The protein folding problem is examined. Specifically, the problem of predicting protein secondary structure from the amino acid sequence is investigated. A literature study is presented into the protein folding process and the different techniques that currently exist to predict protein secondary structures. These techniques include the use of expert rules, statistics, information theory and various computational intelligence techniques, such as neural networks, nearest neighbour methods, Hidden Markov Models and Support Vector Machines. A pattern recognition technique based on statistical analysis is developed to predict protein secondary structure from the amino acid sequence. The technique can be applied to any problem where an input pattern is associated with an output pattern and each element in both the input and output patterns can take its value from a set with finite cardinality. The technique is applied to discover the role that small sequences of amino acids play in the formation of protein secondary structures. By applying the technique, a performance score of Q8 = 59:2% is achieved, with a corresponding Q3 score of 69.7%. This compares well with state of the art techniques, such as OSS-HMM and PSIPRED, which achieve Q3 scores of 67.9% and 66.8% respectively, when predictions on single sequences are made. / Dissertation (MEng)--University of Pretoria, 2009. / Electrical, Electronic and Computer Engineering / unrestricted

In this thesis, we present some new results in distribution theory for both discrete and continuous random variables, together with their motivating applications. We start with some results about the Multivariate Gaussian Distribution and its characterization as a maximizer of the Strichartz Estimates. Then, we present some characterizations of discrete and continuous distributions through ideas coming from optimal transportation. After this, we pass to the Simpson's Paradox and see that it is ubiquitous and it appears in Quantum Mechanics as well. We conclude with a group of results about discrete and continuous distributions invariant under symmetries, in particular invariant under the groups $A_1$, an elliptical version of $O(n)$ and $\mathbb{T}^n$. As mentioned, all the results proved in this thesis are motivated by their applications in different research areas. The applications will be thoroughly discussed. We have tried to keep each chapter self-contained and recalled results from other chapters when needed. The following is a more precise summary of the results discussed in each chapter. In chapter \ref{chapter 2}, we discuss a variational characterization of the Multivariate Normal distribution (MVN) as a maximizer of the Strichartz Estimates. Strichartz Estimates appear as a fundamental tool in the proof of wellposedness results for dispersive PDEs. With respect to the characterization of the MVN distribution as a maximizer of the entropy functional, the characterization as a maximizer of the Strichartz Estimate does not require the constraint of fixed variance. In this chapter, we compute the precise optimal constant for the whole range of Strichartz admissible exponents, discuss the connection of this problem to Restriction Theorems in Fourier analysis and give some statistical properties of the family of Gaussian Distributions which maximize the Strichartz estimates, such as Fisher Information, Index of Dispersion and Stochastic Ordering. We conclude this chapter presenting an optimization algorithm to compute numerically the maximizers. Chapter \ref{chapter 3} is devoted to the characterization of distributions by means of techniques from Optimal Transportation and the Monge-Amp\`{e}re equation. We give emphasis to methods to do statistical inference for distributions that do not possess good regularity, decay or integrability properties. For example, distributions which do not admit a finite expected value, such as the Cauchy distribution. The main tool used here is a modified version of the characteristic function (a particular case of the Fourier Transform). An important motivation to develop these tools come from Big Data analysis and in particular the Consensus Monte Carlo Algorithm. In chapter \ref{chapter 4}, we study the \emph{Simpson's Paradox}. The \emph{Simpson's Paradox} is the phenomenon that appears in some datasets, where subgroups with a common trend (say, all negative trend) show the reverse trend when they are aggregated (say, positive trend). Even if this issue has an elementary mathematical explanation, the statistical implications are deep. Basic examples appear in arithmetic, geometry, linear algebra, statistics, game theory, sociology (e.g. gender bias in the graduate school admission process) and so on and so forth. In our new results, we prove the occurrence of the \emph{Simpson's Paradox} in Quantum Mechanics. In particular, we prove that the \emph{Simpson's Paradox} occurs for solutions of the \emph{Quantum Harmonic Oscillator} both in the stationary case and in the non-stationary case. We prove that the phenomenon is not isolated and that it appears (asymptotically) in the context of the \emph{Nonlinear Schr\"{o}dinger Equation} as well. The likelihood of the \emph{Simpson's Paradox} in Quantum Mechanics and the physical implications are also discussed. Chapter \ref{chapter 5} contains some new results about distributions with symmetries. We first discuss a result on symmetric order statistics. We prove that the symmetry of any of the order statistics is equivalent to the symmetry of the underlying distribution. Then, we characterize elliptical distributions through group invariance and give some properties. Finally, we study geometric probability distributions on the torus with applications to molecular biology. In particular, we introduce a new family of distributions generated through stereographic projection, give several properties of them and compare them with the Von-Mises distribution and its multivariate extensions. / Thesis / Doctor of Philosophy (PhD)