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Comparative Visualization of Protein Secondary Structures
(Peer reviewed; Journal article, 2017-02-15)Background: Protein function is determined by many factors, namely by its constitution, spatial arrangement, and dynamic behavior. Studying these factors helps the biochemists and biologists to better understand the protein ... -
Comparing 17 graph parameters
(Master thesis, 2010-08-02)Many parametrized problems were decided to be FPT or W-hard. However, there is still thousands of problems and parameters for which we do not know yet whether are FPT or W-hard. In this thesis, we provide a tool for extending ... -
Comparison between instrumental variable and mediation-based methods for reconstructing causal gene networks in yeast
(Journal article; Peer reviewed, 2021)Causal gene networks model the flow of information within a cell. Reconstructing causal networks from omics data is challenging because correlation does not imply causation. When genomics and transcriptomics data from a ... -
Comparison of Discrete and Continuous Models for the Pooling Problem
(Chapter; Peer reviewed, 2011)The pooling problem is an important global optimization problem which is encountered in many industrial settings. It is traditionally modeled as a bilinear, nonconvex optimization problem, and solved by branch-and-bound ... -
Comparison of OpenMP and Threading Building Blocks for expressing parallelism on shared-memory systems
(Master thesis, 2011-02-01)The thesis offers a comparison of OpenMP and Intel Threading Building blocks. The two are threading packages used to express parallelism in programs. In addition, the thesis presents a promising scalable algorithm for ... -
Comparison of RNA-folding structures, in-vivo, in-vitro and in-silico
(Master thesis, 2019-10-31)The main objective of the work has been to develop the understanding of the difference between RNA structure probing approaches; in vivo, in vitro and in silico. Similarities and differences between three libraries of data ... -
Comparison of Solving Techniques for Non-linear Sparse Equations over Finite Fields with Application in Cryptanalysis
(Master thesis, 2008)The work on this thesis gives a summary of the Gluing/Agreeing techniques, as well as a reference implementation of this methods. Furthermore widely used SAT-solving techniques are explained and a short insight to the ... -
A Comparison of Vertex and Edge Partitioning Approaches for Parallel Maximal Matching
(Master thesis, 2013-12-09)This thesis will compare two ways of distributing data for parallel graph algorithms: vertex and edge partitioning, using a distributed memory system. Previous studies on the parallelization of graphs has often been focused ... -
Compiler Support for Parallel Evaluation of C++ Constant Expressions
(Journal article; Peer reviewed, 2023)Metaprogramming, the practice of writing programs that manipulate other programs at compile-time, continues to impact software development; enabling new approaches to optimisation, static analysis, and reflection. Nevertheless, ... -
A complexity dichotomy for critical values of the b-chromatic number of graphs
(Journal article; Peer reviewed, 2020)A b-coloring of a graph G is a proper coloring of its vertices such that each color class contains a vertex that has at least one neighbor in all the other color classes. The b-Coloring problem asks whether a graph G has ... -
A complexity dichotomy for critical values of the b-chromatic number of graphs
(Peer reviewed; Journal article, 2019-08-20)A b-coloring of a graph G is a proper coloring of its vertices such that each color class contains a vertex that has at least one neighbor in all the other color classes. The b-Coloring problem asks whether a graph G has ... -
Complexity of Edge Editing to a Connected Graph of Bounded Degrees
(Master thesis, 2019-06-26) -
Complexity of the Steiner Network Problem with Respect to the Number of Terminals
(Journal article; Peer reviewed, 2019)In the Directed Steiner Network problem we are given an arc-weighted digraph G, a set of terminals T subseteq V(G) with |T|=q, and an (unweighted) directed request graph R with V(R)=T. Our task is to output a subgraph H ... -
Composition of multilevel domain-specific modelling languages
(Journal article; Peer reviewed, 2023)Multilevel Modelling (MLM) approaches make it possible for designers and modellers to work with an unlimited number of abstraction levels to specify their domain-specific modelling languages (DSMLs). To fully exploit MLM ... -
Compound Logics for Modification Problems
(Journal article; Peer reviewed, 2023)We introduce a novel model-theoretic framework inspired from graph modification and based on the interplay between model theory and algorithmic graph minors. The core of our framework is a new compound logic operating with ... -
Compressing permutation groups into grammars and polytopes. A graph embedding approach
(Journal article; Peer reviewed, 2020)It can be shown that each permutation group G ⊑ 𝕊_n can be embedded, in a well defined sense, in a connected graph with O(n+|G|) vertices. Some groups, however, require much fewer vertices. For instance, 𝕊_n itself can ... -
Computation of Treespan. A Generalization of Bandwidth to Treelike Structures
(Master thesis, 2012-06-14)Motivated by a search game, Fomin, Heggernes and Telle [Algorithmica, 2005] defined the graph parameter treespan, a generalization of the well studied parameter bandwidth. Treespan is the maximum number of appearances of ... -
Computational analysis of the evolutionary dynamics of proteins on a genomic scale
(Doctoral thesis, 2007-01-16)Biology is primarily concerned with the study of all phenotypic aspects of living organisms and evolutionary biology is more specifically interested in elucidating how different phenotypes evolved. Proteins (and RNA ... -
Computational complexity aspects of super domination
(Journal article; Peer reviewed, 2023)Let G be a graph. A dominating set D ⊆ V (G) is a super dominating set if for every vertex x ∈ V (G) \ D there exists y ∈ D such that NG (y) ∩ (V (G) \ D)) = {x}. The cardinality of a smallest super dominating set of G is ... -
Computational investigation of 0-APN monomials
(Master thesis, 2022-05-18)This thesis is dedicated to exploring methods for deciding whether a power function $F(x) = x^d$ is 0-APN. Any APN function is 0-APN, and so 0-APN-ness is a necessary condition for APN-ness. APN functions are cryptographically ...