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Clinical Interpretation Of Novel Copy Number Variations, Clifton Carey
Clinical Interpretation Of Novel Copy Number Variations, Clifton Carey
All Theses and Dissertations (ETDs)
Copy Number Variations: CNVs) are a significant source of human genetic diversity and are believed to be responsible for a wide variety of phenotypic variation. Recent advances in microarray-based genomic hybridization techniques have facilitated CNV analysis as a viable diagnostic technique in the clinic, and several public databases of well-characterized CNVs are being compiled, but a standard for interpreting uncharacterized CNVs has yet to emerge. This thesis examines the clinical interpretation of uncharacterized CNVs as a multiple instance binary classification problem. We analyze the current state of clinical techniques, then present and test several novel statistical approaches to the problem.
Ns-3 Simulation Of Wimax Networks, Christopher Thomas
Ns-3 Simulation Of Wimax Networks, Christopher Thomas
All Theses and Dissertations (ETDs)
Simulation is a powerful tool for analysis and improvement of networking technologies, and many simulation packages are available. One that is growing in popularity is NS-3, the successor to the popular NS-2. It is a significant departure from NS-2, and offers many advantages and disadvantages. In this thesis, we translate and update a sophisticated WiMAX simulation model from NS-2 to NS-3, and use this experience to investigate the major differences between NS-2 and NS-3, and the relative strengths of each package. We then use the NS-3 simulation model to provide analysis on a new WiMAX OFDMA downlink subframe mapping algorithm.
Empirical Studies For Reliable Home Area Wireless Sensor Networks, Mo Sha
Empirical Studies For Reliable Home Area Wireless Sensor Networks, Mo Sha
All Theses and Dissertations (ETDs)
Home Area Networks: HANs) consisting of wireless sensors have emerged as the enabling technology for important applications such as smart energy and assisted living. A key challenge faced by HANs is maintaining reliable operation in real-world residential environments. In this thesis research, empirical studies on the spectrum usage in the 2.4 GHz band as well as 802.15.4 wireless channels are performed in diversified real residential environments. Based on the insights drawn from empirical studies, network design guideline and practical solution for Home Area Sensor Network are provided.
Decoding Brain Activation From Ipsilateral Cortex Using Ecog Signals In Humans, Yuzong Liu
Decoding Brain Activation From Ipsilateral Cortex Using Ecog Signals In Humans, Yuzong Liu
All Theses and Dissertations (ETDs)
Today, learning from the brain is the most challenging issue in many areas. Neural scientists, computer scientists, and engineers are collaborating in this broad research area. With better techniques, we can extract the brain signals by either non-invasive approach such as EEG: electroencephalography), fMRI, or invasive method such as ECoG: electrocorticography), FP: field potential) and signals from single unit. The challenge is, given the brain signals, how can we possibly decipher them? Brain Computer Interfaces, or BCIs, aim at utilizing the brain signals to control prothetic arms or operate devices. Previously almost all the research on BCIs focuses on decoding …
Low-Impact Profiling Of Streaming, Heterogeneous Applications, Joseph Lancaster
Low-Impact Profiling Of Streaming, Heterogeneous Applications, Joseph Lancaster
All Theses and Dissertations (ETDs)
Computer engineers are continually faced with the task of translating improvements in fabrication process technology: i.e., Moore's Law) into architectures that allow computer scientists to accelerate application performance. As feature-size continues to shrink, architects of commodity processors are designing increasingly more cores on a chip. While additional cores can operate independently with some tasks: e.g. the OS and user tasks), many applications see little to no improvement from adding more processor cores alone. For many applications, heterogeneous systems offer a path toward higher performance. Significant performance and power gains have been realized by combining specialized processors: e.g., Field-Programmable Gate Arrays, …
Computational Methods For Accelerated Discovery And Characterization Of Genes In Emerging Model Organisms, Alan Kwan
All Theses and Dissertations (ETDs)
Cilia are evolutionarily conserved, complex, microtubule-based structures that protrude from many eukaryotic cells. In humans, cilia can be found on almost all cell types. The effect of abnormal or absent cilia has been established as the common underlying cause of a recently emerging class of genetic diseases collectively referred to as ciliopathies. The function and structure of cilia are conserved across all organisms with cilia. One of the most influential model systems used to study ciliopathies has been the ciliated green alga Chlamydomonas reinhardtii, an organism for which there is a sequenced genome with relatively few experimentally validated whole-gene annotations …
A Graph-Based Algorithm To Determine Protein Structure From Cryo-Em Data, Stephen Schuh
A Graph-Based Algorithm To Determine Protein Structure From Cryo-Em Data, Stephen Schuh
All Theses and Dissertations (ETDs)
Cryo-electron microscopy: cryo-EM) provides 3D density maps of proteins, but these maps do not have sufficiently high resolution to directly yield atomic-scale models. Previous work has shown that features known as secondary structures can be located in these density maps. A second source of information about proteins is sequence analysis, which predicts locations of secondary structures along the protein sequence but does not provide any information about the 3D shape of the protein. This thesis presents a graph-based algorithm to find the correspondence between the secondary structures in the density map and sequence. This provides an ordering of secondary structures …
Optimal Control For Autonomous Motor Behavior, Tom Erez
Optimal Control For Autonomous Motor Behavior, Tom Erez
All Theses and Dissertations (ETDs)
This dissertation presents algorithms that allow robots to generate optimal behavior from first principles. Instead of hard-coding every desired behavior, we encode the task as a cost function, and use numerical optimization to find action sequences that can accomplish the task. Using the theoretical framework of optimal control, we develop methods for generating autonomous motor behavior in high-dimensional domains of legged locomotion. We identify three foundational problems that limit the application of existing optimal control algorithms, and present guiding principles that address these issues. First, some traditional algorithms use global optimization, where every possible state is considered. This approach cannot …
Simplifying The Non-Manifold Topology Of Multi-Partitioning Surface Networks, Trung Nguyen
Simplifying The Non-Manifold Topology Of Multi-Partitioning Surface Networks, Trung Nguyen
All Theses and Dissertations (ETDs)
In bio-medical imaging, multi-partitioning surface networks: MPSNs) are very useful to model complex organs with multiple anatomical regions, such as a mouse brain. However, MPSNs are usually constructed from image data and might contain complex geometric and topological features. There has been much research on reducing the geometric complexity of a general surface: non-manifold or not) and the topological complexity of a closed, manifold surface. But there has been no attempt so far to reduce redundant topological features which are unique to non-manifold surfaces, such as curves and points where multiple sheets of surfaces join. In this thesis, we design …
Efficient Automated Planning With New Formulations, Ruoyun Huang
Efficient Automated Planning With New Formulations, Ruoyun Huang
All Theses and Dissertations (ETDs)
Problem solving usually strongly relies on how the problem is formulated. This fact also applies to automated planning, a key field in artificial intelligence research. Classical planning used to be dominated by STRIPS formulation, a simple model based on propositional logic. In the recently introduced SAS+ formulation, the multi-valued variables naturally depict certain invariants that are missed in STRIPS, make SAS+ have many favorable features. Because of its rich structural information SAS+ begins to attract lots of research interest. Existing works, however, are mostly limited to one single thing: to improve heuristic functions. This is in sharp contrast with the …
Towards Real-Time Wireless Sensor Networks, Octav Chipara
Towards Real-Time Wireless Sensor Networks, Octav Chipara
All Theses and Dissertations (ETDs)
Wireless sensor networks are poised to change the way computer systems interact with the physical world. We plan on entrusting sensor systems to collect medical data from patients, monitor the safety of our infrastructure, and control manufacturing processes in our factories. To date, the focus of the sensor network community has been on developing best-effort services. This approach is insufficient for many applications since it does not enable developers to determine if a system's requirements in terms of communication latency, bandwidth utilization, reliability, or energy consumption are met. The focus of this thesis is to develop real-time network support for …
On Motion Parameterizations In Image Sequences From Fixed Viewpoints, Manfred Georg
On Motion Parameterizations In Image Sequences From Fixed Viewpoints, Manfred Georg
All Theses and Dissertations (ETDs)
This dissertation addresses the problem of parameterizing object motion within a set of images taken with a stationary camera. We develop data-driven methods across all image scales: characterizing motion observed at the scale of individual pixels, along extended structures such as roads, and whole image deformations such as lungs deforming over time. The primary contributions include: a) fundamental studies of the relationship between spatio-temporal image derivatives accumulated at a pixel, and the object motions at that pixel,: b) data driven approaches to parameterize breath motion and reconstruct lung CT data volumes, and: c) defining and offering initial results for a …
An Empirical Analysis On Point-Wise Machine Learning Techniques Using Regression Trees For Web-Search Ranking, Ananth Mohan
An Empirical Analysis On Point-Wise Machine Learning Techniques Using Regression Trees For Web-Search Ranking, Ananth Mohan
All Theses and Dissertations (ETDs)
Learning how to rank a set of objects relative to an user defined query has received much interest in the machine learning community during the past decade. In fact, there have been two recent competitions hosted by internationally prominent search companies to encourage research on ranking web site documents. Recent literature on learning to rank has focused on three approaches: point-wise, pair-wise, and list-wise. Many different kinds of classifiers, including boosted decision trees, neural networks, and SVMs have proven successful in the field. This thesis surveys traditional point-wise techniques that use regression trees for web-search ranking. The thesis contains empirical …
Parallelization Of Dynamic Programming Recurrences In Computational Biology, Arpith Jacob
Parallelization Of Dynamic Programming Recurrences In Computational Biology, Arpith Jacob
All Theses and Dissertations (ETDs)
The rapid growth of biosequence databases over the last decade has led to a performance bottleneck in the applications analyzing them. In particular, over the last five years DNA sequencing capacity of next-generation sequencers has been doubling every six months as costs have plummeted. The data produced by these sequencers is overwhelming traditional compute systems. We believe that in the future compute performance, not sequencing, will become the bottleneck in advancing genome science. In this work, we investigate novel computing platforms to accelerate dynamic programming algorithms, which are popular in bioinformatics workloads. We study algorithm-specific hardware architectures that exploit fine-grained …
Abstractions And Algorithms For Control Of Extensible And Heterogeneous Virtualized Network Infrastructures, Charles Wiseman
Abstractions And Algorithms For Control Of Extensible And Heterogeneous Virtualized Network Infrastructures, Charles Wiseman
All Theses and Dissertations (ETDs)
Virtualized network infrastructures are currently deployed in both research and commercial contexts. The complexity of the virtualization layer varies greatly in different deployments, ranging from cloud computing environments, to carrier Ethernet applications using stacked VLANs, to networking testbeds. In all of these cases, many users are sharing the resources of one provider and each user expects their resources to be isolated from all other users. There are many challenges associated with the control and management of these systems, including resource allocation and sharing, resource isolation, system security, and usability. Among the different types of virtualized infrastructures, network testbeds are of …
Modeling And Dynamic Resource Allocation For High Definition And Mobile Video Streams, Abdel-Karim Al-Tamimi
Modeling And Dynamic Resource Allocation For High Definition And Mobile Video Streams, Abdel-Karim Al-Tamimi
All Theses and Dissertations (ETDs)
Video streaming traffic has been surging in the last few years, which has resulted in an increase of its Internet traffic share on a daily basis. The importance of video streaming management has been emphasized with the advent of High Definition: HD) video streaming, as it requires by its nature more network resources. In this dissertation, we provide a better support for managing HD video traffic over both wireless and wired networks through several contributions. We present a simple, general and accurate video source model: Simplified Seasonal ARIMA Model: SAM). SAM is capable of capturing the statistical characteristics of video …
A Geometric Approach For Deciphering Protein Structure From Cryo-Em Volumes, Sasakthi Abeysinghe
A Geometric Approach For Deciphering Protein Structure From Cryo-Em Volumes, Sasakthi Abeysinghe
All Theses and Dissertations (ETDs)
Electron Cryo-Microscopy or cryo-EM is an area that has received much attention in the recent past. Compared to the traditional methods of X-Ray Crystallography and NMR Spectroscopy, cryo-EM can be used to image much larger complexes, in many different conformations, and under a wide range of biochemical conditions. This is because it does not require the complex to be crystallisable. However, cryo-EM reconstructions are limited to intermediate resolutions, with the state-of-the-art being 3.6A, where secondary structure elements can be visually identified but not individual amino acid residues. This lack of atomic level resolution creates new computational challenges for protein structure …
Adaptive Middleware For Resource-Constrained Mobile Ad Hoc And Wireless Sensor Networks, Chien-Liang Fok
Adaptive Middleware For Resource-Constrained Mobile Ad Hoc And Wireless Sensor Networks, Chien-Liang Fok
All Theses and Dissertations (ETDs)
Mobile ad hoc networks: MANETs) and wireless sensor networks: WSNs) are two recently-developed technologies that uniquely function without fixed infrastructure support, and sense at scales, resolutions, and durations previously not possible. While both offer great potential in many applications, developing software for these types of networks is extremely difficult, preventing their wide-spread use. Three primary challenges are: 1) the high level of dynamics within the network in terms of changing wireless links and node hardware configurations,: 2) the wide variety of hardware present in these networks, and: 3) the extremely limited computational and energy resources available. Until now, the burden …
Statistical Aggregation: Theory And Applications, Ruibin Xi
Statistical Aggregation: Theory And Applications, Ruibin Xi
All Theses and Dissertations (ETDs)
Due to their size and complexity, massive data sets bring many computational challenges for statistical analysis, such as overcoming the memory limitation and improving computational efficiency of traditional statistical methods. In the dissertation, I propose the statistical aggregation strategy to conquer such challenges posed by massive data sets. Statistical aggregation partitions the entire data set into smaller subsets, compresses each subset into certain low-dimensional summary statistics and aggregates the summary statistics to approximate the desired computation based on the entire data. Results from statistical aggregation are required to be asymptotically equivalent. Statistical aggregation processes the entire data set part by …
Networking Mechanisms For Delay-Sensitive Applications, Maxim Podlesny
Networking Mechanisms For Delay-Sensitive Applications, Maxim Podlesny
All Theses and Dissertations (ETDs)
The diversity of applications served by the explosively growing Internet is increasing. In particular, applications that are sensitive to end-to-end packet delays become more common and include telephony, video conferencing, and networked games. While the single best-effort service of the current Internet favors throughput-greedy traffic by equipping congested links with large buffers, long queuing at the congested links hurts the delay-sensitive applications. Furthermore, while numerous alternative architectures have been proposed to offer diverse network services, the innovative alternatives failed to gain widespread end-to-end deployment. This dissertation explores different networking mechanisms for supporting low queueing delay required by delay-sensitive applications. In …
Design And Evaluation Of Distributed Algorithms For Placement Of Network Services, Todd Sproull
Design And Evaluation Of Distributed Algorithms For Placement Of Network Services, Todd Sproull
All Theses and Dissertations (ETDs)
Network services play an important role in the Internet today. They serve as data caches for websites, servers for multiplayer games and relay nodes for Voice over IP: VoIP) conversations. While much research has focused on the design of such services, little attention has been focused on their actual placement. This placement can impact the quality of the service, especially if low latency is a requirement. These services can be located on nodes in the network itself, making these nodes supernodes. Typically supernodes are selected in either a proprietary or ad hoc fashion, where a study of this placement is …
Scheduling Policy Design Using Stochastic Dynamic Programming, Robert Glaubius
Scheduling Policy Design Using Stochastic Dynamic Programming, Robert Glaubius
All Theses and Dissertations (ETDs)
Scheduling policies for open soft real-time systems must be able to balance the competing concerns of meeting their objectives under exceptional conditions while achieving good performance in the average case. Balancing these concerns requires modeling strategies that represent the range of possible task behaviors, and solution techniques that are capable of effectively managing uncertainty in order to discover scheduling policies that are effective across the range of system modes. We develop methods for solving a particular class of task scheduling problems in an open soft real-time setting involving repeating, non-preemptable tasks that contend for a single shared resource. We enforce …
Structural Rna Homology Search And Alignment Using Covariance Models, Eric Nawrocki
Structural Rna Homology Search And Alignment Using Covariance Models, Eric Nawrocki
All Theses and Dissertations (ETDs)
Functional RNA elements do not encode proteins, but rather function directly as RNAs. Many different types of RNAs play important roles in a wide range of cellular processes, including protein synthesis, gene regulation, protein transport, splicing, and more. Because important sequence and structural features tend to be evolutionarily conserved, one way to learn about functional RNAs is through comparative sequence analysis - by collecting and aligning examples of homologous RNAs and comparing them. Covariance models: CMs) are powerful computational tools for homology search and alignment that score both the conserved sequence and secondary structure of an RNA family. However, due …