Constructing level-2 phylogenetic networks from trinets

Phylogenetic networks are a generalization of evolutionary trees that can be used to represent reticulate events. Level-k phylogenetic networks are such networks, but with a at most k reticulations per biconnected component of the network. For level-1 networks there exists an algorithm, called TriLoNet (Trinet Level-one Network algorithm), that...

New FPT algorithms for finding the temporal hybridization number for sets of phylogenetic trees

We study the problem of finding a temporal hybridization network for a set of phylogenetic trees that minimizes the number of reticulations. First, we introduce an FPT algorithm for this problem on an arbitrary set of t binary trees with n leaves each with a running time of O(5^k*n*m) where k is the minimum temporal hybridization number. We also...

Tree-child Network Containment

Interest in phylogenetic trees for histories of species and DNA has spawned many problems, one of which is TreeContainment; a problem that asks whether a tree is contained within a network. The TreeContainment problem is proven to be NP-hard for general trees and networks, however it is solvable in polynomial time for networks that meet the tree...

Preventing overfitting in Mixed Integer Optimization based classification tree construction

The global use of azole antifungals as treatment against infections caused by <i>Candida</i> has led to an increase in azole resistance. The primal goal of this BSc thesis is to improve existing Mixed Integer Optimization models to classify azole resistance of <i>C. glabrata</i> more accurately by preventing overfitting. Moreover, these...

Classifying Candida species using Mixed Integer Optimization based optimal classification trees

Global medical use of azole antifungals and echinocandins has led to an enormous increase in resistant <i>Candida</i> species, that are most commonly associated with fungal infections. A possible mechanism causing resistance are single or simultaneous point mutations in the genes responsible for encoding antifungal target enzymes. The aim of...

Parallel Machine Scheduling: with Partition Constraints

Multi-robot parcel sorting systems: Allocation and path finding

The logistics industry is being modernized using information technology and robots. This change encompasses a new set of challenges in warehouses. Recently, some companies have started using robot fleets to sort products and parcels. This thesis studies those systems, and researches the combinatorial problems that arise within them. Three main...

Computing Measures for Tree-Basedness of Phylogenetic Networks

Phylogenetic networks are a type of directed acyclic graph used to represent evolutionary relationships that contain events such as hybridization or horizontal gene transfer. When a network<br/>lacks such events it is a phylogenetic tree. Some phylogenetic networks that are not trees can<br/>however be represented as a tree with additional...

Measuring how far a nonbinary phylogenetic network is from being tree-based

In computational biology, phylogenetic trees are used to describe evolutionary history. This can be done more generally using phylogenetic networks, which can also describe nontreelike events such as hybridization. Some phylogenetic networks can be obtained from a base tree, a rooted spanning tree with the same leaf set, by adding linking edges....

Optimaliseren van de service van een taxisysteem met zelfrijdende voertuigen

Dit project behandelt de programmering en toepassing van een taxiservice, waarbij de passagiers zich vanaf of naar het treinstation willen verplaatsen. Met behulp van geheeltallig lineair programmeren wordt bepaald welke ritten door de taxi's moeten worden gereden, om de winst te maximaliseren. Dit model is gebaseerd op het model wat beschreven...

Parental Parsimony on Phylogenetic Networks: Computing the Maximum Parsimony Scores of Phylogenetic Networks

Phylogenetic networks represent the evolutionary history of organisms and the relationships among them. In the field of phylogenetics research has been done to reconstruct these networks. Several methods for reconstructing those networks have been developed over the years. One of them is the softwired parsimony score and another, a fairly new...

Resource-constrained Machine Scheduling

Background <br/>Scheduling is a form of decision-making that plays a very important<br/>role in manufacturing industries. It is the method by which work<br/>gets assigned to resources that compute it. In this thesis we want to assign<br/>jobs (cycles of a lithography process) to different machines in such a way<br/>that the machines are running...