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As two of the most abundant natural polymers, chitin and lignin not only play critical roles in fungal and plant cell walls but are also important functional materials and promising feedstocks for a variety of chemicals. This study investigated the interactions of chitin and lignin thin films with several other molecules via a quartz crystal microbalance with dissipation monitoring (QCM-D) and atomic force microscopy (AFM). Interactions between chitin and family 18 chitinases are vital for understanding bacterial invasion of fungi and human defense against fungal infection. Regenerated chitin (RChitin) thin films were prepared via chemical conversion and spin-coating. Changes in their mass and viscoelasticity were monitored by a QCM-D in real time during incubation with family 18 chitinases. The optimal temperature for the activity of chitinases on surfaces was lower than bulk solution studies in the literature. Family 18 chitinases showed greater activity on dissolved chitin oligosaccharides while family 19 chitinases showed greater activity on RChitin films, which was attributed to chitin-binding domains in family 19 chitinases. Catechyl lignin (C-lignin) is a promising substrate for lignin valorization. Films of C-lignin were synthesized via adsorbed horseradish peroxidase-catalyzed dehydrogenative polymerization (DHP) of caffeyl alcohol (C-alcohol), and degraded through Fenton chemistry with all processes observed by a QCM-D and AFM. The synthetic rate and yield for C-DHP films was lower than DHP films made from coniferyl alcohol (G-alcohol) and p-coumaryl alcohol (H-alcohol). The C-DHP film underwent complete Fenton mediated degradation in contrast to the G-DHP and H-DHP films regardless of their thicknesses. Conventional lignin suffers from recalcitrance to degradation. Copolymer lignin films were synthesized through surface-initiated copolymerization of C and G or C, G and H monolignols. As the concentration of C-alcohol increased, the percentage degradation of the synthesized DHP copolymer films increased. Almost all the CG-DHP or CGH-DHP films were degraded when the percentage of the C-alcohol in the polymerization feed was ≥ 75% and ≥ 60% for CG-DHP and CGH-DHP, respectively. Doctor of Philosophy Natural polymers are widely considered as an alternative to fossil fuels for the production of biofuels, biochemicals, and biomaterials. The features of their biodegradability, biocompatibility, and sustainability can significantly alleviate concerns about environmental pollution and energy security. The surfaces of natural polymers are critical to their properties and applications. This dissertation focuses on the study of interfacial behaviors occurring at two of the most abundant natural polymers, chitin and lignin, via surface analysis techniques, a quartz crystal microbalance with dissipation monitoring (QCM-D) and atomic force microscopy (AFM). When an endosymbiont bacteria enter a fungal host, they secrete chitinases to soften and loosen the chitin layer in the fungal cell wall. Small chitin fragments will be released from digestion of the chitin layer of the fungal cell wall by chitinases in humans suffering from fungal infections. In order to fully understand the interactions between the fungal chitin layer and chitinases, a chitin thin film was fabricated to mimic the chitin layer, and the changes of the chitin film in mass, viscoelasticity, and morphology during treatment with family 18 chitinases were studied at various temperatures and pH using a QCM-D and AFM. Family 19 chitinases produced greater degradation of chitin thin films than family 18 chitinases, even though the family 18 chitinases had greater activity in solution. Greater surface activity for family 19 chitinases were attributed to chitin-binding domains in their chemical structure that are absent in family 18 chitinases. Millions of tons of lignin are produced in the lignocellulosic biorefinery and are discarded every year due to their recalcitrance to degradation as a result of their heterogeneous and complex structure. A newly discovered lignin, catechyl lignin (C-lignin), has potential for enhancing degradation on account of its simple linear structure. In this dissertation, C-lignin thin films were synthesized on gold-coated QCM-D sensor surfaces via surface-initiated dehydrogenative polymerization of caffeyl alcohol (C-alcohol). Their enzymatic and chemical degradation was investigated. It was found that the C-lignin films underwent complete chelator-mediated Fenton degradation in contrast to conventional lignin films. Although the C-lignin promises to be an ideal substrate for lignin valorization, its narrow distribution in nature severely limits its wide application. In view of this limitation, some people are trying to incorporate C units into conventional lignin through genetically engineered plants. This dissertation demonstrates the successful copolymerization of C-alcohol with conventional monolignols and the improved degradation of the synthesized C unit-containing copolymer lignin films relative to conventional lignin films. The results are expected to inform the design of lignocellulosic biomass for greater utilization.

The high prevalence of work-related musculoskeletal disorders in occupational settings necessitates the development of economic, accurate, and convenient methods for quantifying biomechanical risk exposures. In terms of lifting, the occupational work environment does not provide resources for recording the start and end times of lifting tasks performed by individual workers. As a result, automatic detection of lift starts and ends is required for practical purposes. Occupational lifting styles vary depending on the asymmetry angle, which is the degree of shoulder or trunk rotation required by the lifting task. Predictive or machine learning (ML) algorithms have been increasingly used in the ergonomics field to identify occupational risk factors, such as lifting loads. However, such algorithms are often developed and validated using the dataset collected from the same lab-based experimental set-up, which limits their external validity. The recent development of wearable armbands with surface electromyography (sEMG) electrodes provides a low-cost, wireless, and non-invasive way to collect EMG data beyond laboratory settings. Despite their tremendous potential for field-based workload estimation, these armbands have not been widely implemented yet in automated lift detection and occupational workload estimation. The objective of this study was to evaluate the performance of machine learning (ML) algorithms in the automatic detection of lifts and classification of hand loads during manual lifting tasks from the data acquired by a wearable armband sensor with eight surface electromyography (sEMG) electrodes. Twelve healthy participants (six male and six female) performed repetitive symmetric (S), asymmetric (A), and free dynamic (F) lifts with three different hand-load levels (5 lb, 10 lb and 15 lb) at two origin (24" and 36") and two destination heights (6" and 36"). Three ML algorithms were utilized: Random Forest (RF), Support Vector Machines (SVM) and Gaussian Naïve Bayes (GNB). For lift detection, a subset of four participants was analyzed as a preliminary investigation. RF showed the best performance with the mean start and end errors of 0.53 ± 0.25 seconds and 0.76 ± 0.28 seconds, respectively. The accuracy score of 84.3 ± 3.3% was reported for lift start and 83.3 ± 9.9% for lift end. For hand-load classification, prediction models were developed using four different lifting datasets (S, A, S+A, and F) and were cross-validated using F as the test dataset. Mean classification accuracy was significantly lower in models developed with the S dataset (78.8 ± 7.3%) compared to A (83.3 ± 7.2%), S+A (82.1 ± 7.3%), and F (83.4 ± 8.1%). Overall, findings indicate that the implementation of ML algorithms with wearable EMG armbands for automatic lift detection in occupational settings can be promising. In hand-load classification, models developed with only controlled symmetric lifts were less accurate in predicting loads of more dynamic, unconstrained lifts, which is common in real-world settings. However, since both A and S+A demonstrated equivalent model accuracy with F, EMG armbands possess strong potential for estimating the hand loads of free-dynamic lifts using constrained lift trials involving asymmetric lifts. Master of Science Naturalistic occupational settings involve prolonged, frequent, and physically heavy lifting-lowering tasks that are associated with a high prevalence of musculoskeletal disorders. This necessitates the development of economic, accurate, and convenient methods for quantifying risk exposures such as load magnitude, repetitiveness and duration. In terms of lifting, the occupational work environment does not provide resources for recording the start and end of lifting tasks performed by individual workers for analysis. As a result, automatic detection of lift starts and ends is required for practical purposes. Occupational lifting styles vary depending on the asymmetry angle, which is the degree of shoulder or trunk rotation required by the lifting task. Predictive or machine learning (ML) algorithms have been increasingly used in the ergonomics field to identify occupational risk factors, such as lifting loads. However, such algorithms are often developed and validated using the dataset collected from the same lab-based experimental set-up, which limits their external validity. Electromyographic (EMG) signals representing the neuromuscular activity associated with muscular contractions can be valuable for exposure assessment. The recent development of wearable armbands with surface electromyography (sEMG) electrodes provides a low-cost, wireless, and non-invasive way to collect EMG data beyond laboratory settings. Despite their tremendous potential for field-based workload estimation, these armbands have not been widely implemented yet in automated lift detection and occupational workload estimation. The objective of this study was to evaluate the performance of machine learning (ML) algorithms in the automatic detection of lifts and classification of hand loads during manual lifting tasks from the data acquired by a wearable armband sensor with eight surface electromyography (sEMG) electrodes. Twelve healthy participants (six male and six female) performed repetitive symmetric (S), asymmetric (A), and free dynamic (F) lifts with three different hand-load levels (5 lb, 10 lb and 15 lb) at two origin (24" and 36") and two destination heights (6" and 36"). Three ML algorithms were utilized: Random Forest (RF), Support Vector Machines (SVM) and Gaussian Naïve Bayes (GNB). For lift detection, a subset of four participants was analyzed as a preliminary investigation. RF showed the best performance with the mean start and end errors of 0.53 ± 0.25 seconds and 0.76 ± 0.28 seconds, respectively. The accuracy score of 84.3 ± 3.3% was reported for lift start and 83.3 ± 9.9% for lift end. For hand-load classification, prediction models were developed using four different lifting datasets (S, A, S+A, and F) and were cross-validated using F as the test dataset. Mean classification accuracy was significantly lower in models developed with the S dataset (78.8 ± 7.3%) compared to A (83.3 ± 7.2%), S+A (82.1 ± 7.3%), and F (83.4 ± 8.1%). Overall, findings indicate that the implementation of ML algorithms with wearable EMG armbands for automatic lift detection in occupational settings can be promising. In hand-load classification, models developed with only controlled symmetric lifts were less accurate in predicting loads of more dynamic, unconstrained lifts, which is common in real-world settings. However, since both A and S+A demonstrated equivalent model accuracy with F, EMG armbands possess strong potential for estimating the hand loads of free-dynamic lifts using constrained lift trials involving asymmetric lifts.

Balancing indoor comfort and energy consumption is crucial to building energy efficiency. Occupancy information is a vital aspect in this process, as it determines the energy demand. Although there are various sensors used to gather occupancy information, environmental sensors stand out due to their low cost and privacy benefits. Machine learning algorithms play a critical role in estimating the relationship between occupancy levels and environmental data. To improve performance, more complex models such as deep learning algorithms are necessary. Long Short-Term Memory (LSTM) is a powerful deep learning algorithm that has been utilized in occupancy estimation. However, recently, an algorithm named Attention has emerged with improved performance. The study proposes a more effective model for occupancy level estimation by incorporating Attention into the existing Long Short-Term Memory algorithm. The results show that the proposed model is more accurate than using a single algorithm and has the potential to be integrated into building energy control systems to conserve even more energy. Master of Science The motivation for energy conservation and sustainable development is rapidly increasing, and building energy consumption is a significant part of overall energy use. In order to make buildings more energy efficient, it is necessary to obtain information on the occupancy level of rooms in the building. Environmental sensors are used to measure factors such as humidity and sound to determine occupancy information. However, the relationship between sensor readings and occupancy levels is complex, making it necessary to use machine learning algorithms to establish a connection. As a subfield of machine learning, deep learning is capable of processing complex data. This research aims to utilize advanced deep learning algorithms to estimate building occupancy levels based on environmental sensor data.

In biology and bioinformatics, a variety of data share a common property that challenges numerous cutting-edge research studies: heterogeneities at the individual level with respect to more than one factor. Examples of such heterogeneities include but are not limited to: 1) unequal susceptibility of different patients, and 2) large diversity in gene length, GC content, etc., along with the resulting gene characteristics. For many biological data analysis studies, the critical first step is usually to infer null probability distribution of observed data with the heterogeneities in multiple (confounding) factors taken into account, so that we can further investigate the impact of other factor(s) of interest. Obviously, the heterogeneities heavily influence the potential conclusions that we may draw from statistical analyses of the data. However, modeling such heterogeneities has been challenging, not only due to the inapplicable explicit modeling of all factors with heterogeneous effects on the data, but also because of the non-independence of many factors from one another. Existing methods, either partially/fully neglected the heterogeneity issue at all, or took care of each factor's heterogeneity in isolation. Evidences have shown the insufficiency of such strategies and the errors they may produce in downstream analyses. The emergence of large-scale data sets provides the opportunity to directly and comprehensively learn the heterogeneity from the data without explicitly modeling the mechanisms behind or exerting strong assumptions. The data, as often stored or organized as multidimensional contingency tensors, lead to a natural perspective of modeling heterogeneity with each impact factor of interest being one dimension. The heterogeneity in each factor's impact on the variable of interest can be captured by the marginal property of the data tensor with respect to the corresponding dimension. For instance, in a single-cell sequencing dataset, which can be organized as a matrix with each row representing a gene and each column representing a cell, the heterogeneity caused by both the gene and cell factors can be modeled. In this dissertation, we develop a novel model, Conditional Multifactorial Contingency (CMC), that models the intertwined heterogeneities in all dimensions of the data tensor and infers the probability distribution of each entry of the data tensor jointly conditioned on these heterogeneities. In the proposed CMC model, the problem is formulated as a maximum entropy problem of the contingency tensor's probability distribution subject to the marginal constraints, under the assumption that the individuals within each dimension are independent. The marginal constraints are applied to the expected value instead of observed trial outcomes, which plays a key role in avoiding the innumerable combinations of trial outcomes and leading to an elegant expression form of the entry's probability distribution. The model is first developed for 3D binary data matrix, then extended to multidimensional data tensors and integer data tensors. Furthermore, missing values are taken into account and CMC is extended to be compatible with data with missing values. Being empowered by CMC, we conducted four case studies for real-world bioinformatics research problems: (1) driving transcription factor (TF) identification; (2) scRNA-seq data normalization; (3) cancer-associated gene identification; (4) cell similarity quantification. For each of these case studies, we proposed a whole analysis framework and specific adaptation design for CMC. For the driving-TF identification, compared with traditional methods, we considered the variations in the gene's binding affinity in addition to the typically considered variations in TF's binding affinity. The driving TFs were identified by comparing the observed binding state and the estimated binding probability conditioned on TF/gene binding affinities. For the scRNA-seq data normalization, besides gene factor and cell factor, we figured out one more factor impacting the read counts, cDNA length, and applied CMC to comprehensively analyze the three factors. For cancer-associated gene identification, the CMC model is applied to systematically model the patient, gene, and mutation type factors in the mutation count data. As for the last application, to the best of our knowledge, our solution is the first proposed cell-to-cell-type similarity quantification method, thanks to the availability of CMC to systematically model and remove the impact of cell and gene factors. We studied the theoretical properties of the proposed model and validated the effectiveness and efficiency of our method through experiments. The uniqueness of the probability solution and the convergence of the algorithm was proved. In the endeavor to identify true driving TFs, CMC significantly boosted the best record of success rate, which was proved using data with ground truth. Besides, in an exploratory study without ground truth, in addition to the previously known TFs, Olig1 (ranks 2nd), Olig2 (ranks 3rd), and Sox10 (ranks 4th), we successfully identified Ppp1r14b (ranks 1st) and Zfp36l1 (ranks 6th) that function in oligodendrocyte lineage development, which was validated via biological knock-out experiments and, has led to genuine biological discoveries. In the scRNA-seq data normalization, experimental results show that, by taking the cell, gene, and cDNA-length factors into account, the normalized data achieves lower variances for housekeeping genes than the peer methods. Besides, the data normalized by the CMC model leads to better accuracy of downstream DEG detection than that normalized by peer normalization methods. In cancer-associated gene identification, the CMC model is able to eliminate most of the likely artefactual findings resulted by considering the hidden factors separately. In the cell similarity quantification, CMC based model enables the identification of cell types by establishing between-species cell similarity quantification, regardless of contamination in scRNA-seq data. Doctor of Philosophy Biological data are complicated and typically influenced by numerous factors, including characteristics of biological subjects, physical or chemical properties of molecules, artifacts created by experimental operations, and so on. The information of real interest in a biology/bioinformatics study can be buried in all sorts of irrelevant factors and their impacts on the data. Consider a simple example where a study is conducted to figure out if an association exists between a specific gene and a cancer. Although this gene shows obviously different frequencies of mutation in two groups of people, patients and the normal, we cannot safely confirm the association from this observation. Such differential mutation levels can also be a result of the diversity among all these people in how easily this gene is mutated in a person (related to many characteristics of this person besides "cancer/not"). We call this diversity "heterogeneity", and it actually can be seen everywhere, in people, in genes, in cells, and in cell types, etc. One needs to take good care of such heterogeneities so as to draw firm statistical hence scientific conclusions. However, handling the heterogeneities is far from trivial. On the one hand, it is generally impossible to fully understand the mechanisms behind those diversities, let alone to explicitly and rigorously formulate them. One the other hand, it is not rare that multiple factors intertwine with one another, in which case all these factors must be considered systematically in order to model the data precisely. Existing methods, either partially/fully neglected the heterogeneity issue at all, or took care of each factor's heterogeneity in isolation. Evidences have shown the insufficiency of such strategies and the errors they may produce in downstream analyses. As the exact mechanisms behind heterogeneities are usually not available, we aim to learn and infer the heterogeneities' effects on data from data itself. A large group of biological data can be stored or organized as multidimensional contingency tensors, with each impact factor of interest being one dimension. The heterogeneity in each factor's impact on the variable of interest can be captured by the marginal property of the data tensor with respect to the corresponding dimension, for example, the row sum and the column sum in a 2D tensor. In this dissertation, under the assumption that the individuals of each dimension are independent, we proposed a novel model, Conditional Multifactorial Contingency (CMC), that models the intertwined heterogeneities in all dimensions of the data tensor and infers the probability distribution of each entry of the data tensor jointly conditioned on these heterogeneities. The eventual and most comprehensive version of CMC can work on multidimensional binary or integer data tensors, even in cases where some values in the tensor are missing. CMC was initiated from elegant and simple statistical principles, derived through rigorous theoretical proofs, but ended up as a powerful tool being widely applicable to real-world biology/bioinformatics studies. Being empowered by CMC, we conducted four case studies for real-world bioinformatics research problems: (1) driving transcription factor (TF) identification; (2) scRNA-seq data normalization; (3) cancer-associated gene identification; (4) cell similarity quantification. For each of these case studies, we proposed a whole analysis framework and specific adaptation design for CMC. In each of them, our method based on CMC outperformed existing methods and provided inspiring clues for biological discoveries, which have been validated by biological experiments.

Decision-making is an essential topic for multi-robot coordination and collaboration and is also the main topic of this thesis. Examples can be found in autonomous driving, environmental monitoring, intelligent transportation, etc. To study this problem, we first use multiple applications as motivating examples and then construct the general formulation and solution for those applications. Finally, we extend our investigation from the fundamental problem formulation to resilient and decentralized versions. All those problems are studied in the combinatorial optimization domain with the help of submodular and matroid optimization techniques. As a motivating example, we use a multi-robot environmental monitoring problem to extract the general formulation of a multi-robot decision-making problem. Consider the problem of deploying multi-agent teams for environmental monitoring in a precision farming application. We want to answer the question of when and where to deploy our robots. This is a typical task allocation problem in multi-robot systems. Using the above problem as an example, we first focus on this decision-making problem, e.g., intermittent deployment problem, in a centralized scenario. Given a predictable agriculture environment, we want to make decisions for robots for this monitoring task. The problem is formulated as a combinatorial submodular optimization with matroid constraints. By utilizing the properties of submodularity, we aim to develop a solution with performance guarantees. This motivating example demonstrates how to use a submodular function and matroids to model and solve decision-making problems in multi-robot systems. Based on this framework, we continue to explore the fundamental decision-making problem in several other directions in multi-robot systems, including the robust decision-making problem. All those problems and solutions are formulated and considered in a centralized scenario. In the second part of this thesis, we switch our focus from centralized to decentralized scenarios. We first investigate a case where the robots in a distributed multi-robot system need to work together to guard the system against worst-case attacks while making decisions. By worst-case attacks, we refer to the case where the system may have up to $K$ sensor failures. To increase resilience, we propose a fully distributed algorithm to guide each robot's action selection when the system is attacked. The proposed algorithm guarantees performance in a worst-case scenario where up to a portion of the robots malfunction due to attacks. Based on this specific task allocation problem in robotics, we then create a unified framework for a more general case in a decentralized scenario, e.g., asynchronous decentralized decision-making problems with matroid and knapsack constraints. Finally, several applications in decentralized scenarios are used to validate the theoretical guaranteed performance in robotics. Doctor of Philosophy Robots have been widely used as mobile sensing agents nowadays in various applications. Especially with the help of multi-robot systems and artificial intelligence, our lives have changed dramatically in the last decades. One of the most fundamental questions is how to utilize multi-robot systems to finish tasks successfully. To answer this, we need first to formulate the problem from applications and then find theoretically guaranteed answers to those questions. Meanwhile, the robustness and resilience of the solution also need to be taken care of, as cyber-attacks or system failures can happen everywhere. Motivated by those two main goals, this thesis will first use multiple applications to introduce the thesis's topic. We then provide solutions to those problems in centralized and decentralized scenarios. Meanwhile, to increase the system's ability to handle failures, we need to answer how to improve the robustness and resilience of the proposed solutions. Therefore, the topic of this thesis spread from problem formulation to failure-proof solutions. The result of this thesis can be widely used in multi-robot decision-making applications, including autonomous driving, intelligent transportation, and other cyber-physical systems.

Complex user-end procedures for the execution of computationally expensive processes and tools on high performance computing platforms can hinder the scientific progress of researchers across many domains. In addition, such processes occasionally cannot be executed on user-end platforms either due to insufficient hardware resources or unacceptably long computing times. Such circumstances currently extend to highly sophisticated algorithms and tools utilized for analysis of fluorescent imaging data. Although an extensive collection of cloud-computing solutions exist allowing software developers to resolve these issues, such solutions often abstract both developers and integrators from the executing hardware particulars and can inadvertently incentivize non-ideal software design practices. The discussion herein consists of the theoretical design and real-world realization of an efficient architecture to enable direct multi-user parallel remote utilization of such research tools. Said networked scalable real-time architecture is multi-tier, extensible by design to a vast collection of application archetypes, and is not strictly limited to imaging analysis applications. Transport layer interfaces for packetized binary data transmission, asynchronous command issuance mechanisms, compression and decompression algorithm aggregation, and relational database management systems for inter-tier communication intermediation enable a robust, lightweight, and efficient architecture for networking and remotely interfacing with fluorescent imaging analysis processes. M.S. Collaboration amongst researchers within various technical domains who rely on information processing and analysis tools can be strengthened through the deployment of scientific computing infrastructure that enables their usage via a web interface. The architecture of such infrastructure is preferably efficient, lightweight, and simple while retaining potential future integration capabilities with additional research tools. This work presents the theoretical design and realization of an architecture for networking fluorescent imaging analysis processes so as to make them remotely usable within internal computer networks and across the world wide web.

Longitudinal personalized electronic health record (LPHR) provides a holistic view of health records for individuals and offers a consistent patient-controlled information system for managing the health care of patients. Except for the patients in Veterans Affairs health care service, however, no LPHR is available for the general population in the U.S. that can integrate the existing patients' electronic health records throughout life of care. Such a gap may be contributed mainly by the fact that existing patients' electronic health records are scattered across multiple health care facilities and often not shared due to privacy and security concerns from both patients and health care organizations. The main objective of this dissertation is to address these roadblocks by designing a scalable and interoperable LPHR with patient-controlled and mutually-trusted security and privacy. Privacy and security are complex problems. Specifically, without a set of access control policies, encryption alone cannot secure patient data due to insider threat. Moreover, in a distributed system like LPHR, so-called race condition occurs when access control policies are centralized while decisions making processes are localized. We propose a formal definition of secure LPHR and develop a blockchain-enabled next generation access control (BeNGAC) model. The BeNGAC solution focuses on patient-managed secure authorization for access, and NGAC operates in open access surroundings where users can be centrally known or unknown. We also propose permissioned blockchain technology - Hyperledger Fabric (HF) - to ease the shortcoming of race condition in NGAC that in return enhances the weak confidentiality protection in HF. Built upon BeNGAC, we further design a blockchain-enabled secure and trusted (BEST) LPHR prototype in which data are stored in a distributed yet decentralized database. The unique feature of the proposed BEST-LPHR is the use of blockchain smart contracts allowing BeNGAC policies to govern the security, privacy, confidentiality, data integrity, scalability, sharing, and auditability. The interoperability is achieved by using a health care data exchange standard called Fast Health Care Interoperability Resources. We demonstrated the feasibility of the BEST-LPHR design by the use case studies. Specifically, a small-scale BEST-LPHR is built for sharing platform among a patient and health care organizations. In the study setting, patients have been raising additional ethical concerns related to consent and granular control of LPHR. We engineered a Web-delivered BEST-LPHR sharing platform with patient-controlled consent granularity, security, and privacy realized by BeNGAC. Health organizations that holding the patient's electronic health record (EHR) can join the platform with trust based on the validation from the patient. The mutual trust is established through a rigorous validation process by both the patient and built-in HF consensus mechanism. We measured system scalability and showed millisecond-range performance of LPHR permission changes. In this dissertation, we report the BEST-LPHR solution to electronically sharing and managing patients' electronic health records from multiple organizations, focusing on privacy and security concerns. While the proposed BEST-LPHR solution cannot, expectedly, address all problems in LPHR, this prototype aims to increase EHR adoption rate and reduce LPHR implementation roadblocks. In a long run, the BEST-LPHR will contribute to improving health care efficiency and the quality of life for many patients. Doctor of Philosophy Longitudinal personalized electronic health record (LPHR) provides a holistic view of health records for individuals and offers a consistent patient-controlled information system for managing the health care of patients. Except for the patients in Veterans Affairs health care service, however, no LPHR is available for the general population in the U.S. that can integrate the existing patients' electronic health records throughout life of care. Such a gap may be contributed mainly by the fact that existing patients' electronic health records are scattered across multiple health care facilities and often not shared due to privacy and security concerns from both patients and health care organizations. The main objective of this dissertation is to address these roadblocks by designing a scalable and interoperable LPHR with patient-controlled and mutually-trusted security and privacy. We propose a formal definition of secure LPHR and develop a novel blockchain-enabled next generation access control (BeNGAC) model, that can protect security and privacy of LPHR. Built upon BeNGAC, we further design a blockchain-enabled secure and trusted (BEST) LPHR prototype in which data are stored in a distributed yet decentralized database. The health records on BEST-LPHR are personalized to the patients with patient-controlled security, privacy, and granular consent. The unique feature of the proposed BEST-LPHR is the use of blockchain technology allowing BeNGAC policies to govern the security, privacy, confidentiality, data integrity, scalability, sharing, and auditability. The interoperability is achieved by using a health care data exchange standard. We demonstrated the feasibility of the BEST-LPHR design by the use case studies. Specifically, a small-scale BEST-LPHR is built for sharing platform among a patient and health care organizations. We engineered a Web-delivered BEST-LPHR sharing platform with patient-controlled consent granularity, security, and privacy realized by BeNGAC. Health organizations that holding the patient's electronic health record (EHR) can join the platform with trust based on the validation from the patient. The mutual trust is established through a rigorous validation process by both the patient and built-in blockchain consensus mechanism. We measured system scalability and showed millisecond-range performance of LPHR permission changes. In this dissertation, we report the BEST-LPHR solution to electronically sharing and managing patients' electronic health records from multiple organizations, focusing on privacy and security concerns. While the proposed BEST-LPHR solution cannot, expectedly, address all problems in LPHR, this prototype aims to increase EHR adoption rate and reduce LPHR implementation roadblocks. In a long run, the BEST-LPHR will contribute to improving health care efficiency and the quality of life for many patients.

Real-time computing systems are those that are designed to achieve computing goals by certain deadlines. Real-time computing systems are present in everything from cars to airplanes, pacemakers to industrial-control systems, and other pieces of critical infrastructure. With the increasing interconnectivity of these systems, system security issues and the constant threat of manipulation by malicious external attackers that have plagued general computing systems, now threaten the integrity and safety of real-time systems. This dissertation discusses three different defense techniques that focuses on the role that real-time scheduling theory can play to reduce runtime cost, and guarantee correctness when applying these defense strategies to real-time systems. The first work introduces a novel timing aware defense strategy for the CAN bus that utilizes TrustZone on state-of-the-art ARMv8-M microcontrollers. The second reduces the runtime cost of control-flow integrity (CFI), a popular system security defense technique, by correctly modeling when a real-time system performs I/O, and exploiting the model to schedule CFI procedures efficiently. Finally, the third studies and provides a lightweight mitigation strategy for a recently discovered vulnerability within mixed criticality real-time systems. Doctor of Philosophy Real-time computing systems are those that are designed to achieve computing goals within certain timing constraints. Real-time computing systems are present in everything from cars to airplanes, pacemakers to industrial-control systems, and other pieces of critical infrastructure. With the increasing interconnectivity of these systems, system security issues and the constant threat of manipulation by malicious external attackers that have plagued general computing systems, now threaten the integrity and safety of real-time systems. This dissertation discusses three different defense techniques that focuses on the role that real-time scheduling theory can play to reduce runtime cost, and guarantee correctness when applying these defense strategies to real-time systems. The first work introduces a novel timing aware defense strategy for the Controller Area Network (CAN). CAN is a popular communication system that is at the heart of every modern passenger vehicle and is indispensable for the safe operation of various components such as the engine and transmission systems, and due to its simplicity, may be vulnerable to a variety of attacks. We leverage security advancements in modern processor design to provide a lightweight and predictable (in terms of time taken to perform the operation) defense technique for some of these vulnerabilities. The second work applies a technique called Control-Flow Integrity (CFI) to real-time systems. CFI is a general-purpose defense technique to prevent attackers from modifying software execution, and applying such techniques to real-time systems, particularly those with limited hardware capabilities, may be infeasible. By applying real-time scheduling theory, we propose a strategy to apply CFI to such systems, while reducing its overhead, or cost, without compromising the security guarantees CFI inherently provides. Finally, safety-critical systems may consist of a mix of operations, each having a different level of importance (criticality) with respect to the safe operation of the system. However, due to the complexity of modeling such systems, the models themselves may be vulnerable to attacks. Through simulations we study one such vulnerability and propose a modification to mitigate it.

While increasing number of vehicles on urban roadways create uncontrolled congestion, connectivity among vehicles, traffic lights and other road-side units provide abundant data that paves avenues for novel smart traffic control mechanisms to mitigate traffic congestion and delays. However, increasingly complex vehicular applications have outpaced the computational capabilities of on-board processing units, therefore requiring novel offloading schemes onto additional resources located by the road-side. Adding connectivity and other computational resources on legacy traffic infrastructure may also introduce security vulnerabilities. To ensure that the timeliness and resource constraints of the vehicles using the roadways as well as the applications being deployed on the traffic infrastructure are met, the transportation systems needs to be more predictable. This dissertation discusses three areas that focus on improving the predictability and performance of the connected traffic infrastructure. Firstly, a holistic traffic control strategy is presented that ensures predictable traffic flow by minimizing traffic delays, accounting for unexpected traffic conditions and ensuring timely emergency vehicle traversal through an urban road network. Secondly, a vehicular edge resource management strategy is discussed that incorporates connected traffic lights data to meet timeliness requirements of the vehicular applications. Finally, security vulnerabilities in existing traffic controllers are studied and countermeasures are provided to ensure predictable traffic flow while thwarting attacks on the traffic infrastructure. Doctor of Philosophy Exponentially increasing vehicles especially in urban areas create pollution, delays and uncontrolled traffic congestion. However, improved traffic infrastructure brings connectivity among the vehicles, traffic lights, road-side detectors and other equipment, which can be leveraged to design new and advanced traffic control techniques. The initial work in this dissertation provides a traffic control technique that (i) reduces traffic wait times for the vehicles in urban areas, (ii) ensures safe and quick movements of emergency vehicles even through crowded areas, and (iii) ensures that the traffic keeps moving even under unexpected lane closures or roadblocks. As technology advances, connected vehicles are becoming increasingly automated. This allows the car manufacturers to design novel in-vehicle features where the passengers can now stream media-rich content, play augmented reality (AR)-based games and/or get high definition information about the surroundings on their car's display, while the car is driven through the urban traffic. This is made possible by providing additional computing resources along the road-side that the vehicles can utilize wirelessly to ensure passenger's comfort and improved experience of in-vehicle features. In this dissertation, a technique is provided to manage the computational resources which will allow vehicles (and its passengers) to use multiple features simultaneously. As the traffic infrastructure becomes increasingly inter-connected, it also allows malicious actors to exploit vulnerabilities such as modifying traffic lights, interfering with road-side sensors, etc. This can lead to increased traffic wait times and eventually bring down the traffic network. In the final work, one such vulnerability in traffic infrastructure is studied and mitigating measures are provided so that the traffic keeps moving even when an attack is detected. In all, this dissertation aims to improve safety, security and overall experience of the drivers, passengers and the pedestrians using the connected traffic infrastructure.

We used a 50Hz sampling frequency to collect tri-axle acceleration from the cows. For the traditional Machine learning approach, we segmented the data to calculate features, selected the important features, and applied machine learning algorithms for classification. We compared the performance of various models and found a robust model with relatively low computation and high accuracy. For the deep learning approach, we designed an end-to-end trainable Convolutional Neural Networks (CNN) to predict activities for given segments, applied distillation, and quantization to reduce model size. In addition to the fixed window size approach, we used CNN to predict dense labels that each data point has an individual label, inspired by semantic segmentation. In this way, we could have a more precise measurement for the composition of activities. Summarily, physically monitoring the well-being of crowded animals is labor-intensive, so we proposed a solution for timely and efficient measuring of cattle’s daily activities using wearable sensors and machine learning models. M.S. Animal agriculture has intensified over the past several decades, and animals are managed increasingly as large groups. This group-based management has significantly increased productivity. However, animals are often located remotely on large expanses of pasture, which makes continuous monitoring of daily activities to assess animal health and well-being labor-intensive and challenging [37]. Remote monitoring of animal activities with wireless sensor nodes integrated with machine learning algorithms is a promising solution. The machine learning models will predict the activities of given accelerometer segments, and the pre-dicted result will be uploaded to the cloud. The challenges would be the limitation in power consumption and computation. To propose a precise measurement of individual cattle in the herd, we experimented with several different types of machine learning methods with different advantages and drawbacks in performance and efficiency.

Information mining and knowledge learning from sequential data is a field of growing importance in both industrial and academic fields. Sequential data, which is the natural representation format of the information flow in many applications, usually carries enormous information and is able to help researchers gain insights for various tasks such as airport threat detection, cyber-attack detection, recommender system, point-of-interest (POI) prediction, and citation forecasting. This dissertation focuses on developing the methods for sequential data-driven applications and evolutionary dynamics characterization for various topics such as transit service disruption detection, early event detection on social media, technology opportunity discovery, and traffic incident impact analysis. In particular, four specific applications are studied with four proposed novel methods, including a spatiotemporal feature learning framework for transit service disruption detection, a multi-task learning framework for cybersecurity event detection, citation dynamics modeling via multi-context attentional recurrent neural networks, and traffic incident impact forecasting via hierarchical spatiotemporal graph neural networks. For the first of these methods, the existing transit service disruption detection methods usually suffer from two significant shortcomings: 1) failing to modulate the sparsity of the social media feature domain, i.e., only a few important ``particles'' are indeed related to service disruption among the massive volume of data generated every day and 2) ignoring the real-world geographical connections of transit networks as well as the semantic consistency existing in the problem space. This work makes three contributions: 1) developing a spatiotemporal learning framework for metro disruption detection using open-source data, 2) modeling semantic similarity and spatial connectivity among metro lines in feature space, and 3) developing an optimization algorithm for solving the multi-convex and non-smooth objective function efficiently. For the second of these methods, the conventional studies in cybersecurity detection suffer from the following shortcomings: 1) unable to capture weak signals generated by the cyber-attacks on small organizations or individual accounts, 2) lack of generalization of distinct types of security incidents, and 3) failing to consider the relatedness across different types of cyber-attacks in the feature domain. Three contributions are made in this work: 1) formulating the problem of social media-based cyber-attack detection into the multi-task learning framework, 2) modeling multi-type task relatedness in feature space, and 3) developing an efficient algorithm to solve the non-smooth model with inequality constraints. For the third of these methods, conventional citation forecasting methods are using the traditional temporal point process, which suffers from several drawbacks: 1) unable to predict the technological categories of citing documents and thus are incapable of technological diversity assessment, and 2) require prior domain knowledge and thus are hard to extend to different research areas. Two contributions are made in this work: 1) formulating a novel framework to provide long-term citation predictions in an end-to-end fashion by integrating the process of learning intensity function representations and the process of predicting future citations and 2) designing two novel temporal attention mechanisms to improve the model's ability to modulate complicated temporal dependencies and to allow the model to dynamically combine the observation and prediction sides during the learning process. For the fourth of these methods, the previous work treats the traffic sensor readings as the features and views the incident duration prediction as a feature-driven regression, which typically suffers from three drawbacks: 1) ignoring the existence of the road-sensor hierarchical structure in the real-world traffic network, 2) unable to learn and modulate the hidden temporal patterns in the sensor readings, and 3) lack of consideration of the spatial connectivity between arterial roads and traffic sensors. This work makes three significant contributions: 1) designing a hierarchical graph convolutional network architecture for modeling the road-sensor hierarchy, 2) proposing novel spatiotemporal attention mechanism on the sensor- and road-level features for representation learning, and 3) presenting a graph convolutional network-based method for incident representation learning via spatial connectivity modeling and traffic characteristics modulation. Doctor of Philosophy Information mining and knowledge learning from sequential data is a field of growing importance in both industrial and academic fields. Sequential data, which is the natural representation format of the information flow in many applications, usually carries enormous information and is able to help researchers gain insights for various tasks such as airport threat detection, cyber-attack detection, recommender system, point-of-interest (POI) prediction, and citation forecasting. This dissertation focuses on developing the methods for sequential data-driven applications and evolutionary dynamics characterization for various topics such as transit service disruption detection, early event detection on social media, technology opportunity discovery, and traffic incident impact analysis. In particular, four specific applications are studied with four proposed novel methods, including a spatiotemporal feature learning framework for transit service disruption detection, a multi-task learning framework for cybersecurity event detection, citation dynamics modeling via multi-context attentional recurrent neural networks, and traffic incident impact forecasting via hierarchical spatiotemporal graph neural networks. For the first of these methods, the existing transit service disruption detection methods usually suffer from two significant shortcomings: 1) failing to modulate the sparsity of the social media feature domain, i.e., only a few important ``particles'' are indeed related to service disruption among the massive volume of data generated every day and 2) ignoring the real-world geographical connections of transit networks as well as the semantic consistency existing in the problem space. This work makes three contributions: 1) developing a spatiotemporal learning framework for metro disruption detection using open-source data, 2) modeling semantic similarity and spatial connectivity among metro lines in feature space, and 3) developing an optimization algorithm for solving the multi-convex and non-smooth objective function efficiently. For the second of these methods, the conventional studies in cybersecurity detection suffer from the following shortcomings: 1) unable to capture weak signals generated by the cyber-attacks on small organizations or individual accounts, 2) lack of generalization of distinct types of security incidents, and 3) failing to consider the relatedness across different types of cyber-attacks in the feature domain. Three contributions are made in this work: 1) formulating the problem of social media-based cyber-attack detection into the multi-task learning framework, 2) modeling multi-type task relatedness in feature space, and 3) developing an efficient algorithm to solve the non-smooth model with inequality constraints. For the third of these methods, conventional citation forecasting methods are using the traditional temporal point process, which suffers from several drawbacks: 1) unable to predict the technological categories of citing documents and thus are incapable of technological diversity assessment, and 2) require prior domain knowledge and thus are hard to extend to different research areas. Two contributions are made in this work: 1) formulating a novel framework to provide long-term citation predictions in an end-to-end fashion by integrating the process of learning intensity function representations and the process of predicting future citations and 2) designing two novel temporal attention mechanisms to improve the model's ability to modulate complicated temporal dependencies and to allow the model to dynamically combine the observation and prediction sides during the learning process. For the fourth of these methods, the previous work treats the traffic sensor readings as the features and views the incident duration prediction as a feature-driven regression, which typically suffers from three drawbacks: 1) ignoring the existence of the road-sensor hierarchical structure in the real-world traffic network, 2) unable to learn and modulate the hidden temporal patterns in the sensor readings, and 3) lack of consideration of the spatial connectivity between arterial roads and traffic sensors. This work makes three significant contributions: 1) designing a hierarchical graph convolutional network architecture for modeling the road-sensor hierarchy, 2) proposing novel spatiotemporal attention mechanism on the sensor- and road-level features for representation learning, and 3) presenting a graph convolutional network-based method for incident representation learning via spatial connectivity modeling and traffic characteristics modulation.

Several calamities occur throughout the world each year, resulting in varying losses. Disasters wreak havoc on infrastructures and impair operation. They result in human deaths and injuries and stress people's mental and emotional states. These negative impacts of natural disasters induce significant economic losses, as demonstrated by the $ 423 billion loss in 2011 in Tohoku, Japan, and the $ 133 billion loss in hurricane Harvey, U.S.A. Every year, hurricanes and tropical storms result in 10,000 human deaths worldwide. To mitigate losses, communities' readiness, flexibility, and resilience must be strengthened. To this end, appropriate techniques for forecasting a community's capacity and functionality in the face of impending crises must be developed and suitable community resilience metrics and their quantification must be established. Collaboration between critical infrastructures such as power systems and emergency services and social networks is critical for building a resilient community. As a result, we require metrics that account for both the social and infrastructure aspects of the community. While the literature on critical infrastructures such as power systems discusses the effect of social factors on resilience, they do not model these social factors and metrics due to their complexity. On the other hand, it turns out that the role of critical infrastructures and some critical social characteristics is overlooked in the computational social science literature on community resilience. Thus, this dissertation presents a multi-agent socio-technical model of community resilience, taking into account the interconnection of power systems, emergency services, and social communities. We offer relevant measures for each section and describe dynamic change and its dependence on other metrics using a variety of theories and expertise from social science, psychology, electrical engineering, and emergency services. To validate the model, we used data on two hurricanes (Irma and Harvey) collected from Twitter, GoogleTrends, FEMA, power utilities, CNN, and Snopes (a fact-checking organization). We also describe methods for quantifying social metrics such as anxiety, risk perception, cooperation using social sensing, natural language processing, and text mining tools. Doctor of Philosophy Power systems serve social communities that consist of residential, commercial, and industrial customers. The social behavior and degree of collaboration of all stakeholders, such as consumers, prosumers, and utilities, affect the level of preparedness, mitigation, recovery, adaptability, and, thus, power system resilience. Nonetheless, the literature pays scant attention to stakeholders' social characteristics and collaborative efforts when confronted with a disaster and views the problem solely as a cyber-physical system. However, power system resilience, which is not a standalone discipline, is inherently a cyber-physical-social problem, making it complex to address. To this end, in this dissertation, we develop a socio-technical power system resilience model based on neuroscience, social science, and psychological theories and use the threshold model to simulate the behavior of power system stakeholders during a disaster. We validate our model using datasets of hurricane Harvey of Category 4 that hit Texas in August 2017 and hurricane Irma of Category 5 that made landfall in Florida in September 2017. We retrieve these datasets from Twitter and GoogleTrend and then apply natural language processing and language psychology analysis tools to deduce the social behavior of the end-users.

In this work, we present different deep learning-based digital pre-distorters and compare them based on their performance towards improving the linearity of highly non-linear power amplifiers. The simulation results show that BiLSTM based DPDs work the best in terms of improving the linearity performance. We also compare two methodologies of direct learning and indirect learning to develop deep learning-based digital pre-distorters (DL-DPDs) models and evaluate their improvement on the linearity of Power Amplifiers (PA). We carry out a theoretical analysis on the differences between these training methodologies and verify their performance with simulation results on class-AB and class-F⁻¹ PAs. The simulation results show that both the learning methods lead to an improvement of more than 12 dB and 11dB in the linearity of class-AB and class-F⁻¹ PAs respectively, with indirect learning DL-DPD offering marginally better performance. Moreover, we compare the DL-DPD with memory polynomial models and show that using the former gives a significant improvement over the memory polynomials. Furthermore, we discuss the advantages of exploiting a BiLSTM based neural network architecture for designing direct/indirect DPDs. We demonstrate that BiLSTM DPD can be used to pre distort signals of any size without the drop in linearity. Moreover, based on the insights we develop a frequency domain loss using which further increased the linearity of the PA. Master of Science Wireless communication devices have fundamentally changed the way we interact with people. This increased the user's reliance on communication devices and significantly grew the need for higher data rates and faster internet speeds. But one major obstacle inside the transmitter chain (antenna) with increasing the data rates is the power amplifier, which distorts the signals at these higher powers. This distortion will reduce the efficiency and reliability of communication systems, greatly decreasing the quality of communication. So, we developed a high-performance DPD using deep learning to combat this issue. In this paper, we compare different deep learning-based DPDs and analyze which offers better performance. We also contrast two training methodologies to learn these DL-DPDs, theoretically and with simulation to arrive at which method offers better performing DPDs. We do these experiments on two different types of power amplifiers, and signals of any length. We design a new loss function, such that optimizing it leads to better DL-DPDs.

Throughout stochastic data processing fields, mean and covariance matrices are commonly employed for purposes such as standardizing multivariate data through decorrelation. For practical applications, these matrices are usually estimated, and often, the data used for these estimates are non-Gaussian or may be corrupted by outliers or impulsive noise. To address this, robust estimators should be employed. However, in signal processing, where complex-valued data are common, the robust estimation techniques currently employed, such as M-estimators, provide limited robustness in the multivariate case. For this reason, this dissertation extends, to the complex-valued domain, the high-breakdown-point class of multivariate estimators called S-estimators. This dissertation defines S-estimators in the complex-valued context, and it defines their properties for complex-valued data. One major shortcoming of the leading high-breakdown-point multivariate estimators, such as the Rocke S-estimator and the smoothed hard rejection MM-estimator, is that they lack statistical efficiency at non-Gaussian distributions, which are common with real-world applications. This dissertation proposes a new tunable S-estimator, termed the Sq-estimator, for the general class of elliptically symmetric distributions—a class containing many common families such as the multivariate Gaussian, K-, W-, t-, Cauchy, Laplace, hyperbolic, variance gamma, and normal inverse Gaussian distributions. This dissertation demonstrates the diverse applicability and performance benefits of the Sq-estimator through theoretical analysis, empirical simulation, and the processing of real-world data. Through analytical and empirical means, the Sq-estimator is shown to generally provide higher maximum efficiency than the leading maximum-breakdown estimators, and it is also shown to generally be more stable with respect to initial conditions. To illustrate the theoretical benefits of the Sq for complex-valued applications, the efficiencies and influence functions of adaptive minimum variance distortionless response (MVDR) beamformers based on S- and M-estimators are compared. To illustrate the finite-sample performance benefits of the Sq-estimator, empirical simulation results of multiple signal classification (MUSIC) direction-of-arrival estimation are explored. Additionally, the optimal investment of real-world stock data is used to show the practical performance benefits of the Sq-estimator with respect to robustness to extreme events, estimation efficiency, and prediction performance. Doctor of Philosophy Throughout stochastic processing fields, mean and covariance matrices are commonly employed for purposes such as standardizing multivariate data through decorrelation. For practical applications, these matrices are usually estimated, and often, the data used for these estimates are non-normal or may be corrupted by outliers or large sporadic noise. To address this, estimators should be employed that are robust to these conditions. However, in signal processing, where complex-valued data are common, the robust estimation techniques currently employed provide limited robustness in the multivariate case. For this reason, this dissertation extends, to the complex-valued domain, the highly robust class of multivariate estimators called S-estimators. This dissertation defines S-estimators in the complex-valued context, and it defines their properties for complex-valued data. One major shortcoming of the leading highly robust multivariate estimators is that they may require unreasonably large numbers of samples (i.e. they may have low statistical efficiency) in order to provide good estimates at non-normal distributions, which are common with real-world applications. This dissertation proposes a new tunable S-estimator, termed the Sq-estimator, for the general class of elliptically symmetric distributions—a class containing many common families such as the multivariate Gaussian, K-, W-, t-, Cauchy, Laplace, hyperbolic, variance gamma, and normal inverse Gaussian distributions. This dissertation demonstrates the diverse applicability and performance benefits of the Sq-estimator through theoretical analysis, empirical simulation, and the processing of real-world data. Through analytical and empirical means, the Sq-estimator is shown to generally provide higher maximum efficiency than the leading highly robust estimators, and its solutions are also shown to generally be less sensitive to initial conditions. To illustrate the theoretical benefits of the Sq-estimator for complex-valued applications, the statistical efficiencies and robustness of adaptive beamformers based on various estimators are compared. To illustrate the finite-sample performance benefits of the Sq-estimator, empirical simulation results of signal direction-of-arrival estimation are explored. Additionally, the optimal investment of real-world stock data is used to show the practical performance benefits of the Sq-estimator with respect to robustness to extreme events, estimation efficiency, and prediction performance.

The electric power grid is evolving in terms of generation, transmission and distribution network architecture. On the generation side, distributed energy resources (DER) are participating at a much larger scale. Transmission and distribution networks are transforming to a decentralized architecture from a centralized one. Residential and commercial buildings are now considered as active elements of the electric grid which can participate in grid operation through applications such as the Demand Response (DR). DR is an application through which electric power consumption during the peak demand periods can be curtailed. DR applications ensure an economic and stable operation of the electric grid by eliminating grid stress conditions. In addition to that, DR can be utilized as a mechanism to increase the participation of green electricity in an electric grid. The DR applications, in general, are passive in nature. During the peak demand periods, common practice is to shut down the operation of pre-selected electrical equipment i.e., heating, ventilation and air conditioning (HVAC) and lights to reduce power consumption. This approach, however, is not optimal and does not take into consideration any user preference. Furthermore, this does not provide any information related to demand flexibility beforehand. Under the broad concept of grid modernization, the focus is now on the applications of data analytics in grid operation to ensure an economic, stable and resilient operation of the electric grid. The work presented here utilizes data analytics in DR application that will transform the DR application from a static, look-up-based reactive function to a dynamic, context-aware proactive solution. The dynamic demand response framework presented in this dissertation performs three major functionalities: electrical load forecast, electrical load disaggregation and peak load reduction during DR periods. The building-level electrical load forecasting quantifies required peak load reduction during DR periods. The electrical load disaggregation provides equipment-level power consumption. This will quantify the available building-level demand flexibility. The peak load reduction methodology provides optimal HVAC setpoint and brightness during DR periods to reduce the peak demand of a building. The control scheme takes user preference and context into consideration. A detailed methodology with relevant case studies regarding the design process of the network architecture of a deep learning algorithm for electrical load forecasting and load disaggregation is presented. A case study regarding peak load reduction through HVAC setpoint and brightness adjustment is also presented. To ensure the scalability and interoperability of the proposed framework, a layer-based software architecture to replicate the framework within a cloud environment is demonstrated. Doctor of Philosophy The modern power grid, known as the smart grid, is transforming how electricity is generated, transmitted and distributed across the US. In a legacy power grid, the utilities are the suppliers and the residential or commercial buildings are the consumers of electricity. However, the smart grid considers these buildings as active grid elements which can contribute to the economic, stable and resilient operation of an electric grid. Demand Response (DR) is a grid application that reduces electrical power consumption during peak demand periods. The objective of DR application is to reduce stress conditions of the electric grid. The current DR practice is to shut down pre-selected electrical equipment i.e., HVAC, lights during peak demand periods. However, this approach is static, pre-fixed and does not consider any consumer preference. The proposed framework in this dissertation transforms the DR application from a look-up-based function to a dynamic context-aware solution. The proposed dynamic demand response framework performs three major functionalities: electrical load forecasting, electrical load disaggregation and peak load reduction. The electrical load forecasting quantifies building-level power consumption that needs to be curtailed during the DR periods. The electrical load disaggregation quantifies demand flexibility through equipment-level power consumption disaggregation. The peak load reduction methodology provides actionable intelligence that can be utilized to reduce the peak demand during DR periods. The work leverages functionalities of a deep learning algorithm to increase forecasting accuracy. An interoperable and scalable software implementation is presented to allow integration of the framework with existing energy management systems.

This dissertation explores the idea of inducing grid peak demand curtailment by turning commercial buildings into interactive assets for building owners during the demand control period. The work presented here is useful for both ab initio design of new sites and for existing or retrofitted sites. An analytical hierarchy process (AHP)-based framework is developed to curtail the thermal load effectively across a group of commercial buildings. It gives an insight into the amount of peak demand reduction possible for each building, subject to indoor thermal comfort constraints as per ASHRAE standards. Furthermore, the detailed operation of buildings in communion with the electric grid is illustrated through case studies. This analysis forms an outline for the assessment of transactive energy opportunities for commercial buildings in distribution system operations and lays the foundation for a seamless building-to-grid integration framework. The contribution of this dissertation is fourfold – (a) an efficient method of developing high-fidelity physics-based building energy models for understanding the realistic operation of commercial buildings, (b) identification of minimal dataset to achieve a target accuracy for the building energy models (c) quantification of building peak demand reduction potential and corresponding energy savings across a stipulated range of thermostat setpoint temperatures and (d) AHP-based demand curtailment scheme. By careful modeling, it is shown that commercial building models developed using this methodology are both accurate and robust. As a result, the proposed approach can be extended to other commercial buildings of diverse characteristics, independent of the location. The methodology presented here takes a holistic approach towards building energy modeling by accounting for several building parameters and interactions between them. In addition, parametric analysis is done to identify a useful minimal dataset required to achieve a specified accuracy for the building energy models. This thesis describes the concept of commercial buildings as interactive assets in a transactive grid environment and the idea behind its working. Doctor of Philosophy This dissertation titled "An Expert-based Approach for Grid Peak Demand Curtailment using HVAC Thermostat Setpoint Interventions in Commercial Buildings" tackles two important challenges in the energy management domain: –electric grid peak demand curtailment and energy savings in commercial buildings. The distinguishing feature of the proposed solution lies in addressing these challenges solely through demand-side management (DSM) strategies, which include HVAC thermostat setpoint interventions and lighting control. We present a methodology for developing highly accurate building energy models that serve as digital twins of actual buildings. These digital replicas can be used to quantify the impact of various interventions and reflect the realistic operation of commercial buildings across varied conditions. This enables building owners to control demand intelligently and transact energy effectively in the electricity market. The development of Internet of Things (IoT) market and advanced technologies such as smart meters and smart thermostats allows for the design of novel strategies that address traditional challenges faced by electric grid operators. This dissertation elaborates on how smart buildings can leverage IoT-based solutions to participate in the electricity market during demand control periods. We also developed an expert opinion-based demand curtailment allocation scheme resulting in grid peak demand reduction. The numerical results obtained reinforce the effectiveness of the proposed solution across varied climatic conditions.

The introduction of high-throughput molecular profiling technologies provides the capability of studying diverse biological systems at molecular level. However, due to various limitations of measurement instruments, data preprocessing is often required in biomedical research. Improper preprocessing will have negative impact on the downstream analytics tasks. This thesis studies two important preprocessing topics: missing value imputation and between-sample normalization. Missing data is a major issue in quantitative proteomics data analysis. While many methods have been developed for imputing missing values in high-throughput proteomics data, comparative assessment on the accuracy of existing methods remains inconclusive, mainly because the true missing mechanisms are complex and the existing evaluation methodologies are imperfect. Moreover, few studies have provided an outlook of current and future development. We first report an assessment of eight representative methods collectively targeting three typical missing mechanisms. The selected methods are compared on both realistic simulation and real proteomics datasets, and the performance is evaluated using three quantitative measures. We then discuss fused regularization matrix factorization, a popular low-rank matrix factorization framework with similarity and/or biological regularization, which is extendable to integrating multi-omics data such as gene expressions or clinical variables. We further explore the potential application of convex analysis of mixtures, a biologically inspired latent variable modeling strategy, to missing value imputation. The preliminary results on proteomics data are provided together with an outlook into future development directions. While a few winners emerged from our comparative assessment, data-driven evaluation of imputation methods is imperfect because performance is evaluated indirectly on artificial missing or masked values not authentic missing values. Imputation accuracy may vary with signal intensity. Fused regularization matrix factorization provides a possibility of incorporating external information. Convex analysis of mixtures presents a biologically plausible new approach. Data normalization is essential to ensure accurate inference and comparability of gene expressions across samples or conditions. Ideally, gene expressions should be rescaled based on consistently expressed reference genes. However, for normalizing biologically diverse samples, the most commonly used reference genes have exhibited striking expression variability, and distribution-based approaches can be problematic when differentially expressed genes are significantly asymmetric. We introduce a Cosine score based iterative normalization (Cosbin) strategy to normalize biologically diverse samples. The between-sample normalization is based on iteratively identified consistently expressed genes, where differentially expressed genes are sequentially eliminated according to scale-invariant Cosine scores. We evaluate the performance of Cosbin and four other representative normalization methods (Total count, TMM/edgeR, DESeq2, DEGES/TCC) on both idealistic and realistic simulation data sets. Cosbin consistently outperforms the other methods across various performance criteria. Implemented in open-source R scripts and applicable to grouped or individual samples, the Cosbin tool will allow biologists to detect subtle yet important molecular signals across known or novel phenotypic groups. Master of Science Data preprocessing is often required due to various limitations of measurement instruments in biomedical research. This thesis studies two important preprocessing topics: missing value imputation and between-sample normalization. Missing data is a major issue in quantitative proteomics data analysis. Imputation is the process of substituting for missing values. We propose a more realistic assessment workflow which can preserve the original data distribution, and then assess eight representative general-purpose imputation strategies. We explore two biologically inspired imputation approaches: fused regularization matrix factorization (FRMF) and convex analysis of mixtures (CAM) imputation. FRMF integrates external information such as clinical variables and multi-omics data into imputation, while CAM imputation incorporates biological assumptions. We show that the integration of biological information improves the imputation performance. Data normalization is required to ensure correct comparison. For gene expression data, between sample normalization is needed. We propose a Cosine score based iterative normalization (Cosbin) strategy to normalize biologically diverse samples. We show that Cosbin significantly outperform other methods in both ideal simulation and realistic simulation. Implemented in open-source R scripts and applicable to grouped or individual samples, the Cosbin tool will allow biologists to detect subtle yet important molecular signals across known or novel cell types.

With the huge volume of biological data generated by new technologies and the booming of new machine learning based analytical tools, we expect to advance life science and human health at an unprecedented pace. Unfortunately, there is a significant gap between the complex raw biological data from real life and the data required by mathematical and statistical tools. This gap is contributed by two fundamental and universal problems in biological data that are both related to confounding effects. The first is the intrinsic complexities of the data. An observed sample could be the mixture of multiple underlying sources and we may be only interested in one or part of the sources. The second type of complexities come from the acquisition process of the data. Different samples may be gathered at different time and/or from different locations. Therefore, each sample is associated with specific distortion that must be carefully addressed. These confounding effects obscure the signals of interest in the acquired data. Specifically, this dissertation will address the two major challenges in confounding effects removal: alignment and deconvolution. Liquid chromatography–mass spectrometry (LC-MS) is a standard method for proteomics and metabolomics analysis of biological samples. Unfortunately, it suffers from various changes in the retention time (RT) of the same compound in different samples, and these must be subsequently corrected (aligned) during data processing. Classic alignment methods such as in the popular XCMS package often assume a single time-warping function for each sample. Thus, the potentially varying RT drift for compounds with different masses in a sample is neglected in these methods. Moreover, the systematic change in RT drift across run order is often not considered by alignment algorithms. Therefore, these methods cannot effectively correct all misalignments. To utilize this information, we develop an integrated reference-free profile alignment method, neighbor-wise compound-specific Graphical Time Warping (ncGTW), that can detect misaligned features and align profiles by leveraging expected RT drift structures and compound-specific warping functions. Specifically, ncGTW uses individualized warping functions for different compounds and assigns constraint edges on warping functions of neighboring samples. We applied ncGTW to two large-scale metabolomics LC-MS datasets, which identifies many misaligned features and successfully realigns them. These features would otherwise be discarded or uncorrected using existing methods. When the desired signal is buried in a mixture, deconvolution is needed to recover the pure sources. Many biological questions can be better addressed when the data is in the form of individual sources, instead of mixtures. Though there are some promising supervised deconvolution methods, when there is no a priori information, unsupervised deconvolution is still needed. Among current unsupervised methods, Convex Analysis of Mixtures (CAM) is the most theoretically solid and strongest performing one. However, there are some major limitations of this method. Most importantly, the overall time complexity can be very high, especially when analyzing a large dataset or a dataset with many sources. Also, since there are some stochastic and heuristic steps, the deconvolution result is not accurate enough. To address these problems, we redesigned the modules of CAM. In the feature clustering step, we propose a clustering method, radius-fixed clustering, which could not only control the space size of the cluster, but also find out the outliers simultaneously. Therefore, the disadvantages of K-means clustering, such as instability and the need of cluster number are avoided. Moreover, when identifying the convex hull, we replace Quickhull with linear programming, which decreases the computation time significantly. To avoid the not only heuristic but also approximated step in optimal simplex identification, we propose a greedy search strategy instead. The experimental results demonstrate the vast improvement of computation time. The accuracy of the deconvolution is also shown to be higher than the original CAM. Doctor of Philosophy Due to the complexity of biological data, there are two major pre-processing steps: alignment and deconvolution. The alignment step corrects the time and location related data acquisition distortion by aligning the detected signals to a reference signal. Though many alignment methods are proposed for biological data, most of them fail to consider the relationships among samples carefully. This piece of structure information can help alignment when the data is noisy and/or irregular. To utilize this information, we develop a new method, Neighbor-wise Compound-specific Graphical Time Warping (ncGTW), inspired by graph theory. This new alignment method not only utilizes the structural information but also provides a reference-free solution. We show that the performance of our new method is better than other methods in both simulations and real datasets. When the signal is from a mixture, deconvolution is needed to recover the pure sources. Many biological questions can be better addressed when the data is in the form of single sources, instead of mixtures. There is a classic unsupervised deconvolution method: Convex Analysis of Mixtures (CAM). However, there are some limitations of this method. For example, the time complexity of some steps is very high. Thus, when facing a large dataset or a dataset with many sources, the computation time would be extremely long. Also, since there are some stochastic and heuristic steps, the deconvolution result may be not accurate enough. We improved CAM and the experimental results show that the speed and accuracy of the deconvolution is significantly improved.

Recent breakthroughs in microscopy techniques and fluorescence probes enable the recording of mouse embryogenesis at the cellular level for days, easily generating terabyte-level 3D time-lapse data. Since millions of cells are involved, this information-rich data brings a natural demand for an automated tool for its comprehensive analysis. This tool should automatically (1) detect and segment cells at each time point and (2) track cell migration across time. Most existing cell tracking methods cannot scale to the data with such large size and high complexity. For those purposely designed for embryo data analysis, the accuracy is heavily sacrificed. Here, we present a new computational framework for the mouse embryo data analysis with high accuracy and efficiency. Our framework detects and segments cells with a fully probability-principled method, which not only has high statistical power but also helps determine the desired cell territories and increase the segmentation accuracy. With the cells detected at each time point, our framework reconstructs cell traces with a new minimum-cost circulation-based paradigm, CINDA (CIrculation Network-based DataAssociation). Compared with the widely used minimum-cost flow-based methods, CINDA guarantees the global optimal solution with the best-of-known theoretical worst-case complexity and hundreds to thousands of times practical efficiency improvement. Since the information extracted from a single time point is limited, our framework iteratively refines cell detection and segmentation results based on the cell traces which contain more information from other time points. Results show that this dramatically improves the accuracy of cell detection, segmentation, and tracking. To make our work easy to use, we designed a standalone software, MIVAQ (Microscopic Image Visualization, Annotation, and Quantification), with our framework as the backbone and a user-friendly interface. With MIVAQ, users can easily analyze their data and visually check the results. Doctor of Philosophy Mouse embryogenesis studies mouse embryos from fertilization to tissue and organ formation. The current microscope and fluorescent labeling technique enable the recording of the whole mouse embryo for a long time with high resolution. The generated data can be terabyte-level and contains more than one million cells. This information-rich data brings a natural demand for an automated tool for its comprehensive analysis. This tool should automatically (1) detect and segment cells at each time point to get the information of cell morphology and (2) track cell migration across time. However, the development of analytical tools lags far behind the capability of data generation. Existing tools either cannot scale to the data with such large size and high complexity or sacrifice accuracy heavily for efficiency. In this dissertation, we present a new computational framework for the mouse embryo data analysis with high accuracy and efficiency. To make our framework easy to use, we also designed a standalone software, MIVAQ, with a user-friendly interface. With MIVAQ, users can easily analyze their data and visually check the results.

Advances in time-lapse 3D in vivo fluorescence microscopic imaging techniques enables the observation and investigation into the migration of Oligodendrocyte precursor cells (OPCs) and its role in the central nervous system. However, current practice of image-based OPC motility analysis heavily relies on manual labeling and tracking on 2D max projection of the 3D data, which suffers from massive human labor, subjective biases, weak reproducibility and especially information loss and distortion. Besides, due to the lack of OPC specific genetically encoded indicator, OPCs can only be identified from other oligodendrocyte lineage cells by their observed motion patterns. Automated analytical tools are needed for the identification and tracking of OPCs. In this dissertation work, we proposed an analytical framework, MicTracker (Migrating Cell Tracker), for the integrated task of identifying, segmenting and tracking migrating cells (OPCs) from in vivo time-lapse fluorescence imaging data of high-density cell clusters composed of cells with different modes of motions. As a component of the framework, we presented a novel strategy for cell segmentation with global temporal consistency enforced, tackling the challenges caused by highly clustered cell population and temporally inconsistently blurred boundaries between touching cells. We also designed a data association algorithm to address the violation of usual assumption of small displacements. Recognizing that the violation was in the mixed cell population composed of two cell groups while the assumption held within each group, we proposed to solve the seemingly impossible mission by de-mixing the two groups of cell motion modes without known labels. We demonstrated the effectiveness of MicTracker in solving our problem on in vivo real data. Doctor of Philosophy Oligodendrocyte precursor cells (OPCs) are a type of motile cells in the central nervous system (CNS). OPCs' migration plays a critical role in the repair and re-distribution of myelin sheaths, a structures that helps to accelerate the transmission of electrical signals from neuron to neuron. But the mechanism behind the motility of OPCs is largely unclear. In recent years, advances in genetic fluorescence indicators and time-lapse optical microscopic imaging techniques, especially 3D in vivo imaging, enables neuroscientists to investigate into the puzzle. However, current practice of OPC motility analysis heavily relies on compressing the 3D data into 2D then manually tracking the OPCs, which suffers from not only massive human labor, subjective biases, weak reproducibility and especially information loss and distortion. Automated analytical tools are needed. Due to the limitation of current techniques in fluorescent labeling of cells in live animals, OPCs cannot be distinctively labeled. Instead, in the field of view there are also other irrelevant cells that cannot migrate but locally vibrate. Therefore, the human analyzer or the analytical software is supposed to detect OPCs from a cluster of touching cells containing multiple types of cells by their motion patterns only. In this dissertation, we presented a fully automatic machine learning based algorithm, MicTracker (Migrating Cell Tracker), to identify and track migrating OPCs. The task cannot be straightforwardly solved by existing generic-purpose cell tracking tools due to quite a few special challenges. To tackle the challenges, we also proposed novel methods for two major modules of MicTracker, segmentation and linking, respectively. We demonstrated the effectiveness of MicTracker and its components on real data and compared it with related existing works. The results of experiments showed notable superiority of MicTracker in solving our problem, compared with existing methods.

Since approximately the dawn of the new millennium, neural networks and other machine learning algorithms have become increasingly capable of adeptly performing difficult, dull, and dangerous work conventionally carried out by humans in times of old. As these algorithms become steadily more commonplace in everyday consumer and industry applications, the consideration of how they may be implemented on constrained hardware systems such as smartphones and Internet-of-Things (IoT) peripheral devices in a time- and power- efficient manner while also understanding the scenarios in which they fail is of increasing importance. This work investigates implementations of convolutional neural networks specifically in the context of image inference tasks. Three areas are analyzed: (1) a time- and power-efficient face recognition framework, (2) the development of a COVID-19-related mask classification system suitable for deployment on low-cost, low-power devices, and (3) an investigation into the implementation of spiking neural networks on mobile hardware and their conversion from traditional neural network architectures. Master of Science The subject of machine learning and its associated jargon have become ubiquitous in the past decade as industries seek to develop automated tools and applications and researchers continue to develop new methods for artificial intelligence and improve upon existing ones. Neural networks are a type of machine learning algorithm that can make predictions in complex situations based on input data with human-like (or better) accuracy. Real-time, low-power, and low-cost systems using these algorithms are increasingly used in consumer and industry applications, often improving the efficiency of completing mundane and hazardous tasks traditionally performed by humans. The focus of this work is (1) to explore when and why neural networks may make incorrect decisions in the domain of image-based prediction tasks, (2) the demonstration of a low-power, low-cost machine learning use case using a mask recognition system intended to be suitable for deployment in support of COVID-19-related mask regulations, and (3) the investigation of how neural networks may be implemented on resource-limited technology in an efficient manner using an emerging form of computing.

Generation of high-peak power, microwave ultra-short pulses (USPs) is desirable for ultra-wideband communications and remote sensing. A variety of microwave USP generators exist today, or are described in the literature, and have benefits and limitations depending on application. A new class of pulse compressors for generating USPs using electromagnetic time reversal (TR) techniques have been developed in the last decade, and are the topic of this dissertation. This dissertation presents a compact TR microwave pulse-compression cavity that has ultra-wide bandwidth (5 GHz – 18 GHz), and employs waveguide feeds for high-peak power output over the entire band. The system uses a time-reversal-based pulse compression scheme with one-bit processing (OBTR) to achieve high compression gain. Results from full-wave simulations are presented as well as measurements showing compression gain exceeding 21.2 dB, 22% efficiency, and measured instantaneous peak output powers reaching 39.2 kW. These are all record results for this type of pulse compressor. Additionally presented is new analysis of variation in compression gain due to impulse response recording time and bandwidth variation, new experimental work on the effect of mode stirrer position on compression gain, and a novel RF switch-based technique for reducing time-sidelobes while using OBTR. Finally, a new technique is presented that uses a reverberant cavity with only one feed connected to an ultra-wideband circulator (6.5 GHz to 17 GHz) to perform TRPC. Prior to this work, TRPC has only been demonstrated in electromagnetics using two or more feeds and a reverberant cavity acting as the time-reversal mirror. This new 1-port technique is demonstrated in both simulation and measurement. The proposed system achieves up to a measured 3 dB increase in compression gain and increased efficiency. Also, a novel application of the random coupling model (RCM) to calculate compression gain is presented. The cavity eigenfrequencies are modeled after eigenvalues of random matrices satisfying the Gaussian orthogonal ensembles (GOE) condition. Cavity transfer functions are generated using Monte Carlo simulations, and used to compute the compression gains for many different cavity realizations. Doctor of Philosophy Generation of high-peak power, microwave ultra-short pulses (USPs) is desirable for ultra-wideband communications and remote sensing. A variety of microwave USP generators exist today, or are described in the literature, and have benefits and limitations depending on application. A new class of pulse compressors for generating USPs using electromagnetic time reversal (TR) techniques have been developed in the last decade, and are the topic of this dissertation. This dissertation presents a compact TR-based microwave pulse-compression cavity that has unique features that make it optimal for high-power operations, with results from simulations as well as measurements showing improved performance over other similar cavities published in the literature with a record demonstrated peak output power of 39.2 kW. Additionally, new analysis on the operation and optimization of this cavity for increased performance is also presented. Finally, a new technique is presented that uses a cavity with only one feed that acts as both the input and output. This 1-port technique is demonstrated in both simulation and measurement. The proposed system achieves a two-times increase in compression gain over its 2-port counterpart. In conjunction with these measurements and simulations, a novel technique for predicting the performance of these cavities using Monte Carlo simulation is also presented.

Emerging technologies, including distributed energy resources (DERs), internet-of-things and advanced distribution management systems, are revolutionizing the power industry. They provide benefits like higher operation flexibility and lower bulk grid dependency, and are moving the modern power grid towards a decentralized, interconnected and intelligent direction. Consequently, the emphasis of the system operation management has been shifted from the supply-side to the demand-side. It calls for a reconsideration of the business model for future retail market operators. To address this need, this dissertation proposes an innovative retail market solution tailored to market environments penetrated with price-responsive DERs. The work is presented from aspects of theoretical study, test-bed platform development, and experimental analysis, within which two topics relevant to the retail market operation are investigated in depth. The first topic covers the modeling of key retail market participants. With regard to price-insensitive participants, fixed loads are treated as the representative. Deep learning-based day-ahead load forecasting models are developed in this study, utilizing both recurrent and convolutional neural networks, to predict the part of demands that keep fixed regardless of the market price. With regard to price-sensitive participants, battery storages are selected as the representative. An optimization-based battery arbitrage model is developed in this study to represent their price-responsive behaviors in response to a dynamic price. The second topic further investigates how the retail market model and pricing strategy should be designed to incentivize these market participants. Different from existing works, this study innovatively proposes a profit-neutral double-price-signal retail market model. Such a design differentiates elastic prosumers, who actively offer flexibilities to the system operation, from normal inelastic consumers/generators, based on their sensitivities to the market price. Two price signals, namely retail grid service price and retail energy price, are then introduced to separately quantify values of the flexibility, provided by elastic participants, and the electricity commodity, sold/bought to/from inelastic participants. Within the proposed retail market, a non-profit retail market operator (RMO) manages and settles the market through determining the price signals and supplementary subsidy to minimize the overall system cost. In response to the announced retail grid service price, elastic prosumers adjust their day-ahead operating schedules to maximize their payoffs. Given the interdependency between decisions made by the RMO and elastic participants, a retail pricing scheme, formulated based on a bi-level optimization framework, is proposed. Additional efforts are made on merging and linearizing the original non-convex bi-level problem into a single-level mixed-integer linear programming problem to ensure the computational efficiency of the retail pricing tool. Case studies are conducted on a modified IEEE 34-bus test-bed system, simulating both physical operations of the power grid and financial interactions inside the retail market. Experimental results demonstrate promising properties of the proposed retail market solution: First of all, it is able to provide cost-saving benefits to inelastic customers and create revenues for elastic customers at the same time, justifying the rationalities of these participants to join the market. Second of all, the addition of the grid service subsidy not only strengthens the profitability of the elastic customer, but also ensures that the benefit enjoyed per customer will not be compromised by the competition brought up by a growing number of participants. Furthermore, it is able to properly capture impacts from line losses and voltage constraints on the system efficiency and stability, so as to derive practical pricing solutions that respect the system operating rules. Last but not least, it encourages the technology improvement of elastic assets as elastic assets in better conditions are more profitable and could better save the electricity bills for inelastic customers. Above all, the superiority of the proposed retail market solution is proven. It can serve as a promising start for the retail electricity market reconstruction. Doctor of Philosophy The electricity market plays a critical role in ensuring the economic and secure operation of the power system. The progress made by distributed energy resources (DERs) has reshaped the modern power industry bringing a larger proportion of price-responsive behaviors to the demand-side. It challenges the traditional wholesale-only electricity market and calls for an addition of retail markets to better utilize distributed and elastic assets. Therefore, this dissertation targets at offering a reliable and computational affordable retail market solution to bridge this knowledge gap. Different from existing works, this study assumes that the retail market is managed by a profit-neutral retail market operator (RMO), who oversees and facilitates the system operation for maximizing the system efficiency rather than making profits. Market participants are categorized into two groups: inelastic participants and elastic participants, based on their sensitivity to the market price. The motivation behind this design is that instead of treating elastic participants as normal customers, it is more reasonable to treat them as grid service providers who offer operational flexibilities that benefit the system efficiency. Correspondingly, a double-signal pricing scheme is proposed, such that the flexibility, provided by elastic participants, and the electricity commodity, generated/consumed by inelastic participants, are separately valued by two distinct prices, namely retail grid service price and retail energy price. A grid service subsidy is also introduced in the pricing system to provide supplementary incentives to elastic customers. These two price signals in addition to the subsidy are determined by the RMO via solving a bi-level optimization problem given the interdependency between the prices and reaction of elastic participants. Experimental results indicate that the proposed retail market model and pricing scheme are beneficial for both types of market participants, practical for the network-constrained real-world implementation, and supportive for the technology improvement of elastic assets.

The sun is constantly emitting electrons and ions as magnetized plasma, forming the solar wind and carrying with it the sun’s rotating magnetic field. The solar wind subsequently interacts with Earth’s magnetosphere and the magnetospheres of other planets. Occasionally large amounts of magnetized plasma are released at one time in a Corona mass ejection (CME). When the CME interacts with Earth’s magnetic field, it induces perturbations that may have a significant impact on critical infrastructure, for instance, by disturbing communication systems, and inducing currents on pipelines and electric power lines, which in turn may cause increased corrosion or blackouts, among other effects. In this dissertation, we analyze measured electrical signals provided to us by the Finnish Meteorological Institute, which were induced by geomagnetic storms on pipelines located in Finland and recorded in 2003. Specifically, we perform a wavelet leader multifractal analysis of these current signals to generate singularity spectra, and then using the bootstrapping technique, we apply statistical tests to show that these signals exhibit multifractal characteristics. We also performed surrogate testing to show that these characteristics were unique to the signal. Ph.D. Earth’s weather affects all of us every day. The solar space environment has weather of its own that affects us as well. Storms of a size that far exceed anything on Earth can impact Earth and affect our infrastructure. One of the most powerful phenomena that occur, called solar corona mass ejections, results when the sun ejects a large amount of plasma. This can interact with the Earth’s magnetic field, which in turn induces perturbations that may have a significant impact on critical infrastructure, for instance, by disturbing communication systems, and inducing currents on pipelines and electric power lines. The currents can cause increased corrosion or blackouts, among other effects. In this dissertation, we analyze measured electrical signals provided to us by the Finnish Meteorological Institute, which were induced by geomagnetic storms on pipelines located in Finland and recorded in 2003. Specifically, we perform a statistical analysis of these current signals to decide whether they exhibit multifractal characteristics.

Rapid advances in high-throughput molecular profiling techniques enabled large-scale genomics, transcriptomics, and proteomics-based biomedical studies, generating an enormous amount of multi-omics data. Processing and summarizing multi-omics data, modeling interactions among biomolecules, and detecting condition-specific dysregulation using multi-omics data are some of the most important yet challenging analytics tasks. In the case of detecting somatic DNA copy number aberrations using bulk tumor samples in cancer research, normal cell contamination becomes one significant confounding factor that weakens the power regardless of whichever methods used for detection. To address this problem, we propose a computational approach – BACOM 2.0 to more accurately estimate normal cell fraction and accordingly reconstruct DNA copy number signals in cancer cells. Specifically, by introducing allele-specific absolute normalization, BACOM 2.0 can accurately detect deletion types and aneuploidy in cancer cells directly from DNA copy number data. Genes work through complex networks to support cellular processes. Dysregulated genes can cause structural changes in biological networks, also known as network rewiring. Genes with a large number of rewired edges are more likely to be associated with functional alteration leading phenotype transitions, and hence are potential biomarkers in diseases such as cancers. Differential dependency network (DDN) method was proposed to detect such network rewiring and biomarkers. However, the existing DDN method and software tool has two major drawbacks. Firstly, in imbalanced sample groups, DDN suffers from systematic bias and produces false positive differential dependencies. Secondly, the computational time of the block coordinate descent algorithm in DDN increases rapidly with the number of involved samples and molecular entities. To address the imbalanced sample group problem, we propose a sample-scale-wide normalized formulation to correct systematic bias and design a simulation study for testing the performance. To address high computational complexity, we propose several strategies to accelerate DDN learning, including two reformulated algorithms for block-wise coefficient updating in the DDN optimization problem. Specifically, one strategy on discarding predictors and one strategy on accelerating parallel computing. More importantly, experimental results show that new DDN learning speed with combined accelerating strategies is hundreds of times faster than that of the original method on medium-sized data. We applied the DDN method on several biomedical datasets of omics data and detected significant phenotype-specific network rewiring. With a random-graph-based detection strategy, we discovered the hub node defined biomarkers that helped to generate or validate several novel scientific hypotheses in collaborative research projects. For example, the hub genes detected by the DDN methods in proteomics data from artery samples are significantly enriched in the citric acid cycle pathway that plays a critical role in the development of atherosclerosis. To detect intra-omics and inter-omics network rewirings, we propose a method called multiDDN that uses a multi-layer signaling model to integrate multi-omics data. We adapt the block coordinate descent algorithm to solve the multiDDN optimization problem with accelerating strategies. The simulation study shows that, compared with the DDN method on single omics, the multiDDN method has considerable advantage on higher accuracy of detecting network rewiring. We applied the multiDDN method on the real multi-omics data from CPTAC ovarian cancer dataset, and detected multiple hub genes associated with histone protein deacetylation and were previously reported in independent ovarian cancer data analysis. Doctor of Philosophy We witnessed the start of the human genome project decades ago and stepped into the era of omics since then. Omics are comprehensive approaches for analyzing genome-wide biomolecular profiles. The rapid development of high-throughput technologies enables us to produce an enormous amount of omics data such as genomics, transcriptomics, and proteomics data, which makes researchers swim in a sea of omics information that once never imagined. Yet, the era of omics brings new challenges to us: to process the huge volumes of data, to summarize the data, to reveal the interactions between entities, to link various types of omics data, and to discover mechanisms hidden behind omics data. In processing omics data, one factor that weakens the strengths of follow up data analysis is sample impurity. We call impure tumor samples contaminated by normal cells as heterogeneous samples. The genomic signals measured from heterogeneous samples are a mixture of signals from both tumor cells and normal cells. To correct the mixed signals and get true signals from pure tumor cells, we propose a computational approach called BACOM 2.0 to estimate normal cell fraction and corrected genomics signals accordingly. By introducing a novel normalization method that identifies the neutral component in mixed signals of genomic copy number data, BACOM 2.0 could accurately detect genes' deletion types and abnormal chromosome numbers in tumor cells. In cells, genes connect to other genes and form complex biological networks to perform their functions. Dysregulated genes can cause structural change in biological networks, also known as network rewiring. In a biological network with network rewiring events, a large quantity of network rewiring linking to a single hub gene suggests concentrated gene dysregulation. This hub gene has more impact on the network and hence is more likely to associate with the functional change of the network, which ultimately leads to abnormal phenotypes such as cancer diseases. Therefore, the hub genes linked with network rewiring are potential indicators of disease status or known as biomarkers. Differential dependency network (DDN) method was proposed to detect network rewiring events and biomarkers from omics data. However, the DDN method still has a few drawbacks. Firstly, for two groups of data with unequal sample sizes, DDN consistently detects false targets of network rewiring. The permutation test, which uses the same method on randomly shuffled samples is supposed to distinguish the true targets from random effects, however, is also suffered from the same reason and could let pass those false targets. We propose a new formulation that corrects the mistakes brought by unequal group size and design a simulation study to test the new formulation's correctness. Secondly, the time used for computing in solving DDN problems is unbearably long when processing omics data with a large number of samples scale or a large number of genes. We propose several strategies to increase DDN's computation speed, including three redesigned formulas for efficiently updating the results, one rule to preselect predictor variables, and one accelerating skill of utilizing multiple CPU cores simultaneously. In the timing test, the DDN method with increased computing speed is much faster than the original method. To detect network rewirings within the same omics data or between different types of omics, we propose a method called multiDDN that uses an integrated model to process multiple types of omics data. We solve the new problem by adapting the block coordinate descending algorithm. The test on simulated data shows multiDDN is better than single omics DDN. We applied DDN or multiDDN method on several datasets of omics data and detected significant network rewiring associated with diseases. We detected hub nodes from the network rewiring events. These hub genes as potential biomarkers help us to ask new meaningful questions in related researches.

Tissue heterogeneity, arising from intermingled cellular or tissue subtypes, significantly obscures the analyses of molecular expression data derived from complex tissues. Existing computational methods performing data deconvolution from mixed subtype signals almost exclusively rely on supervising information, requiring subtype-specific markers, the number of subtypes, or subtype compositions in individual samples. We develop a fully unsupervised deconvolution method to dissect complex tissues into molecularly distinctive tissue or cell subtypes directly from mixture expression profiles. We implement an R package, deconvolution by Convex Analysis of Mixtures (debCAM) that can automatically detect tissue or cell-specific markers, determine the number of constituent sub-types, calculate subtype proportions in individual samples, and estimate tissue/cell-specific expression profiles. We demonstrate the performance and biomedical utility of debCAM on gene expression, methylation, and proteomics data. With enhanced data preprocessing and prior knowledge incorporation, debCAM software tool will allow biologists to perform a deep and unbiased characterization of tissue remodeling in many biomedical contexts. Purified expression profiles from physical experiments provide both ground truth and a priori information that can be used to validate unsupervised deconvolution results or improve supervision for various deconvolution methods. Detecting tissue or cell-specific expressed markers from purified expression profiles plays a critical role in molecularly characterizing and determining tissue or cell subtypes. Unfortunately, classic differential analysis assumes a convenient test statistic and associated null distribution that is inconsistent with the definition of markers and thus results in a high false positive rate or lower detection power. We describe a statistically-principled marker detection method, One Versus Everyone Subtype Exclusively-expressed Genes (OVESEG) test, that estimates a mixture null distribution model by applying novel permutation schemes. Validated with realistic synthetic data sets on both type 1 error and detection power, OVESEG-test applied to benchmark gene expression data sets detects many known and de novo subtype-specific expressed markers. Subsequent supervised deconvolution results, obtained using markers detected by the OVESEG-test, showed superior performance when compared with popular peer methods. While the current debCAM approach can dissect mixed signals from multiple samples into the 'averaged' expression profiles of subtypes, many subsequent molecular analyses of complex tissues require sample-specific deconvolution where each sample is a mixture of 'individualized' subtype expression profiles. The between-sample variation embedded in sample-specific subtype signals provides critical information for detecting subtype-specific molecular networks and uncovering hidden crosstalk. However, sample-specific deconvolution is an underdetermined and challenging problem because there are more variables than observations. We propose and develop debCAM2.0 to estimate sample-specific subtype signals by nuclear norm regularization, where the hyperparameter value is determined by random entry exclusion based cross-validation scheme. We also derive an efficient optimization approach based on ADMM to enable debCAM2.0 application in large-scale biological data analyses. Experimental results on realistic simulation data sets show that debCAM2.0 can successfully recover subtype-specific correlation networks that is unobtainable otherwise using existing deconvolution methods. Doctor of Philosophy Tissue samples are essentially mixtures of tissue or cellular subtypes where the proportions of individual subtypes vary across different tissue samples. Data deconvolution aims to dissect tissue heterogeneity into biologically important subtypes, their proportions, and their marker genes. The physical solution to mitigate tissue heterogeneity is to isolate pure tissue components prior to molecular profiling. However, these experimental methods are time-consuming, expensive and may alter the expression values during isolation. Existing literature primarily focuses on supervised deconvolution methods which require a priori information. This approach has an inherent problem as it relies on the quality and accuracy of the a priori information. In this dissertation, we propose and develop a fully unsupervised deconvolution method - deconvolution by Convex Analysis of Mixtures (debCAM) that can estimate the mixing proportions and 'averaged' expression profiles of individual subtypes present in heterogeneous tissue samples. Furthermore, we also propose and develop debCAM2.0 that can estimate 'individualized' expression profiles of participating subtypes in complex tissue samples. Subtype-specific expressed markers, or marker genes (MGs), serves as critical a priori information for supervised deconvolution. MGs are exclusively and consistently expressed in a particular tissue or cell subtype while detecting such unique MGs involving many subtypes constitutes a challenging task. We propose and develop a statistically-principled method - One Versus Everyone Subtype Exclusively-expressed Genes (OVESEG-test) for robust detection of MGs from purified profiles of many subtypes.

The advent of multi-photon microscopes and highly sensitive protein sensors enables the recording of astrocyte activities on a large population of cells over a long-time period in vivo. Existing tools cannot fully characterize these activities, both within single cells and at the population-level, because of the insufficiency of current region-of-interest-based approaches to describe the activity that is often spatially unfixed, size-varying, and propagative. Here, we present Astrocyte Quantitative Analysis (AQuA), an analytical framework that releases astrocyte biologists from the ROI-based paradigm. The framework takes an event-based perspective to model and accurately quantify the complex activity in astrocyte imaging datasets, with an event defined jointly by its spatial occupancy and temporal dynamics. To model the signal propagation in astrocyte, we developed graphical time warping (GTW) to align curves with graph-structured constraints and integrated it into AQuA. To make AQuA easy to use, we designed a comprehensive software package. The software implements the detection pipeline in an intuitive step by step GUI with visual feedback. The software also supports proof-reading and the incorporation of morphology information. With synthetic data, we showed AQuA performed much better in accuracy compared with existing methods developed for astrocytic data and neuronal data. We applied AQuA to a range of ex vivo and in vivo imaging datasets. Since AQuA is data-driven and based on machine learning principles, it can be applied across model organisms, fluorescent indicators, experimental modes, and imaging resolutions and speeds, enabling researchers to elucidate fundamental astrocyte physiology. Doctor of Philosophy Astrocyte is an important type of glial cell in the brain. Unlike neurons, astrocyte cannot be electrically excited. However, the concentrations of many different molecules inside and near astrocytes change over space and time and show complex patterns. Recording, analyzing, and deciphering these activity patterns enables the understanding of various roles astrocyte may play in the nervous system. Many of these important roles, such as sensory-motor integration and brain state modulation, were traditionally considered the territory of neurons, but recently found to be related to astrocytes. These activities can be monitored in the intracellular and extracellular spaces in either brain slices and living animals, thanks to the advancement of microscopes and genetically encoded fluorescent sensors. However, sophisticated analytical tools lag far behind the impressive capability of generating the data. The major reason is that existing tools are all based on the region-of-interest-based (ROI) approach. This approach assumes the field of view can be segmented to many regions, and all pixels in the region should be active together. In neuronal activity analysis, all pixels in an ROI (region of interest) correspond to a neuron and are assumed to share a common activity pattern (curve). This is not true for astrocyte activity data because astrocyte activities are spatially unfixed, size-varying, and propagative. In this dissertation, we developed a framework called AQuA to detect the activities directly. We designed an accurate and flexible detection pipeline that works with different types of astrocyte activity data sets. We designed a machine learning model to characterize the signal propagation for the pipeline. We also implemented a compressive and user-friendly software package. The advantage of AQuA is confirmed in both simulation studies and three different types of real data sets.

This dissertation explores several challenges that plague the hardware-software co-design of popular resource constrained real-time embedded systems. We specifically tackle existing real-world problems, and address them through our design solutions which are highly scalable, and have practical feasibility as verified through our solution implementation on real-world hardware. We address the problem of poor battery life in mobile embedded devices caused due to side-by-side execution of multiple applications in split-screen mode. Existing industry solutions either restricts the number of applications that can run simultaneously, limit their functionality, and/or increase the hardware capacity of the battery associated with the system. We exploit the gap in research on performance and power trade-off in smartphones to propose an integrated energy management solution, that judiciously minimizes the system-wide energy consumption with negligible effect on its quality of service (QoS). Another important real-world requirement in today's interconnected world is the need for security. In the domain of real-time computing, it is not only necessary to secure the system but also maintain its timeliness. Some example security mechanisms that may be used in a hard real-time system include, but are not limited to, security keys, protection of intellectual property (IP) of firmware and application software, one time password (OTP) for software certification on-the-fly, and authenticated computational off-loading. Existing design solutions require expensive, custom-built hardware with long time-to-market or time-to-deployment cycle. A readily available alternative is the use of trusted execution environment (TEE) on commercial off-the-shelf (COTS) embedded processors. However, utilizing TEE creates multiple challenges from a real-time perspective, which includes additional time overhead resulting in possible deadline misses. Second, trusted execution may adversely affect the deterministic execution of the system, as tasks running inside a TEE may need to communicate with other tasks that are executing on the native real-time operating system. We propose three different solutions to address the need for a new task model that can capture the complex relationship between performance and predictability for real-time tasks that require secure execution inside TEE. We also present novel task assignment and scheduling frameworks for real-time trusted execution on COTS processors to improve task set schedulability. We extensively assess the pros and cons of our proposed approaches in comparison to the state-of-the-art techniques in custom-built real-world hardware for feasibility, and simulated environments to test our solutions' scalability. Doctor of Philosophy Today's real-world problems demand real-time solutions. These solutions need to be practically feasible, and scale well with increasing end user demands. They also need to maintain a balance between system performance and predictability, while achieving minimum energy consumption. A recent example of technological design problem involves ways to improve the battery lifetime of mobile embedded devices, for example, smartphones, while still achieving the required performance objectives. For instance, smartphones that run Android OS has the capability to run multiple applications concurrently using a newly introduced split-screen mode of execution, where applications can run side-by-side at the same time on screen while using the same shared resources (e.g., CPU, memory bandwidth, peripheral devices etc.). While this can improve the overall performance of the system, it can also lead to increased energy consumption, thereby directly affecting the battery life. Another technological design problem involves ways to protect confidential proprietary information from being siphoned out of devices by external attackers. Let us consider a surveillance unmanned aerial vehicle (UAV) as an example. The UAV must perform sensitive tasks, such as obtaining coordinates of interest for surveillance, within a given time duration, also known as task deadline. However, an attacker may learn how the UAV communicates with ground control, and take control of the UAV, along with the sensitive information it carries. Therefore, it is crucial to protect such sensitive information from access by an unauthorized party, while maintaining the system's task deadlines. In this dissertation, we explore these two real-world design problems in depth, observe the challenges associated with them, while presenting several solutions to tackle the issues. We extensively assess the pros and cons of our proposed approaches in comparison to the state-of- the-art techniques in custom-built real-world hardware, and simulated environments to test our solutions' scalability.

Deep learning has become an ubiquitous part of research in all fields, including wireless communications. Researchers have shown the ability to leverage deep neural networks (DNNs) that operate on raw in-phase and quadrature samples, termed Radio Frequency Machine Learning (RFML), to synthesize new waveforms, control radio resources, as well as detect and classify signals. While there are numerous advantages to RFML, this thesis answers the question "is it secure?" DNNs have been shown, in other applications such as Computer Vision (CV), to be vulnerable to what are known as adversarial evasion attacks, which consist of corrupting an underlying example with a small, intelligently crafted, perturbation that causes a DNN to misclassify the example. This thesis develops the first threat model that encompasses the unique adversarial goals and capabilities that are present in RFML. Attacks that occur with direct digital access to the RFML classifier are differentiated from physical attacks that must propagate over-the-air (OTA) and are thus subject to impairments due to the wireless channel or inaccuracies in the signal detection stage. This thesis first finds that RFML systems are vulnerable to current adversarial evasion attacks using the well known Fast Gradient Sign Method originally developed for CV applications. However, these current adversarial evasion attacks do not account for the underlying communications and therefore the adversarial advantage is limited because the signal quickly becomes unintelligible. In order to envision new threats, this thesis goes on to develop a new adversarial evasion attack that takes into account the underlying communications and wireless channel models in order to create adversarial evasion attacks with more intelligible underlying communications that generalize to OTA attacks. Master of Science Deep learning is beginning to permeate many commercial products and is being included in prototypes for next generation wireless communications devices. This technology can provide huge breakthroughs in autonomy; however, it is not sufficient to study the effectiveness of deep learning in an idealized laboratory environment, the real world is often harsh and/or adversarial. Therefore, it is important to know how, and when, these deep learning enabled devices will fail in the presence of bad actors before they are deployed in high risk environments, such as battlefields or connected autonomous vehicle communications. This thesis studies a small subset of the security vulnerabilities of deep learning enabled wireless communications devices by attempting to evade deep learning enabled signal classification by an eavesdropper while maintaining effective wireless communications with a cooperative receiver. The primary goal of this thesis is to define the threats to, and identify the current vulnerabilities of, deep learning enabled signal classification systems, because a system can only be secured once its vulnerabilities are known.

An electric power system is a complex network consisting of a large number of power generators and consumers interconnected by transmission and distribution lines. One remarkable thing about the electric grid is that there has to be a continuous balance between the amount of electricity generated and consumed at all times. Maintaining this balance is critical for the stable operation of the grid and this task is achieved in the long term, short term and real-time by operating a three-tier wholesale electricity market consisting of the capacity market, the energy market and the ancillary services market respectively. For a demand resource to participate in the energy and the capacity markets, it needs to be able to reduce the power consumption on-demand, whereas to participate in the ancillary services market, the power consumption of the demand resource needs to be varied continuously following the regulation signal sent by the grid operator. This act of changing the demand to help maintain energy balance is called demand response (DR). The dissertation presents novel algorithms and tools to enable residential buildings to participate as demand resources on such markets to provide DR. Residential sector consumes 37% of the total U.S. electricity consumption and a recent consumer survey showed that 88% of consumers are either eager or supportive of advanced technologies for energy efficiency, including demand response. This indicates that residential sector is a very good target for DR. Two broad solutions for residential DR are presented. The first is a set of efficient algorithms that intelligently controls the customers' heating, ventilating and air conditioning (HVAC) devices for providing DR services to the grid. The second solution is an extensible residential demand response simulation framework that can help evaluate and experiment with different residential demand response algorithms. One of the algorithms presented in this dissertation is to reduce the aggregated demand of a set of HVACs during a DR event while respecting the customers' comfort requirements. The algorithm is shown to be efficient, simple to implement and is proven to be optimal. The second algorithm helps provide the regulation DR while honoring customer comfort requirements. The algorithm is efficient, simple to implement and is shown to perform well in a range of real-world situations. A case study is presented estimating the monetary benefit that can be obtained by implementing the algorithm in a cluster of 100 typical homes and shows promising result. Finally, the dissertation presents the design of a python-based object-oriented residential DR simulation framework which is easy to extend as needed. The framework supports simulation of thermal dynamics of a residential building and supports house hold appliances such as HVAC, water heater, clothes washer/dryer and dish washer. A case study showing the application of the simulation framework for various DR implementation is presented, which shows that the simulation framework performs well and can be a useful tool for future research in residential DR. PHD The total power generation and consumption has to always match in the electric grid. When there is a mismatch because the generation is less than the load, the match can be restored either by increasing the generation or by decreasing the load. Often, during system stress conditions, it is cheaper to decrease certain loads than to increase generation, and this method of achieving power balance is called demand response (DR). Residential sector consumes 37% of the total U.S. electricity consumption and is largely unexplored for demand response purpose, so the focus of the dissertation is on providing solutions to enable residential houses to provide demand response services. This dissertation presents two broad solutions. The first is a set of efficient algorithms that intelligently controls the customers’ heating, ventilating and air conditioning (HVAC) devices for providing DR services to the grid while keeping their comfort in mind. The second solution is a simulation software that can help evaluate and experiment with different residential demand response algorithms. The first algorithm is for reducing the collective power consumption of an aggregation of residential HVAC, whereas the second algorithm is for making the collective power follow a signal sent by the grid operators. It is shown that the algorithms presented can intelligently control the HVAC devices such that DR services can be provided to the grid while ensuring that the temperatures of the houses remain within comfortable range. The algorithms can enable demand response service providers to tap into the residential demand response market and earn revenue, while the simulation software can be valuable for future research in this area. The simulation software is simple to use and is designed with extensibility in mind, so adding new features is easy. The software is shown to work well for studying residential building control for demand response purpose and can be a useful tool for future research in residential DR.

The emergence of blockchain technology and increasing penetration of distributed energy resources (DERs) have created a new opportunity for peer-to-peer (P2P) energy trading. However, challenges arise in such transactive markets to ensure individual rationality, incentive compatibility, budget balance, and economic efficiency during the trading process. This thesis creates an hour-ahead P2P energy trading network based on the Hyperledger Fabric blockchain and explores a comparative analysis of different auction mechanisms that form the basis of smart contracts. Considered auction mechanisms are discriminatory and uniform k-Double Auction with different k values. This thesis also investigates effects of four consumer and prosumer bidding strategies: random, preference factor, price-only game-theoretic approach, and supply-demand game-theoretic approach. A custom simulation framework that models the behavior of the transactive market is developed. Case studies of a 100-home microgrid at various photovoltaic (PV) penetration levels are presented using typical residential load and PV generation profiles in the metropolitan Washington, D.C. area. Results indicate that regardless of PV penetration levels and employed bidding strategies, discriminatory k-DA can outperform uniform k-DA. Despite so, discriminatory k-DA is more sensitive to market conditions than uniform k-DA. Additionally, results show that the price-only game-theoretic bidding strategy leads to near-ideal economic efficiencies regardless of auction mechanisms and PV penetration levels. MS

Among many smart grid technologies, demand response (DR) is gaining increasing popularity. Many utility companies provide a variety of programs to encourage DR participation. Under these circumstances, various building energy management (BEM) systems have emerged to facilitate the building control during a DR event. Nonetheless, due to the cost and return on investment, these solutions mainly target homes and large commercial buildings, leaving aside small- and medium-sized commercial buildings (SMCB). SMCB, however, accounts for 90% of commercial buildings in the US, and offer great potential of load reduction during peak hours. With the advent of Internet-of-Things (IoT) devices and technologies, low cost smart building solutions have become possible for the SMCB; nonetheless, related intelligent algorithms are not widely available. This dissertation work investigates automated building control algorithms, tailored for the SMCB, to realize automatic device control during DR events. To be specific, a control framework for Air-Conditioning (AC) units' coordination is proposed. The goal of such framework is to reduce the aggregated AC power consumption while maintaining the thermal comfort inside a building during DR events. To achieve this goal, three major components of the framework were studied: building thermal property modeling, AC power consumption modeling and control algorithms design. Firstly, to consider occupants' thermal comfort, a reverse thermal model was designed to predict the indoor temperature of thermal zones under different AC control signals. The model was trained with supervised learning using coarse-grained temperature data recorded by smart thermostats; thus, it requires no lengthy configuration as a forward model does. The cost efficiency and plug-and-play feature of the model make it appropriate for SMCB. Secondly, a power disaggregation algorithm is proposed to model the power-outdoor temperature relationship of multiple AC units, using data from a single power meter and thermostats. Finally, algorithms based on mixed integer linear programming (MILP) and reinforcement learning (RL) were devised to coordinate multiple AC units in a building during a DR event. Integrated with the thermal model and AC power consumption model, these algorithms minimize occupants' thermal discomfort while restricting the aggregated AC power consumption below the DR limit. The efficiency of these control algorithms was tested, which demonstrate that they can generate AC control schedule in short notice (5 minutes) ahead of a DR event. Verification and validation of the proposed framework was conducted in both simulation and actual building environments. In addition, though the framework is designed for SMCBs, it can also be applied to large homes with multiple AC units to coordinate. This work is expected to give an insight into the BEM sector, helping the popularization of implementing DR in buildings. The research findings from this dissertation work shows the validity of the proposed algorithms, which can be used in BEM systems and cloud-based smart thermostats to exploit the untapped DR resource in SMCB. PHD For power system operation, the demand and supply should be equal at all time. During peak hours, the demand becomes very high. One way to keep the balance is to provide more generation capacity, and thus more expensive and less efficient generators are brought online, which causes higher production cost and more pollution. Instead, an alternative is to encourage the load reduction via demand response (DR): customers reduce load upon receiving a signal sent by the utility company, usually in exchange for some monetary payback. For buildings to participate in DR, an affordable automation system and related control algorithms are needed. This dissertation proposed a cost-effective, self-learning and data-driven framework to facilitate small- and medium-sized commercial buildings or large homes in air-conditioner (AC) units control during DR events. The devised framework requires little human configuration; it learns the building behavior by analyzing the operation data. Two algorithms are proposed to coordinate multiple AC units in a building with two goals: firstly, reducing the total AC power consumption below certain limit, as agreed between the building owners and their utility company. Secondly, minimizing occupants’ thermal discomfort caused by limiting AC operation. The effectiveness of the framework is investigated in this dissertation based on data collected from a real building.

Engine-triggered tasks are real-time tasks that are released when the crankshaft arrives at certain positions in its path of rotation. This makes the rate of release of these jobs a function of the crankshaft's angular speed and acceleration. In addition, several properties of the engine triggered tasks like the execution time and deadlines are dependent on the speed profile of the crankshaft. Such tasks are referred to as adaptive-variable rate (AVR) tasks. Existing methods to calculate the worst-case demand of AVR tasks are either inaccurate or computationally intractable. We propose a method to efficiently calculate the worst-case demand of AVR tasks by transforming the problem into a variant of the knapsack problem. We then propose a framework to systematically narrow down the search space associated with finding the worst-case demand of AVR tasks. Experimental results show that our approach is at least 10 times faster, with an average runtime improvement of 146 times for randomly generated task sets when compared to the state-of-the-art technique. Master of Science Real-time systems require temporal correctness along with accuracy. This notion of temporal correctness is achieved by specifying deadlines to each of the tasks. In order to ensure that all the deadlines are met, it is important to know the processor requirement, also known as demand, of a task over a given interval. For some tasks, the demand is not constant, instead it depends on several external factors. For such tasks, it becomes necessary to calculate the worst-case demand. Engine-triggered tasks are activated when the crankshaft in an engine is at certain points in its path of rotation. This makes their activation rate dependent on the angular speed and acceleration of the crankshaft. In addition, several properties of the engine triggered tasks like the execution time and deadlines are dependent on the speed profile of the crankshaft. Such tasks are referred to as adaptive-variable rate (AVR) tasks. Existing methods to calculate the worst-case demand of AVR tasks are either inaccurate or computationally intractable. We propose a method to efficiently calculate the worst-case demand of AVR tasks by transforming the problem into a variant of the knapsack problem. We then propose a framework to systematically narrow down the search space associated with finding the worst-case demand of AVR tasks. Experimental results show that our approach is at least 10 times faster, with an average runtime improvement of 146 times for randomly generated task sets when compared to the state-of-the-art technique.

Many data sets have too many features for conventional pattern recognition techniques to work properly. This thesis investigates techniques that alleviate these difficulties. One such technique, biclustering, clusters data in both dimensions and is inherently resistant to the challenges posed by having too many features. However, the algorithms that implement biclustering have limitations in that the user must know at least the structure of the data and how many biclusters to expect. This is where the VIsual Statistical Data Analyzer, or VISDA, can help. It is a visualization tool that successively and progressively explores the structure of the data, identifying clusters along the way. This thesis proposes coupling VISDA with biclustering to overcome some of the challenges of data sets with too many features. Further, to increase the performance, usability, and maintainability as well as reduce costs, VISDA was translated from Matlab to a Python version called VISDApy. Both VISDApy and the overall process were demonstrated with real and synthetic data sets. The results of this work have the potential to improve analysts' understanding of the relationships within complex data sets and their ability to make informed decisions from such data. Master of Science Many data sets have too many features for conventional pattern recognition techniques to work properly. This thesis investigates techniques that alleviate these difficulties. One such technique, biclustering, clusters data in both dimensions and is inherently resistant to the challenges posed by having too many features. However, the algorithms that implement biclustering have limitations in that the user must know at least the structure of the data and how many biclusters to expect. This is where the VIsual Statistical Data Analyzer, or VISDA, can help. It is a visualization tool that successively and progressively explores the structure of the data, identifying clusters along the way. This thesis proposes coupling VISDA with biclustering to overcome some of the challenges of data sets with too many features. Further, to increase the performance, usability, and maintainability as well as reduce costs, VISDA was translated from Matlab to a Python version called VISDApy. Both VISDApy and the overall process were demonstrated with real and synthetic data sets. The results of this work have the potential to improve analysts’ understanding of the relationships within complex data sets and their ability to make informed decisions from such data.

It is a well-known fact that a power system contains many sources of uncertainties. These uncertainties coming from the loads, the renewables, the model and the measurement, etc, are influencing the steady state and dynamic response of the power system. Facing this problem, traditional methods, such as the Monte Carlo method and the Perturbation method, are either too time consuming or suffering from the strong nonlinearity in the system. To solve these, this Dissertation will mainly focus on developing the polynomial chaos based method to replace the traditional ones. Using it, the uncertainties from the model and the measurement are propagated through the polynomial chaos bases at a set of collocation points. The approximated polynomial chaos coefficients contain the statistical information. The method can greatly accelerate the calculation efficiency while not losing the accuracy, even when the system is highly stressed. In this dissertation, both the forward problem and the inverse problem of uncertainty quantification will be discussed. The forward problems will include the probabilistic power flow problem and statistical power system dynamic simulations. The generalized polynomial chaos method, the adaptive polynomial chaos-ANOVA method and the multi-element polynomial chaos method will be introduced and compared. The case studies show that the proposed methods have great performances in the statistical analysis of the large-scale power systems. The inverse problems will include the state and parameter estimation problem. A novel polynomial-chaos-based Kalman filter will be proposed. The comparison studies with other traditional Kalman filter demonstrate the good performances of the proposed Kalman filter. We further explored the area dynamic parameter estimation problem under the Bayesian inference framework. The polynomial-chaos-expansions are treated as the response surface of the full dynamic solver. Combing with hybrid Markov chain Monte Carlo method, the proposed method yields very high estimation accuracy while greatly reducing the computing time. For both the forward problem and the inverse problems, the polynomial chaos based methods haven shown great advantages over the traditional methods. These computational techniques can improve the efficiency and accuracy in power system planning, guarantee the rationality and reliability in power system operations, and, finally, speed up the power system dynamic security assessment. PHD It is a well-known fact that a power system state is inherently stochastic. Sources of stochasticity include load random variations, renewable energy intermittencies, and random outages of generating units, lines, and transformers, to cite a few. These stochasticities translate into uncertainties in the models that are assumed to describe the steady-sate and dynamic behavior of a power system. Now, these models are themselves approximate since they are based on some assumptions that are typically violated in practice. Therefore, it does not come as a surprise if recent research activities in power systems are focusing on how to cope with uncertainties when dealing with power system planning, monitoring and control. This Dissertation is developing polynomial-chaos-based method in quantifying, and managing these uncertainties. Three major topics, including uncertainty quantification, state estimation and parameter estimation are discussed. The developed method can improve the efficiency and accuracy in power system planning, guarantee the rationality and reliability in power system operations in dealing with the uncertainties, and, finally, enhancing the resilience of the power systems.

Smart building's benefits range from improving comfort of occupant, increased productivity, reduction in energy consumption and operating costs, lower CO2 emission, to improved life cycle of utilities, efficient operation of building systems, etc. [65]. Hence, modern building owners are turning towards smart buildings. However, the current smart buildings mostly are not capable of achieving the objectives they are designed for and they can improve a lot better [22]. Therefore, a new technology called, Internet of Things, or IoT, is combined with the smart buildings to improve their performance [23]. IoT is the inter-networking of things embedded with electronics, software, sensors, actuators, and network connectivity to collect and exchange data, and things in this definition is anything and everything around us and even ourselves. Using this technology, e.g. a door can be a thing and can sense how many people have passed it's sensor to enter a space and let the lighting system know to prepare appropriate amount of light, or the HVAC (Heating Ventilation Air Conditioning) system to provide desirable temperature. IoT will provide a lot of useful information that before that accessibility to it was impossible, e.g., condition of water pipes in winter, which helps avoiding damages like frozen or broken pipes. However, despite all the benefits, IoT suffers from being vulnerable to cyber attacks. Examples have been provided later in Chapter 1. In this project among building systems, HVAC system is chosen to be automated with a new control method called MPC (Model Predictive Control). This method is fast, very energy efficient and has a lower than 0.001 rate of error for regulating the space temperature to any temperature that the occupants desire according to the results of this project. Furthermore, a PID (Proportional–Integral–Derivative) controller has been designed for the HVAC system that in the exact same cases MPC shows a much better performance. To design controllers for HVAC system and set the temperature to the desired value a method to automate balancing the heat flow should be found, therefore a thermal model of building should be available that using this model, the amount of heat, flowing in and out of a space in the building disregarding the external weather would be known to estimate. To automate the HVAC system using the programming languages like MATLAB, there is a need to convert the thermal model of the building to a mathematical model. This mathematical model is unique for each building depending on how many floors it has, how wide it is, and what materials have been used to construct the building. This process is needs a lot of effort and time even for buildings with 2 floors and 2 rooms on each floor and at the end the engineer might have done it with error. In this project you will see a software that will do the conversion of thermal model of buildings in any size to their mathematical model automatically, which helps improving the HVAC controllers to set temperature to the value occupants desire and avoid errors and time loss which is put both into calculations and troubleshooting. In addition, a test environment has been designed and constructed as a cyber physical system that allows us to test the IoT- enabled control systems before implementing them on real buildings, observe the performance, and decide if the system is satisfying or not. Also, all cyber threats can be explored and the solutions to those attacks can be evaluated. Even for the systems that are already out there, there is an opportunity to be assessed on this testbed and if there is any vulnerability in case of cyber security, solutions would be evaluated and help the existing systems improve. Master of Science Buildings function as shelters more than any thing else, and this has allowed humans to use it as a space to store important things like private and important information. Therefore, this space should be safe and secure from any vulnerabilities for occupants and their information. Smart buildings, have made a great difference in increasing the comfort level of occupants, but they haven’t been greatly successful achieving their objectives [50]. Therefore, a new technology called, Internet of Things, or IoT, is combined with the smart buildings to improve their performance [23]. IoT is the inter-networking of things embedded with electronics, software, sensors, actuators, and network connectivity to collect and exchange data, and things in this definition is anything and everything around us and even ourselves. Internet of Things (IoT) has helped improving the smart buildings and getting a considerable amount of energy efficiency [27]. But adding Internet of Things has added a network of things connected to internet, which gives the cyber hackers an opportunity to hack the buildings, and get access to the information stored inside the building or put even occupants lives in danger. Therefore, in this thesis the following items have been contributed: • Designing and programming a novel control system for HVAC system of the buildings (Model Predictive Control): This is a new method to control HVAC system of buildings and in comparison with the methods available in the market, it is the most energy efficient, it is faster, and it has a lower error rate in following the desired temperature of the occupants. • Design and construction of IoT- enabled smart building testbed: Since cyber attacks make buildings vulnerable, the author believes it is better to build a test environment to simulate the buildings and the control methods that are used inside the buildings, and try to evaluate performance of the control methods before implementing them on real buildings. Also, by installing IoT sensors inside the test environment, the engineers can perform some cyber attack tests, and also evaluate the solutions for each attack on the testbed. • Design and program a software to convert thermal model of buildings to mathematical model : In designing a new control method for HVAC system of buildings, the first required information is the thermal model of the buildings. Eventually, there is a need to program. Thus, the thermal model should be converted to a mathematical model. However, there is a heavy manual calculation behind it that is really overwhelming, tiring, with a high possibility of error, and time-consuming even for a very small sized building. Therefore, automating this process in terms of a software that takes the information of thermal model of buildings as an input and giving the output of the mathematical model of building is a considerable achievement.

Many machine learning (ML) techniques rely on probability, random variables, and stochastic modeling. Although statistics pervades this field, there is a large disconnect between the copula modeling and the machine learning communities. Copulas are stochastic models that capture the full dependence structure between random variables and allow flexible modeling of multivariate joint distributions. Elidan was the first to recognize this disconnect, and introduced copula based models to the ML community that demonstrated magnitudes of order better performance than the non copula-based models Elidan [2013]. However, the limitation of these is that they are only applicable for continuous random variables and real world data is often naturally modeled jointly as continuous and discrete. This report details our work in bridging this gap of modeling and analyzing data that is jointly continuous and discrete using copulas. Our first research contribution details modeling of jointly continuous and discrete random variables using the copula framework with Bayesian networks, termed Hybrid Copula Bayesian Networks (HCBN) [Karra and Mili, 2016], a continuation of Elidan’s work on Copula Bayesian Networks Elidan [2010]. In this work, we extend the theorems proved by Neslehov ˇ a [2007] from bivariate ´ to multivariate copulas with discrete and continuous marginal distributions. Using the multivariate copula with discrete and continuous marginal distributions as a theoretical basis, we construct an HCBN that can model all possible permutations of discrete and continuous random variables for parent and child nodes, unlike the popular conditional linear Gaussian network model. Finally, we demonstrate on numerous synthetic datasets and a real life dataset that our HCBN compares favorably, from a modeling and flexibility viewpoint, to other hybrid models including the conditional linear Gaussian and the mixture of truncated exponentials models. Our second research contribution then deals with the analysis side, and discusses how one may use copulas for exploratory data analysis. To this end, we introduce a nonparametric copulabased index for detecting the strength and monotonicity structure of linear and nonlinear statistical dependence between pairs of random variables or stochastic signals. Our index, termed Copula Index for Detecting Dependence and Monotonicity (CIM), satisfies several desirable properties of measures of association, including Renyi’s properties, the data processing inequality (DPI), and ´ consequently self-equitability. Synthetic data simulations reveal that the statistical power of CIM compares favorably to other state-of-the-art measures of association that are proven to satisfy the DPI. Simulation results with real-world data reveal CIM’s unique ability to detect the monotonicity structure among stochastic signals to find interesting dependencies in large datasets. Additionally, simulations show that CIM shows favorable performance to estimators of mutual information when discovering Markov network structure. Our third research contribution deals with how to assess an estimator’s performance, in the scenario where multiple estimates of the strength of association between random variables need to be rank ordered. More specifically, we introduce a new property of estimators of the strength of statistical association, which helps characterize how well an estimator will perform in scenarios where dependencies between continuous and discrete random variables need to be rank ordered. The new property, termed the estimator response curve, is easily computable and provides a marginal distribution agnostic way to assess an estimator’s performance. It overcomes notable drawbacks of current metrics of assessment, including statistical power, bias, and consistency. We utilize the estimator response curve to test various measures of the strength of association that satisfy the data processing inequality (DPI), and show that the CIM estimator’s performance compares favorably to kNN, vME, AP, and HMI estimators of mutual information. The estimators which were identified to be suboptimal, according to the estimator response curve, perform worse than the more optimal estimators when tested with real-world data from four different areas of science, all with varying dimensionalities and sizes. Ph. D. Many machine learning (ML) techniques rely on probability, random variables, and stochastic modeling. Although statistics pervades this field, many of the traditional machine learning techniques rely on linear statistical techniques and models. For example, the correlation coefficient, a widely used construct in modern data analysis, is only a measure of linear dependence and cannot fully capture non-linear interactions. In this dissertation, we aim to address some of these gaps, and how they affect machine learning performance, using the mathematical construct of copulas. Our first contribution deals with accurate probabilistic modeling of real-world data, where the underlying data is both continuous and discrete. We show that even though the copula construct has some limitations with respect to discrete data, it is still amenable to modeling large real-world datasets probabilistically. Our second contribution deals with analysis of non-linear datasets. Here, we develop a new measure of statistical association that can handle discrete, continuous, or combinations of such random variables that are related by any general association pattern. We show that our new metric satisfies several desirable properties and compare it’s performance to other measures of statistical association. Our final contribution attempts to provide a framework for understanding how an estimator of statistical association will affect end-to-end machine learning performance. Here, we develop the estimator response curve, and show a new way to characterize the performance of an estimator of statistical association, termed the estimator response curve. We then show that the estimator response curve can help predict how well an estimator performs in algorithms which require statistical associations to be rank ordered.

Pathway analysis is an important task for gaining novel insights into the molecular architecture of many complex diseases. With the advancement of new sequencing technologies, a large amount of quantitative gene expression data have been continuously acquired. The springing up omics data sets such as proteomics has facilitated the investigation on disease relevant pathways. Although much work has previously been done to explore the single omics data, little work has been reported using multi-omics data integration, mainly due to methodological and technological limitations. While a single omic data can provide useful information about the underlying biological processes, multi-omics data integration would be much more comprehensive about the cause-effect processes responsible for diseases and their subtypes. This project investigates the combination of miRNAseq, proteomics, and RNAseq data on seven types of muscular dystrophies and control group. These unique multi-omics data sets provide us with the opportunity to identify disease-specific and most relevant biological pathways. We first perform t-test and OVEPUG test separately to define the differential expressed genes in protein and mRNA data sets. In multi-omics data sets, miRNA also plays a significant role in muscle development by regulating their target genes in mRNA dataset. To exploit the relationship between miRNA and gene expression, we consult with the commonly used gene library - Targetscan to collect all paired miRNA-mRNA and miRNA-protein co-expression pairs. Next, by conducting statistical analysis such as Pearson's correlation coefficient or t-test, we measured the biologically expected correlation of each gene with its upstream miRNAs and identify those showing negative correlation between the aforementioned miRNA-mRNA and miRNA-protein pairs. Furthermore, we identify and assess the most relevant disease-specific pathways by inputting the differential expressed genes and negative correlated genes into the gene-set libraries respectively, and further characterize these prioritized marker subsets using IPA (Ingenuity Pathway Analysis) or KEGG. We will then use Fisher method to combine all these p-values derived from separate gene sets into a joint significance test assessing common pathway relevance. In conclusion, we will find all negative correlated paired miRNA-mRNA and miRNA-protein, and identifying several pathophysiological pathways related to muscular dystrophies by gene set enrichment analysis. This novel multi-omics data integration study and subsequent pathway identification will shed new light on pathophysiological processes in muscular dystrophies and improve our understanding on the molecular pathophysiology of muscle disorders, preventing and treating disease, and make people become healthier in the long term. Master of Science

Recent advances in high-throughput technique enables the generation of a large amount of omic data such as genomics, transcriptomics, proteomics, metabolomics, glycomics etc. Typically, differential expression analysis (e.g., student's t-test, ANOVA) is performed to identify biomolecules (e.g., genes, proteins, metabolites, glycans) with significant changes on individual level between biologically disparate groups (disease cases vs. healthy controls) for cancer biomarker discovery. However, differential expression analysis on independent studies for the same clinical types of patients often led to different sets of significant biomolecules and had only few in common. This may be attributed to the fact that biomolecules are members of strongly intertwined biological pathways and highly interactive with each other. Without considering these interactions, differential expression analysis could lead to biased results. Network-based methods provide a natural framework to study the interactions between biomolecules. Commonly used data-driven network models include relevance network, Bayesian network and Gaussian graphical models. In addition to data-driven network models, there are many publicly available databases such as STRING, KEGG, Reactome, and ConsensusPathDB, where one can extract various types of interactions to build knowledge-driven networks. While both data- and knowledge-driven networks have their pros and cons, an appropriate approach to incorporate the prior biological knowledge from publicly available databases into data-driven network model is desirable for more robust and biologically relevant network reconstruction. Recently, there has been a growing interest in differential network analysis, where the connection in the network represents a statistically significant change in the pairwise interaction between two biomolecules in different groups. From the rewiring interactions shown in differential networks, biomolecules that have strongly altered connectivity between distinct biological groups can be identified. These biomolecules might play an important role in the disease under study. In fact, differential expression and differential network analyses investigate omic data from two complementary perspectives: the former focuses on the change in individual biomolecule level between different groups while the latter concentrates on the change in pairwise biomolecules level. Therefore, an approach that can integrate differential expression and differential network analyses is likely to discover more reliable and powerful biomarkers. To achieve these goals, we start by proposing a novel data-driven network model (i.e., LOPC) to reconstruct sparse biological networks. The sparse networks only contains direct interactions between biomolecules which can help researchers to focus on the more informative connections. Then we propose a novel method (i.e., dwgLASSO) to incorporate prior biological knowledge into data-driven network model to build biologically relevant networks. Differential network analysis is applied based on the networks constructed for biologically disparate groups to identify cancer biomarker candidates. Finally, we propose a novel network-based approach (i.e., INDEED) to integrate differential expression and differential network analyses to identify more reliable and powerful cancer biomarker candidates. INDEED is further expanded as INDEED-M to utilize omic data at different levels of human biological system (e.g., transcriptomics, proteomics, metabolomics), which we believe is promising to increase our understanding of cancer. Matlab and R packages for the proposed methods are developed and available at Github (https://github.com/Hurricaner1989) to share with the research community. Ph. D.

Identification of disease-related alterations in molecular and cellular mechanisms may reveal useful biomarkers for human diseases including cancers. High-throughput omic technologies for identifying and quantifying multi-level biological molecules (e.g., proteins, glycans, and metabolites) have facilitated the advances in biological research in recent years. Liquid (or gas) chromatography coupled with mass spectrometry (LC/GC-MS) has become an essential tool in such large-scale omic studies. Appropriate LC/GC-MS data preprocessing pipelines are needed to detect true differences between biological groups. Challenges exist in several aspects of MS data analysis. Specifically for biomarker discovery, one fundamental challenge in quantitation of biomolecules is owing to the heterogeneous nature of human biospecimens. Although this issue has been a subject of discussion in cancer genomic studies, it has not yet been rigorously investigated in mass spectrometry based omic studies. Purification of mass spectometric data is highly desired prior to subsequent differential analysis. In this research dissertation, we majorly target at addressing the purification problem through probabilistic modeling. We propose an intensity-level purification model (IPM) to computationally purify LC/GC-MS based cancerous data in biomarker discovery studies. We further extend IPM to scan-level purification model (SPM) by considering information from extracted ion chromatogram (EIC, scan-level feature). Both IPM and SPM belong to the category of topic modeling approach, which aims to identify the underlying "topics" (sources) and their mixture proportions in composing the heterogeneous data. Additionally, denoise deconvolution model (DMM) is proposed to capture the noise signals in samples based on purified profiles. Variational expectation-maximization (VEM) and Markov chain Monte Carlo (MCMC) methods are used to draw inference on the latent variables and estimate the model parameters. Before we come to purification, other research topics in related to mass spectrometric data analysis for cancer biomarker discovery are also investigated in this dissertation. Chapter 3 discusses the developed methods in the differential analysis of LC/GC-MS based omic data, specifically for the preprocessing in data of LC-MS profiled glycans. Chapter 4 presents the assumptions and inference details of IPM, SPM, and DDM. A latent Dirichlet allocation (LDA) core is used to model the heterogeneous cancerous data as mixtures of topics consisting of sample-specific pure cancerous source and non-cancerous contaminants. We evaluated the capability of the proposed models in capturing mixture proportions of contaminants and cancer profiles on LC-MS based serum and tissue proteomic and GC-MS based tissue metabolomic datasets acquired from patients with hepatocellular carcinoma (HCC) and liver cirrhosis. Chapter 5 elaborates these applications in cancer biomarker discovery, where typical single omic and integrative analysis of multi-omic studies are included. Ph. D.

Due to the rapid growth of grid-tied solar photovoltaic (PV) systems in the generation mix, the distribution grid will face complex operational challenges. High PV penetration can create overvoltages and voltage fluctuations in the network, which are major concerns for the grid operator. Traditional voltage control devices like switched capacitor banks or line voltage regulators can alleviate slow-moving fluctuations, but these devices need to operate more frequently than usual when PV generation fluctuates due to fast cloud movements. Such frequent operations will impact the life expectancy of these voltage control devices. Advanced PV inverter functionalities enable solar PV systems to provide reliable grid support through controlled real injection and/or reactive power compensation. This dissertation proposes a voltage regulation technique to mitigate probable impacts of high PV penetrations on the distribution voltage profile using smart inverter functionalities. A droop-based reactive power compensation method with active power curtailment is proposed, which uses the local voltage regulation at the inverter end. This technique is further augmented with very short-term PV generation forecasts. A hybrid forecasting algorithm is proposed here which is based on measurement-dependent dynamic modeling of PV systems using the Kalman Filter theory. Physical modeling of the PV system is utilized by this forecasting algorithm. Because of the rise in distributed PV systems, modeling of geographic dispersion is also addressed under PV system modeling. The proposed voltage regulation method is coordinated with existing voltage regulator operations to reduce required number of tap-change operations. Control settings of the voltage regulators are adjusted to achieve minimal number of tap-change operations within a predefined time window. Finally, integration of energy storage is studied to highlight the value of the proposed voltage regulation technique vis-à-vis increased solar energy use. Ph. D.

In the United States, over 40% of the country's total energy consumption is in buildings, most of which are either small-sized (

Data privacy is a globally recognized human right for individuals to control the access to their personal information, and bar the negative consequences from the use of this information. As communication technologies progress, the means to protect data privacy must also evolve to address new challenges come into view. Our research goal in this dissertation is to develop privacy protection frameworks and techniques suitable for the emerging cloud-based data services, in particular privacy-preserving algorithms and protocols for the cloud-based data sharing and data analytics services. Cloud computing has enabled users to store, process, and communicate their personal information through third-party services. It has also raised privacy issues regarding losing control over data, mass harvesting of information, and un-consented disclosure of personal content. Above all, the main concern is the lack of understanding about data privacy in cloud environments. Currently, the cloud service providers either advocate the principle of third-party doctrine and deny users' rights to protect their data stored in the cloud; or rely the notice-and-choice framework and present users with ambiguous, incomprehensible privacy statements without any meaningful privacy guarantee. In this regard, our research has three main contributions. First, to capture users' privacy expectations in cloud environments, we conceptually divide personal data into two categories, i.e., visible data and invisible data. The visible data refer to information users intentionally create, upload to, and share through the cloud; the invisible data refer to users' information retained in the cloud that is aggregated, analyzed, and repurposed without their knowledge or understanding. Second, to address users' privacy concerns raised by cloud computing, we propose two privacy protection frameworks, namely individual control and use limitation. The individual control framework emphasizes users' capability to govern the access to the visible data stored in the cloud. The use limitation framework emphasizes users' expectation to remain anonymous when the invisible data are aggregated and analyzed by cloud-based data services. Finally, we investigate various techniques to accommodate the new privacy protection frameworks, in the context of four cloud-based data services: personal health record sharing, location-based proximity test, link recommendation for social networks, and face tagging in photo management applications. For the first case, we develop a key-based protection technique to enforce fine-grained access control to users' digital health records. For the second case, we develop a key-less protection technique to achieve location-specific user selection. For latter two cases, we develop distributed learning algorithms to prevent large scale data harvesting. We further combine these algorithms with query regulation techniques to achieve user anonymity. The picture that is emerging from the above works is a bleak one. Regarding to personal data, the reality is we can no longer control them all. As communication technologies evolve, the scope of personal data has expanded beyond local, discrete silos, and integrated into the Internet. The traditional understanding of privacy must be updated to reflect these changes. In addition, because privacy is a particularly nuanced problem that is governed by context, there is no one-size-fit-all solution. While some cases can be salvaged either by cryptography or by other means, in others a rethinking of the trade-offs between utility and privacy appears to be necessary. Ph. D.

One of the most common measures of clinical outcomes is the survival time. Accurately linking cancer molecular profiling with survival outcome advances clinical management of cancer. However, existing survival analysis relies intensively on statistical evidence from a single level of data, without paying much attention to the integration of interacting multi-level data and the underlying biology. Advances in genomic techniques provide unprecedented power of characterizing the cancer tissue in a more complete manner than before, opening the opportunity of designing biologically informed and integrative approaches for survival analysis. Many cancer tissues have been profiled for gene expression levels and genomic variants (such as copy number alterations, sequence mutations, DNA methylation, and histone modification). However, it is not clear how to integrate the gene expression and genetic variants to achieve a better prediction and understanding of the cancer survival. To address this challenge, we propose two approaches for data integration in order to both biologically and statistically boost the features selection process for proper detection of the true predictive players of survival. The first approach is data-driven yet biologically informed. Consistent with the biological hierarchy from DNA to RNA, we prioritize each survival-relevant feature with two separate scores, predictive and mechanistic. With mRNA expression levels in concern, predictive features are those mRNAs whose variation in expression levels are associated with the survival outcome, and mechanistic features are those mRNAs whose variation in expression levels are associated with genomic variants (copy number alterations (CNAs) in this study). Further, we propose simultaneously integrating information from both the predictive model and the mechanistic model through our new approach GEMPS (Gene Expression as a Mediator for Predicting Survival). Applied on two cancer types (ovarian and glioblastoma multiforme), our method achieved better prediction power than peer methods. Gene set enrichment analysis confirms that the genes utilized for the final survival analysis are biologically important and relevant. The second approach is a generic mathematical framework to biologically regularize the Cox's proportional hazards model that is widely used in survival analysis. We propose a penalty function that both links the mechanistic model to the clinical model and reflects the biological downstream regulatory effect of the genomic variants on the mRNA expression levels of the target genes. Fast and efficient optimization principles like the coordinate descent and majorization-minimization are adopted in the inference process of the coefficients of the Cox model predictors. Through this model, we develop the regulator-target gene relationship to a new one: regulator-target-outcome relationship of a disease. Assessed via a simulation study and analysis of two real cancer data sets, the proposed method showed better performance in terms of selecting the true predictors and achieving better survival prediction. The proposed method gives insightful and meaningful interpretability to the selected model due to the biological linking of the mechanistic model and the clinical model. Other important forms of clinical outcomes are monitoring angiogenesis (formation of new blood vessels necessary for tumor to nourish itself and sustain its existence) and assessing therapeutic response. This can be done through dynamic imaging, in which a series of images at different time instances are acquired for a specific tumor site after injection of a contrast agent. Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is a noninvasive tool to examine tumor vasculature patterns based on accumulation and washout of the contrast agent. DCE-MRI gives indication about tumor vasculature permeability, which in turn indicates the tumor angiogenic activity. Observing this activity over time can reflect the tumor drug responsiveness and efficacy of the treatment plan. However, due to the limited resolution of the imaging scanners, a partial-volume effect (PVE) problem occurs, which is the result of signals from two or more tissues combining together to produce a single image concentration value within a pixel, with the effect of inaccurate estimation to the values of the pharmacokinetic parameters. A multi-tissue compartmental modeling (CM) technique supported by convex analysis of mixtures is used to mitigate the PVE by clustering pixels and constructing a simplex whose vertices are of a single compartment type. CAM uses the identified pure-volume pixels to estimate the kinetics of the tissues under investigation. We propose an enhanced version of CAM-CM to identify pure-volume pixels more accurately. This includes the consideration of the neighborhood effect on each pixel and the use of a barycentric coordinate system to identify more pure-volume pixels and to test those identified by CAM-CM. Tested on simulated DCE-MRI data, the enhanced CAM-CM achieved better performance in terms of accuracy and reproducibility. Ph. D.

Augmented reality is poised to become the next dominant computing paradigm over the course of the next decade. With the three-dimensional graphics and interactive interfaces that augmented reality promises it will rival the very best science fiction novels. Users will want to have shared experiences in these rich augmented reality scenarios, but surely users will want to restrict who can see their content. It is currently unclear how users of such devices will authenticate one another. Traditional authentication protocols reliant on centralized authorities fall short when different systems with different authorities try to communicate and extra infrastructure means extra resource expenditure. Augmented reality content sharing will usually occur in face-to-face scenarios where it will be advantageous for both performance and usability reasons to keep communications and authentication localized. Looks Good To Me (LGTM) is an authentication protocol for augmented reality headsets that leverages the unique hardware and context provided with augmented reality headsets to solve an old problem in a more usable and more secure way. LGTM works over point to point wireless communications so users can authenticate one another in any circumstance and is designed with usability at its core, requiring users to perform only two actions: one to initiate and one to confirm. LGTM allows users to intuitively authenticate one another, using seemingly only each other's faces. Under the hood LGTM uses a combination of facial recognition and wireless localization to ensure secure and extremely simple authentication. Master of Science

High renewable energy penetration is a goal for many countries to increase energy security and reduce carbon emissions from conventional power plants. Wind energy is one of leading sources among different renewable resources. However, high wind energy penetration in the system brings new challenges to the electric power system due to its variable and stochastic nature, and non-correlation between wind and load profiles. The term non-correlation is used in this research refers to the fact that wind or any other renewable generation, which is nature driven, does not follow the load like conventional power plants. Wind spill is a challenge to utilities with high wind energy penetration levels. This occurs from situations mentioned above and the fact that wind generation sometimes exceeds the servable load minus must-run generation. In these cases there is no option but to curtail non-usable wind generation. This dissertation presents grid-scale energy storage and demand response options as an optimization problem to minimize spilled wind energy. Even after managing this spilled wind energy, there is still a challenge in a system with high wind energy penetration coming from wind power forecast error. Wind power forecast error is handled by having more back-up energy and spilling the non-usable wind power. This research offers a way to use the grid-scale energy storage units to mitigate impacts of wind power forecast error by. A signal processing method is proposed to decompose the fluctuating wind power forecast error signal, based on the fact that each energy storage or conventional unit is more efficient to operate within specific cycling regimes. Finally, an algorithm is proposed schedule energy storage for mitigating both impacts. Ph. D.

Plants have developed specific responses to external stimuli such as drought, cold, high salinity in soil, and precipitation in addition to internal developmental stimuli. These stimuli trigger signal transduction pathways in plants, leading to cellular adaptation. A signal transduction pathway is a network of entities that interact with one another in response to given stimulus. Such participating entities control and affect gene expression in response to stimulus . For computational purposes, a signal transduction pathway is represented as a network where nodes are biological molecules. The interaction of two nodes is a directed edge. A plethora of research has been conducted to understand signal transduction pathways. However, there are a limited number of approaches to explore and integrate signal transduction pathways. Therefore, we need a platform to integrate together and to expand the information of each signal transduction pathway. One of the major computational challenges in inferring signal transduction pathways is that the addition of new nodes and edges can affect the information flow between existing ones in an unknown manner. Here, I develop the Beacon inference engine to address these computational challenges. This software engine employs a network inference approach to predict new edges. First, it uses mutual information and context likelihood relatedness to predict edges from gene expression time-series data. Subsequently, it incorporates prior knowledge to limit false-positive predictions. Finally, a naive Bayes classifier is used to predict new edges. The Beacon inference engine predicts new edges with a recall rate 77.6% and precision 81.4%. 24% of the total predicted edges are new i.e., they are not present in the prior knowledge. Master of Science

Characterizing complex tissues requires precise identification of distinctive cell types, cell-specific signatures, and subpopulation proportions. Tissue heterogeneity, arising from multiple cell types, is a major confounding factor in studying individual subpopulations and repopulation dynamics. Tissue heterogeneity cannot be resolved directly by most global molecular and genomic profiling methods. While signal deconvolution has widespread applications in many real-world problems, there are significant limitations associated with existing methods, mainly unrealistic assumptions and heuristics, leading to inaccurate or incorrect results. In this study, we formulate the signal deconvolution task as a blind source separation problem, and develop novel unsupervised deconvolution methods within the Convex Analysis of Mixtures (CAM) framework, for characterizing multi-scale tissue heterogeneity. We also explanatorily test the application of Significant Intercellular Genomic Heterogeneity (SIGH) method. Unlike existing deconvolution methods, CAM can identify tissue-specific markers directly from mixed signals, a critical task, without relying on any prior knowledge. Fundamental to the success of our approach is a geometric exploitation of tissue-specific markers and signal non-negativity. Using a well-grounded mathematical framework, we have proved new theorems showing that the scatter simplex of mixed signals is a rotated and compressed version of the scatter simplex of pure signals and that the resident markers at the vertices of the scatter simplex are the tissue-specific markers. The algorithm works by geometrically locating the vertices of the scatter simplex of measured signals and their resident markers. The minimum description length (MDL) criterion is applied to determine the number of tissue populations in the sample. Based on CAM principle, we integrated nonnegative independent component analysis (nICA) and convex matrix factorization (CMF) methods, developed CAM-nICA/CMF algorithm, and applied them to multiple gene expression, methylation and protein datasets, achieving very promising results validated by the ground truth or gene enrichment analysis. We integrated CAM with compartment modeling (CM) and developed multi-tissue compartment modeling (MTCM) algorithm, tested on real DCE-MRI data derived from mouse models with consistent and plausible results. We also developed an open-source R-Java software package that implements various CAM based algorithms, including an R package approved by Bioconductor specifically for tumor-stroma deconvolution. While intercellular heterogeneity is often manifested by multiple clones with distinct sequences, systematic efforts to characterize intercellular genomic heterogeneity must effectively distinguish significant genuine clonal sequences from probabilistic fake derivatives. Based on the preliminary studies originally targeting immune T-cells, we tested and applied the SIGH algorithm to characterize intercellular heterogeneity directly from mixed sequencing reads. SIGH works by exploiting the statistical differences in both the sequencing error rates at different nucleobases and the read counts of fake sequences in relation to genuine clones of variable abundance. Ph. D.

State-of-the-art speaker identification and verification (SIV) systems provide near perfect performance under clean conditions. However, their performance deteriorates in the presence of background noise. Many feature compensation, model compensation and signal enhancement techniques have been proposed to improve the noise-robustness of SIV systems. Most of these techniques require extensive training, are computationally expensive or make assumptions about the noise characteristics. There has not been much focus on analyzing the relative importance, or speaker-discriminative power of different speech zones, particularly under noisy conditions. In this work, an automatic, text-independent speaker identification (SI) system and speaker verification (SV) system is proposed using Line Spectral Frequency (LSF) features. The performance of the proposed SI and SV systems are evaluated under various types of background noise. A score-level fusion based technique is implemented to extract complementary information from static and dynamic LSF features. The proposed score-level fusion based SI and SV systems are found to be more robust under noisy conditions. In addition, we investigate the speaker-discriminative power of different speech zones such as vowels, non-vowels and transitions. Rapidly varying regions of speech such as consonant-vowel transitions are found to be most speaker-discriminative in high SNR conditions. Steady, high-energy vowel regions are robust against noise and are hence most speaker-discriminative in low SNR conditions. We show that selectively utilizing features from a combination of transition and steady vowel zones further improves the performance of the score-level fusion based SI and SV systems under noisy conditions. Master of Science