Computer Engineering Commons^™

Modelling And Visualizing Selected Molecular Communication Processes In Biological Organisms: A Multi-Layer Perspective, Aditya Immaneni

School of Computing: Dissertations, Theses, and Student Research

The future pervasive communication and computing devices are envisioned to be tightly integrated with biological systems, i.e., the Internet of Bio-Nano Things. In particular, the study and exploitation of existing processes for the biochemical information exchange and elaboration in biological systems are currently at the forefront of this research direction. Molecular Communication (MC), which studies biochemical information systems with theory and tools from computer communication engineering, has been recently proposed to model and characterize the aforementioned processes. Combined with the rapidly growing field of bio-informatics, which creates a rich profusion of biological data and tools to mine the underlying information, …

Scheduling In Mapreduce Clusters, Chen He

School of Computing: Dissertations, Theses, and Student Research

MapReduce is a framework proposed by Google for processing huge amounts of data in a distributed environment. The simplicity of the programming model and the fault-tolerance feature of the framework make it very popular in Big Data processing.

As MapReduce clusters get popular, their scheduling becomes increasingly important. On one hand, many MapReduce applications have high performance requirements, for example, on response time and/or throughput. On the other hand, with the increasing size of MapReduce clusters, the energy-efficient scheduling of MapReduce clusters becomes inevitable. These scheduling challenges, however, have not been systematically studied.

The objective of this dissertation is to …

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

School of Computing: 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 …

An Unmanned Aerial System For Prescribed Fires, Evan M. Beachly

School of Computing: Dissertations, Theses, and Student Research

Prescribed fires can lessen wildfire severity and control invasive species, but some terrains may be difficult, dangerous, or costly to burn with existing tools. This thesis presents the design of an unmanned aerial system that can ignite prescribed fires from the air, with less cost and risk than with aerial ignition from a manned aircraft. The prototype was evaluated in-lab and successfully used to ignite interior areas of two prescribed fires. Additionally, we introduce an approach that integrates a lightweight fire simulation to autonomously plan safe flight trajectories and suggest effective fire lines. Both components are unique in that they …

Analytical Modeling Of A Communication Channel Based On Subthreshold Stimulation Of Neurobiological Networks, Alireza Khodaei

School of Computing: Dissertations, Theses, and Student Research

The emergence of wearable and implantable machines manufactured artificially or synthesized biologically opens up a new horizon for patient-centered health services such as medical treatment, health monitoring, and rehabilitation with minimized costs and maximized popularity when provided remotely via the Internet. In particular, a swarm of machines at the scale of a single cell down to the nanoscale can be deployed in the body by the non-invasive or minimally invasive operation (e.g., swallowing and injection respectively) to perform various tasks. However, an individual machine is only able to perform basic tasks so it needs to exchange data with the others …

Rate Based Impact Analysis, Nishant Sharma

School of Computing: Dissertations, Theses, and Student Research

Impact Analysis (IA) identifies control and data dependencies to determine the system components that could be affected by a change. Changes to robotic systems as they are updated often alter the flow of control and sensor data. Changes to the rates at which data is published from sensors, controllers, and other parts of the system are particularly subtle and difficult to detect. These rate changes, even if minor (e.g. lowering the frame rate of a camera), can propagate throughout the system and have broad impacts. However, for robotic systems, these changes in flow rate cannot be precisely tracked by just …

Feature Extraction And Parallel Visualization For Large-Scale Scientific Data, Lina Yu

School of Computing: Dissertations, Theses, and Student Research

Advanced computing and sensing technologies enable scientists to study natural and physical phenomena with unprecedented precision, resulting in an explosive growth of data. The unprecedented amounts of data generated from large scientific simulations impose a grand challenge in data analytics and visualization due to the fact that data are too massive for transferring, storing, and processing.

This dissertation makes the first contribution to the design of novel transfer functions and application-aware data replacement policy to facilitate feature classification on highly parallel distributed systems. We design novel transfer functions that advance the classification of continuously changed volume data by combining the …

Deep Learning And Transfer Learning In The Classification Of Eeg Signals, Jacob M. Williams

School of Computing: Dissertations, Theses, and Student Research

Deep learning is seldom used in the classification of electroencephalography (EEG) signals, despite achieving state of the art classification accuracies in other spatial and time series data. Instead, most research has continued to use manual feature extraction followed by a traditional classifier, such as SVMs or logistic regression. This is largely due to the low number of samples per experiment, high-dimensional nature of the data, and the difficulty in finding appropriate deep learning architectures for classification of EEG signals. In this thesis, several deep learning architectures are compared to traditional techniques for the classification of visually evoked EEG signals. We …

Exploring The Telecommunications Properties Of The Human Nervous System: Analytical Modeling And Experimental Validation Of Information Flow Through The Somatosensory System, Natalie Hanisch

School of Computing: Dissertations, Theses, and Student Research

The growing field of Body Area Networks (BANs) is providing solutions to the wireless connectivity of wearable and implantable devices with applications in medicine, entertainment, fitness, and military, amongst others. While electromagnetic wave propagation has been the main BANs' enabling technology, the increasingly pervasive nature of these devices encourages novel solutions with added bio-compatibility and sustainability. In this thesis, a novel communication system is proposed for BANs based on the natural propagation of tactile stimuli through the nervous system. This system is composed of a tactile stimulator coupled to an ElectroEncephaloGraphy (EEG) system, and realizes the propagation of somatosensory signals …

Study Of Comparison Of Ocs And Hybrid Switching In Fso Data Centers, Suraj Yadav

School of Computing: Dissertations, Theses, and Student Research

With the increase in big data applications, it has become the need of the hour to handle data efficiently to handle the growing traffic in the data centers. The popular mechanism is parallel processing using commodity hardware hence it is becoming an interesting research topic to explore new architectures which have high performance, but with an increase in data sizes the architecture has to expand which increases the cabling complexity. Hence the study of Free Space Optical (FSO) communication for the data centers is gaining more importance now than ever. We proposed square OWCELL topology which is a new free …

Investigating Diversity In Open Multiagent Team Formation, Pooja Ahuja

School of Computing: Dissertations, Theses, and Student Research

Team formation is the most rudimentary form of interactions in distributed AI and multiagent systems as it allows coherent collections of agents to work together in a beneficial manner towards a common goal of interest. Basically, individual expertise are assembled together in an additive fashion for accomplishing tasks together. A plethora of the related studies found in the literature often make several unrealistic assumptions such as coordination amongst the agents, or agents having knowledge of the whole environment, or agents and/or tasks are of the same kind, or a static environment setting. Against this background, we argue that there are …

Querying And Visualization Of Moving Objects Using Constraint Databases, Semere M. Woldemariam

School of Computing: Dissertations, Theses, and Student Research

Good querying and visualization of moving objects and their trajectories is still an open problem. This thesis investigates three types of moving objects. First, projectiles, whose parabolic motion is difficult to represent. Second, moving objects that slide down a slope. The representation of these objects is challenging because of their accelerating motion. Third, the motion of migrating animals. The motion of migrating animals is challenging because it also involves some spatio-temporal interpolation. The thesis shows a solution to these problems using ideas from physics and an implementation in the MLPQ constraint databases system. The MLPQ implementation enables several complex spatio-temporal …

Investigating Agent And Task Openness In Adhoc Team Formation, Bin Chen

School of Computing: Dissertations, Theses, and Student Research

When deciding which ad hoc team to join, agents are often required to consider rewards from accomplishing tasks as well as potential benefits from learning when working with others, when solving tasks. We argue that, in order to decide when to learn or when to solve task, agents have to consider the existing agents’ capabilities and tasks available in the environment, and thus agents have to consider agent and task openness—the rate of new, previously unknown agents (and tasks) that are introduced into the environment. We further assume that agents evolve their capabilities intrinsically through learning by observation or learning …

Detection Of Plant Emergence Based On Spatio Temporal Image Sequence Analysis, Bhushit Agarwal

School of Computing: Dissertations, Theses, and Student Research

The phenome of a plant is the sum of all observable phenotypes for that plant. Phenotypes are observable characteristics or traits of a plant. These traits generally reflect a combination of influences from the genotype of the plant and the environment in which the plant has grown and developed. Collecting phenotypic data has traditionally been a slow and costly manual process, albeit one highly necessary for plant breeding and the development of improved agronomic practices. As a result automated methods for plant phenotyping analysis have become an active research field in recent years. Image-based plant phenotyping analysis facilitates extraction of …

Characterization Of Molecular Communication Based On Cell Metabolism Through Mutual Information And Flux Balance Analysis, Zahmeeth Sayed Sakkaff

School of Computing: Dissertations, Theses, and Student Research

Synthetic biology is providing novel tools to engineer cells and access the basis of their molecular information processing, including their communication channels based on chemical reactions and molecule exchange. Molecular communication is a discipline in communication engineering that studies these types of communications and ways to exploit them for novel purposes, such as the development of ubiquitous and heterogeneous communication networks to interconnect biological cells with nano and biotechnology-enabled devices, i.e., the Internet of Bio-Nano Things. One major problem in realizing these goals stands in the development of reliable techniques to control the engineered cells and their behavior from the …

Autonomous Uavs For Near Earth Environmental Sensing, David J. Anthony

School of Computing: Dissertations, Theses, and Student Research

Unmanned aerial vehicles (UAVs) are playing an increasing role in large scale environmental monitoring. Small UAVs are increasingly used to monitor agricultural fields, infrastructure projects, and disaster areas. The combination of their sensors, ease of use, and portability make them an ideal tool for collecting information on demand about geographic regions. These small UAVs do have several significant limitations. The UAVs have very limited autonomy and fly pre-determined flight paths far above the underlying terrain, limiting the spatial resolution of the collected data. Current battery technology severely limits their flight times, which in turn limits the temporal resolution of the …

Optimization Of Irrigation Decision In Cornsoywater, Dharmic Payyala

School of Computing: Dissertations, Theses, and Student Research

A crop simulation model is used to estimate crop production as a function of weather conditions, soil parameters, and plant related inputs. These crop simulation models are extensively used by farmers, corporations and policy makers for agronomical planning and decision making. CornSoyWater is one such application which provides irrigation recommendation for soy and corn farmers using hybrid maize and soy sim models. As this is a simulation technology, the accuracy of results depends on the quality of data provided to it. One such important input parameter is weather data. CornSoyWater simulates field and crop conditions by retrieving the updated weather …

Semeo: A Semantic Equivalence Analysis Framework For Obfuscated Android Applications, Zhen Hu

School of Computing: Dissertations, Theses, and Student Research

Software repackaging is a common approach for creating malware. In this approach, malware authors inject malicious payloads into legitimate applications; then, to ren- der security analysis more difficult, they obfuscate most or all of the code. This forces analysts to spend a large amount of effort filtering out benign obfuscated methods in order to locate potentially malicious methods for further analysis. If an effective mechanism for filtering out benign obfuscated methods were available, the number of methods that must be analyzed could be reduced, allowing analysts to be more productive. In this thesis, we introduce SEMEO, a highly effective and …

Testing The Independence Hypothesis Of Accepted Mutations For Pairs Of Adjacent Amino Acids In Protein Sequences, Jyotsna Ramanan

School of Computing: Dissertations, Theses, and Student Research

Evolutionary studies usually assume that the genetic mutations are independent of each other. However, that does not imply that the observed mutations are independent of each other because it is possible that when a nucleotide is mutated, then it may be biologically beneficial if an adjacent nucleotide mutates too.

With a number of decoded genes currently available in various genome libraries and online databases, it is now possible to have a large-scale computer-based study to test whether the independence assumption holds for pairs of adjacent amino acids. Hence the independence question also arises for pairs of adjacent amino acids within …

Finding Dna Motifs: A Probabilistic Suffix Tree Approach, Abhishek Majumdar

School of Computing: Dissertations, Theses, and Student Research

We address the problem of de novo motif identification. That is, given a set of DNA sequences we try to identify motifs in the dataset without having any prior knowledge about existence of any motifs in the dataset. We propose a method based on Probabilistic Suffix Trees (PSTs) to identify fixed-length motifs from a given set of DNA sequences. Our experiments reveal that our approach successfully discovers true motifs. We compared our method with the popular MEME algorithm, and observed that it detects a larger number of correct and statistically significant motifs than MEME. Our method is highly efficient as …

The Effect Of Frequency Resolution On Intelligibility Sentence And Its Relevance To Cochlear Implant Design, Seth H. Roy

School of Computing: Dissertations, Theses, and Student Research

The purpose of this study is to understand how electrical stimulation (as opposed to acoustical stimulation) of the auditory nerve is used in cochlear implants. Speech is a complex signal that changes rapidly in time and frequency domains. Since phonemes (the smallest unit of speech that distinguishes words) depend on nuanced differences in frequency patterns, it would be expected that a signal with drastically reduced frequency information would be of limited value for conveying speech. Such a frequency-poor signal is the object to be investigated in the present work. It is also the basis of the way speech is represented …

A New System For Human Microrna Functional Evaluation And Network, Jiachun Han

School of Computing: Dissertations, Theses, and Student Research

MicroRNAs are functionally important endogenous non-coding RNAs that silence host genes in animal and plant via destabilizing the mRNAs or preventing the translation. Given the far-reaching implication of microRNA regulation in human health, novel bioinformatics tools are desired to facilitate the mechanistic understanding of microRNA mediated gene regulation, their roles in biological processes, and the functional relevance among microRNAs. However, most state-of-the-art computational methods still focus on the functional study of microRNA targets and there is no e ective strategy to infer the functional similarity among microRNAs. In this study, we developed a new method to quantitatively measure the functional …

On Path Consistency For Binary Constraint Satisfaction Problems, Christopher G. Reeson

School of Computing: Dissertations, Theses, and Student Research

Constraint satisfaction problems (CSPs) provide a flexible and powerful framework for modeling and solving many decision problems of practical importance. Consistency properties and the algorithms for enforcing them on a problem instance are at the heart of Constraint Processing and best distinguish this area from other areas concerned with the same combinatorial problems. In this thesis, we study path consistency (PC) and investigate several algorithms for enforcing it on binary finite CSPs. We also study algorithms for enforcing consistency properties that are related to PC but are stronger or weaker than PC.

We identify and correct errors in the literature …

Power Management In Heterogeneous Mapreduce Cluster, Rojee Sunuwar

School of Computing: Dissertations, Theses, and Student Research

The growing expenses of power in data centers as compared to the operation costs has been a concern for the past several decades. It has been predicted that without an intervention, the energy cost will soon outgrow the infrastructure and operation cost. Therefore, it is of great importance to make data center clusters more energy efficient which is critical for avoiding system overheating and failures. In addition, energy inefficiency causes not only the loss of capital but also environmental pollution. Various Power Management(PM) strategies have been developed over the years to make system more energy efficient and to counteract the …

Rectilinear Steiner Tree Construction, Zhiliu Zhang

School of Computing: Dissertations, Theses, and Student Research

The Minimum Rectilinear Steiner Tree (MRST) problem is to find the minimal spanning tree of a set of points (also called terminals) in the plane that interconnects all the terminals and some extra points (called Steiner points) introduced by intermediate junctions, and in which edge lengths are measured in the L1 (Manhattan) metric. This is one of the oldest optimization problems in mathematics that has been extensively studied and has been proven to be NP-complete, thus efficient approximation heuristics are more applicable than exact algorithms.

In this thesis, we present a new heuristic to construct rectilinear Steiner trees (RSTs) with …

Determination Of Plant Architecture And Component Phenotyping Based On Time-Lapse Image Analysis, Srinidhi Bashyam

School of Computing: Dissertations, Theses, and Student Research

Plant breeding and the development of new food production depend on accurate measurement of different phenotypes (observable physical traits) of a plant. The plant phenotypes play a very important role in the agronomic production. The successful computation of plant phenotypes largely depends on the determination of the architecture of the plant, i.e., the arrangement of its parts (leaves, stems, flowers, etc.) relative to each other, and how the size, shape, and positions of those parts change over time. Researchers and breeders extract valuable information from these types of data to make an informed decision on which individuals to advance to …

Towards Building A Review Recommendation System That Trains Novices By Leveraging The Actions Of Experts, Shilpa Khanal

School of Computing: Dissertations, Theses, and Student Research

Online reviews increase consumer visits, increase the time spent on the website, and create a sense of community among the frequent shoppers. Because of the importance of online reviews, online retailers such as Amazon.com and eOpinions provide detailed guidelines for writing reviews. However, though these guidelines provide instructions on how to write reviews, reviewers are not provided instructions for writing product-specific reviews. As a result, poorly-written reviews are abound and a customer may need to scroll through a large number of reviews, which could be up to 6000 pixels down from the top of the page, in order to find …

Activity Analysis Of Spectator Performer Videos Using Motion Trajectories, Anish Timsina

School of Computing: Dissertations, Theses, and Student Research

Spectator Performer Space (SPS) is a frequently occurring crowd dynamics, composed of one or more central performers, and a peripheral crowd of spectators. Analysis of videos in this space is often complicated due to occlusion and high density of people. Although there are many video analysis approaches, they are targeted for individual actors or low-density crowd and hence are not suitable for SPS videos. In this work, we present two trajectory-based features: Histogram of Trajectories (HoT) and Histogram of Trajectory Clusters (HoTC) to analyze SPS videos. HoT is calculated from the distribution of length and orientation of motion trajectories in …

Improving The Efficiency Of Ci With Uber-Commits, Matias Waterloo

School of Computing: Dissertations, Theses, and Student Research

Continuous Integration (CI) is a software engineering practice where developers break their coding tasks into small changes that can be integrated with the shared code repository on a frequent basis. The primary objectives of CI are to avoid integration problems caused by large change sets and to provide prompt developer feedback so that if a problem is detected, it can be easily and quickly resolved. In this thesis, we argue that while keeping changes small and integrating often is a wise approach for developers, the CI server may be more efficient operating on a different scale. In our approach, the …

Exploring Dynamic Memory Allocations For Bioinformatics Applications, Nitya Kovur

School of Computing: Dissertations, Theses, and Student Research

The progression of scientific data leads to an increase in the demand of powerful high performance computers (HPC) where data can be stored and analyzed. High performance computing is used in several research areas to solve large problems. However, efficient usage of supercomputing resources that are available is a major concern for most of the researchers. The user has to choose the amount of resources needed for execution before submitting the job. Over or under subscription of resources leads to low system utilization and/or low user satisfaction.

Bioinformatics is one such field that heavily relies on HPC. One of the …