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Community Detection on the GPU
(Chapter; Peer reviewed, 2017)We present and evaluate a new GPU algorithm based on the Louvain method for community detection. Our algorithm is the first for this problem that parallelizes the access to individual edges. In this way we can fine tune ... -
Community-driven development for computational biology at Sprints, Hackathons and Codefests
(Peer reviewed; Journal article, 2014-11-27)Background: Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools ... -
A Comparative Analysis of Feature Selection Methods for Biomarker Discovery in Study of Toxicant-Treated Atlantic Cod (Gadus Morhua) Liver
(Communications in Computer and Information Science; 1056, Chapter; Peer reviewed, 2019)Univariate and multivariate feature selection methods can be used for biomarker discovery in analysis of toxicant exposure. Among the univariate methods, differential expression analysis (DEA) is often applied for its ... -
A Comparative Study on Distributed Storage and Erasure Coding Techniques Using Apache Hadoop Over NorNet Core
(Master thesis, 2017)Both private and public sector organizations are constantly looking for new ways to keep their information safe and accessible at all times. Over the past few decades, replication has always been a reliable way to make ... -
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 ... -
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 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 ... -
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 ...