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Pooling Problems with Single-Flow Constraints
(Chapter; Peer reviewed, 2019)The pooling problem is a frequently studied extension of the traditional minimum cost flow problem, in which the composition of the flow is subject to restrictions. In a network consisting of three layers of nodes, the ... -
Population dynamic regulators in an empirical predator-prey system
(Journal article; Peer reviewed, 2021)Capelin (Mallotus villosus) is a short-lived (1–4 years) fish species, that plays a crucial role by dominating the intermediate trophic level in the Barents Sea. Several episodes of extreme biomass decline (collapse) have ... -
A Practical Adaptive Key Recovery Attack on the LGM (GSW-like) Cryptosystem
(Chapter, 2021)We present an adaptive key recovery attack on the leveled homomorphic encryption scheme suggested by Li, Galbraith and Ma (Provsec 2016), which itself is a modification of the GSW cryptosystem designed to resist key recovery ... -
Practical Aspects of the Graph Parameter Boolean-width
(Doctoral thesis, 2014-08-18) -
Precrec: fast and accurate precision-recall and ROC curve calculations in R
(Peer reviewed; Journal article, 2017)The precision–recall plot is more informative than the ROC plot when evaluating classifiers on imbalanced datasets, but fast and accurate curve calculation tools for precision–recall plots are currently not available. We ... -
Predicting employee absenteeism for cost effective interventions
(Journal article; Peer reviewed, 2021)This paper describes a decision support system designed for a Belgian Human Resource (HR) and Well-Being Service Provider. Their goal is to improve health and well-being in the workplace, and to this end, the task is to ... -
Predicting Gene Regulatory Elements in Silico on a Genomic Scale
(Journal article, 1998-05-18)We performed a systematic analysis of gene upstream regions in the yeast genome for occurrences of regular expression-type patterns with the goal of identifying potential regulatory elements. To achieve this goal, we have ... -
Predicting Loss of Inference Accuracy in Bounded Tree-Width Bayesian Networks
(Master thesis, 2019-09-04)A Bayesian network (BN) is a compact way to represent a joint probability distribution graphically. The BN consists of a structure in the form of a directed acyclic graph (DAG) and a set of parameters. The nodes of the DAG ... -
Prediction and analysis of protein structure
(Doctoral thesis, 2010-04-19)This thesis, which contains an introduction and four manuscripts, summarises my efforts during my the past four years to understand proteins, their structure and dynamics. The first manuscript presents a protocol that ... -
Prediction of Polycomb/Trithorax Response Elements using Support Vector Machines
(Master thesis, 2013-06-03)Polycomb/Trithorax Response Elements (PREs) are epigenetic elements that can maintain established transcriptional states over multiple cell divisions. Sequence motifs in known PREs have enabled genome-wide PRE prediction ... -
Present-biased optimization
(Journal article; Peer reviewed, 2022)This paper explores the behavior of present-biased agents, that is, agents who erroneously anticipate the costs of future actions compared to their real costs. Specifically, we extend the original framework proposed by ... -
A Pretty Good Formatting Pipeline
(Lecture Notes in Computer Science; 8225, Chapter; Peer reviewed, 2013)Proper formatting makes the structure of a program apparent and aids program comprehension. The need to format code arises in code generation and transformation, as well as in normal reading and editing situations. Commonly ... -
Privacy, Security, and Repair in Distributed Storage Systems
(Doctoral thesis, 2018-10-17)We are living in the age of information where our lives are shaped by information and communication technologies. As a consequence, there is an explosion in the amount of generated data. Distribute storage systems (DSSs) ... -
Probabilistic analysis on Macaulay matrices over finite fields and complexity of constructing Gröbner bases
(Journal article; Peer reviewed, 2021)Gröbner basis methods are used to solve systems of polynomial equations over finite fields, but their complexity is poorly understood. In this work an upper bound on the time complexity of constructing a Gröbner basis ... -
Profiling of Small Ribosomal Subunits Reveals Modes and Regulation of Translation Initiation
(Journal article; Peer reviewed, 2020)Translation initiation is often attributed as the rate-determining step of eukaryotic protein synthesis and key to gene expression control. Despite this centrality, the series of steps involved in this process is poorly ... -
Program Transformations in Magnolia
(Master thesis, 2017-07-11)We explore program transformations in the context of the Magnolia programming language. We discuss research and implementations of transformation techniques, scenarios to put them to use in Magnolia, interfacing with ... -
Programming Language Technology for Niche Platforms
(Doctoral thesis, 2017-03-03)Developers writing software for a niche platform are denied the luxury of a first-class vendor-supported integrated development environment and a large community crafting platform-tailored libraries, tools, and documentation. ... -
Programming with Explicit Dependencies. A Framework for Portable Parallel Programming
(Doctoral thesis, 2011-05-23)Computational devices are rapidly evolving into massively parallel systems. Multicore processors are already standard; high performance processors such as the Cell/BE processor, graphics processing units (GPUs) ... -
Projecting Art into Virtual Reality. Creating artistic scenes through parametrization utilizing a modern game-engine
(Master thesis, 2018-08-21)Recent advancements in virtual reality both on the hardware and software front have made high-quality virtual reality experiences both cheaper, and easier to obtain. This thesis aims to explore how virtual reality can be ... -
Projective Simulation compared to reinforcement learning
(Master thesis, 2015-06-01)This thesis explores the model of projective simulation (PS), a novel approach for an artificial intelligence (AI) agent. The model of PS learns by interacting with the environment it is situated in, and allows for simulating ...