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Title: 5D Nondestructive Evaluation : Object Reconstruction to Toolpath Generation
Creator: Hamilton, Ciaron Nathan
Date: 2021
Collection: Electronic Theses & Dissertations
Description: The focus of this thesis is to provide virtualization methods for a Cyber-Physical System (CPS) setup that interfaces physical Nondestructive Evaluation (NDE) scanning environments into virtual spaces through virtual-physical interfacing and path planning. In these environments, a probe used for NDE mounted as the end-effector of a robot arm will actuate and acquire data along the surface of a Material Under Test (MUT) within virtual and physical spaces. Such configurations are practical for...
Show moreThe focus of this thesis is to provide virtualization methods for a Cyber-Physical System (CPS) setup that interfaces physical Nondestructive Evaluation (NDE) scanning environments into virtual spaces through virtual-physical interfacing and path planning. In these environments, a probe used for NDE mounted as the end-effector of a robot arm will actuate and acquire data along the surface of a Material Under Test (MUT) within virtual and physical spaces. Such configurations are practical for applications that require damage analysis of certain geometrically complex parts, ranging from automobile to aerospace to military industries. The pipeline of the designed $5D$ actuation system starts by virtually reconstructing the physical MUT and its surrounding environment, generating a toolpath along the surface of the reconstructed MUT, conducting a physical scan along the toolpath which synchronizes the robot's end effector position with retrieved NDE data, and post processing the obtained data. Most of this thesis will focus on virtual topics, including reconstruction from stereo camera images and toolpath planning. Virtual mesh generation of the MUT and surrounding environment are found with stereo camera images, where methods for camera positioning, registration, filtering, and reconstruction are provided. Path planning around the MUT uses a customized path-planner, where a $2D$ grid of rays is generated where each ray intersection across the surface of the MUT's mesh provides the translation and rotation of waypoints for actuation. Experimental setups include both predefined meshes and reconstructed meshes found from several real carbon-fiber automobile components using an Intel RealSense D425i stereo camera, showing both the reconstruction and path planning results. A theoretical review is also included to discuss analytical prospects of the system. The final system is designed to be automated to minimize human interaction to conduct scans, with later reports planned to discuss the scanning and post processing prospects of the system.
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Title: AN EVOLUTIONARY MULTI-OBJECTIVE APPROACH TO SUSTAINABLE AGRICULTURAL WATER AND NUTRIENT OPTIMIZATION
Creator: Kropp, Ian Meyer
Date: 2018
Collection: Electronic Theses & Dissertations
Description: One of the main problems that society is facing in the 21st century is that agricultural production must keep pace with a rapidly increasing global population in an environmentally sustainable manner. One of the solutions to this global problem is a system approach through the application of optimization techniques to manage farm operations. However, unlike existing agricultural optimization research, this work seeks to optimize multiple agricultural objectives at once via multi-objective...
Show moreOne of the main problems that society is facing in the 21st century is that agricultural production must keep pace with a rapidly increasing global population in an environmentally sustainable manner. One of the solutions to this global problem is a system approach through the application of optimization techniques to manage farm operations. However, unlike existing agricultural optimization research, this work seeks to optimize multiple agricultural objectives at once via multi-objective optimization techniques. Specifically, the algorithm Unified Non-dominated Sorting Genetic Algorithm-III (U-NSGA-III) searched for irrigation and nutrient management practices that minimized combinations of environmental objectives (e.g., total irrigation applied, total nitrogen leached) while maximizing crop yield for maize. During optimization, the crop model named the Decision Support System for Agrotechnology Transfer (DSSAT) calculated the yield and nitrogen leaching for each given management practices. This study also developed a novel bi-level optimization framework to improve the performance of the optimization algorithm, employing U-NSGA-III on the upper level and Monte Carlo optimization on the lower level. The multi-objective optimization framework resulted in groups of equally optimal solutions that each offered a unique trade-off among the objectives. As a result, producers can choose the one that best addresses their needs among these groups of solutions, known as Pareto fronts. In addition, the bi-level optimization framework further improved the number, performance, and diversity of solutions within the Pareto fronts.
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Title: ASSURING THE ROBUSTNESS AND RESILIENCY OF LEARNING-ENABLED AUTONOMOUS SYSTEMS
Creator: Langford, Michael Austin
Date: 2022
Collection: Electronic Theses & Dissertations
Description: As Learning-Enabled Systems (LESs) have become more prevalent in safety-critical applications, addressing the assurance of LESs has become increasingly important. Because machine learning models in LESs are not explicitly programmed like traditional software, developers typically have less direct control over the inferences learned by LESs, relying instead on semantically valid and complete patterns to be extracted from the system’s exposure to the environment. As such, the behavior of an LES...
Show moreAs Learning-Enabled Systems (LESs) have become more prevalent in safety-critical applications, addressing the assurance of LESs has become increasingly important. Because machine learning models in LESs are not explicitly programmed like traditional software, developers typically have less direct control over the inferences learned by LESs, relying instead on semantically valid and complete patterns to be extracted from the system’s exposure to the environment. As such, the behavior of an LES is strongly dependent on the quality of its training experience. However, run-time environments are often noisy or not well-defined. Uncertainty in the behavior of an LES can arise when there is inadequate coverage of relevant training/test cases (e.g., corner cases). It is challenging to assure safety-critical LESs will perform as expected when exposed to run-time conditions that have never been experienced during training or validation. This doctoral research contributes automated methods to improve the robustness and resilience of an LES. For this work, a robust LES is less sensitive to noise in the environment, and a resilient LES is able to self-adapt to adverse run-time contexts in order to mitigate system failure. The proposed methods harness diversity-driven evolution-based methods, machine learning, and software assurance cases to train robust LESs, uncover robust system configurations, and foster resiliency through self-adaptation and predictive behavior modeling. This doctoral work demonstrates these capabilities by applying the proposed framework to deep learning and autonomous cyber-physical systems.
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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.
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Title: Adaptive and Automated Deep Recommender Systems
Creator: Zhao, Xiangyu
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Recommender systems are intelligent information retrieval applications, and have been leveraged in numerous domains such as e-commerce, movies, music, books, and point-of-interests. They play a crucial role in the users' information-seeking process, and overcome the information overload issue by recommending personalized items (products, services, or information) that best match users' needs and preferences. Driven by the recent advances in machine learning theories and the prevalence of deep...
Show moreRecommender systems are intelligent information retrieval applications, and have been leveraged in numerous domains such as e-commerce, movies, music, books, and point-of-interests. They play a crucial role in the users' information-seeking process, and overcome the information overload issue by recommending personalized items (products, services, or information) that best match users' needs and preferences. Driven by the recent advances in machine learning theories and the prevalence of deep learning techniques, there have been tremendous interests in developing deep learning based recommender systems. They have unprecedentedly advanced effectiveness of mining the non-linear user-item relationships and learning the feature representations from massive datasets, which produce great vitality and improvements in recommendations from both academic and industry communities.Despite above prominence of existing deep recommender systems, their adaptiveness and automation still remain under-explored. Thus, in this dissertation, we study the problem of adaptive and automated deep recommender systems. Specifically, we present our efforts devoted to building adaptive deep recommender systems to continuously update recommendation strategies according to the dynamic nature of user preference, which maximizes the cumulative reward from users in the practical streaming recommendation scenarios. In addition, we propose a group of automated and systematic approaches that design deep recommender system frameworks effectively and efficiently from a data-driven manner. More importantly, we apply our proposed models into a variety of real-world recommendation platforms and have achieved promising enhancements of social and economic benefits.
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Title: Advanced Operators for Graph Neural Networks
Creator: Ma, Yao
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Graphs, which encode pairwise relations between entities, are a kind of universal data structure for many real-world data, including social networks, transportation networks, and chemical molecules. Many important applications on these data can be treated as computational tasks on graphs. For example, friend recommendation in social networks can be regarded as a link prediction task and predicting properties of chemical compounds can be treated as a graph classification task. An essential...
Show moreGraphs, which encode pairwise relations between entities, are a kind of universal data structure for many real-world data, including social networks, transportation networks, and chemical molecules. Many important applications on these data can be treated as computational tasks on graphs. For example, friend recommendation in social networks can be regarded as a link prediction task and predicting properties of chemical compounds can be treated as a graph classification task. An essential step to facilitate these tasks is to learn vector representations either for nodes or the entire graphs. Given its great success of representation learning in images and text, deep learning offers great promise for graphs. However, compared to images and text, deep learning on graphs faces immense challenges. Graphs are irregular where nodes are unordered and each of them can have a distinct number of neighbors. Thus, traditional deep learning models cannot be directly applied to graphs, which calls for dedicated efforts for designing novel deep graph models. To help meet this pressing demand, we developed and investigated novel GNN algorithms to generalize deep learning techniques to graph-structured data. Two key operations in GNNs are the graph filtering operation, which aims to refine node representations; and the graph pooling operation, which aims to summarize node representations to obtain a graph representation. In this thesis, we provide deep understandings or develop novel algorithms for these two operations from new perspectives. For graph filtering operations, we propose a unified framework from the perspective of graph signal denoising, which demonstrates that most existing graph filtering operations are conducting feature smoothing. Then, we further investigate what information typical graph filtering operations can capture and how they can be understood beyond feature smoothing. For graph pooling operations, we study the procedure of pooling from the perspective of graph spectral theory and present a novel graph pooling operation. We also propose a technique to downsample nodes considering both mode importance and representativeness, which leads to a novel graph pooling operation.
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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: 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: COMBINING FACE AND IRIS FOR PRIVACY PRESERVATION
Creator: Ledala, Achsah Junia
Date: 2021
Collection: Electronic Theses & Dissertations
Description: With the extensive use of biometrics for authenticating users, the need to ensure privacy of biometric data is greater than ever before. Biometric authentication systems are vulnerable to attacks and the loss of biometric data will lead to loss of privacy of an individual. Multibiometrics refers to the use of multiple biometric modalities simultaneously in order to perform matching. In this work, we introduce a multibiometric fusion technique which can be used to ensure that the original raw...
Show moreWith the extensive use of biometrics for authenticating users, the need to ensure privacy of biometric data is greater than ever before. Biometric authentication systems are vulnerable to attacks and the loss of biometric data will lead to loss of privacy of an individual. Multibiometrics refers to the use of multiple biometric modalities simultaneously in order to perform matching. In this work, we introduce a multibiometric fusion technique which can be used to ensure that the original raw biometric data are unlikely to be compromised and, at the same time, recognition can be performed. The face and the iris biometric modalities are fused at the feature-level to produce discriminative embeddings that can be used for recognition. The original face or the iris cannot be retrieved from the combined representation, thus preserving the privacy of the individual. We present the results of this approach, provide analysis, discuss the challenges, and list possible future directions.
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Title: CS1 AND GENDER : UNDERSTANDING EFFECTS OF BACKGROUND AND SELF- EFFICACY ON ACHIEVEMENT AND INTEREST
Creator: Sands, Philip
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Over the past 20 years, the field of computer science has experienced a growth in studentinterest. Despite this increase in participation rates, longstanding gender gaps persist in computer science. Recent research has examined a wide variety of individual factors (e.g., self-efficacy, sense of belonging, etc.) that impact student interest and achievement in computer science; however, these factors are rarely considered in the context of existing learning theories. In this correlational study...
Show moreOver the past 20 years, the field of computer science has experienced a growth in studentinterest. Despite this increase in participation rates, longstanding gender gaps persist in computer science. Recent research has examined a wide variety of individual factors (e.g., self-efficacy, sense of belonging, etc.) that impact student interest and achievement in computer science; however, these factors are rarely considered in the context of existing learning theories. In this correlational study, I explored the relationship between prior knowledge of computer programming, self-efficacy, and the sources of self-efficacy as they differed by gender in a theoretical model of achievement and interest for students in first-year computer science (CS1) courses. This model was based on prior work from Bandura (1997) and others exploring self- efficacy and social cognitive theory in the context of mathematics and science fields. Using cross-sectional data from N=182 CS1 students at two universities, structural regressions were conducted between factors impacting CS1 students across the entire population and for men (N=108) and women (N=70) individually. This data was then used to address the following research questions. (1A) How do prior knowledge of computer programming, the sources of self- efficacy, and self-efficacy for computing predict CS1 achievement and student intentions to continue study in CS? (1B) How does self-efficacy mediate the relationship between student prior knowledge of computer programming and achievement in CS1? (1C) How are thoserelationships moderated by gender? (2) How does feedback in the form of student grades impact intention to continue in CS when considering gender as a moderating factor? For all students, student self-efficacy for CS positively impacted CS1 achievement and post-CS1 interest. Aligning with past research, self-efficacy was derived largely from mastery experiences, with vicarious experiences and social persuasions also contributing to a moderate degree. Social persuasions had a negative effect on self-efficacy, which diverged from research in other fields. The relationship between prior knowledge of computer programming and CS1 achievement was not mediated by self-efficacy and had a small positive effect. For women, vicarious experiences played a stronger role in defining student self-efficacy in CS. Additionally, while the importance of self-efficacy on achievement was similar to that for men, self-efficacy and achievement both played a much stronger role in determining student interest in CS for women. All these findings are in need of further exploration as the analysis was underpowered due to a small, COVID-19 impacted sample size. Future work should focus on the role of feedback on student self-efficacy, the potential misalignment of CS1 feedback and social network feedback, and interventions that address student beliefs about CS abilities to increase opportunities for authentic mastery and vicarious experiences.
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Title: Computational Frameworks for Indel-Aware Evolutionary Analysis using Large-Scale Genomic Sequence Data
Creator: Wang, Wei
Date: 2021
Collection: Electronic Theses & Dissertations
Description: With the development of sequencing techniques, genetic sequencing data has been extensively used in evolutionary studies.The phylogenetic reconstruction problem, which is the reconstruction of evolutionary history from biomolecular sequences, is a fundamental problem. The evolutionary relationship between organisms is often represented by phylogeny, which is a tree or network representation. The most widely-used approach for reconstructing phylogenies from sequencing data involves two phases:...
Show moreWith the development of sequencing techniques, genetic sequencing data has been extensively used in evolutionary studies.The phylogenetic reconstruction problem, which is the reconstruction of evolutionary history from biomolecular sequences, is a fundamental problem. The evolutionary relationship between organisms is often represented by phylogeny, which is a tree or network representation. The most widely-used approach for reconstructing phylogenies from sequencing data involves two phases: multiple sequence alignment and phylogenetic reconstruction from the aligned sequences. As the amount of biomolecular sequence data increases, it has become a major challenge to develop efficient and accurate computational methods for phylogenetic analyses of large-scale sequencing data. Due to the complexity of the phylogenetic reconstruction problem in modern phylogenetic studies, the traditional sequence-based phylogenetic analysis methods involve many over-simplified assumptions. In this thesis, we describe our contribution in relaxing some of these over-simplified assumptions in the phylogenetic analysis.Insertion and deletion events, referred to as indels, carry much phylogenetic information but are often ignored in the reconstruction process of phylogenies. We take into account the indel uncertainties in multiple phylogenetic analyses by applying resampling and re-estimation. Another over-simplified assumption that we contributed to is adopted by many commonly used non-parametric algorithms for the resampling of biomolecular sequences, all sites in an MSA are evolved independently and identically distributed (i.i.d). Many evolution events, such as recombination and hybridization, may produce intra-sequence and functional dependence in biomolecular sequences that violate this assumption. We introduce SERES, a resampling algorithm for biomolecular sequences that can produce resampled replicates that preserve the intra-sequence dependence. We describe the application of the SERES resampling and re-estimation approach to two classical problems: the multiple sequence alignment support estimation and recombination-aware local genealogical inference. We show that these two statistical inference problems greatly benefit from the indel-aware resampling and re-estimation approach and the reservation of intra-sequence dependence.A major drawback of SERES is that it requires parameters to ensure the synchronization of random walks on unaligned sequences.We introduce RAWR, a non-parametric resampling method designed for phylogenetic tree support estimation that does not require extra parameters. We show that the RAWR-based resampling and re-estimation method produces comparable or typically better performance than the traditional bootstrap approach on the phylogenetic tree support estimation problem. We further relax the commonly used assumption of phylogeny.Evolutionary history is usually considered as a tree structure. Evolutionary events that cause reticulated gene flow are ignored. Previous studies show that alignment uncertainty greatly impacts downstream tree inference and learning. However, there is little discussion about the impact of MSA uncertainties on the phylogenetic network reconstruction. We show evidence that the errors introduced in MSA estimation decrease the accuracy of the inferred phylogenetic network, and an indel-aware reconstruction method is needed for phylogenetic network analysis. In this dissertation, we introduce our contribution to phylogenetic estimation using biomolecular sequence data involving complex evolutionary histories, such as sequence insertion and deletion processes and non-tree-like evolution.
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Title: Computational methods to investigate connectivity in evolvable systems
Creator: Ackles, Acacia Lee
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Evolution sheds light on all of biology, and evolutionary dynamics underlie some of the most pressing issues we face today. If we can deepen our understanding of evolution, we can better respond to these various challenges. However, studying such processes directly can be difficult; biological data is naturally messy, easily confounded, and often limited. Fortunately, we can use computational modeling to help simplify and systematically untangle complex evolutionary processes. The aim of this...
Show moreEvolution sheds light on all of biology, and evolutionary dynamics underlie some of the most pressing issues we face today. If we can deepen our understanding of evolution, we can better respond to these various challenges. However, studying such processes directly can be difficult; biological data is naturally messy, easily confounded, and often limited. Fortunately, we can use computational modeling to help simplify and systematically untangle complex evolutionary processes. The aim of this dissertation is therefore to develop innovative computational frameworks to describe, quantify, and build intuition about evolutionary phenomena, with a focus on connectivity within evolvable systems. Here I introduce three such computational frameworks which address the importance of connectivity in systems across scales.First, I introduce rank epistasis, a model of epistasis that does not rely on baseline assumptions of genetic interactions. Rank epistasis borrows rank-based comparison testing from parametric statistics to quantify mutational landscapes around a target locus and identify how much that landscape is perturbed by mutation at that locus. This model is able to correctly identify lack of epistasis where existing models fail, thereby providing better insight into connectivity at the genome level.Next, I describe the comparative hybrid method, an approach to piecewise study of complex phenotypes. This model creates hybridized structures of well-known cognitive substrates in order to address what facilitates the evolution of learning. The comparative hybrid model allowed us to identify both connectivity and discretization as important components to the evolution of cognition, as well as demonstrate how both these components interact in different cognitive structures. This approach highlights the importance of recognizing connected components at the level of the phenotype.Finally, I provide an engineering point of view for Tessevolve, a virtual reality enabled system for viewing fitness landscapes in multiple dimensions. While traditional methods have only allowed for 2D visualization, Tessevolve allows the user to view fitness landscapes scaled across 2D, 3D, and 4D. Visualizing these landscapes in multiple dimensions in an intuitive VR-based system allowed us to identify how landscape traversal changes as dimensions increase, demonstrating the way that connections between points across fitness landscapes are affected by dimensionality. As a whole, this dissertation looks at connectivity in computational structures across a broad range of biological scales. These methods and metrics therefore expand our computational toolkit for studying evolution in multiple systems of interest: genotypic, phenotypic, and at the whole landscape level.
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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: 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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Title: DIGITAL IMAGE FORENSICS IN THE CONTEXT OF BIOMETRICS
Creator: Banerjee, Sudipta
Date: 2020
Collection: Electronic Theses & Dissertations
Description: Digital image forensics entails the deduction of the origin, history and authenticity of a digital image. While a number of powerful techniques have been developed for this purpose, much of the focus has been on images depicting natural scenes and generic objects. In this thesis, we direct our focus on biometric images, viz., iris, ocular and face images.Firstly, we assess the viability of using existing sensor identification schemes developed for visible spectrum images on near-infrared (NIR...
Show moreDigital image forensics entails the deduction of the origin, history and authenticity of a digital image. While a number of powerful techniques have been developed for this purpose, much of the focus has been on images depicting natural scenes and generic objects. In this thesis, we direct our focus on biometric images, viz., iris, ocular and face images.Firstly, we assess the viability of using existing sensor identification schemes developed for visible spectrum images on near-infrared (NIR) iris and ocular images. These schemes are based on estimating the multiplicative sensor noise that is embedded in an input image. Further, we conduct a study analyzing the impact of photometric modifications on the robustness of the schemes. Secondly, we develop a method for sensor de-identificaton, where the sensor noise in an image is suppressed but its biometric utility is retained. This enhances privacy by unlinking an image from its camera sensor and, subsequently, the owner of the camera. Thirdly, we develop methods for constructing an image phylogeny tree from a set of near-duplicate images. An image phylogeny tree captures the relationship between subtly modified images by computing a directed acyclic graph that depicts the sequence in which the images were modified. Our primary contribution in this regard is the use of complex basis functions to model any arbitrary transformation between a pair of images and the design of a likelihood ratio based framework for determining the original and modified image in the pair. We are currently integrating a graph-based deep learning approach with sensor-specific information to refine and improve the performance of the proposed image phylogeny algorithm.
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Title: Deep Convolutional Networks for Modeling Geo-Spatio-Temporal Relationships and Extremes
Creator: Wilson, Tyler
Date: 2021
Collection: Electronic Theses & Dissertations
Description: Geo-spatio-temporal data are valuable for a broad range of applications including traffic forecasting, weather prediction, detection of epidemic outbreaks, and crime monitoring. Data driven approaches to these problems must address several fundamental challenges such as handling the %The two we focus on are the importance ofgeo-spatio-temporal relationships and extreme events. Another recent technological shift has been the success of deep learning especially in applications such as computer...
Show moreGeo-spatio-temporal data are valuable for a broad range of applications including traffic forecasting, weather prediction, detection of epidemic outbreaks, and crime monitoring. Data driven approaches to these problems must address several fundamental challenges such as handling the %The two we focus on are the importance ofgeo-spatio-temporal relationships and extreme events. Another recent technological shift has been the success of deep learning especially in applications such as computer vision, speech recognition, and natural language processing. In this work, we argue that deep learning is a promising approach for many geo-spatio-temporal problems and highlight how it can be used to address the challenges of modeling geo-spatio-temporal relationships and extremes. Though previous research has established techniques for modeling spatio-temporal relationships, these approaches are often limited to gridded spatial data with fixed-length feature vectors and considered only spatial relationships among the features, while ignoring the relationships among model parameters.We begin by describing how the spatial and temporal relationships for non-gridded spatial data can be modeled simultaneously by coupling the graph convolutional network with a long short-term memory (LSTM) network. Unlike previous research, our framework treats the adjacency matrix associated with the spatial data as a model parameter that can be learned from data, with constraints on its sparsity and rank to reduce the number of estimated parameters.Further, we show that the learned adjacency matrix may reveal useful information about the dominant spatial relationships that exist within the data. Second, we explore the varieties of spatial relationships that may exist in a geo-spatial prediction task. Specifically, we distinguish between spatial relationships among predictors and the spatial relationships among model parameters at different locations. We demonstrate an approach for modeling spatial dependencies among model parameters using graph convolution and provide guidance on when convolution of each type can be effectively applied. We evaluate our proposed approach on a climate downscaling and weather prediction tasks. Next, we introduce DeepGPD, a novel deep learning framework for predicting the distribution of geo-spatio-temporal extreme events. We draw on research in extreme value theory and use the generalized Pareto distribution (GPD) to model the distribution of excesses over a threshold. The GPD is integrated into our deep learning framework to learn the distribution of future excess values while incorporating the geo-spatio-temporal relationships present in the data. This requires a novel reparameterization of the GPD to ensure that its constraints are satisfied by the outputs of the neural network. We demonstrate the effectiveness of our proposed approach on a real-world precipitation data set. DeepGPD also employs a deep set architecture to handle the variable-sized feature sets corresponding to excess values from previous time steps as its predictors. Finally, we extend the DeepGPD formulation to simultaneously predict the distribution of extreme events and accurately infer their point estimates. Doing so requires modeling the full distribution of the data not just its extreme values. We propose DEMM, a deep mixture model for modeling the distribution of both excess and non-excess values. To ensure the point estimation of DEMM is a feasible value, new constraints on the output of the neural network are introduced, which requires a new reparameterization of the model parameters of the GPD. We conclude by discussing possibilities for further research at the intersection of deep learning and geo-spatio-temporal data.
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Title: Detecting and Mitigating Bias in Natural Languages
Creator: Liu, Haochen
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Natural language processing (NLP) is an increasingly prominent subfield of artificial intelligence (AI). NLP techniques enable intelligent machines to understand and analyze natural languages and make it possible for humans and machines to communicate through natural languages. However, more and more evidence indicates that NLP applications show human-like discriminatory bias or make unfair decisions. As NLP algorithms play an increasingly irreplaceable role in promoting the automation of...
Show moreNatural language processing (NLP) is an increasingly prominent subfield of artificial intelligence (AI). NLP techniques enable intelligent machines to understand and analyze natural languages and make it possible for humans and machines to communicate through natural languages. However, more and more evidence indicates that NLP applications show human-like discriminatory bias or make unfair decisions. As NLP algorithms play an increasingly irreplaceable role in promoting the automation of people's lives, bias in NLP is closely related to users' vital interests and demands considerable attention.While there are a growing number of studies related to bias in natural languages, the research on this topic is far from complete. In this thesis, we propose several studies to fill up the gaps in the area of bias in NLP in terms of three perspectives. First, existing studies are mainly confined to traditional and relatively mature NLP tasks, but for certain newly emerging tasks such as dialogue generation, the research on how to define, detect, and mitigate the bias in them is still absent. We conduct pioneering studies on bias in dialogue models to answer these questions. Second, previous studies basically focus on explicit bias in NLP algorithms but overlook implicit bias. We investigate the implicit bias in text classification tasks in our studies, where we propose novel methods to detect, explain, and mitigate the implicit bias. Third, existing research on bias in NLP focuses more on in-processing and post-processing bias mitigation strategies, but rarely considers how to avoid bias being produced in the generation process of the training data, especially in the data annotation phase. To this end, we investigate annotator bias in crowdsourced data for NLP tasks and its group effect. We verify the existence of annotator group bias, develop a novel probabilistic graphical framework to capture it, and propose an algorithm to eliminate its negative impact on NLP model learning.
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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: Dissertation : novel parallel algorithms and performance optimization techniques for the multi-level fast multipole algorithm
Creator: Lingg, Michael
Date: 2020
Collection: Electronic Theses & Dissertations
Description: Since Sir Issac Newton determined that characterizing orbits of celestial objects required considering the gravitational interactions among all bodies in the system, the N-Body problem has been a very important tool in physics simulations. Expanding on the early use of the classical N-Body problem for gravitational simulations, the method has proven invaluable in fluid dynamics, molecular simulations and data analytics. The extension of the classical N-Body problem to solve the Helmholtz...
Show moreSince Sir Issac Newton determined that characterizing orbits of celestial objects required considering the gravitational interactions among all bodies in the system, the N-Body problem has been a very important tool in physics simulations. Expanding on the early use of the classical N-Body problem for gravitational simulations, the method has proven invaluable in fluid dynamics, molecular simulations and data analytics. The extension of the classical N-Body problem to solve the Helmholtz equation for groups of particles with oscillatory interactions has allowed for simulations that assist in antenna design, radar cross section prediction, reduction of engine noise, and medical devices that utilize sound waves, to name a sample of possible applications. While N-Body simulations are extremely valuable, the computational cost of directly evaluating interactions among all pairs grows quadratically with the number of particles, rendering large scale simulations infeasible even on the most powerful supercomputers. The Fast Multipole Method (FMM) and the broader class of tree algorithms that it belongs to have significantly reduced the computational complexity of N-body simulations, while providing controllable accuracy guarantees. While FMM provided a significant boost, N-body problems tackled by scientists and engineers continue to grow larger in size, necessitating the development of efficient parallel algorithms and implementations to run on supercomputers. The Laplace variant of FMM, which is used to treat the classical N-body problem, has been extensively researched and optimized to the extent that Laplace FMM codes can scale to tens of thousands of processors for simulations involving over trillion particles. In contrast, the Multi-Level Fast Multipole Algorithm (MLFMA), which is aimed for the Helmholtz kernel variant of FMM, lags significantly behind in efficiency and scaling. The added complexity of an oscillatory potential results in much more intricate data dependency patterns and load balancing requirements among parallel processes, making algorithms and optimizations developed for Laplace FMM mostly ineffective for MLFMA. In this thesis, we propose novel parallel algorithms and performance optimization techniques to improve the performance of MLFMA on modern computer architectures. Proposed algorithms and performance optimizations range from efficient leveraging of the memory hierarchy on multi-core processors to an investigation of the benefits of the emerging concept of task parallelism for MLFMA, and to significant reductions of communication overheads and load imbalances in large scale computations. Parallel algorithms for distributed memory parallel MLFMA are also accompanied by detailed complexity analyses and performance models. We describe efficient implementations of all proposed algorithms and optimization techniques, and analyze their impact in detail. In particular, we show that our work yields significant speedups and much improved scalability compared to existing methods for MLFMA in large geometries designed to test the range of the problem space, as well as in real world problems.
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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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