This thesis presents a successful application of operations research techniques in nonprofit distribution system to improve the distribution efficiency and increase customer service quality. It focuses on truck routing problems faced by St. Mary’s Food Bank Distribution Center. This problem is modeled as a capacitated vehicle routing problem to improve the distribution efficiency and is extended to capacitated vehicle routing problem with time windows to increase customer service quality. Several heuristics are applied to solve these vehicle routing problems and tested in well-known benchmark problems. Algorithms are tested by comparing the results with the plan currently used by St. Mary’s Food Bank Distribution Center. The results suggest heuristics are quite completive: average 17% less trucks and 28.52% less travel time are used in heuristics’ solution.

Modern intelligent transportation systems (ITS) make driving more efficient, easier, and safer. Knowledge of real-time traffic conditions is a critical input for operating ITS. Real-time freeway traffic state estimation approaches have been used to quantify traffic conditions given limited amount of data collected by traffic sensors. Currently, almost all real-time estimation methods have been developed for estimating laterally aggregated traffic conditions in a roadway segment using link-based models which assume homogeneous conditions across multiple lanes. However, with new advances and applications of ITS, knowledge of lane-based traffic conditions is becoming important, where the traffic condition differences among lanes are recognized. In addition, most of the current real-time freeway traffic estimators consider only data from loop detectors. This dissertation develops a bi-level data fusion approach using heterogeneous multi-sensor measurements to estimate real-time lane-based freeway traffic conditions, which integrates a link-level model-based estimator and a lane-level data-driven estimator.

Macroscopic traffic flow models describe the evolution of aggregated traffic characteristics over time and space, which are required by model-based traffic estimation approaches. Since current first-order Lagrangian macroscopic traffic flow model has some unrealistic implicit assumptions (e.g., infinite acceleration), a second-order Lagrangian macroscopic traffic flow model has been developed by incorporating drivers’ anticipation and reaction delay. A multi-sensor extended Kalman filter (MEKF) algorithm has been developed to combine heterogeneous measurements from multiple sources. A MEKF-based traffic estimator, explicitly using the developed second-order traffic flow model and measurements from loop detectors as well as GPS trajectories for given fractions of vehicles, has been proposed which gives real-time link-level traffic estimates in the bi-level estimation system.

The lane-level estimation in the bi-level data fusion system uses the link-level estimates as priors and adopts a data-driven approach to obtain lane-based estimates, where now heterogeneous multi-sensor measurements are combined using parallel spatial-temporal filters.

Experimental analysis shows that the second-order model can more realistically reproduce real world traffic flow patterns (e.g., stop-and-go waves). The MEKF-based link-level estimator exhibits more accurate results than the estimator that uses only a single data source. Evaluation of the lane-level estimator demonstrates that the proposed new bi-level multi-sensor data fusion system can provide very good estimates of real-time lane-based traffic conditions.

Recent advances in medical imaging technology have greatly enhanced imaging based diagnosis which requires computational effective and accurate algorithms to process the images (e.g., measure the objects) for quantitative assessment. In this dissertation, one type of imaging objects is of interest: small blobs. Example small blob objects are cells in histopathology images, small breast lesions in ultrasound images, glomeruli in kidney MR images etc. This problem is particularly challenging because the small blobs often have inhomogeneous intensity distribution and indistinct boundary against the background.

This research develops a generalized four-phased system for small blob detections. The system includes (1) raw image transformation, (2) Hessian pre-segmentation, (3) feature extraction and (4) unsupervised clustering for post-pruning. First, detecting blobs from 2D images is studied where a Hessian-based Laplacian of Gaussian (HLoG) detector is proposed. Using the scale space theory as foundation, the image is smoothed via LoG. Hessian analysis is then launched to identify the single optimal scale based on which a pre-segmentation is conducted. Novel Regional features are extracted from pre-segmented blob candidates and fed to Variational Bayesian Gaussian Mixture Models (VBGMM) for post pruning. Sixteen cell histology images and two hundred cell fluorescent images are tested to demonstrate the performances of HLoG. Next, as an extension, Hessian-based Difference of Gaussians (HDoG) is proposed which is capable to identify the small blobs from 3D images. Specifically, kidney glomeruli segmentation from 3D MRI (6 rats, 3 humans) is investigated. The experimental results show that HDoG has the potential to automatically detect glomeruli, enabling new measurements of renal microstructures and pathology in preclinical and clinical studies. Realizing the computation time is a key factor impacting the clinical adoption, the last phase of this research is to investigate the data reduction technique for VBGMM in HDoG to handle large-scale datasets. A new coreset algorithm is developed for variational Bayesian mixture models. Using the same MRI dataset, it is observed that the four-phased system with coreset-VBGMM has similar performance as using the full dataset but about 20 times faster.

Major advancements in biology and medicine have been realized during recent decades, including massively parallel sequencing, which allows researchers to collect millions or billions of short reads from a DNA or RNA sample. This capability opens the door to a renaissance in personalized medicine if effectively deployed. Three projects that address major and necessary advancements in massively parallel sequencing are included in this dissertation. The first study involves a pair of algorithms to verify patient identity based on single nucleotide polymorphisms (SNPs). In brief, we developed a method that allows de novo construction of sample relationships, e.g., which ones are from the same individuals and which are from different individuals. We also developed a method to confirm the hypothesis that a tumor came from a known individual. The second study derives an algorithm to multiplex multiple Polymerase Chain Reaction (PCR) reactions, while minimizing interference between reactions that compromise results. PCR is a powerful technique that amplifies pre-determined regions of DNA and is often used to selectively amplify DNA and RNA targets that are destined for sequencing. It is highly desirable to multiplex reactions to save on reagent and assay setup costs as well as equalize the effect of minor handling issues across gene targets. Our solution involves a binary integer program that minimizes events that are likely to cause interference between PCR reactions. The third study involves design and analysis methods required to analyze gene expression and copy number results against a reference range in a clinical setting for guiding patient treatments. Our goal is to determine which events are present in a given tumor specimen. These events may be mutation, DNA copy number or RNA expression. All three techniques are being used in major research and diagnostic projects for their intended purpose at the time of writing this manuscript. The SNP matching solution has been selected by The Cancer Genome Atlas to determine sample identity. Paradigm Diagnostics, Viomics and International Genomics Consortium utilize the PCR multiplexing technique to multiplex various types of PCR reactions on multi-million dollar projects. The reference range-based normalization method is used by Paradigm Diagnostics to analyze results from every patient.

Vehicles powered by electricity and alternative-fuels are becoming a more popular form of transportation since they have less of an environmental impact than standard gasoline vehicles. Unfortunately, their success is currently inhibited by the sparseness of locations where the vehicles can refuel as well as the fact that many of the vehicles have a range that is less than those powered by gasoline. These factors together create a "range anxiety" in drivers, which causes the drivers to worry about the utility of alternative-fuel and electric vehicles and makes them less likely to purchase these vehicles. For the new vehicle technologies to thrive it is critical that range anxiety is minimized and performance is increased as much as possible through proper routing and scheduling. In the case of long distance trips taken by individual vehicles, the routes must be chosen such that the vehicles take the shortest routes while not running out of fuel on the trip. When many vehicles are to be routed during the day, if the refueling stations have limited capacity then care must be taken to avoid having too many vehicles arrive at the stations at any time. If the vehicles that will need to be routed in the future are unknown then this problem is stochastic. For fleets of vehicles serving scheduled operations, switching to alternative-fuels requires ensuring the schedules do not cause the vehicles to run out of fuel. This is especially problematic since the locations where the vehicles may refuel are limited due to the technology being new. This dissertation covers three related optimization problems: routing a single electric or alternative-fuel vehicle on a long distance trip, routing many electric vehicles in a network where the stations have limited capacity and the arrivals into the system are stochastic, and scheduling fleets of electric or alternative-fuel vehicles with limited locations to refuel. Different algorithms are proposed to solve each of the three problems, of which some are exact and some are heuristic. The algorithms are tested on both random data and data relating to the State of Arizona.

Multicore processors have proliferated in nearly all forms of computing, from servers, desktop, to smartphones. The primary reason for this large adoption of multicore processors is due to its ability to overcome the power-wall by providing higher performance at a lower power consumption rate. With multi-cores, there is increased need for dynamic energy management (DEM), much more than for single-core processors, as DEM for multi-cores is no more a mechanism just to ensure that a processor is kept under specified temperature limits, but also a set of techniques that manage various processor controls like dynamic voltage and frequency scaling (DVFS), task migration, fan speed, etc. to achieve a stated objective. The objectives span a wide range from maximizing throughput, minimizing power consumption, reducing peak temperature, maximizing energy efficiency, maximizing processor reliability, and so on, along with much more wider constraints of temperature, power, timing, and reliability constraints. Thus DEM can be very complex and challenging to achieve. Since often times many DEMs operate together on a single processor, there is a need to unify various DEM techniques. This dissertation address such a need. In this work, a framework for DEM is proposed that provides a unifying processor model that includes processor power, thermal, timing, and reliability models, supports various DEM control mechanisms, many different objective functions along with equally diverse constraint specifications. Using the framework, a range of novel solutions is derived for instances of DEM problems, that include maximizing processor performance, energy efficiency, or minimizing power consumption, peak temperature under constraints of maximum temperature, memory reliability and task deadlines. Finally, a robust closed-loop controller to implement the above solutions on a real processor platform with a very low operational overhead is proposed. Along with the controller design, a model identification methodology for obtaining the required power and thermal models for the controller is also discussed. The controller is architecture independent and hence easily portable across many platforms. The controller has been successfully deployed on Intel Sandy Bridge processor and the use of the controller has increased the energy efficiency of the processor by over 30%

In this dissertation, an innovative framework for designing a multi-product integrated supply chain network is proposed. Multiple products are shipped from production facilities to retailers through a network of Distribution Centers (DCs). Each retailer has an independent, random demand for multiple products. The particular problem considered in this study also involves mixed-product transshipments between DCs with multiple truck size selection and routing delivery to retailers. Optimally solving such an integrated problem is in general not easy due to its combinatorial nature, especially when transshipments and routing are involved. In order to find out a good solution effectively, a two-phase solution methodology is derived: Phase I solves an integer programming model which includes all the constraints in the original model except that the routings are simplified to direct shipments by using estimated routing cost parameters. Then Phase II model solves the lower level inventory routing problem for each opened DC and its assigned retailers. The accuracy of the estimated routing cost and the effectiveness of the two-phase solution methodology are evaluated, the computational performance is found to be promising. The problem is able to be heuristically solved within a reasonable time frame for a broad range of problem sizes (one hour for the instance of 200 retailers). In addition, a model is generated for a similar network design problem considering direct shipment and consolidation within the same product set opportunities. A genetic algorithm and a specific problem heuristic are designed, tested and compared on several realistic scenarios.

Rapid advance in sensor and information technology has resulted in both spatially and temporally data-rich environment, which creates a pressing need for us to develop novel statistical methods and the associated computational tools to extract intelligent knowledge and informative patterns from these massive datasets. The statistical challenges for addressing these massive datasets lay in their complex structures, such as high-dimensionality, hierarchy, multi-modality, heterogeneity and data uncertainty. Besides the statistical challenges, the associated computational approaches are also considered essential in achieving efficiency, effectiveness, as well as the numerical stability in practice. On the other hand, some recent developments in statistics and machine learning, such as sparse learning, transfer learning, and some traditional methodologies which still hold potential, such as multi-level models, all shed lights on addressing these complex datasets in a statistically powerful and computationally efficient way. In this dissertation, we identify four kinds of general complex datasets, including "high-dimensional datasets", "hierarchically-structured datasets", "multimodality datasets" and "data uncertainties", which are ubiquitous in many domains, such as biology, medicine, neuroscience, health care delivery, manufacturing, etc. We depict the development of novel statistical models to analyze complex datasets which fall under these four categories, and we show how these models can be applied to some real-world applications, such as Alzheimer's disease research, nursing care process, and manufacturing.

Cloud computing has received significant attention recently as it is a new computing infrastructure to enable rapid delivery of computing resources as a utility in a dynamic, scalable, and visualized manner. SaaS (Software-as-a-Service) provide a now paradigm in cloud computing, which goal is to provide an effective and intelligent way to support end users' on-demand requirements to computing resources, including maturity levels of customizable, multi-tenancy and scalability. To meet requirements of on-demand, my thesis discusses several critical research problems and proposed solutions using real application scenarios. Service providers receive multiple requests from customers, how to prioritize those service requests to maximize the business values is one of the most important issues in cloud. An innovative prioritization model is proposed, which uses different types of information, including customer, service, environment and workflow information to optimize the performance of the system. To provide "on-demand" services, an accurate demand prediction and provision become critical for the successful of the cloud computing. An effective demand prediction model is proposed, and applied to a real mortgage application. To support SaaS customization and fulfill the various functional and quality requirements of individual tenants, a unified and innovative multi-layered customization framework is proposed to support and manage the variability of SaaS applications. To support scalable SaaS, a hybrid database design to support SaaS customization with two-layer database partitioning is proposed. To support secure SaaS, O-RBAC, an ontology based RBAC (Role based Access Control) model is used for Multi-Tenancy Architecture in clouds. To support a significant number of tenants, an easy to use SaaS construction framework is proposed. As a summary, this thesis discusses the most important research problems in cloud computing, towards effective and intelligent SaaS. The research in this thesis is critical to the development of cloud computing and provides fundamental solutions to those problems.