Phylogenetic Trees and Their Analysis

Determining the best possible evolutionary history, the lowest-cost phylogenetic tree, to fit a given set of taxa and character sequences using maximum parsimony is an active area of research due to its underlying importance in understanding biological processes. As several steps in this process are NP-Hard when using popular, biologically-motivated optimality criteria, significant amounts of resources are dedicated to both both heuristics and to making exact methods more computationally tractable. We examine both phylogenetic data and the structure of the search space in order to suggest methods to reduce the number of possible trees that must be examined to find an exact solution for any given set of taxa and associated character data. Our work on four related problems combines theoretical insight with empirical study to improve searching of the tree space. First, we show that there is a Hamiltonian path through tree space for the most common tree metrics, answering Bryant\u27s Challenge for the minimal such path. We next examine the topology of the search space under various metrics, showing that some metrics have local maxima and minima even with perfect data, while some others do not. We further characterize conditions for which sequences simulated under the Jukes-Cantor model of evolution yield well-behaved search spaces. Next, we reduce the search space needed for an exact solution by splitting the set of characters into mutually-incompatible subsets of compatible characters, building trees based on the perfect phylogenies implied by these sets, and then searching in the neighborhoods of these trees. We validate this work empirically. Finally, we compare two approaches to the generalized tree alignment problem, or GTAP: Sequence alignment followed by tree search vs. Direct Optimization, on both biological and simulated data

Pattern Recognition

A wealth of advanced pattern recognition algorithms are emerging from the interdiscipline between technologies of effective visual features and the human-brain cognition process. Effective visual features are made possible through the rapid developments in appropriate sensor equipments, novel filter designs, and viable information processing architectures. While the understanding of human-brain cognition process broadens the way in which the computer can perform pattern recognition tasks. The present book is intended to collect representative researches around the globe focusing on low-level vision, filter design, features and image descriptors, data mining and analysis, and biologically inspired algorithms. The 27 chapters coved in this book disclose recent advances and new ideas in promoting the techniques, technology and applications of pattern recognition

Barking up the wrong tree : some obstacles to phylogenetic reconstruction

Phylogenetics is the study of evolutionary relationships between entities, usually biological in nature. The primary aim of such study is to elucidate the structure of these evolutionary histories. Unfortunately, such study can run into a variety of obstacles, both practical and theoretical. In this thesis we explore theoretical obstacles to phylogenetic reconstruction, by examining several scenarios in which distinguishing between similar structures can become quite difficult. In Chapter 2, we consider when metrics on trees and metrics on networks can become indistinguishable, and present several novel results in this area, showing that it is possible for any tree metric to be represented on a non-trivial network, and provide early results on the possible structures of these networks. In Chapter 3, we consider tree-based networks - a phenomenon in which networks have a strong tree-like signal. We present the first findings on these networks in the context of unrooted non-binary networks. We characterise the circumstances under which such networks can become `saturated' by these signals, and provide some graph theoretical results in this area as well. In Chapter 4 we consider the scenario in which two trees can appear similar due to their hierarchical structure. We present a new metric to quantify this similarity, and use simulations to show several promising properties of the metric and the relative accuracy of a function that gives an upper bound to the metric

User mobility prediction and management using machine learning

The next generation mobile networks (NGMNs) are envisioned to overcome current user mobility limitations while improving the network performance. Some of the limitations envisioned for mobility management in the future mobile networks are: addressing the massive traffic growth bottlenecks; providing better quality and experience to end users; supporting ultra high data rates; ensuring ultra low latency, seamless handover (HOs) from one base station (BS) to another, etc. Thus, in order for future networks to manage users mobility through all of the stringent limitations mentioned, artificial intelligence (AI) is deemed to play a key role automating end-to-end process through machine learning (ML). The objectives of this thesis are to explore user mobility predictions and management use-cases using ML. First, background and literature review is presented which covers, current mobile networks overview, and ML-driven applications to enable user’s mobility and management. Followed by the use-cases of mobility prediction in dense mobile networks are analysed and optimised with the use of ML algorithms. The overall framework test accuracy of 91.17% was obtained in comparison to all other mobility prediction algorithms through artificial neural network (ANN). Furthermore, a concept of mobility prediction-based energy consumption is discussed to automate and classify user’s mobility and reduce carbon emissions under smart city transportation achieving 98.82% with k-nearest neighbour (KNN) classifier as an optimal result along with 31.83% energy savings gain. Finally, context-aware handover (HO) skipping scenario is analysed in order to improve over all quality of service (QoS) as a framework of mobility management in next generation networks (NGNs). The framework relies on passenger mobility, trains trajectory, travelling time and frequency, network load and signal ratio data in cardinal directions i.e, North, East, West, and South (NEWS) achieving optimum result of 94.51% through support vector machine (SVM) classifier. These results were fed into HO skipping techniques to analyse, coverage probability, throughput, and HO cost. This work is extended by blockchain-enabled privacy preservation mechanism to provide end-to-end secure platform throughout train passengers mobility