Indiana University-Purdue University Indianapolis (IUPUI) / Yan, Jiaxiang. M.S.E.C.E., Purdue University, May 2013. Modeling, Monitoring and Optimization of Discrete Event Systems Using Petri Nets. Major Professor: Lingxi Li. In last decades, the research of discrete event systems (DESs) has attracts more and more attention because of the fast development of intelligent control strategies. Such control measures combine the conventional control strategies with discrete decision-making processes which simulate human decision-making processes. Due to the scale and complexity of common DESs, the dedicated models, monitoring methods and optimal control strategies for them are necessary. Among various DES models, Petri nets are famous for the advantage in dealing with asynchronous processes. They have been widely applied in intelligent transportation systems (ITS) and communication technology in recent years. With encoding of the Petri net state, we can also enable fault detection and identification capability in DESs and mitigate potential human errors. This thesis studies various problems in the context of DESs that can be modeled by Petri nets. In particular, we focus on systematic modeling, asynchronous monitoring and optimal control strategies design of Petri nets. This thesis starts by looking at the systematic modeling of ITS. A microscopic model of signalized intersection and its two-layer timed Petri net representation is proposed in this thesis, where the first layer is the representation of the intersection and the second layer is the representation of the traffic light system. Deterministic and stochastic transitions are both involved in such Petri net representation. The detailed operation process of such Petri net representation is stated. The improvement of such Petri net representation is also provided with comparison to previous models. Then we study the asynchronous monitoring of sensor networks. An event sequence reconstruction algorithm for a given sensor network based on asynchronous observations of its state changes is proposed in this thesis. We assume that the sensor network is modeled as a Petri net and the asynchronous observations are in the form of state (token) changes at different places in the Petri net. More specifically, the observed sequences of state changes are provided by local sensors and are asynchronous, i.e., they only contain partial information about the ordering of the state changes that occur. We propose an approach that is able to partition the given net into several subnets and reconstruct the event sequence for each subnet. Then we develop an algorithm that is able to reconstruct the event sequences for the entire net that are consistent with: 1) the asynchronous observations of state changes; 2) the event sequences of each subnet; and 3) the structure of the given Petri net. We discuss the algorithmic complexity. The final problem studied in this thesis is the optimal design method of Petri net controllers with fault-tolerant ability. In particular, we consider multiple faults detection and identification in Petri nets that have state machine structures (i.e., every transition in the net has only one input place and one output place). We develop the approximation algorithms to design the fault-tolerant Petri net controller which achieves the minimal number of connections with the original controller. A design example for an automated guided vehicle (AGV) system is also provided to illustrate our approaches.

Indiana University-Purdue University Indianapolis (IUPUI) / Mammographic density is an important risk factor for breast cancer, detecting and screening at an early stage could help save lives. To analyze breast density distribution, a good segmentation algorithm is needed. In this thesis, we compared two popularly used segmentation algorithms, EM-MPM and K-means Clustering. We applied them on twenty cases of synthetic phantom ultrasound tomography (UST), and nine cases of clinical mammogram and UST images. From the synthetic phantom segmentation comparison we found that EM-MPM performs better than K-means Clustering on segmentation accuracy, because the segmentation result fits the ground truth data very well (with superior Tanimoto Coefficient and Parenchyma Percentage). The EM-MPM is able to use a Bayesian prior assumption, which takes advantage of the 3D structure and finds a better localized segmentation. EM-MPM performs significantly better for the highly dense tissue scattered within low density tissue and for volumes with low contrast between high and low density tissues. For the clinical mammogram, image segmentation comparison shows again that EM-MPM outperforms K-means Clustering since it identifies the dense tissue more clearly and accurately than K-means. The superior EM-MPM results shown in this study presents a promising future application to the density proportion and potential cancer risk evaluation.

Indiana University-Purdue University Indianapolis (IUPUI) / Current mainstream computing systems have become increasingly complex. Most of which have Central Processing Units (CPUs) that invoke multiple threads for their computing tasks. The growing issue with these systems is resource contention and with resource contention comes the risk of encountering a deadlock status in the system. Various software and hardware approaches exist that implement deadlock detection/avoidance techniques; however, they lack either the speed or problem size capability needed for real-time systems. The research conducted for this thesis aims to resolve issues present in past approaches by converging the two platforms (software and hardware) by means of the Graphics Processing Unit (GPU). Presented in this thesis are two GPU-based deadlock detection algorithms and one GPU-based deadlock avoidance algorithm. These GPU-based algorithms are: (i) GPU-OSDDA: A GPU-based Single Unit Resource Deadlock Detection Algorithm, (ii) GPU-LMDDA: A GPU-based Multi-Unit Resource Deadlock Detection Algorithm, and (iii) GPU-PBA: A GPU-based Deadlock Avoidance Algorithm. Both GPU-OSDDA and GPU-LMDDA utilize the Resource Allocation Graph (RAG) to represent resource allocation status in the system. However, the RAG is represented using integer-length bit-vectors. The advantages brought forth by this approach are plenty: (i) less memory required for algorithm matrices, (ii) 32 computations performed per instruction (in most cases), and (iii) allows our algorithms to handle large numbers of processes and resources. The deadlock detection algorithms also require minimal interaction with the CPU by implementing matrix storage and algorithm computations on the GPU, thus providing an interactive service type of behavior. As a result of this approach, both algorithms were able to achieve speedups over two orders of magnitude higher than their serial CPU implementations (3.17-317.42x for GPU-OSDDA and 37.17-812.50x for GPU-LMDDA). Lastly, GPU-PBA is the first parallel deadlock avoidance algorithm implemented on the GPU. While it does not achieve two orders of magnitude speedup over its CPU implementation, it does provide a platform for future deadlock avoidance research for the GPU.

Indiana University-Purdue University Indianapolis (IUPUI) / Drug-drug interactions (DDIs) refer to situations where one drug affects the pharmacokinetics or pharmacodynamics of another. DDIs represent a major cause of morbidity and mortality. A common adverse drug reaction (ADR) that can result from, or be exacerbated by DDIs is drug-induced myopathy. Identifying DDIs and understanding their underlying mechanisms is key to the prevention of undesirable effects of DDIs and to efforts to optimize therapeutic outcomes. This dissertation is dedicated to identification of clinically important myopathic DDIs and to elucidation of their underlying mechanisms. Using data mined from the published cytochrome P450 (CYP) drug interaction literature, 13,197 drug pairs were predicted to potentially interact by pairing a substrate and an inhibitor of a major CYP isoform in humans. Prescribing data for these drug pairs and their associations with myopathy were then examined in a large electronic medical record database. The analyses identified fifteen drug pairs as DDIs significantly associated with an increased risk of myopathy. These significant myopathic DDIs involved clinically important drugs including alprazolam, chloroquine, duloxetine, hydroxychloroquine, loratadine, omeprazole, promethazine, quetiapine, risperidone, ropinirole, trazodone and simvastatin. Data from in vitro experiments indicated that the interaction between quetiapine and chloroquine (risk ratio, RR, 2.17, p-value 5.29E-05) may result from the inhibitory effects of quetiapine on chloroquine metabolism by cytochrome P450s (CYPs). The in vitro data also suggested that the interaction between simvastatin and loratadine (RR 1.6, p-value 4.75E-07) may result from synergistic toxicity of simvastatin and desloratadine, the major metabolite of loratadine, to muscle cells, and from the inhibitory effect of simvastatin acid, the active metabolite of simvastatin, on the hepatic uptake of desloratadine via OATP1B1/1B3. Our data not only identified unknown myopathic DDIs of clinical consequence, but also shed light on their underlying pharmacokinetic and pharmacodynamic mechanisms. More importantly, our approach exemplified a new strategy for identification and investigation of DDIs, one that combined literature mining using bioinformatic algorithms, ADR detection using a pharmacoepidemiologic design, and mechanistic studies employing in vitro experimental models.

Indiana University-Purdue University Indianapolis (IUPUI) / A Brain Computer Interface (BCI) is a hardware and software system that establishes direct communication between human brain and the environment. In a BCI system, brain messages pass through wires and external computers instead of the normal pathway of nerves and muscles. General work ow in all BCIs is to measure brain activities, process and then convert them into an output readable for a computer. The measurement of electrical activities in different parts of the brain is called electroencephalography (EEG). There are lots of sensor technologies with different number of electrodes to record brain activities along the scalp. Each of these electrodes captures a weighted sum of activities of all neurons in the area around that electrode. In order to establish a BCI system, it is needed to set a bunch of electrodes on scalp, and a tool to send the signals to a computer for training a system that can find the important information, extract them from the raw signal, and use them to recognize the user's intention. After all, a control signal should be generated based on the application. This thesis describes the step by step training and testing a BCI system that can be used for a person who has lost speaking skills through an accident or surgery, but still has healthy brain tissues. The goal is to establish an algorithm, which recognizes different vowels from EEG signals. It considers a bandpass filter to remove signals' noise and artifacts, periodogram for feature extraction, and Support Vector Machine (SVM) for classification.

Indiana University-Purdue University Indianapolis (IUPUI) / In recent decades, Petri nets (PNs) have been used to model traffic networks for different purposes, such as signal phase control, routing, and traffic flow estimation, etc. Because of the complex nature of traffic networks where both discrete and continuous dynamics come into play, the Hybrid Petri net (HPN) model becomes an important tool for the modeling and analysis of traffic networks. In Chapter 1 a brief historical summery about traffic systems control and then related work is mentioned followed by the major contributions in this research. Chapter 2 provides a theoretical background on Petri nets. In Chapter 3, we develop a HPN model for a single signalized intersection first, then we extend this model to study a simple traffic network that consists of two successive intersections. Time delays between different points of network are also considered in order to make the model suitable for analysis and simulation. In addition to HPN models, we also consider discrete Petri nets where their modeling simplicity enables the characterization of the occurrences of all events in the system. This discrete PN is particularly useful to give a higher-level representation of the traffic network and study its event occurrences and correlations. In Chapter 4, we build a discrete PN model to represent a traffic network with two successive intersections. However, we find that the model leads to unbounded places which cannot accurately reflect the dynamics of the traffic in terms of event occurrences. Hence, we introduce the Modified Binary Petri nets (MBPN) to overcome the limitation and resolve the confliction problem when we design our controllers. This MBPN model is a powerful tool and can be useful for the modeling and analysis of many other applications in traffic networks. Chapter 5 gives a summary for each chapter, provides conclusion and discusses future work for both discrete and hybrid Petri nets.

Indiana University-Purdue University Indianapolis (IUPUI) / In 2009, Indianapolis Emergency Medical Service (I-EMS, formerly Wishard Ambulance Service) launched an electronic medical record system within their ambulances and started to exchange patient data with the Indiana Network for Patient Care (INPC). This unique system allows EMS personnel in an ambulance to get important medical information prior to the patient’s arrival to the accepting hospital from incident scene. In this retrospective cohort study, we found EMS personnel made 3,021 patient data requests (14%) of 21,215 EMS transports during a one-year period, with a “success” match rate of 46%, and a match “failure” rate of 17%. The three major factors for causing match “failure” were (1) ZIP code 55%, (2) Patient Name 22%, and (3) Birth Date 12%. This study shows that the ZIP code is not a robust identifier in the patient identification process and Non-ZIP code identifiers may be a better choice due to inaccuracies and changes of the ZIP code in a patient’s record.