Search results

Title: Distance preserving graphs
Creator: Zahedi, Emad
Date: 2017
Collection: Electronic Theses & Dissertations
Description: "The computational complexity of exploring distance properties of large graphs such as real-world social networks which consist of millions of nodes is extremely expensive. Recomputing distances in subgraphs of the original graph will add to the cost. One way to avoid this is to use subgraphs where the distance between any pair of vertices is the same as in the original graph. Such a subgraph is called isometric. A connected graph is distance preserving, for which we use the abbreviation dp,...
Show more"The computational complexity of exploring distance properties of large graphs such as real-world social networks which consist of millions of nodes is extremely expensive. Recomputing distances in subgraphs of the original graph will add to the cost. One way to avoid this is to use subgraphs where the distance between any pair of vertices is the same as in the original graph. Such a subgraph is called isometric. A connected graph is distance preserving, for which we use the abbreviation dp, if it has an isometric subgraph of every order. In this framework we study dp graphs from both the structural and algorithmic perspectives. First, we study the structural nature of dp graphs. This involves classifying graphs based on the dp property and the relation between dp graphs to other graph classes. Second, we study the recognition problem of dp graphs. We intend to develop efficient algorithms for finding isometric subgraphs as well as deciding whether a graph is dp or not."--Page ii.
Show less

Title: The evolutionary potential of populations on complex fitness landscapes
Creator: Bryson, David Michael
Date: 2012
Collection: Electronic Theses & Dissertations
Description: Evolution is a highly contingent process, where the quality of the solutions produced is affected by many factors. I explore and describe the contributions of three such aspects that influence overall evolutionary potential: the prior history of a population, the type and frequency of mutations that the organisms are subject to, and the composition of the underlying genetic hardware. I have systematically tested changes to a digital evolution system, Avida, measuring evolutionary potential in...
Show moreEvolution is a highly contingent process, where the quality of the solutions produced is affected by many factors. I explore and describe the contributions of three such aspects that influence overall evolutionary potential: the prior history of a population, the type and frequency of mutations that the organisms are subject to, and the composition of the underlying genetic hardware. I have systematically tested changes to a digital evolution system, Avida, measuring evolutionary potential in seven different computational environments ranging in complexity of the underlying fitness landscapes. I have examined trends and general principles that these measurements demonstrate and used my results to optimize the evolutionary potential of the system, broadly enhancing performance. The results of this work show that history and mutation rate play significant roles in evolutionary potential, but the final fitness levels of populations are remarkably stable to substantial changes in the genetic hardware and a broad range of mutation types.
Show less

Title: Fluid animation on deforming surface meshes
Creator: Wang, Xiaojun (Graduate of Michigan State University)
Date: 2017
Collection: Electronic Theses & Dissertations
Description: "We explore methods for visually plausible fluid simulation on deforming surfaces with inhomogeneous diffusion properties. While there are methods for fluid simulation on surfaces, not much research effort focused on the influence of the motion of underlying surface, in particular when it is not a rigid surface, such as knitted or woven textiles in motion. The complexity involved makes the simulation challenging to account for the non-inertial local frames typically used to describe the...
Show more"We explore methods for visually plausible fluid simulation on deforming surfaces with inhomogeneous diffusion properties. While there are methods for fluid simulation on surfaces, not much research effort focused on the influence of the motion of underlying surface, in particular when it is not a rigid surface, such as knitted or woven textiles in motion. The complexity involved makes the simulation challenging to account for the non-inertial local frames typically used to describe the motion and the anisotropic effects in diffusion, absorption, adsorption. Thus, our primary goal is to enable fast and stable method for such scenarios. First, in preparation of the material properties for the surface domain, we describe textiles with salient feature direction by bulk material property tensors in order to reduce the complexity, by employing 2D homogenization technique, which effectively turns microscale inhomogeneous properties into homogeneous properties in macroscale descriptions. We then use standard texture mapping techniques to map these tensors to triangles in the curved surface mesh, taking into account the alignment of each local tangent space with correct feature directions of the macroscale tensor. We show that this homogenization tool is intuitive, flexible and easily adjusted. Second, for efficient description of the deforming surface, we offer a new geometry representation for the surface with solely angles instead of vertex coordinates, to reduce storage for the motion of underlying surface. Since our simulation tool relies heavily on long sequences of 3D curved triangular meshes, it is worthwhile exploring such efficient representations to make our tool practical by reducing the memory access during real-time simulations as well as reducing the file sizes. Inspired by angle-based representations for tetrahedral meshes, we use spectral method to restore curved surface using both angles of the triangles and dihedral angles between adjacent triangles in the mesh. Moreover, in many surface deformation sequences, it is often sufficient to update the dihedral angles while keeping the triangle interior angles fixed. Third, we propose a framework for simulating various effects of fluid flowing on deforming surfaces. We directly applied our simulator on curved surface meshes instead of in parameter domains, whereas many existing simulation methods require a parameterization on the surface. We further demonstrate that fictitious forces induced by the surface motion can be added to the surface-based simulation at a small additional cost. These fictitious forces can be decomposed into different components. Only the rectilinear and Coriolis components are relevant to our choice of local frames. Other effects, such as diffusion, adsorption, absorption, and evaporation are also incorporated for realistic stain simulation. Finally, we explore the extraction of Lagrangian Coherent Structure (LCS), which is often referred to as the skeleton of fluid motion. The LCS structures are often described by ridges of the finite time Lyapunov exponent (FTLE) fields, which describe the extremal stretching of fluid parcels following the flow. We proposed a novel improvement to the ridge marching algorithm, which extract such ridges robustly for the typically noisy FTLE estimates even in well-defined fluid flows. Our results are potentially applicable to visualizing and controlling fluid trajectory patterns. In contrast to current methods for LCS calculation, which are only applicable to flat 2D or 3D domains and sensitive to noise, our ridge extraction is readily applicable to curved surfaces even when they are deforming. The collection of these computational tools will facilitate generation of realistic and easy to adjust surface fluid animation with various physically plausible effects on surface."--Pages ii-iii.
Show less

Title: Signal processing and machine learning approaches to enabling advanced sensing and networking capabilities in everyday infrastructure and electronics
Creator: Ali, Kamran (Scientist)
Date: 2020
Collection: Electronic Theses & Dissertations
Description: Mainstream commercial off-the-shelf (COTS) electronic devices of daily use are usually designed and manufactured to serve a very specific purpose. For example, the WiFi routers and network interface cards (NICs) are designed for high speed wireless communication, RFID readers and tags are designed to identify and track items in supply chain, and smartphone vibrator motors are designed to provide haptic feedback (e.g. notifications in silent mode) to the users. This dissertation focuses on...
Show moreMainstream commercial off-the-shelf (COTS) electronic devices of daily use are usually designed and manufactured to serve a very specific purpose. For example, the WiFi routers and network interface cards (NICs) are designed for high speed wireless communication, RFID readers and tags are designed to identify and track items in supply chain, and smartphone vibrator motors are designed to provide haptic feedback (e.g. notifications in silent mode) to the users. This dissertation focuses on revisiting the physical-layer of various such everyday COTS electronic devices, either to leverage the signals obtained from their physical layers to develop novel sensing applications, or to modify/improve their PHY/MAC layer protocols to enable even more useful deployment scenarios and networking applications - while keeping their original purpose intact - by introducing mere software/firmware level changes and completely avoiding any hardware level changes. Adding such new usefulness and functionalities to existing everyday infrastructure and electronics has advantages both in terms of cost and convenience of use/deployment, as those devices (and their protocols) are already mainstream, easily available, and often already purchased and in use/deployed to serve their mainstream purpose of use.In our works on WiFi signals based sensing, we propose signal processing and machine learning approaches to enable fine-grained gesture recognition and sleep monitoring using COTS WiFi devices. In our work on gesture recognition, we show for the first time thatWiFi signals can be used to recognize small gestures with high accuracy. In our work on sleep monitoring, we propose for the first time aWiFi CSI based sleep quality monitoring scheme which can robustly track breathing and body/limb activity related vital signs during sleep throughout a night in an individual and environment independent manner.In our work on RFID signals based sensing, we propose signal processing and machine learning approaches to effectively image customer activity in front of display items in places such as retail stores using commercial off-the-shelf (COTS) monostatic RFID devices (i.e. which use a single antenna at a time for both transmitting and receiving RFID signals to and from the tags). The key novelty of this work is on achieving multi-person activity tracking in front of display items by constructing coarse grained images via robust, analytical model-driven deep learning based, RFID imaging. We implemented our scheme using a COTS RFID reader and tags.In our work on smartphone's vibration based sensing, we propose a robust and practical vibration based sensing scheme that works with smartphones with different hardware, can extract fine-grained vibration signatures of different surfaces, and is robust to environmental noise and hardware based irregularities. A useful application of this sensing is symbolic localization/tagging, e.g. figuring out whether a user's device is in their hand, pocket, or at their bedroom table, etc. Such symbolic tagging of locations can provide us with indirect information about user activities and intentions without any dedicated infrastructure, based on which we can enable useful services such as context aware notifications/alarms. To make our scheme easily scalable and compatible with COTS smartphones, we design our signal processing and machine learning pipeline such that it relies only on builtin vibration motors and microphone for sensing, and it is robust to hardware irregularities and background environmental noises. We tested our scheme on two different Android smartphones.In our work on powerline communications (PLCs), we propose a distributed spectrum sharing scheme for enterprise level PLC mesh networks. This work is a major step towards using existing COTS PLC devices to connect different types of Internet of Things (IoT) devices for sensing and control related applications in large campuses such as enterprises. Our work is based on identification of a key weakness of the existing HomePlug AV (HPAV) PLC protocol that it does not support spectrum sharing, i.e., currently each link operates over the whole available spectrum, and therefore, only one link can operate at a time. Our proposed spectrum sharing scheme significantly boosts both aggregated and per-link throughputs, by allowing multiple links to communicate concurrently, while requiring a few modifications to the existing HPAV protocol.
Show less

Title: Metamodeling framework for simultaneous multi-objective optimization using efficient evolutionary algorithms
Creator: Roy, Proteek Chandan
Date: 2019
Collection: Electronic Theses & Dissertations
Description: Most real-world problems are comprised of multiple conflicting objectives and solutions to those problems are multiple Pareto-optimal trade-off solutions. The main challenge of these practical problems is that the objectives and constraints do not have any closed functional forms and they are expensive for computation as well. Objectives coming from finite element analysis, computational fluid dynamics software, network flow simulators, crop modeling, weather modeling or any other simulations...
Show moreMost real-world problems are comprised of multiple conflicting objectives and solutions to those problems are multiple Pareto-optimal trade-off solutions. The main challenge of these practical problems is that the objectives and constraints do not have any closed functional forms and they are expensive for computation as well. Objectives coming from finite element analysis, computational fluid dynamics software, network flow simulators, crop modeling, weather modeling or any other simulations which involve partial differential equations are good examples of expensive problems. These problems can also be regarded as l03000300ow-budget'' problems since only a few solution evaluations can be performed given limited time. Nevertheless, parameter estimation and optimization of objectives related to these simulations require a good number of solution evaluations to come up with better parameters or a reasonably good trade-off front. To provide an efficient search process within a limited number of exact evaluations, metamodel-assisted algorithms have been proposed in the literature. These algorithms attempt to construct a computationally inexpensive representative model of the problem, having the same global optima and thereby providing a way to carry out the optimization in metamodel space in an efficient way. Population-based methods like evolutionary algorithms have become standard for solving multi-objective problems and recently Metamodel-based evolutionary algorithms are being used for solving expensive problems. In this thesis, we would like to address a few challenges of metamodel-based optimization algorithms and propose some efficient and innovative ways to construct these algorithms. To approach efficient design of metamodel-based optimization algorithm, one needs to address the choice of metamodeling functions. The most trivial way is to build metamodels for each objective and constraint separately. But we can reduce the number of metamodel constructions by using some aggregated functions and target either single or multiple optima in each step. We propose a taxonomy of possible metamodel-based algorithmic frameworks which not only includes most algorithms from the literature but also suggests some new ones. We improve each of the frameworks by introducing trust region concepts in the multi-objective scenario and present two strategies for building trust regions. Apart from addressing the main bottleneck of the limited number of solution evaluations, we also propose efficient non-dominated sorting methods that further reduce computational time for a basic step of multi-objective optimization. We have carried out extensive experiments over all representative metamodeling frameworks and shown that each of them can solve a good number of test problems. We have not tried to tune the algorithmic parameters yet and it remains as our future work. Our theoretical analyses and extensive experiments suggest that we can achieve efficient metamodel-based multi-objective optimization algorithms for solving test as well as real-world expensive and low-budget problems.
Show less

Title: Secure and efficient spectrum sharing and QoS analysis in OFDM-based heterogeneous wireless networks
Creator: Alahmadi, Ahmed S.
Date: 2016
Collection: Electronic Theses & Dissertations
Description: "The Internet of Things (IoT), which networks versatile devices for information exchange, remote sensing, monitoring and control, is finding promising applications in nearly every field. However, due to its high density and enormous spectrum requirement, the practical development of IoT technology seems to be not available until the release of the large millimeter wave (mmWave) band (30GHz-300GHz). Compared to existing lower band systems (such as 3G, 4G), mmWave band signals generally require...
Show more"The Internet of Things (IoT), which networks versatile devices for information exchange, remote sensing, monitoring and control, is finding promising applications in nearly every field. However, due to its high density and enormous spectrum requirement, the practical development of IoT technology seems to be not available until the release of the large millimeter wave (mmWave) band (30GHz-300GHz). Compared to existing lower band systems (such as 3G, 4G), mmWave band signals generally require line of sight (LOS) path and suffer from severe fading effects, leading to much smaller coverage area. For network design and management, this implies that: (i) MmWave band alone could not support the IoT networks, but has to be integrated with the existing lower band systems through secure and effective spectrum sharing, especially in the lower frequency bands; and (ii) The IoT networks will have very high density node distribution, which is a significant challenge in network design, especially with the scarce energy budget of IoT applications. Motivated by these observations, in this dissertation, we consider three problems: (1) How to achieve secure and effective spectrum sharing? (2) How to accommodate the energy limited IoT devices? (3) How to evaluate the Quality of Service (QoS) in the high density IoT networks? We aim to develop innovative techniques for the design, evaluation and management of future IoT networks under both benign and hostile environments. The main contributions of this dissertation are outlined as follows. First, we develop a secure and efficient spectrum sharing scheme in single-carrier wireless networks. Cognitive radio (CR) is a key enabling technology for spectrum sharing, where the unoccupied spectrum is identified for secondary users (SUs), without interfering with the primary user (PU). A serious security threat to the CR networks is referred to as primary user emulation attack (PUEA), in which a malicious user (MU) emulates the signal characteristics of the PU, thereby causing the SUs to erroneously identify the attacker as the PU. Here, we consider full-band PUEA detection and propose a reliable AES-assisted DTV scheme, where an AES-encrypted reference signal is generated at the DTV transmitter and used as the sync bits of the DTV data frames. For PU detection, we investigate the cross-correlation between the received sequence and reference sequence. The MU detection can be performed by investigating the auto-correlation of the received sequence. We further develop a secure and efficient spectrum sharing scheme in multi-carrier wireless networks. We consider sub-band malicious user detection and propose a secure AES-based DTV scheme, where the existing reference sequence used to generate the pilot symbols in the DVB-T2 frames is encrypted using the AES algorithm. The resulted sequence is exploited for accurate detection of the authorized PU and the MU. Second, we develop an energy efficient transmission scheme in CR networks using energy harvesting. We propose a transmitting scheme for the SUs such that each SU can perform information reception and energy harvesting simultaneously. We perform sum-rate optimization for the SUs under PUEA. It is observed that the sum-rate of the SU network can be improved significantly with the energy harvesting technique. Potentially, the proposed scheme can be applied directly to the energy-constrained IoT networks. Finally, we investigate QoS performance analysis methodologies, which can provide insightful feedbacks to IoT network design and planning. Taking the spatial randomness of the IoT network into consideration, we investigate coverage probability (CP) and blocking probability (BP) in relay-assisted OFDMA networks using stochastic geometry. More specifically, we model the inter-cell interference from the neighboring cells at each typical node, and derive the CP in the downlink transmissions. Based on their data rate requirements, we classify the incoming users into different classes, and calculate the BP using the multi-dimensional loss model."--Pages ii-iii.
Show less

Title: Hidden Markov model-based homology search and gene prediction in NGS ERA
Creator: Techa-angkoon, Prapaporn
Date: 2017
Collection: Electronic Theses & Dissertations
Description: The exponential cost reduction of next-generation sequencing (NGS) enabled researchers to sequence a large number of organisms in order to answer various questions in biology, ecology, health, etc. For newly sequenced genomes, gene prediction and homology search against characterized protein sequence databases are two fundamental tasks for annotating functional elements in the genomes. The main goal of gene prediction is to identify the gene locus and their structures. As there is...
Show moreThe exponential cost reduction of next-generation sequencing (NGS) enabled researchers to sequence a large number of organisms in order to answer various questions in biology, ecology, health, etc. For newly sequenced genomes, gene prediction and homology search against characterized protein sequence databases are two fundamental tasks for annotating functional elements in the genomes. The main goal of gene prediction is to identify the gene locus and their structures. As there is accumulating evidence showing important functions of RNAs (ncRNAs), comprehensive gene prediction should include both protein-coding genes and ncRNAs. Homology search against protein sequences can aid identification of functional elements in genomes. Although there are intensive research in the fields of gene prediction, ncRNA search, and homology search, there are still unaddressed challenges. In this dissertation, I made contributions in these three areas. For gene prediction, I designed an HMM-based ab initio gene prediction tool that considers G+C gradient in grass genomes. For homology search, I designed a method that can align short reads against protein families using profile HMMs. For ncRNA search, I designed a ncRNA alignment tool that can align highly structured ncRNAs using only sequence similarity. Below I summarize my contributions.Despite decades of research about gene prediction, existing gene prediction tools are not carefully designed to deal with variant G+C content and 5'-3' changing patterns inside coding regions. Thus, these tools can miss genes with positive or negative G+C gradient in grass genomes such as rice, maize, sorghum, etc. I implemented a tool named AUGUSTUS-GC that accounts for 5'-3' G+C gradient. Our tool can accurately predict protein-coding genes in plant genomes especially grass genomes.A large number of sequencing projects produced short reads from the whole genomes or transcriptomic data. I designed a short reads homology search tool that employs paired-end reads to improve homology search sensitivity. The experimental results show that our tool can achieve significantly better sensitivity and accuracy in aligning short reads that are part of remote homologs.Despite the extensive studies of ncRNA search, the existing tools that heavily depend on the secondary structure in homology search cannot efficiently handle RNA-seq data that is accumulating rapidly. It will be ideal if we can have a faster ncRNA homology search tool with similar accuracy as those adopting secondary structure. I implemented an accurate ncRNA alignment tool called glu-RNA that can achieve similar accuracy to structural alignment tools while keeping the same running time complexity as sequence alignment tools. The experimental results demonstrate that our tool can achieve more accurate alignments than the popular sequence alignment tools and a well-known structural alignment program.
Show less

Title: Scheduling for CPU Packing and node shutdown to reduce the energy consumption of high performance computing centers
Creator: Vudayagiri, Srikanth Phani
Date: 2010
Collection: Electronic Theses & Dissertations
Description: During the past decade, there has been a tremendous growth in the high performance computing and data center arenas. The huge energy requirements in these sectors have prompted researchers to investigate possible ways to reduce their energy consumption. Reducing the energy consumption is not only beneficial to an organization economically but also to the environment. In this thesis, we focus our attention on high performance scientific computing clusters. We first perform experiments with the...
Show moreDuring the past decade, there has been a tremendous growth in the high performance computing and data center arenas. The huge energy requirements in these sectors have prompted researchers to investigate possible ways to reduce their energy consumption. Reducing the energy consumption is not only beneficial to an organization economically but also to the environment. In this thesis, we focus our attention on high performance scientific computing clusters. We first perform experiments with the CPU Packing feature available in Linux using programs from the SPEC CPU2000 suite. We then look at an energy-aware scheduling algorithm for the cluster that assumes that CPU Packing is enabled on all the nodes. Using simulations, we compare the scheduling done by this algorithm to that done by the existing, commercial Moab scheduler in the cluster. We experiment with the Moab Green Computing feature and based on our observations, we implement the shutdown mechanism used by Moab in our simulations. Our results show that Moab Green Computing could provide about an 13% energy savings on average for the HPC cluster without any noticeable decrease in the performance of jobs.
Show less

Title: Using Eventual Consistency to Improve the Performance of Distributed Graph Computation In Key-Value Stores
Creator: Nguyen, Duong Ngoc
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Key-value stores have gained increasing popularity due to their fast performance and simple data model. A key-value store usually consists of multiple replicas located in different geographical regions to provide higher availability and fault tolerance. Consequently, a protocol is employed to ensure that data are consistent across the replicas.The CAP theorem states the impossibility of simultaneously achieving three desirable properties in a distributed system, namely consistency,...
Show moreKey-value stores have gained increasing popularity due to their fast performance and simple data model. A key-value store usually consists of multiple replicas located in different geographical regions to provide higher availability and fault tolerance. Consequently, a protocol is employed to ensure that data are consistent across the replicas.The CAP theorem states the impossibility of simultaneously achieving three desirable properties in a distributed system, namely consistency, availability, and network partition tolerance. Since failures are a norm in distributed systems and the capability to maintain the service at an acceptable level in the presence of failures is a critical dependability and business requirement of any system, the partition tolerance property is a necessity. Consequently, the trade-off between consistency and availability (performance) is inevitable. Strong consistency is attained at the cost of slow performance and fast performance is attained at the cost of weak consistency, resulting in a spectrum of consistency models suitable for different needs. Among the consistency models, sequential consistency and eventual consistency are two common ones. The former is easier to program with but suffers from poor performance whereas the latter suffers from potential data anomalies while providing higher performance.In this dissertation, we focus on the problem of what a designer should do if he/she is asked to solve a problem on a key-value store that provides eventual consistency. Specifically, we are interested in the approaches that allow the designer to run his/her applications on an eventually consistent key-value store and handle data anomalies if they occur during the computation. To that end, we investigate two options: (1) Using detect-rollback approach, and (2) Using stabilization approach. In the first option, the designer identifies a correctness predicate, say $\Phi$, and continues to run the application as if it was running on sequential consistency, as our system monitors $\Phi$. If $\Phi$ is violated (because the underlying key-value store provides eventual consistency), the system rolls back to a state where $\Phi$ holds and the computation is resumed from there. In the second option, the data anomalies are treated as state perturbations and handled by the convergence property of stabilizing algorithms.We choose LinkedIn's Voldemort key-value store as the example key-value store for our study. We run experiments with several graph-based applications on Amazon AWS platform to evaluate the benefits of the two approaches. From the experiment results, we observe that overall, both approaches provide benefits to the applications when compared to running the applications on sequential consistency. However, stabilization provides higher benefits, especially in the aggressive stabilization mode which trades more perturbations for no locking overhead.The results suggest that while there is some cost associated with making an algorithm stabilizing, there may be a substantial benefit in revising an existing algorithm for the problem at hand to make it stabilizing and reduce the overall runtime under eventual consistency.There are several directions of extension. For the detect-rollback approach, we are working to develop a more general rollback mechanism for the applications and improve the efficiency and accuracy of the monitors. For the stabilization approach, we are working to develop an analytical model for the benefits of eventual consistency in stabilizing programs. Our current work focuses on silent stabilization and we plan to extend our approach to other variations of stabilization.
Show less

Title: Achieving reliable distributed systems : through efficient run-time monitoring and predicate detection
Creator: Tekken Valapil, Vidhya
Date: 2020
Collection: Electronic Theses & Dissertations
Description: Runtime monitoring of distributed systems to perform predicate detection is critical as well as a challenging task. It is critical because it ensures the reliability of the system by detecting all possible violations of system requirements. It is challenging because to guarantee lack of violations one has to analyze every possible ordering of system events and this is an expensive task. In this report, wefocus on ordering events in a system run using HLC (Hybrid Logical Clocks) timestamps,...
Show moreRuntime monitoring of distributed systems to perform predicate detection is critical as well as a challenging task. It is critical because it ensures the reliability of the system by detecting all possible violations of system requirements. It is challenging because to guarantee lack of violations one has to analyze every possible ordering of system events and this is an expensive task. In this report, wefocus on ordering events in a system run using HLC (Hybrid Logical Clocks) timestamps, which are O(1) sized timestamps, and present some efficient algorithms to perform predicate detection using HLC. Since, with HLC, the runtime monitor cannot find all possible orderings of systems events, we present a new type of clock called Biased Hybrid Logical Clocks (BHLC), that are capable of finding more possible orderings than HLC. Thus we show that BHLC based predicate detection can find more violations than HLC based predicate detection. Since predicate detection based on both HLC and BHLC do not guarantee detection of all possible violations in a system run, we present an SMT (Satisfiability Modulo Theories) solver based predicate detection approach, that guarantees the detection of all possible violations in a system run. While a runtime monitor that performs predicate detection using SMT solvers is accurate, the time taken by the solver to detect the presence or absence of a violation can be high. To reduce the time taken by the runtime monitor, we propose the use of an efficient two-layered monitoring approach, where the first layer of the monitor is efficient but less accurate and the second layer is accurate but less efficient. Together they reduce the overall time taken to perform predicate detection drastically and also guarantee detection of all possible violations.
Show less

Title: A study of Bluetooth Frequency Hopping sequence : modeling and a practical attack
Creator: Albazrqaoe, Wahhab
Date: 2011
Collection: Electronic Theses & Dissertations
Description: The Bluetooth is a wireless interface that enables electronic devices to establish short-range, ad-hoc wireless connections. This kind of short-range wireless networking is known as Wireless Personal Area Networks (WPAN). Because of its attractive features of small size, low cost, and low power, Bluetooth gains a world wide usage. It is embedded in many portable computing devices and considered as a good replacement for local wire connections. Since wireless data is inherently exposed to...
Show moreThe Bluetooth is a wireless interface that enables electronic devices to establish short-range, ad-hoc wireless connections. This kind of short-range wireless networking is known as Wireless Personal Area Networks (WPAN). Because of its attractive features of small size, low cost, and low power, Bluetooth gains a world wide usage. It is embedded in many portable computing devices and considered as a good replacement for local wire connections. Since wireless data is inherently exposed to eavesdropping, the security and confidentiality is a central issue for wireless standard as well as Bluetooth. To maintain security and confidentiality of wireless packets, the Bluetooth system mainly relies on the Frequency Hopping mechanism to equivocate an adversary. By this technique, a wireless channel is accessed for transmitting a packet. For each wireless packet, a single channel is selected in a pseudo random way. This kind of randomness in channel selection makes it difficult for an eavesdropped to predict the next channel to be accessed. Hence, capturing Bluetooth wireless packets is a challenge. In this work, we investigate the Frequency Hopping sequence and specifically the hop selection kernel. We analyze the operation of the kernel hardware by partitioning it into three parts. Based on this modeling, we propose an attacking method for the hop selection kernel. The proposed method shows how to expose the clock value hidden in the kernel. This helps to predict Bluetooth hopping sequence and, hence, capturing Bluetooth wireless packet is possible.
Show less

Title: Consistency for distributed data stores
Creator: Roohitavaf, Mohammad
Date: 2019
Collection: Electronic Theses & Dissertations
Description: Geo-replicated data stores are one of the integral parts of today's Internet services. Service providers usually replicate their data on different data centers worldwide to achieve higher performance and data durability. However, when we use this approach, the consistency between replicas becomes a concern. At the highest level of consistency, we want strong consistency that provides the illusion of having only a single copy of the data. However, strong consistency comes with high performance...
Show moreGeo-replicated data stores are one of the integral parts of today's Internet services. Service providers usually replicate their data on different data centers worldwide to achieve higher performance and data durability. However, when we use this approach, the consistency between replicas becomes a concern. At the highest level of consistency, we want strong consistency that provides the illusion of having only a single copy of the data. However, strong consistency comes with high performance and availability costs. In this work, we focus on weaker consistency models that allow us to provide high performance and availability while preventing certain inconsistencies. Session guarantees (aka. client-centric consistency models) are one of such weaker consistency models that prevent some of the inconsistencies from occurring in a client session. We provide modified versions of session guarantees that, unlike traditional session guarantees, do not cause the problem of slowdown cascade for partitioned systems. We present a protocol to provide session guarantees for eBay NuKV that is a key-value store designed for eBay's internal services with high performance and availability requirements. We utilize Hybrid Logical Clocks (HLCs) to provide wait-free write operations while providing session guarantees. Our experiments, done on eBay cloud platform, show our protocol does not cause significant overhead compared with eventual consistency. In addition to session guarantees, a large portion of this dissertation is dedicated to causal consistency. Causal consistency is especially interesting as it is has been proved to be the strongest consistency model that allows the system to be available even during network partitions. We provide CausalSpartanX protocol that, using HLCs, improves current time-based protocols by eliminating the effect of clock anomalies such as clock skew between servers. CausalSpartanX also supports non-blocking causally consistent read-only transactions that allow applications to read a set of values that are causally consistent with each other. Read-only transactions provide a powerful abstraction that is impossible to be replaced by a set of basic read operations. CausalSpartanX, like other causal consistency protocols, assumes sticky clients (i.e. clients that never change the replica that they access). We prove if one wants immediate visibility for local updates in a data center, clients have to be sticky. Based on the structure of CausalSpartanX, we provide our Adaptive Causal Consistency Framework (ACCF) that is a configurable framework that generalizes current consistency protocols. ACCF provides a basis for designing adaptive protocols that can constantly monitor the system and clients' usage pattern and change themselves to provide better performance and availability. Finally, we present our Distributed Key-Value Framework (DKVF), a framework for rapid prototyping and benchmarking consistency protocols. DKVF lets protocol designers only focus on their high-level protocols, delegating all lower level communication and storage tasks to the framework.
Show less

Title: Automated addition of fault-tolerance via lazy repair and graceful degradation
Creator: Lin, Yiyan
Date: 2015
Collection: Electronic Theses & Dissertations
Description: In this dissertation, we concentrate on the problem of automated addition of fault-tolerance that transforms a fault-intolerant program to be a fault-tolerant program. We solve this problem via model repair. Model repair is a correct-by-construct technique to revise an existing model so that the revised model satisfies the given correctness criteria, such as safety, liveness, or fault-tolerance. We consider two problems of using model repair to add fault-tolerance. First, if the repaired...
Show moreIn this dissertation, we concentrate on the problem of automated addition of fault-tolerance that transforms a fault-intolerant program to be a fault-tolerant program. We solve this problem via model repair. Model repair is a correct-by-construct technique to revise an existing model so that the revised model satisfies the given correctness criteria, such as safety, liveness, or fault-tolerance. We consider two problems of using model repair to add fault-tolerance. First, if the repaired model violates the assumptions (e.g., partial observability, inability to detect crashed processes, etc) made in the underlying system, then it cannot be implemented. We denote these requirements as realizability constraints. Second, the addition of fault-tolerance may fail if the program cannot fully recover after certain faults occur. In this dissertation, we propose a lazy repair approach to address realizability issues in adding fault-tolerance. Additionally, we propose a technique to automatically add graceful degradation to a program, so that the program can recover with partial functionality (that is identified by the designer to be the critical functionality) if full recovery is impossible.A model repair technique transforms a model to another model that satisfies a new set of properties. Such a transformation should also maintain the mapping between the model and the underlying program. For example, in a distributed program, every process is restricted to read (or write) some variables in other processes. A model that represents this program should also disallow the process to read (or write) those inaccessable variables. If these constraints are violated, then the corresponding model will be unrealizable. An unrealizable model (in this context, a model that violates the read/write restrictions) may make it impossible to obtain the corresponding implementation.%In this dissertation, we call the read (or write) restriction as a realizability constraint in distributed systems. An unrealizable model (a model that violates the realizability constraints) may complicate the implementation by introducing extra amount of modification to the program. Such modification may in turn break the program's correctness.Resolving realizability constraints increases the complexity of model repair. Existing model repair techniques introduce heuristics to reduce the complexity. However, this heuristic-based approach is designed and optimized specifically for distributed programs. We need a more generic model repair approach for other types of programs, e.g., synchronous programs, cyber-physical programs, etc. Hence, in this dissertation, we propose a model repair technique, i.e., lazy repair, to add fault-tolerance to programs with different types of realizability constraints. It involves two steps. First, we only focus on repairing to obtain a model that satisfies correctness criteria while ignoring realizability constraints. In the second step, we repair this model further by removing behaviors while ensuring that the desired specification is preserved. The lazy repair approach simplifies the process of developing heuristics, and provides a tradeoff in terms of the time saved in the first step and the extra work required in the second step. We demonstrate that lazy repair is applicable in the context of distributed systems, synchronous systems and cyber-physical systems.In addition, safety critical systems such as airplanes, automobiles and elevators should operate with high dependability in the presence of faults. If the occurrence of faults breaks down some components, the system may not be able to fully recover. In this scenario, the system can still operate with remaining resources and deliver partial but core functionality, i.e., to display graceful degradation. Existing model repair approaches, such as addition of fault-tolerance, cannot transform a program to provide graceful degradation. In this dissertation, we propose a technique to add fault-tolerance to a program with graceful degradation. In the absence of faults, such a program exhibits ideal behaviors. In the presence of faults, the program is allowed to recover with reduced functionality. This technique involves two steps. First, it automatically generates a program with graceful degradation based on the input fault-intolerant program. Second, it adds fault-tolerance to the output program from first step. We demonstrate that this technique is applicable in the context of high atomicity programs as well as low atomicity programs (i.e., distributed programs). We also present a case study on adding multi-graceful degradation to a dangerous gas detection and ventilation system. Through this case study, we show that our approach can assist the designer to obtain a program that behaves like the deployed system.
Show less

Title: Computational identification and analysis of non-coding RNAs in large-scale biological data
Creator: Lei, Jikai
Date: 2015
Collection: Electronic Theses & Dissertations
Description: Non-protein-coding RNAs (ncRNAs) are RNA molecules that function directly at the level of RNA without translating into protein. They play important biological functions in all three domains of life, i.e. Eukarya, Bacteria and Archaea. To understand the working mechanisms and the functions of ncRNAs in various species, a fundamental step is to identify both known and novel ncRNAs from large-scale biological data.Large-scale genomic data includes both genomic sequence data and NGS sequencing...
Show moreNon-protein-coding RNAs (ncRNAs) are RNA molecules that function directly at the level of RNA without translating into protein. They play important biological functions in all three domains of life, i.e. Eukarya, Bacteria and Archaea. To understand the working mechanisms and the functions of ncRNAs in various species, a fundamental step is to identify both known and novel ncRNAs from large-scale biological data.Large-scale genomic data includes both genomic sequence data and NGS sequencing data. Both types of genomic data provide great opportunity for identifying ncRNAs. For genomic sequence data, a lot of ncRNA identification tools that use comparative sequence analysis have been developed. These methods work well for ncRNAs that have strong sequence similarity. However, they are not well-suited for detecting ncRNAs that are remotely homologous. Next generation sequencing (NGS), while it opens a new horizon for annotating and understanding known and novel ncRNAs, also introduces many challenges. First, existing genomic sequence searching tools can not be readily applied to NGS data because NGS technology produces short, fragmentary reads. Second, most NGS data sets are large-scale. Existing algorithms are infeasible on NGS data because of high resource requirements. Third, metagenomic sequencing, which utilizes NGS technology to sequence uncultured, complex microbial communities directly from their natural inhabitants, further aggravates the difficulties. Thus, massive amount of genomic sequence data and NGS data calls for efficient algorithms and tools for ncRNA annotation.In this dissertation, I present three computational methods and tools to efficiently identify ncRNAs from large-scale biological data. Chain-RNA is a tool that combines both sequence similarity and structure similarity to locate cross-species conserved RNA elements with low sequence similarity in genomic sequence data. It can achieve significantly higher sensitivity in identifying remotely conserved ncRNA elements than sequence based methods such as BLAST, and is much faster than existing structural alignment tools. miR-PREFeR (miRNA PREdiction From small RNA-Seq data) utilizes expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples. It is sensitive, accurate, fast and has low-memory footprint. metaCRISPR focuses on identifying Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) from large-scale metagenomic sequencing data. It uses a kmer hash table to efficiently detect reads that belong to CRISPRs from the raw metagonmic data set. Overlap graph based clustering is then conducted on the reduced data set to separate different CRSIPRs. A set of graph based algorithms are used to assemble and recover CRISPRs from the clusters.
Show less

Title: Statistical and learning algorithms for the design, analysis, measurement, and modeling of networking and security systems
Creator: Shahzad, Muhammad (College teacher)
Date: 2015
Collection: Electronic Theses & Dissertations
Description: "The goal of this thesis is to develop statistical and learning algorithms for the design, analysis, measurement, and modeling of networking and security systems with specific focus on RFID systems, network performance metrics, user security, and software security. Next, I give a brief overview of these four areas of focus." -- Abstract.

Title: Near duplicate image search
Creator: Li, Fengjie
Date: 2014
Collection: Electronic Theses & Dissertations
Description: Information retrieval addresses the fundamental problem of how to identify the objects from database that satisfies the information needs of users. Facing the information overload, the major challenge in search algorithm design is to ensure that useful information can be found both accurately and efficiently from large databases.To address this challenge, different indexing and retrieval methods had been proposed for different types of data, namely sparse data (e.g. documents), dense data (e...
Show moreInformation retrieval addresses the fundamental problem of how to identify the objects from database that satisfies the information needs of users. Facing the information overload, the major challenge in search algorithm design is to ensure that useful information can be found both accurately and efficiently from large databases.To address this challenge, different indexing and retrieval methods had been proposed for different types of data, namely sparse data (e.g. documents), dense data (e.g. dense feature vectors) and bag-of-features (e.g. local feature represented images). For sparse data, inverted index and document retrieval models had been proved to be very effective for large scale retrieval problems. For dense data and bag-of-feature data, however, there are still some open problems. For example, Locality Sensitive Hashing, a state-of-the-art method for searching high dimensional vectors, often fails to make a good tradeoff between precision and recall. Namely, it tends to achieve high preci- sion but with low recall or vice versa. The bag-of-words model, a popular approach for searching objects represented bag-of-features, has a limited performance because of the information loss during the quantization procedure.Since the general problem of searching objects represented in dense vectors and bag-of-features may be too challenging, in this dissertation, we focus on nearly duplicate search, in which the matched objects is almost identical to the query. By effectively exploring the statistical proper- ties of near duplicities, we will be able to design more effective indexing schemes and search algorithms. Thus, the focus of this dissertation is to design new indexing methods and retrieval algorithms, for near duplicate search in large scale databases, that accurately capture the data simi- larity and delivers more accurate and efficient search. Below, we summarize the main contributions of this dissertation:Our first contribution is a new algorithm for searching near duplicate bag-of-features data. The proposed algorithm, named random seeding quantization, is more efficient in generating bag-of- words representations for near duplicate images. The new scheme is motivated by approximating the optimal partial matching between bag-of-features, and thus produces a bag-of-words representation capturing the true similarities of the data, leading to more accurate and efficient retrieval of bag-of-features data.Our second contribution, termed Random Projection Filtering, is a search algorithm designed for efficient near duplicate vector search. By explicitly exploiting the statistical properties of near duplicity, the algorithm projects high dimensional vectors into lower dimensional space and filter out irrelevant items. Our effective filtering procedure makes RPF more accurate and efficient to identify nearly duplicate objects in databases.Our third contribution is to develop and evaluate a new randomized range search algorithm for near duplicate vectors in high dimensional spaces, termed as Random Projection Search. Different from RPF, the algorithm presented in this chapter is suitable for a wider range of applications be- cause it does not require the sparsity constrains for high search accuracy. The key idea is to project both the data points and the query point into an one dimensional space by a random projection, and perform one dimensional range search to find the subset of data points that are within the range of a given query using binary search. We prove the theoretical guarantee for the proposed algorithm and evaluate its empirical performance on a dataset of 1.1 billion image features.
Show less

Title: Novel computational approaches to investigate microbial diversity
Creator: Zhang, Qingpeng
Date: 2015
Collection: Electronic Theses & Dissertations
Description: Species diversity is an important measurement of ecological communities.Scientists believe that there is a strong relationship between speciesdiversity and ecosystem processes. However efforts to investigate microbialdiversity using whole genome shotgun reads data are still scarce. With novel applications of data structuresand the development of novel algorithms, firstly we developed an efficient k-mer countingapproach and approaches to enable scalable streaming analysis of large and error...
Show moreSpecies diversity is an important measurement of ecological communities.Scientists believe that there is a strong relationship between speciesdiversity and ecosystem processes. However efforts to investigate microbialdiversity using whole genome shotgun reads data are still scarce. With novel applications of data structuresand the development of novel algorithms, firstly we developed an efficient k-mer countingapproach and approaches to enable scalable streaming analysis of large and error-prone short-read shotgun data sets. Then based on these efforts, we developed a statistical framework allowing for scalable diversity analysis of large,complex metagenomes without the need for assembly or reference sequences. Thismethod is evaluated on multiple large metagenomes from differentenvironments, such as seawater, human microbiome, soil. Given the velocity ingrowth of sequencing data, this method is promising for analyzing highlydiverse samples with relatively low computational requirements. Further, as themethod does not depend on reference genomes, it also provides opportunities totackle the large amounts of unknowns we find in metagenomicdatasets.
Show less

Title: Exploiting cross-technology interference for efficient network services in wireless systems
Creator: Zhou, Ruogu
Date: 2014
Collection: Electronic Theses & Dissertations
Description: In the last decade, we have witnessed the wide adoption of a variety of wireless technologies like WiFi, Cellular, Bluetooth, ZigBee, and Near-field Communication(NFC). However, the fast growth of wireless networks generates significant cross-technology interference, which leads to network performance degradation and potential security breach. In this dissertation, we propose two novel physical layer techniques to deal with the interference, and improve the performance and security of sensor...
Show moreIn the last decade, we have witnessed the wide adoption of a variety of wireless technologies like WiFi, Cellular, Bluetooth, ZigBee, and Near-field Communication(NFC). However, the fast growth of wireless networks generates significant cross-technology interference, which leads to network performance degradation and potential security breach. In this dissertation, we propose two novel physical layer techniques to deal with the interference, and improve the performance and security of sensor networks and mobile systems, respectively. First, we exploit the WiFi interference as a ``blessing" in the design of sensor networks and develop novel WiFi interference detection techniques for ZigBee sensors. Second, utilizing these techniques, we design three efficient network services: WiFi discovery which detects the existence of nearby WiFi networks using ZigBee sensors, WiFi performance monitoring which measures and tracks performance of WiFi networks using a ZigBee sensor network, and time synchronization which provides synchronized clocks for sensor networks based on WiFi signals. Third, we design a novel, noninvasive NFC security system called {\em nShield} to reduce the transmission power of NFC radios, which protects NFC against passive eavesdropping. nShield implements a novel adaptive RF attenuation scheme, in which the extra RF energy of NFC transmissions is determined and absorbed by nShield. At the same time, nShield scavenges the extra RF energy to sustain the perpetual operation. Together with the extremely lo-power design, it enables nShield to provide the host uninterrupted protection against malicious eavesdropping. The above systems are implemented and extensively evaluated on a testbed of sensor networks and smartphones.
Show less

Title: Geometric and topological modeling techniques for large and complex shapes
Creator: Feng, Xin
Date: 2014
Collection: Electronic Theses & Dissertations
Description: The past few decades have witnessed the incredible advancements in modeling, digitizing and visualizing techniques for three–dimensional shapes. Those advancements led to an explosion in the number of three–dimensional models being created for design, manufacture, architecture, medical imaging, etc. At the same time, the structure, function, stability, and dynamics of proteins, subcellular structures, organelles, and multiprotein complexes have emerged as a leading interest in...
Show moreThe past few decades have witnessed the incredible advancements in modeling, digitizing and visualizing techniques for three–dimensional shapes. Those advancements led to an explosion in the number of three–dimensional models being created for design, manufacture, architecture, medical imaging, etc. At the same time, the structure, function, stability, and dynamics of proteins, subcellular structures, organelles, and multiprotein complexes have emerged as a leading interest in structural biology, another major source of large and complex geometric models. Geometric modeling not only provides visualizations of shapes for large biomolecular complexes but also fills the gap between structural information and theoretical modeling, and enables the understanding of function, stability, and dynamics.We first propose, for tessellated volumes of arbitrary topology, a compact data structure that offers constant–time–complexity incidence queries among cells of any dimensions. Our data structure is simple to implement, easy to use, and allows for arbitrary, user–defined 3–cells such as prisms and hexahedra, while remaining highly efficient in memory usage compared to previous work. We also provide the analysis on its time complexity for commonly–used incidence and adjacency queries such as vertex and edge one–rings.We then introduce a suite of computational tools for volumetric data processing, information extraction, surface mesh rendering, geometric measurement, and curvature estimation for biomolecular complexes. Particular emphasis is given to the modeling of Electron Microscopy Data Bank (EMDB) data and Protein Data Bank (PDB) data. Lagrangian and Cartesian representations are discussed for the surface presentation. Based on these representations, practical algorithms are developed for surface area and surface–enclosed volume calculation, and curvature estimation. Methods for volumetric meshing have also been presented. Because the technological development in computer science and mathematics has led to a variety of choices at each stage of the geometric modeling, we discuss the rationales in the design and selection of various algorithms. Analytical test models are designed to verify the computational accuracy and convergence of proposed algorithms. We selected six EMDB data and six PDB data to demonstrate the efficacy of the proposed algorithms in handling biomolecular surfaces and explore their capability of geometric characterization of binding targets. Thus, our toolkit offers a comprehensive protocol for the geometric modeling of proteins, subcellular structures, organelles, and multiprotein complexes.Furthermore, we present a method for computing “choking” loops—a set of surface loops that describe the narrowing of the volumes inside/outside of the surface and extend the notion of surface homology and homotopy loops. The intuition behind their definition is that a choking loop represents the region where an offset of the original surface would get pinched. Our generalized loops naturally include the usual 2g handles/tunnels computed based on the topology of the genus–g surface, but also include loops that identify chokepoints or bottlenecks, i.e., boundaries of small membranes separating the inside or outside volume of the surface into disconnected regions. Our definition is based on persistent homology theory, which gives a measure to topological structures, thus providing resilience to noise and a well–defined way to determine topological feature size.Finally, we explore the application of persistent homology theory in protein folding analysis. The extremely complex process of protein folding brings challenges for both experimental study and theoretical modeling. The persistent homology approach studies the Euler characteristics of the protein conformations during the folding process. More precisely, the persistence is measured by the variation of van der Waals radius, which leads to the change of protein 3D structures and uncovers the inter–connectivity. Our results on fullerenes demonstrate the potential of our geometric and topological approach to protein stability analysis.
Show less

Title: Distance-preserving graphs
Creator: Nussbaum, Ronald
Date: 2014
Collection: Electronic Theses & Dissertations
Description: Let G be a simple graph on n vertices, where d_G(u,v) denotes the distance between vertices u and v in G. An induced subgraph H of G is isometric if d_H(u,v)=d_G(u,v) for all u,v in V(H). We say that G is a distance-preserving graph if G contains at least one isometric subgraph of order k for every k where 1<=k<=n.A number of sufficient conditions exist for a graph to be distance-preserving. We show that all hypercubes and graphs with delta(G)>=2n/3-1 are distance-preserving. Towards this end...
Show moreLet G be a simple graph on n vertices, where d_G(u,v) denotes the distance between vertices u and v in G. An induced subgraph H of G is isometric if d_H(u,v)=d_G(u,v) for all u,v in V(H). We say that G is a distance-preserving graph if G contains at least one isometric subgraph of order k for every k where 1<=k<=n.A number of sufficient conditions exist for a graph to be distance-preserving. We show that all hypercubes and graphs with delta(G)>=2n/3-1 are distance-preserving. Towards this end, we carefully examine the role of "forbidden" subgraphs. We discuss our observations, and provide some conjectures which we computationally verified for small values of n. We say that a distance-preserving graph is sequentially distance-preserving if each subgraph in the set of isometric subgraphs is a superset of the previous one, and consider this special case as well.There are a number of questions involving the construction of distance-preserving graphs. We show that it is always possible to add an edge to a non-complete sequentially distance-preserving graph such that the augmented graph is still sequentially distance-preserving. We further conjecture that the same is true of all distance-preserving graphs. We discuss our observations on making non-distance-preserving graphs into distance preserving ones via adding edges. We show methods for constructing regular distance-preserving graphs, and consider constructing distance-preserving graphs for arbitrary degree sequences. As before, all conjectures here have been computationally verified for small values of n.
Show less

MSU Libraries

Digital Repository

Enabled Filters

Pages

Pages

MSU Libraries

Digital Repository

You are here

Search results

Pages

Pages