular ad-hoc networks (VANETs) are used for vehicle-to-vehicle (V2V) and vehicle-to-infrastructure (V2I) communications. The IEEE 802.11p/WAVE (Wireless Access in Vehicular Environment) and with WAVE Short Messaging Protocol (WSMP) has been proposed as the standard protocol for designing applications for VANETs. This communication protocol must be thoroughly tested before reliable and efficient applications can be built using its protocols. In this paper, we perform on-road experiments in a variety of scenarios to evaluate the performance of the standard. We use commercial VANET devices with 802.11p/WAVE compliant chipsets for both BSM (basic safety messages) as well as video streaming applications using WSMP as a communication protocol. We show that while the standard performs well for BSM application in lightly loaded conditions, the performance becomes inferior when traffic and other performance metric increases. Furthermore, we also show that the standard is not suitable for video streaming due to the bursty nature of traffic and the bandwidth throttling, which is a major shortcoming for V2X applications.

The widely used vector model maintains its popularity because of its simplicity, fast speed, and the appeal of using spatial proximity for semantic proximity. However, this model faces a disadvantage that is associated with the vagueness from keywords overlapping. Efforts have been made to improve the vector model. The research on improving document representation has been focused on four areas, namely, statistical co-occurrence of related items, forming term phrases, grouping of related words, and representing the content of documents. In this thesis, we propose the idea-indexing model to improve document representation for the filtering task in IR. The idea-indexing model matches document terms with the ideas they express and indexes the document with these ideas. This indexing scheme represents the document with its semantics instead of sets of independent terms. We show in this thesis that indexing with ideas leads to better performance.

One of the greatest problems facing researchers in the sub field of Artificial Intelligence known as Intelligent Tutoring Systems (ITS) is the selection of a knowledge base designs that will facilitate the modification of the knowledge base. The Class-Entity-Relationship-Attribute (CERA), proposed by R. P. Brazile, holds certain promise as a more generic knowledge base design framework upon which can be built robust and efficient ITS. This study has a twofold purpose. The first is to demonstrate that a CERA knowledge base can be constructed for an ITS on a subset of the domain of Cretaceous paleontology and function as the "expert module" of the ITS. The second is to test the validity of the ideas that students guided through a lesson learn more factual knowledge, while those who explore the knowledge base that underlies the lesson through query at their own pace will be able to formulate their own integrative knowledge from the knowledge gained in their explorations and spend more time on the system. This study concludes that a CERA-based system can be constructed as an effective teaching tool. However, while an ITS - treatment provides for statistically significant gains in achievement test scores, the type of treatment seems …

This thesis compares the file organization techniques that are implemented on two different types of computer systems, the large-scale and the small-scale. File organizations from representative computers in each class are examined in detail: the IBM System/370 (OS/370) and the Harris 1600 Distributed Processing System with the Extended Communications Operating System (ECOS). In order to establish the basic framework for comparison, an introduction to file organizations is presented. Additionally, the functional requirements for file organizations are described by their characteristics and user demands. Concluding remarks compare file organization techniques and discuss likely future developments of file systems.

There are three main results in this dissertation. They are PLS-completeness of discrete Hopfield network convergence with eight different restrictions, (degree 3, bipartite and degree 3, 8-neighbor mesh, dual of the knight's graph, hypercube, butterfly, cube-connected cycles and shuffle-exchange), exponential convergence behavior of discrete Hopfield network, and simulation of Turing machines by discrete Hopfield Network.

Many infectious diseases are spread through interactions between susceptible and infectious individuals. Keeping track of where each exposure to the disease took place, when it took place, and which individuals were involved in the exposure can give public health officials important information that they may use to formulate their interventions. Further, knowing which individuals in the population are at the highest risk of becoming infected with the disease may prove to be a useful tool for public health officials trying to curtail the spread of the disease. Epidemiological models are needed to allow epidemiologists to study the population dynamics of transmission of infectious agents and the potential impact of infectious disease control programs. While many agent-based computational epidemiological models exist in the literature, they focus on the spread of disease rather than exposure risk. These models are designed to simulate very large populations, representing individuals as agents, and using random experiments and probabilities in an attempt to more realistically guide the course of the modeled disease outbreak. The work presented in this thesis focuses on tracking exposure risk to chickenpox in an elementary school setting. This setting is chosen due to the high level of detailed information realistically available to …

Publicly available datasets in health science are often large and observational, in contrast to experimental datasets where a small number of data are collected in controlled experiments. Variables' causal relationships in the observational dataset are yet to be determined. However, there is a significant interest in health science to discover and analyze causal relationships from health data since identified causal relationships will greatly facilitate medical professionals to prevent diseases or to mitigate the negative effects of the disease. Recent advances in Computer Science, particularly in Bayesian networks, has initiated a renewed interest for causality research. Causal relationships can be possibly discovered through learning the network structures from data. However, the number of candidate graphs grows in a more than exponential rate with the increase of variables. Exact learning for obtaining the optimal structure is thus computationally infeasible in practice. As a result, heuristic approaches are imperative to alleviate the difficulty of computations. This research provides effective and efficient learning tools for local causal discoveries and novel methods of learning causal structures with a combination of background knowledge. Specifically in the direction of constraint based structural learning, polynomial-time algorithms for constructing causal structures are designed with first-order conditional independence. Algorithms of …

POD (Point of Dispensing)-based emergency response plans involving mass prophylaxis may seem feasible when considering the choice of dispensing points within a region, overall population density, and estimated traffic demands. However, the plan may fail to serve particular vulnerable sub-populations, resulting in access disparities during emergency response. Federal authorities emphasize on the need to identify sub-populations that cannot avail regular services during an emergency due to their special needs to ensure effective response. Vulnerable individuals require the targeted allocation of appropriate resources to serve their special needs. Devising schemes to address the needs of vulnerable sub-populations is essential for the effectiveness of response plans. This research focuses on data-driven computational methods to quantify and address vulnerabilities in response plans that require the allocation of targeted resources. Data-driven methods to identify and quantify vulnerabilities in response plans are developed as part of this research. Addressing vulnerabilities requires the targeted allocation of appropriate resources to PODs. The problem of resource allocation to PODs during public health emergencies is introduced and the variants of the resource allocation problem such as the spatial allocation, spatio-temporal allocation and optimal resource subset variants are formulated. Generating optimal resource allocation and scheduling solutions can be computationally hard …

Synthetic seismograms are a computer-generated aid in the search for hydrocarbons. Heretofore the solution has been done by z-transforms. This thesis presents a solution based on the method of finite differences. The resulting algorithm is fast and compact. The method is applied to three variations of the problem, all three are reduced to the same approximating equation, which is shown to be optimal, in that grid refinement does not change it. Two types of algorithms are derived from the equation. The number of obvious multiplications, additions and subtractions of each is analyzed. Critical section of each requires one multiplication, two additions and two subtractions. Four sample synthetic seismograms are shown. Implementation of the new algorithm runs twice as fast as previous computer program.

This study models the human process of music cognition on the digital computer. The definition of music cognition is derived from the work in music cognition done by the researchers Carol Krumhansl and Edward Kessler, and by Mari Jones, as well as from the music theories of Heinrich Schenker. The computer implementation functions in three stages. First, it translates a musical "performance" in the form of MIDI (Musical Instrument Digital Interface) messages into LISP structures. Second, the various parameters of the performance are examined separately a la Jones's joint accent structure, quantified according to psychological findings, and adjusted to a common scale. The findings of Krumhansl and Kessler are used to evaluate the consonance of each note with respect to the key of the piece and with respect to the immediately sounding harmony. This process yields a multidimensional set of points, each of which is a cognitive evaluation of a single musical event within the context of the piece of music within which it occurred. This set of points forms a metric space in multi-dimensional Euclidean space. The third phase of the analysis maps the set of points into a topology-preserving data structure for a Schenkerian-like middleground structural analysis. This …

This investigation dealt with locating and measuring x-ray absorption of radiographic images. The methods developed provide a fast, accurate, minicomputer control, for analysis of embedded objects. A PDP/8 computer system was interfaced with a Joyce Loebl 3CS Microdensitometer and a Leeds & Northrup Recorder. Proposed algorithms for bone location and data smoothing work on a twelve-bit minicomputer. Designs of a software control program and operational procedure are presented. The filter made wedge and limb scans monotonic from minima to maxima. It was tested for various convoluted intervals. Ability to resmooth the same data in multiple passes was tested. An interval size of fifteen works well in one pass.

The problem of interest as indicated is to develop a general purpose technique that is a combination of the structural approach, and an extension of the Finite Inductive Sequence (FI) technique. FI technology is pre-algebra, and deals with patterns for which an alphabet can be formulated.

Streaming multimedia content with UDP has become popular over distributed systems such as an Internet. This may encounter many losses due to dropped packets or late arrivals at destination since UDP can only provide best effort delivery. Even UDP doesn't have any self-recovery mechanism from congestion collapse or bursty loss to inform sender of the data to adjust future transmission rate of data like in TCP. So there is a need to incorporate various control schemes like forward error control, interleaving, and congestion control and error concealment into real-time transmission to prevent from effect of losses. Loss can be repaired by retransmission if roundtrip delay is allowed, otherwise error concealment techniques will be used based on the type and amount of loss. This paper implements the interleaving technique with packet spacing of varying interleaver block size for protecting real-time data from loss and its effect during transformation across the Internet. The packets are interleaved and maintain some time gap between two consecutive packets before being transmitted into the Internet. Thus loss of packets can be reduced from congestion and preventing loss of consecutive packets of information when a burst of several packets are lost. Several experiments have been conducted with …

Managing large-scale dynamical systems (e.g., transportation systems, complex information systems, and power networks, etc.) in real-time is very challenging considering their complicated system dynamics, intricate network interactions, large scale, and especially the existence of various uncertainties. To address this issue, intelligent techniques which can quickly design decision-making strategies that are robust to uncertainties are needed. This dissertation aims to conquer these challenges by exploring a data-driven decision-making framework, which leverages big-data techniques and scalable uncertainty evaluation approaches to quickly solve optimal control problems. In particular, following techniques have been developed along this direction: 1) system modeling approaches to simplify the system analysis and design procedures for multiple applications; 2) effective simulation and analytical based approaches to efficiently evaluate system performance and design control strategies under uncertainty; and 3) big-data techniques that allow some computations of control strategies to be completed offline. These techniques and tools for analysis, design and control contribute to a wide range of applications including air traffic flow management, complex information systems, and airborne networks.

This problem is intended to be an introduction to the design of a software system which translates PDP-8 assembly language source into it's machine-readable object code. This assembler runs on the IBM 360/50. It is assumed that the reader is familiar with the basic PDP-8 assembly language. For the description and use of this assembler the reader is referred to the PAL-III SYMBOLIC ASSEMBLER PROGRAMMING MANUAL from DEC (order number DIGITAL 8-3-5, Digital Equipment Corporation: Maynard, Massachusetts, 1965.). The Second problem of the study concerns the design of a simulator for the PDP-8 computer.

Operatorless Prolog text is LL(1) in nature and any standard LL parser generator tool can be used to parse it. However, the Prolog text that conforms to the ISO Prolog standard allows the definition of dynamic operators. Since Prolog operators can be defined at run-time, operator symbols are not present in the grammar rules of the language. Unless the parser generator allows for some flexibility in the specification of the grammar rules, it is very difficult to generate a parser for such text. In this thesis we discuss the existing parsing methods and their modified versions to parse languages with dynamic operator capabilities. Implementation details of a parser using Javacc as a parser generator tool to parse standard Prolog text is provided. The output of the parser is an “Abstract Syntax Tree” that reflects the correct precedence and associativity rules among the various operators (static and dynamic) of the language. Empirical results are provided that show that a Prolog parser that is generated by the parser generator like Javacc is comparable in efficiency to a hand-coded parser.

In this thesis, the gate matrix layout problem in VLSI design is considered where the goal is to minimize the number of tracks required to layout a given circuit and a taxonomy of approaches to its solution is presented. An efficient hybrid heuristic is also proposed for this combinatorial optimization problem, which is based on the combination of probabilistic hill-climbing technique and greedy method. This heuristic is tested experimentally with respect to four existing algorithms. As test cases, five benchmark problems from the literature as well as randomly generated problem instances are considered. The experimental results show that the proposed hybrid algorithm, on the average, performs better than other heuristics in terms of the required computation time and/or the quality of solution. Due to the computation-intensive nature of the problem, an exact solution within reasonable time limits is impossible. So, it is difficult to judge the effectiveness of any heuristic in terms of the quality of solution (number of tracks required). A probabilistic model of the gate matrix layout problem that computes the expected number of tracks from the given input parameters, is useful to this respect. Such a probabilistic model is proposed in this thesis, and its performance is …

Extracting information from a stack of data is a tedious task and the scenario is no different in proteomics. Volumes of research papers are published about study of various proteins in several species, their interactions with other proteins and identification of protein(s) as possible biomarker in causing diseases. It is a challenging task for biologists to keep track of these developments manually by reading through the literatures. Several tools have been developed by computer linguists to assist identification, extraction and hypotheses generation of proteins and protein-protein interactions from biomedical publications and protein databases. However, they are confronted with the challenges of term variation, term ambiguity, access only to abstracts and inconsistencies in time-consuming manual curation of protein and protein-protein interaction repositories. This work attempts to attenuate the challenges by extracting protein-protein interactions in humans and elicit possible interactions using associative rule mining on full text, abstracts and captions from figures available from publicly available biomedical literature databases. Two such databases are used in our study: Directory of Open Access Journals (DOAJ) and PubMed Central (PMC). A corpus is built using articles based on search terms. A dataset of more than 38,000 protein-protein interactions from the Human Protein Reference Database (HPRD) …