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Item Automatic Modeling and Simulation of Networked Components(2011) Bruce, Nathaniel William; Koskie, Sarah; Chen, Yaobin; Li, LingxiTesting and verification are essential to safe and consistent products. Simulation is a widely accepted method used for verification and testing of distributed components. Generally, one of the major hurdles in using simulation is the development of detailed and accurate models. Since there are time constraints on projects, fast and effective methods of simulation model creation emerge as essential for testing. This thesis proposes to solve these issues by presenting a method to automatically generate a simulation model and run a random walk simulation using that model. The method is automated so that a modeler spends as little time as possible creating a simulation model and the errors normally associated with manual modeling are eliminated. The simulation is automated to allow a human to focus attention on the device that should be tested. The communications transactions between two nodes on a network are recorded as a trace file. This trace file is used to automatically generate a finite state machine model. The model can be adjusted by a designer to add missing information and then simulated in real-time using a software-in-the-loop approach. The innovations in this thesis include adaptation of a synthesis method for use in simulation, introduction of a random simulation method, and introduction of a practical evaluation method for two finite state machines. Test results indicate that nodes can be adequately replaced by models generated automatically by these methods. In addition, model construction time is reduced when comparing to the from scratch model creation method.Item Investigating Disease Mechanisms and Drug Response Differences in Transcriptomics Sequencing Data(2022-01) Simpson, Edward Ronald Jr.; Liu, Yunlong; Janga, Sarath; Wan, Jun; Wu, Huanmei; Yan, JingwenIn eukaryotes, genetic information is encoded by DNA, transcribed to precursor messenger RNA (pre-mRNA), processed into mature messenger RNA (mRNA), and translated into functional proteins. Splicing of pre-mRNA is an important epigenetic process that alters the function of proteins through modifying the exon structure of mature mRNA transcripts and is known to greatly contribute to diversity of the human proteome. The vast majority of human genes are expressed through multiple transcript isoforms. Expression of genes through splicing of pre-mRNA plays crucial roles in cellular development, identity, and processes. Both the identity of genes selected for transcription and the specific transcript isoforms that are expressed are essential for normal cellular function. Deviations in gene expression or isoform proportion can be an indication or the cause of disease. RNA sequencing (RNAseq) is a high-throughput next-generation sequencing technology that allows for the interrogation of gene expression on a massive scale. RNAseq generates short sequences that reflect pieces of mRNAs present in a sample. RNAseq can therefore be used to explore differences in gene expression, reveal transcript isoform identities and compare changes in isoform proportions. In this dissertation, I design and apply advanced analysis techniques to RNAseq, phenotypic and drug response data to investigate disease mechanisms and drug sensitivity. Research Goals: The work described in this dissertation accomplishes 4 aims. Aim 1) Evaluate the gene expression signature of concussion in collegiate athletes and identify potential biomarkers for response and recovery. Aim 2) Implement a machine-learning algorithm to determine if splicing can predict drug response in cancer cell lines. Aim 3) Design a fast, scalable method to identify differentially spliced events related to cancer drug response. Aim 4) Construct a drug-splicing network and use a systems biology approach to search for similarities in underlying splicing events.Item Solving Prediction Problems from Temporal Event Data on Networks(2021-08) Sha, Hao; Mohler, George; Hasan, Mohammad; Dundar, Murat; Mukhopadhyay, SnehasisMany complex processes can be viewed as sequential events on a network. In this thesis, we study the interplay between a network and the event sequences on it. We first focus on predicting events on a known network. Examples of such include: modeling retweet cascades, forecasting earthquakes, and tracing the source of a pandemic. In specific, given the network structure, we solve two types of problems - (1) forecasting future events based on the historical events, and (2) identifying the initial event(s) based on some later observations of the dynamics. The inverse problem of inferring the unknown network topology or links, based on the events, is also of great important. Examples along this line include: constructing influence networks among Twitter users from their tweets, soliciting new members to join an event based on their participation history, and recommending positions for job seekers according to their work experience. Following this direction, we study two types of problems - (1) recovering influence networks, and (2) predicting links between a node and a group of nodes, from event sequences.