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A Graph-Neural-Network Approach for Reconstructing Temporal Networks

Broeders, Theo (author)

Reconstructing a minimum reticulation network from phylogenetic trees is used in evolutionary studies. In this thesis, we focus on finding temporal networks using cherry-picking sequences for binary trees with all taxa. Finding such a minimum reticulation temporal network is NP-hard.<br/><br/>We introduce an algorithm to find a minimum...

master thesis 2024

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Forest-Based Binary Phylogenetic Networks: Finding Optimal Base Forests with Integer Linear Programming

van Gruijthuijsen, Merel (author)

Phylogenetic trees are commonly utilised in evolutionary biology. These trees represent the evolution of a set of species. In case of gene transfer however, a phylogenetic tree is insufficient. In such cases, tree-based phylogenetic networks are more suitable as they can depict reticulate evolution.<br/>Nonetheless, tree-based phylogenetic...

bachelor thesis 2023

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Computing the Scanwidth of Directed Acyclic Graphs

Holtgrefe, Niels (author)

Phylogenetic networks are a specific type of directed acyclic graph (DAG), used to depict evolutionary relationships among, for example, species or other groups of organisms. To solve computationally hard problems, treewidth has been used to parametrize algorithms in phylogenetics. In the hope of simplifying the algorithmic design process, Berry...

master thesis 2023

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Creating phylogenetic networks from clusters

Keur, Hans (author)

In biology, phylogenetics is the study of the evolutionary history of and relations between e.g. species. Such data are often represented in trees. Remarkably, trees lack the representation of reticulation events, such as hybridization, while such events are believed to be important. One of the reasons why trees are widely used, is the enormous...

master thesis 2023

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Treewidth based algorithms for Tree Containment in phylogenetics

Huijsman, Robbert (author)

TreeContainment is a well-known problem within phylogenetics, which asks whether a binary phylogenetic tree is embedded in a binary phylogenetic network. For this problem, Jones, Weller and van Iersel (2022) have created an algorithm that uses dynamic programming on tree-decompositions to achieve a running time that is exponential in the tree...

master thesis 2023

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Box set optimization for e-commerce warehouses: Applied to bol.com

van der Made, Frank (author)

The problem considered in this thesis is the box set optimization problem. In<br/>this problem the goal is to find the optimal dimensions of a number of shipping<br/>boxes which have to provide an optimal fit on a set of items. The application<br/>considered is e-commerce, and hence the number of items is relatively large<br/>compared to other...

master thesis 2022

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Enumeration of Minimal Separators with Special Properties

Nardi Dei Da Filicaia Dotti, Andrea (author)

In this paper we give a historical and theoretical background to minimal triangulation and its relation to minimal separators.<br/>We introduce a new type of minimal separators, the minimal meta separator, which its size is a lower bound for the treewidth problem, its fill-in is a lower bound for the minimum fill-in problem and can be used for...

master thesis 2022

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A new polynomial for describing Phylogenetic Networks

van de Klok, Margot (author)

Describing phylogenetic trees or networks with a polynomial is a tool to distinguish between them. In this thesis, a new polynomial for describing rooted binary internally labeled phylogenetic networks and trees is introduced based on the research of P. Liu and J. Pons et al. Two different cases are considered, one where the reticulation nodes...

bachelor thesis 2022

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Encoding undirected and semi-directed binary phylogenetic networks by quarnets

Nipius, Leonie (author)

Phylogenetic networks generalize evolutionary trees and are commonly used to represent evolutionary relationships between species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer. In this thesis all quarnets, networks on four species, of a network are assumed to be known. We prove that...

master thesis 2022

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Making phylogenetic networks orchard: Algorithms to determine if a phylogenetic network is orchard and to transform non-orchard to orchard networks

Susanna, Merel (author)

Phylogenetic networks are used to represent evolutionary histories of a set of taxa. In this thesis, we look at a certain network class, called orchard networks. <br/>In the beginning of this thesis, definitions concerning phylogenetic networks and specifically orchard networks are introduced. The characterization of orchard networks involves...

bachelor thesis 2022

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Optimizing Shunting Operations: A case-study at Kijfhoek shunting yard

Druijf, Teun (author)

In the current economy, there is an increasing focus on sustainability. Green transport solutions, like rail freight, are becoming more and more popular. We will look into the shunting operations at Kijfhoek shunting yard. This yard functions as the central hub for DB Cargo Nederland and connects the Port of Rotterdam with the hinterland. About...

master thesis 2022

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Exploring deep learning to improve allelic peak calling in forensic DNA analysis

van Belkom, Myrte (author)

When processing a trace DNA sample at the Netherlands Forensic Institute, an STR electropherogram can be created. An analyst uses this electropherogram and analysis software to read out peaks signifying DNA. After analysis, the DNA profile is used in the interpretation process, which can include the comparison to a reference DNA profile of a...

master thesis 2021

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Algorithmic study of 2-interval graphs

Simon, Alexandre (author)

Interval graphs play an important role in graph theory and have intensively been studied for over sixty years due to their wide range of applications and because most NP-hard problems on general graphs become solvable in linear time on interval graphs. However, the class of interval graphs is restricted and does not even contain a cycle of...

master thesis 2021

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Encoding level-k phylogenetic networks

Janisse, Frank (author)

Phylogenetic networks are used to describe evolutionary histories and are a generalisation of evolutionary trees. They can contain so called reticulations, representing reticulate evolution, such as hybridization, lateral gene transfer and recombination. Methods are being developed to construct certain rooted phylogenetic networks from their...

master thesis 2021

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Using reinforcement learning for finding the optimal quantum annealing schedule

Dijksman, Calvin (author)

For NP-hard optimisation problems no polynomial-time algorithms exist for finding a solution. Therefore, heuristic methods are often used, especially when approximate solutions can be satisfactory. One such method is quantum annealing, a method where some initial Hamiltonian is slowly perturbed to anneal towards a problem Hamiltonian. The...

bachelor thesis 2021

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Different reduction rules for the Maximum Parsimony distance on phylogenetic trees

Deen, Elise (author)

In this report, the bounded Maximum Parsimony distance will be considered when<br/>applying three different reduction rules. The distance is a measure on how dissimilar two trees are and is calculated based on the number of mutations that occur when looking at heritable traits. The first rule considered, is the chain reduction. For this rule, it...

bachelor thesis 2021

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Investment Optimized Airport Infrastructure for Battery and Hydrogen Canister Swaps

van Oosterom, Simon (author)

In this thesis, we consider investment optimization for airport infrastructure which is required charge and refuel electric and hydrogen powered aircraft using battery and hydrogen canister swaps respectively. The task at hand is to determine the most cost-effective infrastructure, consisting of spare batteries, and battery chargers for electric...

master thesis 2021

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Improving algorithms in phylogenetics using machine learning

Versendaal, Bryan (author)

In this thesis we look at three different algorithms within the field of phylogenetics and create a proof of concept for using machine learning to improve the algorithms. The problems are the maximum agreement forest problem, the hybridization number problem and finally the tail move problem. A study of the problems show that they can all...

master thesis 2020

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Reconstruction of Phylogenetic Networks: An algorithm for deconstructing and reconstructing Level-2 Binary Networks based on their distances

Mol, Riche (author)

Van Iersel, Moulton, and Murakami (2020) proved that a level-2 binary phylogenetic network can be uniquely reconstructed based on the matrix of mulitsets of the distances of the leaves. Using a handful of lemma’s each<br/>describing the steps of identifying cherries, uncontained leaves and blobs in the network, I created an algorithm for...

bachelor thesis 2020

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Tail move rearrangement algorithm for rooted binary phylogenetic networks

Husanović, Selma (author)

A common tool for exploring the space of phylogenetic networks is applying rearrangement moves, such as <i>tail moves</i>. Recently, it has been shown by Janssen et al that, given a rooted binary phylogenetic network, it is possible to generate any other alternative network, using only tail moves. The aim of this report is to translate this...

bachelor thesis 2020