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Title: High-precision and Personalized Wearable Sensing Systems for Healthcare Applications
Creator: Tu, Linlin
Date: 2022
Collection: Electronic Theses & Dissertations
Description: The cyber-physical system (CPS) has been discussed and studied extensively since 2010. It provides various solutions for monitoring the user's physical and psychological health states, enhancing the user's experience, and improving the lifestyle. A variety of mobile internet devices with built-in sensors, such as accelerators, cameras, PPG sensors, pressure sensors, and the microphone, can be leveraged to build mobile cyber-physical applications that collected sensing data from the real world...
Show moreThe cyber-physical system (CPS) has been discussed and studied extensively since 2010. It provides various solutions for monitoring the user's physical and psychological health states, enhancing the user's experience, and improving the lifestyle. A variety of mobile internet devices with built-in sensors, such as accelerators, cameras, PPG sensors, pressure sensors, and the microphone, can be leveraged to build mobile cyber-physical applications that collected sensing data from the real world, had data processed, communicated to the internet services and transformed into behavioral and physiological models. The detected results can be used as feedback to help the user understand his/her behavior, improve the lifestyle, or avoid danger. They can also be delivered to therapists to facilitate their diagnose. Designing CPS for health monitoring is challenging due to multiple factors. First of all, high estimation accuracy is necessary for health monitoring. However, some systems suffer irregular noise. For example, PPG sensors for cardiac health state monitoring are extremely vulnerable to motion noise. Second, to include human in the loop, health monitoring systems are required to be user-friendly. However, some systems involve cumbersome equipment for a long time of data collection, which is not feasible for daily monitoring. Most importantly, large-scale high-level health-related monitoring systems, such as the systems for human activity recognition, require high accuracy and communication efficiency. However, with users' raw data uploading to the server, centralized learning fails to protect users' private information and is communication-inefficient. The research introduced in this dissertation addressed the above three significant challenges in developing health-related monitoring systems. We build a lightweight system for accurate heart rate measurement during exercise, design a smart in-home breathing training system with bio-Feedback via virtual reality (VR) game, and propose federated learning via dynamic layer sharing for human activity recognition.
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Title: Variational Bayes inference of Ising models and their applications
Creator: Kim, Minwoo
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Ising models originated in statistical physics have been widely used in modeling spatialdata and computer vision problems. However, statistical inference of this model and its application to many practical fields remain challenging due to intractable nature of the normalizing constant in the likelihood. This dissertation consists of two main themes, (1) parameter estimation of Ising model and (2) structured variable selection based on the Ising model using variational Bayes (VB).In Chapter 1,...
Show moreIsing models originated in statistical physics have been widely used in modeling spatialdata and computer vision problems. However, statistical inference of this model and its application to many practical fields remain challenging due to intractable nature of the normalizing constant in the likelihood. This dissertation consists of two main themes, (1) parameter estimation of Ising model and (2) structured variable selection based on the Ising model using variational Bayes (VB).In Chapter 1, we review the background, research questions and development of Isingmodel, variational Bayes, and other statistical concepts. An Ising model basically deal with a binary random vector in which each component is dependent on its neighbors. There exist various versions of Ising model depending on parameterization and neighboring structure. In Chapter 2, with two-parameter Ising model, we describe a novel procedure for the pa- rameter estimation based on VB which is computationally efficient and accurate compared to existing methods. Traditional pseudo maximum likelihood estimate (PMLE) can pro- vide accurate results only for smaller number of neighbors. A Bayesian approach based on Markov chain Monte Carlo (MCMC) performs better even with a large number of neighbors. Computational costs of MCMC, however, are quite expensive in terms of time. Accordingly, we propose a VB method with two variational families, mean-field (MF) Gaussian family and bivariate normal (BN) family. Extensive simulation studies validate the efficacy of the families. Using our VB methods, computing times are remarkably decreased without dete- rioration in performance accuracy, or in some scenarios we get much more accurate output. In addition, we demonstrates theoretical properties of the proposed VB method under MF family. The main theoretical contribution of our work lies in establishing the consistency of the variational posterior for the Ising model with the true likelihood replaced by the pseudo- likelihood. Under certain conditions, we first derive the rates at which the true posterior based on the pseudo-likelihood concentrates around the εn- shrinking neighborhoods of the true parameters. With a suitable bound on the Kullback-Leibler distance between the true and the variational posterior, we next establish the rate of contraction for the variational pos- terior and demonstrate that the variational posterior also concentrates around εn-shrinking neighborhoods of the true parameter.In Chapter 3, we propose a Bayesian variable selection technique for a regression setupin which the regression coefficients hold structural dependency. We employ spike and slab priors on the regression coefficients as follows: (i) In order to capture the intrinsic structure, we first consider Ising prior on latent binary variables. If a latent variable takes one, the corresponding regression coefficient is active, otherwise, it is inactive. (ii) Employing spike and slab prior, we put Gaussian priors (slab) on the active coefficients and inactive coefficients will be zeros with probability one (spike).
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Title: Solving Computationally Expensive Problems Using Surrogate-Assisted Optimization : Methods and Applications
Creator: Blank, Julian
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Optimization is omnipresent in many research areas and has become a critical component across industries. However, while researchers often focus on a theoretical analysis or convergence proof of an optimization algorithm, practitioners face various other challenges in real-world applications. This thesis focuses on one of the biggest challenges when applying optimization in practice: computational expense, often caused by the necessity of calling a third-party software package. To address the...
Show moreOptimization is omnipresent in many research areas and has become a critical component across industries. However, while researchers often focus on a theoretical analysis or convergence proof of an optimization algorithm, practitioners face various other challenges in real-world applications. This thesis focuses on one of the biggest challenges when applying optimization in practice: computational expense, often caused by the necessity of calling a third-party software package. To address the time-consuming evaluation, we propose a generalizable probabilistic surrogate-assisted framework that dynamically incorporates predictions of approximation models. Besides the framework's capability of handling multiple objectives and constraints simultaneously, the novelty is its applicability to all kinds of metaheuristics. Moreover, often multiple disciplines are involved in optimization, resulting in different types of software packages utilized for performance assessment. Therefore, the resulting optimization problem typically consists of multiple independently evaluable objectives and constraints with varying computational expenses. Besides providing a taxonomy describing different ways of independent evaluation calls, this thesis also proposes a methodology to handle inexpensive constraints with expensive objective functions and a more generic concept for any type of heterogeneously expensive optimization problem. Furthermore, two case studies of real-world optimization problems from the automobile industry are discussed, a blueprint for solving optimization problems in practice is provided, and a widely-used optimization framework focusing on multi-objective optimization (founded and maintained by the author of this thesis) is presented. Altogether, this thesis shall pave the way to solve (computationally expensive) real-world optimization more efficiently and bridge the gap between theory and practice.
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Title: Towards Accurate Ranging and Versatile Authentication for Smart Mobile Devices
Creator: Li, Lingkun
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Internet of Things (IoTs) was rapidly developed during past years. Smart devices, such as smartphones, smartwatches, and smart assistants, which are equipped with smart chips as well as sensors, provide users with many easy used functions and lead them to a more convenient life. In this dissertation, we carefully studied the birefringence of the transparent tape, the nonlinear effects of the microphone, and the phase characteristic of the reflected ultrasound, and make use of such effects to...
Show moreInternet of Things (IoTs) was rapidly developed during past years. Smart devices, such as smartphones, smartwatches, and smart assistants, which are equipped with smart chips as well as sensors, provide users with many easy used functions and lead them to a more convenient life. In this dissertation, we carefully studied the birefringence of the transparent tape, the nonlinear effects of the microphone, and the phase characteristic of the reflected ultrasound, and make use of such effects to design three systems, RainbowLight, Patronus, and BreathPass, to provide users with accurate localization, privacy protection, and authentication, respectively.RainbowLight leverages observation direction-varied spectrum generated by a polarized light passing through a birefringence material, i.e., transparent tape, to provide localization service. We characterize the relationship between observe direction, light interference and the special spectrum, and using it to calculate the direction to a chip after taking a photo containing the chip. With multiple chips, RainbowLight designs a direction intersection based method to derive the location. In this dissertation, we build the theoretical basis of using polarized light and birefringence phenomenon to perform localization. Based on the theoretical model, we design and implement the RainbowLight on the mobile device, and evaluate the performance of the system. The evaluation results show that RainbowLight achieves 1.68 cm of the median error in the X-axis, 2 cm of the median error in the Y-axis, 5.74 cm of the median error in Z-axis, and 7.04 cm of the median error with the whole dimension.It is the first system that could only use the reflected lights in the space to perform visible light positioning. Patronus prevents unauthorized speech recording by leveraging the nonlinear effects of commercial off-the-shelf microphones. The inaudible ultrasound scramble interferes recording of unauthorized devices and can be canceled on authorized devices through an adaptive filter. In this dissertation, we carefully studied the nonlinear effects of ultrasound on commercial microphones. Based on the study, we proposed an optimized configuration to generate the scramble. It would provide privacy protection againist unauthorized recordings that does not disturb normal conversations. We designed, implemented a system including hardware and software components. Experiments results show that only 19.7% of words protected by Patronus' scramble can be recognized by unauthorized devices. Furthermore, authorized recordings have 1.6x higher perceptual evaluation of speech quality (PESQ) score and, on average, 50% lower speech recognition error rates than unauthorized recordings. BreathPass uses speakers to emit ultrasound signals. The signals are reflected off the chest wall and abdomen and then back to the microphone, which records the reflected signals. The system then extracts the fingerprints from the breathing pattern, and use these fingerprints to perform authentication. In this dissertation, we characterized the challenge of conducting authentication with the breathing pattern. After addressing these challenges, we designed such a system and implemented a proof-of-concept application on Android platform.We also conducted comprehensive experiments to evaluate the performance under different scenarios. BreathPass achieves an overall accuracy of 83%, a true positive rate of 73%, and a false positive rate of 5%, according to performance evaluation results. In general, this dissertation provides an enhanced ranging and versatile authentication systems of Internet of Things.
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Title: Investigating the Role of Sensor Based Technologies to Support Domestic Activities in Sub-Saharan Africa
Creator: Chidziwisano, George Hope
Date: 2022
Collection: Electronic Theses & Dissertations
Description: In sub-Saharan Africa (SSA), homes face various challenges including insecurity, unreliable power supply, and extreme weather conditions. While the use of sensor-based technologies is increasing in industrialized countries, it is unclear how they can be used to support domestic activities in SSA. The availability of low-cost sensors and the widespread adoption of mobile phones presents an opportunity to collect real-time data and utilize proactive methods to monitor these challenges. This...
Show moreIn sub-Saharan Africa (SSA), homes face various challenges including insecurity, unreliable power supply, and extreme weather conditions. While the use of sensor-based technologies is increasing in industrialized countries, it is unclear how they can be used to support domestic activities in SSA. The availability of low-cost sensors and the widespread adoption of mobile phones presents an opportunity to collect real-time data and utilize proactive methods to monitor these challenges. This dissertation presents three studies that build upon each other to explore the role of sensor-based technologies in SSA. I used a technology probes method to develop three sensor-based systems that support domestic security (M-Kulinda), power blackout monitoring (GridAlert) and poultry farming (NkhukuApp). I deployed M-Kulinda in 20 Kenyan homes, GridAlert in 18 Kenyan homes, and NkhukuProbe in 15 Malawian home-based chicken coops for one month. I used interview, observation, diary, and data logging methods to understand participants’ experiences using the probes. Findings from these studies suggest that people in Kenya and Malawi want to incorporate sensor-based technologies into their everyday activities, and they quickly find unexpected ways to use them. Participants’ interactions with the probes prompted detailed reflections about how they would integrate sensor-based technologies in their homes (e.g., monitoring non-digital tools). These reflections are useful for motivating new design concepts in HCI. I use these findings to motivate a discussion about unexplored areas that could benefit from sensor-based technologies. Further, I discuss recommendations for designing sensor-based technologies that support activities in some Kenyan and Malawian homes. This research contributes to HCI by providing design implications for sensor-based applications in Kenyan and Malawian homes, employing a technology probes method in a non-traditional context, and developing prototypes of three novel systems.
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Title: EFFICIENT AND PORTABLE SPARSE SOLVERS FOR HETEROGENEOUS HIGH PERFORMANCE COMPUTING SYSTEMS
Creator: Rabbi, Md Fazlay
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Sparse matrix computations arise in the form of the solution of systems of linear equations, matrix factorization, linear least-squares problems, and eigenvalue problems in numerous computational disciplines ranging from quantum many-body problems, computational fluid dynamics, machine learning and graph analytics. The scale of problems in these scientific applications typically necessitates execution on massively parallel architectures. Moreover, due to the irregular data access patterns and...
Show moreSparse matrix computations arise in the form of the solution of systems of linear equations, matrix factorization, linear least-squares problems, and eigenvalue problems in numerous computational disciplines ranging from quantum many-body problems, computational fluid dynamics, machine learning and graph analytics. The scale of problems in these scientific applications typically necessitates execution on massively parallel architectures. Moreover, due to the irregular data access patterns and low arithmetic intensities of sparse matrix computations, achieving high performance and scalability is very difficult. These challenges are further exacerbated by the increasingly complex deep memory hierarchies of the modern architectures as they typically integrate several layers of memory storage. Data movement is an important bottleneck against efficiency and energy consumption in large-scale sparse matrix computations. Minimizing data movement across layers of the memory and overlapping data movement with computations are keys to achieving high performance in sparse matrix computations. My thesis work contributes towards systematically identifying algorithmic challenges of the sparse solvers and providing optimized and high performing solutions for both shared memory architectures and heterogeneous architectures by minimizing data movements between different memory layers. For this purpose, we first introduce a shared memory task-parallel framework focusing on optimizing the entire solvers rather than a specific kernel. As most of the recent (or upcoming) supercomputers are equipped with Graphics Processing Unit (GPU), we decided to evaluate the efficacy of the directive-based programming models (i.e., OpenMP and OpenACC) in offloading computations on GPU to achieve performance portability. Being inspired by the promising results of this work, we port and optimize our shared memory task-parallel framework on GPU accelerated systems to execute problem sizes that exceed device memory.
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Title: Non-coding RNA identification in large-scale genomic data
Creator: Yuan, Cheng
Date: 2014
Collection: Electronic Theses & Dissertations
Description: Noncoding RNAs (ncRNAs), which function directly as RNAs without translating into proteins, play diverse and important biological functions. ncRNAs function not only through their primary structures, but also secondary structures, which are defined by interactions between Watson-Crick and wobble base pairs. Common types of ncRNA include microRNA, rRNA, snoRNA, tRNA. Functions of ncRNAs vary among different types. Recent studies suggest the existence of large number of ncRNA genes....
Show moreNoncoding RNAs (ncRNAs), which function directly as RNAs without translating into proteins, play diverse and important biological functions. ncRNAs function not only through their primary structures, but also secondary structures, which are defined by interactions between Watson-Crick and wobble base pairs. Common types of ncRNA include microRNA, rRNA, snoRNA, tRNA. Functions of ncRNAs vary among different types. Recent studies suggest the existence of large number of ncRNA genes. Identification of novel and known ncRNAs becomes increasingly important in order to understand their functionalities and the underlying communities.Next-generation sequencing (NGS) technology sheds lights on more comprehensive and sensitive ncRNA annotation. Lowly transcribed ncRNAs or ncRNAs from rare species with low abundance may be identified via deep sequencing. However, there exist several challenges in ncRNA identification in large-scale genomic data. First, the massive volume of datasets could lead to very long computation time, making existing algorithms infeasible. Second, NGS has relatively high error rate, which could further complicate the problem. Third, high sequence similarity among related ncRNAs could make them difficult to identify, resulting in incorrect output. Fourth, while secondary structures should be adopted for accurate ncRNA identification, they usually incur high computational complexity. In particular, some ncRNAs contain pseudoknot structures, which cannot be effectively modeled by the state-of-the-art approach. As a result, ncRNAs containing pseudoknots are hard to annotate.In my PhD work, I aimed to tackle the above challenges in ncRNA identification. First, I designed a progressive search pipeline to identify ncRNAs containing pseudoknot structures. The algorithms are more efficient than the state-of-the-art approaches and can be used for large-scale data. Second, I designed a ncRNA classification tool for short reads in NGS data lacking quality reference genomes. The initial homology search phase significantly reduces size of the original input, making the tool feasible for large-scale data. Last, I focused on identifying 16S ribosomal RNAs from NGS data. 16S ribosomal RNAs are very important type of ncRNAs, which can be used for phylogenic study. A set of graph based assembly algorithms were applied to form longer or full-length 16S rRNA contigs. I utilized paired-end information in NGS data, so lowly abundant 16S genes can also be identified. To reduce the complexity of problem and make the tool practical for large-scale data, I designed a list of error correction and graph reduction techniques for graph simplification.
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Title: Finding optimized bounding boxes of polytopes in d-dimensional space and their properties in k-dimensional projections
Creator: Shahid, Salman (Of Michigan State University)
Date: 2014
Collection: Electronic Theses & Dissertations
Description: Using minimal bounding boxes to encapsulate or approximate a set of points in d-dimensional space is a non-trivial problem that has applications in a variety of fields including collision detection, object rendering, high dimensional databases and statistical analysis to name a few. While a significant amount of work has been done on the three dimensional variant of the problem (i.e. finding the minimum volume bounding box of a set of points in three dimensions), it is difficult to find a...
Show moreUsing minimal bounding boxes to encapsulate or approximate a set of points in d-dimensional space is a non-trivial problem that has applications in a variety of fields including collision detection, object rendering, high dimensional databases and statistical analysis to name a few. While a significant amount of work has been done on the three dimensional variant of the problem (i.e. finding the minimum volume bounding box of a set of points in three dimensions), it is difficult to find a simple method to do the same for higher dimensions. Even in three dimensions existing methods suffer from either high time complexity or suboptimal results with a speed up in execution time. In this thesis we present a new approach to find the optimized minimum bounding boxes of a set of points defining convex polytopes in d-dimensional space. The solution also gives the optimal bounding box in three dimensions with a much simpler implementation while significantly speeding up the execution time for a large number of vertices. The basis of the proposed approach is a series of unique properties of the k-dimensional projections that are leveraged into an algorithm. This algorithm works by constructing the convex hulls of a given set of points and optimizing the projections of those hulls in two dimensional space using the new concept of Simultaneous Local Optimal. We show that the proposed algorithm provides significantly better performances than those of the current state of the art approach on the basis of time and accuracy. To illustrate the importance of the result in terms of a real world application, the optimized bounding box algorithm is used to develop a method for carrying out range queries in high dimensional databases. This method uses data transformation techniques in conjunction with a set of heuristics to provide significant performance improvement.
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Title: Semi=supervised learning with side information : graph-based approaches
Creator: Liu, Yi
Date: 2007
Collection: Electronic Theses & Dissertations

Title: Some contributions to semi-supervised learning
Creator: Mallapragada, Paven Kumar
Date: 2010
Collection: Electronic Theses & Dissertations

Title: Algorithms for deep packet inspection
Creator: Patel, Jignesh
Date: 2012
Collection: Electronic Theses & Dissertations
Description: The core operation in network intrusion detection and prevention systems is Deep Packet Inspection (DPI), in which each security threat is represented as a signature, and the payload of each data packet is matched against the set of current security threat signatures. DPI is also used for other networking applications like advanced QoS mechanisms, protocol identification etc.. In the past, attack signatures were specified as strings, and a great deal of research has been done in string...
Show moreThe core operation in network intrusion detection and prevention systems is Deep Packet Inspection (DPI), in which each security threat is represented as a signature, and the payload of each data packet is matched against the set of current security threat signatures. DPI is also used for other networking applications like advanced QoS mechanisms, protocol identification etc.. In the past, attack signatures were specified as strings, and a great deal of research has been done in string matching for network applications. Today most DPI systems use Regular Expression (RE) to represent signatures. RE matching is more diffcult than string matching, and current string matching solutions don't work well for REs. RE matching for networking applications is diffcult for several reasons. First, the DPI application is usually implemented in network devices, which have limited computing resources. Second, as new threats are discovered, size of the signature set grows over time. Last, the matching needs to be done at network speeds, the growth of which out paces improvements in computing speed; so there is a need for novel solutions that can deliver higher throughput. So RE matching for DPI is a very important and active research area.In our research, we investigate the existing methods proposed for RE matching, identify their limitations, and propose new methods to overcome these limitations. RE matching remains a fundamentally challenging problem due to the diffculty in compactly encoding DFA. While the DFA for any one RE is typically small, the DFA that corresponds to the entire set of REs is usually too large to be constructed or deployed. To address this issue, many alternative automata implementations that compress the size of the final automaton have been proposed. However, previously proposed automata construction algorithms employ a “Union then Minimize” framework where the automata for each RE are first joined before minimization occurs. This leads to expensive minimization on a large automata, and a large intermediate memory footprint. We propose a “Minimize then Union” framework for constructing compact alternative automata, which minimizes smaller automata first before combining them. This approach required much less time and memory, allowing us to handle a much larger RE set. Prior hardware based RE matching algorithms typically use FPGA. The drawback of FPGA is that resynthesizing and updating FPGA circuitry to handle RE updates is slow and diffcult. We propose the first hardware-based RE matching approach that uses Ternary Content Addressable Memory (TCAM). TCAMs have already been widely used in modern networking devices for tasks such as packet classification, so our solutions can be easily deployed. Our methods support easy RE updates, and we show that we can achieve very high throughput. The main reason combined DFAs for multiple REs grow exponentially in size is because of replication of states. We developed a new overlay automata model which exploit this replication to compress the size of the DFA. The idea is to group together the replicated DFA structures instead of repeating them multiple times. The result is that we get a final automata size that is close to that of a NFA (which is linear in the size of the RE set), and simultaneously achieve fast deterministic matching speed of a DFA.
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Title: Replaying Life's Virtual Tape : Examining the Role of History in Experiments with Digital Organisms
Creator: Bundy, Jason Nyerere
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Evolution is a complex process with a simple recipe. Evolutionary change involves three essential “ingredients” interacting over many generations: adaptation (selection), chance (random variation), and history (inheritance). In 1989’s Wonderful Life, the late paleontologist Stephen Jay Gould advocated for the importance of historical contingency—the way unique events throughout history influence future possibilities—using a clever thought experiment of “replaying life’s tape”. But not...
Show moreEvolution is a complex process with a simple recipe. Evolutionary change involves three essential “ingredients” interacting over many generations: adaptation (selection), chance (random variation), and history (inheritance). In 1989’s Wonderful Life, the late paleontologist Stephen Jay Gould advocated for the importance of historical contingency—the way unique events throughout history influence future possibilities—using a clever thought experiment of “replaying life’s tape”. But not everyone was convinced. Some believed that chance was the primary driver of evolutionary change, while others insisted that natural selection was the most powerful influence. Since then, “replaying life’s tape” has become a core method in experimental evolution for measuring the relative contributions of adaptation, chance, and history. In this dissertation, I focus on the effects associated with history in evolving populations of digital organisms—computer programs that self-replicate, mutate, compete, and evolve in virtual environments. In Chapter 1, I discuss the philosophical significance of Gould’s thought experiment and its influence on experimental methods. I argue that his thought experiment was a challenge to anthropocentric reasoning about natural history that is still popular, particularly outside of the scientific community. In this regard, it was his way of advocating for a “radical” view of evolution. In Chapter 2—Richard Lenski, Charles Ofria, and I describe a two-phase, virtual, “long-term” evolution experiment with digital organisms using the Avida software. In Phase I, we evolved 10 replicate populations, in parallel, from a single genotype for around 65,000 generations. This part of the experiment is similar to the design of Lenski’s E. coli Long-term Evolution Experiment (LTEE). We isolated the dominant genotype from each population around 3,000 generations (shallow history) into Phase I and then again at the end of Phase I (deep history). In Phase II, we evolved 10 populations from each of the genotypes we isolated from Phase I in two new environments, one similar and one dissimilar to the old environment used for Phase I. Following Phase II, we estimated the contributions of adaptation, chance, and history to the evolution of fitness and genome length in each new environment. This unique experimental design allowed us to see how the contributions of adaptation, chance, and history changed as we extended the depth of history from Phase I. We were also able to determine whether the results depended on the extent of environmental change (similar or dissimilar new environment). In Chapter 3, we report an extended analysis of the experiment from the previous chapter to further examine how extensive adaptation to the Phase I environment shaped the evolution of replicates during Phase II. We show how the form of pleiotropy (antagonistic or synergistic) between the old (Phase I) and new (Phase II) habitats was influenced by the depth of history from Phase I (shallow or deep) and the extent of environmental change (similar or dissimilar new environment). In the final chapter Zachary Blount, Richard Lenski, and I describe an exercise we developed using the educational version of Avida (Avida-ED). The exercise features a two-phase, “replaying life’s tape” activity. Students are able to explore how the unique history of founders that we pre-evolved during Phase I influences the acquisition of new functions by descendent populations during Phase II, which the students perform during the activity.
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Title: Evolving Phenotypically Plastic Digital Organisms
Creator: Lalejini, Alexander
Date: 2021
Collection: Electronic Theses & Dissertations
Description: The ability to dynamically respond to cues from the environment is a fundamental feature of most adaptive systems. In biological systems, changes to an organism based on environmental cues is called phenotypic plasticity. Indeed, phenotypic plasticity underlies many of the adaptive traits and developmental patterns found in nature and serves as a key mechanism for responding to spatially or temporally variable environments. Most computer programs require phenotypic plasticity, as they must...
Show moreThe ability to dynamically respond to cues from the environment is a fundamental feature of most adaptive systems. In biological systems, changes to an organism based on environmental cues is called phenotypic plasticity. Indeed, phenotypic plasticity underlies many of the adaptive traits and developmental patterns found in nature and serves as a key mechanism for responding to spatially or temporally variable environments. Most computer programs require phenotypic plasticity, as they must respond dynamically to stimuli such as user input, sensor data, et cetera. As such, phenotypic plasticity also has practical applications in genetic programming, wherein we apply the natural principles of evolution to automatically synthesize computer programs rather than writing them by hand. In this dissertation, I achieve two synergistic aims: (1) I use populations of self-replicating computer programs (digital organisms) to empirically study the conditions under which adaptive phenotypic plasticity evolves and how its evolution shapes subsequent evolutionary outcomes; and (2) I transfer insights from biology to develop novel genetic programming techniques in order to evolve more responsive (i.e., phenotypically plastic) computer programs. First, I illustrate the importance of mutation rate, environmental change, and partially-plastic building blocks for the evolution of adaptive plasticity. Next, I show that adaptive phenotypic plasticity stabilizes populations against environmental change, allowing them to more easily retain novel adaptive traits. Finally, I improve our ability to evolve phenotypically plastic computer programs with three novel genetic programming techniques: (1) SignalGP, which provides mechanisms to control code expression based on environmental cues, (2) tag-based genetic regulation to adjust code expression based on current context, and (3) tag-accessed memory to provide more dynamic mechanisms for storing data.
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Title: Automated Speaker Recognition in Non-ideal Audio Signals Using Deep Neural Networks
Creator: Chowdhury, Anurag
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Speaker recognition entails the use of the human voice as a biometric modality for recognizing individuals. While speaker recognition systems are gaining popularity in consumer applications, most of these systems are negatively affected by non-ideal audio conditions, such as audio degradations, multi-lingual speech, and varying duration audio. This thesis focuses on developing speaker recognition systems robust to non-ideal audio conditions.Firstly, a 1-Dimensional Convolutional Neural...
Show moreSpeaker recognition entails the use of the human voice as a biometric modality for recognizing individuals. While speaker recognition systems are gaining popularity in consumer applications, most of these systems are negatively affected by non-ideal audio conditions, such as audio degradations, multi-lingual speech, and varying duration audio. This thesis focuses on developing speaker recognition systems robust to non-ideal audio conditions.Firstly, a 1-Dimensional Convolutional Neural Network (1D-CNN) is developed to extract noise-robust speaker-dependent speech characteristics from the Mel Frequency Cepstral Coefficients (MFCC). Secondly, the 1D-CNN-based approach is extended to develop a triplet-learning-based feature-fusion framework, called 1D-Triplet-CNN, for improving speaker recognition performance by judiciously combining MFCC and Linear Predictive Coding (LPC) features. Our hypothesis rests on the observation that MFCC and LPC capture two distinct aspects of speech: speech perception and speech production. Thirdly, a time-domain filterbank called DeepVOX is learned from vast amounts of raw speech audio to replace commonly-used hand-crafted filterbanks, such as the Mel filterbank, in speech feature extractors. Finally, a vocal style encoding network called DeepTalk is developed to learn speaker-dependent behavioral voice characteristics to improve speaker recognition performance. The primary contribution of the thesis is the development of deep learning-based techniques to extract discriminative, noise-robust physical and behavioral voice characteristics from non-ideal speech audio. A large number of experiments conducted on the TIMIT, NTIMIT, SITW, NIST SRE (2008, 2010, and 2018), Fisher, VOXCeleb, and JukeBox datasets convey the efficacy of the proposed techniques and their importance in improving speaker recognition performance in non-ideal audio conditions.
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Title: Energy Conservation in Heterogeneous Smartphone Ad Hoc Networks
Creator: Mariani, James
Date: 2018
Collection: Electronic Theses & Dissertations
Description: In recent years mobile computing has been rapidly expanding to the point that there are now more devices than there are people. While once it was common for every household to have one PC, it is now common for every person to have a mobile device. With the increased use of smartphone devices, there has also been an increase in the need for mobile ad hoc networks, in which phones connect directly to each other without the need for an intermediate router. Most modern smart phones are equipped...
Show moreIn recent years mobile computing has been rapidly expanding to the point that there are now more devices than there are people. While once it was common for every household to have one PC, it is now common for every person to have a mobile device. With the increased use of smartphone devices, there has also been an increase in the need for mobile ad hoc networks, in which phones connect directly to each other without the need for an intermediate router. Most modern smart phones are equipped with both Bluetooth and Wifi Direct, where Wifi Direct has a better transmission range and rate and Bluetooth is more energy efficient. However only one or the other is used in a smartphone ad hoc network. We propose a Heterogeneous Smartphone Ad Hoc Network, HSNet, a framework to enable the automatic switching between Wifi Direct and Bluetooth to emphasize minimizing energy consumption while still maintaining an efficient network. We develop an application to evaluate the HSNet framework which shows significant energy savings when utilizing our switching algorithm to send messages by a less energy intensive technology in situations where energy conservation is desired. We discuss additional features of HSNet such as load balancing to help increase the lifetime of the network by more evenly distributing slave nodes among connected master nodes. Finally, we show that the throughput of our system is not affected due to technology switching for most scenarios. Future work of this project includes exploring energy efficient routing as well as simulation/scale testing for larger and more diverse smartphone ad hoc networks.
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Title: Contributions to Fingerprint Recognition
Creator: Engelsma, Joshua James
Date: 2021
Collection: Electronic Theses & Dissertations
Description: From the early days of the mid to late nineteenth century when scientific research first began to focus on fingerprints, to the present day fingerprint recognition systems we find deployed on our day to day devices, the science of fingerprint recognition has come a long way. In spite of this progress, there remains challenging problems to be solved. This thesis highlights a few of these problems, and proposes solutions to address them. One area of further research that must be conducted on...
Show moreFrom the early days of the mid to late nineteenth century when scientific research first began to focus on fingerprints, to the present day fingerprint recognition systems we find deployed on our day to day devices, the science of fingerprint recognition has come a long way. In spite of this progress, there remains challenging problems to be solved. This thesis highlights a few of these problems, and proposes solutions to address them. One area of further research that must be conducted on fingerprint recognition systems is that of robust, operational evaluations. In chapter two of this thesis, we show how the current practices of using calibration patterns to evaluate fingerprint readers are limited. We then propose a realistic fake finger called the Universal Target. The Universal Target is a realistic, 3D, fake finger (or phantom) which can be imaged by all major types of fingerprint sensing technologies. We show the entire manufacturing (molding and casting) process for fabricating the Universal Targets. Then, we show a series of evaluations which demonstrate how the Universal Targets can be used to operationally evaluate current commercial fingerprint readers. Our Universal Target is a significant step forward in enabling more realistic, standardized evaluations of fingerprint readers. In our third chapter, we shift gears from improving the evaluation standards of fingerprint readers to instead focus on the security of fingerprint readers. In particular, we turn our attention towards detecting fake fingerprint (spoof) attacks. To do so, we open source a fingerprint reader (built from low-cost ubiquitous components), called RaspiReader. RaspiReader is a high-resolution fingerprint reader customized with both direct-view imaging and FTIR imaging in order to better detect fingerprint spoofs. We show through a number of experiments that RaspiReader enables state-of-the-art fingerprint spoof detection accuracy. We also demonstrate that RaspiReader enables better generalization to what are known as "unseen attacks" (those attacks which were not seen during training of the spoof detector). Finally, we show that fingerprints captured by RaspiReader are completely compatible with images captured by legacy fingerprint readers for matching.In chapter four, we move on to propose a major improvement to the fingerprint feature extraction and matching sub-modules of fingerprint recognition systems. In particular, we propose a deep network, called DeepPrint, to extract a 200 byte fixed-length fingerprint representation. While prevailing fingerprint matchers primarily utilize minutiae points and expensive graph matching algorithms for comparison, two DeepPrint representations can be compared with only 192 multiplications and 191 additions. This is extremely useful for large scale search where potentially billions of pairwise fingerprint comparisons must be made. The DeepPrint representation also enables practical encrypted matching using a fully homomorphic encryption scheme. This enables better protection of the fingerprint templates which are stored in the database. While discriminative fixed-length representations are available for both face and iris recognition, such a representation has eluded fingerprint recognition. This chapter aims to fill that void.Finally, we conclude our thesis by working to extend fingerprint recognition to all ages. While current fingerprint recognition systems are being used by billions of teenagers and adults around the world, the youngest people among us remain disenfranchised. In particular, modern day fingerprint recognition systems do not work well on infants and young children. In this penultimate chapter, we aim to rectify this major shortcoming. To that end, we prototype a high-resolution (1900 ppi) infant fingerprint reader. Then, we track and fingerprint 315 infants (under the age of 3 months at enrollment) at the Dayalbagh Children's Hospital in Agra India over the course of 1 year (4 different sessions). To match the infant fingerprints, we develop our own high-resolution infant fingerprint matcher. Our experimental results demonstrate significant promise for the extension of fingerprint recognition to all ages. This work has the potential for major global good as all young infants and children could be given a verifiable digital identity for better vaccination tracking as a child and for government benefits and assistance as an adult. In summary, this thesis makes major contributions to the entire end-to-end fingerprint recognition system and extends its use case to all ages.
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Title: Discrete de Rham-Hodge Theory
Creator: Zhao, Rundong
Date: 2020
Collection: Electronic Theses & Dissertations
Description: We present a systematic treatment to 3D shape analysis based on the well-established de Rham-Hodge theory in differential geometry and topology. The computational tools we developed are widely applicable to research areas such as computer graphics, computer vision, and computational biology. We extensively tested it in the context of 3D structure analysis of biological macromolecules to demonstrate the efficacy and efficiency of our method in potential applications. Our contributions are...
Show moreWe present a systematic treatment to 3D shape analysis based on the well-established de Rham-Hodge theory in differential geometry and topology. The computational tools we developed are widely applicable to research areas such as computer graphics, computer vision, and computational biology. We extensively tested it in the context of 3D structure analysis of biological macromolecules to demonstrate the efficacy and efficiency of our method in potential applications. Our contributions are summarized in the following aspects. First, we present a compendium of discrete Hodge decompositions of vector fields, which provides the primary building block of the de Rham-Hodge theory for computations performed on the commonly used tetrahedral meshes embedded in the 3D Euclidean space. Second, we present a real-world application of the above computational tool to 3D shape analysis on biological macromolecules. Finally, we extend the above method to an evolutionary de Rham-Hodge method to provide a unified paradigm for the multiscale geometric and topological analysis of evolving manifolds constructed from a filtration, which induces a family of evolutionary de Rham complexes. Our work on the decomposition of vector fields, spectral shape analysis on static shapes, and evolving shapes has already shown its effectiveness in biomolecular applications and will lead to a rich set of features for machine learning-based shape analysis currently under development.
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Title: I AM DOING MORE THAN CODING : A QUALITATIVE STUDY OF BLACK WOMEN HBCU UNDERGRADUATES’ PERSISTENCE IN COMPUTING
Creator: Benton, Amber V.
Date: 2020
Collection: Electronic Theses & Dissertations
Description: The purpose of my study is to explore why and how Black women undergraduates at historically Black colleges and universities (HBCUs) persist in computing. By centering the experiences of Black women undergraduates and their stories, this dissertation expands traditional, dominant ways of understanding student persistence in higher education. Critical Race Feminism (CRF) was applied as a conceptual framework to the stories of 11 Black women undergraduates in computing and drew on the small...
Show moreThe purpose of my study is to explore why and how Black women undergraduates at historically Black colleges and universities (HBCUs) persist in computing. By centering the experiences of Black women undergraduates and their stories, this dissertation expands traditional, dominant ways of understanding student persistence in higher education. Critical Race Feminism (CRF) was applied as a conceptual framework to the stories of 11 Black women undergraduates in computing and drew on the small stories qualitative approach to examine the day-to-day experiences of Black women undergraduates at HBCUs as they persisted in their computing degree programs. The findings suggest that: (a) gender underrepresentation in computing affects Black women’s experiences, (b) computing culture at HBCUs directly affect Black women in computing, (c) Black women need access to resources and opportunities to persist in computing, (d) computing-related internships are beneficial professional opportunities but are also sites of gendered racism for Black women, (e) connectedness between Black people is innate but also needs to be fostered, (f) Black women want to engage in computing that contributes to social impact and community uplift, and (g) science identity is not a primary identity for Black women in computing. This paper also argues that disciplinary focused efforts contribute to the persistence of Black women in computing.
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Title: Optimal Learning of Deployment and Search Strategies for Robotic Teams
Creator: Wei, Lai
Date: 2021
Collection: Electronic Theses & Dissertations
Description: In the problem of optimal learning, the dilemma of exploration and exploitation stems from the fact that gathering information and exploiting it are, in many cases, two mutually exclusive activities. The key to optimal learning is to strike a balance between exploration and exploitation. The Multi-Armed Bandit (MAB) problem is a prototypical example of such an explore-exploit tradeoff, in which a decision-maker sequentially allocates a single resource by repeatedly choosing one among a set of...
Show moreIn the problem of optimal learning, the dilemma of exploration and exploitation stems from the fact that gathering information and exploiting it are, in many cases, two mutually exclusive activities. The key to optimal learning is to strike a balance between exploration and exploitation. The Multi-Armed Bandit (MAB) problem is a prototypical example of such an explore-exploit tradeoff, in which a decision-maker sequentially allocates a single resource by repeatedly choosing one among a set of options that provide stochastic rewards. The MAB setup has been applied in many robotics problems such as foraging, surveillance, and target search, wherein the task of robots can be modeled as collecting stochastic rewards. The theoretical work of this dissertation is based on the MAB setup and three problem variations, namely heavy-tailed bandits, nonstationary bandits, and multi-player bandits, are studied. The first two variations capture two key features of stochastic feedback in complex and uncertain environments: heavy-tailed distributions and nonstationarity; while the last one addresses the problem of achieving coordination in uncertain environments. We design several algorithms that are robust to heavy-tailed distributions and nonstationary environments. Besides, two distributed policies that require no communication among agents are designed for the multi-player stochastic bandits in a piece-wise stationary environment.The MAB problems provide a natural framework to study robotic search problems. The above variations of the MAB problems directly map to robotic search tasks in which a robot team searches for a target from a fixed set of view-points (arms). We further focus on the class of search problems involving the search of an unknown number of targets in a large or continuous space. We view the multi-target search problem as a hot-spots identification problem in which, instead of the global maximum of the field, all locations with a value greater than a threshold need to be identified. We consider a robot moving in 3D space with a downward-facing camera sensor. We model the robot's sensing output using a multi-fidelity Gaussian Process (GP) that systematically describes the sensing information available at different altitudes from the floor. Based on the sensing model, we design a novel algorithm that (i) addresses the coverage-accuracy tradeoff: sampling at a location farther from the floor provides a wider field of view but less accurate measurements, (ii) computes an occupancy map of the floor within a prescribed accuracy and quickly eliminates unoccupied regions from the search space, and (iii) travels efficiently to collect the required samples for target detection. We rigorously analyze the algorithm and establish formal guarantees on the target detection accuracy and the detection time.An approach to extend the single robot search policy to multiple robots is to partition the environment into multiple regions such that workload is equitably distributed among all regions and then assign a robot to each region. The coverage control focuses on such equitable partitioning and the workload is equivalent to the so-called service demands in the coverage control literature. In particular, we study the adaptive coverage control problem, in which the demands of robotic service within the environment are modeled as a GP. To optimize the coverage of service demands in the environment, the team of robots aims to partition the environment and achieve a configuration that minimizes the coverage cost, which is a measure of the average distance of a service demand from the nearest robot. The robots need to address the explore-exploit tradeoff: to minimize coverage cost, they need to gather information about demands within the environment, whereas information gathering deviates them from maintaining a good coverage configuration. We propose an algorithm that schedules learning and coverage epochs such that its emphasis gradually shifts from exploration to exploitation while never fully ceasing to learn. Using a novel definition of coverage regret, we analyze the algorithm and characterizes its coverage performance over a finite time horizon.
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Title: Coreference Resolution for Downstream NLP Tasks
Creator: Pani, Sushanta Kumar
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Natural Language Processing (NLP) tasks have witnessed a significant improvement in performance by utilizing the power of end-to-end neural network models. An NLP system built for one job can contribute to other closely related tasks. Coreference Resolution (CR) systems work on resolving references and are at the core of many NLP tasks. The coreference resolution refers to the linking of repeated object references in a text. CR systems can boost the performance of downstream NLP tasks, such...
Show moreNatural Language Processing (NLP) tasks have witnessed a significant improvement in performance by utilizing the power of end-to-end neural network models. An NLP system built for one job can contribute to other closely related tasks. Coreference Resolution (CR) systems work on resolving references and are at the core of many NLP tasks. The coreference resolution refers to the linking of repeated object references in a text. CR systems can boost the performance of downstream NLP tasks, such as Text Summarization, Question Answering, Machine Translation, etc. We provide a detailed comparative error analysis of two state-of-the-art coreference resolution systems to understand error distribution in the predicted output. The understanding of error distribution is helpful to interpret the system behavior. Eventually, this will contribute to the selection of an optimal CR system for a specific target task.
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