Physical Sciences and Mathematics Commons^™

High-Performance Computing Frameworks For Large-Scale Genome Assembly, Sayan Goswami

LSU Doctoral Dissertations

Genome sequencing technology has witnessed tremendous progress in terms of throughput and cost per base pair, resulting in an explosion in the size of data. Typical de Bruijn graph-based assembly tools demand a lot of processing power and memory and cannot assemble big datasets unless running on a scaled-up server with terabytes of RAMs or scaled-out cluster with several dozens of nodes. In the first part of this work, we present a distributed next-generation sequence (NGS) assembler called Lazer, that achieves both scalability and memory efficiency by using partitioned de Bruijn graphs. By enhancing the memory-to-disk swapping and reducing the …

Mobile Music Development Tools For Creative Coders, Daniel Stuart Holmes

LSU Doctoral Dissertations

This project is a body of work that facilitates the creation of musical mobile artworks. The project includes a code toolkit that enhances and simplifies the development of mobile music iOS applications, a flexible notation system designed for mobile musical interactions, and example apps and scored compositions to demonstrate the toolkit and notation system.

The code library is designed to simplify the technical aspect of user-centered design and development with a more direct connection between concept and deliverable. This sim- plification addresses learning problems (such as motivation, self-efficacy, and self-perceived understanding) by bridging the gap between idea and functional prototype …

Geometric Problems In Robot Exploration, Wyatt Preston Clements

LSU Doctoral Dissertations

Robots are increasingly utilized to perform tasks in today's world. This has varied from vacuuming to building advanced structures. With robots being used for tasks such as these, new challenges are introduced. Problems that have been previously researched to be performed, either theoretically or implemented, need to be redesigned to be able to better handle these challenges. In this thesis, I will discuss multiple problems that have previously been researched and I have redesigned to be possible to be implemented by robots or that I have developed a new way for the robots to solve the problem. I focus on …

Modeling Crowd Feedback In The Mobile App Market, Grant S. Williams

LSU Doctoral Dissertations

Mobile application (app) stores, such as Google Play and the Apple App Store, have recently emerged as a new model of online distribution platform. These stores have expanded in size in the past five years to host millions of apps, offering end-users of mobile software virtually unlimited options to choose from. In such a competitive market, no app is too big to fail. In fact, recent evidence has shown that most apps lose their users within the first 90 days after initial release. Therefore, app developers have to remain up-to-date with their end-users’ needs in order to survive. Staying close …

Effective Visualization Approaches For Ultra-High Dimensional Datasets, Gurminder Kaur

LSU Doctoral Dissertations

Multivariate informational data, which are abstract as well as complex, are becoming increasingly common in many areas such as scientific, medical, social, business, and so on. Displaying and analyzing large amounts of multivariate data with more than three variables of different types is quite challenging. Visualization of such multivariate data suffers from a high degree of clutter when the numbers of dimensions/variables and data observations become too large. We propose multiple approaches to effectively visualize large datasets of ultrahigh number of dimensions by generalizing two standard multivariate visualization methods, namely star plot and parallel coordinates plot. We refine three variants …

Bipartite Quantum Interactions: Entangling And Information Processing Abilities, Siddhartha Das

LSU Doctoral Dissertations

The aim of this thesis is to advance the theory behind quantum information processing tasks, by deriving fundamental limits on bipartite quantum interactions and dynamics. A bipartite quantum interaction corresponds to an underlying Hamiltonian that governs the physical transformation of a two-body open quantum system. Under such an interaction, the physical transformation of a bipartite quantum system is considered in the presence of a bath, which may be inaccessible to an observer. The goal is to determine entangling abilities of such arbitrary bipartite quantum interactions. Doing so provides fundamental limitations on information processing tasks, including entanglement distillation and secret key …

Development Of A Slab-Based Monte Carlo Proton Dose Algorithm With A Robust Material-Dependent Nuclear Halo Model, John Wesley Chapman Jr

LSU Doctoral Dissertations

Pencil beam algorithms (PBAs) are often utilized for dose calculation in proton therapy treatment planning because they are fast and accurate under most conditions. However, as discussed in Chapman et al (2017), the accuracy of a PBA can be limited under certain conditions because of two major assumptions: (1) the central-axis semi-infinite slab approximation; and, (2) the lack of material dependence in the nuclear halo model. To address these limitations, we transported individual protons using a class II condensed history Monte Carlo and added a novel energy loss method that scaled the nuclear halo equation in water to arbitrary geometry. …

Entropic Bounds On Two-Way Assisted Secret-Key Agreement Capacities Of Quantum Channels, Noah Anthony Davis

LSU Doctoral Dissertations

In order to efficiently put quantum technologies into action, we must know the characteristics of the underlying quantum systems and effects. An interesting example is the use of the secret-key-agreement capacity of a quantum channel as a guide and measure for the implementation of quantum key distribution (QKD) and distributed quantum computation. We define the communication task of establishing a secret key over a quantum channel subject to an energy constraint on the input state and while allowing for unlimited local operations and classical communication (LOCC) between a sender and receiver. We then use the energy-constrained squashed entanglement to bound …

An Optimizing Java Translation Framework For Automated Checkpointing And Strong Mobility, Arvind Kumar Saini

LSU Doctoral Dissertations

Long-running programs, e.g., in high-performance computing, need to

write periodic checkpoints of their execution state to disk to allow

them to recover from node failure. Manually adding checkpointing code

to an application, however, is very tedious. The mechanisms needed

for writing the execution state of a program to disk and restoring it

are similar to those needed for migrating a running thread or a mobile

object. We have extended a source-to-source translation scheme that

allows the migration of mobile Java objects with running threads to

make it more general and allow it to be used for automated

checkpointing. Our translation …

Hierarchical Fusion Based Deep Learning Framework For Lung Nodule Classification, Kazim Sekeroglu

LSU Doctoral Dissertations

Lung cancer is the leading cancer type that causes the mortality in both men and women. Computer aided detection (CAD) and diagnosis systems can play a very important role for helping the physicians in cancer treatments. This dissertation proposes a CAD framework that utilizes a hierarchical fusion based deep learning model for detection of nodules from the stacks of 2D images. In the proposed hierarchical approach, a decision is made at each level individually employing the decisions from the previous level. Further, individual decisions are computed for several perspectives of a volume of interest (VOI). This study explores three different …

Information Theoretic Study Of Gaussian Graphical Models And Their Applications, Ali Moharrer

LSU Doctoral Dissertations

In many problems we are dealing with characterizing a behavior of a complex stochastic system or its response to a set of particular inputs. Such problems span over several topics such as machine learning, complex networks, e.g., social or communication networks; biology, etc. Probabilistic graphical models (PGMs) are powerful tools that offer a compact modeling of complex systems. They are designed to capture the random behavior, i.e., the joint distribution of the system to the best possible accuracy. Our goal is to study certain algebraic and topological properties of a special class of graphical models, known as Gaussian graphs. First, …

Succinct Data Structures For Parameterized Pattern Matching And Related Problems, Arnab Ganguly

LSU Doctoral Dissertations

Let T be a fixed text-string of length n and P be a varying pattern-string of length |P| <= n. Both T and P contain characters from a totally ordered alphabet Sigma of size sigma <= n. Suffix tree is the ubiquitous data structure for answering a pattern matching query: report all the positions i in T such that T[i + k - 1] = P[k], 1 <= k <= |P|. Compressed data structures support pattern matching queries, using much lesser space than the suffix tree, mainly by relying on a crucial property of the leaves in the tree. Unfortunately, in many suffix tree variants (such as parameterized suffix tree, order-preserving suffix tree, and 2-dimensional suffix tree), this property does not hold. Consequently, compressed representations of these suffix tree variants have been elusive. We present the first compressed data structures for two important variants of the pattern matching problem: (1) Parameterized Matching -- report a position i in T if T[i + k - 1] = f(P[k]), 1 <= k <= |P|, for a one-to-one function f that renames the characters in P to the characters in T[i,i+|P|-1], and (2) Order-preserving Matching -- report a position i in T if T[i + j - 1] and T[i + k -1] have the same relative order as that of P[j] and P[k], 1 <= j < k <= |P|. For each of these two problems, the existing suffix tree variant requires O(n*log n) bits of space and answers a query in O(|P|*log sigma + occ) time, where occ is the number of starting positions where a match exists. We present data structures that require O(n*log sigma) bits of space and answer a query in O((|P|+occ) poly(log n)) time. As a byproduct, we obtain compressed data structures for a few other variants, as well as introduce two new techniques (of independent interest) for designing compressed data structures for pattern matching.

Empirically Tuning Hpc Kernels With Ifko, Md Majedul Haque Sujon

LSU Doctoral Dissertations

iFKO (iterative Floating point Kernel Optimizer) is an open-source iterative empirical compilation framework which can be used to tune high performance computing (HPC) kernels. The goal of our research is to advance iterative empirical compilation to the degree that the performance it can achieve is comparable to that delivered by painstaking hand tuning in assembly. This will allow many HPC researchers to spend precious development time on higher level aspects of tuning such as parallelization, as well as enabling computational scientists to develop new algorithms that demand new high performance kernels. At present, algorithms that cannot use hand-tuned performance libraries …

Decentralized Scheduling For Many-Task Applications In The Hybrid Cloud, Brian Lyle Peterson

LSU Doctoral Dissertations

While Cloud Computing has transformed how we solve many computing tasks, some scientific and many-task applications are not efficiently executed on cloud resources. Decentralized scheduling, as studied in grid computing, can provide a scalable system to organize cloud resources and schedule a variety of work. By measuring simulations of two algorithms, the fully decentralized Organic Grid, and the partially decentralized Air Traffic Controller from IBM, we establish that decentralization is a workable approach, and that there are bottlenecks that can impact partially centralized algorithms. Through measurements in the cloud, we verify that our simulation approach is sound, and assess the …

Maintaining High Performance Across All Problem Sizes And Parallel Scales Using Microkernel-Based Linear Algebra, Md Rakib Hasan

LSU Doctoral Dissertations

Linear algebra underlies a large proportion of computational problems. With the continuous increase of scale on modern hardware, performance of small sized linear algebra has become increasingly important. To overcome the shortcomings of conventional approaches, we employ a new approach using a microkernel framework provided by ATLAS to improve the performance of a few linear algebra routines for all problem sizes. Our initial research consists of improving the performance of parallel LU factorization in ATLAS for which we were able to achieve up to 2.07x and 2.66x speedup for small problems, up to 91% and 87% of theoretical peak performance …

Symbolic And Deep Learning Based Data Representation Methods For Activity Recognition And Image Understanding At Pixel Level, Manohar Karki

LSU Doctoral Dissertations

Efficient representation of large amount of data particularly images and video helps in the analysis, processing and overall understanding of the data. In this work, we present two frameworks that encapsulate the information present in such data. At first, we present an automated symbolic framework to recognize particular activities in real time from videos. The framework uses regular expressions for symbolically representing (possibly infinite) sets of motion characteristics obtained from a video. It is a uniform framework that handles trajectory-based and periodic articulated activities and provides polynomial time graph algorithms for fast recognition. The regular expressions representing motion characteristics can …

Fairness And Approximation In Multi-Version Transactional Memory., Basem Ibrahim Assiri

LSU Doctoral Dissertations

Shared memory multi-core systems bene_x000C_t from transactional memory implementations due to the inherent avoidance of deadlocks and progress guarantees. In this research, we examine how the system performance is a_x000B_ected by transaction fairness in scheduling and by the precision in consistency. We _x000C_rst explore the fairness aspect using a Lazy Snapshot (multi-version) Algorithm. The fairness of transactions scheduling aims to balance the load between read-only and update transactions. We implement a fairness mechanism based on machine learning techniques that improve fairness decisions according to the transaction execution history. Experimental analysis shows that the throughput of the Lazy Snapshot Algorithm is …

Probabilistic And Deep Learning Algorithms For The Analysis Of Imagery Data, Saikat Basu

LSU Doctoral Dissertations

Accurate object classification is a challenging problem for various low to high resolution imagery data. This applies to both natural as well as synthetic image datasets. However, each object recognition dataset poses its own distinct set of domain-specific problems. In order to address these issues, we need to devise intelligent learning algorithms which require a deep understanding and careful analysis of the feature space. In this thesis, we introduce three new learning frameworks for the analysis of both airborne images (NAIP dataset) and handwritten digit datasets without and with noise (MNIST and n-MNIST respectively). First, we propose a probabilistic framework …

A Novel Recurrent Convolutional Neural Network For Ocean And Weather Forecasting, Robert James Firth

LSU Doctoral Dissertations

Numerical weather prediction is a computationally expensive task that requires not only the numerical solution to a complex set of non-linear partial differential equations, but also the creation of a parameterization scheme to estimate sub-grid scale phenomenon. The proposed method is an alternative approach to developing a mesoscale meteorological model – a modified recurrent convolutional neural network that learns to simulate the solution to these equations. Along with an appropriate time integration scheme and learning algorithm, this method can be used to create multi-day forecasts for a large region. The learning method presented is an extended form of Backpropagation Through …

Garbage Collection For General Graphs, Hari Krishnan

LSU Doctoral Dissertations

Garbage collection is moving from being a utility to a requirement of every modern programming language. With multi-core and distributed systems, most programs written recently are heavily multi-threaded and distributed. Distributed and multi-threaded programs are called concurrent programs. Manual memory management is cumbersome and difficult in concurrent programs. Concurrent programming is characterized by multiple independent processes/threads, communication between processes/threads, and uncertainty in the order of concurrent operations. The uncertainty in the order of operations makes manual memory management of concurrent programs difficult. A popular alternative to garbage collection in concurrent programs is to use smart pointers. Smart pointers can collect …

Pattern Mining And Events Discovery In Molecular Dynamics Simulations Data, Shobhit Sandesh Shakya

LSU Doctoral Dissertations

Molecular dynamics simulation method is widely used to calculate and understand a wide range of properties of materials. A lot of research efforts have been focused on simulation techniques but relatively fewer works are done on methods for analyzing the simulation results. Large-scale simulations usually generate massive amounts of data, which make manual analysis infeasible, particularly when it is necessary to look into the details of the simulation results. In this dissertation, we propose a system that uses computational method to automatically perform analysis of simulation data, which represent atomic position-time series. The system identifies, in an automated fashion, the …

A Trust-Based Relay Selection Approach To The Multi-Hop Network Formation Problem In Cognitive Radio Networks, Brandy Michelle Tyson

LSU Doctoral Dissertations

One of the major challenges for today’s wireless communications is to meet the growing demand for supporting an increasing diversity of wireless applications with limited spectrum resource. In cooperative communications and networking, users share resources and collaborate in a distributed approach, similar to entities of active social groups in self organizational communities. Users’ information may be shared by the user and also by the cooperative users, in distributed transmission. Cooperative communications and networking is a fairly new communication paradigm that promises significant capacity and multiplexing gain increase in wireless networks. This research will provide a cooperative relay selection framework that …

Real-Time Shadows For Gigapixel Displacement Maps, Kevin Anthony Cherry

LSU Doctoral Dissertations

Shadows portray helpful information in scenes. From a scientific visualization standpoint, they help to add data without unnecessary clutter. In video games they add realism and depth. In common graphics pipelines, due to the independent and parallel rendering of geometric primitives, shadows are difficult to achieve. Objects require knowledge of each other and therefore multiple renders are needed to collect the necessary data. The collection of this data comes with its own set of trade offs. Our research involves adding shadows into a lunar rendering framework developed by Dr. Robert Kooima. The NASA-collected data contains a multi-gigapixel displacement map describing …

Classification In The Presence Of Ordered Classes And Weighted Evaluative Attributes, Forrest Justin Osterman

LSU Doctoral Dissertations

We are interested in an important family of problems in the interface of the Multi-Attribute Decision-Making and Data Mining fields. This is a special case of the general classification problem, in which records describing entities of interest have been expressed in terms of a number of evaluative attributes. These attributes are associated with weights of importance, and both the data and the classes are ordinal. Our goal is to use historical records and the corresponding decisions to best estimate the class values of new data points in a way consistent with prior classification decisions, without knowledge of the weights of …

Seavipers - Computer Vision And Inertial Position Reference Sensor System (Cviprss), Justin Lee Erdman

LSU Doctoral Dissertations

This work describes the design and development of an optical, Computer Vision (CV) based sensor for use as a Position Reference System (PRS) in Dynamic Positioning (DP). Using a combination of robotics and CV techniques, the sensor provides range and heading information to a selected reference object. The proposed optical system is superior to existing ones because it does not depend upon special reflectors nor does it require a lengthy set-up time. This system, the Computer Vision and Inertial Position Reference Sensor System (CVIPRSS, pronounced \nickname), combines a laser rangefinder, infrared camera, and a pan--tilt unit with the robust TLD …

String Searching With Ranking Constraints And Uncertainty, Sudip Biswas

LSU Doctoral Dissertations

Strings play an important role in many areas of computer science. Searching pattern in a string or string collection is one of the most classic problems. Different variations of this problem such as document retrieval, ranked document retrieval, dictionary matching has been well studied. Enormous growth of internet, large genomic projects, sensor networks, digital libraries necessitates not just efficient algorithms and data structures for the general string indexing, but indexes for texts with fuzzy information and support for queries with different constraints. This dissertation addresses some of these problems and proposes indexing solutions. One such variation is document retrieval query …

Synthesis With Hypergraphs, Christopher Thomas Alvin

LSU Doctoral Dissertations

Many problems related to synthesis with intelligent tutoring may be phrased as program synthesis problems using AI-style search and formal reasoning techniques. The _x000C_first two results in this dissertation focus on problem synthesis as an aspect of intelligent tutoring systems applied to STEM-based education frameworks, specifically high school geometry. Given a geometric _x000C_figure as input, our technique constructs a hypergraph representing logical deduction of facts, and then traverses the hypergraph to synthesize problems and their corresponding solutions. Using similar techniques, our third result is focused on exhaustive synthesis of molecules. This synthesis process involves bonding sets of basic, molecular `fragments' …

Large-Scale Geometric Data Decomposition, Processing And Structured Mesh Generation, Wuyi Yu

LSU Doctoral Dissertations

Mesh generation is a fundamental and critical problem in geometric data modeling and processing. In most scientific and engineering tasks that involve numerical computations and simulations on 2D/3D regions or on curved geometric objects, discretizing or approximating the geometric data using a polygonal or polyhedral meshes is always the first step of the procedure. The quality of this tessellation often dictates the subsequent computation accuracy, efficiency, and numerical stability. When compared with unstructured meshes, the structured meshes are favored in many scientific/engineering tasks due to their good properties. However, generating high-quality structured mesh remains challenging, especially for complex or large-scale …

Parallel Processes In Hpx: Designing An Infrastructure For Adaptive Resource Management, Vinay Chandra Amatya

LSU Doctoral Dissertations

Advancement in cutting edge technologies have enabled better energy efficiency as well as scaling computational power for the latest High Performance Computing(HPC) systems. However, complexity, due to hybrid architectures as well as emerging classes of applications, have shown poor computational scalability using conventional execution models. Thus alternative means of computation, that addresses the bottlenecks in computation, is warranted. More precisely, dynamic adaptive resource management feature, both from systems as well as application's perspective, is essential for better computational scalability and efficiency. This research presents and expands the notion of Parallel Processes as a placeholder for procedure definitions, targeted at one …

A Persistent Storage Model For Extreme Computing, Shuangyang Yang

LSU Doctoral Dissertations

The continuing technological progress resulted in a dramatic growth in aggregate computational performance of the largest supercomputing systems. Unfortunately, these advances did not translate to the required extent into accompanying I/O systems and little more in terms of architecture or effective access latency. New classes of algorithms developed for massively parallel applications, that gracefully handle the challenges of asynchrony, heavily multi-threaded distributed codes, and message-driven computation, must be matched by similar advances in I/O methods and algorithms to produce a well performing and balanced supercomputing system. This dissertation proposes PXFS, a storage model for persistent objects inspired by the ParalleX …