Doctor of Philosopy (PhD) / Wireless communication always attracts extensive research interest, as it is a core part of modern communication technology. During my PhD study, I have focused on two research areas of wireless communication: IEEE 802.11 network performance analysis, and wireless cooperative retransmission. The first part of this thesis focuses on IEEE 802.11 network performance analysis. Since IEEE 802.11 technology is the most popular wireless access technology, IEEE 802.11 network performance analysis is always an important research area. In this area, my work includes the development of three analytical models for various aspects of IEEE 802.11 network performance analysis. First, a two-dimensional Markov chain model is proposed for analysing the performance of IEEE 802.11e EDCA (Enhanced Distributed Channel Access). With this analytical model, the saturated throughput is obtained. Compared with the existing analytical models of EDCA, the proposed model includes more correct details of EDCA, and accordingly its results are more accurate. This better accuracy is also proved by the simulation study. Second, another two-dimensional Markov chain model is proposed for analysing the coexistence performance of IEEE 802.11 DCF (Distributed Coordination Function) and IEEE 802.11e EDCA wireless devices. The saturated throughput is obtained with the proposed analytical model. The simulation study verifies the proposed analytical model, and it shows that the channel access priority of DCF is similar to that of the best effort access category in EDCA in the coexistence environment. The final work in this area is a hierarchical Markov chain model for investigating the impact of data-rate switching on the performance of IEEE 802.11 DCF. With this analytical model，the saturated throughput can be obtained. The simulation study verifies the accuracy of the model and shows the impact of the data-rate switching under different network conditions. A series of threshold values for the channel condition as well as the number of stations are obtained to decide whether the data-rate switching should be active or not. The second part of this thesis focuses on wireless cooperative retransmission. In this thesis, two uncoordinated distributed wireless cooperative retransmission strategies for single-hop connection are presented. In the proposed strategies, each uncoordinated cooperative neighbour randomly decide whether it should transmit to help the frame delivery depending on some pre-calculated optimal transmission probabilities. In Strategy 1, the source only transmits once in the first slot, and only the neighbours are involved in the retransmission attempts in the subsequent slots. In Strategy 2, both the source and the neighbours participate in the retransmission attempts. Both strategies are first analysed with a simple memoryless channel model, and the results show the superior performance of Strategy 2. With the elementary results for the memoryless channel model, a more realistic two-state Markov fading channel model is used to investigate the performance of Strategy 2. The simulation study verifies the accuracy of our analysis and indicates the superior performance of Strategy 2 compared with the simple retransmission strategy and the traditional two-hop strategy.

The determination of economic control charts and the determination of specification limits with minimum cost are two different research topics. In this study, we first combine the design of economic control charts and the determination of specification limits to maximize the expected profit per unit time for the smaller the better quality variable following the gamma distribution. Because of the asymmetric distribution, we design the EWMA control chart with asymmetric control limits. We simultaneously determine the economic EWMA control chart and upper specification limit with maximum expected profit per unit time. Then, extend the approach to determine the economic variable sampling interval EWMA control chart and upper specification limit with maximum expected profit per unit time. In all our numerical examples of the two profit models, the optimum expected profit per unit time under inspection is higher than that of no inspection. The detection ability of the EWMA chart with an appropriate weight is always better than the X-bar probability chart. The detection ability of the VSI EWMA chart is also superior to that of the fixed sampling interval EWMA chart. Sensitivity analyses are provided to determine the significant parameters for the optimal design parameters and the optimal expected profit per unit time.

This paper presents a model and analysis of a synchronous tandem flow line that produces different part types on unreliable machines. The machines operate according to a static priority rule, operating on the highest priority part whenever possible, and operating on lower priority parts only when unable to produce those with higher priorities. We develop a new decomposition method to analyze the behavior of the manufacturing system by decomposing the long production line into small analytically tractable components. As a first step in modeling a production line with more than one part type, we restrict ourselves to the case where there are two part types. Detailed modeling and derivations are presented with a small two-part-type production line that consists of two processing machines and two demand machines. Then, a generalized longer flow line is analyzed. Furthermore, estimates for performance measures, such as average buffer levels and production rates, are presented and compared to extensive discrete event simulation. The quantitative behavior of the two-part type processing line under different demand scenarios is also provided. / Singapore-MIT Alliance (SMA)

The journal cited frequency is usually an index to weigh an academic research achievement and may provide useful information for the academic society. However, it is spectulated that it may be influenced by factors such as the citing frequencies of other journals, the price of the journal and so on. In this work, as an initial attempt we will investigate the correlation between the citing frequency and cited frequency in the same journal. The data is taken the JCR (Journal Citation Reports) annually published by ISI (Institute for Scientific Information) to understand the relationship between citing and cited patterns. Moreover, Impact Factor from the JCR has also been used as a basis of ranking, we will discuss about the variation in journal ranking in all fields based on Markov chain modeling. The ranking based on a modified impact factor will be used to compare with that by the original impact factor provided by the JCR.

The aim of this thesis is to formulate and implement an algorithm that calculates the probability for two genes being orthologs, given a gene tree and a species tree. To do this, reconciliations between the gene tree and the species trees are used. A birth and death process is used to model the evolution, and used to calculate the orthology probability. The birth and death parameters are approximated with a Markov Chain Monte Carlo (MCMC). A MCMC framework for probability calculations of reconciliations written by Arvestad et al. (2003) is used. Rules for orthologous reconciliations are developed and implemented to calculate the probability for the reconciliations that have two genes as orthologs. The rules where integrated with the Arvestad et al. (2003) framework, and the algorithm was then validated and tested.

This thesis develops models and associated Bayesian inference methods for flexible univariate and multivariate conditional density estimation. The models are flexible in the sense that they can capture widely differing shapes of the data. The estimation methods are specifically designed to achieve flexibility while still avoiding overfitting. The models are flexible both for a given covariate value, but also across covariate space. A key contribution of this thesis is that it provides general approaches of density estimation with highly efficient Markov chain Monte Carlo methods. The methods are illustrated on several challenging non-linear and non-normal datasets. In the first paper, a general model is proposed for flexibly estimating the density of a continuous response variable conditional on a possibly high-dimensional set of covariates. The model is a finite mixture of asymmetric student-t densities with covariate-dependent mixture weights. The four parameters of the components, the mean, degrees of freedom, scale and skewness, are all modeled as functions of the covariates. The second paper explores how well a smooth mixture of symmetric components can capture skewed data. Simulations and applications on real data show that including covariate-dependent skewness in the components can lead to substantially improved performance on skewed data, often using a much smaller number of components. We also introduce smooth mixtures of gamma and log-normal components to model positively-valued response variables. In the third paper we propose a multivariate Gaussian surface regression model that combines both additive splines and interactive splines, and a highly efficient MCMC algorithm that updates all the multi-dimensional knot locations jointly. We use shrinkage priors to avoid overfitting with different estimated shrinkage factors for the additive and surface part of the model, and also different shrinkage parameters for the different response variables. In the last paper we present a general Bayesian approach for directly modeling dependencies between variables as function of explanatory variables in a flexible copula context. In particular, the Joe-Clayton copula is extended to have covariate-dependent tail dependence and correlations. Posterior inference is carried out using a novel and efficient simulation method. The appendix of the thesis documents the computational implementation details. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: In press. Paper 4: Manuscript.</p>

We say that (weak/strong) time duality holds for continuous time quasi-birth-and-death-processes if, starting from a fixed level, the first hitting time of the next upper level and the first hitting time of the next lower level have the same distribution. We present here a criterion for time duality in the case where transitions from one level to another have to pass through a given single state, the so-called bottleneck property. We also prove that a weaker form of reversibility called balanced under permutation is sufficient for the time duality to hold. We then discuss the general case.

Amongst the many complex processes taking place in living cells, transport of cargoes across the cytosceleton is fundamental to cell viability and activity. To move cargoes between the different cell parts, cells employ Molecular Motors. The motors operate by transporting cargoes along the so-called cellular micro-tubules, namely rope-like structures that connect, for instance, the cell-nucleus and outer membrane. We introduce a new Markov Chain, the killed Quasi-Random-Walk, for such transport molecules and derive properties like the maximal run length and time. Furthermore we introduce permuted balance, which is a more flexible extension of the ordinary reversibility and introduce the notion of Time Duality, which compares certain passage times pathwise. We give a number of sufficient conditions for Time Duality based on the geometry of the transition graph. Both notions are closely related to properties of the killed Quasi-Random-Walk.

Longitudinal studies, where data on study subjects are collected over time, is increasingly involving multivariate longitudinal responses. Frequently, the heterogeneity observed in a multivariate longitudinal response can be attributed to underlying unobserved disease states in addition to any between-subject differences. We propose modeling such disease states using a hidden Markov model (HMM) approach and expand upon previous work, which incorporated random effects into HMMs for the analysis of univariate longitudinal data, to the setting of a multivariate longitudinal response. Multivariate longitudinal data are modeled jointly using separate but correlated random effects between longitudinal responses of mixed data types in addition to a shared underlying hidden process. We use a computationally efficient Bayesian approach via Markov chain Monte Carlo (MCMC) to fit such models. We apply this methodology to bivariate longitudinal response data from a smoking cessation clinical trial. Under these models, we examine how to incorporate a treatment effect on the disease states, as well as develop methods to classify observations by disease state and to attempt to understand patient dropout. Simulation studies were performed to evaluate the properties of such models and their applications under a variety of realistic situations.

We study here a model for a strand passage in a ring polymer about a randomly chosen location at which two strands of the polymer have been brought gcloseh together. The model is based on ¦-SAPs, which are unknotted self-avoiding polygons in Z^3 that contain a fixed structure ¦ that forces two segments of the polygon to be close together. To study this model, the Composite Markov Chain Monte Carlo (CMCMC) algorithm, referred to as the CMC ¦-BFACF algorithm, that I developed and proved to be ergodic for unknotted ¦-SAPs in my M. Sc. Thesis, is used. Ten simulations (each consisting of 9.6~10^10 time steps) of the CMC ¦-BFACF algorithm are performed and the results from a statistical analysis of the simulated data are presented. To this end, a new maximum likelihood method, based on previous work of Berretti and Sokal, is developed for obtaining maximum likelihood estimates of the growth constants and critical exponents associated respectively with the numbers of unknotted (2n)-edge ¦-SAPs, unknotted (2n)-edge successful-strand-passage ¦-SAPs, unknotted (2n)-edge failed-strand-passage ¦-SAPs, and (2n)-edge after-strand-passage-knot-type-K unknotted successful-strand-passage ¦-SAPs. The maximum likelihood estimates are consistent with the result (proved here) that the growth constants are all equal, and provide evidence that the associated critical exponents are all equal.<p> We then investigate the question gGiven that a successful local strand passage occurs at a random location in a (2n)-edge knot-type K ¦-SAP, with what probability will the ¦-SAP have knot-type Kf after the strand passage?h. To this end, the CMCMC data is used to obtain estimates for the probability of knotting given a (2n)-edge successful-strand-passage ¦-SAP and the probability of an after-strand-passage polygon having knot-type K given a (2n)-edge successful-strand-passage ¦-SAP. The computed estimates numerically support the unproven conjecture that these probabilities, in the n¨ limit, go to a value lying strictly between 0 and 1. We further prove here that the rate of approach to each of these limits (should the limits exist) is less than exponential.<p> We conclude with a study of whether or not there is a difference in the gsizeh of an unknotted successful-strand-passage ¦-SAP whose after-strand-passage knot-type is K when compared to the gsizeh of a ¦-SAP whose knot-type does not change after strand passage. The two measures of gsizeh used are the expected lengths of, and the expected mean-square radius of gyration of, subsets of ¦-SAPs. How these two measures of gsizeh behave as a function of a polygonfs length and its after-strand-passage knot-type is investigated.