<p>This PhD thesis consists of an introduction and five papers, dealing with statistical methods in phylogenetics.</p><p>A phylogenetic tree describes the evolutionary relationships among species assuming that they share a common ancestor and that evolution takes place in a tree like manner. Our aim is to reconstruct the evolutionary relationships from aligned DNA sequences.</p><p>In the first two papers we investigate two measures of confidence for likelihood based methods, bootstrap frequencies with Maximum Likelihood (ML) and Bayesian posterior probabilities. We show that an earlier claimed approximate equivalence between them holds under certain conditions, but not in the current implementations of the two methods.</p><p>In the following two papers the divergence times of the internal nodes are considered. The ML estimate of the divergence time of the root is improved if longer sequences are analyzed or if more taxa are added. We show that the gain in precision is faster with longer sequences than with more taxa. We also show that the algorithm of the software package PATHd8 may give biased estimates if the global molecular clock is violated. A change of the algorithm to obtain unbiased estimates is therefore suggested.</p><p>The last paper deals with non-informative priors when using the Bayesian approach in phylogenetics. The term is not uniquely defined in the literature. We adopt the idea of data translated likelihoods and derive the so called Jeffreys' prior for branch lengths using Jukes Cantor model of evolution.</p>

Thesis (Ph. D.)--Ohio State University, 2006. / Title from first page of PDF file. Includes bibliographical references (p. 145-151).

This PhD thesis consists of an introduction and five papers, dealing with statistical methods in phylogenetics. A phylogenetic tree describes the evolutionary relationships among species assuming that they share a common ancestor and that evolution takes place in a tree like manner. Our aim is to reconstruct the evolutionary relationships from aligned DNA sequences. In the first two papers we investigate two measures of confidence for likelihood based methods, bootstrap frequencies with Maximum Likelihood (ML) and Bayesian posterior probabilities. We show that an earlier claimed approximate equivalence between them holds under certain conditions, but not in the current implementations of the two methods. In the following two papers the divergence times of the internal nodes are considered. The ML estimate of the divergence time of the root is improved if longer sequences are analyzed or if more taxa are added. We show that the gain in precision is faster with longer sequences than with more taxa. We also show that the algorithm of the software package PATHd8 may give biased estimates if the global molecular clock is violated. A change of the algorithm to obtain unbiased estimates is therefore suggested. The last paper deals with non-informative priors when using the Bayesian approach in phylogenetics. The term is not uniquely defined in the literature. We adopt the idea of data translated likelihoods and derive the so called Jeffreys' prior for branch lengths using Jukes Cantor model of evolution.

In regression with near collinear explanatory variables, the least squares predictor has large variance. Ordinary least squares regression (OLSR) often leads to unrealistic regression coefficients. Several regularized regression methods have been proposed as alternatives. Well-known are principal components regression (PCR), ridge regression (RR) and continuum regression (CR). The latter two involve a continuous metaparameter, offering additional flexibility. For a univariate response variable, CR incorporates OLSR, PLSR, and PCR as special cases, for special values of the metaparameter. CR is also closely related to RR. However, CR can in fact yield regressors that vary discontinuously with the metaparameter. Thus, the relation between CR and RR is not always one-to-one. We develop a new class of regression methods, LSRR, essentially the same as CR, but without discontinuities, and prove that any optimization principle will yield a regressor proportional to a RR, provided only that the principle implies maximizing some function of the regressor's sample correlation coefficient and its sample variance. For a multivariate response vector we demonstrate that a number of well-established regression methods are related, in that they are special cases of basically one general procedure. We try a more general method based on this procedure, with two meta-parameters. In a simulation study we compare this method to ridge regression, multivariate PLSR and repeated univariate PLSR. For most types of data studied, all methods do approximately equally well. There are cases where RR and LSRR yield larger errors than the other methods, and we conclude that one-factor methods are not adequate for situations where more than one latent variable are needed to describe the data. Among those based on latent variables, none of the methods tried is superior to the others in any obvious way.

I denna avhandling studerar vi nödvändiga och tillräckliga villkor för svag konvergens av första-sällan-händelsetider för semi-Markovska processer. I introduktionen ger vi nödvändiga grundläggande definitioner och beskrivningar av modeller som betraktas i avhandlingen, samt ger några exempel på situationer i vilka metoder av första-sällan-händelsetider kan vara lämpliga att använda. Dessutom analyserar vi publicerade resultat om asymptotiska problem för stokastiska funktionaler som definieras på semi-Markovska processer. I artikel A betraktar vi första-sällan-händelsetider för semi-Markovska processer med en ändlig mängd av lägen. Vi ger också en sammanfattning av våra resultat om nödvändiga och tillräckliga villkor för svag konvergens, samt diskuterar möjliga tillämpningar inom aktuarie-området. I artikel B redovisar vi i detalj de resultat som annonseras i artikel A och bevisen för dem. Vi ger också nödvändiga och tillräckliga villkor för svag konvergens av första-sällan-händelsetider för semi-Markovska processer med en ändlig mängd av lägen i ett icke-triangulärt tillstånd. Dessutom beskriver vi med hjälp av Laplacetransformationen klassen av alla möjliga gränsfördelningar. I artikel C studerar vi villkor av svag konvergens av flöden av sällan-händelser i ett icke-triangulärt tillstånd. Vi formulerar nödvändiga och tillräckliga villkor för konvergens, och beskriver klassen av alla möjliga gränsflöden. Vi tillämpar också våra resultat i asymptotisk analys av icke-ruin-sannolikheten för störda riskprocesser. I artikel D ger vi nödvändiga och tillräckliga villkor för svag konvergens av första-sällan-händelsetider för semi-Markovska rocesser med en ändlig mängd av lägen i ett triangulärt tillstånd, samt beskriver klassen av alla möjliga gränsfördelningar. Resultaten utvidgar slutsatser från artikel B till att gälla för ett allmänt triangulärt tillstånd. I artikel E ger vi nödvändiga och tillräckliga villkor för svag konvergens av flöden av sällan-händelser för semi-Markovska processer i ett triangulärt tillstånd. Detta generaliserar resultaten från artikel C till att beskriva ett allmänt triangulärt tillstånd. Vidare ger vi tillämpningar av våra resultat på asymptotiska problem av störda riskprocesser och till kösystemen med snabb service. / In this thesis we study necessary and sufficient conditions for weak convergence of first-rare-event times for semi-Markov processes, we describe the class of all possible limit distributions, and give the applications of the results to risk theory and queueing systems. In paper <b>A</b>, we consider first-rare-event times for semi-Markov processes with a finite set of states, and give a summary of our results concerning necessary and sufficient conditions for weak convergence of first-rare-event times and their actuarial applications. In paper <b>B</b>, we present in detail results announced in paper <b>A</b> as well as their proofs. We give necessary and sufficient conditions for weak convergence of first-rare-event times for semi-Markov processes with a finite set of states in non-triangular-array mode and describe the class of all possible limit distributions in terms of their Laplace transforms. In paper <b>C</b>, we study the conditions for weak convergence for flows of rare events for semi-Markov processes with a finite set of states in non-triangular array mode. We formulate necessary and sufficient conditions of convergence and describe the class of all possible limit stochastic flows. In the second part of the paper, we apply our results to the asymptotical analysis of non-ruin probabilities for perturbed risk processes. In paper <b>D</b>, we give necessary and sufficient conditions for the weak convergence of first-rare-event times for semi-Markov processes with a finite set of states in triangular array mode as well as describing the class of all possible limit distributions. The results of paper <b>D</b> extend results obtained in paper <b>B</b> to a general triangular array mode. In paper <b>E</b>, we give the necessary and sufficient conditions for weak convergence for the flows of rare events for semi-Markov processes with a finite set of states in triangular array case. This paper generalizes results obtained in paper <b>C</b> to a general triangular array mode. In the second part of the paper, we present applications of our results to asymptotical problems of perturbed risk processes and to queueing systems with quick service

Optimal stopping and mathematical finance are intimately connected since the value of an American option is given as the solution to an optimal stopping problem. Such a problem can be viewed as a game in which we are trying to maximize an expected reward. The solution involves finding the best possible strategy, or equivalently, an optimal stopping time for the game. Moreover, the reward corresponding to this optimal time should be determined. It is also of interest to know how the solution depends on the model parameters. For example, when pricing and hedging an American option, the volatility needs to be estimated and it is of great practical importance to know how the price and hedging portfolio are affected by a possible misspecification. The first paper of this thesis investigates the performance of the delta hedging strategy for a class of American options with non-convex payoffs. It turns out that an option writer who overestimates the volatility will obtain a superhedge for the option when using the misspecified hedging portfolio. In the second paper we consider the valuation of a so-called stock loan when the lender is allowed to issue a margin call. We show that the price of such an instrument is equivalent to that of an American down-and-out barrier option with a rebate. The value of this option is determined explicitly together with the optimal repayment strategy of the stock loan. The third paper considers the problem of how to optimally stop a Brownian bridge. A finite horizon optimal stopping problem like this can rarely be solved explicitly. However, one expects the value function and the optimal stopping boundary to satisfy a time-dependent free boundary problem. By assuming a special form of the boundary, we are able to transform this problem into one which does not depend on time and solving this we obtain candidates for the value function and the boundary. Using stochastic calculus we then verify that these indeed satisfy our original problem. In the fourth paper we consider an investor wanting to take advantage of a mispricing in the market by purchasing a bull spread, which is liquidated in case of a market downturn. We show that this can be formulated as an optimal stopping problem which we then, using similar techniques as in the third paper, solve explicitly. In the fifth and final paper we study convexity preservation of option prices in a model with jumps. This is done by finding a sufficient condition for the no-crossing property to hold in a jump-diffusion setting.

We investigate mathematical tools, Edgeworth series expansion and the saddle point method, which are approximation techniques that help us to estimate the distribution function for the standardized mean of independent identical distributed random variables where we will take into consideration the lattice case. Later on we will describe one important application for these mathematical tools where game developing companies can use them to reduce the amount of time needed to satisfy their standard requests before they approve any game

An important issue in finance is model calibration. The calibration problem is the inverse of the option pricing problem. Calibration is performed on a set of option prices generated from a given exponential L´evy model. By numerical examples, it is shown that the usual formulation of the inverse problem via Non-linear Least Squares is an ill-posed problem. To achieve well-posedness of the problem, some regularization is needed. Therefore a regularization method based on relative entropy is applied.

Investigation of stains from crime scenes are commonly used in the search for criminals. At The National Laboratory of Forensic Science, where these stains are examined, a number of questions of theoretical and practical interest regarding the databases of DNA profiles and the strength of DNA evidence against a suspect in a trial are not fully investigated. The first part of this thesis deals with how a sample of DNA profiles from a population is used in the process of estimating the strength of DNA evidence in a trial, taking population genetic factors into account. We then consider how to combine hypotheses regarding the relationship between a suspect and other possible donors of the stain from the crime scene by two applications of Bayes’ theorem. After that we assess the DNA profiles that minimize the strength of DNA evidence against a suspect, and investigate how the strength is affected by sampling error using the bootstrap method and a Bayesian method. In the last part of the thesis we examine discrepancies between different databases of DNA profiles by both descriptive and inferential statistics, including likelihood ratio tests and Bayes factor tests. Little evidence of major differences is found.

In this thesis we investigate the case of monitoring of stocks havingjust been introduced for public trading on the nancial market. Theempirical distribution of the change-point for 20 assets for 60 days was calculated to check the support for the assumption that the priceinitially drop or rise to some steady level.The price process X = {Xt : t in Z} is assumed to be an AR(1) process with a shift in the mean value from a slope to a constant. The Shiryaev-Roberts, Shewhart, EWMA, Likelihood ratio and CUSUM proceduresfor detecting a change-point in such a process are derived. The expecteddelay of the motivated alarm according to these methods is achievedunder the assumptions of a Poisson, uniform, binomial and geometric distributed by means of simulations.